I want to create input file of cardanol (C21H36O) and compute some properties in GAMESS software. The coordinates of C21H36O are required in the input file. I have tried to check in chemspider but no success.
Dear Radwan Alnajjar
Thanks for your help, I also succeeded to get it from chemspider.
Mr. Jacob,
Please find as attachment 3 conformers of cardanol as *.gjf files. In addition there is a figure with the FF optimized structures. Conformer (a)-1 appears the most stable. While (a)-2 has energy difference comparing with (a)-1 DE = 1 kcal.mol-1. Conformer (c) has energy difference comparing with (a)-2 DE = 0.02 kcal.mol-1.
Studying flexible molecules you should bear in mind that the initial state is weakly affected by the level of optimization. So there should be carried out preliminary conformational analysis like the shown data in order to select a representative set(s) of conformational situations. because of if you have an interest from crystalline state computations or by the solution ones the molecular geometry at the global minimum of PES frequently does not correspond to the real observable one due to effect of solute-solute or solute-solvent interactions in condense phases.
In this context the common boundary of DE = 0.5 kcal.mol-1 energy difference between conformers using computational analysis of an isolated molecule in gas-phase does not express so realistic the real conformations when complex flexible molecules are objects of analysis.
Simply speaking there are needed a larger set of computations in order to reproduce realistic the experimentally observed state in condense phases.
For conformational search there can be used Avogadro (free of charge program package, https://avogadro.cc/docs/optimizing-geometry/conformers/)
The *.gjf files you could process by Gabedit (free of charge, http://gabedit.sourceforge.net/). The latter program can be used to create Gamess' inp-files, using the coordinates in *.gjf files.
In addition the latter program package can be used to generate 3D inputs of molecular systems as well.
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