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href="https://sorbonne-fr.academia.edu/">Sorbonne University</a>, <a class="u-tcGrayDarker" href="https://sorbonne-fr.academia.edu/Departments/Chemistry/Documents">Chemistry</a>, <span class="u-tcGrayDarker">Faculty Member</span></div></div></div></div><div class="sidebar-cta-container"><button class="ds2-5-button hidden profile-cta-button grow js-profile-follow-button" data-broccoli-component="user-info.follow-button" data-click-track="profile-user-info-follow-button" data-follow-user-fname="Jean-Philip" data-follow-user-id="35445" data-follow-user-source="profile_button" data-has-google="false"><span class="material-symbols-outlined" style="font-size: 20px" translate="no">add</span>Follow</button><button class="ds2-5-button hidden profile-cta-button grow js-profile-unfollow-button" data-broccoli-component="user-info.unfollow-button" data-click-track="profile-user-info-unfollow-button" data-unfollow-user-id="35445"><span class="material-symbols-outlined" style="font-size: 20px" 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style="margin: 0px;">Theoretical chemistry<br /><span class="u-fw700">Phone: </span>33 1 44 27 25 04<br /><b>Address: </b>Laboratoire de Chimie Théorique, <br />Université Pierre et Marie Curie, Paris 6, <br />CC 137, 4 place Jussieu, <br />75252 Paris Cedex 05, France.<br /><div class="js-profile-less-about u-linkUnstyled u-tcGrayDarker u-textDecorationUnderline u-displayNone">less</div></div></div><div class="ri-section"><div class="ri-section-header"><span>Interests</span><a class="ri-more-link js-profile-ri-list-card" data-click-track="profile-user-info-primary-research-interest" data-has-card-for-ri-list="35445">View All (6)</a></div><div class="ri-tags-container"><a data-click-track="profile-user-info-expand-research-interests" data-has-card-for-ri-list="35445" href="https://www.academia.edu/Documents/in/Chemistry"><div id="js-react-on-rails-context" style="display:none" 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class="user-content-wrapper"><div class="uploads-container" id="social-redesign-work-container"><div class="upload-header"><h2 class="ds2-5-heading-sans-serif-xs">Uploads</h2></div><div class="documents-container backbone-social-profile-documents" style="width: 100%;"><div class="u-taCenter"></div><div class="profile--tab_content_container js-tab-pane tab-pane active" id="all"><div class="profile--tab_heading_container js-section-heading" data-section="Papers" id="Papers"><h3 class="profile--tab_heading_container">Papers by Jean-Philip Piquemal</h3></div><div class="js-work-strip profile--work_container" data-work-id="35314545"><div class="profile--work_thumbnail hidden-xs"><a class="js-work-strip-work-link" data-click-track="profile-work-strip-thumbnail" href="https://www.academia.edu/35314545/Tinker_HP_a_Massively_Parallel_Molecular_Dynamics_Package_for_Multiscale_Simulations_of_Large_Complex_Systems_with_Advanced_Point_Dipole_Polarizable_Force_Fields"><img alt="Research paper thumbnail of Tinker-HP: a Massively Parallel Molecular Dynamics Package for Multiscale Simulations of Large Complex Systems with Advanced Point Dipole Polarizable Force Fields" class="work-thumbnail" src="https://attachments.academia-assets.com/55175253/thumbnails/1.jpg" /></a></div><div class="wp-workCard wp-workCard_itemContainer"><div class="wp-workCard_item wp-workCard--title"><a class="js-work-strip-work-link text-gray-darker" data-click-track="profile-work-strip-title" href="https://www.academia.edu/35314545/Tinker_HP_a_Massively_Parallel_Molecular_Dynamics_Package_for_Multiscale_Simulations_of_Large_Complex_Systems_with_Advanced_Point_Dipole_Polarizable_Force_Fields">Tinker-HP: a Massively Parallel Molecular Dynamics Package for Multiscale Simulations of Large Complex Systems with Advanced Point Dipole Polarizable Force Fields</a></div><div class="wp-workCard_item wp-workCard--coauthors"><span>by </span><span><a class="" data-click-track="profile-work-strip-authors" href="https://sorbonne-fr.academia.edu/JeanPhilipPiquemal">Jean-Philip Piquemal</a> and <a class="" data-click-track="profile-work-strip-authors" href="https://uni-mainz.academia.edu/FilippoLipparini">Filippo Lipparini</a></span></div><div class="wp-workCard_item"><span class="js-work-more-abstract-truncated">We present Tinker-HP, a massively MPI parallel package dedicated to classical molecular dynamics ...</span><a class="js-work-more-abstract" data-broccoli-component="work_strip.more_abstract" data-click-track="profile-work-strip-more-abstract" href="javascript:;"><span> more </span><span><i class="fa fa-caret-down"></i></span></a><span class="js-work-more-abstract-untruncated hidden">We present Tinker-HP, a massively MPI parallel package dedicated to classical molecular dynamics (MD) and to multiscale simulations, using advanced polarizable force fields (PFF) encompassing distributed multipoles electrostatics. Tinker-HP is an evolution of the popular Tinker package code that conserves its simplicity of use and its reference double precision implementation for CPUs. Grounded on interdisciplinary efforts with applied mathematics, Tinker-HP allows for long polarizable MD simulations on large systems up to millions of atoms.We detail in the paper the newly developed extension of massively parallel 3D spatial decomposition to point dipole polarizable models as well as their coupling to efficient Krylov iterative and non-iterative polarization solvers. The design of the code allows the use of various computer systems ranging from laboratory workstations to modern petascale supercomputers with thousands of cores. Tinker-HP proposes therefore the first high-performance scalable CPU computing environment for the development of next generation point dipole PFFs and for production simulations. Strategies linking Tinker-HP to Quantum Mechanics (QM) in the framework of multiscale polarizable self-consistent QM/MD simulations are also provided. The possibilities, performances and scalability of the software are demonstrated via benchmarks calculations using the polarizable AMOEBA force field on systems ranging from large water boxes of increasing size and ionic liquids to (very) large biosystems encompassing several proteins as well as the complete satellite tobacco mosaic virus and ribosome structures. For small systems, Tinker-HP appears to be competitive with the Tinker-OpenMM GPU implementation of Tinker. As the system size grows, Tinker-HP remains operational thanks to its access to distributed memory and takes advantage of its new algorithmic enabling for stable long timescale polarizable simulations. Overall, a several thousand-fold acceleration over a single-core computation is observed for the largest systems. The extension of the present CPU implementation of Tinker-HP to other computational platforms is discussed.</span></div><div class="wp-workCard_item wp-workCard--actions"><span class="work-strip-bookmark-button-container"></span><a id="9cdb9921b054f820062b2435d0659816" class="wp-workCard--action" rel="nofollow" data-click-track="profile-work-strip-download" data-download="{"attachment_id":55175253,"asset_id":35314545,"asset_type":"Work","button_location":"profile"}" href="https://www.academia.edu/attachments/55175253/download_file?st=MTczMjM3NTk4Myw4LjIyMi4yMDguMTQ2&s=profile"><span><i class="fa fa-arrow-down"></i></span><span>Download</span></a><span class="wp-workCard--action visible-if-viewed-by-owner inline-block" style="display: none;"><span class="js-profile-work-strip-edit-button-wrapper profile-work-strip-edit-button-wrapper" data-work-id="35314545"><a class="js-profile-work-strip-edit-button" tabindex="0"><span><i class="fa fa-pencil"></i></span><span>Edit</span></a></span></span><span id="work-strip-rankings-button-container"></span></div><div class="wp-workCard_item wp-workCard--stats"><span><span><span class="js-view-count view-count u-mr2x" data-work-id="35314545"><i class="fa fa-spinner fa-spin"></i></span><script>$(function () { var workId = 35314545; window.Academia.workViewCountsFetcher.queue(workId, function (count) { var description = window.$h.commaizeInt(count) + " " + window.$h.pluralize(count, 'View'); $(".js-view-count[data-work-id=35314545]").text(description); $(".js-view-count[data-work-id=35314545]").attr('title', description).tooltip(); }); });</script></span></span><span><span class="percentile-widget hidden"><span class="u-mr2x work-percentile"></span></span><script>$(function () { var workId = 35314545; window.Academia.workPercentilesFetcher.queue(workId, function (percentileText) { var container = $(".js-work-strip[data-work-id='35314545']"); container.find('.work-percentile').text(percentileText.charAt(0).toUpperCase() + percentileText.slice(1)); container.find('.percentile-widget').show(); container.find('.percentile-widget').removeClass('hidden'); }); });</script></span><span><script>$(function() { new Works.PaperRankView({ workId: 35314545, container: "", }); });</script></span></div><div id="work-strip-premium-row-container"></div></div></div><script> require.config({ waitSeconds: 90 })(["https://a.academia-assets.com/assets/wow_profile-f77ea15d77ce96025a6048a514272ad8becbad23c641fc2b3bd6e24ca6ff1932.js","https://a.academia-assets.com/assets/work_edit-ad038b8c047c1a8d4fa01b402d530ff93c45fee2137a149a4a5398bc8ad67560.js"], function() { // from javascript_helper.rb var dispatcherData = {} if (true){ window.WowProfile.dispatcher = window.WowProfile.dispatcher || _.clone(Backbone.Events); dispatcherData = { dispatcher: window.WowProfile.dispatcher, downloadLinkId: "9cdb9921b054f820062b2435d0659816" } } $('.js-work-strip[data-work-id=35314545]').each(function() { if (!$(this).data('initialized')) { new WowProfile.WorkStripView({ el: this, workJSON: {"id":35314545,"title":"Tinker-HP: a Massively Parallel Molecular Dynamics Package for Multiscale Simulations of Large Complex Systems with Advanced Point Dipole Polarizable Force Fields","translated_title":"","metadata":{"abstract":"We present Tinker-HP, a massively MPI parallel package dedicated to classical molecular dynamics (MD) and to multiscale simulations, using advanced polarizable force fields (PFF) encompassing distributed multipoles electrostatics. 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$(this).data('initialized', true); } }); $a.trackClickSource(".js-work-strip-work-link", "profile_work_strip") }); </script> <div class="js-work-strip profile--work_container" data-work-id="35181718"><div class="profile--work_thumbnail hidden-xs"><a class="js-work-strip-work-link" data-click-track="profile-work-strip-thumbnail" href="https://www.academia.edu/35181718/A_QM_MM_Approach_Using_the_AMOEBA_Polarizable_Embedding_From_Ground_State_Energies_to_Electronic_Excitations"><img alt="Research paper thumbnail of A QM/MM Approach Using the AMOEBA Polarizable Embedding: From Ground State Energies to Electronic Excitations" class="work-thumbnail" src="https://a.academia-assets.com/images/blank-paper.jpg" /></a></div><div class="wp-workCard wp-workCard_itemContainer"><div class="wp-workCard_item wp-workCard--title"><a class="js-work-strip-work-link text-gray-darker" data-click-track="profile-work-strip-title" href="https://www.academia.edu/35181718/A_QM_MM_Approach_Using_the_AMOEBA_Polarizable_Embedding_From_Ground_State_Energies_to_Electronic_Excitations">A QM/MM Approach Using the AMOEBA Polarizable Embedding: From Ground State Energies to Electronic Excitations</a></div><div class="wp-workCard_item"><span>Journal of chemical theory and computation</span><span>, Jan 11, 2016</span></div><div class="wp-workCard_item"><span class="js-work-more-abstract-truncated">A fully polarizable implementation of the hybrid quantum mechanics/molecular mechanics approach i...</span><a class="js-work-more-abstract" data-broccoli-component="work_strip.more_abstract" data-click-track="profile-work-strip-more-abstract" href="javascript:;"><span> more </span><span><i class="fa fa-caret-down"></i></span></a><span class="js-work-more-abstract-untruncated hidden">A fully polarizable implementation of the hybrid quantum mechanics/molecular mechanics approach is presented, where the classical environment is described through the AMOEBA polarizable force field. A variational formalism, offering a self-consistent relaxation of both the MM induced dipoles and the QM electronic density, is used for ground state energies and extended to electronic excitations in the framework of time-dependent density functional theory combined with a state specific response of the classical part. An application to the calculation of the solvatochromism of the pyridinium N-phenolate betaine dye used to define the solvent ET(30) scale is presented. The results show that the QM/AMOEBA model not only properly describes specific and bulk effects in the ground state but it also correctly responds to the large change in the solute electronic charge distribution upon excitation.</span></div><div class="wp-workCard_item wp-workCard--actions"><span class="work-strip-bookmark-button-container"></span><span class="wp-workCard--action visible-if-viewed-by-owner inline-block" style="display: none;"><span class="js-profile-work-strip-edit-button-wrapper profile-work-strip-edit-button-wrapper" data-work-id="35181718"><a class="js-profile-work-strip-edit-button" tabindex="0"><span><i class="fa fa-pencil"></i></span><span>Edit</span></a></span></span><span id="work-strip-rankings-button-container"></span></div><div class="wp-workCard_item wp-workCard--stats"><span><span><span class="js-view-count view-count u-mr2x" data-work-id="35181718"><i class="fa fa-spinner fa-spin"></i></span><script>$(function () { var workId = 35181718; window.Academia.workViewCountsFetcher.queue(workId, function (count) { var description = window.$h.commaizeInt(count) + " " + window.$h.pluralize(count, 'View'); $(".js-view-count[data-work-id=35181718]").text(description); $(".js-view-count[data-work-id=35181718]").attr('title', description).tooltip(); }); });</script></span></span><span><span class="percentile-widget hidden"><span class="u-mr2x work-percentile"></span></span><script>$(function () { var workId = 35181718; window.Academia.workPercentilesFetcher.queue(workId, function (percentileText) { var container = $(".js-work-strip[data-work-id='35181718']"); container.find('.work-percentile').text(percentileText.charAt(0).toUpperCase() + percentileText.slice(1)); container.find('.percentile-widget').show(); container.find('.percentile-widget').removeClass('hidden'); }); });</script></span><span><script>$(function() { new Works.PaperRankView({ workId: 35181718, container: "", }); });</script></span></div><div id="work-strip-premium-row-container"></div></div></div><script> require.config({ waitSeconds: 90 })(["https://a.academia-assets.com/assets/wow_profile-f77ea15d77ce96025a6048a514272ad8becbad23c641fc2b3bd6e24ca6ff1932.js","https://a.academia-assets.com/assets/work_edit-ad038b8c047c1a8d4fa01b402d530ff93c45fee2137a149a4a5398bc8ad67560.js"], function() { // from javascript_helper.rb var dispatcherData = {} if (false){ window.WowProfile.dispatcher = window.WowProfile.dispatcher || _.clone(Backbone.Events); dispatcherData = { dispatcher: window.WowProfile.dispatcher, downloadLinkId: "-1" } } $('.js-work-strip[data-work-id=35181718]').each(function() { if (!$(this).data('initialized')) { new WowProfile.WorkStripView({ el: this, workJSON: {"id":35181718,"title":"A QM/MM Approach Using the AMOEBA Polarizable Embedding: From Ground State Energies to Electronic Excitations","translated_title":"","metadata":{"abstract":"A fully polarizable implementation of the hybrid quantum mechanics/molecular mechanics approach is presented, where the classical environment is described through the AMOEBA polarizable force field. 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The results show that the QM/AMOEBA model not only properly describes specific and bulk effects in the ground state but it also correctly responds to the large change in the solute electronic charge distribution upon excitation.","publication_date":{"day":11,"month":1,"year":2016,"errors":{}},"publication_name":"Journal of chemical theory and computation"},"translated_abstract":"A fully polarizable implementation of the hybrid quantum mechanics/molecular mechanics approach is presented, where the classical environment is described through the AMOEBA polarizable force field. A variational formalism, offering a self-consistent relaxation of both the MM induced dipoles and the QM electronic density, is used for ground state energies and extended to electronic excitations in the framework of time-dependent density functional theory combined with a state specific response of the classical part. An application to the calculation of the solvatochromism of the pyridinium N-phenolate betaine dye used to define the solvent ET(30) scale is presented. The results show that the QM/AMOEBA model not only properly describes specific and bulk effects in the ground state but it also correctly responds to the large change in the solute electronic charge distribution upon excitation.","internal_url":"https://www.academia.edu/35181718/A_QM_MM_Approach_Using_the_AMOEBA_Polarizable_Embedding_From_Ground_State_Energies_to_Electronic_Excitations","translated_internal_url":"","created_at":"2017-11-18T07:17:50.340-08:00","preview_url":null,"current_user_can_edit":null,"current_user_is_owner":null,"owner_id":35445,"coauthors_can_edit":true,"document_type":"paper","co_author_tags":[],"downloadable_attachments":[],"slug":"A_QM_MM_Approach_Using_the_AMOEBA_Polarizable_Embedding_From_Ground_State_Energies_to_Electronic_Excitations","translated_slug":"","page_count":null,"language":"en","content_type":"Work","owner":{"id":35445,"first_name":"Jean-Philip","middle_initials":null,"last_name":"Piquemal","page_name":"JeanPhilipPiquemal","domain_name":"sorbonne-fr","created_at":"2009-03-17T04:43:24.569-07:00","display_name":"Jean-Philip Piquemal","url":"https://sorbonne-fr.academia.edu/JeanPhilipPiquemal"},"attachments":[],"research_interests":[{"id":645605,"name":"THEORETICAL AND COMPUTATIONAL CHEMISTRY","url":"https://www.academia.edu/Documents/in/THEORETICAL_AND_COMPUTATIONAL_CHEMISTRY"}],"urls":[]}, dispatcherData: dispatcherData }); $(this).data('initialized', true); } }); $a.trackClickSource(".js-work-strip-work-link", "profile_work_strip") }); </script> <div class="js-work-strip profile--work_container" data-work-id="35181717"><div class="profile--work_thumbnail hidden-xs"><a class="js-work-strip-work-link" data-click-track="profile-work-strip-thumbnail" href="https://www.academia.edu/35181717/LICHEM_A_QM_MM_program_for_simulations_with_multipolar_and_polarizable_force_fields"><img alt="Research paper thumbnail of LICHEM: A QM/MM program for simulations with multipolar and polarizable force fields" class="work-thumbnail" src="https://a.academia-assets.com/images/blank-paper.jpg" /></a></div><div class="wp-workCard wp-workCard_itemContainer"><div class="wp-workCard_item wp-workCard--title"><a class="js-work-strip-work-link text-gray-darker" data-click-track="profile-work-strip-title" href="https://www.academia.edu/35181717/LICHEM_A_QM_MM_program_for_simulations_with_multipolar_and_polarizable_force_fields">LICHEM: A QM/MM program for simulations with multipolar and polarizable force fields</a></div><div class="wp-workCard_item"><span>Journal of Computational Chemistry</span><span>, 2016</span></div><div class="wp-workCard_item"><span class="js-work-more-abstract-truncated">We introduce an initial implementation of the LICHEM software package. LICHEM can interface with ...</span><a class="js-work-more-abstract" data-broccoli-component="work_strip.more_abstract" data-click-track="profile-work-strip-more-abstract" href="javascript:;"><span> more </span><span><i class="fa fa-caret-down"></i></span></a><span class="js-work-more-abstract-untruncated hidden">We introduce an initial implementation of the LICHEM software package. LICHEM can interface with Gaussian, PSI4, NWChem, TINKER, and TINKER-HP to enable QM/MM calculations using multipolar/polarizable force fields. LICHEM extracts forces and energies from unmodified QM and MM software packages to perform geometry optimizations, single-point energy calculations, or Monte Carlo simulations. When the QM and MM regions are connected by covalent bonds, the pseudo-bond approach is employed to smoothly transition between the QM region and the polarizable force field. A series of water clusters and small peptides have been employed to test our initial implementation. The results obtained from these test systems show the capabilities of the new software and highlight the importance of including explicit polarization. © 2016 Wiley Periodicals, Inc.</span></div><div class="wp-workCard_item wp-workCard--actions"><span class="work-strip-bookmark-button-container"></span><span class="wp-workCard--action visible-if-viewed-by-owner inline-block" style="display: none;"><span class="js-profile-work-strip-edit-button-wrapper profile-work-strip-edit-button-wrapper" data-work-id="35181717"><a class="js-profile-work-strip-edit-button" tabindex="0"><span><i class="fa fa-pencil"></i></span><span>Edit</span></a></span></span><span id="work-strip-rankings-button-container"></span></div><div class="wp-workCard_item wp-workCard--stats"><span><span><span class="js-view-count view-count u-mr2x" data-work-id="35181717"><i class="fa fa-spinner fa-spin"></i></span><script>$(function () { var workId = 35181717; window.Academia.workViewCountsFetcher.queue(workId, function (count) { var description = window.$h.commaizeInt(count) + " " + window.$h.pluralize(count, 'View'); $(".js-view-count[data-work-id=35181717]").text(description); $(".js-view-count[data-work-id=35181717]").attr('title', description).tooltip(); }); });</script></span></span><span><span class="percentile-widget hidden"><span class="u-mr2x work-percentile"></span></span><script>$(function () { var workId = 35181717; window.Academia.workPercentilesFetcher.queue(workId, function (percentileText) { var container = $(".js-work-strip[data-work-id='35181717']"); container.find('.work-percentile').text(percentileText.charAt(0).toUpperCase() + percentileText.slice(1)); container.find('.percentile-widget').show(); container.find('.percentile-widget').removeClass('hidden'); }); });</script></span><span><script>$(function() { new Works.PaperRankView({ workId: 35181717, container: "", }); });</script></span></div><div id="work-strip-premium-row-container"></div></div></div><script> require.config({ waitSeconds: 90 })(["https://a.academia-assets.com/assets/wow_profile-f77ea15d77ce96025a6048a514272ad8becbad23c641fc2b3bd6e24ca6ff1932.js","https://a.academia-assets.com/assets/work_edit-ad038b8c047c1a8d4fa01b402d530ff93c45fee2137a149a4a5398bc8ad67560.js"], function() { // from javascript_helper.rb var dispatcherData = {} if (false){ window.WowProfile.dispatcher = window.WowProfile.dispatcher || _.clone(Backbone.Events); dispatcherData = { dispatcher: window.WowProfile.dispatcher, downloadLinkId: "-1" } } $('.js-work-strip[data-work-id=35181717]').each(function() { if (!$(this).data('initialized')) { new WowProfile.WorkStripView({ el: this, workJSON: {"id":35181717,"title":"LICHEM: A QM/MM program for simulations with multipolar and polarizable force fields","translated_title":"","metadata":{"abstract":"We introduce an initial implementation of the LICHEM software package. 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The results obtained from these test systems show the capabilities of the new software and highlight the importance of including explicit polarization. © 2016 Wiley Periodicals, Inc.","publisher":"Wiley-Blackwell","publication_date":{"day":null,"month":null,"year":2016,"errors":{}},"publication_name":"Journal of Computational Chemistry"},"translated_abstract":"We introduce an initial implementation of the LICHEM software package. LICHEM can interface with Gaussian, PSI4, NWChem, TINKER, and TINKER-HP to enable QM/MM calculations using multipolar/polarizable force fields. LICHEM extracts forces and energies from unmodified QM and MM software packages to perform geometry optimizations, single-point energy calculations, or Monte Carlo simulations. When the QM and MM regions are connected by covalent bonds, the pseudo-bond approach is employed to smoothly transition between the QM region and the polarizable force field. A series of water clusters and small peptides have been employed to test our initial implementation. The results obtained from these test systems show the capabilities of the new software and highlight the importance of including explicit polarization. © 2016 Wiley Periodicals, Inc.","internal_url":"https://www.academia.edu/35181717/LICHEM_A_QM_MM_program_for_simulations_with_multipolar_and_polarizable_force_fields","translated_internal_url":"","created_at":"2017-11-18T07:17:50.166-08:00","preview_url":null,"current_user_can_edit":null,"current_user_is_owner":null,"owner_id":35445,"coauthors_can_edit":true,"document_type":"paper","co_author_tags":[],"downloadable_attachments":[],"slug":"LICHEM_A_QM_MM_program_for_simulations_with_multipolar_and_polarizable_force_fields","translated_slug":"","page_count":null,"language":"en","content_type":"Work","owner":{"id":35445,"first_name":"Jean-Philip","middle_initials":null,"last_name":"Piquemal","page_name":"JeanPhilipPiquemal","domain_name":"sorbonne-fr","created_at":"2009-03-17T04:43:24.569-07:00","display_name":"Jean-Philip Piquemal","url":"https://sorbonne-fr.academia.edu/JeanPhilipPiquemal"},"attachments":[],"research_interests":[{"id":528,"name":"Computational Chemistry","url":"https://www.academia.edu/Documents/in/Computational_Chemistry"},{"id":6811,"name":"Quantum Theory","url":"https://www.academia.edu/Documents/in/Quantum_Theory"},{"id":53293,"name":"Software","url":"https://www.academia.edu/Documents/in/Software"},{"id":645605,"name":"THEORETICAL AND COMPUTATIONAL CHEMISTRY","url":"https://www.academia.edu/Documents/in/THEORETICAL_AND_COMPUTATIONAL_CHEMISTRY"},{"id":1333436,"name":"Monte Carlo Method","url":"https://www.academia.edu/Documents/in/Monte_Carlo_Method"}],"urls":[]}, dispatcherData: dispatcherData }); $(this).data('initialized', true); } }); $a.trackClickSource(".js-work-strip-work-link", "profile_work_strip") }); </script> <div class="js-work-strip profile--work_container" data-work-id="35181716"><div class="profile--work_thumbnail hidden-xs"><a class="js-work-strip-work-link" data-click-track="profile-work-strip-thumbnail" href="https://www.academia.edu/35181716/Scalable_improvement_of_SPME_multipolar_electrostatics_in_anisotropic_polarizable_molecular_mechanics_using_a_general_short_range_penetration_correction_up_to_quadrupoles"><img alt="Research paper thumbnail of Scalable improvement of SPME multipolar electrostatics in anisotropic polarizable molecular mechanics using a general short-range penetration correction up to quadrupoles" class="work-thumbnail" src="https://a.academia-assets.com/images/blank-paper.jpg" /></a></div><div class="wp-workCard wp-workCard_itemContainer"><div class="wp-workCard_item wp-workCard--title"><a class="js-work-strip-work-link text-gray-darker" data-click-track="profile-work-strip-title" href="https://www.academia.edu/35181716/Scalable_improvement_of_SPME_multipolar_electrostatics_in_anisotropic_polarizable_molecular_mechanics_using_a_general_short_range_penetration_correction_up_to_quadrupoles">Scalable improvement of SPME multipolar electrostatics in anisotropic polarizable molecular mechanics using a general short-range penetration correction up to quadrupoles</a></div><div class="wp-workCard_item"><span>Journal of Computational Chemistry</span><span>, 2016</span></div><div class="wp-workCard_item"><span class="js-work-more-abstract-truncated">We propose a general coupling of the Smooth Particle Mesh Ewald SPME approach for distributed mul...</span><a class="js-work-more-abstract" data-broccoli-component="work_strip.more_abstract" data-click-track="profile-work-strip-more-abstract" href="javascript:;"><span> more </span><span><i class="fa fa-caret-down"></i></span></a><span class="js-work-more-abstract-untruncated hidden">We propose a general coupling of the Smooth Particle Mesh Ewald SPME approach for distributed multipoles to a short-range charge penetration correction modifying the charge-charge, charge-dipole and charge-quadrupole energies. Such an approach significantly improves electrostatics when compared to ab initio values and has been calibrated on Symmetry-Adapted Perturbation Theory reference data. Various neutral molecular dimers have been tested and results on the complexes of mono- and divalent cations with a water ligand are also provided. Transferability of the correction is adressed in the context of the implementation of the AMOEBA and SIBFA polarizable force fields in the TINKER-HP software. As the choices of the multipolar distribution are discussed, conclusions are drawn for the future penetration-corrected polarizable force fields highlighting the mandatory need of non-spurious procedures for the obtention of well balanced and physically meaningful distributed moments. Finally, scalability and parallelism of the short-range corrected SPME approach are addressed, demonstrating that the damping function is computationally affordable and accurate for molecular dynamics simulations of complex bio- or bioinorganic systems in periodic boundary conditions. © 2016 Wiley Periodicals, Inc.</span></div><div class="wp-workCard_item wp-workCard--actions"><span class="work-strip-bookmark-button-container"></span><span class="wp-workCard--action visible-if-viewed-by-owner inline-block" style="display: none;"><span class="js-profile-work-strip-edit-button-wrapper profile-work-strip-edit-button-wrapper" data-work-id="35181716"><a class="js-profile-work-strip-edit-button" tabindex="0"><span><i class="fa fa-pencil"></i></span><span>Edit</span></a></span></span><span id="work-strip-rankings-button-container"></span></div><div class="wp-workCard_item wp-workCard--stats"><span><span><span class="js-view-count view-count u-mr2x" data-work-id="35181716"><i class="fa fa-spinner fa-spin"></i></span><script>$(function () { var workId = 35181716; window.Academia.workViewCountsFetcher.queue(workId, function (count) { var description = window.$h.commaizeInt(count) + " " + window.$h.pluralize(count, 'View'); $(".js-view-count[data-work-id=35181716]").text(description); $(".js-view-count[data-work-id=35181716]").attr('title', description).tooltip(); }); });</script></span></span><span><span class="percentile-widget hidden"><span class="u-mr2x work-percentile"></span></span><script>$(function () { var workId = 35181716; window.Academia.workPercentilesFetcher.queue(workId, function (percentileText) { var container = $(".js-work-strip[data-work-id='35181716']"); container.find('.work-percentile').text(percentileText.charAt(0).toUpperCase() + percentileText.slice(1)); container.find('.percentile-widget').show(); container.find('.percentile-widget').removeClass('hidden'); }); });</script></span><span><script>$(function() { new Works.PaperRankView({ workId: 35181716, container: "", }); });</script></span></div><div id="work-strip-premium-row-container"></div></div></div><script> require.config({ waitSeconds: 90 })(["https://a.academia-assets.com/assets/wow_profile-f77ea15d77ce96025a6048a514272ad8becbad23c641fc2b3bd6e24ca6ff1932.js","https://a.academia-assets.com/assets/work_edit-ad038b8c047c1a8d4fa01b402d530ff93c45fee2137a149a4a5398bc8ad67560.js"], function() { // from javascript_helper.rb var dispatcherData = {} if (false){ window.WowProfile.dispatcher = window.WowProfile.dispatcher || _.clone(Backbone.Events); dispatcherData = { dispatcher: window.WowProfile.dispatcher, downloadLinkId: "-1" } } $('.js-work-strip[data-work-id=35181716]').each(function() { if (!