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Z-matrix (chemistry)
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<h2 id="example">Example</h2> <p>The <a href="/facts/Methane/kBHneYnh">methane</a> molecule can be described by the following Cartesian coordinates (in <a href="/facts/%C3%85ngstr%C3%B6m/T5mjdd97">Ångströms</a>): </p> C 0.000000 0.000000 0.000000 H 0.000000 0.000000 1.089000 H 1.026719 0.000000 -0.363000 H -0.513360 -0.889165 -0.363000 H -0.513360 0.889165 -0.363000 <p>Reorienting the molecule leads to Cartesian coordinates that make the symmetry more obvious. This removes the bond length of 1.089 from the explicit parameters. </p> C 0.000000 0.000000 0.000000 H 0.628736 0.628736 0.628736 H -0.628736 -0.628736 0.628736 H -0.628736 0.628736 -0.628736 H 0.628736 -0.628736 -0.628736 <p>The corresponding Z-matrix, which starts from the carbon atom, could look like this: </p> C H 1 1.089000 H 1 1.089000 2 109.4710 H 1 1.089000 2 109.4710 3 120.0000 H 1 1.089000 2 109.4710 3 -120.0000 <p>Only the 1.089000 value is not fixed by <a href="/facts/Tetrahedral_symmetry/hIVlf9pu">tetrahedral symmetry</a>. </p> <h2 id="external-links">External links</h2> <ul><li>Parsons, Jerod; Holmes, J. Bradley; Rojas, J. Maurice; Tsai, Jerry; Strauss, Charlie E. M. (2005). "Practical conversion from torsion space to Cartesian space forin silico protein synthesis". <i>Journal of Computational Chemistry</i>. 26 (10): 1063–1068. <a href="/facts/Doi_(identifier)/muM9Etpq">doi</a>:<a href="https://doi.org/10.1002%2Fjcc.20237">10.1002/jcc.20237</a>. <a href="/facts/PMID_(identifier)/JlHAvMHt">PMID</a> <a href="https://pubmed.ncbi.nlm.nih.gov/15898109">15898109</a>. <a href="/facts/S2CID_(identifier)/ldJsHa2Y">S2CID</a> <a href="https://api.semanticscholar.org/CorpusID:2279574">2279574</a>.</li> <li><a href="http://bioshell.chem.uw.edu.pl/api/de/dab/a00319.html#_details">Java implementation of the NERF conversion algorithm</a></li> <li><a href="https://github.com/kylelutz/chemkit/blob/master/src/chemkit/internalcoordinates.cpp">C++ implementation of the NERF conversion algorithm</a></li> <li><a href="http://www.shodor.org/chemviz/zmatrices/babel.html">Z-Matrix to Cartesian Coordinate Conversion Page</a></li> <li><a href="https://metacpan.org/module/Chemistry::InternalCoords::Builder">Chemistry::InternalCoords::Builder</a> — <a href="/facts/Perl/fx31kjlT">Perl</a> module to build a Z-matrix from Cartesian coordinates.</li></ul> <h2 id="references">References</h2> <ol> <li id="fn:1"><p>Parsons, Jerod; Holmes, J. Bradley; Rojas, J. Maurice; Tsai, Jerry; Strauss, Charlie E. M. (2005). "Practical conversion from torsion space to Cartesian space for in silico protein synthesis". Journal of Computational Chemistry. 26 (10): 1063–1068. CiteSeerX 10.1.1.83.8235. doi:10.1002/jcc.20237. PMID 15898109. S2CID 2279574. <a href="/wiki/CiteSeerX_(identifier)" target="_blank">/wiki/CiteSeerX_(identifier)</a> <a href="#fnref:1" class="footnote-back-ref">↩</a></p></li> <li id="fn:2"><p>Gordon, M. S.; Pople, J. A. (1968). "Approximate Self-Consistent Molecular-Orbital Theory. VI. INDO Calculated Equilibrium Geometries". The Journal of Chemical Physics. 49 (10): 4643–4650. Bibcode:1968JChPh..49.4643G. doi:10.1063/1.1669925. <a href="/wiki/Bibcode_(identifier)" target="_blank">/wiki/Bibcode_(identifier)</a> <a href="#fnref:2" class="footnote-back-ref">↩</a></p></li> <li id="fn:3"><p>Parsons, Jerod; Holmes, J. Bradley; Rojas, J. Maurice; Tsai, Jerry; Strauss, Charlie E. M. (2005). "Practical conversion from torsion space to Cartesian space for in silico protein synthesis". Journal of Computational Chemistry. 26 (10): 1063–1068. CiteSeerX 10.1.1.83.8235. doi:10.1002/jcc.20237. PMID 15898109. S2CID 2279574. <a href="/wiki/CiteSeerX_(identifier)" target="_blank">/wiki/CiteSeerX_(identifier)</a> <a href="#fnref:3" class="footnote-back-ref">↩</a></p></li> <li id="fn:4"><p>Parsons, Jerod; Holmes, J. Bradley; Rojas, J. Maurice; Tsai, Jerry; Strauss, Charlie E. M. (2005). "Practical conversion from torsion space to Cartesian space for in silico protein synthesis". Journal of Computational Chemistry. 26 (10): 1063–1068. CiteSeerX 10.1.1.83.8235. doi:10.1002/jcc.20237. PMID 15898109. S2CID 2279574. <a href="/wiki/CiteSeerX_(identifier)" target="_blank">/wiki/CiteSeerX_(identifier)</a> <a href="#fnref:4" class="footnote-back-ref">↩</a></p></li> </ol>