MolecularGeometry - Maple Help
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QuantumChemistry

 MolecularGeometry
 returns the geometry of a molecule

 Calling Sequence MolecularGeometry(molecule)

Parameters

 molecule - string, integer; name of the molecule as a string, CID number as an integer, or SMILES formula (see below for format)

Description

 • MolecularGeometry(molecule) returns the geometry of a molecule.
 • The molecule can be a name, CID number, or SMILES formula in the format "smiles=formula".
 • MolecularGeometry returns the molecular geometry as a Maple list of lists in the standard molecular geometry format of the QuantumChemistry package.
 • The standard geometry format of the QuantumChemistry package is a Maple list of lists which each list has 4 elements, the string of an atom's symbol and atom's x, y, and z coordinates.
 • Geometries and structures are retrieved from a web database.  A connection to the internet is required.  Currently, the procedure has access to over 96 million molecules contained in the PubChem database.
 References Kim S, Chen J, Cheng T, Gindulyte A, He J, He S, Li Q, Shoemaker BA, Thiessen PA, Yu B, Zaslavsky L, Zhang J, Bolton EE. PubChem 2023 update. Nucleic Acids Res. 2023 Jan 6;51(D1):D1373-D1380. doi:10.1093/nar/gkac956. PMID: 36305812.

Examples

 > $\mathrm{with}\left(\mathrm{QuantumChemistry}\right):$

Retrieve the geometry of hydrogen fluoride

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 ${\mathrm{mol}}{≔}{"hydrogenfluoride"}$ (1)
 >
 ${\mathrm{geom}}{≔}\left[\left[{"F"}{,}{0}{,}{0}{,}{0}\right]{,}\left[{"H"}{,}{0.43580000}{,}{-0.14770000}{,}{-0.81880000}\right]\right]$ (2)

Retrieve the geometry of benzene

 >
 ${\mathrm{mol}}{≔}{"benzene"}$ (3)
 >
 ${\mathrm{geom}}{≔}\left[\left[{"C"}{,}{-1.21310000}{,}{-0.68840000}{,}{0}\right]{,}\left[{"C"}{,}{-1.20280000}{,}{0.70640000}{,}{0.00010000}\right]{,}\left[{"C"}{,}{-0.01030000}{,}{-1.39480000}{,}{0}\right]{,}\left[{"C"}{,}{0.01040000}{,}{1.39480000}{,}{-0.00010000}\right]{,}\left[{"C"}{,}{1.20280000}{,}{-0.70630000}{,}{0}\right]{,}\left[{"C"}{,}{1.21310000}{,}{0.68840000}{,}{0}\right]{,}\left[{"H"}{,}{-2.15770000}{,}{-1.22440000}{,}{0}\right]{,}\left[{"H"}{,}{-2.13930000}{,}{1.25640000}{,}{0.00010000}\right]{,}\left[{"H"}{,}{-0.01840000}{,}{-2.48090000}{,}{-0.00010000}\right]{,}\left[{"H"}{,}{0.01840000}{,}{2.48080000}{,}{0}\right]{,}\left[{"H"}{,}{2.13940000}{,}{-1.25630000}{,}{0.00010000}\right]{,}\left[{"H"}{,}{2.15770000}{,}{1.22450000}{,}{0}\right]\right]$ (4)