$(this).data('initialized')) { new WowProfile.WorkStripView({ el: this, workJSON: {"id":35181716,"title":"Scalable improvement of SPME multipolar electrostatics in anisotropic polarizable molecular mechanics using a general short-range penetration correction up to quadrupoles","translated_title":"","metadata":{"abstract":"We propose a general coupling of the Smooth Particle Mesh Ewald SPME approach for distributed multipoles to a short-range charge penetration correction modifying the charge-charge, charge-dipole and charge-quadrupole energies. Such an approach significantly improves electrostatics when compared to ab initio values and has been calibrated on Symmetry-Adapted Perturbation Theory reference data. Various neutral molecular dimers have been tested and results on the complexes of mono- and divalent cations with a water ligand are also provided. Transferability of the correction is adressed in the context of the implementation of the AMOEBA and SIBFA polarizable force fields in the TINKER-HP software. As the choices of the multipolar distribution are discussed, conclusions are drawn for the future penetration-corrected polarizable force fields highlighting the mandatory need of non-spurious procedures for the obtention of well balanced and physically meaningful distributed moments. Finally, scalability and parallelism of the short-range corrected SPME approach are addressed, demonstrating that the damping function is computationally affordable and accurate for molecular dynamics simulations of complex bio- or bioinorganic systems in periodic boundary conditions. © 2016 Wiley Periodicals, Inc.","publisher":"Wiley-Blackwell","publication_date":{"day":null,"month":null,"year":2016,"errors":{}},"publication_name":"Journal of Computational Chemistry"},"translated_abstract":"We propose a general coupling of the Smooth Particle Mesh Ewald SPME approach for distributed multipoles to a short-range charge penetration correction modifying the charge-charge, charge-dipole and charge-quadrupole energies. Such an approach significantly improves electrostatics when compared to ab initio values and has been calibrated on Symmetry-Adapted Perturbation Theory reference data. Various neutral molecular dimers have been tested and results on the complexes of mono- and divalent cations with a water ligand are also provided. Transferability of the correction is adressed in the context of the implementation of the AMOEBA and SIBFA polarizable force fields in the TINKER-HP software. As the choices of the multipolar distribution are discussed, conclusions are drawn for the future penetration-corrected polarizable force fields highlighting the mandatory need of non-spurious procedures for the obtention of well balanced and physically meaningful distributed moments. Finally, scalability and parallelism of the short-range corrected SPME approach are addressed, demonstrating that the damping function is computationally affordable and accurate for molecular dynamics simulations of complex bio- or bioinorganic systems in periodic boundary conditions. © 2016 Wiley Periodicals, Inc.","internal_url":"https://www.academia.edu/35181716/Scalable_improvement_of_SPME_multipolar_electrostatics_in_anisotropic_polarizable_molecular_mechanics_using_a_general_short_range_penetration_correction_up_to_quadrupoles","translated_internal_url":"","created_at":"2017-11-18T07:17:50.013-08:00","preview_url":null,"current_user_can_edit":null,"current_user_is_owner":null,"owner_id":35445,"coauthors_can_edit":true,"document_type":"paper","co_author_tags":[],"downloadable_attachments":[],"slug":"Scalable_improvement_of_SPME_multipolar_electrostatics_in_anisotropic_polarizable_molecular_mechanics_using_a_general_short_range_penetration_correction_up_to_quadrupoles","translated_slug":"","page_count":null,"language":"en","content_type":"Work","owner":{"id":35445,"first_name":"Jean-Philip","middle_initials":null,"last_name":"Piquemal","page_name":"JeanPhilipPiquemal","domain_name":"sorbonne-fr","created_at":"2009-03-17T04:43:24.569-07:00","display_name":"Jean-Philip Piquemal","url":"https://sorbonne-fr.academia.edu/JeanPhilipPiquemal"},"attachments":[],"research_interests":[{"id":522,"name":"Thermodynamics","url":"https://www.academia.edu/Documents/in/Thermodynamics"},{"id":528,"name":"Computational Chemistry","url":"https://www.academia.edu/Documents/in/Computational_Chemistry"},{"id":2215,"name":"Water","url":"https://www.academia.edu/Documents/in/Water"},{"id":2736,"name":"Molecular Dynamics Simulation","url":"https://www.academia.edu/Documents/in/Molecular_Dynamics_Simulation"},{"id":4987,"name":"Kinetics","url":"https://www.academia.edu/Documents/in/Kinetics"},{"id":6811,"name":"Quantum Theory","url":"https://www.academia.edu/Documents/in/Quantum_Theory"},{"id":37333,"name":"Anisotropy","url":"https://www.academia.edu/Documents/in/Anisotropy"},{"id":53293,"name":"Software","url":"https://www.academia.edu/Documents/in/Software"},{"id":414692,"name":"Solutions","url":"https://www.academia.edu/Documents/in/Solutions"},{"id":606320,"name":"Benzene","url":"https://www.academia.edu/Documents/in/Benzene"},{"id":645605,"name":"THEORETICAL AND COMPUTATIONAL CHEMISTRY","url":"https://www.academia.edu/Documents/in/THEORETICAL_AND_COMPUTATIONAL_CHEMISTRY"},{"id":1154485,"name":"Mechanical Processes","url":"https://www.academia.edu/Documents/in/Mechanical_Processes"},{"id":1451660,"name":"Static Electricity","url":"https://www.academia.edu/Documents/in/Static_Electricity"},{"id":1809037,"name":"Dimerization","url":"https://www.academia.edu/Documents/in/Dimerization"}],"urls":[]}, dispatcherData: dispatcherData }); $(this).data('initialized', true); } }); $a.trackClickSource(".js-work-strip-work-link", "profile_work_strip") }); </script> <div class="js-work-strip profile--work_container" data-work-id="35181715"><div class="profile--work_thumbnail hidden-xs"><a class="js-work-strip-work-link" data-click-track="profile-work-strip-thumbnail" href="https://www.academia.edu/35181715/Addressing_the_Issues_of_Non_isotropy_and_Non_additivity_in_the_Development_of_Quantum_Chemistry_Grounded_Polarizable_Molecular_Mechanics"><img alt="Research paper thumbnail of Addressing the Issues of Non-isotropy and Non-additivity in the Development of Quantum Chemistry-Grounded Polarizable Molecular Mechanics" class="work-thumbnail" src="https://a.academia-assets.com/images/blank-paper.jpg" /></a></div><div class="wp-workCard wp-workCard_itemContainer"><div class="wp-workCard_item wp-workCard--title"><a class="js-work-strip-work-link text-gray-darker" data-click-track="profile-work-strip-title" href="https://www.academia.edu/35181715/Addressing_the_Issues_of_Non_isotropy_and_Non_additivity_in_the_Development_of_Quantum_Chemistry_Grounded_Polarizable_Molecular_Mechanics">Addressing the Issues of Non-isotropy and Non-additivity in the Development of Quantum Chemistry-Grounded Polarizable Molecular Mechanics</a></div><div class="wp-workCard_item"><span>Quantum Modeling of Complex Molecular Systems</span><span>, 2015</span></div><div class="wp-workCard_item"><span class="js-work-more-abstract-truncated">ABSTRACT We review two essential features of the intermolecular interaction energies (ΔE) compute...</span><a class="js-work-more-abstract" data-broccoli-component="work_strip.more_abstract" data-click-track="profile-work-strip-more-abstract" href="javascript:;"><span> more </span><span><i class="fa fa-caret-down"></i></span></a><span class="js-work-more-abstract-untruncated hidden">ABSTRACT We review two essential features of the intermolecular interaction energies (ΔE) computed in the context of quantum chemistry (QC): non-isotropy and non-additivity. Energy-decomposition analyses show the extent to which each comes into play in the separate ΔE contributions, namely electrostatic, short-range repulsion, polarization, charge-transfer and dispersion. Such contributions have their counterparts in anisotropic, polarizable molecular mechanics (APMM), and each of these should display the same features as in QC. We review examples to evaluate the performances of APMM in this respect. They bear on the complexes of one or several ligands with metal cations, and on multiply H-bonded complexes. We also comment on the involvement of polarization, a key contributor to non-additivity, in the issues of multipole transferability and conjugation. In the last section we provide recent examples of APMM validations by QC, which relate to interactions taking place in the recognition sites of kinases and metalloproteins. We conclude by mentioning prospects of extensive applications of APMM.</span></div><div class="wp-workCard_item wp-workCard--actions"><span class="work-strip-bookmark-button-container"></span><span class="wp-workCard--action visible-if-viewed-by-owner inline-block" style="display: none;"><span class="js-profile-work-strip-edit-button-wrapper profile-work-strip-edit-button-wrapper" data-work-id="35181715"><a class="js-profile-work-strip-edit-button" tabindex="0"><span><i class="fa fa-pencil"></i></span><span>Edit</span></a></span></span><span id="work-strip-rankings-button-container"></span></div><div class="wp-workCard_item wp-workCard--stats"><span><span><span class="js-view-count view-count u-mr2x" data-work-id="35181715"><i class="fa fa-spinner fa-spin"></i></span><script>$(function () { var workId = 35181715; window.Academia.workViewCountsFetcher.queue(workId, function (count) { var description = window.$h.commaizeInt(count) + " " + window.$h.pluralize(count, 'View'); $(".js-view-count[data-work-id=35181715]").text(description); $(".js-view-count[data-work-id=35181715]").attr('title', description).tooltip(); }); });</script></span></span><span><span class="percentile-widget hidden"><span class="u-mr2x work-percentile"></span></span><script>$(function () { var workId = 35181715; window.Academia.workPercentilesFetcher.queue(workId, function (percentileText) { var container = $(".js-work-strip[data-work-id='35181715']"); container.find('.work-percentile').text(percentileText.charAt(0).toUpperCase() + percentileText.slice(1)); container.find('.percentile-widget').show(); container.find('.percentile-widget').removeClass('hidden'); }); });</script></span><span><script>$(function() { new Works.PaperRankView({ workId: 35181715, container: "", }); });</script></span></div><div id="work-strip-premium-row-container"></div></div></div><script> require.config({ waitSeconds: 90 })(["https://a.academia-assets.com/assets/wow_profile-f77ea15d77ce96025a6048a514272ad8becbad23c641fc2b3bd6e24ca6ff1932.js","https://a.academia-assets.com/assets/work_edit-ad038b8c047c1a8d4fa01b402d530ff93c45fee2137a149a4a5398bc8ad67560.js"], function() { // from javascript_helper.rb var dispatcherData = {} if (false){ window.WowProfile.dispatcher = window.WowProfile.dispatcher || _.clone(Backbone.Events); dispatcherData = { dispatcher: window.WowProfile.dispatcher, downloadLinkId: "-1" } } $('.js-work-strip[data-work-id=35181715]').each(function() { if (!$(this).data('initialized')) { new WowProfile.WorkStripView({ el: this, workJSON: {"id":35181715,"title":"Addressing the Issues of Non-isotropy and Non-additivity in the Development of Quantum Chemistry-Grounded Polarizable Molecular Mechanics","translated_title":"","metadata":{"abstract":"ABSTRACT We review two essential features of the intermolecular interaction energies (ΔE) computed in the context of quantum chemistry (QC): non-isotropy and non-additivity. Energy-decomposition analyses show the extent to which each comes into play in the separate ΔE contributions, namely electrostatic, short-range repulsion, polarization, charge-transfer and dispersion. Such contributions have their counterparts in anisotropic, polarizable molecular mechanics (APMM), and each of these should display the same features as in QC. We review examples to evaluate the performances of APMM in this respect. They bear on the complexes of one or several ligands with metal cations, and on multiply H-bonded complexes. We also comment on the involvement of polarization, a key contributor to non-additivity, in the issues of multipole transferability and conjugation. In the last section we provide recent examples of APMM validations by QC, which relate to interactions taking place in the recognition sites of kinases and metalloproteins. We conclude by mentioning prospects of extensive applications of APMM.","publication_date":{"day":null,"month":null,"year":2015,"errors":{}},"publication_name":"Quantum Modeling of Complex Molecular Systems"},"translated_abstract":"ABSTRACT We review two essential features of the intermolecular interaction energies (ΔE) computed in the context of quantum chemistry (QC): non-isotropy and non-additivity. Energy-decomposition analyses show the extent to which each comes into play in the separate ΔE contributions, namely electrostatic, short-range repulsion, polarization, charge-transfer and dispersion. Such contributions have their counterparts in anisotropic, polarizable molecular mechanics (APMM), and each of these should display the same features as in QC. We review examples to evaluate the performances of APMM in this respect. They bear on the complexes of one or several ligands with metal cations, and on multiply H-bonded complexes. We also comment on the involvement of polarization, a key contributor to non-additivity, in the issues of multipole transferability and conjugation. In the last section we provide recent examples of APMM validations by QC, which relate to interactions taking place in the recognition sites of kinases and metalloproteins. We conclude by mentioning prospects of extensive applications of APMM.","internal_url":"https://www.academia.edu/35181715/Addressing_the_Issues_of_Non_isotropy_and_Non_additivity_in_the_Development_of_Quantum_Chemistry_Grounded_Polarizable_Molecular_Mechanics","translated_internal_url":"","created_at":"2017-11-18T07:17:49.862-08:00","preview_url":null,"current_user_can_edit":null,"current_user_is_owner":null,"owner_id":35445,"coauthors_can_edit":true,"document_type":"paper","co_author_tags":[],"downloadable_attachments":[],"slug":"Addressing_the_Issues_of_Non_isotropy_and_Non_additivity_in_the_Development_of_Quantum_Chemistry_Grounded_Polarizable_Molecular_Mechanics","translated_slug":"","page_count":null,"language":"en","content_type":"Work","owner":{"id":35445,"first_name":"Jean-Philip","middle_initials":null,"last_name":"Piquemal","page_name":"JeanPhilipPiquemal","domain_name":"sorbonne-fr","created_at":"2009-03-17T04:43:24.569-07:00","display_name":"Jean-Philip Piquemal","url":"https://sorbonne-fr.academia.edu/JeanPhilipPiquemal"},"attachments":[],"research_interests":[],"urls":[]}, dispatcherData: dispatcherData }); $(this).data('initialized', true); } }); $a.trackClickSource(".js-work-strip-work-link", "profile_work_strip") }); </script> <div class="js-work-strip profile--work_container" data-work-id="35181714"><div class="profile--work_thumbnail hidden-xs"><a class="js-work-strip-work-link" data-click-track="profile-work-strip-thumbnail" href="https://www.academia.edu/35181714/Approaching_the_double_faceted_nature_of_the_CX_bond_in_halobenzenes_with_a_bifunctional_probe"><img alt="Research paper thumbnail of Approaching the double-faceted nature of the CX bond in halobenzenes with a bifunctional probe" class="work-thumbnail" src="https://a.academia-assets.com/images/blank-paper.jpg" /></a></div><div class="wp-workCard wp-workCard_itemContainer"><div class="wp-workCard_item wp-workCard--title"><a class="js-work-strip-work-link text-gray-darker" data-click-track="profile-work-strip-title" href="https://www.academia.edu/35181714/Approaching_the_double_faceted_nature_of_the_CX_bond_in_halobenzenes_with_a_bifunctional_probe">Approaching the double-faceted nature of the CX bond in halobenzenes with a bifunctional probe</a></div><div class="wp-workCard_item"><span>Chemical Physics Letters</span><span>, 2015</span></div><div class="wp-workCard_item"><span class="js-work-more-abstract-truncated">ABSTRACT In halobenzenes, the CX bond (X = Cl, Br) is doubly faceted, electron-deficient along th...</span><a class="js-work-more-abstract" data-broccoli-component="work_strip.more_abstract" data-click-track="profile-work-strip-more-abstract" href="javascript:;"><span> more </span><span><i class="fa fa-caret-down"></i></span></a><span class="js-work-more-abstract-untruncated hidden">ABSTRACT In halobenzenes, the CX bond (X = Cl, Br) is doubly faceted, electron-deficient along the CX direction, and electron-rich on its flanks. We have recently shown that both features could be enhanced by appropriate electron-withdrawing and electron-donating groups, respectively. In this paper we further highlight this dual character by approaching a bifunctional probe, N-methylformamide, to both regions in representative substituted halobenzenes. We report the results of interaction energy computations, ELF, and NCI analyses. These methods used in conjunction show the responsiveness of the CX bond to both kinds of substitutions, enabling significant interaction energy gains with respect to the parent compound.</span></div><div class="wp-workCard_item wp-workCard--actions"><span class="work-strip-bookmark-button-container"></span><span class="wp-workCard--action visible-if-viewed-by-owner inline-block" style="display: none;"><span class="js-profile-work-strip-edit-button-wrapper profile-work-strip-edit-button-wrapper" data-work-id="35181714"><a class="js-profile-work-strip-edit-button" tabindex="0"><span><i class="fa fa-pencil"></i></span><span>Edit</span></a></span></span><span id="work-strip-rankings-button-container"></span></div><div class="wp-workCard_item wp-workCard--stats"><span><span><span class="js-view-count view-count u-mr2x" data-work-id="35181714"><i class="fa fa-spinner fa-spin"></i></span><script>$(function () { var workId = 35181714; window.Academia.workViewCountsFetcher.queue(workId, function (count) { var description = window.$h.commaizeInt(count) + " " + window.$h.pluralize(count, 'View'); $(".js-view-count[data-work-id=35181714]").text(description); $(".js-view-count[data-work-id=35181714]").attr('title', description).tooltip(); }); });</script></span></span><span><span class="percentile-widget hidden"><span class="u-mr2x work-percentile"></span></span><script>$(function () { var workId = 35181714; window.Academia.workPercentilesFetcher.queue(workId, function (percentileText) { var container = $(".js-work-strip[data-work-id='35181714']"); container.find('.work-percentile').text(percentileText.charAt(0).toUpperCase() + percentileText.slice(1)); container.find('.percentile-widget').show(); container.find('.percentile-widget').removeClass('hidden'); }); });</script></span><span><script>$(function() { new Works.PaperRankView({ workId: 35181714, container: "", }); });</script></span></div><div id="work-strip-premium-row-container"></div></div></div><script> require.config({ waitSeconds: 90 })(["https://a.academia-assets.com/assets/wow_profile-f77ea15d77ce96025a6048a514272ad8becbad23c641fc2b3bd6e24ca6ff1932.js","https://a.academia-assets.com/assets/work_edit-ad038b8c047c1a8d4fa01b402d530ff93c45fee2137a149a4a5398bc8ad67560.js"], function() { // from javascript_helper.rb var dispatcherData = {} if (false){ window.WowProfile.dispatcher = window.WowProfile.dispatcher || _.clone(Backbone.Events); dispatcherData = { dispatcher: window.WowProfile.dispatcher, downloadLinkId: "-1" } } $('.js-work-strip[data-work-id=35181714]').each(function() { if (!$(this).data('initialized')) { new WowProfile.WorkStripView({ el: this, workJSON: {"id":35181714,"title":"Approaching the double-faceted nature of the CX bond in halobenzenes with a bifunctional probe","translated_title":"","metadata":{"abstract":"ABSTRACT In halobenzenes, the CX bond (X = Cl, Br) is doubly faceted, electron-deficient along the CX direction, and electron-rich on its flanks. We have recently shown that both features could be enhanced by appropriate electron-withdrawing and electron-donating groups, respectively. In this paper we further highlight this dual character by approaching a bifunctional probe, N-methylformamide, to both regions in representative substituted halobenzenes. We report the results of interaction energy computations, ELF, and NCI analyses. These methods used in conjunction show the responsiveness of the CX bond to both kinds of substitutions, enabling significant interaction energy gains with respect to the parent compound.","publisher":"Elsevier BV","publication_date":{"day":null,"month":null,"year":2015,"errors":{}},"publication_name":"Chemical Physics Letters"},"translated_abstract":"ABSTRACT In halobenzenes, the CX bond (X = Cl, Br) is doubly faceted, electron-deficient along the CX direction, and electron-rich on its flanks. We have recently shown that both features could be enhanced by appropriate electron-withdrawing and electron-donating groups, respectively. In this paper we further highlight this dual character by approaching a bifunctional probe, N-methylformamide, to both regions in representative substituted halobenzenes. We report the results of interaction energy computations, ELF, and NCI analyses. These methods used in conjunction show the responsiveness of the CX bond to both kinds of substitutions, enabling significant interaction energy gains with respect to the parent compound.","internal_url":"https://www.academia.edu/35181714/Approaching_the_double_faceted_nature_of_the_CX_bond_in_halobenzenes_with_a_bifunctional_probe","translated_internal_url":"","created_at":"2017-11-18T07:17:49.671-08:00","preview_url":null,"current_user_can_edit":null,"current_user_is_owner":null,"owner_id":35445,"coauthors_can_edit":true,"document_type":"paper","co_author_tags":[],"downloadable_attachments":[],"slug":"Approaching_the_double_faceted_nature_of_the_CX_bond_in_halobenzenes_with_a_bifunctional_probe","translated_slug":"","page_count":null,"language":"en","content_type":"Work","owner":{"id":35445,"first_name":"Jean-Philip","middle_initials":null,"last_name":"Piquemal","page_name":"JeanPhilipPiquemal","domain_name":"sorbonne-fr","created_at":"2009-03-17T04:43:24.569-07:00","display_name":"Jean-Philip Piquemal","url":"https://sorbonne-fr.academia.edu/JeanPhilipPiquemal"},"attachments":[],"research_interests":[{"id":923,"name":"Technology","url":"https://www.academia.edu/Documents/in/Technology"},{"id":118582,"name":"Physical sciences","url":"https://www.academia.edu/Documents/in/Physical_sciences"},{"id":260118,"name":"CHEMICAL SCIENCES","url":"https://www.academia.edu/Documents/in/CHEMICAL_SCIENCES"}],"urls":[]}, dispatcherData: dispatcherData }); $(this).data('initialized', true); } }); $a.trackClickSource(".js-work-strip-work-link", "profile_work_strip") }); </script> <div class="js-work-strip profile--work_container" data-work-id="35181713"><div class="profile--work_thumbnail hidden-xs"><a class="js-work-strip-work-link" data-click-track="profile-work-strip-thumbnail" href="https://www.academia.edu/35181713/Stacked_and_H_bonded_Cytosine_Dimers_Analysis_of_the_Intermolecular_Interaction_Energies_by_Parallel_Quantum_Chemistry_and_Polarizable_Molecular_Mechanics"><img alt="Research paper thumbnail of Stacked and H-bonded Cytosine Dimers. Analysis of the Intermolecular Interaction Energies by Parallel Quantum Chemistry and Polarizable Molecular Mechanics" class="work-thumbnail" src="https://a.academia-assets.com/images/blank-paper.jpg" /></a></div><div class="wp-workCard wp-workCard_itemContainer"><div class="wp-workCard_item wp-workCard--title"><a class="js-work-strip-work-link text-gray-darker" data-click-track="profile-work-strip-title" href="https://www.academia.edu/35181713/Stacked_and_H_bonded_Cytosine_Dimers_Analysis_of_the_Intermolecular_Interaction_Energies_by_Parallel_Quantum_Chemistry_and_Polarizable_Molecular_Mechanics">Stacked and H-bonded Cytosine Dimers. Analysis of the Intermolecular Interaction Energies by Parallel Quantum Chemistry and Polarizable Molecular Mechanics</a></div><div class="wp-workCard_item"><span>The journal of physical chemistry. B</span><span>, Jan 29, 2015</span></div><div class="wp-workCard_item"><span class="js-work-more-abstract-truncated">Until now, atomistic simulations of DNA and RNA and their complexes have been executed using well...</span><a class="js-work-more-abstract" data-broccoli-component="work_strip.more_abstract" data-click-track="profile-work-strip-more-abstract" href="javascript:;"><span> more </span><span><i class="fa fa-caret-down"></i></span></a><span class="js-work-more-abstract-untruncated hidden">Until now, atomistic simulations of DNA and RNA and their complexes have been executed using well calibrated but conceptually simple pair-additive empirical potentials (force fields). Although such simulations provided many valuable results, it is well established that simple force fields also introduce errors into the description, underlying the need for development of alternative anisotropic, polarizable molecular mechanics (APMM) potentials. One of the most abundant forces in all kinds on nucleic acids topologies is base stacking. Intra- and interstrand stacking is assumed to be the most essential factor affecting local conformational variations of B-DNA. However, stacking also contributes to formation of all kinds of non-canonical nucleic acids structures, such as quadruplexes or folded RNAs. The present study focuses on fourteen stacked cytosine (Cyt) dimers and the doubly H-bonded dimer. We evaluate the extent to which an APMM procedure, SIBFA, could account quantitatively for...</span></div><div class="wp-workCard_item wp-workCard--actions"><span class="work-strip-bookmark-button-container"></span><span class="wp-workCard--action visible-if-viewed-by-owner inline-block" style="display: none;"><span class="js-profile-work-strip-edit-button-wrapper profile-work-strip-edit-button-wrapper" data-work-id="35181713"><a class="js-profile-work-strip-edit-button" tabindex="0"><span><i class="fa fa-pencil"></i></span><span>Edit</span></a></span></span><span id="work-strip-rankings-button-container"></span></div><div class="wp-workCard_item wp-workCard--stats"><span><span><span class="js-view-count view-count u-mr2x" data-work-id="35181713"><i class="fa fa-spinner fa-spin"></i></span><script>$(function () { var workId = 35181713; window.Academia.workViewCountsFetcher.queue(workId, function (count) { var description = window.$h.commaizeInt(count) + " " + window.$h.pluralize(count, 'View'); $(".js-view-count[data-work-id=35181713]").text(description); $(".js-view-count[data-work-id=35181713]").attr('title', description).tooltip(); }); });</script></span></span><span><span class="percentile-widget hidden"><span class="u-mr2x work-percentile"></span></span><script>$(function () { var workId = 35181713; window.Academia.workPercentilesFetcher.queue(workId, function (percentileText) { var container = $(".js-work-strip[data-work-id='35181713']"); container.find('.work-percentile').text(percentileText.charAt(0).toUpperCase() + percentileText.slice(1)); container.find('.percentile-widget').show(); container.find('.percentile-widget').removeClass('hidden'); }); });</script></span><span><script>$(function() { new Works.PaperRankView({ workId: 35181713, container: "", }); });</script></span></div><div id="work-strip-premium-row-container"></div></div></div><script> require.config({ waitSeconds: 90 })(["https://a.academia-assets.com/assets/wow_profile-f77ea15d77ce96025a6048a514272ad8becbad23c641fc2b3bd6e24ca6ff1932.js","https://a.academia-assets.com/assets/work_edit-ad038b8c047c1a8d4fa01b402d530ff93c45fee2137a149a4a5398bc8ad67560.js"], function() { // from javascript_helper.rb var dispatcherData = {} if (false){ window.WowProfile.dispatcher = window.WowProfile.dispatcher || _.clone(Backbone.Events); dispatcherData = { dispatcher: window.WowProfile.dispatcher, downloadLinkId: "-1" } } $('.js-work-strip[data-work-id=35181713]').each(function() { if (!$(this).data('initialized')) { new WowProfile.WorkStripView({ el: this, workJSON: {"id":35181713,"title":"Stacked and H-bonded Cytosine Dimers. Analysis of the Intermolecular Interaction Energies by Parallel Quantum Chemistry and Polarizable Molecular Mechanics","translated_title":"","metadata":{"abstract":"Until now, atomistic simulations of DNA and RNA and their complexes have been executed using well calibrated but conceptually simple pair-additive empirical potentials (force fields). Although such simulations provided many valuable results, it is well established that simple force fields also introduce errors into the description, underlying the need for development of alternative anisotropic, polarizable molecular mechanics (APMM) potentials. One of the most abundant forces in all kinds on nucleic acids topologies is base stacking. Intra- and interstrand stacking is assumed to be the most essential factor affecting local conformational variations of B-DNA. However, stacking also contributes to formation of all kinds of non-canonical nucleic acids structures, such as quadruplexes or folded RNAs. The present study focuses on fourteen stacked cytosine (Cyt) dimers and the doubly H-bonded dimer. We evaluate the extent to which an APMM procedure, SIBFA, could account quantitatively for...","publication_date":{"day":29,"month":1,"year":2015,"errors":{}},"publication_name":"The journal of physical chemistry. B"},"translated_abstract":"Until now, atomistic simulations of DNA and RNA and their complexes have been executed using well calibrated but conceptually simple pair-additive empirical potentials (force fields). Although such simulations provided many valuable results, it is well established that simple force fields also introduce errors into the description, underlying the need for development of alternative anisotropic, polarizable molecular mechanics (APMM) potentials. One of the most abundant forces in all kinds on nucleic acids topologies is base stacking. Intra- and interstrand stacking is assumed to be the most essential factor affecting local conformational variations of B-DNA. However, stacking also contributes to formation of all kinds of non-canonical nucleic acids structures, such as quadruplexes or folded RNAs. The present study focuses on fourteen stacked cytosine (Cyt) dimers and the doubly H-bonded dimer. We evaluate the extent to which an APMM procedure, SIBFA, could account quantitatively for...","internal_url":"https://www.academia.edu/35181713/Stacked_and_H_bonded_Cytosine_Dimers_Analysis_of_the_Intermolecular_Interaction_Energies_by_Parallel_Quantum_Chemistry_and_Polarizable_Molecular_Mechanics","translated_internal_url":"","created_at":"2017-11-18T07:17:49.508-08:00","preview_url":null,"current_user_can_edit":null,"current_user_is_owner":null,"owner_id":35445,"coauthors_can_edit":true,"document_type":"paper","co_author_tags":[],"downloadable_attachments":[],"slug":"Stacked_and_H_bonded_Cytosine_Dimers_Analysis_of_the_Intermolecular_Interaction_Energies_by_Parallel_Quantum_Chemistry_and_Polarizable_Molecular_Mechanics","translated_slug":"","page_count":null,"language":"en","content_type":"Work","owner":{"id":35445,"first_name":"Jean-Philip","middle_initials":null,"last_name":"Piquemal","page_name":"JeanPhilipPiquemal","domain_name":"sorbonne-fr","created_at":"2009-03-17T04:43:24.569-07:00","display_name":"Jean-Philip Piquemal","url":"https://sorbonne-fr.academia.edu/JeanPhilipPiquemal"},"attachments":[],"research_interests":[{"id":48,"name":"Engineering","url":"https://www.academia.edu/Documents/in/Engineering"},{"id":522,"name":"Thermodynamics","url":"https://www.academia.edu/Documents/in/Thermodynamics"},{"id":2215,"name":"Water","url":"https://www.academia.edu/Documents/in/Water"},{"id":6811,"name":"Quantum Theory","url":"https://www.academia.edu/Documents/in/Quantum_Theory"},{"id":48057,"name":"DNA","url":"https://www.academia.edu/Documents/in/DNA"},{"id":70902,"name":"Magnesium","url":"https://www.academia.edu/Documents/in/Magnesium"},{"id":118582,"name":"Physical sciences","url":"https://www.academia.edu/Documents/in/Physical_sciences"},{"id":260118,"name":"CHEMICAL SCIENCES","url":"https://www.academia.edu/Documents/in/CHEMICAL_SCIENCES"},{"id":296798,"name":"Hydrogen Bonding","url":"https://www.academia.edu/Documents/in/Hydrogen_Bonding"},{"id":649537,"name":"Molecular Conformation","url":"https://www.academia.edu/Documents/in/Molecular_Conformation"},{"id":1809037,"name":"Dimerization","url":"https://www.academia.edu/Documents/in/Dimerization"}],"urls":[]}, dispatcherData: dispatcherData }); $(this).data('initialized', true); } }); $a.trackClickSource(".js-work-strip-work-link", "profile_work_strip") }); </script> <div class="js-work-strip profile--work_container" data-work-id="35181712"><div class="profile--work_thumbnail hidden-xs"><a class="js-work-strip-work-link" data-click-track="profile-work-strip-thumbnail" href="https://www.academia.edu/35181712/General_Model_for_Treating_Short_Range_Electrostatic_Penetration_in_a_Molecular_Mechanics_Force_Field"><img alt="Research paper thumbnail of General Model for Treating Short-Range Electrostatic Penetration in a Molecular Mechanics Force Field" class="work-thumbnail" src="https://a.academia-assets.com/images/blank-paper.jpg" /></a></div><div class="wp-workCard wp-workCard_itemContainer"><div class="wp-workCard_item wp-workCard--title"><a class="js-work-strip-work-link text-gray-darker" data-click-track="profile-work-strip-title" href="https://www.academia.edu/35181712/General_Model_for_Treating_Short_Range_Electrostatic_Penetration_in_a_Molecular_Mechanics_Force_Field">General Model for Treating Short-Range Electrostatic Penetration in a Molecular Mechanics Force Field</a></div><div class="wp-workCard_item"><span>Journal of Chemical Theory and Computation</span><span>, 2015</span></div><div class="wp-workCard_item"><span class="js-work-more-abstract-truncated">Classical molecular mechanics force fields typically model interatomic electrostatic interactions...</span><a class="js-work-more-abstract" data-broccoli-component="work_strip.more_abstract" data-click-track="profile-work-strip-more-abstract" href="javascript:;"><span> more </span><span><i class="fa fa-caret-down"></i></span></a><span class="js-work-more-abstract-untruncated hidden">Classical molecular mechanics force fields typically model interatomic electrostatic interactions with point charges or multipole expansions, which can fail for atoms in close contact due to the lack of a description of penetration effects between their electron clouds. These short-range penetration effects can be significant and are essential for accurate modeling of intermolecular interactions. In this work we report parametrization of an empirical charge-charge function previously reported (Piquemal J.-P.; J. Phys. Chem. A2003, 107, 10353) to correct for the missing penetration term in standard molecular mechanics force fields. For this purpose, we have developed a database (S101×7) of 101 unique molecular dimers, each at 7 different intermolecular distances. Electrostatic, induction/polarization, repulsion, and dispersion energies, as well as the total interaction energy for each complex in the database are calculated using the SAPT2+ method (Parker T. M.; J. Chem. Phys.2014, 140, 094106). This empirical penetration model significantly improves agreement between point multipole and quantum mechanical electrostatic energies across the set of dimers and distances, while using only a limited set of parameters for each chemical element. Given the simplicity and effectiveness of the model, we expect the electrostatic penetration correction will become a standard component of future molecular mechanics force fields.</span></div><div class="wp-workCard_item wp-workCard--actions"><span class="work-strip-bookmark-button-container"></span><span class="wp-workCard--action visible-if-viewed-by-owner inline-block" style="display: none;"><span class="js-profile-work-strip-edit-button-wrapper profile-work-strip-edit-button-wrapper" data-work-id="35181712"><a class="js-profile-work-strip-edit-button" tabindex="0"><span><i class="fa fa-pencil"></i></span><span>Edit</span></a></span></span><span id="work-strip-rankings-button-container"></span></div><div class="wp-workCard_item wp-workCard--stats"><span><span><span class="js-view-count view-count u-mr2x" data-work-id="35181712"><i class="fa fa-spinner fa-spin"></i></span><script>$(function () { var workId = 35181712; window.Academia.workViewCountsFetcher.queue(workId, function (count) { var description = window.$h.commaizeInt(count) + " " + window.$h.pluralize(count, 'View'); $(".js-view-count[data-work-id=35181712]").text(description); $(".js-view-count[data-work-id=35181712]").attr('title', description).tooltip(); }); });</script></span></span><span><span class="percentile-widget hidden"><span class="u-mr2x work-percentile"></span></span><script>$(function () { var workId = 35181712; window.Academia.workPercentilesFetcher.queue(workId, function (percentileText) { var container = $(".js-work-strip[data-work-id='35181712']"); container.find('.work-percentile').text(percentileText.charAt(0).toUpperCase() + percentileText.slice(1)); container.find('.percentile-widget').show(); container.find('.percentile-widget').removeClass('hidden'); }); });</script></span><span><script>$(function() { new Works.PaperRankView({ workId: 35181712, container: "", }); });</script></span></div><div id="work-strip-premium-row-container"></div></div></div><script> require.config({ waitSeconds: 90 })(["https://a.academia-assets.com/assets/wow_profile-f77ea15d77ce96025a6048a514272ad8becbad23c641fc2b3bd6e24ca6ff1932.js","https://a.academia-assets.com/assets/work_edit-ad038b8c047c1a8d4fa01b402d530ff93c45fee2137a149a4a5398bc8ad67560.js"], function() { // from javascript_helper.rb var dispatcherData = {} if (false){ window.WowProfile.dispatcher = window.WowProfile.dispatcher || _.clone(Backbone.Events); dispatcherData = { dispatcher: window.WowProfile.dispatcher, downloadLinkId: "-1" } } $('.js-work-strip[data-work-id=35181712]').each(function() { if (!