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class="menu nav navbar-nav"><li class="first leaf active"><a href="/chemdex/" class="active">Home</a></li> <li class="leaf"><a href="/chemdex/chemistry/vn_element_selection">VN grid</a></li> <li class="leaf"><a href="/chemdex/chemistry/on_element_selection">ON Grid</a></li> <li class="leaf"><a href="/chemdex/chemistry/cn_element_selection">CN grid</a></li> <li class="leaf"><a href="/chemdex/chemistry/en_element_selection">EN grid</a></li> <li class="leaf"><a href="/chemdex/chemistry/xn_element_selection" title="">XN grid</a></li> <li class="leaf"><a href="/chemdex/chemistry/ln_element_selection">LN grid</a></li> <li class="leaf"><a href="/chemdex/chemistry/zn_element_selection">ZN grid</a></li> <li class="leaf"><a href="/chemdex/chemistry/bn_element_selection">BN grid</a></li> <li class="leaf"><a href="/chemdex/chemistry/vn_cn_element_selection" title="VN vs. CN">VN–CN</a></li> <li class="leaf"><a href="/chemdex/chemistry/vn_en_element_selection" title="VN vs. EN plot">VN–EN</a></li> <li class="leaf"><a href="/chemdex/chemistry/vn_on_element_selection" title="VN vs. ON">VN–ON</a></li> <li class="leaf"><a href="/chemdex/chemistry/on_cn_element_selection" title="ON vs. CN">ON–CN</a></li> <li class="leaf"><a href="/chemdex/chemistry/on_en_element_selection" title="ON vs. EN">ON–EN</a></li> <li class="leaf"><a href="/chemdex/chemistry/xn_cn_element_selection" title="X vs. CN">XN–CN</a></li> <li class="leaf"><a href="/chemdex/chemistry/cn_en_element_selection">CN–EN</a></li> <li class="leaf"><a href="/chemdex/chemistry/ln_bn_element_selection" title="LN vs. BN">LN–BN</a></li> <li class="leaf"><a href="/chemdex/chemistry/vn_bn_element_selection" title="VN vs. BN">VN–BN</a></li> <li class="leaf"><a href="/chemdex/chemistry/on_bn_element_selection" title="ON vs. BN">ON–BN</a></li> <li class="leaf"><a href="/chemdex/chemistry/cn_bn_element_selection">CN–BN</a></li> <li class="leaf"><a href="/chemdex/chemistry/mlxz_grid_element_selection">MLXZ grid</a></li> <li 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taxonomy</a></li> <li class="leaf"><a href="/chemdex/taxonomy/geometry">Geometry</a></li> <li class="leaf"><a href="/chemdex/taxonomy/compound_type" title="Compound type">Compound type</a></li> <li class="last leaf"><a href="/chemdex/taxonomy/isomer_label">Isomer label</a></li> </ul></li> <li class="leaf"><a href="/chemdex/taxonomy/chemicals" title="">Search</a></li> <li class="last leaf"><a href="/chemdex/documentation" title="Documentation">Documentation</a></li> </ul> </nav> </div> </div> </header> <div class="main-container container"> <header role="banner" id="page-header"> <p class="lead">Atom taxonomy: classification of atoms in compounds</p> </header>  <div class="row"> <section class="col-sm-12"> <a id="main-content"></a> <div class="region region-content"> <section id="block-system-main" class="block block-system clearfix"> <article id="node-1" class="node node-page node-promoted node-teaser clearfix" about="/chemdex/node/1" typeof="foaf:Document"> <header> <h2><a href="/chemdex/node/1">Chemdex</a></h2> <span property="dc:title" content="Chemdex" class="rdf-meta element-hidden"></span> </header> <div class="field field-name-body field-type-text-with-summary field-label-hidden"><div class="field-items"><div class="field-item even" property="content:encoded"><h2>About Chemdex</h2> <p>Chemdex contains more than 73,000 atom environments. This is the <strong>November 2024</strong> data version. The Chemdex system calculates or records several classifications (listed below) for each compound. <strong>Quick start</strong> (no need to log in) - try the following links to view periodic trends for any of the following:</p> <ul> <li><strong><a href="/chemdex/chemistry/vn_element_selection">VN</a></strong>: <strong>V</strong>alence <strong>N</strong>umber;</li> <li><strong><a href="/chemdex/chemistry/on_element_selection">ON</a></strong>: <strong>O</strong>xidation <strong>N</strong>umber;</li> <li><strong><a href="/chemdex/chemistry/cn_element_selection">CN</a></strong>: <strong>C</strong>oordination <strong>N</strong>umber;</li> <li><strong><a href="/chemdex/chemistry/en_element_selection">EN</a></strong>: <strong>E</strong>lectron <strong>N</strong>umber;</li> <li><strong><a href="/chemdex/chemistry/xn_element_selection">XN</a></strong>: <strong>X</strong> <strong>N</strong>umber;</li> <li><strong><a href="/chemdex/chemistry/ln_element_selection">LN</a></strong>: <strong>L</strong> <strong>N</strong>umber;</li> <li><strong><a href="/chemdex/chemistry/zn_element_selection">ZN</a></strong>: <strong>Z</strong> <strong>N</strong>umber;</li> <li><strong><a href="/chemdex/chemistry/mlxzq_grid_element_selection">MLXZ<sup><em>q</em></sup></a></strong> class (<strong><em>q</em></strong>: overall charge of the compound) and the <strong><a href="/chemdex/chemistry/mlxz_grid_element_selection">MLXZ</a></strong> equivalent neutral class (ENC);</li> <li><strong><a href="/chemdex/chemistry/bn_element_selection">BN</a></strong>:<strong> B</strong>ond <strong>N</strong>umber, or <strong>LBN</strong>: <strong>L</strong>igand <strong>B</strong>ond <strong>N</strong>umber;</li> </ul> <p><strong>Update</strong>. A paper about Chemdex in Dalton Transactions is now available and I'm pleased to say it is open access. See <em>Chemdex: quantification and distributions of valence numbers, oxidation numbers, coordination numbers, electron numbers, and covalent bond classes for the elements</em>, Dalton Trans., 2024, <strong>51</strong>, 493-511, <a href="https://doi.org/10.1039/D3DT03738J">https://doi.org/10.1039/D3DT03738J</a>.</p> <p>I wish to acknowledge the use of the EPSRC funded <a href="https://psds.ac.uk/">Physical Sciences Data-science Service</a> hosted by the University of Southampton and STFC under grant number EP/S020357/1. <a href="https://www.ukri.org/who-we-are/stfc/locations/daresbury-laboratory/">The Daresbury Laboratory</a> runs the <a href="https://cds.dl.ac.uk/">CrystalWorks</a> system for the PSDS and I am grateful to the <a href="https://www.scd.stfc.ac.uk/">Daresbury Laboratory Scientific Computing</a> staff for access to, and assistance with, <a href="https://cds.dl.ac.uk/">CrystalWorks</a>. The Chemdex site is hosted by <a href="https:www.shef.ac.uk">The University of Sheffield</a>.</p> <p>There is no online documentation as yet. Use the menu items at the top to explore - or select from the below table. If you feel it would be useful to plot other pairs of classifications please let me know. You can also use the menu items to plot one property against another for one or more elements. The interface for element selection is a periodic table whose organisation is based upon the empirical data contained within Chemdex.</p> <div class="table-responsive"> <table style="text-align: center;" id="plot_grid"> <tr style="text-align: center;"> <th class="th_top70 w60"> </th> <th class="th_top70 w70"><a href="/chemdex/chemistry/vn_element_selection">VN</a></th> <th class="th_top70 w70"><a href="/chemdex/chemistry/on_element_selection">ON</a></th> <th class="th_top70 w70"><a href="/chemdex/chemistry/cn_element_selection">XN</a></th> <th class="th_top70 w70"><a href="/chemdex/chemistry/cn_element_selection">CN</a></th> <th class="th_top70 w70"><a href="/chemdex/chemistry/vn_element_selection">EN</a></th> <th class="th_top70 w70"><a href="/chemdex/chemistry/on_element_selection">LN</a></th> <th class="th_top70 w70"><a href="/chemdex/chemistry/on_element_selection">ZN</a></th> <th class="th_top70 w70"><a href="/chemdex/chemistry/on_element_selection">BN</a></th> </tr> <tr style="text-align: