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type="text/json">{"id":181847,"name":"First-Order Logic","url":"https://www.academia.edu/Documents/in/First-Order_Logic?f_ri=32927","nofollow":false}</script><a class="InlineList-item-text" data-has-card-for-ri="396848" href="https://www.academia.edu/Documents/in/Formic_Acid">Formic Acid</a><script data-card-contents-for-ri="396848" type="text/json">{"id":396848,"name":"Formic Acid","url":"https://www.academia.edu/Documents/in/Formic_Acid?f_ri=32927","nofollow":false}</script></span></li><script>(function(){ if (true) { new Aedu.ResearchInterestListCard({ el: $('*[data-has-card-for-ri-list=18505453]'), work: {"id":18505453,"title":"Decarboxylation of Δ9-tetrahydrocannabinol: Kinetics and molecular 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u-lineHeight1_3"><a class="u-tcGrayDarkest js-work-link" href="https://www.academia.edu/78211482/Solvent_effects_on_the_structures_and_vibrational_features_of_zwitterionic_dipeptides_L_diglycine_and_L_dialanine">Solvent effects on the structures and vibrational features of zwitterionic dipeptides: L-diglycine and L-dialanine</a></div></div><div class="u-pb4x u-mt3x"><div class="summary u-fs14 u-fw300 u-lineHeight1_5 u-tcGrayDarkest"><div class="summarized">Calculations were done by applying the B3LYP/6-31++G(d) method on the zwitterionic L-diglycine and L-dialanine to study the solvent effects on their structures and vibrational features. Three models of solvation (implicit, explicit, and... <a class="more_link u-tcGrayDark u-linkUnstyled" data-container=".work_78211482" data-show=".complete" data-hide=".summarized" data-more-link-behavior="true" href="#">more</a></div><div class="complete hidden">Calculations were done by applying the B3LYP/6-31++G(d) method on the zwitterionic L-diglycine and L-dialanine to study the solvent effects on their structures and vibrational features. Three models of solvation (implicit, explicit, and explicit in implicit) were used and the subsequent resulting values compared. Even though both dipeptides surrounded by 12 water molecules seem sufficient to stabilize their zwitterionic characters, notably to avoid the proton transfer between the backbone (N t H[Formula: see text], COO (-)) groups, the hybrid model of solvation (explicit in implicit noted 12W/Continuum) appears to be in better agreement with available IR and Raman experiments than explicit and implicit models. The harmonic vibrational modes derived from geometry optimization of L-diglycine and L-dialanine in 12W/Continuum, agree with the available IR and Raman experimental values within 1 % for L-diglycine and 2 % for L-dialanine, and they appear more accurate than those found using the explicit model (12W). Graphical Abstract DFT/6-31++G∗ Optimized structures of L-diglycine (top) and L-dialanine (bottom) surrounded by 12 water molecules all embedded in a continuum.</div></div></div><ul class="InlineList u-ph0x u-fs13"><li class="InlineList-item logged_in_only"><div class="share_on_academia_work_button"><a class="academia_share Button Button--inverseBlue Button--sm js-bookmark-button" data-academia-share="Work/78211482" data-share-source="work_strip" data-spinner="small_white_hide_contents"><i class="fa fa-plus"></i><span class="work-strip-link-text u-ml1x" data-content="button_text">Bookmark</span></a></div></li><li class="InlineList-item"><ul class="InlineList InlineList--bordered u-ph0x"><li class="InlineList-item InlineList-item--bordered"><span class="InlineList-item-text">by <span itemscope="itemscope" itemprop="author" itemtype="https://schema.org/Person"><a class="u-tcGrayDark u-fw700" data-has-card-for-user="59370181" href="https://univ-bangui.academia.edu/JKOYAMBO">Jonathan KOYAMBO</a><script data-card-contents-for-user="59370181" type="text/json">{"id":59370181,"first_name":"Jonathan","last_name":"KOYAMBO","domain_name":"univ-bangui","page_name":"JKOYAMBO","display_name":"Jonathan KOYAMBO","profile_url":"https://univ-bangui.academia.edu/JKOYAMBO?f_ri=32927","photo":"https://0.academia-photos.com/59370181/17498723/17572243/s65_jonathan.koyambo.jpg"}</script></span></span></li><li class="js-paper-rank-work_78211482 InlineList-item InlineList-item--bordered hidden"><span class="js-paper-rank-view hidden u-tcGrayDark" data-paper-rank-work-id="78211482"><i class="u-m1x fa fa-bar-chart"></i><strong class="js-paper-rank"></strong></span><script>$(function() { new Works.PaperRankView({ workId: 78211482, container: ".js-paper-rank-work_78211482", }); 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Three models of solvation (implicit, explicit, and explicit in implicit) were used and the subsequent resulting values compared. Even though both dipeptides surrounded by 12 water molecules seem sufficient to stabilize their zwitterionic characters, notably to avoid the proton transfer between the backbone (N t H[Formula: see text], COO (-)) groups, the hybrid model of solvation (explicit in implicit noted 12W/Continuum) appears to be in better agreement with available IR and Raman experiments than explicit and implicit models. The harmonic vibrational modes derived from geometry optimization of L-diglycine and L-dialanine in 12W/Continuum, agree with the available IR and Raman experimental values within 1 % for L-diglycine and 2 % for L-dialanine, and they appear more accurate than those found using the explicit model (12W). Graphical Abstract DFT/6-31++G∗ Optimized structures of L-diglycine (top) and L-dialanine (bottom) surrounded by 12 water molecules all embedded in a continuum.","downloadable_attachments":[],"ordered_authors":[{"id":59370181,"first_name":"Jonathan","last_name":"KOYAMBO","domain_name":"univ-bangui","page_name":"JKOYAMBO","display_name":"Jonathan KOYAMBO","profile_url":"https://univ-bangui.academia.edu/JKOYAMBO?f_ri=32927","photo":"https://0.academia-photos.com/59370181/17498723/17572243/s65_jonathan.koyambo.jpg"}],"research_interests":[{"id":523,"name":"Chemistry","url":"https://www.academia.edu/Documents/in/Chemistry?f_ri=32927","nofollow":false},{"id":2215,"name":"Water","url":"https://www.academia.edu/Documents/in/Water?f_ri=32927","nofollow":false},{"id":26327,"name":"Medicine","url":"https://www.academia.edu/Documents/in/Medicine?f_ri=32927","nofollow":false},{"id":32927,"name":"Molecular modeling","url":"https://www.academia.edu/Documents/in/Molecular_modeling?f_ri=32927","nofollow":false},{"id":645605,"name":"THEORETICAL AND COMPUTATIONAL CHEMISTRY","url":"https://www.academia.edu/Documents/in/THEORETICAL_AND_COMPUTATIONAL_CHEMISTRY?f_ri=32927"},{"id":1745595,"name":"Solvents","url":"https://www.academia.edu/Documents/in/Solvents?f_ri=32927"}]}, }) } })();</script></ul></li></ul></div></div><div class="u-borderBottom1 u-borderColorGrayLighter"><div class="clearfix u-pv7x u-mb0x js-work-card work_64455467" data-work_id="64455467" itemscope="itemscope" itemtype="https://schema.org/ScholarlyArticle"><div class="header"><div class="title u-fontSerif u-fs22 u-lineHeight1_3"><a class="u-tcGrayDarkest js-work-link" href="https://www.academia.edu/64455467/Many_scale_molecular_simulation_for_ABS_MMT_nanocomposites_Upgrading_of_industrial_scraps">Many-scale molecular simulation for ABS-MMT nanocomposites: Upgrading of industrial scraps</a></div></div><div class="u-pb4x u-mt3x"><div class="summary u-fs14 u-fw300 u-lineHeight1_5 u-tcGrayDarkest"><div class="summarized">In this work, we simulated modified organoclay exfoliation and intercalation at an atomistic level, thus providing information about the rational choice of compatibilizers and polymer insertions behavior. Phase morphology and segregation... <a class="more_link u-tcGrayDark u-linkUnstyled" data-container=".work_64455467" data-show=".complete" data-hide=".summarized" data-more-link-behavior="true" href="#">more</a></div><div class="complete hidden">In this work, we simulated modified organoclay exfoliation and intercalation at an atomistic level, thus providing information about the rational choice of compatibilizers and polymer insertions behavior. Phase morphology and segregation domains have then been obtained ...