$(this).data('initialized')) { new WowProfile.WorkStripView({ el: this, workJSON: {"id":35181712,"title":"General Model for Treating Short-Range Electrostatic Penetration in a Molecular Mechanics Force Field","translated_title":"","metadata":{"abstract":"Classical molecular mechanics force fields typically model interatomic electrostatic interactions with point charges or multipole expansions, which can fail for atoms in close contact due to the lack of a description of penetration effects between their electron clouds. These short-range penetration effects can be significant and are essential for accurate modeling of intermolecular interactions. In this work we report parametrization of an empirical charge-charge function previously reported (Piquemal J.-P.; J. Phys. Chem. A2003, 107, 10353) to correct for the missing penetration term in standard molecular mechanics force fields. For this purpose, we have developed a database (S101×7) of 101 unique molecular dimers, each at 7 different intermolecular distances. Electrostatic, induction/polarization, repulsion, and dispersion energies, as well as the total interaction energy for each complex in the database are calculated using the SAPT2+ method (Parker T. M.; J. Chem. Phys.2014, 140, 094106). This empirical penetration model significantly improves agreement between point multipole and quantum mechanical electrostatic energies across the set of dimers and distances, while using only a limited set of parameters for each chemical element. Given the simplicity and effectiveness of the model, we expect the electrostatic penetration correction will become a standard component of future molecular mechanics force fields.","publisher":"American Chemical Society (ACS)","publication_date":{"day":null,"month":null,"year":2015,"errors":{}},"publication_name":"Journal of Chemical Theory and Computation"},"translated_abstract":"Classical molecular mechanics force fields typically model interatomic electrostatic interactions with point charges or multipole expansions, which can fail for atoms in close contact due to the lack of a description of penetration effects between their electron clouds. These short-range penetration effects can be significant and are essential for accurate modeling of intermolecular interactions. In this work we report parametrization of an empirical charge-charge function previously reported (Piquemal J.-P.; J. Phys. Chem. A2003, 107, 10353) to correct for the missing penetration term in standard molecular mechanics force fields. For this purpose, we have developed a database (S101×7) of 101 unique molecular dimers, each at 7 different intermolecular distances. Electrostatic, induction/polarization, repulsion, and dispersion energies, as well as the total interaction energy for each complex in the database are calculated using the SAPT2+ method (Parker T. M.; J. Chem. Phys.2014, 140, 094106). This empirical penetration model significantly improves agreement between point multipole and quantum mechanical electrostatic energies across the set of dimers and distances, while using only a limited set of parameters for each chemical element. Given the simplicity and effectiveness of the model, we expect the electrostatic penetration correction will become a standard component of future molecular mechanics force fields.","internal_url":"https://www.academia.edu/35181712/General_Model_for_Treating_Short_Range_Electrostatic_Penetration_in_a_Molecular_Mechanics_Force_Field","translated_internal_url":"","created_at":"2017-11-18T07:17:49.354-08:00","preview_url":null,"current_user_can_edit":null,"current_user_is_owner":null,"owner_id":35445,"coauthors_can_edit":true,"document_type":"paper","co_author_tags":[],"downloadable_attachments":[],"slug":"General_Model_for_Treating_Short_Range_Electrostatic_Penetration_in_a_Molecular_Mechanics_Force_Field","translated_slug":"","page_count":null,"language":"en","content_type":"Work","owner":{"id":35445,"first_name":"Jean-Philip","middle_initials":null,"last_name":"Piquemal","page_name":"JeanPhilipPiquemal","domain_name":"sorbonne-fr","created_at":"2009-03-17T04:43:24.569-07:00","display_name":"Jean-Philip Piquemal","url":"https://sorbonne-fr.academia.edu/JeanPhilipPiquemal"},"attachments":[],"research_interests":[{"id":645605,"name":"THEORETICAL AND COMPUTATIONAL CHEMISTRY","url":"https://www.academia.edu/Documents/in/THEORETICAL_AND_COMPUTATIONAL_CHEMISTRY"}],"urls":[]}, dispatcherData: dispatcherData }); $(this).data('initialized', true); } }); $a.trackClickSource(".js-work-strip-work-link", "profile_work_strip") }); </script> <div class="js-work-strip profile--work_container" data-work-id="35181711"><div class="profile--work_thumbnail hidden-xs"><a class="js-work-strip-work-link" data-click-track="profile-work-strip-thumbnail" href="https://www.academia.edu/35181711/Polarizable_Force_Fields_for_Biomolecular_Modeling"><img alt="Research paper thumbnail of Polarizable Force Fields for Biomolecular Modeling" class="work-thumbnail" src="https://a.academia-assets.com/images/blank-paper.jpg" /></a></div><div class="wp-workCard wp-workCard_itemContainer"><div class="wp-workCard_item wp-workCard--title"><a class="js-work-strip-work-link text-gray-darker" data-click-track="profile-work-strip-title" href="https://www.academia.edu/35181711/Polarizable_Force_Fields_for_Biomolecular_Modeling">Polarizable Force Fields for Biomolecular Modeling</a></div><div class="wp-workCard_item"><span>Reviews in Computational Chemistry</span><span>, 2015</span></div><div class="wp-workCard_item"><span class="js-work-more-abstract-truncated">ABSTRACT This chapter focuses on the recent developments in different polarizable force fields. T...</span><a class="js-work-more-abstract" data-broccoli-component="work_strip.more_abstract" data-click-track="profile-work-strip-more-abstract" href="javascript:;"><span> more </span><span><i class="fa fa-caret-down"></i></span></a><span class="js-work-more-abstract-untruncated hidden">ABSTRACT This chapter focuses on the recent developments in different polarizable force fields. These include atomic multipole optimized energetics for biomolecular applications (AMOEBA), sum of interactions between fragments ab initio computed (SIBFA), nonempirical molecular orbital (NEMO), CHARMM fluctuating charge model (FQ), and polarizable protein force field (PFF). The chapter begins with a brief introduction to the basic principles and formulae underlying alternative models. It reviews recent progress of several well-developed polarizable force fields. Finally, the chapter presents applications of polarizable models to a range of molecular systems, including water and other small molecules, ion solvation, peptides, proteins, and lipid systems. Beyond polarization, modeling the conformational flexibility and corresponding intermolecular energetics of organic molecules via sampling methods such as molecular dynamics is essential to predicting the thermodynamic properties of crystals. The importance of polarization still needs to be established systematically for a wide range of biological systems.</span></div><div class="wp-workCard_item wp-workCard--actions"><span class="work-strip-bookmark-button-container"></span><span class="wp-workCard--action visible-if-viewed-by-owner inline-block" style="display: none;"><span class="js-profile-work-strip-edit-button-wrapper profile-work-strip-edit-button-wrapper" data-work-id="35181711"><a class="js-profile-work-strip-edit-button" tabindex="0"><span><i class="fa fa-pencil"></i></span><span>Edit</span></a></span></span><span id="work-strip-rankings-button-container"></span></div><div class="wp-workCard_item wp-workCard--stats"><span><span><span class="js-view-count view-count u-mr2x" data-work-id="35181711"><i class="fa fa-spinner fa-spin"></i></span><script>$(function () { var workId = 35181711; window.Academia.workViewCountsFetcher.queue(workId, function (count) { var description = window.$h.commaizeInt(count) + " " + window.$h.pluralize(count, 'View'); $(".js-view-count[data-work-id=35181711]").text(description); $(".js-view-count[data-work-id=35181711]").attr('title', description).tooltip(); }); });</script></span></span><span><span class="percentile-widget hidden"><span class="u-mr2x work-percentile"></span></span><script>$(function () { var workId = 35181711; window.Academia.workPercentilesFetcher.queue(workId, function (percentileText) { var container = $(".js-work-strip[data-work-id='35181711']"); container.find('.work-percentile').text(percentileText.charAt(0).toUpperCase() + percentileText.slice(1)); container.find('.percentile-widget').show(); container.find('.percentile-widget').removeClass('hidden'); }); });</script></span><span><script>$(function() { new Works.PaperRankView({ workId: 35181711, container: "", }); });</script></span></div><div id="work-strip-premium-row-container"></div></div></div><script> require.config({ waitSeconds: 90 })(["https://a.academia-assets.com/assets/wow_profile-f77ea15d77ce96025a6048a514272ad8becbad23c641fc2b3bd6e24ca6ff1932.js","https://a.academia-assets.com/assets/work_edit-ad038b8c047c1a8d4fa01b402d530ff93c45fee2137a149a4a5398bc8ad67560.js"], function() { // from javascript_helper.rb var dispatcherData = {} if (false){ window.WowProfile.dispatcher = window.WowProfile.dispatcher || _.clone(Backbone.Events); dispatcherData = { dispatcher: window.WowProfile.dispatcher, downloadLinkId: "-1" } } $('.js-work-strip[data-work-id=35181711]').each(function() { if (!$(this).data('initialized')) { new WowProfile.WorkStripView({ el: this, workJSON: {"id":35181711,"title":"Polarizable Force Fields for Biomolecular Modeling","translated_title":"","metadata":{"abstract":"ABSTRACT This chapter focuses on the recent developments in different polarizable force fields. These include atomic multipole optimized energetics for biomolecular applications (AMOEBA), sum of interactions between fragments ab initio computed (SIBFA), nonempirical molecular orbital (NEMO), CHARMM fluctuating charge model (FQ), and polarizable protein force field (PFF). The chapter begins with a brief introduction to the basic principles and formulae underlying alternative models. It reviews recent progress of several well-developed polarizable force fields. Finally, the chapter presents applications of polarizable models to a range of molecular systems, including water and other small molecules, ion solvation, peptides, proteins, and lipid systems. Beyond polarization, modeling the conformational flexibility and corresponding intermolecular energetics of organic molecules via sampling methods such as molecular dynamics is essential to predicting the thermodynamic properties of crystals. The importance of polarization still needs to be established systematically for a wide range of biological systems.","publisher":"John Wiley \u0026 Sons, Inc","publication_date":{"day":null,"month":null,"year":2015,"errors":{}},"publication_name":"Reviews in Computational Chemistry"},"translated_abstract":"ABSTRACT This chapter focuses on the recent developments in different polarizable force fields. These include atomic multipole optimized energetics for biomolecular applications (AMOEBA), sum of interactions between fragments ab initio computed (SIBFA), nonempirical molecular orbital (NEMO), CHARMM fluctuating charge model (FQ), and polarizable protein force field (PFF). The chapter begins with a brief introduction to the basic principles and formulae underlying alternative models. It reviews recent progress of several well-developed polarizable force fields. Finally, the chapter presents applications of polarizable models to a range of molecular systems, including water and other small molecules, ion solvation, peptides, proteins, and lipid systems. Beyond polarization, modeling the conformational flexibility and corresponding intermolecular energetics of organic molecules via sampling methods such as molecular dynamics is essential to predicting the thermodynamic properties of crystals. The importance of polarization still needs to be established systematically for a wide range of biological systems.","internal_url":"https://www.academia.edu/35181711/Polarizable_Force_Fields_for_Biomolecular_Modeling","translated_internal_url":"","created_at":"2017-11-18T07:17:49.207-08:00","preview_url":null,"current_user_can_edit":null,"current_user_is_owner":null,"owner_id":35445,"coauthors_can_edit":true,"document_type":"paper","co_author_tags":[],"downloadable_attachments":[],"slug":"Polarizable_Force_Fields_for_Biomolecular_Modeling","translated_slug":"","page_count":null,"language":"en","content_type":"Work","owner":{"id":35445,"first_name":"Jean-Philip","middle_initials":null,"last_name":"Piquemal","page_name":"JeanPhilipPiquemal","domain_name":"sorbonne-fr","created_at":"2009-03-17T04:43:24.569-07:00","display_name":"Jean-Philip Piquemal","url":"https://sorbonne-fr.academia.edu/JeanPhilipPiquemal"},"attachments":[],"research_interests":[{"id":181569,"name":"Proteins","url":"https://www.academia.edu/Documents/in/Proteins"},{"id":645605,"name":"THEORETICAL AND COMPUTATIONAL CHEMISTRY","url":"https://www.academia.edu/Documents/in/THEORETICAL_AND_COMPUTATIONAL_CHEMISTRY"}],"urls":[]}, dispatcherData: dispatcherData }); $(this).data('initialized', true); } }); $a.trackClickSource(".js-work-strip-work-link", "profile_work_strip") }); </script> <div class="js-work-strip profile--work_container" data-work-id="35181710"><div class="profile--work_thumbnail hidden-xs"><a class="js-work-strip-work-link" data-click-track="profile-work-strip-thumbnail" href="https://www.academia.edu/35181710/Polarizable_Molecular_Dynamics_in_a_Polarizable_Continuum_Solvent"><img alt="Research paper thumbnail of Polarizable Molecular Dynamics in a Polarizable Continuum Solvent" class="work-thumbnail" src="https://a.academia-assets.com/images/blank-paper.jpg" /></a></div><div class="wp-workCard wp-workCard_itemContainer"><div class="wp-workCard_item wp-workCard--title"><a class="js-work-strip-work-link text-gray-darker" data-click-track="profile-work-strip-title" href="https://www.academia.edu/35181710/Polarizable_Molecular_Dynamics_in_a_Polarizable_Continuum_Solvent">Polarizable Molecular Dynamics in a Polarizable Continuum Solvent</a></div><div class="wp-workCard_item"><span>Journal of Chemical Theory and Computation</span><span>, 2015</span></div><div class="wp-workCard_item"><span class="js-work-more-abstract-truncated">We present for the first time scalable polarizable molecular dynamics (MD) simulations within a p...</span><a class="js-work-more-abstract" data-broccoli-component="work_strip.more_abstract" data-click-track="profile-work-strip-more-abstract" href="javascript:;"><span> more </span><span><i class="fa fa-caret-down"></i></span></a><span class="js-work-more-abstract-untruncated hidden">We present for the first time scalable polarizable molecular dynamics (MD) simulations within a polarizable continuum solvent with molecular shape cavities and exact solution of the mutual polarization. The key ingredients are a very efficient algorithm for solving the equations associated with the polarizable continuum, in particular, the domain decomposition Conductor-like Screening Model (ddCOSMO), a rigorous coupling of the continuum with the polarizable force field achieved through a robust variational formulation and an effective strategy to solve the coupled equations. The coupling of ddCOSMO with non variational force fields, including AMOEBA, is also addressed. The MD simulations are feasible, for real life systems, on standard cluster nodes; a scalable parallel implementation allows for further speed up in the context of a newly developed module in Tinker, named Tinker-HP. NVE simulations are stable and long term energy conservation can be achieved. This paper is focused on the methodological developments, on the analysis of the algorithm and on the stability of the simulations; a proof-of-concept application is also presented to attest the possibilities of this newly developed technique.</span></div><div class="wp-workCard_item wp-workCard--actions"><span class="work-strip-bookmark-button-container"></span><span class="wp-workCard--action visible-if-viewed-by-owner inline-block" style="display: none;"><span class="js-profile-work-strip-edit-button-wrapper profile-work-strip-edit-button-wrapper" data-work-id="35181710"><a class="js-profile-work-strip-edit-button" tabindex="0"><span><i class="fa fa-pencil"></i></span><span>Edit</span></a></span></span><span id="work-strip-rankings-button-container"></span></div><div class="wp-workCard_item wp-workCard--stats"><span><span><span class="js-view-count view-count u-mr2x" data-work-id="35181710"><i class="fa fa-spinner fa-spin"></i></span><script>$(function () { var workId = 35181710; window.Academia.workViewCountsFetcher.queue(workId, function (count) { var description = window.$h.commaizeInt(count) + " " + window.$h.pluralize(count, 'View'); $(".js-view-count[data-work-id=35181710]").text(description); $(".js-view-count[data-work-id=35181710]").attr('title', description).tooltip(); }); });</script></span></span><span><span class="percentile-widget hidden"><span class="u-mr2x work-percentile"></span></span><script>$(function () { var workId = 35181710; window.Academia.workPercentilesFetcher.queue(workId, function (percentileText) { var container = $(".js-work-strip[data-work-id='35181710']"); container.find('.work-percentile').text(percentileText.charAt(0).toUpperCase() + percentileText.slice(1)); container.find('.percentile-widget').show(); container.find('.percentile-widget').removeClass('hidden'); }); });</script></span><span><script>$(function() { new Works.PaperRankView({ workId: 35181710, container: "", }); });</script></span></div><div id="work-strip-premium-row-container"></div></div></div><script> require.config({ waitSeconds: 90 })(["https://a.academia-assets.com/assets/wow_profile-f77ea15d77ce96025a6048a514272ad8becbad23c641fc2b3bd6e24ca6ff1932.js","https://a.academia-assets.com/assets/work_edit-ad038b8c047c1a8d4fa01b402d530ff93c45fee2137a149a4a5398bc8ad67560.js"], function() { // from javascript_helper.rb var dispatcherData = {} if (false){ window.WowProfile.dispatcher = window.WowProfile.dispatcher || _.clone(Backbone.Events); dispatcherData = { dispatcher: window.WowProfile.dispatcher, downloadLinkId: "-1" } } $('.js-work-strip[data-work-id=35181710]').each(function() { if (!$(this).data('initialized')) { new WowProfile.WorkStripView({ el: this, workJSON: {"id":35181710,"title":"Polarizable Molecular Dynamics in a Polarizable Continuum Solvent","translated_title":"","metadata":{"abstract":"We present for the first time scalable polarizable molecular dynamics (MD) simulations within a polarizable continuum solvent with molecular shape cavities and exact solution of the mutual polarization. The key ingredients are a very efficient algorithm for solving the equations associated with the polarizable continuum, in particular, the domain decomposition Conductor-like Screening Model (ddCOSMO), a rigorous coupling of the continuum with the polarizable force field achieved through a robust variational formulation and an effective strategy to solve the coupled equations. The coupling of ddCOSMO with non variational force fields, including AMOEBA, is also addressed. The MD simulations are feasible, for real life systems, on standard cluster nodes; a scalable parallel implementation allows for further speed up in the context of a newly developed module in Tinker, named Tinker-HP. NVE simulations are stable and long term energy conservation can be achieved. This paper is focused on the methodological developments, on the analysis of the algorithm and on the stability of the simulations; a proof-of-concept application is also presented to attest the possibilities of this newly developed technique.","publisher":"American Chemical Society (ACS)","publication_date":{"day":null,"month":null,"year":2015,"errors":{}},"publication_name":"Journal of Chemical Theory and Computation"},"translated_abstract":"We present for the first time scalable polarizable molecular dynamics (MD) simulations within a polarizable continuum solvent with molecular shape cavities and exact solution of the mutual polarization. The key ingredients are a very efficient algorithm for solving the equations associated with the polarizable continuum, in particular, the domain decomposition Conductor-like Screening Model (ddCOSMO), a rigorous coupling of the continuum with the polarizable force field achieved through a robust variational formulation and an effective strategy to solve the coupled equations. The coupling of ddCOSMO with non variational force fields, including AMOEBA, is also addressed. The MD simulations are feasible, for real life systems, on standard cluster nodes; a scalable parallel implementation allows for further speed up in the context of a newly developed module in Tinker, named Tinker-HP. NVE simulations are stable and long term energy conservation can be achieved. This paper is focused on the methodological developments, on the analysis of the algorithm and on the stability of the simulations; a proof-of-concept application is also presented to attest the possibilities of this newly developed technique.","internal_url":"https://www.academia.edu/35181710/Polarizable_Molecular_Dynamics_in_a_Polarizable_Continuum_Solvent","translated_internal_url":"","created_at":"2017-11-18T07:17:49.034-08:00","preview_url":null,"current_user_can_edit":null,"current_user_is_owner":null,"owner_id":35445,"coauthors_can_edit":true,"document_type":"paper","co_author_tags":[],"downloadable_attachments":[],"slug":"Polarizable_Molecular_Dynamics_in_a_Polarizable_Continuum_Solvent","translated_slug":"","page_count":null,"language":"en","content_type":"Work","owner":{"id":35445,"first_name":"Jean-Philip","middle_initials":null,"last_name":"Piquemal","page_name":"JeanPhilipPiquemal","domain_name":"sorbonne-fr","created_at":"2009-03-17T04:43:24.569-07:00","display_name":"Jean-Philip Piquemal","url":"https://sorbonne-fr.academia.edu/JeanPhilipPiquemal"},"attachments":[],"research_interests":[{"id":428,"name":"Algorithms","url":"https://www.academia.edu/Documents/in/Algorithms"},{"id":2736,"name":"Molecular Dynamics Simulation","url":"https://www.academia.edu/Documents/in/Molecular_Dynamics_Simulation"},{"id":151086,"name":"Peptides","url":"https://www.academia.edu/Documents/in/Peptides"},{"id":645605,"name":"THEORETICAL AND COMPUTATIONAL CHEMISTRY","url":"https://www.academia.edu/Documents/in/THEORETICAL_AND_COMPUTATIONAL_CHEMISTRY"},{"id":1745595,"name":"Solvents","url":"https://www.academia.edu/Documents/in/Solvents"}],"urls":[]}, dispatcherData: dispatcherData }); $(this).data('initialized', true); } }); $a.trackClickSource(".js-work-strip-work-link", "profile_work_strip") }); </script> <div class="js-work-strip profile--work_container" data-work-id="35181709"><div class="profile--work_thumbnail hidden-xs"><a class="js-work-strip-work-link" data-click-track="profile-work-strip-thumbnail" href="https://www.academia.edu/35181709/Bridging_Organometallics_and_Quantum_Chemical_Topology_Understanding_Electronic_Relocalisation_During_Palladium_Catalyzed_Reductive_Elimination"><img alt="Research paper thumbnail of Bridging Organometallics and Quantum Chemical Topology: Understanding Electronic Relocalisation During Palladium-Catalyzed Reductive Elimination" class="work-thumbnail" src="https://a.academia-assets.com/images/blank-paper.jpg" /></a></div><div class="wp-workCard wp-workCard_itemContainer"><div class="wp-workCard_item wp-workCard--title"><a class="js-work-strip-work-link text-gray-darker" data-click-track="profile-work-strip-title" href="https://www.academia.edu/35181709/Bridging_Organometallics_and_Quantum_Chemical_Topology_Understanding_Electronic_Relocalisation_During_Palladium_Catalyzed_Reductive_Elimination">Bridging Organometallics and Quantum Chemical Topology: Understanding Electronic Relocalisation During Palladium-Catalyzed Reductive Elimination</a></div><div class="wp-workCard_item"><span>Journal of computational chemistry</span><span>, Jan 21, 2015</span></div><div class="wp-workCard_item"><span class="js-work-more-abstract-truncated">This article proposes to bridge two fields, namely organometallics and quantum chemical topology....</span><a class="js-work-more-abstract" data-broccoli-component="work_strip.more_abstract" data-click-track="profile-work-strip-more-abstract" href="javascript:;"><span> more </span><span><i class="fa fa-caret-down"></i></span></a><span class="js-work-more-abstract-untruncated hidden">This article proposes to bridge two fields, namely organometallics and quantum chemical topology. To do so, Palladium-catalyzed reductive elimination is studied. Such reaction is a classical elementary step in organometallic chemistry, where the directionality of electrons delocalization is not well understood. New computational evidences highlighting the accepted mechanism are proposed following a strategy coupling quantum theory of atoms in molecules and electron localization function topological analyses and enabling an extended quantification of donated/back-donated electrons fluxes along reaction paths going beyond the usual Dewar-Chatt-Duncanson model. Indeed, if the ligands coordination mode (phosphine, carbene) is commonly described as dative, it appears that ligands lone pairs stay centered on ligands as electrons are shared between metal and ligand with strong delocalization toward the latter. Overall, through strong trans effects coming from the carbon involved in the red...</span></div><div class="wp-workCard_item wp-workCard--actions"><span class="work-strip-bookmark-button-container"></span><span class="wp-workCard--action visible-if-viewed-by-owner inline-block" style="display: none;"><span class="js-profile-work-strip-edit-button-wrapper profile-work-strip-edit-button-wrapper" data-work-id="35181709"><a class="js-profile-work-strip-edit-button" tabindex="0"><span><i class="fa fa-pencil"></i></span><span>Edit</span></a></span></span><span id="work-strip-rankings-button-container"></span></div><div class="wp-workCard_item wp-workCard--stats"><span><span><span class="js-view-count view-count u-mr2x" data-work-id="35181709"><i class="fa fa-spinner fa-spin"></i></span><script>$(function () { var workId = 35181709; window.Academia.workViewCountsFetcher.queue(workId, function (count) { var description = window.$h.commaizeInt(count) + " " + window.$h.pluralize(count, 'View'); $(".js-view-count[data-work-id=35181709]").text(description); $(".js-view-count[data-work-id=35181709]").attr('title', description).tooltip(); }); });</script></span></span><span><span class="percentile-widget hidden"><span class="u-mr2x work-percentile"></span></span><script>$(function () { var workId = 35181709; window.Academia.workPercentilesFetcher.queue(workId, function (percentileText) { var container = $(".js-work-strip[data-work-id='35181709']"); container.find('.work-percentile').text(percentileText.charAt(0).toUpperCase() + percentileText.slice(1)); container.find('.percentile-widget').show(); container.find('.percentile-widget').removeClass('hidden'); }); });</script></span><span><script>$(function() { new Works.PaperRankView({ workId: 35181709, container: "", }); });</script></span></div><div id="work-strip-premium-row-container"></div></div></div><script> require.config({ waitSeconds: 90 })(["https://a.academia-assets.com/assets/wow_profile-f77ea15d77ce96025a6048a514272ad8becbad23c641fc2b3bd6e24ca6ff1932.js","https://a.academia-assets.com/assets/work_edit-ad038b8c047c1a8d4fa01b402d530ff93c45fee2137a149a4a5398bc8ad67560.js"], function() { // from javascript_helper.rb var dispatcherData = {} if (false){ window.WowProfile.dispatcher = window.WowProfile.dispatcher || _.clone(Backbone.Events); dispatcherData = { dispatcher: window.WowProfile.dispatcher, downloadLinkId: "-1" } } $('.js-work-strip[data-work-id=35181709]').each(function() { if (!$(this).data('initialized')) { new WowProfile.WorkStripView({ el: this, workJSON: {"id":35181709,"title":"Bridging Organometallics and Quantum Chemical Topology: Understanding Electronic Relocalisation During Palladium-Catalyzed Reductive Elimination","translated_title":"","metadata":{"abstract":"This article proposes to bridge two fields, namely organometallics and quantum chemical topology. To do so, Palladium-catalyzed reductive elimination is studied. Such reaction is a classical elementary step in organometallic chemistry, where the directionality of electrons delocalization is not well understood. New computational evidences highlighting the accepted mechanism are proposed following a strategy coupling quantum theory of atoms in molecules and electron localization function topological analyses and enabling an extended quantification of donated/back-donated electrons fluxes along reaction paths going beyond the usual Dewar-Chatt-Duncanson model. Indeed, if the ligands coordination mode (phosphine, carbene) is commonly described as dative, it appears that ligands lone pairs stay centered on ligands as electrons are shared between metal and ligand with strong delocalization toward the latter. Overall, through strong trans effects coming from the carbon involved in the red...","publication_date":{"day":21,"month":1,"year":2015,"errors":{}},"publication_name":"Journal of computational chemistry"},"translated_abstract":"This article proposes to bridge two fields, namely organometallics and quantum chemical topology. To do so, Palladium-catalyzed reductive elimination is studied. Such reaction is a classical elementary step in organometallic chemistry, where the directionality of electrons delocalization is not well understood. New computational evidences highlighting the accepted mechanism are proposed following a strategy coupling quantum theory of atoms in molecules and electron localization function topological analyses and enabling an extended quantification of donated/back-donated electrons fluxes along reaction paths going beyond the usual Dewar-Chatt-Duncanson model. Indeed, if the ligands coordination mode (phosphine, carbene) is commonly described as dative, it appears that ligands lone pairs stay centered on ligands as electrons are shared between metal and ligand with strong delocalization toward the latter. Overall, through strong trans effects coming from the carbon involved in the red...","internal_url":"https://www.academia.edu/35181709/Bridging_Organometallics_and_Quantum_Chemical_Topology_Understanding_Electronic_Relocalisation_During_Palladium_Catalyzed_Reductive_Elimination","translated_internal_url":"","created_at":"2017-11-18T07:17:48.856-08:00","preview_url":null,"current_user_can_edit":null,"current_user_is_owner":null,"owner_id":35445,"coauthors_can_edit":true,"document_type":"paper","co_author_tags":[],"downloadable_attachments":[],"slug":"Bridging_Organometallics_and_Quantum_Chemical_Topology_Understanding_Electronic_Relocalisation_During_Palladium_Catalyzed_Reductive_Elimination","translated_slug":"","page_count":null,"language":"en","content_type":"Work","owner":{"id":35445,"first_name":"Jean-Philip","middle_initials":null,"last_name":"Piquemal","page_name":"JeanPhilipPiquemal","domain_name":"sorbonne-fr","created_at":"2009-03-17T04:43:24.569-07:00","display_name":"Jean-Philip Piquemal","url":"https://sorbonne-fr.academia.edu/JeanPhilipPiquemal"},"attachments":[],"research_interests":[{"id":528,"name":"Computational Chemistry","url":"https://www.academia.edu/Documents/in/Computational_Chemistry"},{"id":645605,"name":"THEORETICAL AND COMPUTATIONAL CHEMISTRY","url":"https://www.academia.edu/Documents/in/THEORETICAL_AND_COMPUTATIONAL_CHEMISTRY"}],"urls":[]}, dispatcherData: dispatcherData }); $(this).data('initialized', true); } }); $a.trackClickSource(".js-work-strip-work-link", "profile_work_strip") }); </script> <div class="js-work-strip profile--work_container" data-work-id="18536578"><div class="profile--work_thumbnail hidden-xs"><a class="js-work-strip-work-link" data-click-track="profile-work-strip-thumbnail" href="https://www.academia.edu/18536578/Hydration_Gibbs_free_energies_of_open_and_closed_shell_trivalent_lanthanide_and_actinide_cations_from_polarizable_molecular_dynamics"><img alt="Research paper thumbnail of Hydration Gibbs free energies of open and closed shell trivalent lanthanide and actinide cations from polarizable molecular dynamics" class="work-thumbnail" src="https://a.academia-assets.com/images/blank-paper.jpg" /></a></div><div class="wp-workCard wp-workCard_itemContainer"><div class="wp-workCard_item wp-workCard--title"><a class="js-work-strip-work-link text-gray-darker" data-click-track="profile-work-strip-title" href="https://www.academia.edu/18536578/Hydration_Gibbs_free_energies_of_open_and_closed_shell_trivalent_lanthanide_and_actinide_cations_from_polarizable_molecular_dynamics">Hydration Gibbs free energies of open and closed shell trivalent lanthanide and actinide cations from polarizable molecular dynamics</a></div><div class="wp-workCard_item wp-workCard--coauthors"><span>by </span><span><a class="" data-click-track="profile-work-strip-authors" href="https://pitt.academia.edu/AMarjolin">A. Marjolin</a> and <a class="" data-click-track="profile-work-strip-authors" href="https://sorbonne-fr.academia.edu/JeanPhilipPiquemal">Jean-Philip Piquemal</a></span></div><div class="wp-workCard_item"><span>Journal of molecular modeling</span><span>, 2014</span></div><div class="wp-workCard_item"><span class="js-work-more-abstract-truncated">The hydration free energies, structures, and dynamics of open- and closed-shell trivalent lanthan...</span><a class="js-work-more-abstract" data-broccoli-component="work_strip.more_abstract" data-click-track="profile-work-strip-more-abstract" href="javascript:;"><span> more </span><span><i class="fa fa-caret-down"></i></span></a><span class="js-work-more-abstract-untruncated hidden">The hydration free energies, structures, and dynamics of open- and closed-shell trivalent lanthanide and actinide metal cations are studied using molecular dynamics simulations (MD) based on a polarizable force field. Parameters for the metal cations are derived from an ab initio bottom-up strategy. MD simulations of six cations solvated in bulk water are subsequently performed with the AMOEBA polarizable force field. The calculated first-and second shell hydration numbers, water residence times, and free energies of hydration are consistent with experimental/theoretical values leading to a predictive modeling of f-elements compounds.