From chemistry-request@www.ccl.net Thu Feb 25 07:05:02 1999 Received: from mail-b.bcc.ac.uk (mail-b.bcc.ac.uk [144.82.100.22]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id HAA28828 Thu, 25 Feb 1999 07:04:55 -0500 (EST) Received: from socrates-a.ucl.ac.uk by mail-b.bcc.ac.uk with SMTP (XT-PP); Thu, 25 Feb 1999 11:49:02 +0000 From: uccatvm Message-Id: <14876.199902251149@socrates-a.ucl.ac.uk> Subject: Re: BSSE in calc. of activation energies? To: chemistry@www.ccl.net (CCL) Date: Thu, 25 Feb 1999 11:49:01 +0000 (GMT) X-Mailer: ELM [version 2.4 PL25] MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Dear Kalju, First of all, my apologies for the late reply. I think that your way to correct for BSSE is correct, assuming at least that BSSE is only important *between* (and not within) A and B, as it is in my ArHF example below. If you would calculate your energy difference simply as: E_act = E(TS,TS_basis_in_TS_geometry)-E(RC,RC_basis_in_RC_geometry) then you would not correct for BSSE at all! Assuming the BSSE within the monomers can be neglected, you can compare with a diatomic AB (like He2, for example). In this case, you also have to correct for BSSE at each individual point of the potential energy curve. Simply substracting two AB dimer energies does not produce a BSSE-free energy difference, since the uncorrected potential energy curve will be distorted. Also in this case, for each different interatomic distance the ghost orbitals are at different geometrical positions. As another example: For ArHF, which has 2 linear minima and a T-shaped TS, the correct way to compute the stationary points would be, in my opinion, to substract from the dimer energy the Ar and HF energies computed in the ArHF basis set, and you would do this for the 2 different minima (Ar...HF and Ar...FH), as well as for the TS. The barrier height is then the difference between the minimum and TS interaction energy. This of course assumes that the BSSE within HF can be neglected. For this example, I can reference 2 papers (I must confess I am on the author list of both): JCP 107, 2451 (1997) and Adv. Quant. Chem. 31, 105, 1999. You already mentioned the review article by van Duijneveldt et al. I hope this answers your question, Best regards, Tanja -- ==================================================================== Tanja van Mourik phone University College London work: +44 (0)171-504-4665 Christopher Ingold Laboratories home: +44 (0)1895-259-312 20 Gordon Street e-mail London WC1H 0AJ work: T.vanMourik@ucl.ac.uk United Kingdom home: tanja@netcomuk.co.uk ==================================================================== > Dear CCLers, > > I realize there has been some controversy about basis set > superposition error (BSSE), and that the current consensus > favors the view that full counterpoise procedure (CP) of > Boys and Bernardini is a good way to correct for BSSE. > (e.g. van Duijneveldt et. al. in Chem. Rev, 1994, 94, 1873-1885) > > My question concerns application of BSSE correction via CP > to bimolecular reactions. Let's take gas phase SN2 > displacement as an example. Here we have a two reactants, A and B, > forming first a bimolecular "reactants complex" (RC), followed by > transition state (TS): > A + B -> (A...B)[RC] -> A-B[TS] > The activation barrier can be defined as an energy difference > between TS and RC. What is the correct way to calculate this > energy difference? (Assuming Born-Oppenheimer approximation, > and dealing with size-consistent methods, e.g. HF level of theory) > > My own answer would be: > If one accepts a view that energies of both RC and TS > (relative to isolated reactants) are affected by BSSE, > one should correct both according to the CP scheme, and now: > E_act = E(TS,TS_basis_in_TS_geometry)-E(RC,RC_basis_in_RC_geometry)- > E(A,TS_basis_in_TS_geometry) -E(B,TS_basis_in_TS_geometry)+ > E(A,RC_basis_in_RC_geometry) +E(B,RC_basis_in_RC_geometry) > > Obviously, the number of