</div></div></div><ul class="InlineList u-ph0x u-fs13"><li class="InlineList-item logged_in_only"><div class="share_on_academia_work_button"><a class="academia_share Button Button--inverseBlue Button--sm js-bookmark-button" data-academia-share="Work/64455467" data-share-source="work_strip" data-spinner="small_white_hide_contents"><i class="fa fa-plus"></i><span class="work-strip-link-text u-ml1x" data-content="button_text">Bookmark</span></a></div></li><li class="InlineList-item"><div class="download"><a id="623f5f76985aa961eb013d6b2da28bc0" rel="nofollow" data-download="{"attachment_id":76485425,"asset_id":64455467,"asset_type":"Work","always_allow_download":false,"track":null,"button_location":"work_strip","source":null,"hide_modal":null}" class="Button Button--sm Button--inverseGreen js-download-button prompt_button doc_download" href="https://www.academia.edu/attachments/76485425/download_file?st=MTczMjk3MDIyOSw4LjIyMi4yMDguMTQ2&s=work_strip"><i class="fa fa-arrow-circle-o-down fa-lg"></i><span class="u-textUppercase u-ml1x" data-content="button_text">Download</span></a></div></li><li class="InlineList-item"><ul class="InlineList InlineList--bordered u-ph0x"><li class="InlineList-item InlineList-item--bordered"><span class="InlineList-item-text">by <span itemscope="itemscope" itemprop="author" itemtype="https://schema.org/Person"><a class="u-tcGrayDark u-fw700" data-has-card-for-user="437780" href="https://units.academia.edu/MaurizioFermeglia">Maurizio Fermeglia</a><script data-card-contents-for-user="437780" type="text/json">{"id":437780,"first_name":"Maurizio","last_name":"Fermeglia","domain_name":"units","page_name":"MaurizioFermeglia","display_name":"Maurizio Fermeglia","profile_url":"https://units.academia.edu/MaurizioFermeglia?f_ri=32927","photo":"https://0.academia-photos.com/437780/139882/162246/s65_maurizio.fermeglia.jpg"}</script></span></span></li><li class="js-paper-rank-work_64455467 InlineList-item InlineList-item--bordered hidden"><span class="js-paper-rank-view hidden u-tcGrayDark" data-paper-rank-work-id="64455467"><i class="u-m1x fa fa-bar-chart"></i><strong class="js-paper-rank"></strong></span><script>$(function() { new Works.PaperRankView({ workId: 64455467, container: ".js-paper-rank-work_64455467", }); 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type="text/json">{"id":2541,"name":"Structural Biology","url":"https://www.academia.edu/Documents/in/Structural_Biology?f_ri=32927","nofollow":false}</script><a class="InlineList-item-text" data-has-card-for-ri="4233" href="https://www.academia.edu/Documents/in/Computational_Biology">Computational Biology</a>, <script data-card-contents-for-ri="4233" type="text/json">{"id":4233,"name":"Computational Biology","url":"https://www.academia.edu/Documents/in/Computational_Biology?f_ri=32927","nofollow":false}</script><a class="InlineList-item-text" data-has-card-for-ri="32927" href="https://www.academia.edu/Documents/in/Molecular_modeling">Molecular modeling</a><script data-card-contents-for-ri="32927" type="text/json">{"id":32927,"name":"Molecular modeling","url":"https://www.academia.edu/Documents/in/Molecular_modeling?f_ri=32927","nofollow":false}</script></span></li><script>(function(){ if (true) { new Aedu.ResearchInterestListCard({ el: $('*[data-has-card-for-ri-list=15307099]'), work: 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itemtype="https://schema.org/Person"><a class="u-tcGrayDark u-fw700" data-has-card-for-user="50412544" href="https://independent.academia.edu/MonicaCivera">Monica Civera</a><script data-card-contents-for-user="50412544" type="text/json">{"id":50412544,"first_name":"Monica","last_name":"Civera","domain_name":"independent","page_name":"MonicaCivera","display_name":"Monica Civera","profile_url":"https://independent.academia.edu/MonicaCivera?f_ri=32927","photo":"/images/s65_no_pic.png"}</script></span></span><span class="u-displayInlineBlock InlineList-item-text"> and <span class="u-textDecorationUnderline u-clickable InlineList-item-text js-work-more-authors-26458104">+3</span><div class="hidden js-additional-users-26458104"><div><span itemscope="itemscope" itemprop="author" itemtype="https://schema.org/Person"><a href="https://independent.academia.edu/RaffaeleColombo">Raffaele Colombo</a></span></div><div><span itemscope="itemscope" itemprop="author" 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and structure of N-(substituted 5-bromo hydroxyphenylaldiminate) Co(II) complexes</a></div></div><div class="u-pb4x u-mt3x"><div class="summary u-fs14 u-fw300 u-lineHeight1_5 u-tcGrayDarkest"><div class="summarized">The medium and far IR spectra of the title compounds are discussed and related to the molecular structure. The spectral analysis is supported by a normal coordinate treatment based on a simplified molecular model. Bands near 375 and 290... <a class="more_link u-tcGrayDark u-linkUnstyled" data-container=".work_72667682" data-show=".complete" data-hide=".summarized" data-more-link-behavior="true" href="#">more</a></div><div class="complete hidden">The medium and far IR spectra of the title compounds are discussed and related to the molecular structure. The spectral analysis is supported by a normal coordinate treatment based on a simplified molecular model. Bands near 375 and 290 cm−1 are assigned to the Co-O and Co-N stretching vibrations, respectively; the corresponding force constants are estimated to be 1.11 and</div></div></div><ul class="InlineList u-ph0x u-fs13"><li class="InlineList-item logged_in_only"><div class="share_on_academia_work_button"><a class="academia_share Button Button--inverseBlue Button--sm js-bookmark-button" data-academia-share="Work/72667682" data-share-source="work_strip" data-spinner="small_white_hide_contents"><i class="fa fa-plus"></i><span class="work-strip-link-text u-ml1x" data-content="button_text">Bookmark</span></a></div></li><li class="InlineList-item"><div class="download"><a id="11b365e8a9dfe6450aa7b7cfcd820ce8" rel="nofollow" data-download="{"attachment_id":81505223,"asset_id":72667682,"asset_type":"Work","always_allow_download":false,"track":null,"button_location":"work_strip","source":null,"hide_modal":null}" class="Button Button--sm Button--inverseGreen js-download-button