</span></div><div class="wp-workCard_item wp-workCard--actions"><span class="work-strip-bookmark-button-container"></span><span class="wp-workCard--action visible-if-viewed-by-owner inline-block" style="display: none;"><span class="js-profile-work-strip-edit-button-wrapper profile-work-strip-edit-button-wrapper" data-work-id="18536578"><a class="js-profile-work-strip-edit-button" tabindex="0"><span><i class="fa fa-pencil"></i></span><span>Edit</span></a></span></span><span id="work-strip-rankings-button-container"></span></div><div class="wp-workCard_item wp-workCard--stats"><span><span><span class="js-view-count view-count u-mr2x" data-work-id="18536578"><i class="fa fa-spinner fa-spin"></i></span><script>$(function () { var workId = 18536578; window.Academia.workViewCountsFetcher.queue(workId, function (count) { var description = window.$h.commaizeInt(count) + " " + window.$h.pluralize(count, 'View'); $(".js-view-count[data-work-id=18536578]").text(description); $(".js-view-count[data-work-id=18536578]").attr('title', description).tooltip(); }); });</script></span></span><span><span class="percentile-widget hidden"><span class="u-mr2x work-percentile"></span></span><script>$(function () { var workId = 18536578; window.Academia.workPercentilesFetcher.queue(workId, function (percentileText) { var container = $(".js-work-strip[data-work-id='18536578']"); container.find('.work-percentile').text(percentileText.charAt(0).toUpperCase() + percentileText.slice(1)); container.find('.percentile-widget').show(); container.find('.percentile-widget').removeClass('hidden'); }); });</script></span><span><script>$(function() { new Works.PaperRankView({ workId: 18536578, container: "", }); });</script></span></div><div id="work-strip-premium-row-container"></div></div></div><script> require.config({ waitSeconds: 90 })(["https://a.academia-assets.com/assets/wow_profile-f77ea15d77ce96025a6048a514272ad8becbad23c641fc2b3bd6e24ca6ff1932.js","https://a.academia-assets.com/assets/work_edit-ad038b8c047c1a8d4fa01b402d530ff93c45fee2137a149a4a5398bc8ad67560.js"], function() { // from javascript_helper.rb var dispatcherData = {} if (false){ window.WowProfile.dispatcher = window.WowProfile.dispatcher || _.clone(Backbone.Events); dispatcherData = { dispatcher: window.WowProfile.dispatcher, downloadLinkId: "-1" } } $('.js-work-strip[data-work-id=18536578]').each(function() { if (!$(this).data('initialized')) { new WowProfile.WorkStripView({ el: this, workJSON: {"id":18536578,"title":"Hydration Gibbs free energies of open and closed shell trivalent lanthanide and actinide cations from polarizable molecular dynamics","translated_title":"","metadata":{"abstract":"The hydration free energies, structures, and dynamics of open- and closed-shell trivalent lanthanide and actinide metal cations are studied using molecular dynamics simulations (MD) based on a polarizable force field. 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The calculated first-and second shell hydration numbers, water residence times, and free energies of hydration are consistent with experimental/theoretical values leading to a predictive modeling of f-elements compounds.","internal_url":"https://www.academia.edu/18536578/Hydration_Gibbs_free_energies_of_open_and_closed_shell_trivalent_lanthanide_and_actinide_cations_from_polarizable_molecular_dynamics","translated_internal_url":"","created_at":"2015-11-17T14:09:06.310-08:00","preview_url":null,"current_user_can_edit":null,"current_user_is_owner":null,"owner_id":38393997,"coauthors_can_edit":true,"document_type":"paper","co_author_tags":[{"id":12532643,"work_id":18536578,"tagging_user_id":38393997,"tagged_user_id":null,"co_author_invite_id":2343916,"email":"j***n@gmail.com","display_order":0,"name":"Jean-pierre Dognon","title":"Hydration Gibbs free energies of open and closed shell trivalent lanthanide and actinide cations from polarizable molecular dynamics"},{"id":12532644,"work_id":18536578,"tagging_user_id":38393997,"tagged_user_id":37239238,"co_author_invite_id":null,"email":"m***s@uiowa.edu","affiliation":"The University of Iowa","display_order":4194304,"name":"Michael Schnieders","title":"Hydration Gibbs free energies of open and closed shell trivalent lanthanide and actinide cations from polarizable molecular dynamics"},{"id":12532645,"work_id":18536578,"tagging_user_id":38393997,"tagged_user_id":35445,"co_author_invite_id":null,"email":"j***p@lct.jussieu.fr","affiliation":"Sorbonne University","display_order":6291456,"name":"Jean-Philip Piquemal","title":"Hydration Gibbs free energies of open and closed shell trivalent lanthanide and actinide cations from polarizable molecular dynamics"},{"id":12532646,"work_id":18536578,"tagging_user_id":38393997,"tagged_user_id":32699940,"co_author_invite_id":null,"email":"p***n@mail.utexas.edu","affiliation":"The University of Texas at Austin","display_order":7340032,"name":"Pengyu Ren","title":"Hydration Gibbs free energies of open and closed shell trivalent lanthanide and actinide cations from polarizable molecular dynamics"}],"downloadable_attachments":[],"slug":"Hydration_Gibbs_free_energies_of_open_and_closed_shell_trivalent_lanthanide_and_actinide_cations_from_polarizable_molecular_dynamics","translated_slug":"","page_count":null,"language":"en","content_type":"Work","owner":{"id":38393997,"first_name":"A.","middle_initials":null,"last_name":"Marjolin","page_name":"AMarjolin","domain_name":"pitt","created_at":"2015-11-15T13:07:23.000-08:00","display_name":"A. Marjolin","url":"https://pitt.academia.edu/AMarjolin"},"attachments":[],"research_interests":[{"id":2215,"name":"Water","url":"https://www.academia.edu/Documents/in/Water"},{"id":2736,"name":"Molecular Dynamics Simulation","url":"https://www.academia.edu/Documents/in/Molecular_Dynamics_Simulation"},{"id":32927,"name":"Molecular modeling","url":"https://www.academia.edu/Documents/in/Molecular_modeling"},{"id":645605,"name":"THEORETICAL AND COMPUTATIONAL CHEMISTRY","url":"https://www.academia.edu/Documents/in/THEORETICAL_AND_COMPUTATIONAL_CHEMISTRY"},{"id":717129,"name":"Energy Transfer","url":"https://www.academia.edu/Documents/in/Energy_Transfer"},{"id":967839,"name":"Structure activity Relationship","url":"https://www.academia.edu/Documents/in/Structure_activity_Relationship"},{"id":1013858,"name":"Cations","url":"https://www.academia.edu/Documents/in/Cations"},{"id":1724844,"name":"Molecular Structure","url":"https://www.academia.edu/Documents/in/Molecular_Structure"},{"id":1745595,"name":"Solvents","url":"https://www.academia.edu/Documents/in/Solvents"}],"urls":[]}, dispatcherData: dispatcherData }); $(this).data('initialized', true); } }); $a.trackClickSource(".js-work-strip-work-link", "profile_work_strip") }); </script> <div class="js-work-strip profile--work_container" data-work-id="35181708"><div class="profile--work_thumbnail hidden-xs"><a class="js-work-strip-work-link" data-click-track="profile-work-strip-thumbnail" href="https://www.academia.edu/35181708/A_supervised_fitting_approach_to_force_field_parametrization_with_application_to_the_SIBFA_polarizable_force_field"><img alt="Research paper thumbnail of A supervised fitting approach to force field parametrization with application to the SIBFA polarizable force field" class="work-thumbnail" src="https://a.academia-assets.com/images/blank-paper.jpg" /></a></div><div class="wp-workCard wp-workCard_itemContainer"><div class="wp-workCard_item wp-workCard--title"><a class="js-work-strip-work-link text-gray-darker" data-click-track="profile-work-strip-title" href="https://www.academia.edu/35181708/A_supervised_fitting_approach_to_force_field_parametrization_with_application_to_the_SIBFA_polarizable_force_field">A supervised fitting approach to force field parametrization with application to the SIBFA polarizable force field</a></div><div class="wp-workCard_item"><span>Journal of computational chemistry</span><span>, Jan 5, 2014</span></div><div class="wp-workCard_item"><span class="js-work-more-abstract-truncated">A supervised, semiautomated approach to force field parameter fitting is described and applied to...</span><a class="js-work-more-abstract" data-broccoli-component="work_strip.more_abstract" data-click-track="profile-work-strip-more-abstract" href="javascript:;"><span> more </span><span><i class="fa fa-caret-down"></i></span></a><span class="js-work-more-abstract-untruncated hidden">A supervised, semiautomated approach to force field parameter fitting is described and applied to the SIBFA polarizable force field. The I-NoLLS interactive, nonlinear least squares fitting program is used as an engine for parameter refinement while keeping parameter values within a physical range. Interactive fitting is shown to avoid many of the stability problems that frequently afflict highly correlated, nonlinear fitting problems occurring in force field parametrizations. The method is used to obtain parameters for the H2O, formamide, and imidazole molecular fragments and their complexes with the Mg(2+) cation. Reference data obtained from ab initio calculations using an auc-cc-pVTZ basis set exploit advances in modern computer hardware to provide a more accurate parametrization of SIBFA than has previously been available.</span></div><div class="wp-workCard_item wp-workCard--actions"><span class="work-strip-bookmark-button-container"></span><span class="wp-workCard--action visible-if-viewed-by-owner inline-block" style="display: none;"><span class="js-profile-work-strip-edit-button-wrapper profile-work-strip-edit-button-wrapper" data-work-id="35181708"><a class="js-profile-work-strip-edit-button" tabindex="0"><span><i class="fa fa-pencil"></i></span><span>Edit</span></a></span></span><span id="work-strip-rankings-button-container"></span></div><div class="wp-workCard_item wp-workCard--stats"><span><span><span class="js-view-count view-count u-mr2x" data-work-id="35181708"><i class="fa fa-spinner fa-spin"></i></span><script>$(function () { var workId = 35181708; window.Academia.workViewCountsFetcher.queue(workId, function (count) { var description = window.$h.commaizeInt(count) + " " + window.$h.pluralize(count, 'View'); $(".js-view-count[data-work-id=35181708]").text(description); $(".js-view-count[data-work-id=35181708]").attr('title', description).tooltip(); }); });</script></span></span><span><span class="percentile-widget hidden"><span class="u-mr2x work-percentile"></span></span><script>$(function () { var workId = 35181708; window.Academia.workPercentilesFetcher.queue(workId, function (percentileText) { var container = $(".js-work-strip[data-work-id='35181708']"); container.find('.work-percentile').text(percentileText.charAt(0).toUpperCase() + percentileText.slice(1)); container.find('.percentile-widget').show(); container.find('.percentile-widget').removeClass('hidden'); }); });</script></span><span><script>$(function() { new Works.PaperRankView({ workId: 35181708, container: "", }); });</script></span></div><div id="work-strip-premium-row-container"></div></div></div><script> require.config({ waitSeconds: 90 })(["https://a.academia-assets.com/assets/wow_profile-f77ea15d77ce96025a6048a514272ad8becbad23c641fc2b3bd6e24ca6ff1932.js","https://a.academia-assets.com/assets/work_edit-ad038b8c047c1a8d4fa01b402d530ff93c45fee2137a149a4a5398bc8ad67560.js"], function() { // from javascript_helper.rb var dispatcherData = {} if (false){ window.WowProfile.dispatcher = window.WowProfile.dispatcher || _.clone(Backbone.Events); dispatcherData = { dispatcher: window.WowProfile.dispatcher, downloadLinkId: "-1" } } $('.js-work-strip[data-work-id=35181708]').each(function() { if (!$(this).data('initialized')) { new WowProfile.WorkStripView({ el: this, workJSON: {"id":35181708,"title":"A supervised fitting approach to force field parametrization with application to the SIBFA polarizable force field","translated_title":"","metadata":{"abstract":"A supervised, semiautomated approach to force field parameter fitting is described and applied to the SIBFA polarizable force field. The I-NoLLS interactive, nonlinear least squares fitting program is used as an engine for parameter refinement while keeping parameter values within a physical range. Interactive fitting is shown to avoid many of the stability problems that frequently afflict highly correlated, nonlinear fitting problems occurring in force field parametrizations. The method is used to obtain parameters for the H2O, formamide, and imidazole molecular fragments and their complexes with the Mg(2+) cation. Reference data obtained from ab initio calculations using an auc-cc-pVTZ basis set exploit advances in modern computer hardware to provide a more accurate parametrization of SIBFA than has previously been available.","publication_date":{"day":5,"month":1,"year":2014,"errors":{}},"publication_name":"Journal of computational chemistry"},"translated_abstract":"A supervised, semiautomated approach to force field parameter fitting is described and applied to the SIBFA polarizable force field. The I-NoLLS interactive, nonlinear least squares fitting program is used as an engine for parameter refinement while keeping parameter values within a physical range. Interactive fitting is shown to avoid many of the stability problems that frequently afflict highly correlated, nonlinear fitting problems occurring in force field parametrizations. The method is used to obtain parameters for the H2O, formamide, and imidazole molecular fragments and their complexes with the Mg(2+) cation. Reference data obtained from ab initio calculations using an auc-cc-pVTZ basis set exploit advances in modern computer hardware to provide a more accurate parametrization of SIBFA than has previously been available.","internal_url":"https://www.academia.edu/35181708/A_supervised_fitting_approach_to_force_field_parametrization_with_application_to_the_SIBFA_polarizable_force_field","translated_internal_url":"","created_at":"2017-11-18T07:17:48.544-08:00","preview_url":null,"current_user_can_edit":null,"current_user_is_owner":null,"owner_id":35445,"coauthors_can_edit":true,"document_type":"paper","co_author_tags":[],"downloadable_attachments":[],"slug":"A_supervised_fitting_approach_to_force_field_parametrization_with_application_to_the_SIBFA_polarizable_force_field","translated_slug":"","page_count":null,"language":"en","content_type":"Work","owner":{"id":35445,"first_name":"Jean-Philip","middle_initials":null,"last_name":"Piquemal","page_name":"JeanPhilipPiquemal","domain_name":"sorbonne-fr","created_at":"2009-03-17T04:43:24.569-07:00","display_name":"Jean-Philip Piquemal","url":"https://sorbonne-fr.academia.edu/JeanPhilipPiquemal"},"attachments":[],"research_interests":[{"id":528,"name":"Computational Chemistry","url":"https://www.academia.edu/Documents/in/Computational_Chemistry"},{"id":2215,"name":"Water","url":"https://www.academia.edu/Documents/in/Water"},{"id":69542,"name":"Computer Simulation","url":"https://www.academia.edu/Documents/in/Computer_Simulation"},{"id":70902,"name":"Magnesium","url":"https://www.academia.edu/Documents/in/Magnesium"},{"id":645605,"name":"THEORETICAL AND COMPUTATIONAL CHEMISTRY","url":"https://www.academia.edu/Documents/in/THEORETICAL_AND_COMPUTATIONAL_CHEMISTRY"},{"id":801409,"name":"Imidazoles","url":"https://www.academia.edu/Documents/in/Imidazoles"},{"id":2819832,"name":"Parametrization","url":"https://www.academia.edu/Documents/in/Parametrization"}],"urls":[]}, dispatcherData: dispatcherData }); $(this).data('initialized', true); } }); $a.trackClickSource(".js-work-strip-work-link", "profile_work_strip") }); </script> <div class="js-work-strip profile--work_container" data-work-id="35181707"><div class="profile--work_thumbnail hidden-xs"><a class="js-work-strip-work-link" data-click-track="profile-work-strip-thumbnail" href="https://www.academia.edu/35181707/Characterizing_Molecular_Interactions_in_Chemical_Systems"><img alt="Research paper thumbnail of Characterizing Molecular Interactions in Chemical Systems" class="work-thumbnail" src="https://a.academia-assets.com/images/blank-paper.jpg" /></a></div><div class="wp-workCard wp-workCard_itemContainer"><div class="wp-workCard_item wp-workCard--title"><a class="js-work-strip-work-link text-gray-darker" data-click-track="profile-work-strip-title" href="https://www.academia.edu/35181707/Characterizing_Molecular_Interactions_in_Chemical_Systems">Characterizing Molecular Interactions in Chemical Systems</a></div><div class="wp-workCard_item"><span>IEEE Transactions on Visualization and Computer Graphics</span><span>, 2014</span></div><div class="wp-workCard_item"><span class="js-work-more-abstract-truncated">Interactions between atoms have a major influence on the chemical properties of molecular systems...</span><a class="js-work-more-abstract" data-broccoli-component="work_strip.more_abstract" data-click-track="profile-work-strip-more-abstract" href="javascript:;"><span> more </span><span><i class="fa fa-caret-down"></i></span></a><span class="js-work-more-abstract-untruncated hidden">Interactions between atoms have a major influence on the chemical properties of molecular systems. While covalent interactions impose the structural integrity of molecules, noncovalent interactions govern more subtle phenomena such as protein folding, bonding or self assembly. The understanding of these types of interactions is necessary for the interpretation of many biological processes and chemical design tasks. While traditionally the electron density is analyzed to interpret the quantum chemistry of a molecular system, noncovalent interactions are characterized by low electron densities and only slight variations of them--challenging their extraction and characterization. Recently, the signed electron density and the reduced gradient, two scalar fields derived from the electron density, have drawn much attention in quantum chemistry since they enable a qualitative visualization of these interactions even in complex molecular systems and experimental measurements. In this work, we present the first combinatorial algorithm for the automated extraction and characterization of covalent and noncovalent interactions in molecular systems. The proposed algorithm is based on a joint topological analysis of the signed electron density and the reduced gradient. Combining the connectivity information of the critical points of these two scalar fields enables to visualize, enumerate, classify and investigate molecular interactions in a robust manner. Experiments on a variety of molecular systems, from simple dimers to proteins or DNA, demonstrate the ability of our technique to robustly extract these interactions and to reveal their structural relations to the atoms and bonds forming the molecules. For simple systems, our analysis corroborates the observations made by the chemists while it provides new visual and quantitative insights on chemical interactions for larger molecular systems.</span></div><div class="wp-workCard_item wp-workCard--actions"><span class="work-strip-bookmark-button-container"></span><span class="wp-workCard--action visible-if-viewed-by-owner inline-block" style="display: none;"><span class="js-profile-work-strip-edit-button-wrapper profile-work-strip-edit-button-wrapper" data-work-id="35181707"><a class="js-profile-work-strip-edit-button" tabindex="0"><span><i class="fa fa-pencil"></i></span><span>Edit</span></a></span></span><span id="work-strip-rankings-button-container"></span></div><div class="wp-workCard_item wp-workCard--stats"><span><span><span class="js-view-count view-count u-mr2x" data-work-id="35181707"><i class="fa fa-spinner fa-spin"></i></span><script>$(function () { var workId = 35181707; window.Academia.workViewCountsFetcher.queue(workId, function (count) { var description = window.$h.commaizeInt(count) + " " + window.$h.pluralize(count, 'View'); $(".js-view-count[data-work-id=35181707]").text(description); $(".js-view-count[data-work-id=35181707]").attr('title', description).tooltip(); }); });</script></span></span><span><span class="percentile-widget hidden"><span class="u-mr2x work-percentile"></span></span><script>$(function () { var workId = 35181707; window.Academia.workPercentilesFetcher.queue(workId, function (percentileText) { var container = $(".js-work-strip[data-work-id='35181707']"); container.find('.work-percentile').text(percentileText.charAt(0).toUpperCase() + percentileText.slice(1)); container.find('.percentile-widget').show(); container.find('.percentile-widget').removeClass('hidden'); }); });</script></span><span><script>$(function() { new Works.PaperRankView({ workId: 35181707, container: "", }); });</script></span></div><div id="work-strip-premium-row-container"></div></div></div><script> require.config({ waitSeconds: 90 })(["https://a.academia-assets.com/assets/wow_profile-f77ea15d77ce96025a6048a514272ad8becbad23c641fc2b3bd6e24ca6ff1932.js","https://a.academia-assets.com/assets/work_edit-ad038b8c047c1a8d4fa01b402d530ff93c45fee2137a149a4a5398bc8ad67560.js"], function() { // from javascript_helper.rb var dispatcherData = {} if (false){ window.WowProfile.dispatcher = window.WowProfile.dispatcher || _.clone(Backbone.Events); dispatcherData = { dispatcher: window.WowProfile.dispatcher, downloadLinkId: "-1" } } $('.js-work-strip[data-work-id=35181707]').each(function() { if (!$(this).data('initialized')) { new WowProfile.WorkStripView({ el: this, workJSON: {"id":35181707,"title":"Characterizing Molecular Interactions in Chemical Systems","translated_title":"","metadata":{"abstract":"Interactions between atoms have a major influence on the chemical properties of molecular systems. While covalent interactions impose the structural integrity of molecules, noncovalent interactions govern more subtle phenomena such as protein folding, bonding or self assembly. The understanding of these types of interactions is necessary for the interpretation of many biological processes and chemical design tasks. While traditionally the electron density is analyzed to interpret the quantum chemistry of a molecular system, noncovalent interactions are characterized by low electron densities and only slight variations of them--challenging their extraction and characterization. Recently, the signed electron density and the reduced gradient, two scalar fields derived from the electron density, have drawn much attention in quantum chemistry since they enable a qualitative visualization of these interactions even in complex molecular systems and experimental measurements. In this work, we present the first combinatorial algorithm for the automated extraction and characterization of covalent and noncovalent interactions in molecular systems. The proposed algorithm is based on a joint topological analysis of the signed electron density and the reduced gradient. Combining the connectivity information of the critical points of these two scalar fields enables to visualize, enumerate, classify and investigate molecular interactions in a robust manner. Experiments on a variety of molecular systems, from simple dimers to proteins or DNA, demonstrate the ability of our technique to robustly extract these interactions and to reveal their structural relations to the atoms and bonds forming the molecules. For simple systems, our analysis corroborates the observations made by the chemists while it provides new visual and quantitative insights on chemical interactions for larger molecular systems.","publisher":"Institute of Electrical and Electronics Engineers (IEEE)","publication_date":{"day":null,"month":null,"year":2014,"errors":{}},"publication_name":"IEEE Transactions on Visualization and Computer Graphics"},"translated_abstract":"Interactions between atoms have a major influence on the chemical properties of molecular systems. While covalent interactions impose the structural integrity of molecules, noncovalent interactions govern more subtle phenomena such as protein folding, bonding or self assembly. The understanding of these types of interactions is necessary for the interpretation of many biological processes and chemical design tasks. While traditionally the electron density is analyzed to interpret the quantum chemistry of a molecular system, noncovalent interactions are characterized by low electron densities and only slight variations of them--challenging their extraction and characterization. Recently, the signed electron density and the reduced gradient, two scalar fields derived from the electron density, have drawn much attention in quantum chemistry since they enable a qualitative visualization of these interactions even in complex molecular systems and experimental measurements. In this work, we present the first combinatorial algorithm for the automated extraction and characterization of covalent and noncovalent interactions in molecular systems. The proposed algorithm is based on a joint topological analysis of the signed electron density and the reduced gradient. Combining the connectivity information of the critical points of these two scalar fields enables to visualize, enumerate, classify and investigate molecular interactions in a robust manner. Experiments on a variety of molecular systems, from simple dimers to proteins or DNA, demonstrate the ability of our technique to robustly extract these interactions and to reveal their structural relations to the atoms and bonds forming the molecules. For simple systems, our analysis corroborates the observations made by the chemists while it provides new visual and quantitative insights on chemical interactions for larger molecular systems.","internal_url":"https://www.academia.edu/35181707/Characterizing_Molecular_Interactions_in_Chemical_Systems","translated_internal_url":"","created_at":"2017-11-18T07:17:48.392-08:00","preview_url":null,"current_user_can_edit":null,"current_user_is_owner":null,"owner_id":35445,"coauthors_can_edit":true,"document_type":"paper","co_author_tags":[],"downloadable_attachments":[],"slug":"Characterizing_Molecular_Interactions_in_Chemical_Systems","translated_slug":"","page_count":null,"language":"en","content_type":"Work","owner":{"id":35445,"first_name":"Jean-Philip","middle_initials":null,"last_name":"Piquemal","page_name":"JeanPhilipPiquemal","domain_name":"sorbonne-fr","created_at":"2009-03-17T04:43:24.569-07:00","display_name":"Jean-Philip Piquemal","url":"https://sorbonne-fr.academia.edu/JeanPhilipPiquemal"},"attachments":[],"research_interests":[{"id":445,"name":"Computer Graphics","url":"https://www.academia.edu/Documents/in/Computer_Graphics"},{"id":4233,"name":"Computational Biology","url":"https://www.academia.edu/Documents/in/Computational_Biology"},{"id":48057,"name":"DNA","url":"https://www.academia.edu/Documents/in/DNA"},{"id":181569,"name":"Proteins","url":"https://www.academia.edu/Documents/in/Proteins"},{"id":372917,"name":"Protein Secondary Structure Prediction","url":"https://www.academia.edu/Documents/in/Protein_Secondary_Structure_Prediction"},{"id":649537,"name":"Molecular Conformation","url":"https://www.academia.edu/Documents/in/Molecular_Conformation"}],"urls":[]}, dispatcherData: dispatcherData }); $(this).data('initialized', true); } }); $a.trackClickSource(".js-work-strip-work-link", "profile_work_strip") }); </script> <div class="js-work-strip profile--work_container" data-work-id="35181706"><div class="profile--work_thumbnail hidden-xs"><a class="js-work-strip-work-link" data-click-track="profile-work-strip-thumbnail" href="https://www.academia.edu/35181706/Synthesis_and_structure_activity_relationship_of_non_peptidic_antagonists_of_neuropilin_1_receptor"><img alt="Research paper thumbnail of Synthesis and structure-activity relationship of non-peptidic antagonists of neuropilin-1 receptor" class="work-thumbnail" src="https://a.academia-assets.com/images/blank-paper.jpg" /></a></div><div class="wp-workCard wp-workCard_itemContainer"><div class="wp-workCard_item wp-workCard--title"><a class="js-work-strip-work-link text-gray-darker" data-click-track="profile-work-strip-title" href="https://www.academia.edu/35181706/Synthesis_and_structure_activity_relationship_of_non_peptidic_antagonists_of_neuropilin_1_receptor">Synthesis and structure-activity relationship of non-peptidic antagonists of neuropilin-1 receptor</a></div><div class="wp-workCard_item"><span>Bioorganic & medicinal chemistry letters</span><span>, 2014</span></div><div class="wp-workCard_item"><span class="js-work-more-abstract-truncated">Neuropilins (NRPs) are VEGF-A165 co-receptors over-expressed in tumor cells, and considered as ta...</span><a class="js-work-more-abstract" data-broccoli-component="work_strip.more_abstract" data-click-track="profile-work-strip-more-abstract" href="javascript:;"><span> more </span><span><i class="fa fa-caret-down"></i></span></a><span class="js-work-more-abstract-untruncated hidden">Neuropilins (NRPs) are VEGF-A165 co-receptors over-expressed in tumor cells, and considered as targets in angiogenic-related pathologies. We previously identified compound 1, the first non-peptidic antagonist of the VEGF-A165/NRP binding, which exhibits in vivo anti-angiogenic and anti-tumor activities. We report here the synthesis and biological evaluations of new antagonists structurally-related to compound 1. Among these molecules, 4a, 4c and 4d show cytotoxic effects on HUVEC and MDA-MB-31 cells, and antagonize VEGF-A165/NRP-1 binding. This study confirmed our key structure-activity relationships hypothesis and paved the way to compound 1 &#39;hit to lead&#39; optimization.</span></div><div class="wp-workCard_item wp-workCard--actions"><span class="work-strip-bookmark-button-container"></span><span class="wp-workCard--action visible-if-viewed-by-owner inline-block" style="display: none;"><span class="js-profile-work-strip-edit-button-wrapper profile-work-strip-edit-button-wrapper" data-work-id="35181706"><a class="js-profile-work-strip-edit-button" tabindex="0"><span><i class="fa fa-pencil"></i></span><span>Edit</span></a></span></span><span id="work-strip-rankings-button-container"></span></div><div class="wp-workCard_item wp-workCard--stats"><span><span><span class="js-view-count view-count u-mr2x" data-work-id="35181706"><i class="fa fa-spinner fa-spin"></i></span><script>$(function () { var workId = 35181706; window.Academia.workViewCountsFetcher.queue(workId, function (count) { var description = window.$h.commaizeInt(count) + " " + window.$h.pluralize(count, 'View'); $(".js-view-count[data-work-id=35181706]").text(description); $(".js-view-count[data-work-id=35181706]").attr('title', description).tooltip(); }); });</script></span></span><span><span class="percentile-widget hidden"><span class="u-mr2x work-percentile"></span></span><script>$(function () { var workId = 35181706; window.Academia.workPercentilesFetcher.queue(workId, function (percentileText) { var container = $(".js-work-strip[data-work-id='35181706']"); container.find('.work-percentile').text(percentileText.charAt(0).toUpperCase() + percentileText.slice(1)); container.find('.percentile-widget').show(); container.find('.percentile-widget').removeClass('hidden'); }); });</script></span><span><script>$(function() { new Works.PaperRankView({ workId: 35181706, container: "", }); });</script></span></div><div id="work-strip-premium-row-container"></div></div></div><script> require.config({ waitSeconds: 90 })(["https://a.academia-assets.com/assets/wow_profile-f77ea15d77ce96025a6048a514272ad8becbad23c641fc2b3bd6e24ca6ff1932.js","https://a.academia-assets.com/assets/work_edit-ad038b8c047c1a8d4fa01b402d530ff93c45fee2137a149a4a5398bc8ad67560.js"], function() { // from javascript_helper.rb var dispatcherData = {} if (false){ window.WowProfile.dispatcher = window.WowProfile.dispatcher || _.clone(Backbone.Events); dispatcherData = { dispatcher: window.WowProfile.dispatcher, downloadLinkId: "-1" } } $('.js-work-strip[data-work-id=35181706]').each(function() { if (!$(this).data('initialized')) { new WowProfile.WorkStripView({ el: this, workJSON: {"id":35181706,"title":"Synthesis and structure-activity relationship of non-peptidic antagonists of neuropilin-1 receptor","translated_title":"","metadata":{"abstract":"Neuropilins (NRPs) are VEGF-A165 co-receptors over-expressed in tumor cells, and considered as targets in angiogenic-related pathologies. We previously identified compound 1, the first non-peptidic antagonist of the VEGF-A165/NRP binding, which exhibits in vivo anti-angiogenic and anti-tumor activities. We report here the synthesis and biological evaluations of new antagonists structurally-related to compound 1. Among these molecules, 4a, 4c and 4d show cytotoxic effects on HUVEC and MDA-MB-31 cells, and antagonize VEGF-A165/NRP-1 binding. This study confirmed our key structure-activity relationships hypothesis and paved the way to compound 1 \u0026#39;hit to lead\u0026#39; optimization.","publication_date":{"day":null,"month":null,"year":2014,"errors":{}},"publication_name":"Bioorganic \u0026 medicinal chemistry letters"},"translated_abstract":"Neuropilins (NRPs) are VEGF-A165 co-receptors over-expressed in tumor cells, and considered as targets in angiogenic-related pathologies. We previously identified compound 1, the first non-peptidic antagonist of the VEGF-A165/NRP binding, which exhibits in vivo anti-angiogenic and anti-tumor activities. We report here the synthesis and biological evaluations of new antagonists structurally-related to compound 1. Among these molecules, 4a, 4c and 4d show cytotoxic effects on HUVEC and MDA-MB-31 cells, and antagonize VEGF-A165/NRP-1 binding. This study confirmed our key structure-activity relationships hypothesis and paved the way to compound 1 \u0026#39;hit to lead\u0026#39; optimization.","internal_url":"https://www.academia.edu/35181706/Synthesis_and_structure_activity_relationship_of_non_peptidic_antagonists_of_neuropilin_1_receptor","translated_internal_url":"","created_at":"2017-11-18T07:17:48.248-08:00","preview_url":null,"current_user_can_edit":null,"current_user_is_owner":null,"owner_id":35445,"coauthors_can_edit":true,"document_type":"paper","co_author_tags":[],"downloadable_attachments":[],"slug":"Synthesis_and_structure_activity_relationship_of_non_peptidic_antagonists_of_neuropilin_1_receptor","translated_slug":"","page_count":null,"language":"en","content_type":"Work","owner":{"id":35445,"first_name":"Jean-Philip","middle_initials":null,"last_name":"Piquemal","page_name":"JeanPhilipPiquemal","domain_name":"sorbonne-fr","created_at":"2009-03-17T04:43:24.569-07:00","display_name":"Jean-Philip Piquemal","url":"https://sorbonne-fr.academia.edu/JeanPhilipPiquemal"},"attachments":[],"research_interests":[],"urls":[]}, dispatcherData: dispatcherData }); 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$(this).data('initialized', true); } }); $a.trackClickSource(".js-work-strip-work-link", "profile_work_strip") }); </script> </div><div class="profile--tab_content_container js-tab-pane tab-pane" data-section-id="4708" id="papers"><div class="js-work-strip profile--work_container" data-work-id="35314545"><div class="profile--work_thumbnail hidden-xs"><a class="js-work-strip-work-link" data-click-track="profile-work-strip-thumbnail" href="https://www.academia.edu/35314545/Tinker_HP_a_Massively_Parallel_Molecular_Dynamics_Package_for_Multiscale_Simulations_of_Large_Complex_Systems_with_Advanced_Point_Dipole_Polarizable_Force_Fields"><img alt="Research paper thumbnail of Tinker-HP: a Massively Parallel Molecular Dynamics Package for Multiscale Simulations of Large Complex Systems with Advanced Point Dipole Polarizable Force Fields" class="work-thumbnail" src="https://attachments.academia-assets.com/55175253/thumbnails/1.jpg" /></a></div><div class="wp-workCard wp-workCard_itemContainer"><div class="wp-workCard_item wp-workCard--title"><a class="js-work-strip-work-link text-gray-darker" data-click-track="profile-work-strip-title" href="https://www.academia.edu/35314545/Tinker_HP_a_Massively_Parallel_Molecular_Dynamics_Package_for_Multiscale_Simulations_of_Large_Complex_Systems_with_Advanced_Point_Dipole_Polarizable_Force_Fields">Tinker-HP: a Massively Parallel Molecular Dynamics Package for Multiscale Simulations of Large Complex Systems with Advanced Point Dipole Polarizable Force Fields</a></div><div class="wp-workCard_item wp-workCard--coauthors"><span>by </span><span><a class="" data-click-track="profile-work-strip-authors" href="https://sorbonne-fr.academia.edu/JeanPhilipPiquemal">Jean-Philip Piquemal</a> and <a class="" data-click-track="profile-work-strip-authors" href="https://uni-mainz.academia.edu/FilippoLipparini">Filippo Lipparini</a></span></div><div class="wp-workCard_item"><span class="js-work-more-abstract-truncated">We present Tinker-HP, a massively MPI parallel package dedicated to classical molecular dynamics ...