Retrieve the geometry of aspirin

 >
 ${\mathrm{mol}}{≔}{"aspirin"}$ (5)
 >
 ${\mathrm{geom}}{≔}\left[\left[{"O"}{,}{1.23330000}{,}{0.55400000}{,}{0.77920000}\right]{,}\left[{"O"}{,}{-0.69520000}{,}{-2.71480000}{,}{-0.75020000}\right]{,}\left[{"O"}{,}{0.79580000}{,}{-2.18430000}{,}{0.86850000}\right]{,}\left[{"O"}{,}{1.78130000}{,}{0.81050000}{,}{-1.48210000}\right]{,}\left[{"C"}{,}{-0.08570000}{,}{0.60880000}{,}{0.44030000}\right]{,}\left[{"C"}{,}{-0.79270000}{,}{-0.55150000}{,}{0.12440000}\right]{,}\left[{"C"}{,}{-0.72880000}{,}{1.84640000}{,}{0.41330000}\right]{,}\left[{"C"}{,}{-2.14260000}{,}{-0.47410000}{,}{-0.21840000}\right]{,}\left[{"C"}{,}{-2.07870000}{,}{1.92380000}{,}{0.07060000}\right]{,}\left[{"C"}{,}{-2.78550000}{,}{0.76360000}{,}{-0.24530000}\right]{,}\left[{"C"}{,}{-0.14090000}{,}{-1.85360000}{,}{0.14770000}\right]{,}\left[{"C"}{,}{2.10940000}{,}{0.67150000}{,}{-0.31130000}\right]{,}\left[{"C"}{,}{3.53050000}{,}{0.59960000}{,}{0.16350000}\right]{,}\left[{"H"}{,}{-0.18510000}{,}{2.75450000}{,}{0.65930000}\right]{,}\left[{"H"}{,}{-2.72470000}{,}{-1.36050000}{,}{-0.45640000}\right]{,}\left[{"H"}{,}{-2.57970000}{,}{2.88720000}{,}{0.05060000}\right]{,}\left[{"H"}{,}{-3.83740000}{,}{0.82380000}{,}{-0.50900000}\right]{,}\left[{"H"}{,}{3.72900000}{,}{1.41840000}{,}{0.85930000}\right]{,}\left[{"H"}{,}{4.20450000}{,}{0.69690000}{,}{-0.69240000}\right]{,}\left[{"H"}{,}{3.71050000}{,}{-0.36590000}{,}{0.64260000}\right]{,}\left[{"H"}{,}{-0.25550000}{,}{-3.59160000}{,}{-0.73370000}\right]\right]$ (6)

Use SMILES to retrieve the geometry of glucose

 >
 ${\mathrm{geom}}{≔}\left[\left[{"O"}{,}{-0.66790000}{,}{1.15870000}{,}{0.25700000}\right]{,}\left[{"O"}{,}{-0.88700000}{,}{-2.44830000}{,}{-0.33880000}\right]{,}\left[{"O"}{,}{1.86230000}{,}{-2.06930000}{,}{0.46960000}\right]{,}\left[{"O"}{,}{2.86090000}{,}{0.54140000}{,}{-0.46190000}\right]{,}\left[{"O"}{,}{1.12220000}{,}{2.65520000}{,}{0.25740000}\right]{,}\left[{"O"}{,}{-3.37420000}{,}{0.97170000}{,}{-0.18650000}\right]{,}\left[{"C"}{,}{-0.37270000}{,}{-1.24700000}{,}{0.23000000}\right]{,}\left[{"C"}{,}{1.08560000}{,}{-1.07090000}{,}{-0.19400000}\right]{,}\left[{"C"}{,}{-1.22110000}{,}{-0.06210000}{,}{-0.23750000}\right]{,}\left[{"C"}{,}{1.60820000}{,}{0.31510000}{,}{0.18390000}\right]{,}\left[{"C"}{,}{0.63880000}{,}{1.41320000}{,}{-0.25340000}\right]{,}\left[{"C"}{,}{-2.65500000}{,}{-0.15770000}{,}{0.27400000}\right]{,}\left[{"H"}{,}{-0.42480000}{,}{-1.35220000}{,}{1.32060000}\right]{,}\left[{"H"}{,}{1.20660000}{,}{-1.24870000}{,}{-1.26970000}\right]{,}\left[{"H"}{,}{-1.25480000}{,}{-0.00980000}{,}{-1.33430000}\right]{,}\left[{"H"}{,}{1.79520000}{,}{0.35980000}{,}{1.26360000}\right]{,}\left[{"H"}{,}{0.59670000}{,}{1.51410000}{,}{-1.34400000}\right]{,}\left[{"H"}{,}{-2.69160000}{,}{-0.15350000}{,}{1.36850000}\right]{,}\left[{"H"}{,}{-3.15640000}{,}{-1.05810000}{,}{-0.09220000}\right]{,}\left[{"H"}{,}{-0.85140000}{,}{-2.36150000}{,}{-1.30660000}\right]{,}\left[{"H"}{,}{1.49730000}{,}{-2.93560000}{,}{0.22000000}\right]{,}\left[{"H"}{,}{2.71650000}{,}{0.49890000}{,}{-1.42270000}\right]{,}\left[{"H"}{,}{1.48760000}{,}{2.50330000}{,}{1.14480000}\right]{,}\left[{"H"}{,}{-2.91920000}{,}{1.76520000}{,}{0.14400000}\right]\right]$ (7)
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