Ceilidh ... Re^4: Binding Energies for Receptor Ligand Systems

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Re^4: Binding Energies for Receptor Ligand Systems

Hello Solntsev Pasha:

Thank you for the reference and recommendation. I do have structures optimized with hybrid DFT method, also in good agreement with X-Ray crystal structures (MP2 optimization would be prohibitively expensive in my case). I should be able to run single point energy calculations at MP2 level with large basis set (like the 6-311++(d,p) you indicated for your run). I did not see the input and output file sample for the Hessian job run that should allow me to make the zero point vibrational energy (ZPVE) corrections.

Can you post some sample input and output files for the hessian job runs that will do this and any methodology if possible? What scaling factor did you use for these MP2 job runs with the large basis sets on the vibrational frequencies to calculate the ZPVE from? I believe that is just the simple job type is set to Hessian the factor will default to 1.0 per the GAMESS-US input.doc guide (reproduced below).

Thanks again for any help.

SCLFAC = scale factor for vibrational frequencies, used in calculating the zero point vibrational energy. Some workers correct for the usual overestimate in SCF frequencies by a factor 0.89. �ZPE or other methods might employ other factors, see A.P.Scott, L.Radom �J.Phys.Chem. �100, 16502-16513 (1996). The output always prints unscaled frequencies, so this value is used only during the thermochemical analysis. (Default is 1.0)

I found an example (using a much lower level of theory) that I thought might be germane posted at:

http://www.usc.es/congresos/ecsoc/7/papers/C007/C007.htm http://www.usc.es/congresos/ecsoc/7/papers/C007/C007.htm http://www.usc.es/congresos/ecsoc/7/papers/C007/C007.htm http://www.usc.es/congresos/ecsoc/7/papers/C007/C007.htm

The portion that describes the ZPVE correction is in a footnote:

Zero-point vibrational energy (ZPVE) corrections were calculated from harmonic vibrational frequencies determined at the RHF 6-31G(d) level and scaled by a factor of 1.00 in accord with known overestimates at this level. DeltaH(STD) =D(E + ZPVE) + CpT and DeltaG(STD) = DeltaH(STD) +T*DeltaS(STD). are the relative gas-phase enthalpy and free energy, respectively.

Best Regards,

Thomas Patko

On Wed Dec 17 '08 10:16am, Solntsev Pasha wrote
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>I also performed computation of binding energy for simple model. If you have complex A***B with very week binding energy (few kcal/mol), then firstly you should make geometry optimization of complex AB. I used MP2 method at 6-311++(d,p) for system which include C,H,N elements only. Optimized geometry was with full agreement to x-ray analysis. In some cases DFT method excepted too. Then you should performed geometry optimization of moieties A and B.
> E_bind = E(A***B) - (E(A) + E(B))

>To get true binding energy you should make BSSE correction (see http://classic.chem.msu.su/cgi-bin/ceilidh.exe/gran/gamess/forum/?C358d654d7eOC-6535-0-00.htm http://classic.chem.msu.su/cgi-bin/ceilidh.exe/gran/gamess/forum/?C358d654d7eOC-6535-0-00.htm http://classic.chem.msu.su/cgi-bin/ceilidh.exe/gran/gamess/forum/?C358d654d7eOC-6535-0-00.htm http://classic.chem.msu.su/cgi-bin/ceilidh.exe/gran/gamess/forum/?C358d654d7eOC-6535-0-00.htm http://classic.chem.msu.su/cgi-bin/ceilidh.exe/gran/gamess/forum/?C358d654d7eOC-6535-0-00.htm http://classic.chem.msu.su/cgi-bin/ceilidh.exe/gran/gamess/forum/?C358d654d7eOC-6535-0-00.htm http://classic.chem.msu.su/cgi-bin/ceilidh.exe/gran/gamess/forum/?C358d654d7eOC-6535-0-00.htm http://classic.chem.msu.su/cgi-bin/ceilidh.exe/gran/gamess/forum/?C358d654d7eOC-6535-0-00.htm) �
>and zero point energy (see $HESSIAN input and read carefully output)

>Also you can use google(or other) to get answers for general question.

[ This message was edited on Wed Dec 17 '08 at 5:13pm by the author ]

Wed Dec 17 '08 5:13pm

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