</span><a class="js-work-more-abstract" data-broccoli-component="work_strip.more_abstract" data-click-track="profile-work-strip-more-abstract" href="javascript:;"><span> more </span><span><i class="fa fa-caret-down"></i></span></a><span class="js-work-more-abstract-untruncated hidden">We present Tinker-HP, a massively MPI parallel package dedicated to classical molecular dynamics (MD) and to multiscale simulations, using advanced polarizable force fields (PFF) encompassing distributed multipoles electrostatics. Tinker-HP is an evolution of the popular Tinker package code that conserves its simplicity of use and its reference double precision implementation for CPUs. Grounded on interdisciplinary efforts with applied mathematics, Tinker-HP allows for long polarizable MD simulations on large systems up to millions of atoms.We detail in the paper the newly developed extension of massively parallel 3D spatial decomposition to point dipole polarizable models as well as their coupling to efficient Krylov iterative and non-iterative polarization solvers. The design of the code allows the use of various computer systems ranging from laboratory workstations to modern petascale supercomputers with thousands of cores. Tinker-HP proposes therefore the first high-performance scalable CPU computing environment for the development of next generation point dipole PFFs and for production simulations. Strategies linking Tinker-HP to Quantum Mechanics (QM) in the framework of multiscale polarizable self-consistent QM/MD simulations are also provided. The possibilities, performances and scalability of the software are demonstrated via benchmarks calculations using the polarizable AMOEBA force field on systems ranging from large water boxes of increasing size and ionic liquids to (very) large biosystems encompassing several proteins as well as the complete satellite tobacco mosaic virus and ribosome structures. For small systems, Tinker-HP appears to be competitive with the Tinker-OpenMM GPU implementation of Tinker. As the system size grows, Tinker-HP remains operational thanks to its access to distributed memory and takes advantage of its new algorithmic enabling for stable long timescale polarizable simulations. Overall, a several thousand-fold acceleration over a single-core computation is observed for the largest systems. The extension of the present CPU implementation of Tinker-HP to other computational platforms is discussed.</span></div><div class="wp-workCard_item wp-workCard--actions"><span class="work-strip-bookmark-button-container"></span><a id="9cdb9921b054f820062b2435d0659816" class="wp-workCard--action" rel="nofollow" data-click-track="profile-work-strip-download" data-download="{"attachment_id":55175253,"asset_id":35314545,"asset_type":"Work","button_location":"profile"}" href="https://www.academia.edu/attachments/55175253/download_file?st=MTczMjM3NTk4Myw4LjIyMi4yMDguMTQ2&s=profile"><span><i class="fa fa-arrow-down"></i></span><span>Download</span></a><span class="wp-workCard--action visible-if-viewed-by-owner inline-block" style="display: none;"><span class="js-profile-work-strip-edit-button-wrapper profile-work-strip-edit-button-wrapper" data-work-id="35314545"><a class="js-profile-work-strip-edit-button" tabindex="0"><span><i class="fa fa-pencil"></i></span><span>Edit</span></a></span></span><span id="work-strip-rankings-button-container"></span></div><div class="wp-workCard_item wp-workCard--stats"><span><span><span class="js-view-count view-count u-mr2x" data-work-id="35314545"><i class="fa fa-spinner fa-spin"></i></span><script>$(function () { var workId = 35314545; window.Academia.workViewCountsFetcher.queue(workId, function (count) { var description = window.$h.commaizeInt(count) + " " + window.$h.pluralize(count, 'View'); $(".js-view-count[data-work-id=35314545]").text(description); $(".js-view-count[data-work-id=35314545]").attr('title', description).tooltip(); }); });</script></span></span><span><span class="percentile-widget hidden"><span class="u-mr2x work-percentile"></span></span><script>$(function () { var workId = 35314545; window.Academia.workPercentilesFetcher.queue(workId, function (percentileText) { var container = $(".js-work-strip[data-work-id='35314545']"); container.find('.work-percentile').text(percentileText.charAt(0).toUpperCase() + percentileText.slice(1)); container.find('.percentile-widget').show(); container.find('.percentile-widget').removeClass('hidden'); }); });</script></span><span><script>$(function() { new Works.PaperRankView({ workId: 35314545, container: "", }); });</script></span></div><div id="work-strip-premium-row-container"></div></div></div><script> require.config({ waitSeconds: 90 })(["https://a.academia-assets.com/assets/wow_profile-f77ea15d77ce96025a6048a514272ad8becbad23c641fc2b3bd6e24ca6ff1932.js","https://a.academia-assets.com/assets/work_edit-ad038b8c047c1a8d4fa01b402d530ff93c45fee2137a149a4a5398bc8ad67560.js"], function() { // from javascript_helper.rb var dispatcherData = {} if (true){ window.WowProfile.dispatcher = window.WowProfile.dispatcher || _.clone(Backbone.Events); dispatcherData = { dispatcher: window.WowProfile.dispatcher, downloadLinkId: "9cdb9921b054f820062b2435d0659816" } } $('.js-work-strip[data-work-id=35314545]').each(function() { if (!$(this).data('initialized')) { new WowProfile.WorkStripView({ el: this, workJSON: {"id":35314545,"title":"Tinker-HP: a Massively Parallel Molecular Dynamics Package for Multiscale Simulations of Large Complex Systems with Advanced Point Dipole Polarizable Force Fields","translated_title":"","metadata":{"abstract":"We present Tinker-HP, a massively MPI parallel package dedicated to classical molecular dynamics (MD) and to multiscale simulations, using advanced polarizable force fields (PFF) encompassing distributed multipoles electrostatics. 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The design of the code allows the use of various computer systems ranging from laboratory workstations to modern petascale supercomputers with thousands of cores. Tinker-HP proposes therefore the first high-performance scalable CPU computing environment for the development of next generation point dipole PFFs and for production simulations. Strategies linking Tinker-HP to Quantum Mechanics (QM) in the framework of multiscale polarizable self-consistent QM/MD simulations are also provided. The possibilities, performances and scalability of the software are demonstrated via benchmarks calculations using the polarizable AMOEBA force field on systems ranging from large water boxes of increasing size and ionic liquids to (very) large biosystems encompassing several proteins as well as the complete satellite tobacco mosaic virus and ribosome structures. For small systems, Tinker-HP appears to be competitive with the Tinker-OpenMM GPU implementation of Tinker. 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$(this).data('initialized', true); } }); $a.trackClickSource(".js-work-strip-work-link", "profile_work_strip") }); </script> <div class="js-work-strip profile--work_container" data-work-id="35181719"><div class="profile--work_thumbnail hidden-xs"><a class="js-work-strip-work-link" data-click-track="profile-work-strip-thumbnail" href="https://www.academia.edu/35181719/Status_of_the_Gaussian_Electrostatic_Model_a_Density_Based_Polarizable_Force_Field"><img alt="Research paper thumbnail of Status of the Gaussian Electrostatic Model, a Density-Based Polarizable Force Field" class="work-thumbnail" src="https://a.academia-assets.com/images/blank-paper.jpg" /></a></div><div class="wp-workCard wp-workCard_itemContainer"><div class="wp-workCard_item wp-workCard--title"><a class="js-work-strip-work-link text-gray-darker" data-click-track="profile-work-strip-title" href="https://www.academia.edu/35181719/Status_of_the_Gaussian_Electrostatic_Model_a_Density_Based_Polarizable_Force_Field">Status of the Gaussian Electrostatic Model, a Density-Based Polarizable Force Field</a></div><div class="wp-workCard_item"><span>Many-Body Effects and Electrostatics in Biomolecules</span><span>, 2016</span></div><div class="wp-workCard_item wp-workCard--actions"><span class="work-strip-bookmark-button-container"></span><span class="wp-workCard--action visible-if-viewed-by-owner inline-block" style="display: none;"><span class="js-profile-work-strip-edit-button-wrapper profile-work-strip-edit-button-wrapper" data-work-id="35181719"><a class="js-profile-work-strip-edit-button" tabindex="0"><span><i class="fa fa-pencil"></i></span><span>Edit</span></a></span></span><span id="work-strip-rankings-button-container"></span></div><div class="wp-workCard_item wp-workCard--stats"><span><span><span class="js-view-count view-count u-mr2x" data-work-id="35181719"><i class="fa fa-spinner fa-spin"></i></span><script>$(function () { var workId = 35181719; 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$(this).data('initialized', true); } }); $a.trackClickSource(".js-work-strip-work-link", "profile_work_strip") }); </script> <div class="js-work-strip profile--work_container" data-work-id="35181718"><div class="profile--work_thumbnail hidden-xs"><a class="js-work-strip-work-link" data-click-track="profile-work-strip-thumbnail" href="https://www.academia.edu/35181718/A_QM_MM_Approach_Using_the_AMOEBA_Polarizable_Embedding_From_Ground_State_Energies_to_Electronic_Excitations"><img alt="Research paper thumbnail of A QM/MM Approach Using the AMOEBA Polarizable Embedding: From Ground State Energies to Electronic Excitations" class="work-thumbnail" src="https://a.academia-assets.com/images/blank-paper.jpg" /></a></div><div class="wp-workCard wp-workCard_itemContainer"><div class="wp-workCard_item wp-workCard--title"><a class="js-work-strip-work-link text-gray-darker" data-click-track="profile-work-strip-title" href="https://www.academia.edu/35181718/A_QM_MM_Approach_Using_the_AMOEBA_Polarizable_Embedding_From_Ground_State_Energies_to_Electronic_Excitations">A QM/MM Approach Using the AMOEBA Polarizable Embedding: From Ground State Energies to Electronic Excitations</a></div><div class="wp-workCard_item"><span>Journal of chemical theory and computation</span><span>, Jan 11, 2016</span></div><div class="wp-workCard_item"><span class="js-work-more-abstract-truncated">A fully polarizable implementation of the hybrid quantum mechanics/molecular mechanics approach i...</span><a class="js-work-more-abstract" data-broccoli-component="work_strip.more_abstract" data-click-track="profile-work-strip-more-abstract" href="javascript:;"><span> more </span><span><i class="fa fa-caret-down"></i></span></a><span class="js-work-more-abstract-untruncated hidden">A fully polarizable implementation of the hybrid quantum mechanics/molecular mechanics approach is presented, where the classical environment is described through the AMOEBA polarizable force field. A variational formalism, offering a self-consistent relaxation of both the MM induced dipoles and the QM electronic density, is used for ground state energies and extended to electronic excitations in the framework of time-dependent density functional theory combined with a state specific response of the classical part. An application to the calculation of the solvatochromism of the pyridinium N-phenolate betaine dye used to define the solvent ET(30) scale is presented. The results show that the QM/AMOEBA model not only properly describes specific and bulk effects in the ground state but it also correctly responds to the large change in the solute electronic charge distribution upon excitation.</span></div><div class="wp-workCard_item wp-workCard--actions"><span class="work-strip-bookmark-button-container"></span><span class="wp-workCard--action visible-if-viewed-by-owner inline-block" style="display: none;"><span class="js-profile-work-strip-edit-button-wrapper profile-work-strip-edit-button-wrapper" data-work-id="35181718"><a class="js-profile-work-strip-edit-button" tabindex="0"><span><i class="fa fa-pencil"></i></span><span>Edit</span></a></span></span><span id="work-strip-rankings-button-container"></span></div><div class="wp-workCard_item wp-workCard--stats"><span><span><span class="js-view-count view-count u-mr2x" data-work-id="35181718"><i class="fa fa-spinner fa-spin"></i></span><script>$(function () { var workId = 35181718; window.Academia.workViewCountsFetcher.queue(workId, function (count) { var description = window.$h.commaizeInt(count) + " " + window.$h.pluralize(count, 'View'); $(".js-view-count[data-work-id=35181718]").text(description); $(".js-view-count[data-work-id=35181718]").attr('title', description).tooltip(); }); });</script></span></span><span><span class="percentile-widget hidden"><span class="u-mr2x work-percentile"></span></span><script>$(function () { var workId = 35181718; window.Academia.workPercentilesFetcher.queue(workId, function (percentileText) { var container = $(".js-work-strip[data-work-id='35181718']"); container.find('.work-percentile').text(percentileText.charAt(0).toUpperCase() + percentileText.slice(1)); container.find('.percentile-widget').show(); container.find('.percentile-widget').removeClass('hidden'); }); });</script></span><span><script>$(function() { new Works.PaperRankView({ workId: 35181718, container: "", }); });</script></span></div><div id="work-strip-premium-row-container"></div></div></div><script> require.config({ waitSeconds: 90 })(["https://a.academia-assets.com/assets/wow_profile-f77ea15d77ce96025a6048a514272ad8becbad23c641fc2b3bd6e24ca6ff1932.js","https://a.academia-assets.com/assets/work_edit-ad038b8c047c1a8d4fa01b402d530ff93c45fee2137a149a4a5398bc8ad67560.js"], function() { // from javascript_helper.rb var dispatcherData = {} if (false){ window.WowProfile.dispatcher = window.WowProfile.dispatcher || _.clone(Backbone.Events); dispatcherData = { dispatcher: window.WowProfile.dispatcher, downloadLinkId: "-1" } } $('.js-work-strip[data-work-id=35181718]').each(function() { if (!$(this).data('initialized')) { new WowProfile.WorkStripView({ el: this, workJSON: {"id":35181718,"title":"A QM/MM Approach Using the AMOEBA Polarizable Embedding: From Ground State Energies to Electronic Excitations","translated_title":"","metadata":{"abstract":"A fully polarizable implementation of the hybrid quantum mechanics/molecular mechanics approach is presented, where the classical environment is described through the AMOEBA polarizable force field. 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The results show that the QM/AMOEBA model not only properly describes specific and bulk effects in the ground state but it also correctly responds to the large change in the solute electronic charge distribution upon excitation.","publication_date":{"day":11,"month":1,"year":2016,"errors":{}},"publication_name":"Journal of chemical theory and computation"},"translated_abstract":"A fully polarizable implementation of the hybrid quantum mechanics/molecular mechanics approach is presented, where the classical environment is described through the AMOEBA polarizable force field. A variational formalism, offering a self-consistent relaxation of both the MM induced dipoles and the QM electronic density, is used for ground state energies and extended to electronic excitations in the framework of time-dependent density functional theory combined with a state specific response of the classical part. An application to the calculation of the solvatochromism of the pyridinium N-phenolate betaine dye used to define the solvent ET(30) scale is presented. The results show that the QM/AMOEBA model not only properly describes specific and bulk effects in the ground state but it also correctly responds to the large change in the solute electronic charge distribution upon excitation.","internal_url":"https://www.academia.edu/35181718/A_QM_MM_Approach_Using_the_AMOEBA_Polarizable_Embedding_From_Ground_State_Energies_to_Electronic_Excitations","translated_internal_url":"","created_at":"2017-11-18T07:17:50.340-08:00","preview_url":null,"current_user_can_edit":null,"current_user_is_owner":null,"owner_id":35445,"coauthors_can_edit":true,"document_type":"paper","co_author_tags":[],"downloadable_attachments":[],"slug":"A_QM_MM_Approach_Using_the_AMOEBA_Polarizable_Embedding_From_Ground_State_Energies_to_Electronic_Excitations","translated_slug":"","page_count":null,"language":"en","content_type":"Work","owner":{"id":35445,"first_name":"Jean-Philip","middle_initials":null,"last_name":"Piquemal","page_name":"JeanPhilipPiquemal","domain_name":"sorbonne-fr","created_at":"2009-03-17T04:43:24.569-07:00","display_name":"Jean-Philip Piquemal","url":"https://sorbonne-fr.academia.edu/JeanPhilipPiquemal"},"attachments":[],"research_interests":[{"id":645605,"name":"THEORETICAL AND COMPUTATIONAL CHEMISTRY","url":"https://www.academia.edu/Documents/in/THEORETICAL_AND_COMPUTATIONAL_CHEMISTRY"}],"urls":[]}, dispatcherData: dispatcherData }); $(this).data('initialized', true); } }); $a.trackClickSource(".js-work-strip-work-link", "profile_work_strip") }); </script> <div class="js-work-strip profile--work_container" data-work-id="35181717"><div class="profile--work_thumbnail hidden-xs"><a class="js-work-strip-work-link" data-click-track="profile-work-strip-thumbnail" href="https://www.academia.edu/35181717/LICHEM_A_QM_MM_program_for_simulations_with_multipolar_and_polarizable_force_fields"><img alt="Research paper thumbnail of LICHEM: A QM/MM program for simulations with multipolar and polarizable force fields" class="work-thumbnail" src="https://a.academia-assets.com/images/blank-paper.jpg" /></a></div><div class="wp-workCard wp-workCard_itemContainer"><div class="wp-workCard_item wp-workCard--title"><a class="js-work-strip-work-link text-gray-darker" data-click-track="profile-work-strip-title" href="https://www.academia.edu/35181717/LICHEM_A_QM_MM_program_for_simulations_with_multipolar_and_polarizable_force_fields">LICHEM: A QM/MM program for simulations with multipolar and polarizable force fields</a></div><div class="wp-workCard_item"><span>Journal of Computational Chemistry</span><span>, 2016</span></div><div class="wp-workCard_item"><span class="js-work-more-abstract-truncated">We introduce an initial implementation of the LICHEM software package. LICHEM can interface with ...</span><a class="js-work-more-abstract" data-broccoli-component="work_strip.more_abstract" data-click-track="profile-work-strip-more-abstract" href="javascript:;"><span> more </span><span><i class="fa fa-caret-down"></i></span></a><span class="js-work-more-abstract-untruncated hidden">We introduce an initial implementation of the LICHEM software package. LICHEM can interface with Gaussian, PSI4, NWChem, TINKER, and TINKER-HP to enable QM/MM calculations using multipolar/polarizable force fields. LICHEM extracts forces and energies from unmodified QM and MM software packages to perform geometry optimizations, single-point energy calculations, or Monte Carlo simulations. When the QM and MM regions are connected by covalent bonds, the pseudo-bond approach is employed to smoothly transition between the QM region and the polarizable force field. A series of water clusters and small peptides have been employed to test our initial implementation. The results obtained from these test systems show the capabilities of the new software and highlight the importance of including explicit polarization. © 2016 Wiley Periodicals, Inc.</span></div><div class="wp-workCard_item wp-workCard--actions"><span class="work-strip-bookmark-button-container"></span><span class="wp-workCard--action visible-if-viewed-by-owner inline-block" style="display: none;"><span class="js-profile-work-strip-edit-button-wrapper profile-work-strip-edit-button-wrapper" data-work-id="35181717"><a class="js-profile-work-strip-edit-button" tabindex="0"><span><i class="fa fa-pencil"></i></span><span>Edit</span></a></span></span><span id="work-strip-rankings-button-container"></span></div><div class="wp-workCard_item wp-workCard--stats"><span><span><span class="js-view-count view-count u-mr2x" data-work-id="35181717"><i class="fa fa-spinner fa-spin"></i></span><script>$(function () { var workId = 35181717; window.Academia.workViewCountsFetcher.queue(workId, function (count) { var description = window.$h.commaizeInt(count) + " " + window.$h.pluralize(count, 'View'); $(".js-view-count[data-work-id=35181717]").text(description); $(".js-view-count[data-work-id=35181717]").attr('title', description).tooltip(); }); });</script></span></span><span><span class="percentile-widget hidden"><span class="u-mr2x work-percentile"></span></span><script>$(function () { var workId = 35181717; window.Academia.workPercentilesFetcher.queue(workId, function (percentileText) { var container = $(".js-work-strip[data-work-id='35181717']"); container.find('.work-percentile').text(percentileText.charAt(0).toUpperCase() + percentileText.slice(1)); container.find('.percentile-widget').show(); container.find('.percentile-widget').removeClass('hidden'); }); });</script></span><span><script>$(function() { new Works.PaperRankView({ workId: 35181717, container: "", }); });</script></span></div><div id="work-strip-premium-row-container"></div></div></div><script> require.config({ waitSeconds: 90 })(["https://a.academia-assets.com/assets/wow_profile-f77ea15d77ce96025a6048a514272ad8becbad23c641fc2b3bd6e24ca6ff1932.js","https://a.academia-assets.com/assets/work_edit-ad038b8c047c1a8d4fa01b402d530ff93c45fee2137a149a4a5398bc8ad67560.js"], function() { // from javascript_helper.rb var dispatcherData = {} if (false){ window.WowProfile.dispatcher = window.WowProfile.dispatcher || _.clone(Backbone.Events); dispatcherData = { dispatcher: window.WowProfile.dispatcher, downloadLinkId: "-1" } } $('.js-work-strip[data-work-id=35181717]').each(function() { if (!$(this).data('initialized')) { new WowProfile.WorkStripView({ el: this, workJSON: {"id":35181717,"title":"LICHEM: A QM/MM program for simulations with multipolar and polarizable force fields","translated_title":"","metadata":{"abstract":"We introduce an initial implementation of the LICHEM software package. 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The results obtained from these test systems show the capabilities of the new software and highlight the importance of including explicit polarization. © 2016 Wiley Periodicals, Inc.","publisher":"Wiley-Blackwell","publication_date":{"day":null,"month":null,"year":2016,"errors":{}},"publication_name":"Journal of Computational Chemistry"},"translated_abstract":"We introduce an initial implementation of the LICHEM software package. LICHEM can interface with Gaussian, PSI4, NWChem, TINKER, and TINKER-HP to enable QM/MM calculations using multipolar/polarizable force fields. LICHEM extracts forces and energies from unmodified QM and MM software packages to perform geometry optimizations, single-point energy calculations, or Monte Carlo simulations. When the QM and MM regions are connected by covalent bonds, the pseudo-bond approach is employed to smoothly transition between the QM region and the polarizable force field. A series of water clusters and small peptides have been employed to test our initial implementation. The results obtained from these test systems show the capabilities of the new software and highlight the importance of including explicit polarization. © 2016 Wiley Periodicals, Inc.","internal_url":"https://www.academia.edu/35181717/LICHEM_A_QM_MM_program_for_simulations_with_multipolar_and_polarizable_force_fields","translated_internal_url":"","created_at":"2017-11-18T07:17:50.166-08:00","preview_url":null,"current_user_can_edit":null,"current_user_is_owner":null,"owner_id":35445,"coauthors_can_edit":true,"document_type":"paper","co_author_tags":[],"downloadable_attachments":[],"slug":"LICHEM_A_QM_MM_program_for_simulations_with_multipolar_and_polarizable_force_fields","translated_slug":"","page_count":null,"language":"en","content_type":"Work","owner":{"id":35445,"first_name":"Jean-Philip","middle_initials":null,"last_name":"Piquemal","page_name":"JeanPhilipPiquemal","domain_name":"sorbonne-fr","created_at":"2009-03-17T04:43:24.569-07:00","display_name":"Jean-Philip Piquemal","url":"https://sorbonne-fr.academia.edu/JeanPhilipPiquemal"},"attachments":[],"research_interests":[{"id":528,"name":"Computational Chemistry","url":"https://www.academia.edu/Documents/in/Computational_Chemistry"},{"id":6811,"name":"Quantum Theory","url":"https://www.academia.edu/Documents/in/Quantum_Theory"},{"id":53293,"name":"Software","url":"https://www.academia.edu/Documents/in/Software"},{"id":645605,"name":"THEORETICAL AND COMPUTATIONAL CHEMISTRY","url":"https://www.academia.edu/Documents/in/THEORETICAL_AND_COMPUTATIONAL_CHEMISTRY"},{"id":1333436,"name":"Monte Carlo Method","url":"https://www.academia.edu/Documents/in/Monte_Carlo_Method"}],"urls":[]}, dispatcherData: dispatcherData }); $(this).data('initialized', true); } }); $a.trackClickSource(".js-work-strip-work-link", "profile_work_strip") }); </script> <div class="js-work-strip profile--work_container" data-work-id="35181716"><div class="profile--work_thumbnail hidden-xs"><a class="js-work-strip-work-link" data-click-track="profile-work-strip-thumbnail" href="https://www.academia.edu/35181716/Scalable_improvement_of_SPME_multipolar_electrostatics_in_anisotropic_polarizable_molecular_mechanics_using_a_general_short_range_penetration_correction_up_to_quadrupoles"><img alt="Research paper thumbnail of Scalable improvement of SPME multipolar electrostatics in anisotropic polarizable molecular mechanics using a general short-range penetration correction up to quadrupoles" class="work-thumbnail" src="https://a.academia-assets.com/images/blank-paper.jpg" /></a></div><div class="wp-workCard wp-workCard_itemContainer"><div class="wp-workCard_item wp-workCard--title"><a class="js-work-strip-work-link text-gray-darker" data-click-track="profile-work-strip-title" href="https://www.academia.edu/35181716/Scalable_improvement_of_SPME_multipolar_electrostatics_in_anisotropic_polarizable_molecular_mechanics_using_a_general_short_range_penetration_correction_up_to_quadrupoles">Scalable improvement of SPME multipolar electrostatics in anisotropic polarizable molecular mechanics using a general short-range penetration correction up to quadrupoles</a></div><div class="wp-workCard_item"><span>Journal of Computational Chemistry</span><span>, 2016</span></div><div class="wp-workCard_item"><span class="js-work-more-abstract-truncated">We propose a general coupling of the Smooth Particle Mesh Ewald SPME approach for distributed mul...</span><a class="js-work-more-abstract" data-broccoli-component="work_strip.more_abstract" data-click-track="profile-work-strip-more-abstract" href="javascript:;"><span> more </span><span><i class="fa fa-caret-down"></i></span></a><span class="js-work-more-abstract-untruncated hidden">We propose a general coupling of the Smooth Particle Mesh Ewald SPME approach for distributed multipoles to a short-range charge penetration correction modifying the charge-charge, charge-dipole and charge-quadrupole energies. Such an approach significantly improves electrostatics when compared to ab initio values and has been calibrated on Symmetry-Adapted Perturbation Theory reference data. Various neutral molecular dimers have been tested and results on the complexes of mono- and divalent cations with a water ligand are also provided. Transferability of the correction is adressed in the context of the implementation of the AMOEBA and SIBFA polarizable force fields in the TINKER-HP software. As the choices of the multipolar distribution are discussed, conclusions are drawn for the future penetration-corrected polarizable force fields highlighting the mandatory need of non-spurious procedures for the obtention of well balanced and physically meaningful distributed moments. Finally, scalability and parallelism of the short-range corrected SPME approach are addressed, demonstrating that the damping function is computationally affordable and accurate for molecular dynamics simulations of complex bio- or bioinorganic systems in periodic boundary conditions. © 2016 Wiley Periodicals, Inc.</span></div><div class="wp-workCard_item wp-workCard--actions"><span class="work-strip-bookmark-button-container"></span><span class="wp-workCard--action visible-if-viewed-by-owner inline-block" style="display: none;"><span class="js-profile-work-strip-edit-button-wrapper profile-work-strip-edit-button-wrapper" data-work-id="35181716"><a class="js-profile-work-strip-edit-button" tabindex="0"><span><i class="fa fa-pencil"></i></span><span>Edit</span></a></span></span><span id="work-strip-rankings-button-container"></span></div><div class="wp-workCard_item wp-workCard--stats"><span><span><span class="js-view-count view-count u-mr2x" data-work-id="35181716"><i class="fa fa-spinner fa-spin"></i></span><script>$(function () { var workId = 35181716; window.Academia.workViewCountsFetcher.queue(workId, function (count) { var description = window.$h.commaizeInt(count) + " " + window.$h.pluralize(count, 'View'); $(".js-view-count[data-work-id=35181716]").text(description); $(".js-view-count[data-work-id=35181716]").attr('title', description).tooltip(); }); });</script></span></span><span><span class="percentile-widget hidden"><span class="u-mr2x work-percentile"></span></span><script>$(function () { var workId = 35181716; window.Academia.workPercentilesFetcher.queue(workId, function (percentileText) { var container = $(".js-work-strip[data-work-id='35181716']"); container.find('.work-percentile').text(percentileText.charAt(0).toUpperCase() + percentileText.slice(1)); container.find('.percentile-widget').show(); container.find('.percentile-widget').removeClass('hidden'); }); });</script></span><span><script>$(function() { new Works.PaperRankView({ workId: 35181716, container: "", }); });</script></span></div><div id="work-strip-premium-row-container"></div></div></div><script> require.config({ waitSeconds: 90 })(["https://a.academia-assets.com/assets/wow_profile-f77ea15d77ce96025a6048a514272ad8becbad23c641fc2b3bd6e24ca6ff1932.js","https://a.academia-assets.com/assets/work_edit-ad038b8c047c1a8d4fa01b402d530ff93c45fee2137a149a4a5398bc8ad67560.js"], function() { // from javascript_helper.rb var dispatcherData = {} if (false){ window.WowProfile.dispatcher = window.WowProfile.dispatcher || _.clone(Backbone.Events); dispatcherData = { dispatcher: window.WowProfile.dispatcher, downloadLinkId: "-1" } } $('.js-work-strip[data-work-id=35181716]').each(function() { if (!