From chemistry-request@ccl.net Mon Jul 22 14:57:52 1991 Date: Mon, 22 Jul 91 14:41 EDT From: "Scott Le Grand" Subject: Conformational Entropy Summary To: chemistry@ccl.net Status: R Here is a repost of my original question about conformational entropy and the various replies which described methods of estimating it that I received. Thanks for the help everyone! Scott Date: Tue, 25 Jun 91 00:56 EDT From: "Scott Le Grand" Subject: Conformational Entropy To: chemistry@ccl.net Sender: chemistry-request@ccl.net Errors-To: owner-chemistry@ccl.net Precedence: bulk Is there any way to crudely estimate the conformational entropy of a particular conformation of a molecule that does not involve the O(n"3) matrix inversion of the Hessian matrix of the potential energy function? I'm unfortunately betting that there isn't... Scott Le Grand Date: Tue, 25 Jun 1991 05:42:35 PDT Sender: Sundar_Sundararajan.XRCC@xerox.com From: sundar.XRCC@xerox.com Subject: Blank Mail Note To: sml108@psuvm.psu.edu Reply-to: "sundar.xrcc-ns@xerox.com".XRCC@xerox.com Message-ID: <"25-Jun-91 8:42:28".*.Sundar_Sundararajan.XRCC@Xerox.com> Dear Scott, As for the conformational entropy, in the case of polymers, it is often calculated with the energy and the partition function. See for example, P.R. Sundararajan, Macromolecules, 23, 2600 (1990) Regards Sundar Date: Tue, 25 Jun 91 10:57:31 -0500 From: "Richard A. Caldwell" To: SML108%PSUVM.PSU.EDU@vm.utdallas.edu Subject: Re: Conformational Entropy how crude is crude? The Benson group equivalent technique (Benson, S. W., "Thermochemical Kinetics," 2nd Edition, John WIley & Sons, N. Y., 1976) provides a CNQM (figure it out!) technique which gives heats of formation to +/- 1 kcal/mol in many cases and also provides a way to estimate standard entropies of formation. I ahve no personal experience with the latter but expect it to be comparably good. It isn't generally used for isolated conformations but seems to me adaptable with a little ingenuity. Dick Caldwell 09:45:02 EDT Date: Wed, 26 Jun 91 09:45:02 EDT From: jacque@isadora.albany.edu (Jacque Fetrow) Message-Id: <9106261345.AA24623@isadora.albany.edu> To: sml108@psuvm.psu.edu Subject: entropy scott - i don't know anything about a matrix inversion of the hessian matrix, so this suggestion may not make any sense, but... couldn't you estimate the entropy of a residue using the good old equation S=k(lnW) where W is the number of ways of arranging the system. you can estimate W from a rotamer library--you know the possible allowed conformations. i don't know if this will work for what you want... Date: Thu, 27 Jun 91 08:05:22 -0400 Message-Id: <9106271205.AA05285@esds01.es.dupont.com> From: fredvc@esvax.DNET.dupont.com To: "sml108@psuvm.psu.edu"@ESDS01.DNET.dupont.com Cc: FREDVC@esds01.es.dupont.com Subject: Conformational entropy: part II Conformational entropy, as I understand it, is simply {sum over i} Xi*ln(Xi) where Xi is the mole fraction of the i-th conformation. This, in turn, is given by exp[-Ei/RT]/{sum over j} exp[-Ej/RT] where Ei is the (relative) energy of the i-th conformation. Is there something special in the realm of protein/peptide chemistry that I am missing??? Frederic A. Van-Catledge Office: (302) 695-1187 Scientific Computing Div. FAX: (302) 695-9658 Central Res. & Dev. Dept. The Du Pont Company P. O. Box 80320 Wilmington DE 19880-0320 Internet address: fredvc@esvax.dnet.dupont.com ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ NEW E-MAIL ADDRESS From chemistry-request@ccl.net Mon Jul 22 16:17:04 1991 Date: Mon, 22 Jul 91 16:00:52 EDT From: Shi Yi Yue To: chemistry@ccl.net Subject: Summary of Force Constant Calculations Status: R Hi, Here is a repost of my original question about force constant calculation and the various replies I received. Thanks for the help everyone! ! ! Hi, ! I will be very appreciated if someone could point out that ! there has been any approvements from Gaussian 80, 82, 86, 88 ! to Gaussian 90 for the calculation of the Force Constant. ! The reason for asking this question is that what I have in ! hand is Gaussian 80. But what I want to carry out is some bond ! constants from the combination of {C, N, O}. I hope Gaussian ! 80 is not too old for this job. ! By the way, I think STO-3G is OK for this calculation ! because of the size of the molecules I have to calculate. ! Any comments, any suggestions? ! Thank you in advance! ! --------------------------------------------------------------------- >From rbw@msc.edu Fri May 10 21:46:05 1991 You might wish to read sections 6.3.1 through 6.3.10 in the book Ab Initio Molecular Theory where 3-21G basis sets are recommended. Richard Walsh Minnesota Supercomputer Center -------------------------------------------------------------------- >From cpaulse@magnus.acs.ohio-state.edu Fri May 10 22:27:19 1991 For hartree fock calculations, gaussian 82 and 86, 88, and 90 most definitely use the method of analytic second derivatives for force constant evaluation. As for gaussian 80, I'm not sure. You should be able to check the documentation quite easily in order to find this out. As for improvements, other than a more efficient algorithm found in gaussian 88-up for evaluation of second derivative integrals, there should be no difference in the numbers you obtain using any of the newer programs, provided the calculation is analytic. Hope this helps. Chris ------------------------------------------------------------------- >From oles@ulrik.uio.no Sat May 11 08:57:21 1991 You suggest: > By the way, I think STO-3G is OK for this calculation >because of the size of the molecules I have to calculate. > Any comments, any suggestions? Indeed. Bond constants for [C,N,O] containing molecules will probably be better modeled by a modern semiempiric method such as AM1. Minimal basis Hartree-Fock calculations cost more and will probably give you less. ------------------------------------------------------------------ >From ryanmd%phvax.dnet@smithkline.com Sat May 11 14:12:33 1991 I concur with the recent posting about sto3g, but several additional cautions are needed. Semi-empirical calculations can in some cases get the optimized geometries quite wrong in torsion angles, and therefore you need to check for this in the literature. If you need force constants for force field calculations you also need to worry about values that will fit with the other terms of the field. I do not feel that sto-3g will do this well at all, in fact 6-31G** would be more suitable, and then not even force constants may be correct but rather a set of discrete points along the bond stretch you are interested in could be better. You will also have to deal with the transformation from normal modes (what a frequency calculation will give you) to internal coordinate representation if you do not carry out many calculations along the bond stretch desired. Normal modes of vibration are *not* the same as internal coordinates. If you need this for a force field you may also have to worry about balancing non-bonded terms and other angle or coupling terms to your new ones. Charges in particular can be troublesome, and you should use atom charges fitted to a potential field using at least a split-valence basis set. Finally, G80 is a dinosaur. G90 will probably be 10 to 50 times faster and has features that will permit you to calculate much larger molecules as well. I have found G90 to be ~3-5x G88, which was another 3-10x G86 which was in turn faster than predecessors. There are also alternatives, I would recommend Spartan, faster and tied to the graphical interface, very nice. Call Wavefunction at 714-955-2120. There is much to be considered if you hope to get numbers that won't lead you astray, I strongly suggest spending a large chunk of time in the literature. M. Dominic Ryan, Ph.D