From chan@uni-muenster.de Thu May 15 03:43:17 1997 Received: from asterix.uni-muenster.de for chan@uni-muenster.de by www.ccl.net (8.8.3/950822.1) id DAA16706; Thu, 15 May 1997 03:09:31 -0400 (EDT) Received: from localhost (chan@localhost) by asterix.uni-muenster.de (8.7.5/8.7.5) with SMTP id JAA104316 for ; Thu, 15 May 1997 09:09:16 +0200 X-Authentication-Warning: asterix.uni-muenster.de: chan owned process doing -bs Date: Thu, 15 May 1997 09:09:16 +0200 (MES) From: "Jerry C.C. Chan" To: chemistry@www.ccl.net Subject: Summary: Chemical Softness by DFT In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCLers, Thanks are due to all who response to my questions concerning the chemical hardness. I am happy that many experienced CCLers did share with me their valuable expertise. Sincere thanks, Jerry > Last week I posted a question concerning the determination of > chemical hardness (or softness) of the metal centre of a TM complexes. > Maybe the way I asked the question was not specific enough, I just > received two mails asking for the summary. So I try to write down my > thinking explicitly and hope that someone in the net, who could not > tolerate the naiveness or even mistakes of my post, would kindly comment > on it. I will summarize. > > I want to determine the chemical hardness of the metal centre of a charged > TM complexes. The method that comes to my mind is to do a HF calculation > and get the MO spectrum. Based on the Koopmans' theorem the hardness of > the complexes would be (E_LUMO - E_HOMO)/2. > > Even my thinking is correct, HF calculation seems to be unreliable for TM > complexes and correlated methods are usually very expensive. Therefore > last time I enquired the possibility of using DFT methods as an > alternative although Koopman's theorem does not hold for KS orbitals. > > By the way, I have heard that Fukui function is somehow related to the > chemical hardness but I don't have the recipe. ++++++++++++++++++++++++++++++++ Stefan Fau Pascal HEBANT Xavier Assfeld Hogue, Pat (AZ76) R.G. Parr and W. Yang, "Density-Functional Theory of Atoms and Molecules" (Oxford University Press, 1989, New York). Ian Fleming, "Frontier Orbitals and Organic Chemical Reactions" "Hardness and softness in Density Functional Theory in Chemical Hardness", K.D. Sen Ed., Coll. Structure and Bonding 80, (Springer-Verlag, Berlin, 1993). R.G. Pearson: J.Am. Chem. Soc. 85, 3533 ('63) N.K. Ray, L. Samuels, R.G. Parr: J.Chem. Phys. 70, 3680 ('79) M.S. Gopinathan, M.A. Whitehead: Isr. J. Chem. 19, 209 ('80) J.P. Perdew, R.G. Parr, M. Levy, J.L. Balduz: Phys. Rev. Lett. 49, 1691 ('82) R.G. Parr, R.G. Pearson: J. Am. Chem. Soc 105, 7512 ('83) R.F. Nalewajski: J. Am. Chem. Soc. 106, 944 ('84) R.G. Parr, W. Yang: J. Am. Chem. Soc. 106, 4049 ('84) W. Yang, W.J. Mortier: J. Am. Chem. Soc. 108, 5708 ('86) R.G. Pearson: J. Chem. Ed. 64, 561 ('87) A.R. Orsky, M.A. Whitehead: Can. J. Chem. 65, 1970 ('87) M. Berkowitz, R.G. Parr: J. Chem. Phys. 88, 2554 ('88) R.G. Parr, P.K. Chattaraj: J. Am. Chem. Soc. 113, 1854 ('91) P.K. Chattaraj, H. Lee, R.G. Parr: J. Am. Chem. Soc. 113, 1855 ('91) D. Datta, S.N. Singh: JCS Dalton Trans. 