center;"> <th class="th_param_list"><a href="/chemdex/chemistry/vn_element_selection">VN</a></th> <td class="void"></td> <td>•</td> <td>•</td> <td>•</td> <td>•</td> <td>•</td> <td>•</td> <td>•</td> </tr> <tr style="text-align: center;"> <th class="th_param_list"><a href="/chemdex/chemistry/on_element_selection">ON</a></th> <td><a href="/chemdex/chemistry/vn_on_element_selection">VN vs. ON</a></td> <td class="void"></td> <td>•</td> <td>•</td> <td>•</td> <td>•</td> <td>•</td> <td>•</td> </tr> <tr style="text-align: center;"> <th class="th_param_list"><a href="/chemdex/chemistry/cn_element_selection">XN</a></th> <td>•</td> <td>•</td> <td class="void"></td> <td>•</td> <td>•</td> <td>•</td> <td>•</td> <td>•</td> </tr> <tr style="text-align: center;"> <th class="th_param_list"><a href="/chemdex/chemistry/cn_element_selection">CN</a></th> <td><a href="/chemdex/chemistry/vn_cn_element_selection">VN vs. CN</a></td> <td><a href="/chemdex/chemistry/on_cn_element_selection">ON vs. CN</a></td> <td><a href="/chemdex/chemistry/xn_cn_element_selection">XN vs. CN</a></td> <td class="void"></td> <td>•</td> <td>•</td> <td>•</td> <td>•</td> </tr> <tr style="text-align: center;"> <th class="th_param_list"><a href="/chemdex/chemistry/vn_element_selection">EN</a></th> <td><a href="/chemdex/chemistry/vn_en_element_selection">VN vs. EN</a></td> <td><a href="/chemdex/chemistry/on_en_element_selection">ON vs. EN</a></td> <td>•</td> <td><a href="/chemdex/chemistry/cn_en_element_selection">CN vs. EN</a></td> <td class="void"></td> <td>•</td> <td>•</td> <td>•</td> </tr> <tr style="text-align: center;"> <th class="th_param_list"><a href="/chemdex/chemistry/on_element_selection">LN</a></th> <td>•</td> <td>•</td> <td>•</td> <td>•</td> <td>•</td> <td class="void"></td> <td>•</td> <td>•</td> </tr> <tr style="text-align: center;"> <th class="th_param_list"><a href="/chemdex/chemistry/on_element_selection">ZN</a></th> <td>•</td> <td>•</td> <td>•</td> <td>•</td> <td>•</td> <td>•</td> <td class="void"></td> <td>•</td> </tr> <tr style="text-align: center;"> <th class="th_param_list"><a href="/chemdex/chemistry/on_element_selection">BN</a></th> <td><a href="/chemdex/chemistry/vn_bn_element_selection">VN vs. BN</a></td> <td><a href="/chemdex/chemistry/on_bn_element_selection">ON vs. BN</a></td> <td>•</td> <td><a href="/chemdex/chemistry/cn_bn_element_selection">CN vs. BN</a></td> <td>•</td> <td><a href="/chemdex/chemistry/ln_bn_element_selection">LN vs. BN</a></td> <td>•</td> <td class="void"></td> </tr> </table> </div> <h2>Chemdex Notes</h2> <p>You don't need an account to browse. Please understand the compound entries are still pretty messy (necessary for debugging and programming purposes).</p> <p>Chemdex contains compounds for which there is a crystal structure <em>with coordinates</em> on deposit and for which there is a <a href="https://www.doi.org/">Digital Object Identifier (DOI)</a> link.</p> <p>If you see a pink box with a message please let me know - it indicates an error, probably in programming. Please tell me the text, the URL, what you were doing, and maybe a screenshot if you think that would help me to fix it.</p> <p>Other errors: if you spot an error in the data (shouldn't be difficult) please let me know the compound and what you think is wrong. Typical errors might be incorrect attached group, incorrect attached group number, wrong name, and so on.... A good way to search for errors is to look at the outliers on the data plots. An outlier is either an interesting compound or I've made an error regarding that compound (quite likely). Note that agostic interactions are not included as primary bonding.</p> <p>Chemdex should display just fine on a mobile device. It works for me on an iPhone and an iPad. Does it work on your devices? 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