prompt_button doc_download" href="https://www.academia.edu/attachments/81505223/download_file?st=MTczMjk3MDIzMCw4LjIyMi4yMDguMTQ2&s=work_strip"><i class="fa fa-arrow-circle-o-down fa-lg"></i><span class="u-textUppercase u-ml1x" data-content="button_text">Download</span></a></div></li><li class="InlineList-item"><ul class="InlineList InlineList--bordered u-ph0x"><li class="InlineList-item InlineList-item--bordered"><span class="InlineList-item-text">by <span itemscope="itemscope" itemprop="author" itemtype="https://schema.org/Person"><a class="u-tcGrayDark u-fw700" data-has-card-for-user="53044701" href="https://independent.academia.edu/VictorPobletePulgar">Victor Poblete Pulgar</a><script data-card-contents-for-user="53044701" type="text/json">{"id":53044701,"first_name":"Victor","last_name":"Poblete Pulgar","domain_name":"independent","page_name":"VictorPobletePulgar","display_name":"Victor Poblete Pulgar","profile_url":"https://independent.academia.edu/VictorPobletePulgar?f_ri=32927","photo":"/images/s65_no_pic.png"}</script></span></span></li><li class="js-paper-rank-work_72667682 InlineList-item InlineList-item--bordered hidden"><span class="js-paper-rank-view hidden u-tcGrayDark" data-paper-rank-work-id="72667682"><i class="u-m1x fa fa-bar-chart"></i><strong class="js-paper-rank"></strong></span><script>$(function() { new Works.PaperRankView({ workId: 72667682, container: ".js-paper-rank-work_72667682", }); 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discovery of new potent inhibitors, drugs for acute leukemias: A Virtual Screening, Molecular Docking, ADME & Tox study</a></div></div><div class="u-pb4x u-mt3x"><div class="summary u-fs14 u-fw300 u-lineHeight1_5 u-tcGrayDarkest"><div class="summarized">Mixed lineage leukemia (MLL) is an aggressive form of leukemia that affects both infants and adults and typically carries a poor prognosis. The underlying genetic defect is a chromosomal translocation that fuses the MLL gene to a variety... <a class="more_link u-tcGrayDark u-linkUnstyled" data-container=".work_41767986" data-show=".complete" data-hide=".summarized" data-more-link-behavior="true" href="#">more</a></div><div class="complete hidden">Mixed lineage leukemia (MLL) is an aggressive form of leukemia that affects both infants and adults and typically carries a poor prognosis. The underlying genetic defect is a chromosomal translocation that fuses the MLL gene to a variety of partners, and the resulting oncogenic fusion proteins gain the ability to interact with at least 3 known protein complexes, one of which contains DOT1L, a histone methyltransferase that catalyzes the methylation of histone H3 (H3K79). As DOT1L is essential for leukemic transformation, small-molecule inhibitors of DOT1L function are an attractive therapeutic target for this type of leukemia.<br />As per the previous researches show anti-cancer activity of Pyrazolone we have presumed that derivates of this moeity can be good inhibitor for DOT1L. With the help of virtual screening and molecular docking approach using Lamarckian Genetic Algorithm we have performed the binding mode of derivates of Pyrazolone with DOT1L.<br /><br />The study involved virtual screening of 6000 molecules on the basis of structure similarity of Pyrazolone from different chemical databases. Molecular docking using Lamarckian Genetic Algorithm was carried out for these ligands and the result gave binding energies which were in the range of -11.18 kcal/mol to -1.25 kcal/mol. The top molecules were selected on the basis of minimum binding energy and protein-ligand complex was created. They were then visualized using UCSF chimera for H-bond interaction between ligand and active site residues of DOT1L which resulted in finding intricate atomic scale properties between ligand and residues PHE 223, ASP 161 and GLU 186. The top molecules then were run for in-silico ADMET and druglikeness properties in which we got promising results.  Further in-vitro and in-vivo study is required on these molecules to test the inhibition of DOT1L.</div></div></div><ul class="InlineList u-ph0x u-fs13"><li class="InlineList-item logged_in_only"><div class="share_on_academia_work_button"><a class="academia_share Button Button--inverseBlue Button--sm js-bookmark-button" data-academia-share="Work/41767986" data-share-source="work_strip" data-spinner="small_white_hide_contents"><i class="fa fa-plus"></i><span class="work-strip-link-text u-ml1x" data-content="button_text">Bookmark</span></a></div></li><li class="InlineList-item"><div class="download"><a id="90fb36240672c92d96815e40c9ae7555" rel="nofollow" data-download="{"attachment_id":61926138,"asset_id":41767986,"asset_type":"Work","always_allow_download":false,"track":null,"button_location":"work_strip","source":null,"hide_modal":null}" class="Button Button--sm Button--inverseGreen js-download-button prompt_button doc_download" href="https://www.academia.edu/attachments/61926138/download_file?st=MTczMjk3MDIzMCw4LjIyMi4yMDguMTQ2&s=work_strip"><i class="fa fa-arrow-circle-o-down fa-lg"></i><span class="u-textUppercase u-ml1x" data-content="button_text">Download</span></a></div></li><li class="InlineList-item"><ul class="InlineList InlineList--bordered u-ph0x"><li class="InlineList-item InlineList-item--bordered"><span class="InlineList-item-text">by <span itemscope="itemscope" itemprop="author" itemtype="https://schema.org/Person"><a class="u-tcGrayDark u-fw700" data-has-card-for-user="509804" href="https://amity.academia.edu/asif">Asif Naqvi</a><script data-card-contents-for-user="509804" type="text/json">{"id":509804,"first_name":"Asif","last_name":"Naqvi","domain_name":"amity","page_name":"asif","display_name":"Asif Naqvi","profile_url":"https://amity.academia.edu/asif?f_ri=32927","photo":"https://0.academia-photos.com/509804/177232/32505789/s65_asif.naqvi.jpg"}</script></span></span></li><li class="js-paper-rank-work_41767986 InlineList-item InlineList-item--bordered hidden"><span class="js-paper-rank-view hidden u-tcGrayDark" data-paper-rank-work-id="41767986"><i class="u-m1x fa fa-bar-chart"></i><strong class="js-paper-rank"></strong></span><script>$(function() { new Works.PaperRankView({ workId: 41767986, container: ".js-paper-rank-work_41767986", }); 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The underlying genetic defect is a chromosomal translocation that fuses the MLL gene to a variety of partners, and the resulting oncogenic fusion proteins gain the ability to interact with at least 3 known protein complexes, one of which contains DOT1L, a histone methyltransferase that catalyzes the methylation of histone H3 (H3K79). As DOT1L is essential for leukemic transformation, small-molecule inhibitors of DOT1L function are an attractive therapeutic target for this type of leukemia.\nAs per the previous researches show anti-cancer activity of Pyrazolone we have presumed that derivates of this moeity can be good inhibitor for DOT1L. With the help of virtual screening and molecular docking approach using Lamarckian Genetic Algorithm we have performed the binding mode of derivates of Pyrazolone with DOT1L.