1541, ('91) J. Cioslowski, S.T. Mixon: J. Am. Chem. Soc. 115, 1084 ('93) J. Cioslowski & B.B. Stefanov: J. Chem. Phys. 99, 5151 ('93) R.G. Pearson: Acc. Chem. Res. 26, 250 ('93) P.K. Chattaraj, P.v.R. Schleyer: J. Am. Chem. Soc. 116, 1067 ('94) F. Mendez, J.L. Gasquez: J. Am. Chem. Soc. 116, 9298 ('94) W. Kohn, A.D. Becke, R.G. Parr: J. Phys. Chem. 100, 12974 ('96) +++++++++++++++++++++++++++++++++++++++++ From: Liang Lou There is an equivalence in DFT calculations which is called Slater's transition state method. In this method, the EA and IP are approximated by the values of an halfly occupied orbital. For example, for IP, you put +0.5e on the molecule and run a full SCF. Then you check the eigenvalue for the one-particle state with an 0.5 occupation number. This gives a good estimate of the IP. For EA, charge the molecule with -0.5e. The formal explanation of this "transition state" method was given by Janet (coauthor of the book "calculation of electronic structure in metals"). It is roughly as follows. The total energy of an N-electron system in LDA can be written as E=sum[n_k * epsilon_k] + ..., where n_k is the occupation of the eigenstate k and epsilon_k is the corresponding eigenvalue. The eigenvalue of the one-particle state k is simply epsilon_k=dE/dn_k. This is an equivalence of the koopmans' theorem in LDA. The Slater's transition state is a "finite-difference" approximation to the infinitesimal d(n_k). The error of this method, from my experience, is in the range between 0.1-0.3eV, approximately the same as from a small-delta SCF calculation (e.g., dE(EA) = E(N) - E(N+1)). +++++++++++++++++++++++ From: Rene Fournier > although Koopman's theorem does not hold for KS orbitals. I would not worry about that. First, Koopman's theorem is not so great anyway. It equates two theoretical constructs: the energy difference between the GS and a HYPOTHETICAL excited state with orbitals identical to those of the GS on one hand, and the difference between the HOMO and LUMO HF orbital energies on the other. Actually, I would say that Kohn-Sham DFT is THE IDEAL theory for your problem. It has two useful theorems: (a) the negative of the KS HOMO energy is equal to the TRUE ionization energy of the system (relates a theoretical construct to an observable). CAVEAT: this theorem holds only in the limit of an "exact" XC potential. [ But how could one expect exact calculation of observables in any approximate theory anyway? At least, in KS-DFT, the framework for exact calculations of this kind is there. ] (b) the derivative of the KS-DFT energy w.r.t. number of electrons, whether the XC is exact or approximate, is precisely equal to the energy of the highest partly occupied orbital (Janak's theorem) The hardness is most conveniently defined as being half the second derivative of the energy w.r.t. number of electrons; the finite difference approximation to that is (I-A)/2; and that in turn can be approximated as (E_LUMO - E_HOMO)/2 . Thanks to Janak's theorem, you can get some derivatives (dE/dN) simply by looking up orbital energies. There is an excellent discussion of hardness and Fukui function in Parr and Yang's book "Density-Functional Theory of Atoms and Molecules" (Oxford University Press, 1989, New York). BTW, the Fukui function is the derivative of the electron density at point r w.r.t. total number of electrons, N. If the sum of nuclei charges is M, then: f(r) is roughly the density associated with the LUMO for N = M+delta f(r) is roughly the density associated with the HOMO for N = M-delta f(r) is roughly the average of the above two for N=M ++++++++++++++++++++++++++++++++++++ From: "N. Sukumar" Hardness in DFT is given by the partial second derivative of the energy functional with respect to the electron density, at constant external potential, ie. (d^{2}E/d\{rho}^2)_v See Parr & Yang's book and the references therein for details, including relations to the Fukui functional (which is the mixed partial derivative of the energy functional with respect to density annd external potential) : Robert G. Parr & Weitao Yang, "Density Functional Theory of Atoms and