basis functions in TS_basis and RC_basis > is the same, but the geometrical position of ghost orbitals relative > to partner molecule are different in TS_geometry and RC_geometry. > So, the last four terms do not cancel out. > > This seems a right way to account for BSSE, but the above method > was quoted as "misinterpretation of the BSSE concept" by Dr. J. A. Sordo > in "Comment on "Ab initio investigation of internal rotation in the > ethylene-sulfur dioxide dimer"" (J. Chem. Phys., 106(14), 6204). > > Could somebody kindly explain me how do I misinterpret the BSSE > concept here? Or do we need to be concerned about BSSE when > calculating ab initio activation barriers? > > Thanks a lot, Kalju > > P.S. I will summarize your responses. > > P.S.2. Happy Valentine's Day! > > ****************************************************************** > Kalju Kahn kalju@bioorganic.ucsb.edu > Chemistry Department tel: (805)-893-7158 > University of California Santa Barbara > Santa Barbara, CA 93106 > ################################################################## > From chemistry-request@www.ccl.net Thu Feb 25 09:53:37 1999 Received: from foreman.ac.rwth-aachen.de (foreman.ac.RWTH-Aachen.DE [134.130.100.31]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id JAA03207 Thu, 25 Feb 1999 09:53:26 -0500 (EST) Received: (from landrum@localhost) by foreman.ac.rwth-aachen.de (AIX4.2/UCB 8.7/8.7) id PAA27910; Thu, 25 Feb 1999 15:53:03 +0100 (NFT) Date: Thu, 25 Feb 1999 15:53:03 +0100 (NFT) From: "Gregory A. Landrum" To: chemistry@www.ccl.net Subject: Re: CCL:Summary: AMD-K6/linux for G98 In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Normally I stay silent on these things, but this comment was just a bit too indicative of general "benchmark abuse". > For pinene using DFT/B3LYP with large basis sets, for >example, the machine i bought for $11,000 was faster than a Cray T3E-600 >with 4 processors and only 15% slower than a Cray T3E-1200 with 4 >processors, both running parallel Gaussian 94. (The G94 calculations were >done by Sosa and Frisch, so were probably pretty well optimized for the >machine, see last July 15 number of J. Comput. Chem. Sosa et al. Vol 19, >p. 1053). I haven't priced those machines but they must be >$100k. If you >want to benchmark against one of your own machines, Pulay would be happy >to do some calculations for you. The comparison here is *completely* invalid. If you want to compare the speed of machines, you must be running the same program. In this case, a highly-optimized DFT implementation (the one from Pulay) is being compared to an implementation which can charitably be called "not so great", this does not say a single thing about the relative speeds of the computers running those programs. Having Pulay do a benchmark for you would be altering two variables at the same time: (a) the hardware (b) the software it is impossible to decouple the effects of the two changes. One more time, for good measure: If you want reliable benchmarks of *hardware* performance, you must compare the same programs on the different hardware. -greg -- --------------------- Dr. Greg Landrum (landrum@foreman.ac.rwth-aachen.de) Institute of Inorganic Chemistry Aachen University of Technology Prof.-Pirlet-Str. 1, D-52074 Aachen, Germany Phone: 049-241-80-7004 Fax: 049-241-8888-288 From chemistry-request@www.ccl.net Thu Feb 25 12:07:00 1999 Received: from bgnet0.bgsu.edu (bgnet0.bgsu.edu [129.1.2.15]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id MAA07808 Thu, 25 Feb 1999 12:07:00 -0500 (EST) Received: from lzang (ppp-198-84.bgsu.edu [129.1.198.84]) by bgnet0.bgsu.edu (8.8.5/8.8.5) with SMTP id MAA32378 for ; Thu, 25 Feb 1999 12:06:59 -0500 (EST) Reply-To: From: "Xiaomei Yang" To: Subject: FW: Biological relevance of aluminium Date: Thu, 25 Feb 1999 12:09:45 -0500 Message-ID: <000201be60e1$a465ddc0$54c60181@lzang.bgsu.edu> MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook 8.5, Build 4.71.2173.0 