Comments for Dr. Joaquin Barroso's Blog

Comment on Leave a question! (new*) by vasanth.v

vasanth.v — Fri, 24 Feb 2012 06:21:50 +0000

respected sir
i want to study the solvent effects on my molecule. For this i used syntax

#t scf=maxcycles=1000 b3lyp/6-311+g scrf=(cpcm,solvent=nitromethane,read) freq=raman

but 1301.exe is stopped working message is being displayed after few seconds?

pl help in this regard

Comment on Analyzing Natural Bond Orbitals (NBO) results from Gaussian ’03 & ’09 by steve

steve — Fri, 24 Feb 2012 00:12:42 +0000

Great blog!
Quick question. We are trying to determine the relative interaction with a protein and a inhibitor. We have crystal structure data (from a .pdb) for the protein and are attempting to put different inhibitors in the pocket (which we assume we know where it is). We have optimized ONIOM calculations for several inhibitors and now want to look at NBO’s to distinguish what interactions are important.

However when i run a NBO with the following (obtained from your site, many thanks!)
#P opt rhf/6-31G(d,p) pop=(full,nboread) gfoldprint geom=connectivity

stuff
blank iine
$NBO PLOT $END

i am seeing the structure of our cut out piece of protein and inhibitor move with the different cycles. This seems alarming to me as we spent much time trying to get their optimal structure already. Is this the correct way to go about gleaming interactions between a protein and a inhibitor? And should i be worried about the movement of the molecules?

Comment on How to calculate Fukui indices by Abdel-Illah Djelloul Smir

Abdel-Illah Djelloul Smir — Thu, 23 Feb 2012 16:49:06 +0000

Dear Professor, I ask you a stone pertmet information about the calculation of indices fukui. In fact, for the molecule H2C = C (CN) (Morpholyno), I try to calculate indices of fukui two doubly bonded carbon. I, unwanted DFT/B3LYP/6-31G the *. I managed easily optimize the neutral molecule and quite difficult to negatively charged molecule. However, I can not optimize the positively charged molecule!
The question I ask the technical point, how to use the optimization of the neutral molecule to optimize the positively charged molecule.
Thank you for your help

Comment on Analyzing Natural Bond Orbitals (NBO) results from Gaussian ’03 & ’09 by sam john

sam john — Thu, 23 Feb 2012 07:39:06 +0000

Respected Sir

Natural Bond Orbitals (Summary) consist numerous values. From which how we interpret the calculation results. Sir any common methods is used for sorting these results.

Senior research fellow
Dept of chemistry
University of calicut

Comment on Green Chemistry and sustainable development by gautam18

gautam18 — Thu, 23 Feb 2012 06:14:32 +0000

Dear sir ,
i have a problem with the calculation of excited state optimization.For trial i have done this with benzene molecule and worked out well. But for my molecule “6-anilinopurine”, it is ending with error notification such as “transformation cannot fit into max disk” and some error via 1104.exe. Kindly help me to solve this.Thank you sir.

Comment on Leave a question! (new*) by Rajesh

Rajesh — Sun, 19 Feb 2012 09:05:04 +0000

Hi,

Recently I have perfomed a NBO analyis on metal-alkene complex. I have found that the stablization energy (E2) given by the second order pertubation analysis on donor-acceptor interactions is very high (ranging from 30-50 kcal/mol different alkene complexes). .I don’t think I can take this value in a quantitave manner). The total binding energy for those metal-alekene complexes are ranges from 15-21 kcal/mol..Can u pls explain to me this discrepancies in these values?

Comment on Leave a question! (new*) by joaquinbarroso

joaquinbarroso — Fri, 17 Feb 2012 15:13:45 +0000

In this blog there is a post about the use of the GEN keyword. Try searching it with the search field at the left side of the page

Comment on Leave a question! (new*) by Bijan Mondal

Bijan Mondal — Fri, 17 Feb 2012 07:35:38 +0000

Dear Brady,

Please share how you solve your problems regarding gen keyword and EMSL basis set, and how you assigned uv-vis peaks to their natural orbital exited transition in a TD calculation?

Many thanks

With best regards,
Bijan Mondal

Comment on Rigid and Relaxed Potential Energy Surface Scans (PES Scan) in Gaussian 03 and Gaussian 09 by joaquinbarroso

joaquinbarroso — Fri, 17 Feb 2012 06:14:50 +0000

Sorry, Yali. You have only one little mistake in that email: It is barroso with two ‘o’s

I’m waiting for your files

Comment on Research by joaquinbarroso

joaquinbarroso — Fri, 17 Feb 2012 06:13:10 +0000

Glad I could help!