$(this).data('initialized')) { new WowProfile.WorkStripView({ el: this, workJSON: {"id":35181716,"title":"Scalable improvement of SPME multipolar electrostatics in anisotropic polarizable molecular mechanics using a general short-range penetration correction up to quadrupoles","translated_title":"","metadata":{"abstract":"We propose a general coupling of the Smooth Particle Mesh Ewald SPME approach for distributed multipoles to a short-range charge penetration correction modifying the charge-charge, charge-dipole and charge-quadrupole energies. Such an approach significantly improves electrostatics when compared to ab initio values and has been calibrated on Symmetry-Adapted Perturbation Theory reference data. Various neutral molecular dimers have been tested and results on the complexes of mono- and divalent cations with a water ligand are also provided. Transferability of the correction is adressed in the context of the implementation of the AMOEBA and SIBFA polarizable force fields in the TINKER-HP software. As the choices of the multipolar distribution are discussed, conclusions are drawn for the future penetration-corrected polarizable force fields highlighting the mandatory need of non-spurious procedures for the obtention of well balanced and physically meaningful distributed moments. Finally, scalability and parallelism of the short-range corrected SPME approach are addressed, demonstrating that the damping function is computationally affordable and accurate for molecular dynamics simulations of complex bio- or bioinorganic systems in periodic boundary conditions. © 2016 Wiley Periodicals, Inc.","publisher":"Wiley-Blackwell","publication_date":{"day":null,"month":null,"year":2016,"errors":{}},"publication_name":"Journal of Computational Chemistry"},"translated_abstract":"We propose a general coupling of the Smooth Particle Mesh Ewald SPME approach for distributed multipoles to a short-range charge penetration correction modifying the charge-charge, charge-dipole and charge-quadrupole energies. Such an approach significantly improves electrostatics when compared to ab initio values and has been calibrated on Symmetry-Adapted Perturbation Theory reference data. Various neutral molecular dimers have been tested and results on the complexes of mono- and divalent cations with a water ligand are also provided. Transferability of the correction is adressed in the context of the implementation of the AMOEBA and SIBFA polarizable force fields in the TINKER-HP software. As the choices of the multipolar distribution are discussed, conclusions are drawn for the future penetration-corrected polarizable force fields highlighting the mandatory need of non-spurious procedures for the obtention of well balanced and physically meaningful distributed moments. Finally, scalability and parallelism of the short-range corrected SPME approach are addressed, demonstrating that the damping function is computationally affordable and accurate for molecular dynamics simulations of complex bio- or bioinorganic systems in periodic boundary conditions. © 2016 Wiley Periodicals, Inc.","internal_url":"https://www.academia.edu/35181716/Scalable_improvement_of_SPME_multipolar_electrostatics_in_anisotropic_polarizable_molecular_mechanics_using_a_general_short_range_penetration_correction_up_to_quadrupoles","translated_internal_url":"","created_at":"2017-11-18T07:17:50.013-08:00","preview_url":null,"current_user_can_edit":null,"current_user_is_owner":null,"owner_id":35445,"coauthors_can_edit":true,"document_type":"paper","co_author_tags":[],"downloadable_attachments":[],"slug":"Scalable_improvement_of_SPME_multipolar_electrostatics_in_anisotropic_polarizable_molecular_mechanics_using_a_general_short_range_penetration_correction_up_to_quadrupoles","translated_slug":"","page_count":null,"language":"en","content_type":"Work","owner":{"id":35445,"first_name":"Jean-Philip","middle_initials":null,"last_name":"Piquemal","page_name":"JeanPhilipPiquemal","domain_name":"sorbonne-fr","created_at":"2009-03-17T04:43:24.569-07:00","display_name":"Jean-Philip Piquemal","url":"https://sorbonne-fr.academia.edu/JeanPhilipPiquemal"},"attachments":[],"research_interests":[{"id":522,"name":"Thermodynamics","url":"https://www.academia.edu/Documents/in/Thermodynamics"},{"id":528,"name":"Computational Chemistry","url":"https://www.academia.edu/Documents/in/Computational_Chemistry"},{"id":2215,"name":"Water","url":"https://www.academia.edu/Documents/in/Water"},{"id":2736,"name":"Molecular Dynamics Simulation","url":"https://www.academia.edu/Documents/in/Molecular_Dynamics_Simulation"},{"id":4987,"name":"Kinetics","url":"https://www.academia.edu/Documents/in/Kinetics"},{"id":6811,"name":"Quantum Theory","url":"https://www.academia.edu/Documents/in/Quantum_Theory"},{"id":37333,"name":"Anisotropy","url":"https://www.academia.edu/Documents/in/Anisotropy"},{"id":53293,"name":"Software","url":"https://www.academia.edu/Documents/in/Software"},{"id":414692,"name":"Solutions","url":"https://www.academia.edu/Documents/in/Solutions"},{"id":606320,"name":"Benzene","url":"https://www.academia.edu/Documents/in/Benzene"},{"id":645605,"name":"THEORETICAL AND COMPUTATIONAL CHEMISTRY","url":"https://www.academia.edu/Documents/in/THEORETICAL_AND_COMPUTATIONAL_CHEMISTRY"},{"id":1154485,"name":"Mechanical Processes","url":"https://www.academia.edu/Documents/in/Mechanical_Processes"},{"id":1451660,"name":"Static Electricity","url":"https://www.academia.edu/Documents/in/Static_Electricity"},{"id":1809037,"name":"Dimerization","url":"https://www.academia.edu/Documents/in/Dimerization"}],"urls":[]}, dispatcherData: dispatcherData }); $(this).data('initialized', true); } }); $a.trackClickSource(".js-work-strip-work-link", "profile_work_strip") }); </script> <div class="js-work-strip profile--work_container" data-work-id="35181715"><div class="profile--work_thumbnail hidden-xs"><a class="js-work-strip-work-link" data-click-track="profile-work-strip-thumbnail" href="https://www.academia.edu/35181715/Addressing_the_Issues_of_Non_isotropy_and_Non_additivity_in_the_Development_of_Quantum_Chemistry_Grounded_Polarizable_Molecular_Mechanics"><img alt="Research paper thumbnail of Addressing the Issues of Non-isotropy and Non-additivity in the Development of Quantum Chemistry-Grounded Polarizable Molecular Mechanics" class="work-thumbnail" src="https://a.academia-assets.com/images/blank-paper.jpg" /></a></div><div class="wp-workCard wp-workCard_itemContainer"><div class="wp-workCard_item wp-workCard--title"><a class="js-work-strip-work-link text-gray-darker" data-click-track="profile-work-strip-title" href="https://www.academia.edu/35181715/Addressing_the_Issues_of_Non_isotropy_and_Non_additivity_in_the_Development_of_Quantum_Chemistry_Grounded_Polarizable_Molecular_Mechanics">Addressing the Issues of Non-isotropy and Non-additivity in the Development of Quantum Chemistry-Grounded Polarizable Molecular Mechanics</a></div><div class="wp-workCard_item"><span>Quantum Modeling of Complex Molecular Systems</span><span>, 2015</span></div><div class="wp-workCard_item"><span class="js-work-more-abstract-truncated">ABSTRACT We review two essential features of the intermolecular interaction energies (ΔE) compute...</span><a class="js-work-more-abstract" data-broccoli-component="work_strip.more_abstract" data-click-track="profile-work-strip-more-abstract" href="javascript:;"><span> more </span><span><i class="fa fa-caret-down"></i></span></a><span class="js-work-more-abstract-untruncated hidden">ABSTRACT We review two essential features of the intermolecular interaction energies (ΔE) computed in the context of quantum chemistry (QC): non-isotropy and non-additivity. Energy-decomposition analyses show the extent to which each comes into play in the separate ΔE contributions, namely electrostatic, short-range repulsion, polarization, charge-transfer and dispersion. Such contributions have their counterparts in anisotropic, polarizable molecular mechanics (APMM), and each of these should display the same features as in QC. We review examples to evaluate the performances of APMM in this respect. They bear on the complexes of one or several ligands with metal cations, and on multiply H-bonded complexes. We also comment on the involvement of polarization, a key contributor to non-additivity, in the issues of multipole transferability and conjugation. In the last section we provide recent examples of APMM validations by QC, which relate to interactions taking place in the recognition sites of kinases and metalloproteins. We conclude by mentioning prospects of extensive applications of APMM.</span></div><div class="wp-workCard_item wp-workCard--actions"><span class="work-strip-bookmark-button-container"></span><span class="wp-workCard--action visible-if-viewed-by-owner inline-block" style="display: none;"><span class="js-profile-work-strip-edit-button-wrapper profile-work-strip-edit-button-wrapper" data-work-id="35181715"><a class="js-profile-work-strip-edit-button" tabindex="0"><span><i class="fa fa-pencil"></i></span><span>Edit</span></a></span></span><span id="work-strip-rankings-button-container"></span></div><div class="wp-workCard_item wp-workCard--stats"><span><span><span class="js-view-count view-count u-mr2x" data-work-id="35181715"><i class="fa fa-spinner fa-spin"></i></span><script>$(function () { var workId = 35181715; window.Academia.workViewCountsFetcher.queue(workId, function (count) { var description = window.$h.commaizeInt(count) + " " + window.$h.pluralize(count, 'View'); $(".js-view-count[data-work-id=35181715]").text(description); $(".js-view-count[data-work-id=35181715]").attr('title', description).tooltip(); }); });</script></span></span><span><span class="percentile-widget hidden"><span class="u-mr2x work-percentile"></span></span><script>$(function () { var workId = 35181715; window.Academia.workPercentilesFetcher.queue(workId, function (percentileText) { var container = $(".js-work-strip[data-work-id='35181715']"); container.find('.work-percentile').text(percentileText.charAt(0).toUpperCase() + percentileText.slice(1)); container.find('.percentile-widget').show(); container.find('.percentile-widget').removeClass('hidden'); }); });</script></span><span><script>$(function() { new Works.PaperRankView({ workId: 35181715, container: "", }); });</script></span></div><div id="work-strip-premium-row-container"></div></div></div><script> require.config({ waitSeconds: 90 })(["https://a.academia-assets.com/assets/wow_profile-f77ea15d77ce96025a6048a514272ad8becbad23c641fc2b3bd6e24ca6ff1932.js","https://a.academia-assets.com/assets/work_edit-ad038b8c047c1a8d4fa01b402d530ff93c45fee2137a149a4a5398bc8ad67560.js"], function() { // from javascript_helper.rb var dispatcherData = {} if (false){ window.WowProfile.dispatcher = window.WowProfile.dispatcher || _.clone(Backbone.Events); dispatcherData = { dispatcher: window.WowProfile.dispatcher, downloadLinkId: "-1" } } $('.js-work-strip[data-work-id=35181715]').each(function() { if (!$(this).data('initialized')) { new WowProfile.WorkStripView({ el: this, workJSON: {"id":35181715,"title":"Addressing the Issues of Non-isotropy and Non-additivity in the Development of Quantum Chemistry-Grounded Polarizable Molecular Mechanics","translated_title":"","metadata":{"abstract":"ABSTRACT We review two essential features of the intermolecular interaction energies (ΔE) computed in the context of quantum chemistry (QC): non-isotropy and non-additivity. Energy-decomposition analyses show the extent to which each comes into play in the separate ΔE contributions, namely electrostatic, short-range repulsion, polarization, charge-transfer and dispersion. Such contributions have their counterparts in anisotropic, polarizable molecular mechanics (APMM), and each of these should display the same features as in QC. We review examples to evaluate the performances of APMM in this respect. They bear on the complexes of one or several ligands with metal cations, and on multiply H-bonded complexes. We also comment on the involvement of polarization, a key contributor to non-additivity, in the issues of multipole transferability and conjugation. In the last section we provide recent examples of APMM validations by QC, which relate to interactions taking place in the recognition sites of kinases and metalloproteins. We conclude by mentioning prospects of extensive applications of APMM.","publication_date":{"day":null,"month":null,"year":2015,"errors":{}},"publication_name":"Quantum Modeling of Complex Molecular Systems"},"translated_abstract":"ABSTRACT We review two essential features of the intermolecular interaction energies (ΔE) computed in the context of quantum chemistry (QC): non-isotropy and non-additivity. Energy-decomposition analyses show the extent to which each comes into play in the separate ΔE contributions, namely electrostatic, short-range repulsion, polarization, charge-transfer and dispersion. Such contributions have their counterparts in anisotropic, polarizable molecular mechanics (APMM), and each of these should display the same features as in QC. We review examples to evaluate the performances of APMM in this respect. They bear on the complexes of one or several ligands with metal cations, and on multiply H-bonded complexes. We also comment on the involvement of polarization, a key contributor to non-additivity, in the issues of multipole transferability and conjugation. In the last section we provide recent examples of APMM validations by QC, which relate to interactions taking place in the recognition sites of kinases and metalloproteins. We conclude by mentioning prospects of extensive applications of APMM.","internal_url":"https://www.academia.edu/35181715/Addressing_the_Issues_of_Non_isotropy_and_Non_additivity_in_the_Development_of_Quantum_Chemistry_Grounded_Polarizable_Molecular_Mechanics","translated_internal_url":"","created_at":"2017-11-18T07:17:49.862-08:00","preview_url":null,"current_user_can_edit":null,"current_user_is_owner":null,"owner_id":35445,"coauthors_can_edit":true,"document_type":"paper","co_author_tags":[],"downloadable_attachments":[],"slug":"Addressing_the_Issues_of_Non_isotropy_and_Non_additivity_in_the_Development_of_Quantum_Chemistry_Grounded_Polarizable_Molecular_Mechanics","translated_slug":"","page_count":null,"language":"en","content_type":"Work","owner":{"id":35445,"first_name":"Jean-Philip","middle_initials":null,"last_name":"Piquemal","page_name":"JeanPhilipPiquemal","domain_name":"sorbonne-fr","created_at":"2009-03-17T04:43:24.569-07:00","display_name":"Jean-Philip Piquemal","url":"https://sorbonne-fr.academia.edu/JeanPhilipPiquemal"},"attachments":[],"research_interests":[],"urls":[]}, dispatcherData: dispatcherData }); $(this).data('initialized', true); } }); $a.trackClickSource(".js-work-strip-work-link", "profile_work_strip") }); </script> <div class="js-work-strip profile--work_container" data-work-id="35181714"><div class="profile--work_thumbnail hidden-xs"><a class="js-work-strip-work-link" data-click-track="profile-work-strip-thumbnail" href="https://www.academia.edu/35181714/Approaching_the_double_faceted_nature_of_the_CX_bond_in_halobenzenes_with_a_bifunctional_probe"><img alt="Research paper thumbnail of Approaching the double-faceted nature of the CX bond in halobenzenes with a bifunctional probe" class="work-thumbnail" src="https://a.academia-assets.com/images/blank-paper.jpg" /></a></div><div class="wp-workCard wp-workCard_itemContainer"><div class="wp-workCard_item wp-workCard--title"><a class="js-work-strip-work-link text-gray-darker" data-click-track="profile-work-strip-title" href="https://www.academia.edu/35181714/Approaching_the_double_faceted_nature_of_the_CX_bond_in_halobenzenes_with_a_bifunctional_probe">Approaching the double-faceted nature of the CX bond in halobenzenes with a bifunctional probe</a></div><div class="wp-workCard_item"><span>Chemical Physics Letters</span><span>, 2015</span></div><div class="wp-workCard_item"><span class="js-work-more-abstract-truncated">ABSTRACT In halobenzenes, the CX bond (X = Cl, Br) is doubly faceted, electron-deficient along th...</span><a class="js-work-more-abstract" data-broccoli-component="work_strip.more_abstract" data-click-track="profile-work-strip-more-abstract" href="javascript:;"><span> more </span><span><i class="fa fa-caret-down"></i></span></a><span class="js-work-more-abstract-untruncated hidden">ABSTRACT In halobenzenes, the CX bond (X = Cl, Br) is doubly faceted, electron-deficient along the CX direction, and electron-rich on its flanks. We have recently shown that both features could be enhanced by appropriate electron-withdrawing and electron-donating groups, respectively. In this paper we further highlight this dual character by approaching a bifunctional probe, N-methylformamide, to both regions in representative substituted halobenzenes. We report the results of interaction energy computations, ELF, and NCI analyses. These methods used in conjunction show the responsiveness of the CX bond to both kinds of substitutions, enabling significant interaction energy gains with respect to the parent compound.</span></div><div class="wp-workCard_item wp-workCard--actions"><span class="work-strip-bookmark-button-container"></span><span class="wp-workCard--action visible-if-viewed-by-owner inline-block" style="display: none;"><span class="js-profile-work-strip-edit-button-wrapper profile-work-strip-edit-button-wrapper" data-work-id="35181714"><a class="js-profile-work-strip-edit-button" tabindex="0"><span><i class="fa fa-pencil"></i></span><span>Edit</span></a></span></span><span id="work-strip-rankings-button-container"></span></div><div class="wp-workCard_item wp-workCard--stats"><span><span><span class="js-view-count view-count u-mr2x" data-work-id="35181714"><i class="fa fa-spinner fa-spin"></i></span><script>$(function () { var workId = 35181714; window.Academia.workViewCountsFetcher.queue(workId, function (count) { var description = window.$h.commaizeInt(count) + " " + window.$h.pluralize(count, 'View'); $(".js-view-count[data-work-id=35181714]").text(description); $(".js-view-count[data-work-id=35181714]").attr('title', description).tooltip(); }); });</script></span></span><span><span class="percentile-widget hidden"><span class="u-mr2x work-percentile"></span></span><script>$(function () { var workId = 35181714; window.Academia.workPercentilesFetcher.queue(workId, function (percentileText) { var container = $(".js-work-strip[data-work-id='35181714']"); container.find('.work-percentile').text(percentileText.charAt(0).toUpperCase() + percentileText.slice(1)); container.find('.percentile-widget').show(); container.find('.percentile-widget').removeClass('hidden'); }); });</script></span><span><script>$(function() { new Works.PaperRankView({ workId: 35181714, container: "", }); });</script></span></div><div id="work-strip-premium-row-container"></div></div></div><script> require.config({ waitSeconds: 90 })(["https://a.academia-assets.com/assets/wow_profile-f77ea15d77ce96025a6048a514272ad8becbad23c641fc2b3bd6e24ca6ff1932.js","https://a.academia-assets.com/assets/work_edit-ad038b8c047c1a8d4fa01b402d530ff93c45fee2137a149a4a5398bc8ad67560.js"], function() { // from javascript_helper.rb var dispatcherData = {} if (false){ window.WowProfile.dispatcher = window.WowProfile.dispatcher || _.clone(Backbone.Events); dispatcherData = { dispatcher: window.WowProfile.dispatcher, downloadLinkId: "-1" } } $('.js-work-strip[data-work-id=35181714]').each(function() { if (!$(this).data('initialized')) { new WowProfile.WorkStripView({ el: this, workJSON: {"id":35181714,"title":"Approaching the double-faceted nature of the CX bond in halobenzenes with a bifunctional probe","translated_title":"","metadata":{"abstract":"ABSTRACT In halobenzenes, the CX bond (X = Cl, Br) is doubly faceted, electron-deficient along the CX direction, and electron-rich on its flanks. We have recently shown that both features could be enhanced by appropriate electron-withdrawing and electron-donating groups, respectively. In this paper we further highlight this dual character by approaching a bifunctional probe, N-methylformamide, to both regions in representative substituted halobenzenes. We report the results of interaction energy computations, ELF, and NCI analyses. These methods used in conjunction show the responsiveness of the CX bond to both kinds of substitutions, enabling significant interaction energy gains with respect to the parent compound.","publisher":"Elsevier BV","publication_date":{"day":null,"month":null,"year":2015,"errors":{}},"publication_name":"Chemical Physics Letters"},"translated_abstract":"ABSTRACT In halobenzenes, the CX bond (X = Cl, Br) is doubly faceted, electron-deficient along the CX direction, and electron-rich on its flanks. We have recently shown that both features could be enhanced by appropriate electron-withdrawing and electron-donating groups, respectively. In this paper we further highlight this dual character by approaching a bifunctional probe, N-methylformamide, to both regions in representative substituted halobenzenes. We report the results of interaction energy computations, ELF, and NCI analyses. These methods used in conjunction show the responsiveness of the CX bond to both kinds of substitutions, enabling significant interaction energy gains with respect to the parent compound.","internal_url":"https://www.academia.edu/35181714/Approaching_the_double_faceted_nature_of_the_CX_bond_in_halobenzenes_with_a_bifunctional_probe","translated_internal_url":"","created_at":"2017-11-18T07:17:49.671-08:00","preview_url":null,"current_user_can_edit":null,"current_user_is_owner":null,"owner_id":35445,"coauthors_can_edit":true,"document_type":"paper","co_author_tags":[],"downloadable_attachments":[],"slug":"Approaching_the_double_faceted_nature_of_the_CX_bond_in_halobenzenes_with_a_bifunctional_probe","translated_slug":"","page_count":null,"language":"en","content_type":"Work","owner":{"id":35445,"first_name":"Jean-Philip","middle_initials":null,"last_name":"Piquemal","page_name":"JeanPhilipPiquemal","domain_name":"sorbonne-fr","created_at":"2009-03-17T04:43:24.569-07:00","display_name":"Jean-Philip Piquemal","url":"https://sorbonne-fr.academia.edu/JeanPhilipPiquemal"},"attachments":[],"research_interests":[{"id":923,"name":"Technology","url":"https://www.academia.edu/Documents/in/Technology"},{"id":118582,"name":"Physical sciences","url":"https://www.academia.edu/Documents/in/Physical_sciences"},{"id":260118,"name":"CHEMICAL SCIENCES","url":"https://www.academia.edu/Documents/in/CHEMICAL_SCIENCES"}],"urls":[]}, dispatcherData: dispatcherData }); $(this).data('initialized', true); } }); $a.trackClickSource(".js-work-strip-work-link", "profile_work_strip") }); </script> <div class="js-work-strip profile--work_container" data-work-id="35181713"><div class="profile--work_thumbnail hidden-xs"><a class="js-work-strip-work-link" data-click-track="profile-work-strip-thumbnail" href="https://www.academia.edu/35181713/Stacked_and_H_bonded_Cytosine_Dimers_Analysis_of_the_Intermolecular_Interaction_Energies_by_Parallel_Quantum_Chemistry_and_Polarizable_Molecular_Mechanics"><img alt="Research paper thumbnail of Stacked and H-bonded Cytosine Dimers. Analysis of the Intermolecular Interaction Energies by Parallel Quantum Chemistry and Polarizable Molecular Mechanics" class="work-thumbnail" src="https://a.academia-assets.com/images/blank-paper.jpg" /></a></div><div class="wp-workCard wp-workCard_itemContainer"><div class="wp-workCard_item wp-workCard--title"><a class="js-work-strip-work-link text-gray-darker" data-click-track="profile-work-strip-title" href="https://www.academia.edu/35181713/Stacked_and_H_bonded_Cytosine_Dimers_Analysis_of_the_Intermolecular_Interaction_Energies_by_Parallel_Quantum_Chemistry_and_Polarizable_Molecular_Mechanics">Stacked and H-bonded Cytosine Dimers. Analysis of the Intermolecular Interaction Energies by Parallel Quantum Chemistry and Polarizable Molecular Mechanics</a></div><div class="wp-workCard_item"><span>The journal of physical chemistry. B</span><span>, Jan 29, 2015</span></div><div class="wp-workCard_item"><span class="js-work-more-abstract-truncated">Until now, atomistic simulations of DNA and RNA and their complexes have been executed using well...</span><a class="js-work-more-abstract" data-broccoli-component="work_strip.more_abstract" data-click-track="profile-work-strip-more-abstract" href="javascript:;"><span> more </span><span><i class="fa fa-caret-down"></i></span></a><span class="js-work-more-abstract-untruncated hidden">Until now, atomistic simulations of DNA and RNA and their complexes have been executed using well calibrated but conceptually simple pair-additive empirical potentials (force fields). Although such simulations provided many valuable results, it is well established that simple force fields also introduce errors into the description, underlying the need for development of alternative anisotropic, polarizable molecular mechanics (APMM) potentials. One of the most abundant forces in all kinds on nucleic acids topologies is base stacking. Intra- and interstrand stacking is assumed to be the most essential factor affecting local conformational variations of B-DNA. However, stacking also contributes to formation of all kinds of non-canonical nucleic acids structures, such as quadruplexes or folded RNAs. The present study focuses on fourteen stacked cytosine (Cyt) dimers and the doubly H-bonded dimer. We evaluate the extent to which an APMM procedure, SIBFA, could account quantitatively for...</span></div><div class="wp-workCard_item wp-workCard--actions"><span class="work-strip-bookmark-button-container"></span><span class="wp-workCard--action visible-if-viewed-by-owner inline-block" style="display: none;"><span class="js-profile-work-strip-edit-button-wrapper profile-work-strip-edit-button-wrapper" data-work-id="35181713"><a class="js-profile-work-strip-edit-button" tabindex="0"><span><i class="fa fa-pencil"></i></span><span>Edit</span></a></span></span><span id="work-strip-rankings-button-container"></span></div><div class="wp-workCard_item wp-workCard--stats"><span><span><span class="js-view-count view-count u-mr2x" data-work-id="35181713"><i class="fa fa-spinner fa-spin"></i></span><script>$(function () { var workId = 35181713; window.Academia.workViewCountsFetcher.queue(workId, function (count) { var description = window.$h.commaizeInt(count) + " " + window.$h.pluralize(count, 'View'); $(".js-view-count[data-work-id=35181713]").text(description); $(".js-view-count[data-work-id=35181713]").attr('title', description).tooltip(); }); });</script></span></span><span><span class="percentile-widget hidden"><span class="u-mr2x work-percentile"></span></span><script>$(function () { var workId = 35181713; window.Academia.workPercentilesFetcher.queue(workId, function (percentileText) { var container = $(".js-work-strip[data-work-id='35181713']"); container.find('.work-percentile').text(percentileText.charAt(0).toUpperCase() + percentileText.slice(1)); container.find('.percentile-widget').show(); container.find('.percentile-widget').removeClass('hidden'); }); });</script></span><span><script>$(function() { new Works.PaperRankView({ workId: 35181713, container: "", }); });</script></span></div><div id="work-strip-premium-row-container"></div></div></div><script> require.config({ waitSeconds: 90 })(["https://a.academia-assets.com/assets/wow_profile-f77ea15d77ce96025a6048a514272ad8becbad23c641fc2b3bd6e24ca6ff1932.js","https://a.academia-assets.com/assets/work_edit-ad038b8c047c1a8d4fa01b402d530ff93c45fee2137a149a4a5398bc8ad67560.js"], function() { // from javascript_helper.rb var dispatcherData = {} if (false){ window.WowProfile.dispatcher = window.WowProfile.dispatcher || _.clone(Backbone.Events); dispatcherData = { dispatcher: window.WowProfile.dispatcher, downloadLinkId: "-1" } } $('.js-work-strip[data-work-id=35181713]').each(function() { if (!$(this).data('initialized')) { new WowProfile.WorkStripView({ el: this, workJSON: {"id":35181713,"title":"Stacked and H-bonded Cytosine Dimers. Analysis of the Intermolecular Interaction Energies by Parallel Quantum Chemistry and Polarizable Molecular Mechanics","translated_title":"","metadata":{"abstract":"Until now, atomistic simulations of DNA and RNA and their complexes have been executed using well calibrated but conceptually simple pair-additive empirical potentials (force fields). Although such simulations provided many valuable results, it is well established that simple force fields also introduce errors into the description, underlying the need for development of alternative anisotropic, polarizable molecular mechanics (APMM) potentials. One of the most abundant forces in all kinds on nucleic acids topologies is base stacking. Intra- and interstrand stacking is assumed to be the most essential factor affecting local conformational variations of B-DNA. However, stacking also contributes to formation of all kinds of non-canonical nucleic acids structures, such as quadruplexes or folded RNAs. The present study focuses on fourteen stacked cytosine (Cyt) dimers and the doubly H-bonded dimer. We evaluate the extent to which an APMM procedure, SIBFA, could account quantitatively for...","publication_date":{"day":29,"month":1,"year":2015,"errors":{}},"publication_name":"The journal of physical chemistry. B"},"translated_abstract":"Until now, atomistic simulations of DNA and RNA and their complexes have been executed using well calibrated but conceptually simple pair-additive empirical potentials (force fields). Although such simulations provided many valuable results, it is well established that simple force fields also introduce errors into the description, underlying the need for development of alternative anisotropic, polarizable molecular mechanics (APMM) potentials. One of the most abundant forces in all kinds on nucleic acids topologies is base stacking. Intra- and interstrand stacking is assumed to be the most essential factor affecting local conformational variations of B-DNA. However, stacking also contributes to formation of all kinds of non-canonical nucleic acids structures, such as quadruplexes or folded RNAs. The present study focuses on fourteen stacked cytosine (Cyt) dimers and the doubly H-bonded dimer. We evaluate the extent to which an APMM procedure, SIBFA, could account quantitatively for...","internal_url":"https://www.academia.edu/35181713/Stacked_and_H_bonded_Cytosine_Dimers_Analysis_of_the_Intermolecular_Interaction_Energies_by_Parallel_Quantum_Chemistry_and_Polarizable_Molecular_Mechanics","translated_internal_url":"","created_at":"2017-11-18T07:17:49.508-08:00","preview_url":null,"current_user_can_edit":null,"current_user_is_owner":null,"owner_id":35445,"coauthors_can_edit":true,"document_type":"paper","co_author_tags":[],"downloadable_attachments":[],"slug":"Stacked_and_H_bonded_Cytosine_Dimers_Analysis_of_the_Intermolecular_Interaction_Energies_by_Parallel_Quantum_Chemistry_and_Polarizable_Molecular_Mechanics","translated_slug":"","page_count":null,"language":"en","content_type":"Work","owner":{"id":35445,"first_name":"Jean-Philip","middle_initials":null,"last_name":"Piquemal","page_name":"JeanPhilipPiquemal","domain_name":"sorbonne-fr","created_at":"2009-03-17T04:43:24.569-07:00","display_name":"Jean-Philip Piquemal","url":"https://sorbonne-fr.academia.edu/JeanPhilipPiquemal"},"attachments":[],"research_interests":[{"id":48,"name":"Engineering","url":"https://www.academia.edu/Documents/in/Engineering"},{"id":522,"name":"Thermodynamics","url":"https://www.academia.edu/Documents/in/Thermodynamics"},{"id":2215,"name":"Water","url":"https://www.academia.edu/Documents/in/Water"},{"id":6811,"name":"Quantum Theory","url":"https://www.academia.edu/Documents/in/Quantum_Theory"},{"id":48057,"name":"DNA","url":"https://www.academia.edu/Documents/in/DNA"},{"id":70902,"name":"Magnesium","url":"https://www.academia.edu/Documents/in/Magnesium"},{"id":118582,"name":"Physical sciences","url":"https://www.academia.edu/Documents/in/Physical_sciences"},{"id":260118,"name":"CHEMICAL SCIENCES","url":"https://www.academia.edu/Documents/in/CHEMICAL_SCIENCES"},{"id":296798,"name":"Hydrogen Bonding","url":"https://www.academia.edu/Documents/in/Hydrogen_Bonding"},{"id":649537,"name":"Molecular Conformation","url":"https://www.academia.edu/Documents/in/Molecular_Conformation"},{"id":1809037,"name":"Dimerization","url":"https://www.academia.edu/Documents/in/Dimerization"}],"urls":[]}, dispatcherData: dispatcherData }); $(this).data('initialized', true); } }); $a.trackClickSource(".js-work-strip-work-link", "profile_work_strip") }); </script> <div class="js-work-strip profile--work_container" data-work-id="35181712"><div class="profile--work_thumbnail hidden-xs"><a class="js-work-strip-work-link" data-click-track="profile-work-strip-thumbnail" href="https://www.academia.edu/35181712/General_Model_for_Treating_Short_Range_Electrostatic_Penetration_in_a_Molecular_Mechanics_Force_Field"><img alt="Research paper thumbnail of General Model for Treating Short-Range Electrostatic Penetration in a Molecular Mechanics Force Field" class="work-thumbnail" src="https://a.academia-assets.com/images/blank-paper.jpg" /></a></div><div class="wp-workCard wp-workCard_itemContainer"><div class="wp-workCard_item wp-workCard--title"><a class="js-work-strip-work-link text-gray-darker" data-click-track="profile-work-strip-title" href="https://www.academia.edu/35181712/General_Model_for_Treating_Short_Range_Electrostatic_Penetration_in_a_Molecular_Mechanics_Force_Field">General Model for Treating Short-Range Electrostatic Penetration in a Molecular Mechanics Force Field</a></div><div class="wp-workCard_item"><span>Journal of Chemical Theory and Computation</span><span>, 2015</span></div><div class="wp-workCard_item"><span class="js-work-more-abstract-truncated">Classical molecular mechanics force fields typically model interatomic electrostatic interactions...</span><a class="js-work-more-abstract" data-broccoli-component="work_strip.more_abstract" data-click-track="profile-work-strip-more-abstract" href="javascript:;"><span> more </span><span><i class="fa fa-caret-down"></i></span></a><span class="js-work-more-abstract-untruncated hidden">Classical molecular mechanics force fields typically model interatomic electrostatic interactions with point charges or multipole expansions, which can fail for atoms in close contact due to the lack of a description of penetration effects between their electron clouds. These short-range penetration effects can be significant and are essential for accurate modeling of intermolecular interactions. In this work we report parametrization of an empirical charge-charge function previously reported (Piquemal J.-P.; J. Phys. Chem. A2003, 107, 10353) to correct for the missing penetration term in standard molecular mechanics force fields. For this purpose, we have developed a database (S101×7) of 101 unique molecular dimers, each at 7 different intermolecular distances. Electrostatic, induction/polarization, repulsion, and dispersion energies, as well as the total interaction energy for each complex in the database are calculated using the SAPT2+ method (Parker T. M.; J. Chem. Phys.2014, 140, 094106). This empirical penetration model significantly improves agreement between point multipole and quantum mechanical electrostatic energies across the set of dimers and distances, while using only a limited set of parameters for each chemical element. Given the simplicity and effectiveness of the model, we expect the electrostatic penetration correction will become a standard component of future molecular mechanics force fields.</span></div><div class="wp-workCard_item wp-workCard--actions"><span class="work-strip-bookmark-button-container"></span><span class="wp-workCard--action visible-if-viewed-by-owner inline-block" style="display: none;"><span class="js-profile-work-strip-edit-button-wrapper profile-work-strip-edit-button-wrapper" data-work-id="35181712"><a class="js-profile-work-strip-edit-button" tabindex="0"><span><i class="fa fa-pencil"></i></span><span>Edit</span></a></span></span><span id="work-strip-rankings-button-container"></span></div><div class="wp-workCard_item wp-workCard--stats"><span><span><span class="js-view-count view-count u-mr2x" data-work-id="35181712"><i class="fa fa-spinner fa-spin"></i></span><script>$(function () { var workId = 35181712; window.Academia.workViewCountsFetcher.queue(workId, function (count) { var description = window.$h.commaizeInt(count) + " " + window.$h.pluralize(count, 'View'); $(".js-view-count[data-work-id=35181712]").text(description); $(".js-view-count[data-work-id=35181712]").attr('title', description).tooltip(); }); });</script></span></span><span><span class="percentile-widget hidden"><span class="u-mr2x work-percentile"></span></span><script>$(function () { var workId = 35181712; window.Academia.workPercentilesFetcher.queue(workId, function (percentileText) { var container = $(".js-work-strip[data-work-id='35181712']"); container.find('.work-percentile').text(percentileText.charAt(0).toUpperCase() + percentileText.slice(1)); container.find('.percentile-widget').show(); container.find('.percentile-widget').removeClass('hidden'); }); });</script></span><span><script>$(function() { new Works.PaperRankView({ workId: 35181712, container: "", }); });</script></span></div><div id="work-strip-premium-row-container"></div></div></div><script> require.config({ waitSeconds: 90 })(["https://a.academia-assets.com/assets/wow_profile-f77ea15d77ce96025a6048a514272ad8becbad23c641fc2b3bd6e24ca6ff1932.js","https://a.academia-assets.com/assets/work_edit-ad038b8c047c1a8d4fa01b402d530ff93c45fee2137a149a4a5398bc8ad67560.js"], function() { // from javascript_helper.rb var dispatcherData = {} if (false){ window.WowProfile.dispatcher = window.WowProfile.dispatcher || _.clone(Backbone.Events); dispatcherData = { dispatcher: window.WowProfile.dispatcher, downloadLinkId: "-1" } } $('.js-work-strip[data-work-id=35181712]').each(function() { if (!