Importance: Normal X-MimeOLE: Produced By Microsoft MimeOLE V4.72.3110.3 -----Original Message----- From: Xiaomei Yang [mailto:xiaomei_yang@usa.net] Sent: Wednesday, February 24, 1999 11:13 PM To: chaudash@aston.ac.uk Subject: RE: Biological relevance of aluminium Hi there, I happen to be reading a book titled, "metals in biological systems", 1992 by M. J. Kendrick, etal. that may give you some information about aluminum in biological systems (chap 12). There is reportedly an accumulation of Al in the brains of patients with several neurological disorders, like Alzheimer's disease, Parkinson's disease, dialysis dementia. You could get more information from the refs listed, for an example, Crapper, D. R.; Dalton, A. J.; Krishnan, S. S. Science 1973, 180, 511. Xiaomei From chemistry-request@www.ccl.net Fri Feb 26 06:40:32 1999 Received: from harfang.CC.UMontreal.CA (harfang.CC.UMontreal.CA [132.204.2.102]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id GAA15794 Fri, 26 Feb 1999 06:40:32 -0500 (EST) Received: from esi21.ESI.UMontreal.CA (esi21.ESI.UMontreal.CA [132.204.2.91]) by harfang.CC.UMontreal.CA (8.8.8/8.8.8) with ESMTP id GAA17291; Fri, 26 Feb 1999 06:40:34 -0500 (EST) Received: from localhost (proynov@localhost) by esi21.ESI.UMontreal.CA with SMTP id GAA26804 (8.8.7/IDA-1.6); Fri, 26 Feb 1999 06:40:33 -0500 (EST) X-Authentication-Warning: esi21.ESI.UMontreal.CA: proynov owned process doing -bs Date: Fri, 26 Feb 1999 06:40:29 -0500 (EST) From: Proynov Emil X-Sender: proynov@esi21.ESI.UMontreal.CA To: Keith Refson cc: chemistry@www.ccl.net Subject: Re: CCL:Comment on DFT & Hydrogen bonds In-Reply-To: <14037.22677.427440.751227@gargle.gargle.HOWL> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from QUOTED-PRINTABLE to 8bit by www.ccl.net id GAA15795 Dear Keith, On Thu, 25 Feb 1999, Keith Refson wrote: > > Is 0.14eV good or bad? The reason I ask will become apparent if you > read > > D. R. Hamman, Phys. Rev. B 55(16) R10157-10160 (1997) > > In this paper Hamman compares the sublimation energies of Ice with > various functionals. (Although his claimed experimental value is a bit > suspect at 0.58eV. I thought is was 0.491). > n the case of Hé2 dimer BP gives a dimerization energy of about 4.7 kcal/mol with a TZVP2 basis and a bit lower elergy with bases containing diffuse and pllarization functions. This matches well with recent experimental estimates of about 4.7 p.m. 0.3 kcal/mol. Ice is more hard example of course, and I agree that an error of about 0.14 eV (about 3 kcal/mol) sounds less encouraging... I personally have not tried to test various Exc on ice, this may be a very good idea by the way to do! Best wishes, Emil Proynov From chemistry-request@www.ccl.net Fri Feb 26 12:27:57 1999 Received: from MIT.EDU (PACIFIC-CARRIER-ANNEX.MIT.EDU [18.69.0.28]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id MAA18809 Fri, 26 Feb 1999 12:27:56 -0500 (EST) Received: from KFJ1-SGI.MIT.EDU by MIT.EDU with SMTP id AA29926; Fri, 26 Feb 99 12:28:33 EST Received: by kfj1-sgi.mit.edu (950413.SGI.8.6.12/4.7) id MAA10507; Fri, 26 Feb 1999 12:27:59 -0500 Message-Id: <199902261727.MAA10507@kfj1-sgi.mit.edu> To: chemistry@www.ccl.net Subject: HELP: G98 Freq job dies with segmentation fault Date: Fri, 26 Feb 1999 12:27:59 EST From: Vijay Gupta Hi ! I have a geometry optimization followed by a frequency job for a molecule which is close to linear. I am using Gaussian 98, Revision A.5 running on an HP workstation (HPUX 10.20). The job runs fine using G94. The same job using G98 optimizes the geometry but dies during the frequency calculations. I am using the internal redundant coordinates during geom opt. Since the geometry optimization proceeds without any problems, I assume that the geometry specification is not a problem. The frequency job calculates the frequencies and the partition functions and then mysteriously dies giving a "Segmentation Fault" error. The only difference I can see is that in