Molecules" (Oxford University Press, New York, 1989) Jerzy Cioslowski in Florida has done some ab initio (Hartree-Fock level) calculations (on small molecules) using the DFT definition of hardness, without relying on the Koopman's theorem. Some references are : J. Cioslowski & S. T. Mixon, J. Amer. Chem. Soc. 115, 1084 (1993) J. Cioslowski & B. B. Stefanov, J. Chem. Phys. 99, 5151 (1993) see also references therein (since the above two papers are primarily concerned with BOND hardness). +++++++++++++++++++++++++++++++ From: Oliver Warschkow You have asked about hardness/softness calculations. I dont have any experiences in such calculations myself, but there is a recent review by Kohn, Becke and Parr (J.Phys.Chem (1996), 100, 12974) where hardness,softness and fukui-functions in the framework of DFT are discussed. The explicit expression given in there (eq.3.4) is hardness = (del mu / del N) at const. V where mu is the chemical potential (or fermi leve Ef) of the system. So, it probably boils down to running a two DFT calculations on the system with slightly (that is fractionally) different number of electrons and to see how the HOMO orbital energy (or Ef if you use a Fermi-Dirac orbital occupation scheme) changes. Well, that would be my guess how to do it. You are right in that you are probably better off in doing DFT instead of HF on TM systems and according to the review, concepts like hardness,softness etc are quite natural to DFT. +++++++++++++++++++++++++++++ From: "Jack A. Smith" I think a good reference for you would be "Density Functional Theory of Atoms and Molecules" by Parr and Yang (Oxford Press, 1989), particularly chapters 4 & 5. You'll see that the KS orbitals of DFT are actually more directly related to the chemical potential, hardness, Fukui functions, etc. than canonical HF orbitals [Grand Canonical HF, on the other hand, can be viewed as a natural extension of HF to DFT which includes proper exchange (see J. Linderberg, IJQC 12:supp 1, p267) but no extra correlation, and whose orbitals allow similar interpretation as do KS orbitals]. -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= From: Liang Lou > Thank you very much for your reply. Since I always work on closed shell > system, I would like to know if I understand your suggestion correctly: > > If I have a +3 TM complexes, in G94 I can simply change the the charge > from +3 to +3.5 and the multiplicity from 1 to 2 and then do a DFT > calculation. No special keywords are needed. Repeat the calculation > with the charge of +2.5. I may have difficulties to get the SCF > convergence for these +3.5 and +2.5 systems but using vshift should be > able to solve it (though I don't have any experience on it). As far as I know, Gaussian is not particularly strong for metals, especially in the sense of the efficiency of basis sets. Other DFT program packages could do better (with either highly optimized Gaussian bases or Slater type bases, or numerical bases). I guess the level shifting would result in artificial values for orbital energy near the separation of HOMO and LUMO. When calculating electron removal energies, IP and EA, the system always changes spin multiplicity and there are always associated uncertainties. Usually, the orbital energy values do not change in the first few decimal places after he total energy has converged to under, say, 10**(-4). Therefore, higher convergence of total energy will not affect comparing with experiment. From JARP@WCHUWR.CHEM.UNI.WROC.PL Thu May 15 05:43:17 1997 Received: from indigo2 for JARP@WCHUWR.CHEM.UNI.WROC.PL by www.ccl.net (8.8.3/950822.1) id FAA17385; Thu, 15 May 1997 