\n\nThe study involved virtual screening of 6000 molecules on the basis of structure similarity of Pyrazolone from different chemical databases. Molecular docking using Lamarckian Genetic Algorithm was carried out for these ligands and the result gave binding energies which were in the range of -11.18 kcal/mol to -1.25 kcal/mol. The top molecules were selected on the basis of minimum binding energy and protein-ligand complex was created. They were then visualized using UCSF chimera for H-bond interaction between ligand and active site residues of DOT1L which resulted in finding intricate atomic scale properties between ligand and residues PHE 223, ASP 161 and GLU 186. The top molecules then were run for in-silico ADMET and druglikeness properties in which we got promising results. Further in-vitro and in-vivo study is required on these molecules to test the inhibition of DOT1L.","downloadable_attachments":[{"id":61926138,"asset_id":41767986,"asset_type":"Work","always_allow_download":false}],"ordered_authors":[{"id":509804,"first_name":"Asif","last_name":"Naqvi","domain_name":"amity","page_name":"asif","display_name":"Asif Naqvi","profile_url":"https://amity.academia.edu/asif?f_ri=32927","photo":"https://0.academia-photos.com/509804/177232/32505789/s65_asif.naqvi.jpg"}],"research_interests":[{"id":146,"name":"Bioinformatics","url":"https://www.academia.edu/Documents/in/Bioinformatics?f_ri=32927","nofollow":false},{"id":32927,"name":"Molecular modeling","url":"https://www.academia.edu/Documents/in/Molecular_modeling?f_ri=32927","nofollow":false},{"id":141235,"name":"Molecular docking","url":"https://www.academia.edu/Documents/in/Molecular_docking?f_ri=32927","nofollow":false},{"id":838409,"name":"Small Molecule 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Simulation","url":"https://www.academia.edu/Documents/in/Molecular_Dynamic_Simulation?f_ri=32927"},{"id":1333505,"name":"Solution Structure","url":"https://www.academia.edu/Documents/in/Solution_Structure?f_ri=32927"},{"id":1362652,"name":"Nucleic Acid Conformation","url":"https://www.academia.edu/Documents/in/Nucleic_Acid_Conformation?f_ri=32927"},{"id":1681026,"name":"Biochemistry and cell biology","url":"https://www.academia.edu/Documents/in/Biochemistry_and_cell_biology?f_ri=32927"}]}, }) } })();</script></ul></li></ul></div></div><div class="u-borderBottom1 u-borderColorGrayLighter"><div class="clearfix u-pv7x u-mb0x js-work-card work_5120995" data-work_id="5120995" itemscope="itemscope" itemtype="https://schema.org/ScholarlyArticle"><div class="header"><div class="title u-fontSerif u-fs22 u-lineHeight1_3"><a class="u-tcGrayDarkest js-work-link" href="https://www.academia.edu/5120995/The_cognitive_life_of_mechanical_molecular_models">The cognitive life of mechanical molecular models</a></div></div><div class="u-pb4x u-mt3x"><div class="summary u-fs14 u-fw300 u-lineHeight1_5 u-tcGrayDarkest"><div class="summarized">The use of physical models of molecular structures as research tools has been central to the development of biochemistry and molecular biology. Intriguingly, it has received little attention from scholars of science. In this paper, I... <a class="more_link u-tcGrayDark u-linkUnstyled" data-container=".work_5120995" data-show=".complete" data-hide=".summarized" data-more-link-behavior="true" href="#">more</a></div><div class="complete hidden">The use of physical models of molecular structures as research tools has been central to the development of biochemistry and molecular biology. Intriguingly, it has received little attention from scholars of science. In this paper, I argue that these physical models are not mere three-dimensional representations but that they are in fact very special research tools: they are cognitive augmentations. Despite the fact that they are external props, these models serve as cognitive tools that augment and extend the modeler’s cognitive capacities and performance in molecular modeling tasks. This cognitive enhancement is obtained because of the way the modeler interacts with these models, the models’ materiality contributing to the solving of the molecule’s structure. Furthermore, I argue that these material models and their component parts were designed, built and used specifically to serve as cognitive facilitators and cognitive augmentations.</div></div></div><ul class="InlineList u-ph0x u-fs13"><li class="InlineList-item logged_in_only"><div class="share_on_academia_work_button"><a class="academia_share Button Button--inverseBlue Button--sm js-bookmark-button" data-academia-share="Work/5120995" data-share-source="work_strip" data-spinner="small_white_hide_contents"><i class="fa fa-plus"></i><span class="work-strip-link-text u-ml1x" data-content="button_text">Bookmark</span></a></div></li><li class="InlineList-item"><div class="download"><a id="fa644d35f638a210f33df54b85773e09" rel="nofollow" data-download="{"attachment_id":33946348,"asset_id":5120995,"asset_type":"Work","always_allow_download":false,"track":null,"button_location":"work_strip","source":null,"hide_modal":null}" class="Button Button--sm Button--inverseGreen js-download-button prompt_button doc_download" href="https://www.academia.edu/attachments/33946348/download_file?st=MTczMjk3MDIzMCw4LjIyMi4yMDguMTQ2&s=work_strip"><i class="fa fa-arrow-circle-o-down fa-lg"></i><span class="u-textUppercase u-ml1x" data-content="button_text">Download</span></a></div></li><li class="InlineList-item"><ul class="InlineList InlineList--bordered u-ph0x"><li class="InlineList-item InlineList-item--bordered"><span class="InlineList-item-text">by <span itemscope="itemscope" itemprop="author" itemtype="https://schema.org/Person"><a class="u-tcGrayDark u-fw700" data-has-card-for-user="4870231" href="https://ceu.academia.edu/MathieuCharbonneau">Mathieu Charbonneau</a><script data-card-contents-for-user="4870231" type="text/json">{"id":4870231,"first_name":"Mathieu","last_name":"Charbonneau","domain_name":"ceu","page_name":"MathieuCharbonneau","display_name":"Mathieu Charbonneau","profile_url":"https://ceu.academia.edu/MathieuCharbonneau?f_ri=32927","photo":"https://0.academia-photos.com/4870231/2920646/52406446/s65_mathieu.charbonneau.jpg"}</script></span></span></li><li class="js-paper-rank-work_5120995 InlineList-item InlineList-item--bordered hidden"><span class="js-paper-rank-view hidden u-tcGrayDark" data-paper-rank-work-id="5120995"><i class="u-m1x fa fa-bar-chart"></i><strong class="js-paper-rank"></strong></span><script>$(function() { new Works.PaperRankView({ workId: 5120995, container: ".js-paper-rank-work_5120995", }); 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Intriguingly, it has received little attention from scholars of science. In this paper, I argue that these physical models are not mere three-dimensional representations but that they are in fact very special research tools: they are cognitive augmentations. Despite the fact that they are external props, these models serve as cognitive tools that augment and extend the modeler’s cognitive capacities and performance in molecular modeling tasks. This cognitive enhancement is obtained because of the way the modeler interacts with these models, the models’ materiality contributing to the solving