$(this).data('initialized')) { new WowProfile.WorkStripView({ el: this, workJSON: {"id":35181712,"title":"General Model for Treating Short-Range Electrostatic Penetration in a Molecular Mechanics Force Field","translated_title":"","metadata":{"abstract":"Classical molecular mechanics force fields typically model interatomic electrostatic interactions with point charges or multipole expansions, which can fail for atoms in close contact due to the lack of a description of penetration effects between their electron clouds. These short-range penetration effects can be significant and are essential for accurate modeling of intermolecular interactions. In this work we report parametrization of an empirical charge-charge function previously reported (Piquemal J.-P.; J. Phys. Chem. A2003, 107, 10353) to correct for the missing penetration term in standard molecular mechanics force fields. For this purpose, we have developed a database (S101×7) of 101 unique molecular dimers, each at 7 different intermolecular distances. Electrostatic, induction/polarization, repulsion, and dispersion energies, as well as the total interaction energy for each complex in the database are calculated using the SAPT2+ method (Parker T. M.; J. Chem. Phys.2014, 140, 094106). This empirical penetration model significantly improves agreement between point multipole and quantum mechanical electrostatic energies across the set of dimers and distances, while using only a limited set of parameters for each chemical element. Given the simplicity and effectiveness of the model, we expect the electrostatic penetration correction will become a standard component of future molecular mechanics force fields.","publisher":"American Chemical Society (ACS)","publication_date":{"day":null,"month":null,"year":2015,"errors":{}},"publication_name":"Journal of Chemical Theory and Computation"},"translated_abstract":"Classical molecular mechanics force fields typically model interatomic electrostatic interactions with point charges or multipole expansions, which can fail for atoms in close contact due to the lack of a description of penetration effects between their electron clouds. These short-range penetration effects can be significant and are essential for accurate modeling of intermolecular interactions. In this work we report parametrization of an empirical charge-charge function previously reported (Piquemal J.-P.; J. Phys. Chem. A2003, 107, 10353) to correct for the missing penetration term in standard molecular mechanics force fields. For this purpose, we have developed a database (S101×7) of 101 unique molecular dimers, each at 7 different intermolecular distances. Electrostatic, induction/polarization, repulsion, and dispersion energies, as well as the total interaction energy for each complex in the database are calculated using the SAPT2+ method (Parker T. M.; J. Chem. Phys.2014, 140, 094106). This empirical penetration model significantly improves agreement between point multipole and quantum mechanical electrostatic energies across the set of dimers and distances, while using only a limited set of parameters for each chemical element. Given the simplicity and effectiveness of the model, we expect the electrostatic penetration correction will become a standard component of future molecular mechanics force fields.","internal_url":"https://www.academia.edu/35181712/General_Model_for_Treating_Short_Range_Electrostatic_Penetration_in_a_Molecular_Mechanics_Force_Field","translated_internal_url":"","created_at":"2017-11-18T07:17:49.354-08:00","preview_url":null,"current_user_can_edit":null,"current_user_is_owner":null,"owner_id":35445,"coauthors_can_edit":true,"document_type":"paper","co_author_tags":[],"downloadable_attachments":[],"slug":"General_Model_for_Treating_Short_Range_Electrostatic_Penetration_in_a_Molecular_Mechanics_Force_Field","translated_slug":"","page_count":null,"language":"en","content_type":"Work","owner":{"id":35445,"first_name":"Jean-Philip","middle_initials":null,"last_name":"Piquemal","page_name":"JeanPhilipPiquemal","domain_name":"sorbonne-fr","created_at":"2009-03-17T04:43:24.569-07:00","display_name":"Jean-Philip Piquemal","url":"https://sorbonne-fr.academia.edu/JeanPhilipPiquemal"},"attachments":[],"research_interests":[{"id":645605,"name":"THEORETICAL AND COMPUTATIONAL CHEMISTRY","url":"https://www.academia.edu/Documents/in/THEORETICAL_AND_COMPUTATIONAL_CHEMISTRY"}],"urls":[]}, dispatcherData: dispatcherData }); $(this).data('initialized', true); } }); $a.trackClickSource(".js-work-strip-work-link", "profile_work_strip") }); </script> <div class="js-work-strip profile--work_container" data-work-id="35181711"><div class="profile--work_thumbnail hidden-xs"><a class="js-work-strip-work-link" data-click-track="profile-work-strip-thumbnail" href="https://www.academia.edu/35181711/Polarizable_Force_Fields_for_Biomolecular_Modeling"><img alt="Research paper thumbnail of Polarizable Force Fields for Biomolecular Modeling" class="work-thumbnail" src="https://a.academia-assets.com/images/blank-paper.jpg" /></a></div><div class="wp-workCard wp-workCard_itemContainer"><div class="wp-workCard_item wp-workCard--title"><a class="js-work-strip-work-link text-gray-darker" data-click-track="profile-work-strip-title" href="https://www.academia.edu/35181711/Polarizable_Force_Fields_for_Biomolecular_Modeling">Polarizable Force Fields for Biomolecular Modeling</a></div><div class="wp-workCard_item"><span>Reviews in Computational Chemistry</span><span>, 2015</span></div><div class="wp-workCard_item"><span class="js-work-more-abstract-truncated">ABSTRACT This chapter focuses on the recent developments in different polarizable force fields. T...</span><a class="js-work-more-abstract" data-broccoli-component="work_strip.more_abstract" data-click-track="profile-work-strip-more-abstract" href="javascript:;"><span> more </span><span><i class="fa fa-caret-down"></i></span></a><span class="js-work-more-abstract-untruncated hidden">ABSTRACT This chapter focuses on the recent developments in different polarizable force fields. These include atomic multipole optimized energetics for biomolecular applications (AMOEBA), sum of interactions between fragments ab initio computed (SIBFA), nonempirical molecular orbital (NEMO), CHARMM fluctuating charge model (FQ), and polarizable protein force field (PFF). The chapter begins with a brief introduction to the basic principles and formulae underlying alternative models. It reviews recent progress of several well-developed polarizable force fields. Finally, the chapter presents applications of polarizable models to a range of molecular systems, including water and other small molecules, ion solvation, peptides, proteins, and lipid systems. Beyond polarization, modeling the conformational flexibility and corresponding intermolecular energetics of organic molecules via sampling methods such as molecular dynamics is essential to predicting the thermodynamic properties of crystals. The importance of polarization still needs to be established systematically for a wide range of biological systems.</span></div><div class="wp-workCard_item wp-workCard--actions"><span class="work-strip-bookmark-button-container"></span><span class="wp-workCard--action visible-if-viewed-by-owner inline-block" style="display: none;"><span class="js-profile-work-strip-edit-button-wrapper profile-work-strip-edit-button-wrapper" data-work-id="35181711"><a class="js-profile-work-strip-edit-button" tabindex="0"><span><i class="fa fa-pencil"></i></span><span>Edit</span></a></span></span><span id="work-strip-rankings-button-container"></span></div><div class="wp-workCard_item wp-workCard--stats"><span><span><span class="js-view-count view-count u-mr2x" data-work-id="35181711"><i class="fa fa-spinner fa-spin"></i></span><script>$(function () { var workId = 35181711; window.Academia.workViewCountsFetcher.queue(workId, function (count) { var description = window.$h.commaizeInt(count) + " " + window.$h.pluralize(count, 'View'); $(".js-view-count[data-work-id=35181711]").text(description); $(".js-view-count[data-work-id=35181711]").attr('title', description).tooltip(); }); });</script></span></span><span><span class="percentile-widget hidden"><span class="u-mr2x work-percentile"></span></span><script>$(function () { var workId = 35181711; window.Academia.workPercentilesFetcher.queue(workId, function (percentileText) { var container = $(".js-work-strip[data-work-id='35181711']"); container.find('.work-percentile').text(percentileText.charAt(0).toUpperCase() + percentileText.slice(1)); container.find('.percentile-widget').show(); container.find('.percentile-widget').removeClass('hidden'); }); });</script></span><span><script>$(function() { new Works.PaperRankView({ workId: 35181711, container: "", }); });</script></span></div><div id="work-strip-premium-row-container"></div></div></div><script> require.config({ waitSeconds: 90 })(["https://a.academia-assets.com/assets/wow_profile-f77ea15d77ce96025a6048a514272ad8becbad23c641fc2b3bd6e24ca6ff1932.js","https://a.academia-assets.com/assets/work_edit-ad038b8c047c1a8d4fa01b402d530ff93c45fee2137a149a4a5398bc8ad67560.js"], function() { // from javascript_helper.rb var dispatcherData = {} if (false){ window.WowProfile.dispatcher = window.WowProfile.dispatcher || _.clone(Backbone.Events); dispatcherData = { dispatcher: window.WowProfile.dispatcher, downloadLinkId: "-1" } } $('.js-work-strip[data-work-id=35181711]').each(function() { if (!$(this).data('initialized')) { new WowProfile.WorkStripView({ el: this, workJSON: {"id":35181711,"title":"Polarizable Force Fields for Biomolecular Modeling","translated_title":"","metadata":{"abstract":"ABSTRACT This chapter focuses on the recent developments in different polarizable force fields. These include atomic multipole optimized energetics for biomolecular applications (AMOEBA), sum of interactions between fragments ab initio computed (SIBFA), nonempirical molecular orbital (NEMO), CHARMM fluctuating charge model (FQ), and polarizable protein force field (PFF). The chapter begins with a brief introduction to the basic principles and formulae underlying alternative models. It reviews recent progress of several well-developed polarizable force fields. Finally, the chapter presents applications of polarizable models to a range of molecular systems, including water and other small molecules, ion solvation, peptides, proteins, and lipid systems. Beyond polarization, modeling the conformational flexibility and corresponding intermolecular energetics of organic molecules via sampling methods such as molecular dynamics is essential to predicting the thermodynamic properties of crystals. The importance of polarization still needs to be established systematically for a wide range of biological systems.","publisher":"John Wiley \u0026 Sons, Inc","publication_date":{"day":null,"month":null,"year":2015,"errors":{}},"publication_name":"Reviews in Computational Chemistry"},"translated_abstract":"ABSTRACT This chapter focuses on the recent developments in different polarizable force fields. These include atomic multipole optimized energetics for biomolecular applications (AMOEBA), sum of interactions between fragments ab initio computed (SIBFA), nonempirical molecular orbital (NEMO), CHARMM fluctuating charge model (FQ), and polarizable protein force field (PFF). The chapter begins with a brief introduction to the basic principles and formulae underlying alternative models. It reviews recent progress of several well-developed polarizable force fields. Finally, the chapter presents applications of polarizable models to a range of molecular systems, including water and other small molecules, ion solvation, peptides, proteins, and lipid systems. Beyond polarization, modeling the conformational flexibility and corresponding intermolecular energetics of organic molecules via sampling methods such as molecular dynamics is essential to predicting the thermodynamic properties of crystals. The importance of polarization still needs to be established systematically for a wide range of biological systems.","internal_url":"https://www.academia.edu/35181711/Polarizable_Force_Fields_for_Biomolecular_Modeling","translated_internal_url":"","created_at":"2017-11-18T07:17:49.207-08:00","preview_url":null,"current_user_can_edit":null,"current_user_is_owner":null,"owner_id":35445,"coauthors_can_edit":true,"document_type":"paper","co_author_tags":[],"downloadable_attachments":[],"slug":"Polarizable_Force_Fields_for_Biomolecular_Modeling","translated_slug":"","page_count":null,"language":"en","content_type":"Work","owner":{"id":35445,"first_name":"Jean-Philip","middle_initials":null,"last_name":"Piquemal","page_name":"JeanPhilipPiquemal","domain_name":"sorbonne-fr","created_at":"2009-03-17T04:43:24.569-07:00","display_name":"Jean-Philip Piquemal","url":"https://sorbonne-fr.academia.edu/JeanPhilipPiquemal"},"attachments":[],"research_interests":[{"id":181569,"name":"Proteins","url":"https://www.academia.edu/Documents/in/Proteins"},{"id":645605,"name":"THEORETICAL AND COMPUTATIONAL CHEMISTRY","url":"https://www.academia.edu/Documents/in/THEORETICAL_AND_COMPUTATIONAL_CHEMISTRY"}],"urls":[]}, dispatcherData: dispatcherData }); $(this).data('initialized', true); } }); $a.trackClickSource(".js-work-strip-work-link", "profile_work_strip") }); </script> <div class="js-work-strip profile--work_container" data-work-id="35181710"><div class="profile--work_thumbnail hidden-xs"><a class="js-work-strip-work-link" data-click-track="profile-work-strip-thumbnail" href="https://www.academia.edu/35181710/Polarizable_Molecular_Dynamics_in_a_Polarizable_Continuum_Solvent"><img alt="Research paper thumbnail of Polarizable Molecular Dynamics in a Polarizable Continuum Solvent" class="work-thumbnail" src="https://a.academia-assets.com/images/blank-paper.jpg" /></a></div><div class="wp-workCard wp-workCard_itemContainer"><div class="wp-workCard_item wp-workCard--title"><a class="js-work-strip-work-link text-gray-darker" data-click-track="profile-work-strip-title" href="https://www.academia.edu/35181710/Polarizable_Molecular_Dynamics_in_a_Polarizable_Continuum_Solvent">Polarizable Molecular Dynamics in a Polarizable Continuum Solvent</a></div><div class="wp-workCard_item"><span>Journal of Chemical Theory and Computation</span><span>, 2015</span></div><div class="wp-workCard_item"><span class="js-work-more-abstract-truncated">We present for the first time scalable polarizable molecular dynamics (MD) simulations within a p...</span><a class="js-work-more-abstract" data-broccoli-component="work_strip.more_abstract" data-click-track="profile-work-strip-more-abstract" href="javascript:;"><span> more </span><span><i class="fa fa-caret-down"></i></span></a><span class="js-work-more-abstract-untruncated hidden">We present for the first time scalable polarizable molecular dynamics (MD) simulations within a polarizable continuum solvent with molecular shape cavities and exact solution of the mutual polarization. The key ingredients are a very efficient algorithm for solving the equations associated with the polarizable continuum, in particular, the domain decomposition Conductor-like Screening Model (ddCOSMO), a rigorous coupling of the continuum with the polarizable force field achieved through a robust variational formulation and an effective strategy to solve the coupled equations. The coupling of ddCOSMO with non variational force fields, including AMOEBA, is also addressed. The MD simulations are feasible, for real life systems, on standard cluster nodes; a scalable parallel implementation allows for further speed up in the context of a newly developed module in Tinker, named Tinker-HP. NVE simulations are stable and long term energy conservation can be achieved. This paper is focused on the methodological developments, on the analysis of the algorithm and on the stability of the simulations; a proof-of-concept application is also presented to attest the possibilities of this newly developed technique.</span></div><div class="wp-workCard_item wp-workCard--actions"><span class="work-strip-bookmark-button-container"></span><span class="wp-workCard--action visible-if-viewed-by-owner inline-block" style="display: none;"><span class="js-profile-work-strip-edit-button-wrapper profile-work-strip-edit-button-wrapper" data-work-id="35181710"><a class="js-profile-work-strip-edit-button" tabindex="0"><span><i class="fa fa-pencil"></i></span><span>Edit</span></a></span></span><span id="work-strip-rankings-button-container"></span></div><div class="wp-workCard_item wp-workCard--stats"><span><span><span class="js-view-count view-count u-mr2x" data-work-id="35181710"><i class="fa fa-spinner fa-spin"></i></span><script>$(function () { var workId = 35181710; window.Academia.workViewCountsFetcher.queue(workId, function (count) { var description = window.$h.commaizeInt(count) + " " + window.$h.pluralize(count, 'View'); $(".js-view-count[data-work-id=35181710]").text(description); $(".js-view-count[data-work-id=35181710]").attr('title', description).tooltip(); }); });</script></span></span><span><span class="percentile-widget hidden"><span class="u-mr2x work-percentile"></span></span><script>$(function () { var workId = 35181710; window.Academia.workPercentilesFetcher.queue(workId, function (percentileText) { var container = $(".js-work-strip[data-work-id='35181710']"); container.find('.work-percentile').text(percentileText.charAt(0).toUpperCase() + percentileText.slice(1)); container.find('.percentile-widget').show(); container.find('.percentile-widget').removeClass('hidden'); }); });</script></span><span><script>$(function() { new Works.PaperRankView({ workId: 35181710, container: "", }); });</script></span></div><div id="work-strip-premium-row-container"></div></div></div><script> require.config({ waitSeconds: 90 })(["https://a.academia-assets.com/assets/wow_profile-f77ea15d77ce96025a6048a514272ad8becbad23c641fc2b3bd6e24ca6ff1932.js","https://a.academia-assets.com/assets/work_edit-ad038b8c047c1a8d4fa01b402d530ff93c45fee2137a149a4a5398bc8ad67560.js"], function() { // from javascript_helper.rb var dispatcherData = {} if (false){ window.WowProfile.dispatcher = window.WowProfile.dispatcher || _.clone(Backbone.Events); dispatcherData = { dispatcher: window.WowProfile.dispatcher, downloadLinkId: "-1" } } $('.js-work-strip[data-work-id=35181710]').each(function() { if (!$(this).data('initialized')) { new WowProfile.WorkStripView({ el: this, workJSON: {"id":35181710,"title":"Polarizable Molecular Dynamics in a Polarizable Continuum Solvent","translated_title":"","metadata":{"abstract":"We present for the first time scalable polarizable molecular dynamics (MD) simulations within a polarizable continuum solvent with molecular shape cavities and exact solution of the mutual polarization. The key ingredients are a very efficient algorithm for solving the equations associated with the polarizable continuum, in particular, the domain decomposition Conductor-like Screening Model (ddCOSMO), a rigorous coupling of the continuum with the polarizable force field achieved through a robust variational formulation and an effective strategy to solve the coupled equations. The coupling of ddCOSMO with non variational force fields, including AMOEBA, is also addressed. The MD simulations are feasible, for real life systems, on standard cluster nodes; a scalable parallel implementation allows for further speed up in the context of a newly developed module in Tinker, named Tinker-HP. NVE simulations are stable and long term energy conservation can be achieved. This paper is focused on the methodological developments, on the analysis of the algorithm and on the stability of the simulations; a proof-of-concept application is also presented to attest the possibilities of this newly developed technique.","publisher":"American Chemical Society (ACS)","publication_date":{"day":null,"month":null,"year":2015,"errors":{}},"publication_name":"Journal of Chemical Theory and Computation"},"translated_abstract":"We present for the first time scalable polarizable molecular dynamics (MD) simulations within a polarizable continuum solvent with molecular shape cavities and exact solution of the mutual polarization. The key ingredients are a very efficient algorithm for solving the equations associated with the polarizable continuum, in particular, the domain decomposition Conductor-like Screening Model (ddCOSMO), a rigorous coupling of the continuum with the polarizable force field achieved through a robust variational formulation and an effective strategy to solve the coupled equations. The coupling of ddCOSMO with non variational force fields, including AMOEBA, is also addressed. The MD simulations are feasible, for real life systems, on standard cluster nodes; a scalable parallel implementation allows for further speed up in the context of a newly developed module in Tinker, named Tinker-HP. NVE simulations are stable and long term energy conservation can be achieved. This paper is focused on the methodological developments, on the analysis of the algorithm and on the stability of the simulations; a proof-of-concept application is also presented to attest the possibilities of this newly developed technique.","internal_url":"https://www.academia.edu/35181710/Polarizable_Molecular_Dynamics_in_a_Polarizable_Continuum_Solvent","translated_internal_url":"","created_at":"2017-11-18T07:17:49.034-08:00","preview_url":null,"current_user_can_edit":null,"current_user_is_owner":null,"owner_id":35445,"coauthors_can_edit":true,"document_type":"paper","co_author_tags":[],"downloadable_attachments":[],"slug":"Polarizable_Molecular_Dynamics_in_a_Polarizable_Continuum_Solvent","translated_slug":"","page_count":null,"language":"en","content_type":"Work","owner":{"id":35445,"first_name":"Jean-Philip","middle_initials":null,"last_name":"Piquemal","page_name":"JeanPhilipPiquemal","domain_name":"sorbonne-fr","created_at":"2009-03-17T04:43:24.569-07:00","display_name":"Jean-Philip Piquemal","url":"https://sorbonne-fr.academia.edu/JeanPhilipPiquemal"},"attachments":[],"research_interests":[{"id":428,"name":"Algorithms","url":"https://www.academia.edu/Documents/in/Algorithms"},{"id":2736,"name":"Molecular Dynamics Simulation","url":"https://www.academia.edu/Documents/in/Molecular_Dynamics_Simulation"},{"id":151086,"name":"Peptides","url":"https://www.academia.edu/Documents/in/Peptides"},{"id":645605,"name":"THEORETICAL AND COMPUTATIONAL CHEMISTRY","url":"https://www.academia.edu/Documents/in/THEORETICAL_AND_COMPUTATIONAL_CHEMISTRY"},{"id":1745595,"name":"Solvents","url":"https://www.academia.edu/Documents/in/Solvents"}],"urls":[]}, dispatcherData: dispatcherData }); $(this).data('initialized', true); } }); $a.trackClickSource(".js-work-strip-work-link", "profile_work_strip") }); </script> <div class="js-work-strip profile--work_container" data-work-id="35181709"><div class="profile--work_thumbnail hidden-xs"><a class="js-work-strip-work-link" data-click-track="profile-work-strip-thumbnail" href="https://www.academia.edu/35181709/Bridging_Organometallics_and_Quantum_Chemical_Topology_Understanding_Electronic_Relocalisation_During_Palladium_Catalyzed_Reductive_Elimination"><img alt="Research paper thumbnail of Bridging Organometallics and Quantum Chemical Topology: Understanding Electronic Relocalisation During Palladium-Catalyzed Reductive Elimination" class="work-thumbnail" src="https://a.academia-assets.com/images/blank-paper.jpg" /></a></div><div class="wp-workCard wp-workCard_itemContainer"><div class="wp-workCard_item wp-workCard--title"><a class="js-work-strip-work-link text-gray-darker" data-click-track="profile-work-strip-title" href="https://www.academia.edu/35181709/Bridging_Organometallics_and_Quantum_Chemical_Topology_Understanding_Electronic_Relocalisation_During_Palladium_Catalyzed_Reductive_Elimination">Bridging Organometallics and Quantum Chemical Topology: Understanding Electronic Relocalisation During Palladium-Catalyzed Reductive Elimination</a></div><div class="wp-workCard_item"><span>Journal of computational chemistry</span><span>, Jan 21, 2015</span></div><div class="wp-workCard_item"><span class="js-work-more-abstract-truncated">This article proposes to bridge two fields, namely organometallics and quantum chemical topology....</span><a class="js-work-more-abstract" data-broccoli-component="work_strip.more_abstract" data-click-track="profile-work-strip-more-abstract" href="javascript:;"><span> more </span><span><i class="fa fa-caret-down"></i></span></a><span class="js-work-more-abstract-untruncated hidden">This article proposes to bridge two fields, namely organometallics and quantum chemical topology. To do so, Palladium-catalyzed reductive elimination is studied. Such reaction is a classical elementary step in organometallic chemistry, where the directionality of electrons delocalization is not well understood. New computational evidences highlighting the accepted mechanism are proposed following a strategy coupling quantum theory of atoms in molecules and electron localization function topological analyses and enabling an extended quantification of donated/back-donated electrons fluxes along reaction paths going beyond the usual Dewar-Chatt-Duncanson model. Indeed, if the ligands coordination mode (phosphine, carbene) is commonly described as dative, it appears that ligands lone pairs stay centered on ligands as electrons are shared between metal and ligand with strong delocalization toward the latter. Overall, through strong trans effects coming from the carbon involved in the red...</span></div><div class="wp-workCard_item wp-workCard--actions"><span class="work-strip-bookmark-button-container"></span><span class="wp-workCard--action visible-if-viewed-by-owner inline-block" style="display: none;"><span class="js-profile-work-strip-edit-button-wrapper profile-work-strip-edit-button-wrapper" data-work-id="35181709"><a class="js-profile-work-strip-edit-button" tabindex="0"><span><i class="fa fa-pencil"></i></span><span>Edit</span></a></span></span><span id="work-strip-rankings-button-container"></span></div><div class="wp-workCard_item wp-workCard--stats"><span><span><span class="js-view-count view-count u-mr2x" data-work-id="35181709"><i class="fa fa-spinner fa-spin"></i></span><script>$(function () { var workId = 35181709; window.Academia.workViewCountsFetcher.queue(workId, function (count) { var description = window.$h.commaizeInt(count) + " " + window.$h.pluralize(count, 'View'); $(".js-view-count[data-work-id=35181709]").text(description); $(".js-view-count[data-work-id=35181709]").attr('title', description).tooltip(); }); });</script></span></span><span><span class="percentile-widget hidden"><span class="u-mr2x work-percentile"></span></span><script>$(function () { var workId = 35181709; window.Academia.workPercentilesFetcher.queue(workId, function (percentileText) { var container = $(".js-work-strip[data-work-id='35181709']"); container.find('.work-percentile').text(percentileText.charAt(0).toUpperCase() + percentileText.slice(1)); container.find('.percentile-widget').show(); container.find('.percentile-widget').removeClass('hidden'); }); });</script></span><span><script>$(function() { new Works.PaperRankView({ workId: 35181709, container: "", }); });</script></span></div><div id="work-strip-premium-row-container"></div></div></div><script> require.config({ waitSeconds: 90 })(["https://a.academia-assets.com/assets/wow_profile-f77ea15d77ce96025a6048a514272ad8becbad23c641fc2b3bd6e24ca6ff1932.js","https://a.academia-assets.com/assets/work_edit-ad038b8c047c1a8d4fa01b402d530ff93c45fee2137a149a4a5398bc8ad67560.js"], function() { // from javascript_helper.rb var dispatcherData = {} if (false){ window.WowProfile.dispatcher = window.WowProfile.dispatcher || _.clone(Backbone.Events); dispatcherData = { dispatcher: window.WowProfile.dispatcher, downloadLinkId: "-1" } } $('.js-work-strip[data-work-id=35181709]').each(function() { if (!$(this).data('initialized')) { new WowProfile.WorkStripView({ el: this, workJSON: {"id":35181709,"title":"Bridging Organometallics and Quantum Chemical Topology: Understanding Electronic Relocalisation During Palladium-Catalyzed Reductive Elimination","translated_title":"","metadata":{"abstract":"This article proposes to bridge two fields, namely organometallics and quantum chemical topology. To do so, Palladium-catalyzed reductive elimination is studied. Such reaction is a classical elementary step in organometallic chemistry, where the directionality of electrons delocalization is not well understood. New computational evidences highlighting the accepted mechanism are proposed following a strategy coupling quantum theory of atoms in molecules and electron localization function topological analyses and enabling an extended quantification of donated/back-donated electrons fluxes along reaction paths going beyond the usual Dewar-Chatt-Duncanson model. Indeed, if the ligands coordination mode (phosphine, carbene) is commonly described as dative, it appears that ligands lone pairs stay centered on ligands as electrons are shared between metal and ligand with strong delocalization toward the latter. Overall, through strong trans effects coming from the carbon involved in the red...","publication_date":{"day":21,"month":1,"year":2015,"errors":{}},"publication_name":"Journal of computational chemistry"},"translated_abstract":"This article proposes to bridge two fields, namely organometallics and quantum chemical topology. To do so, Palladium-catalyzed reductive elimination is studied. Such reaction is a classical elementary step in organometallic chemistry, where the directionality of electrons delocalization is not well understood. New computational evidences highlighting the accepted mechanism are proposed following a strategy coupling quantum theory of atoms in molecules and electron localization function topological analyses and enabling an extended quantification of donated/back-donated electrons fluxes along reaction paths going beyond the usual Dewar-Chatt-Duncanson model. Indeed, if the ligands coordination mode (phosphine, carbene) is commonly described as dative, it appears that ligands lone pairs stay centered on ligands as electrons are shared between metal and ligand with strong delocalization toward the latter. Overall, through strong trans effects coming from the carbon involved in the red...","internal_url":"https://www.academia.edu/35181709/Bridging_Organometallics_and_Quantum_Chemical_Topology_Understanding_Electronic_Relocalisation_During_Palladium_Catalyzed_Reductive_Elimination","translated_internal_url":"","created_at":"2017-11-18T07:17:48.856-08:00","preview_url":null,"current_user_can_edit":null,"current_user_is_owner":null,"owner_id":35445,"coauthors_can_edit":true,"document_type":"paper","co_author_tags":[],"downloadable_attachments":[],"slug":"Bridging_Organometallics_and_Quantum_Chemical_Topology_Understanding_Electronic_Relocalisation_During_Palladium_Catalyzed_Reductive_Elimination","translated_slug":"","page_count":null,"language":"en","content_type":"Work","owner":{"id":35445,"first_name":"Jean-Philip","middle_initials":null,"last_name":"Piquemal","page_name":"JeanPhilipPiquemal","domain_name":"sorbonne-fr","created_at":"2009-03-17T04:43:24.569-07:00","display_name":"Jean-Philip Piquemal","url":"https://sorbonne-fr.academia.edu/JeanPhilipPiquemal"},"attachments":[],"research_interests":[{"id":528,"name":"Computational Chemistry","url":"https://www.academia.edu/Documents/in/Computational_Chemistry"},{"id":645605,"name":"THEORETICAL AND COMPUTATIONAL CHEMISTRY","url":"https://www.academia.edu/Documents/in/THEORETICAL_AND_COMPUTATIONAL_CHEMISTRY"}],"urls":[]}, dispatcherData: dispatcherData }); $(this).data('initialized', true); } }); $a.trackClickSource(".js-work-strip-work-link", "profile_work_strip") }); </script> <div class="js-work-strip profile--work_container" data-work-id="18536578"><div class="profile--work_thumbnail hidden-xs"><a class="js-work-strip-work-link" data-click-track="profile-work-strip-thumbnail" href="https://www.academia.edu/18536578/Hydration_Gibbs_free_energies_of_open_and_closed_shell_trivalent_lanthanide_and_actinide_cations_from_polarizable_molecular_dynamics"><img alt="Research paper thumbnail of Hydration Gibbs free energies of open and closed shell trivalent lanthanide and actinide cations from polarizable molecular dynamics" class="work-thumbnail" src="https://a.academia-assets.com/images/blank-paper.jpg" /></a></div><div class="wp-workCard wp-workCard_itemContainer"><div class="wp-workCard_item wp-workCard--title"><a class="js-work-strip-work-link text-gray-darker" data-click-track="profile-work-strip-title" href="https://www.academia.edu/18536578/Hydration_Gibbs_free_energies_of_open_and_closed_shell_trivalent_lanthanide_and_actinide_cations_from_polarizable_molecular_dynamics">Hydration Gibbs free energies of open and closed shell trivalent lanthanide and actinide cations from polarizable molecular dynamics</a></div><div class="wp-workCard_item wp-workCard--coauthors"><span>by </span><span><a class="" data-click-track="profile-work-strip-authors" href="https://pitt.academia.edu/AMarjolin">A. Marjolin</a> and <a class="" data-click-track="profile-work-strip-authors" href="https://sorbonne-fr.academia.edu/JeanPhilipPiquemal">Jean-Philip Piquemal</a></span></div><div class="wp-workCard_item"><span>Journal of molecular modeling</span><span>, 2014</span></div><div class="wp-workCard_item"><span class="js-work-more-abstract-truncated">The hydration free energies, structures, and dynamics of open- and closed-shell trivalent lanthan...</span><a class="js-work-more-abstract" data-broccoli-component="work_strip.more_abstract" data-click-track="profile-work-strip-more-abstract" href="javascript:;"><span> more </span><span><i class="fa fa-caret-down"></i></span></a><span class="js-work-more-abstract-untruncated hidden">The hydration free energies, structures, and dynamics of open- and closed-shell trivalent lanthanide and actinide metal cations are studied using molecular dynamics simulations (MD) based on a polarizable force field. Parameters for the metal cations are derived from an ab initio bottom-up strategy. MD simulations of six cations solvated in bulk water are subsequently performed with the AMOEBA polarizable force field. The calculated first-and second shell hydration numbers, water residence times, and free energies of hydration are consistent with experimental/theoretical values leading to a predictive modeling of f-elements compounds.