G98 geom opt output, there are some extra angles which appear such as : A13 L(2,1,4,7,-1) 179.9891 estimate D2E/DX2 A14 L(2,1,4,7,-2) 180.0002 estimate D2E/DX2 The angle A14 get optimized to a value above 180 degrees and that might be causing the problem in the Frequency analysis. Does anybody know what the "L" stands for here? Has anybody else experienced similar problems? I sent an e-mail to Gaussian but have not received any reply. I will summarize all the replies for the list. Thanks Vijay Gupta ======================================================================== Vijay Gupta E-mail: vgupta@mit.edu Department of Chemical Engineering Massachusetts Institute of Technology Cambridge, MA 02139 ======================================================================== From chemistry-request@www.ccl.net Fri Feb 26 20:27:33 1999 Received: from hotmail.com (f96.hotmail.com [207.82.250.215]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id UAA24834 Fri, 26 Feb 1999 20:27:32 -0500 (EST) Received: (qmail 24241 invoked by uid 0); 27 Feb 1999 01:27:05 -0000 Message-ID: <19990227012705.24240.qmail@hotmail.com> Received: from 206.49.136.140 by www.hotmail.com with HTTP; Fri, 26 Feb 1999 17:27:04 PST X-Originating-IP: [206.49.136.140] From: "fernando betancur" To: CHEMISTRY@www.ccl.net Subject: Information about ... Date: Fri, 26 Feb 1999 17:27:04 PST Mime-Version: 1.0 Content-type: text/plain Srs: I need some information about the procces to make sodium bisulfite. The kinethics, the basic equipment and all your cant send me to my e-mail : betafernando@hotmail.com Thanks a lot ______________________________________________________ Get Your Private, Free Email at http://www.hotmail.com From chemistry-request@www.ccl.net Sat Feb 27 19:36:17 1999 Received: from alchemy.chem.utoronto.ca (alchemy.chem.utoronto.ca [142.150.224.224]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id TAA01013 Sat, 27 Feb 1999 19:36:16 -0500 (EST) Received: (from elewars@localhost) by alchemy.chem.utoronto.ca (8.9.3/8.9.3) id TAA25742 for chemistry@www.ccl.net; Sat, 27 Feb 1999 19:36:14 -0500 (EST) Date: Sat, 27 Feb 1999 19:36:14 -0500 (EST) From: "E. Lewars" Message-Id: <199902280036.TAA25742@alchemy.chem.utoronto.ca> To: chemistry@www.ccl.net Subject: IR INTENSITIES 1999 Feb 26 I have a question about calculating the relative intensities of IR vibrations. Let me say at the outset that my interest here is to *illustrate* in a simple way how intensities can be calc from the change in dipole moment accompanying the normal-mode vibration; I know there are sophisticated algorithms for calculating the intensity of IR bands. I just want to show how, in principle, one might get relative intensities in a conceptually simple way. The intensity of a normal-mode vibration is approximately I = k(dm/dq)**2 where k is a proportionality constant (we are interested in _relative_ intensities) m = dipole moment q = a geometric parameter like bond length Approximating the derivative as the ratio of finite increments enables us to readily calculate relative intensities for the single mode of diatomic molecules: I = k(delta m/delta q)**2 Thus for H-F and HCl, using HF/6-31G* calcs: H-F r(0.9109=r-equil), m = 1.9719 D; r(0.9209), m = 1.9897 I = k(0.0178/0.01)**2 = 3.17k H-Cl r(1.2662=r-equil), m = 1.5017 D; r(1.2762), m = 1.5081 I = k(0.0064/0.01)**2 = 0.41k Intensity ratio, I(HF)/I(HCl) = 3.17/0.41 = 7.7 A calc using Gaussian 98 gives an intensity ratio of 141.5/24.3 = 5.8 Fine. ------------- QUESTION: Suppose we have, say H2O, and want to calc the relative intensities of the asym and the sym stretching modes. In principle we can distort the geom a little (as for H-F and H-Cl, above) and calc the change in dipole moment, delta m. But what do we take as delta q when there is not just *one* simple geometric parameter like r=(H--X)? I suppose either q is composite, or the expression for I has several terms. O / \ H H Thanks E. Lewars ==================