of the molecule’s structure. Furthermore, I argue that these material models and their component parts were designed, built and used specifically to serve as cognitive facilitators and cognitive augmentations.","downloadable_attachments":[{"id":33946348,"asset_id":5120995,"asset_type":"Work","always_allow_download":false}],"ordered_authors":[{"id":4870231,"first_name":"Mathieu","last_name":"Charbonneau","domain_name":"ceu","page_name":"MathieuCharbonneau","display_name":"Mathieu Charbonneau","profile_url":"https://ceu.academia.edu/MathieuCharbonneau?f_ri=32927","photo":"https://0.academia-photos.com/4870231/2920646/52406446/s65_mathieu.charbonneau.jpg"}],"research_interests":[{"id":2513,"name":"Molecular Biology","url":"https://www.academia.edu/Documents/in/Molecular_Biology?f_ri=32927","nofollow":false},{"id":3939,"name":"History and Philosophy of Biology","url":"https://www.academia.edu/Documents/in/History_and_Philosophy_of_Biology?f_ri=32927","nofollow":false},{"id":4418,"name":"Distributed Cognition","url":"https://www.academia.edu/Documents/in/Distributed_Cognition?f_ri=32927","nofollow":false},{"id":31989,"name":"Embodied and Distributed Cognition","url":"https://www.academia.edu/Documents/in/Embodied_and_Distributed_Cognition?f_ri=32927","nofollow":false},{"id":32927,"name":"Molecular modeling","url":"https://www.academia.edu/Documents/in/Molecular_modeling?f_ri=32927"},{"id":813810,"name":"History of Biological Sciences","url":"https://www.academia.edu/Documents/in/History_of_Biological_Sciences?f_ri=32927"}]}, }) } })();</script></ul></li></ul></div></div><div class="u-borderBottom1 u-borderColorGrayLighter"><div class="clearfix u-pv7x u-mb0x js-work-card work_7777170 coauthored" data-work_id="7777170" itemscope="itemscope" itemtype="https://schema.org/ScholarlyArticle"><div class="header"><div class="title u-fontSerif u-fs22 u-lineHeight1_3"><a class="u-tcGrayDarkest js-work-link" href="https://www.academia.edu/7777170/Docking_of_the_alkaloid_geissospermine_into_acetylcholinesterase_a_natural_scaffold_targeting_the_treatment_of_Alzheimers_disease">Docking of the alkaloid geissospermine into acetylcholinesterase: a natural scaffold targeting the treatment of Alzheimer's disease</a></div></div><div class="u-pb4x u-mt3x"><div class="summary u-fs14 u-fw300 u-lineHeight1_5 u-tcGrayDarkest"><div class="summarized">Pharmacological studies from our group [Lima et al. Pharmacol Biochem Behav 92:508, (2009)] revealed that geissospermine (GSP), the major alkaloid of the bark extract of Brazilian Geissospermum vellosii, inhibits acetylcholinesterases... <a class="more_link u-tcGrayDark u-linkUnstyled" data-container=".work_7777170" data-show=".complete" data-hide=".summarized" data-more-link-behavior="true" href="#">more</a></div><div class="complete hidden">Pharmacological studies from our group [Lima et al. Pharmacol Biochem Behav 92:508, (2009)] revealed that geissospermine (GSP), the major alkaloid of the bark extract of Brazilian Geissospermum vellosii, inhibits acetylcholinesterases (AChEs) in the brains of rats and electric eels (Electrophorus electricus). However, the binding mode (i.e., conformation and orientation) of this indole-indoline alkaloid into the AChE active site is unknown. Therefore, in order to propose a plausible binding mode between GSP and AChE, which might explain the observed experimental inhibitory activity, we performed comparative automatic molecular docking simulations using the AutoDock and Molegro Virtual Docker (MVD) programs. A sample of ten crystal structures of the Pacific electric ray (Torpedo californica) TcAChE, in complex with ten diverse active site ligands, was selected as a robust re-docking validation test, and also for GSP docking. The MVD results indicate a preferential binding mode between GSP and AChE, in which GSP functional groups may perform specific interactions with residues in the enzyme active site, according to the ligand–protein contacts detected by the LPC/CSU server. Four hydrogen bonds were detected between GSP and Tyr121, Ser122, Ser200, and His440, in which the last two residues belong to the catalytic triad (Ser200···His440···Glu327). Hydrophobic and π–π stacking interactions were also detected between GSP and Phe330 and Trp84, respectively; these are involved in substrate stabilization at the active site. This study provides the basis to propose structural changes to the GSP structure, such as molecular simplification and isosteric replacement, in order to aid the design of new potential AChE inhibitors that are relevant to the treatment of Alzheimer’s disease. Figure GSP/1DX6 (Molegro Virtual Docker)</div></div></div><ul class="InlineList u-ph0x u-fs13"><li class="InlineList-item logged_in_only"><div class="share_on_academia_work_button"><a class="academia_share Button Button--inverseBlue Button--sm js-bookmark-button" data-academia-share="Work/7777170" data-share-source="work_strip" data-spinner="small_white_hide_contents"><i class="fa fa-plus"></i><span class="work-strip-link-text u-ml1x" data-content="button_text">Bookmark</span></a></div></li><li class="InlineList-item"><div class="download"><a id="400f4b341c81ed4760b105dab94a8d49" rel="nofollow" data-download="{"attachment_id":48345124,"asset_id":7777170,"asset_type":"Work","always_allow_download":false,"track":null,"button_location":"work_strip","source":null,"hide_modal":null}" class="Button Button--sm Button--inverseGreen js-download-button prompt_button doc_download" href="https://www.academia.edu/attachments/48345124/download_file?st=MTczMjk3MDIzMCw4LjIyMi4yMDguMTQ2&s=work_strip"><i class="fa fa-arrow-circle-o-down fa-lg"></i><span class="u-textUppercase u-ml1x" data-content="button_text">Download</span></a></div></li><li class="InlineList-item"><ul class="InlineList InlineList--bordered u-ph0x"><li class="InlineList-item InlineList-item--bordered"><span class="InlineList-item-text">by <span itemscope="itemscope" itemprop="author" itemtype="https://schema.org/Person"><a class="u-tcGrayDark u-fw700" data-has-card-for-user="48065689" href="https://oi.academia.edu/JoseliaLima">Josélia Lima</a><script data-card-contents-for-user="48065689" type="text/json">{"id":48065689,"first_name":"Josélia","last_name":"Lima","domain_name":"oi","page_name":"JoseliaLima","display_name":"Josélia Lima","profile_url":"https://oi.academia.edu/JoseliaLima?f_ri=32927","photo":"/images/s65_no_pic.png"}</script></span></span><span class="u-displayInlineBlock InlineList-item-text"> and <span class="u-textDecorationUnderline u-clickable InlineList-item-text js-work-more-authors-7777170">+2</span><div class="hidden js-additional-users-7777170"><div><span itemscope="itemscope" itemprop="author" itemtype="https://schema.org/Person"><a href="https://ufrj.academia.edu/MagalyAlbuquerque">Magaly G Albuquerque</a></span></div><div><span itemscope="itemscope" itemprop="author" itemtype="https://schema.org/Person"><a href="https://ufrj.academia.edu/RicardoBiccadeAlencastro">Ricardo Bicca de Alencastro</a></span></div></div></span><script>(function(){ var popoverSettings = { el: $('.js-work-more-authors-7777170'), placement: 'bottom', hide_delay: 200, html: true, content: function(){ return $('.js-additional-users-7777170').html(); 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Pharmacol Biochem Behav 92:508, (2009)] revealed that geissospermine (GSP), the major alkaloid of the bark extract of Brazilian Geissospermum vellosii, inhibits acetylcholinesterases (AChEs) in the brains of rats and electric eels (Electrophorus electricus). However, the binding mode (i.e., conformation and orientation) of this indole-indoline alkaloid into the AChE active site is unknown. Therefore, in order to propose a plausible binding mode between GSP and AChE, which might explain the observed experimental inhibitory activity, we performed comparative automatic molecular docking simulations using the AutoDock and Molegro Virtual Docker (MVD) programs. A sample of ten crystal structures of the Pacific electric ray (Torpedo californica) TcAChE, in complex with ten diverse active site ligands, was selected as a robust re-docking validation test, and also for GSP docking. The MVD results indicate a preferential binding mode between GSP and AChE, in which GSP functional groups may perform specific interactions with residues in the enzyme active site, according to the ligand–protein contacts detected by the LPC/CSU server. Four hydrogen bonds were detected between GSP and Tyr121, Ser122, Ser200, and His440, in which the last two residues belong to the catalytic triad (Ser200···His440···Glu327). Hydrophobic and π–π stacking interactions were also detected between GSP and Phe330 and Trp84, respectively; these are involved in substrate stabilization at the active site. This study provides the basis to propose structural changes to the GSP structure, such as molecular simplification and isosteric replacement, in order to aid the design of new potential AChE inhibitors that are relevant to the treatment of Alzheimer’s disease. Figure GSP/1DX6 (Molegro Virtual Docker)","downloadable_attachments":[{"id":48345124,"asset_id":7777170,"asset_type":"Work","always_allow_download":false}],"ordered_authors":[{"id":48065689,"first_name":"Josélia","last_name":"Lima","domain_name":"oi","page_name":"JoseliaLima","display_name":"Josélia Lima","profile_url":"https://oi.academia.edu/JoseliaLima?f_ri=32927","photo":"/images/s65_no_pic.png"},{"id":14314428,"first_name":"Magaly","last_name":"Albuquerque","domain_name":"ufrj","page_name":"MagalyAlbuquerque","display_name":"Magaly G Albuquerque","profile_url":"https://ufrj.academia.edu/MagalyAlbuquerque?f_ri=32927","photo":"https://0.academia-photos.com/14314428/3917987/4581223/s65_magaly.albuquerque.jpg"},{"id":37732846,"first_name":"Ricardo Bicca de","last_name":"Alencastro","domain_name":"ufrj","page_name":"RicardoBiccadeAlencastro","display_name":"Ricardo Bicca de 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Change","url":"https://www.academia.edu/Documents/in/Structural_Change?f_ri=32927"},{"id":240148,"name":"Hydrogen Bond","url":"https://www.academia.edu/Documents/in/Hydrogen_Bond?f_ri=32927"},{"id":296798,"name":"Hydrogen Bonding","url":"https://www.academia.edu/Documents/in/Hydrogen_Bonding?f_ri=32927"},{"id":354019,"name":"Active site","url":"https://www.academia.edu/Documents/in/Active_site?f_ri=32927"},{"id":519926,"name":"Functional Group","url":"https://www.academia.edu/Documents/in/Functional_Group?f_ri=32927"},{"id":583568,"name":"Enzyme activity","url":"https://www.academia.edu/Documents/in/Enzyme_activity?f_ri=32927"},{"id":645605,"name":"THEORETICAL AND COMPUTATIONAL CHEMISTRY","url":"https://www.academia.edu/Documents/in/THEORETICAL_AND_COMPUTATIONAL_CHEMISTRY?f_ri=32927"},{"id":649537,"name":"Molecular Conformation","url":"https://www.academia.edu/Documents/in/Molecular_Conformation?f_ri=32927"},{"id":653665,"name":"Protein Conformation","url":"https://www.academia.edu/Documents/in/Protein_Conformation?f_ri=32927"},{"id":1010725,"name":"Protein Binding","url":"https://www.academia.edu/Documents/in/Protein_Binding?f_ri=32927"},{"id":1120234,"name":"Alzheimer Disease","url":"https://www.academia.edu/Documents/in/Alzheimer_Disease?f_ri=32927"},{"id":1222191,"name":"Ligands","url":"https://www.academia.edu/Documents/in/Ligands?f_ri=32927"},{"id":1241261,"name":"Indole Alkaloids","url":"https://www.academia.edu/Documents/in/Indole_Alkaloids?f_ri=32927"}]}, }) } })();</script></ul></li></ul></div></div><div class="u-borderBottom1 u-borderColorGrayLighter"><div class="clearfix u-pv7x u-mb0x js-work-card work_9367249" data-work_id="9367249" itemscope="itemscope" itemtype="https://schema.org/ScholarlyArticle"><div class="header"><div class="title u-fontSerif u-fs22 u-lineHeight1_3"><a class="u-tcGrayDarkest js-work-link" href="https://www.academia.edu/9367249/Dynamic_Mechanical_Properties_of_Body_Wall_Dermis_in_Various_Mechanical_States_and_Their_Implications_for_the_Behavior_of_Sea_Cucumbers">Dynamic Mechanical Properties of Body-Wall Dermis in Various Mechanical States and Their Implications for the Behavior of Sea Cucumbers</a></div></div><div class="u-pb4x u-mt3x"></div><ul class="InlineList u-ph0x u-fs13"><li class="InlineList-item logged_in_only"><div class="share_on_academia_work_button"><a class="academia_share Button Button--inverseBlue Button--sm js-bookmark-button" data-academia-share="Work/9367249" data-share-source="work_strip" data-spinner="small_white_hide_contents"><i class="fa fa-plus"></i><span class="work-strip-link-text u-ml1x" data-content="button_text">Bookmark</span></a></div></li><li class="InlineList-item"><div class="download"><a id="c4b4adc736b98444a993d62b279a92b6" rel="nofollow" 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class="u-tcGrayDark u-fw700" data-has-card-for-user="33363372" href="https://ku-dk.academia.edu/S%C3%B8renEngelsen">Søren B Engelsen</a><script data-card-contents-for-user="33363372" type="text/json">{"id":33363372,"first_name":"Søren","last_name":"Engelsen","domain_name":"ku-dk","page_name":"SørenEngelsen","display_name":"Søren B Engelsen","profile_url":"https://ku-dk.academia.edu/S%C3%B8renEngelsen?f_ri=32927","photo":"/images/s65_no_pic.png"}</script></span></span><span class="u-displayInlineBlock InlineList-item-text"> and <span class="u-textDecorationUnderline u-clickable InlineList-item-text js-work-more-authors-14421719">+4</span><div class="hidden js-additional-users-14421719"><div><span itemscope="itemscope" itemprop="author" itemtype="https://schema.org/Person"><a href="https://ku-dk.academia.edu/BirtheJespersen">Birthe Jespersen</a></span></div><div><span itemscope="itemscope" itemprop="author" itemtype="https://schema.org/Person"><a 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Csizmadia","profile_url":"https://independent.academia.edu/ICsizmadia?f_ri=32927","photo":"/images/s65_no_pic.png"}],"research_interests":[{"id":32927,"name":"Molecular modeling","url":"https://www.academia.edu/Documents/in/Molecular_modeling?f_ri=32927","nofollow":false},{"id":118582,"name":"Physical sciences","url":"https://www.academia.edu/Documents/in/Physical_sciences?f_ri=32927","nofollow":false},{"id":1114938,"name":"Ab Initio Calculation","url":"https://www.academia.edu/Documents/in/Ab_Initio_Calculation?f_ri=32927","nofollow":false}]}, }) } })();</script></ul></li></ul></div></div><div