</span></div><div class="wp-workCard_item wp-workCard--actions"><span class="work-strip-bookmark-button-container"></span><span class="wp-workCard--action visible-if-viewed-by-owner inline-block" style="display: none;"><span class="js-profile-work-strip-edit-button-wrapper profile-work-strip-edit-button-wrapper" data-work-id="18536578"><a class="js-profile-work-strip-edit-button" tabindex="0"><span><i class="fa fa-pencil"></i></span><span>Edit</span></a></span></span><span id="work-strip-rankings-button-container"></span></div><div class="wp-workCard_item wp-workCard--stats"><span><span><span class="js-view-count view-count u-mr2x" data-work-id="18536578"><i class="fa fa-spinner fa-spin"></i></span><script>$(function () { var workId = 18536578; window.Academia.workViewCountsFetcher.queue(workId, function (count) { var description = window.$h.commaizeInt(count) + " " + window.$h.pluralize(count, 'View'); $(".js-view-count[data-work-id=18536578]").text(description); $(".js-view-count[data-work-id=18536578]").attr('title', description).tooltip(); }); });</script></span></span><span><span class="percentile-widget hidden"><span class="u-mr2x work-percentile"></span></span><script>$(function () { var workId = 18536578; window.Academia.workPercentilesFetcher.queue(workId, function (percentileText) { var container = $(".js-work-strip[data-work-id='18536578']"); container.find('.work-percentile').text(percentileText.charAt(0).toUpperCase() + percentileText.slice(1)); container.find('.percentile-widget').show(); container.find('.percentile-widget').removeClass('hidden'); }); });</script></span><span><script>$(function() { new Works.PaperRankView({ workId: 18536578, container: "", }); });</script></span></div><div id="work-strip-premium-row-container"></div></div></div><script> require.config({ waitSeconds: 90 })(["https://a.academia-assets.com/assets/wow_profile-f77ea15d77ce96025a6048a514272ad8becbad23c641fc2b3bd6e24ca6ff1932.js","https://a.academia-assets.com/assets/work_edit-ad038b8c047c1a8d4fa01b402d530ff93c45fee2137a149a4a5398bc8ad67560.js"], function() { // from javascript_helper.rb var dispatcherData = {} if (false){ window.WowProfile.dispatcher = window.WowProfile.dispatcher || _.clone(Backbone.Events); dispatcherData = { dispatcher: window.WowProfile.dispatcher, downloadLinkId: "-1" } } $('.js-work-strip[data-work-id=18536578]').each(function() { if (!$(this).data('initialized')) { new WowProfile.WorkStripView({ el: this, workJSON: {"id":18536578,"title":"Hydration Gibbs free energies of open and closed shell trivalent lanthanide and actinide cations from polarizable molecular dynamics","translated_title":"","metadata":{"abstract":"The hydration free energies, structures, and dynamics of open- and closed-shell trivalent lanthanide and actinide metal cations are studied using molecular dynamics simulations (MD) based on a polarizable force field. 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The calculated first-and second shell hydration numbers, water residence times, and free energies of hydration are consistent with experimental/theoretical values leading to a predictive modeling of f-elements compounds.","internal_url":"https://www.academia.edu/18536578/Hydration_Gibbs_free_energies_of_open_and_closed_shell_trivalent_lanthanide_and_actinide_cations_from_polarizable_molecular_dynamics","translated_internal_url":"","created_at":"2015-11-17T14:09:06.310-08:00","preview_url":null,"current_user_can_edit":null,"current_user_is_owner":null,"owner_id":38393997,"coauthors_can_edit":true,"document_type":"paper","co_author_tags":[{"id":12532643,"work_id":18536578,"tagging_user_id":38393997,"tagged_user_id":null,"co_author_invite_id":2343916,"email":"j***n@gmail.com","display_order":0,"name":"Jean-pierre Dognon","title":"Hydration Gibbs free energies of open and closed shell trivalent lanthanide and actinide cations from polarizable molecular dynamics"},{"id":12532644,"work_id":18536578,"tagging_user_id":38393997,"tagged_user_id":37239238,"co_author_invite_id":null,"email":"m***s@uiowa.edu","affiliation":"The University of Iowa","display_order":4194304,"name":"Michael Schnieders","title":"Hydration Gibbs free energies of open and closed shell trivalent lanthanide and actinide cations from polarizable molecular dynamics"},{"id":12532645,"work_id":18536578,"tagging_user_id":38393997,"tagged_user_id":35445,"co_author_invite_id":null,"email":"j***p@lct.jussieu.fr","affiliation":"Sorbonne University","display_order":6291456,"name":"Jean-Philip Piquemal","title":"Hydration Gibbs free energies of open and closed shell trivalent lanthanide and actinide cations from polarizable molecular dynamics"},{"id":12532646,"work_id":18536578,"tagging_user_id":38393997,"tagged_user_id":32699940,"co_author_invite_id":null,"email":"p***n@mail.utexas.edu","affiliation":"The University of Texas at Austin","display_order":7340032,"name":"Pengyu Ren","title":"Hydration Gibbs free energies of open and closed shell trivalent lanthanide and actinide cations from polarizable molecular dynamics"}],"downloadable_attachments":[],"slug":"Hydration_Gibbs_free_energies_of_open_and_closed_shell_trivalent_lanthanide_and_actinide_cations_from_polarizable_molecular_dynamics","translated_slug":"","page_count":null,"language":"en","content_type":"Work","owner":{"id":38393997,"first_name":"A.","middle_initials":null,"last_name":"Marjolin","page_name":"AMarjolin","domain_name":"pitt","created_at":"2015-11-15T13:07:23.000-08:00","display_name":"A. Marjolin","url":"https://pitt.academia.edu/AMarjolin"},"attachments":[],"research_interests":[{"id":2215,"name":"Water","url":"https://www.academia.edu/Documents/in/Water"},{"id":2736,"name":"Molecular Dynamics Simulation","url":"https://www.academia.edu/Documents/in/Molecular_Dynamics_Simulation"},{"id":32927,"name":"Molecular modeling","url":"https://www.academia.edu/Documents/in/Molecular_modeling"},{"id":645605,"name":"THEORETICAL AND COMPUTATIONAL CHEMISTRY","url":"https://www.academia.edu/Documents/in/THEORETICAL_AND_COMPUTATIONAL_CHEMISTRY"},{"id":717129,"name":"Energy Transfer","url":"https://www.academia.edu/Documents/in/Energy_Transfer"},{"id":967839,"name":"Structure activity Relationship","url":"https://www.academia.edu/Documents/in/Structure_activity_Relationship"},{"id":1013858,"name":"Cations","url":"https://www.academia.edu/Documents/in/Cations"},{"id":1724844,"name":"Molecular Structure","url":"https://www.academia.edu/Documents/in/Molecular_Structure"},{"id":1745595,"name":"Solvents","url":"https://www.academia.edu/Documents/in/Solvents"}],"urls":[]}, dispatcherData: dispatcherData }); $(this).data('initialized', true); } }); $a.trackClickSource(".js-work-strip-work-link", "profile_work_strip") }); </script> <div class="js-work-strip profile--work_container" data-work-id="35181708"><div class="profile--work_thumbnail hidden-xs"><a class="js-work-strip-work-link" data-click-track="profile-work-strip-thumbnail" href="https://www.academia.edu/35181708/A_supervised_fitting_approach_to_force_field_parametrization_with_application_to_the_SIBFA_polarizable_force_field"><img alt="Research paper thumbnail of A supervised fitting approach to force field parametrization with application to the SIBFA polarizable force field" class="work-thumbnail" src="https://a.academia-assets.com/images/blank-paper.jpg" /></a></div><div class="wp-workCard wp-workCard_itemContainer"><div class="wp-workCard_item wp-workCard--title"><a class="js-work-strip-work-link text-gray-darker" data-click-track="profile-work-strip-title" href="https://www.academia.edu/35181708/A_supervised_fitting_approach_to_force_field_parametrization_with_application_to_the_SIBFA_polarizable_force_field">A supervised fitting approach to force field parametrization with application to the SIBFA polarizable force field</a></div><div class="wp-workCard_item"><span>Journal of computational chemistry</span><span>, Jan 5, 2014</span></div><div class="wp-workCard_item"><span class="js-work-more-abstract-truncated">A supervised, semiautomated approach to force field parameter fitting is described and applied to...</span><a class="js-work-more-abstract" data-broccoli-component="work_strip.more_abstract" data-click-track="profile-work-strip-more-abstract" href="javascript:;"><span> more </span><span><i class="fa fa-caret-down"></i></span></a><span class="js-work-more-abstract-untruncated hidden">A supervised, semiautomated approach to force field parameter fitting is described and applied to the SIBFA polarizable force field. The I-NoLLS interactive, nonlinear least squares fitting program is used as an engine for parameter refinement while keeping parameter values within a physical range. Interactive fitting is shown to avoid many of the stability problems that frequently afflict highly correlated, nonlinear fitting problems occurring in force field parametrizations. The method is used to obtain parameters for the H2O, formamide, and imidazole molecular fragments and their complexes with the Mg(2+) cation. Reference data obtained from ab initio calculations using an auc-cc-pVTZ basis set exploit advances in modern computer hardware to provide a more accurate parametrization of SIBFA than has previously been available.</span></div><div class="wp-workCard_item wp-workCard--actions"><span class="work-strip-bookmark-button-container"></span><span class="wp-workCard--action visible-if-viewed-by-owner inline-block" style="display: none;"><span class="js-profile-work-strip-edit-button-wrapper profile-work-strip-edit-button-wrapper" data-work-id="35181708"><a class="js-profile-work-strip-edit-button" tabindex="0"><span><i class="fa fa-pencil"></i></span><span>Edit</span></a></span></span><span id="work-strip-rankings-button-container"></span></div><div class="wp-workCard_item wp-workCard--stats"><span><span><span class="js-view-count view-count u-mr2x" data-work-id="35181708"><i class="fa fa-spinner fa-spin"></i></span><script>$(function () { var workId = 35181708; window.Academia.workViewCountsFetcher.queue(workId, function (count) { var description = window.$h.commaizeInt(count) + " " + window.$h.pluralize(count, 'View'); $(".js-view-count[data-work-id=35181708]").text(description); $(".js-view-count[data-work-id=35181708]").attr('title', description).tooltip(); }); });</script></span></span><span><span class="percentile-widget hidden"><span class="u-mr2x work-percentile"></span></span><script>$(function () { var workId = 35181708; window.Academia.workPercentilesFetcher.queue(workId, function (percentileText) { var container = $(".js-work-strip[data-work-id='35181708']"); container.find('.work-percentile').text(percentileText.charAt(0).toUpperCase() + percentileText.slice(1)); container.find('.percentile-widget').show(); container.find('.percentile-widget').removeClass('hidden'); }); });</script></span><span><script>$(function() { new Works.PaperRankView({ workId: 35181708, container: "", }); });</script></span></div><div id="work-strip-premium-row-container"></div></div></div><script> require.config({ waitSeconds: 90 })(["https://a.academia-assets.com/assets/wow_profile-f77ea15d77ce96025a6048a514272ad8becbad23c641fc2b3bd6e24ca6ff1932.js","https://a.academia-assets.com/assets/work_edit-ad038b8c047c1a8d4fa01b402d530ff93c45fee2137a149a4a5398bc8ad67560.js"], function() { // from javascript_helper.rb var dispatcherData = {} if (false){ window.WowProfile.dispatcher = window.WowProfile.dispatcher || _.clone(Backbone.Events); dispatcherData = { dispatcher: window.WowProfile.dispatcher, downloadLinkId: "-1" } } $('.js-work-strip[data-work-id=35181708]').each(function() { if (!$(this).data('initialized')) { new WowProfile.WorkStripView({ el: this, workJSON: {"id":35181708,"title":"A supervised fitting approach to force field parametrization with application to the SIBFA polarizable force field","translated_title":"","metadata":{"abstract":"A supervised, semiautomated approach to force field parameter fitting is described and applied to the SIBFA polarizable force field. The I-NoLLS interactive, nonlinear least squares fitting program is used as an engine for parameter refinement while keeping parameter values within a physical range. Interactive fitting is shown to avoid many of the stability problems that frequently afflict highly correlated, nonlinear fitting problems occurring in force field parametrizations. The method is used to obtain parameters for the H2O, formamide, and imidazole molecular fragments and their complexes with the Mg(2+) cation. Reference data obtained from ab initio calculations using an auc-cc-pVTZ basis set exploit advances in modern computer hardware to provide a more accurate parametrization of SIBFA than has previously been available.","publication_date":{"day":5,"month":1,"year":2014,"errors":{}},"publication_name":"Journal of computational chemistry"},"translated_abstract":"A supervised, semiautomated approach to force field parameter fitting is described and applied to the SIBFA polarizable force field. The I-NoLLS interactive, nonlinear least squares fitting program is used as an engine for parameter refinement while keeping parameter values within a physical range. Interactive fitting is shown to avoid many of the stability problems that frequently afflict highly correlated, nonlinear fitting problems occurring in force field parametrizations. The method is used to obtain parameters for the H2O, formamide, and imidazole molecular fragments and their complexes with the Mg(2+) cation. Reference data obtained from ab initio calculations using an auc-cc-pVTZ basis set exploit advances in modern computer hardware to provide a more accurate parametrization of SIBFA than has previously been available.","internal_url":"https://www.academia.edu/35181708/A_supervised_fitting_approach_to_force_field_parametrization_with_application_to_the_SIBFA_polarizable_force_field","translated_internal_url":"","created_at":"2017-11-18T07:17:48.544-08:00","preview_url":null,"current_user_can_edit":null,"current_user_is_owner":null,"owner_id":35445,"coauthors_can_edit":true,"document_type":"paper","co_author_tags":[],"downloadable_attachments":[],"slug":"A_supervised_fitting_approach_to_force_field_parametrization_with_application_to_the_SIBFA_polarizable_force_field","translated_slug":"","page_count":null,"language":"en","content_type":"Work","owner":{"id":35445,"first_name":"Jean-Philip","middle_initials":null,"last_name":"Piquemal","page_name":"JeanPhilipPiquemal","domain_name":"sorbonne-fr","created_at":"2009-03-17T04:43:24.569-07:00","display_name":"Jean-Philip Piquemal","url":"https://sorbonne-fr.academia.edu/JeanPhilipPiquemal"},"attachments":[],"research_interests":[{"id":528,"name":"Computational Chemistry","url":"https://www.academia.edu/Documents/in/Computational_Chemistry"},{"id":2215,"name":"Water","url":"https://www.academia.edu/Documents/in/Water"},{"id":69542,"name":"Computer Simulation","url":"https://www.academia.edu/Documents/in/Computer_Simulation"},{"id":70902,"name":"Magnesium","url":"https://www.academia.edu/Documents/in/Magnesium"},{"id":645605,"name":"THEORETICAL AND COMPUTATIONAL CHEMISTRY","url":"https://www.academia.edu/Documents/in/THEORETICAL_AND_COMPUTATIONAL_CHEMISTRY"},{"id":801409,"name":"Imidazoles","url":"https://www.academia.edu/Documents/in/Imidazoles"},{"id":2819832,"name":"Parametrization","url":"https://www.academia.edu/Documents/in/Parametrization"}],"urls":[]}, dispatcherData: dispatcherData }); $(this).data('initialized', true); } }); $a.trackClickSource(".js-work-strip-work-link", "profile_work_strip") }); </script> <div class="js-work-strip profile--work_container" data-work-id="35181707"><div class="profile--work_thumbnail hidden-xs"><a class="js-work-strip-work-link" data-click-track="profile-work-strip-thumbnail" href="https://www.academia.edu/35181707/Characterizing_Molecular_Interactions_in_Chemical_Systems"><img alt="Research paper thumbnail of Characterizing Molecular Interactions in Chemical Systems" class="work-thumbnail" src="https://a.academia-assets.com/images/blank-paper.jpg" /></a></div><div class="wp-workCard wp-workCard_itemContainer"><div class="wp-workCard_item wp-workCard--title"><a class="js-work-strip-work-link text-gray-darker" data-click-track="profile-work-strip-title" href="https://www.academia.edu/35181707/Characterizing_Molecular_Interactions_in_Chemical_Systems">Characterizing Molecular Interactions in Chemical Systems</a></div><div class="wp-workCard_item"><span>IEEE Transactions on Visualization and Computer Graphics</span><span>, 2014</span></div><div class="wp-workCard_item"><span class="js-work-more-abstract-truncated">Interactions between atoms have a major influence on the chemical properties of molecular systems...</span><a class="js-work-more-abstract" data-broccoli-component="work_strip.more_abstract" data-click-track="profile-work-strip-more-abstract" href="javascript:;"><span> more </span><span><i class="fa fa-caret-down"></i></span></a><span class="js-work-more-abstract-untruncated hidden">Interactions between atoms have a major influence on the chemical properties of molecular systems. While covalent interactions impose the structural integrity of molecules, noncovalent interactions govern more subtle phenomena such as protein folding, bonding or self assembly. The understanding of these types of interactions is necessary for the interpretation of many biological processes and chemical design tasks. While traditionally the electron density is analyzed to interpret the quantum chemistry of a molecular system, noncovalent interactions are characterized by low electron densities and only slight variations of them--challenging their extraction and characterization. Recently, the signed electron density and the reduced gradient, two scalar fields derived from the electron density, have drawn much attention in quantum chemistry since they enable a qualitative visualization of these interactions even in complex molecular systems and experimental measurements. In this work, we present the first combinatorial algorithm for the automated extraction and characterization of covalent and noncovalent interactions in molecular systems. The proposed algorithm is based on a joint topological analysis of the signed electron density and the reduced gradient. Combining the connectivity information of the critical points of these two scalar fields enables to visualize, enumerate, classify and investigate molecular interactions in a robust manner. Experiments on a variety of molecular systems, from simple dimers to proteins or DNA, demonstrate the ability of our technique to robustly extract these interactions and to reveal their structural relations to the atoms and bonds forming the molecules. For simple systems, our analysis corroborates the observations made by the chemists while it provides new visual and quantitative insights on chemical interactions for larger molecular systems.</span></div><div class="wp-workCard_item wp-workCard--actions"><span class="work-strip-bookmark-button-container"></span><span class="wp-workCard--action visible-if-viewed-by-owner inline-block" style="display: none;"><span class="js-profile-work-strip-edit-button-wrapper profile-work-strip-edit-button-wrapper" data-work-id="35181707"><a class="js-profile-work-strip-edit-button" tabindex="0"><span><i class="fa fa-pencil"></i></span><span>Edit</span></a></span></span><span id="work-strip-rankings-button-container"></span></div><div class="wp-workCard_item wp-workCard--stats"><span><span><span class="js-view-count view-count u-mr2x" data-work-id="35181707"><i class="fa fa-spinner fa-spin"></i></span><script>$(function () { var workId = 35181707; window.Academia.workViewCountsFetcher.queue(workId, function (count) { var description = window.$h.commaizeInt(count) + " " + window.$h.pluralize(count, 'View'); $(".js-view-count[data-work-id=35181707]").text(description); $(".js-view-count[data-work-id=35181707]").attr('title', description).tooltip(); }); });</script></span></span><span><span class="percentile-widget hidden"><span class="u-mr2x work-percentile"></span></span><script>$(function () { var workId = 35181707; window.Academia.workPercentilesFetcher.queue(workId, function (percentileText) { var container = $(".js-work-strip[data-work-id='35181707']"); container.find('.work-percentile').text(percentileText.charAt(0).toUpperCase() + percentileText.slice(1)); container.find('.percentile-widget').show(); container.find('.percentile-widget').removeClass('hidden'); }); });</script></span><span><script>$(function() { new Works.PaperRankView({ workId: 35181707, container: "", }); });</script></span></div><div id="work-strip-premium-row-container"></div></div></div><script> require.config({ waitSeconds: 90 })(["https://a.academia-assets.com/assets/wow_profile-f77ea15d77ce96025a6048a514272ad8becbad23c641fc2b3bd6e24ca6ff1932.js","https://a.academia-assets.com/assets/work_edit-ad038b8c047c1a8d4fa01b402d530ff93c45fee2137a149a4a5398bc8ad67560.js"], function() { // from javascript_helper.rb var dispatcherData = {} if (false){ window.WowProfile.dispatcher = window.WowProfile.dispatcher || _.clone(Backbone.Events); dispatcherData = { dispatcher: window.WowProfile.dispatcher, downloadLinkId: "-1" } } $('.js-work-strip[data-work-id=35181707]').each(function() { if (!$(this).data('initialized')) { new WowProfile.WorkStripView({ el: this, workJSON: {"id":35181707,"title":"Characterizing Molecular Interactions in Chemical Systems","translated_title":"","metadata":{"abstract":"Interactions between atoms have a major influence on the chemical properties of molecular systems. While covalent interactions impose the structural integrity of molecules, noncovalent interactions govern more subtle phenomena such as protein folding, bonding or self assembly. The understanding of these types of interactions is necessary for the interpretation of many biological processes and chemical design tasks. While traditionally the electron density is analyzed to interpret the quantum chemistry of a molecular system, noncovalent interactions are characterized by low electron densities and only slight variations of them--challenging their extraction and characterization. Recently, the signed electron density and the reduced gradient, two scalar fields derived from the electron density, have drawn much attention in quantum chemistry since they enable a qualitative visualization of these interactions even in complex molecular systems and experimental measurements. In this work, we present the first combinatorial algorithm for the automated extraction and characterization of covalent and noncovalent interactions in molecular systems. The proposed algorithm is based on a joint topological analysis of the signed electron density and the reduced gradient. Combining the connectivity information of the critical points of these two scalar fields enables to visualize, enumerate, classify and investigate molecular interactions in a robust manner. Experiments on a variety of molecular systems, from simple dimers to proteins or DNA, demonstrate the ability of our technique to robustly extract these interactions and to reveal their structural relations to the atoms and bonds forming the molecules. For simple systems, our analysis corroborates the observations made by the chemists while it provides new visual and quantitative insights on chemical interactions for larger molecular systems.","publisher":"Institute of Electrical and Electronics Engineers (IEEE)","publication_date":{"day":null,"month":null,"year":2014,"errors":{}},"publication_name":"IEEE Transactions on Visualization and Computer Graphics"},"translated_abstract":"Interactions between atoms have a major influence on the chemical properties of molecular systems. While covalent interactions impose the structural integrity of molecules, noncovalent interactions govern more subtle phenomena such as protein folding, bonding or self assembly. The understanding of these types of interactions is necessary for the interpretation of many biological processes and chemical design tasks. While traditionally the electron density is analyzed to interpret the quantum chemistry of a molecular system, noncovalent interactions are characterized by low electron densities and only slight variations of them--challenging their extraction and characterization. Recently, the signed electron density and the reduced gradient, two scalar fields derived from the electron density, have drawn much attention in quantum chemistry since they enable a qualitative visualization of these interactions even in complex molecular systems and experimental measurements. In this work, we present the first combinatorial algorithm for the automated extraction and characterization of covalent and noncovalent interactions in molecular systems. The proposed algorithm is based on a joint topological analysis of the signed electron density and the reduced gradient. Combining the connectivity information of the critical points of these two scalar fields enables to visualize, enumerate, classify and investigate molecular interactions in a robust manner. Experiments on a variety of molecular systems, from simple dimers to proteins or DNA, demonstrate the ability of our technique to robustly extract these interactions and to reveal their structural relations to the atoms and bonds forming the molecules. For simple systems, our analysis corroborates the observations made by the chemists while it provides new visual and quantitative insights on chemical interactions for larger molecular systems.","internal_url":"https://www.academia.edu/35181707/Characterizing_Molecular_Interactions_in_Chemical_Systems","translated_internal_url":"","created_at":"2017-11-18T07:17:48.392-08:00","preview_url":null,"current_user_can_edit":null,"current_user_is_owner":null,"owner_id":35445,"coauthors_can_edit":true,"document_type":"paper","co_author_tags":[],"downloadable_attachments":[],"slug":"Characterizing_Molecular_Interactions_in_Chemical_Systems","translated_slug":"","page_count":null,"language":"en","content_type":"Work","owner":{"id":35445,"first_name":"Jean-Philip","middle_initials":null,"last_name":"Piquemal","page_name":"JeanPhilipPiquemal","domain_name":"sorbonne-fr","created_at":"2009-03-17T04:43:24.569-07:00","display_name":"Jean-Philip Piquemal","url":"https://sorbonne-fr.academia.edu/JeanPhilipPiquemal"},"attachments":[],"research_interests":[{"id":445,"name":"Computer Graphics","url":"https://www.academia.edu/Documents/in/Computer_Graphics"},{"id":4233,"name":"Computational Biology","url":"https://www.academia.edu/Documents/in/Computational_Biology"},{"id":48057,"name":"DNA","url":"https://www.academia.edu/Documents/in/DNA"},{"id":181569,"name":"Proteins","url":"https://www.academia.edu/Documents/in/Proteins"},{"id":372917,"name":"Protein Secondary Structure Prediction","url":"https://www.academia.edu/Documents/in/Protein_Secondary_Structure_Prediction"},{"id":649537,"name":"Molecular Conformation","url":"https://www.academia.edu/Documents/in/Molecular_Conformation"}],"urls":[]}, dispatcherData: dispatcherData }); $(this).data('initialized', true); } }); $a.trackClickSource(".js-work-strip-work-link", "profile_work_strip") }); </script> <div class="js-work-strip profile--work_container" data-work-id="35181706"><div class="profile--work_thumbnail hidden-xs"><a class="js-work-strip-work-link" data-click-track="profile-work-strip-thumbnail" href="https://www.academia.edu/35181706/Synthesis_and_structure_activity_relationship_of_non_peptidic_antagonists_of_neuropilin_1_receptor"><img alt="Research paper thumbnail of Synthesis and structure-activity relationship of non-peptidic antagonists of neuropilin-1 receptor" class="work-thumbnail" src="https://a.academia-assets.com/images/blank-paper.jpg" /></a></div><div class="wp-workCard wp-workCard_itemContainer"><div class="wp-workCard_item wp-workCard--title"><a class="js-work-strip-work-link text-gray-darker" data-click-track="profile-work-strip-title" href="https://www.academia.edu/35181706/Synthesis_and_structure_activity_relationship_of_non_peptidic_antagonists_of_neuropilin_1_receptor">Synthesis and structure-activity relationship of non-peptidic antagonists of neuropilin-1 receptor</a></div><div class="wp-workCard_item"><span>Bioorganic & medicinal chemistry letters</span><span>, 2014</span></div><div class="wp-workCard_item"><span class="js-work-more-abstract-truncated">Neuropilins (NRPs) are VEGF-A165 co-receptors over-expressed in tumor cells, and considered as ta...</span><a class="js-work-more-abstract" data-broccoli-component="work_strip.more_abstract" data-click-track="profile-work-strip-more-abstract" href="javascript:;"><span> more </span><span><i class="fa fa-caret-down"></i></span></a><span class="js-work-more-abstract-untruncated hidden">Neuropilins (NRPs) are VEGF-A165 co-receptors over-expressed in tumor cells, and considered as targets in angiogenic-related pathologies. We previously identified compound 1, the first non-peptidic antagonist of the VEGF-A165/NRP binding, which exhibits in vivo anti-angiogenic and anti-tumor activities. We report here the synthesis and biological evaluations of new antagonists structurally-related to compound 1. Among these molecules, 4a, 4c and 4d show cytotoxic effects on HUVEC and MDA-MB-31 cells, and antagonize VEGF-A165/NRP-1 binding. This study confirmed our key structure-activity relationships hypothesis and paved the way to compound 1 &#39;hit to lead&#39; optimization.</span></div><div class="wp-workCard_item wp-workCard--actions"><span class="work-strip-bookmark-button-container"></span><span class="wp-workCard--action visible-if-viewed-by-owner inline-block" style="display: none;"><span class="js-profile-work-strip-edit-button-wrapper profile-work-strip-edit-button-wrapper" data-work-id="35181706"><a class="js-profile-work-strip-edit-button" tabindex="0"><span><i class="fa fa-pencil"></i></span><span>Edit</span></a></span></span><span id="work-strip-rankings-button-container"></span></div><div class="wp-workCard_item wp-workCard--stats"><span><span><span class="js-view-count view-count u-mr2x" data-work-id="35181706"><i class="fa fa-spinner fa-spin"></i></span><script>$(function () { var workId = 35181706; window.Academia.workViewCountsFetcher.queue(workId, function (count) { var description = window.$h.commaizeInt(count) + " " + window.$h.pluralize(count, 'View'); $(".js-view-count[data-work-id=35181706]").text(description); $(".js-view-count[data-work-id=35181706]").attr('title', description).tooltip(); }); });</script></span></span><span><span class="percentile-widget hidden"><span class="u-mr2x work-percentile"></span></span><script>$(function () { var workId = 35181706; window.Academia.workPercentilesFetcher.queue(workId, function (percentileText) { var container = $(".js-work-strip[data-work-id='35181706']"); container.find('.work-percentile').text(percentileText.charAt(0).toUpperCase() + percentileText.slice(1)); container.find('.percentile-widget').show(); container.find('.percentile-widget').removeClass('hidden'); }); });</script></span><span><script>$(function() { new Works.PaperRankView({ workId: 35181706, container: "", }); });</script></span></div><div id="work-strip-premium-row-container"></div></div></div><script> require.config({ waitSeconds: 90 })(["https://a.academia-assets.com/assets/wow_profile-f77ea15d77ce96025a6048a514272ad8becbad23c641fc2b3bd6e24ca6ff1932.js","https://a.academia-assets.com/assets/work_edit-ad038b8c047c1a8d4fa01b402d530ff93c45fee2137a149a4a5398bc8ad67560.js"], function() { // from javascript_helper.rb var dispatcherData = {} if (false){ window.WowProfile.dispatcher = window.WowProfile.dispatcher || _.clone(Backbone.Events); dispatcherData = { dispatcher: window.WowProfile.dispatcher, downloadLinkId: "-1" } } $('.js-work-strip[data-work-id=35181706]').each(function() { if (!$(this).data('initialized')) { new WowProfile.WorkStripView({ el: this, workJSON: {"id":35181706,"title":"Synthesis and structure-activity relationship of non-peptidic antagonists of neuropilin-1 receptor","translated_title":"","metadata":{"abstract":"Neuropilins (NRPs) are VEGF-A165 co-receptors over-expressed in tumor cells, and considered as targets in angiogenic-related pathologies. We previously identified compound 1, the first non-peptidic antagonist of the VEGF-A165/NRP binding, which exhibits in vivo anti-angiogenic and anti-tumor activities. We report here the synthesis and biological evaluations of new antagonists structurally-related to compound 1. Among these molecules, 4a, 4c and 4d show cytotoxic effects on HUVEC and MDA-MB-31 cells, and antagonize VEGF-A165/NRP-1 binding. This study confirmed our key structure-activity relationships hypothesis and paved the way to compound 1 \u0026#39;hit to lead\u0026#39; optimization.","publication_date":{"day":null,"month":null,"year":2014,"errors":{}},"publication_name":"Bioorganic \u0026 medicinal chemistry letters"},"translated_abstract":"Neuropilins (NRPs) are VEGF-A165 co-receptors over-expressed in tumor cells, and considered as targets in angiogenic-related pathologies. We previously identified compound 1, the first non-peptidic antagonist of the VEGF-A165/NRP binding, which exhibits in vivo anti-angiogenic and anti-tumor activities. We report here the synthesis and biological evaluations of new antagonists structurally-related to compound 1. Among these molecules, 4a, 4c and 4d show cytotoxic effects on HUVEC and MDA-MB-31 cells, and antagonize VEGF-A165/NRP-1 binding. This study confirmed our key structure-activity relationships hypothesis and paved the way to compound 1 \u0026#39;hit to lead\u0026#39; optimization.","internal_url":"https://www.academia.edu/35181706/Synthesis_and_structure_activity_relationship_of_non_peptidic_antagonists_of_neuropilin_1_receptor","translated_internal_url":"","created_at":"2017-11-18T07:17:48.248-08:00","preview_url":null,"current_user_can_edit":null,"current_user_is_owner":null,"owner_id":35445,"coauthors_can_edit":true,"document_type":"paper","co_author_tags":[],"downloadable_attachments":[],"slug":"Synthesis_and_structure_activity_relationship_of_non_peptidic_antagonists_of_neuropilin_1_receptor","translated_slug":"","page_count":null,"language":"en","content_type":"Work","owner":{"id":35445,"first_name":"Jean-Philip","middle_initials":null,"last_name":"Piquemal","page_name":"JeanPhilipPiquemal","domain_name":"sorbonne-fr","created_at":"2009-03-17T04:43:24.569-07:00","display_name":"Jean-Philip Piquemal","url":"https://sorbonne-fr.academia.edu/JeanPhilipPiquemal"},"attachments":[],"research_interests":[],"urls":[]}, dispatcherData: dispatcherData }); 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