I need to calculate 10 properties for 270 molecules using Gaussian 09. Could you please suggest me what is the best and shortest way to have the structure of 270 molecules (in the format .com or .xyz)?

Is there any website which collected all the molecular structures?

  • 5
    $\begingroup$ I'm confused. You want 270 random molecules? Or you have a list of 270 molecules that you'd like to run? (In which case, what format do you have the list?) $\endgroup$ – Geoff Hutchison Mar 17 '16 at 14:26
  • $\begingroup$ What keeps you from drawing or writing the initial geometries by yourself? $\endgroup$ – Klaus-Dieter Warzecha Mar 17 '16 at 14:42
  • $\begingroup$ @Geoff Hutchison: I have the list of 270 molecules. I found the .xyz for some of them but for most of them I did not find .xyz $\endgroup$ – Tohid Borhani Mar 17 '16 at 15:37
  • $\begingroup$ @Klaus Warzecha: As you know drawing 270 molecule is time consuming procedure and unfortunately I do not have enough time for that. I first want to find a faster way $\endgroup$ – Tohid Borhani Mar 17 '16 at 15:39

There are a few resources that can get you what you want, but you'll probably want to consider some level of scripting automation. A search for 270 molecules isn't enormous, but doing it by hand would still be tedious.

  • PubChem: Run by the NIH, it offers many types of searching, and 3D coordinates for most compounds.
  • ChemSpider: Run by the RSC, it allows searching by name and has 3D structures for many (if not most) compounds. I'm less sure on quality, since they don't clarify how they generate their 3D coordinates.
  • NIH Chemical Resolver: Run by the NIH as well, it converts between different representations, including name to 3D structure.

Each offers automation tools, including Python interfaces called PubChemPy, ChemSpiPy, and CIRpy.

My choice would probably be the chemical resolver, partly because the access is very simple to automate:

https://cactus.nci.nih.gov/chemical/structure/"structure identifier"/"representation"

So you'd set up a URL like: https://cactus.nci.nih.gov/chemical/structure/aspirin/sdf?get3d=true

The result will be in SD format, but it's easy to convert that to XYZ or Gaussian files with Open Babel.

  • $\begingroup$ Dear Geoff Hutchison. Thank you very much for your nice suggestions. I have another question: I found that the structure e.g. for Ethanol is different when I used the .xyz from two different resources. How we can find that the initial structure is correct? (I am new Gaussian user) $\endgroup$ – Tohid Borhani Mar 17 '16 at 16:51
  • $\begingroup$ Most likely both are correct. BTW, are you going to run geometry optimization on all 270 molecules? $\endgroup$ – Ivan Neretin Mar 17 '16 at 16:52
  • $\begingroup$ I need to calculate HOMO, LUMO, Ionization Potential, Heat of formation, Dipole Moment, Electronegativity, Total energy at 0 K, Entropy at 298 K for 270 molecules using DFT/B3LYP/6-31G(d,p) and then use these properties as descriptors in QSPR study. Which type of calculation is proper for that? $\endgroup$ – Tohid Borhani Mar 17 '16 at 16:55
  • $\begingroup$ Don't calculate the values you can get experimentally. $\endgroup$ – Mark Apr 8 '18 at 3:42

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