I have found many organic molecule databases, such as PubChem or chEMBL. But they don't provide the atomic coordinates of each atom on the structure. I'm especially interested in organic molecules that contain silicon. Where can I find these atomic coordinates?
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asked Dec 13, 2021 at 18:34
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1$\begingroup$ You have to look carefully. For example, in chEMBL, in the Representations section, you have the option to download the structure in SDF format. $\endgroup$– Camps ♦Dec 13, 2021 at 19:09
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$\begingroup$ Thanks, don't know why I didn't see them. $\endgroup$– Carlos Andrés del ValleDec 14, 2021 at 3:04
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1 Answer
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There are a few sites where you can find geometries, for example
- PubChem https://pubchem.ncbi.nlm.nih.gov/
- CCCBDB: Computational Chemistry Comparison and Benchmark Database https://cccbdb.nist.gov/geom1x.asp
- ChemSpider http://www.chemspider.com/
- NIST Chemistry WebBook https://webbook.nist.gov/chemistry/
- Public Computational Chemistry Database http://pccdb.org/
The problem with the database structures is that they are often of poor quality: the coordinates are typically optimized at B3LYP/6-31G* level of theory, and I'm not sure whether they correspond to the lowest-lying conformation.
You didn't say what purpose you have in mind for the geometries, and how large molecules you are interested in. My general advice is to try to find a general database, and extract the kinds of molecules you are interested in. For instance, the tmQM transition metal dataset J. Chem. Inf. Model. 2020, 60, 12, 6135 appears to have also molecules with silicon atoms in it.
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$\begingroup$ Thanks for your answer. Very useful. I want to do DFT calculations on the molecules. Iḿ not sure yet how big I want the molecules to be. But I want an initial structure in which I can relax the coordinates and then compare My results with some literature results. $\endgroup$ Dec 13, 2021 at 23:47
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2$\begingroup$ @CarlosAndrésdelValle you can use a GUI like Avogadro or IQmol to draw the molecules you want, then use something like xtb to perform geometry optimization and conformational sampling, and then do the DFT calculations to refine the geometry. We have some examples in our preprint at chemrxiv.org/engage/chemrxiv/article-details/… $\endgroup$ Dec 14, 2021 at 0:07
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$\begingroup$ Yeah, thanks. I dint consider that option. But sometimes I work whit molecules with more than 100 atoms. There are few occasions where I can draw the molecule, so I dint know that trick. that's the main reason I was seeking coordinate files. $\endgroup$ Dec 14, 2021 at 3:03
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