class="u-borderBottom1 u-borderColorGrayLighter"><div class="clearfix u-pv7x u-mb0x js-work-card work_48293984" data-work_id="48293984" itemscope="itemscope" itemtype="https://schema.org/ScholarlyArticle"><div class="header"><div class="title u-fontSerif u-fs22 u-lineHeight1_3"><a class="u-tcGrayDarkest js-work-link" href="https://www.academia.edu/48293984/Time_Dependent_Density_Functional_Theory_Study_of_Structure_Property_Relationships_in_Diarylethene_Photochromic_Compounds">Time-Dependent Density Functional Theory Study of Structure-Property Relationships in Diarylethene Photochromic Compounds</a></div></div><div class="u-pb4x u-mt3x"><div class="summary u-fs14 u-fw300 u-lineHeight1_5 u-tcGrayDarkest"><div class="summarized">Photochromic compounds exhibit reversible transition between closed and open isomeric forms upon irradiation accompanied by change in their color. The two isomeric forms differ not only in absorption spectra, but also in various physical... <a class="more_link u-tcGrayDark u-linkUnstyled" data-container=".work_48293984" data-show=".complete" data-hide=".summarized" data-more-link-behavior="true" href="#">more</a></div><div class="complete hidden">Photochromic compounds exhibit reversible transition between closed and open isomeric forms upon irradiation accompanied by change in their color. The two isomeric forms differ not only in absorption spectra, but also in various physical and chemical properties and find applications as optical switching and data storage materials. In this contribution we apply Density Functional Theory (DFT) and Time-Dependent DFT (TD-DFT) to predict the equilibrium geometry and absorption spectra of a benchmark set of diarylethene based photochromic compounds in open and closed forms (before and after photocyclization). Comparison of the calculated Bond Length Alternation parameters with those available from the X-ray data indicates M05-2x functional to be the best method for geometry optimization when basis set includes polarization functions. We found M05 functional accurately predicts the maximum absorption wavelength when solvent is taken into account. 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We recommend combined theory level TD-M05/...","downloadable_attachments":[{"id":66988993,"asset_id":48293984,"asset_type":"Work","always_allow_download":false}],"ordered_authors":[{"id":32765818,"first_name":"Artëm","last_name":"Masunov","domain_name":"ucf","page_name":"Artem_Masunov","display_name":"Artëm E Masunov","profile_url":"https://ucf.academia.edu/Artem_Masunov?f_ri=32927","photo":"https://0.academia-photos.com/32765818/9766883/10880846/s65_art_m.masunov.jpg_oh_2eaaa7b8cf2eba3358ed3e48e6c67ea1_oe_5633e381___gda___1445104878_90470c7ab3a218acf152b7616947e828"}],"research_interests":[{"id":48,"name":"Engineering","url":"https://www.academia.edu/Documents/in/Engineering?f_ri=32927","nofollow":false},{"id":528,"name":"Computational Chemistry","url":"https://www.academia.edu/Documents/in/Computational_Chemistry?f_ri=32927","nofollow":false},{"id":529,"name":"Quantum 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href="https://www.academia.edu/17883830/Isolation_and_identification_of_a_ferulic_acid_dehydrotrimer_from_saponified_maize_bran_insoluble_fiber">Isolation and identification of a ferulic acid dehydrotrimer from saponified maize bran insoluble fiber</a></div></div><div class="u-pb4x u-mt3x"></div><ul class="InlineList u-ph0x u-fs13"><li class="InlineList-item logged_in_only"><div class="share_on_academia_work_button"><a class="academia_share Button Button--inverseBlue Button--sm js-bookmark-button" data-academia-share="Work/17883830" data-share-source="work_strip" data-spinner="small_white_hide_contents"><i class="fa fa-plus"></i><span class="work-strip-link-text u-ml1x" data-content="button_text">Bookmark</span></a></div></li><li class="InlineList-item"><div class="download"><a id="61448c12484fec8d9389a437f1f9a3af" rel="nofollow" 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Biotechnology","url":"https://www.academia.edu/Documents/in/Industrial_Biotechnology?f_ri=32927","nofollow":false}</script><a class="InlineList-item-text" data-has-card-for-ri="32927" href="https://www.academia.edu/Documents/in/Molecular_modeling">Molecular modeling</a>, <script data-card-contents-for-ri="32927" type="text/json">{"id":32927,"name":"Molecular modeling","url":"https://www.academia.edu/Documents/in/Molecular_modeling?f_ri=32927","nofollow":false}</script><a class="InlineList-item-text" data-has-card-for-ri="84384" href="https://www.academia.edu/Documents/in/Maize">Maize</a><script data-card-contents-for-ri="84384" type="text/json">{"id":84384,"name":"Maize","url":"https://www.academia.edu/Documents/in/Maize?f_ri=32927","nofollow":false}</script></span></li><script>(function(){ if (true) { new Aedu.ResearchInterestListCard({ el: $('*[data-has-card-for-ri-list=17883830]'), work: {"id":17883830,"title":"Isolation and identification of a ferulic acid dehydrotrimer from 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class="u-tcGrayDarkest js-work-link" href="https://www.academia.edu/13587795/Density_functional_theory_study_of_small_nickel_clusters">Density functional theory study of small nickel clusters</a></div></div><div class="u-pb4x u-mt3x"></div><ul class="InlineList u-ph0x u-fs13"><li class="InlineList-item logged_in_only"><div class="share_on_academia_work_button"><a class="academia_share Button Button--inverseBlue Button--sm js-bookmark-button" data-academia-share="Work/13587795" data-share-source="work_strip" data-spinner="small_white_hide_contents"><i class="fa fa-plus"></i><span class="work-strip-link-text u-ml1x" data-content="button_text">Bookmark</span></a></div></li><li class="InlineList-item"><div class="download"><a id="f7b22e94f2d13850d9d3a54630be5f28" rel="nofollow" data-download="{"attachment_id":45182355,"asset_id":13587795,"asset_type":"Work","always_allow_download":false,"track":null,"button_location":"work_strip","source":null,"hide_modal":null}" class="Button Button--sm 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href="https://www.academia.edu/Documents/in/Molecular_modeling">Molecular modeling</a>, <script data-card-contents-for-ri="32927" type="text/json">{"id":32927,"name":"Molecular modeling","url":"https://www.academia.edu/Documents/in/Molecular_modeling?f_ri=32927","nofollow":false}</script><a class="InlineList-item-text" data-has-card-for-ri="194828" href="https://www.academia.edu/Documents/in/Nickel">Nickel</a>, <script data-card-contents-for-ri="194828" type="text/json">{"id":194828,"name":"Nickel","url":"https://www.academia.edu/Documents/in/Nickel?f_ri=32927","nofollow":false}</script><a class="InlineList-item-text" data-has-card-for-ri="214560" href="https://www.academia.edu/Documents/in/Electron_Density">Electron Density</a>, <script data-card-contents-for-ri="214560" type="text/json">{"id":214560,"name":"Electron Density","url":"https://www.academia.edu/Documents/in/Electron_Density?f_ri=32927","nofollow":false}</script><a class="InlineList-item-text" data-has-card-for-ri="645605" 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This paper considers the use of quaternions in matching two conformations of a molecule, in interpolating rotations, in performing statistics on orientational... <a class="more_link u-tcGrayDark u-linkUnstyled" data-container=".work_37564858" data-show=".complete" data-hide=".summarized" data-more-link-behavior="true" href="#">more</a></div><div class="complete hidden">Quaternions are an important tool to describe the orientation of a molecule. This paper considers the use of quaternions in matching two conformations of a molecule, in interpolating rotations, in performing statistics on orientational data, in the random sampling of rotations, and in establishing grids in orientation space. These examples show that many of the rotational problems that arise in molecular modeling may be handled simply and efficiently using quaternions.