QuantumChemistry
MolecularGeometry
returns the geometry of a molecule
Calling Sequence
Parameters
Description
References Examples
MolecularGeometry(molecule)
molecule
-
string, integer; name of the molecule as a string, CID number as an integer, or SMILES formula (see below for format)
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
withQuantumChemistry:
Retrieve the geometry of hydrogen fluoride
mol≔ hydrogenfluoride;
mol≔hydrogenfluoride
geom≔ MolecularGeometrymol;
geom≔F,0,0,0,H,0.43580000,−0.14770000,−0.81880000
Retrieve the geometry of benzene
mol≔ benzene;
mol≔benzene
geom≔C,−1.21310000,−0.68840000,0,C,−1.20280000,0.70640000,0.00010000,C,−0.01030000,−1.39480000,0,C,0.01040000,1.39480000,−0.00010000,C,1.20280000,−0.70630000,0,C,1.21310000,0.68840000,0,H,−2.15770000,−1.22440000,0,H,−2.13930000,1.25640000,0.00010000,H,−0.01840000,−2.48090000,−0.00010000,H,0.01840000,2.48080000,0,H,2.13940000,−1.25630000,0.00010000,H,2.15770000,1.22450000,0
Retrieve the geometry of aspirin
mol≔ aspirin;
mol≔aspirin
geom≔O,1.23330000,0.55400000,0.77920000,O,−0.69520000,−2.71480000,−0.75020000,O,0.79580000,−2.18430000,0.86850000,O,1.78130000,0.81050000,−1.48210000,C,−0.08570000,0.60880000,0.44030000,C,−0.79270000,−0.55150000,0.12440000,C,−0.72880000,1.84640000,0.41330000,C,−2.14260000,−0.47410000,−0.21840000,C,−2.07870000,1.92380000,0.07060000,C,−2.78550000,0.76360000,−0.24530000,C,−0.14090000,−1.85360000,0.14770000,C,2.10940000,0.67150000,−0.31130000,C,3.53050000,0.59960000,0.16350000,H,−0.18510000,2.75450000,0.65930000,H,−2.72470000,−1.36050000,−0.45640000,H,−2.57970000,2.88720000,0.05060000,H,−3.83740000,0.82380000,−0.50900000,H,3.72900000,1.41840000,0.85930000,H,4.20450000,0.69690000,−0.69240000,H,3.71050000,−0.36590000,0.64260000,H,−0.25550000,−3.59160000,−0.73370000
Use SMILES to retrieve the geometry of glucose
geom ≔ MolecularGeometrysmiles=OC[C@@H](O1)[C@@H](O)[C@H](O)[C@@H](O)[C@H](O)1;
geom≔O,−0.66790000,1.15870000,0.25700000,O,−0.88700000,−2.44830000,−0.33880000,O,1.86230000,−2.06930000,0.46960000,O,2.86090000,0.54140000,−0.46190000,O,1.12220000,2.65520000,0.25740000,O,−3.37420000,0.97170000,−0.18650000,C,−0.37270000,−1.24700000,0.23000000,C,1.08560000,−1.07090000,−0.19400000,C,−1.22110000,−0.06210000,−0.23750000,C,1.60820000,0.31510000,0.18390000,C,0.63880000,1.41320000,−0.25340000,C,−2.65500000,−0.15770000,0.27400000,H,−0.42480000,−1.35220000,1.32060000,H,1.20660000,−1.24870000,−1.26970000,H,−1.25480000,−0.00980000,−1.33430000,H,1.79520000,0.35980000,1.26360000,H,0.59670000,1.51410000,−1.34400000,H,−2.69160000,−0.15350000,1.36850000,H,−3.15640000,−1.05810000,−0.09220000,H,−0.85140000,−2.36150000,−1.30660000,H,1.49730000,−2.93560000,0.22000000,H,2.71650000,0.49890000,−1.42270000,H,1.48760000,2.50330000,1.14480000,H,−2.91920000,1.76520000,0.14400000
See Also
MolecularData
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