</div></div></div><ul class="InlineList u-ph0x u-fs13"><li class="InlineList-item logged_in_only"><div class="share_on_academia_work_button"><a class="academia_share Button Button--inverseBlue Button--sm js-bookmark-button" data-academia-share="Work/37564858" data-share-source="work_strip" data-spinner="small_white_hide_contents"><i class="fa fa-plus"></i><span class="work-strip-link-text u-ml1x" data-content="button_text">Bookmark</span></a></div></li><li class="InlineList-item"><div class="download"><a id="d4f1924d29e377f619c57a0ddacc3c4c" rel="nofollow" data-download="{"attachment_id":57541953,"asset_id":37564858,"asset_type":"Work","always_allow_download":false,"track":null,"button_location":"work_strip","source":null,"hide_modal":null}" class="Button Button--sm Button--inverseGreen js-download-button prompt_button doc_download" href="https://www.academia.edu/attachments/57541953/download_file?st=MTczMjk3MDIzMCw4LjIyMi4yMDguMTQ2&s=work_strip"><i class="fa fa-arrow-circle-o-down fa-lg"></i><span class="u-textUppercase u-ml1x" data-content="button_text">Download</span></a></div></li><li class="InlineList-item"><ul class="InlineList InlineList--bordered u-ph0x"><li class="InlineList-item InlineList-item--bordered"><span class="InlineList-item-text">by <span itemscope="itemscope" itemprop="author" itemtype="https://schema.org/Person"><a class="u-tcGrayDark u-fw700" data-has-card-for-user="90516873" href="https://sri.academia.edu/CharlesKarney">Charles Karney</a><script data-card-contents-for-user="90516873" type="text/json">{"id":90516873,"first_name":"Charles","last_name":"Karney","domain_name":"sri","page_name":"CharlesKarney","display_name":"Charles Karney","profile_url":"https://sri.academia.edu/CharlesKarney?f_ri=32927","photo":"https://gravatar.com/avatar/a28b30bf91dd62ffdad4235850d00145?s=65"}</script></span></span></li><li class="js-paper-rank-work_37564858 InlineList-item InlineList-item--bordered hidden"><span class="js-paper-rank-view hidden u-tcGrayDark" data-paper-rank-work-id="37564858"><i class="u-m1x fa fa-bar-chart"></i><strong class="js-paper-rank"></strong></span><script>$(function() { new Works.PaperRankView({ workId: 37564858, container: ".js-paper-rank-work_37564858", }); 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These examples show that many of the rotational problems that arise in molecular modeling may be handled simply and efficiently using quaternions.","downloadable_attachments":[{"id":57541953,"asset_id":37564858,"asset_type":"Work","always_allow_download":false}],"ordered_authors":[{"id":90516873,"first_name":"Charles","last_name":"Karney","domain_name":"sri","page_name":"CharlesKarney","display_name":"Charles Karney","profile_url":"https://sri.academia.edu/CharlesKarney?f_ri=32927","photo":"https://gravatar.com/avatar/a28b30bf91dd62ffdad4235850d00145?s=65"}],"research_interests":[{"id":300,"name":"Mathematics","url":"https://www.academia.edu/Documents/in/Mathematics?f_ri=32927","nofollow":false},{"id":32927,"name":"Molecular modeling","url":"https://www.academia.edu/Documents/in/Molecular_modeling?f_ri=32927","nofollow":false},{"id":64561,"name":"Computer Software","url":"https://www.academia.edu/Documents/in/Computer_Software?f_ri=32927","nofollow":false},{"id":69542,"name":"Computer Simulation","url":"https://www.academia.edu/Documents/in/Computer_Simulation?f_ri=32927","nofollow":false},{"id":84365,"name":"Molecular Simulation","url":"https://www.academia.edu/Documents/in/Molecular_Simulation?f_ri=32927"},{"id":398499,"name":"Random sampling","url":"https://www.academia.edu/Documents/in/Random_sampling?f_ri=32927"},{"id":645605,"name":"THEORETICAL AND COMPUTATIONAL CHEMISTRY","url":"https://www.academia.edu/Documents/in/THEORETICAL_AND_COMPUTATIONAL_CHEMISTRY?f_ri=32927"},{"id":649537,"name":"Molecular Conformation","url":"https://www.academia.edu/Documents/in/Molecular_Conformation?f_ri=32927"},{"id":1681026,"name":"Biochemistry and cell biology","url":"https://www.academia.edu/Documents/in/Biochemistry_and_cell_biology?f_ri=32927"}]}, }) } })();</script></ul></li></ul></div></div><div class="u-borderBottom1 u-borderColorGrayLighter"><div class="clearfix u-pv7x u-mb0x js-work-card work_27934028" data-work_id="27934028" itemscope="itemscope" itemtype="https://schema.org/ScholarlyArticle"><div class="header"><div class="title u-fontSerif u-fs22 u-lineHeight1_3"><a class="u-tcGrayDarkest js-work-link" href="https://www.academia.edu/27934028/Ras_oncoprotein_inhibitors_The_discovery_of_potent_ras_nucleotide_exchange_inhibitors_and_the_structural_determination_of_a_drug_protein_complex">Ras oncoprotein inhibitors: The discovery of potent, ras nucleotide exchange inhibitors and the structural determination of a drug-protein complex</a></div></div><div class="u-pb4x u-mt3x"></div><ul class="InlineList u-ph0x u-fs13"><li class="InlineList-item logged_in_only"><div class="share_on_academia_work_button"><a class="academia_share Button Button--inverseBlue Button--sm js-bookmark-button" data-academia-share="Work/27934028" data-share-source="work_strip" data-spinner="small_white_hide_contents"><i class="fa fa-plus"></i><span class="work-strip-link-text u-ml1x" data-content="button_text">Bookmark</span></a></div></li><li class="InlineList-item"><div class="download"><a id="5c50e86b6010a3ab4c53979a0e0f9beb" rel="nofollow" data-download="{"attachment_id":48242258,"asset_id":27934028,"asset_type":"Work","always_allow_download":false,"track":null,"button_location":"work_strip","source":null,"hide_modal":null}" class="Button Button--sm Button--inverseGreen js-download-button prompt_button doc_download" href="https://www.academia.edu/attachments/48242258/download_file?st=MTczMjk3MDIzMCw4LjIyMi4yMDguMTQ2&s=work_strip"><i class="fa fa-arrow-circle-o-down fa-lg"></i><span class="u-textUppercase u-ml1x" data-content="button_text">Download</span></a></div></li><li class="InlineList-item"><ul class="InlineList InlineList--bordered u-ph0x"><li class="InlineList-item InlineList-item--bordered"><span class="InlineList-item-text">by <span itemscope="itemscope" itemprop="author" itemtype="https://schema.org/Person"><a class="u-tcGrayDark u-fw700" data-has-card-for-user="52344040" href="https://independent.academia.edu/DelisleD">D. 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