05:03:06 -0400 (EDT) Received: from wchuwr.chem.uni.wroc.pl by indigo2 via SMTP (940816.SGI.8.6.9/930416.SGI) for id LAA02172; Thu, 15 May 1997 11:01:08 GMT Received: from ICHUWR/SMTPQueue by wchuwr.chem.uni.wroc.pl (Mercury 1.11); Thu, 15 May 97 11:03:18 +0100 Received: from Mailqueue by ICHUWR (Mercury 1.11); Thu, 15 May 97 11:02:42 +0100 From: "Jaroslaw Panek" Organization: University of Wroclaw (Chemistry) To: chemistry@www.ccl.net Date: Thu, 15 May 1997 11:02:41 GMT+1 Subject: CCL: First Brillouin zone ? X-pmrqc: 1 Priority: normal X-mailer: Pegasus Mail v3.1 (R1) Message-ID: <4D0EEB4508@wchuwr.chem.uni.wroc.pl> Help me, help me please... I would like to know how looks FIRST BRILLOUIN ZONE for TETRAGONAL SYSTEM, SPACE GROUP I(-4)2d. I'd be very grateful for your answers Grzegorz Gajewski & Jaroslaw Panek jarp@wchuwr.chem.uni.wroc.pl Faculty of Chemistry, Wroclaw University Wroclaw, Poland From oliver@mpi-sb.mpg.de Thu May 15 12:43:22 1997 Received: from mpi-sb.mpg.de for oliver@mpi-sb.mpg.de by www.ccl.net (8.8.3/950822.1) id MAA19855; Thu, 15 May 1997 12:25:28 -0400 (EDT) Received: from mpii-ol.ag1.mpi-sb.mpg.de (mpii-ol [139.19.10.174]) by mpi-sb.mpg.de (8.8.5/8.8.5) with ESMTP id SAA23466 for ; Thu, 15 May 1997 18:25:54 +0200 (MET DST) Received: from mpii-ol (localhost [127.0.0.1]) by mpii-ol.ag1.mpi-sb.mpg.de (8.7.1/8.7.3) with ESMTP id SAA08529 for ; Thu, 15 May 1997 18:24:29 +0200 (MET DST) Message-Id: <199705151624.SAA08529@mpii-ol.ag1.mpi-sb.mpg.de> X-Mailer: exmh version 1.6.9 8/22/96 To: chemistry@www.ccl.net Subject: Comparison of force fields Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Date: Thu, 15 May 1997 18:24:28 +0200 From: Oliver Kohlbacher Dear Netters, I'm trying to compare the total energies of different conformations of large protein complexes (preferably in water). The only obvious possibility to get these energies seems to be the use of a molecular mechanics force field. But there's quite a lot of different force field out there, most of them are optimized (according to their authors) especially for proteins. But there must be a difference! So, there's my question: Has anyone compared the quality of different force fields or has knowledge of recent publications concerning this problem? Thank you Oliver Kohlbacher -- ---- Oliver Kohlbacher (oliver@mpi-sb.mpg.de) Max-Planck-Institut fuer Informatik, Im Stadtwald, 66121 Saarbruecken Tel.: 0681-9325-505 Fax: 0681-9325-199 From gdp@ppco.com Thu May 15 12:57:23 1997 Received: from relay.ppco.com for gdp@ppco.com by www.ccl.net (8.8.3/950822.1) id MAA19814; Thu, 15 May 1997 12:13:31 -0400 (EDT) Received: by relay.ppco.com id AA01024 (InterLock SMTP Gateway 3.0 for chemistry@www.ccl.net); Thu, 15 May 1997 11:13:30 -0500 Message-Id: <199705151613.AA01024@relay.ppco.com> Received: by relay.ppco.com (Internal Mail Agent-1); Thu, 15 May 1997 11:13:30 -0500 X-Sender: gdp@pop3-host.ppco.com X-Mailer: Windows Eudora Light Version 3.0.1 (32) Date: Thu, 15 May 1997 11:13:28 -0500 To: chemistry@www.ccl.net From: "George D. Parks" Subject: Gaussian Windows vs. Linux: Addendum Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Peter Burger has sent some additional information on GAUSSIAN performance under Windows and Linux. His results using the latest revision of Gaussian for Windows shows performance comparable to Linux. He shows an improvement of greater than 2x under the new Windows version compared to the old one. George Parks gdp@ppco.com ======================================================== Dear George, Test178 old G94W version 1 h 8 min!!!!! new G94W version: Test178 under WIN-NT 4.0 28min 10 sec Test178 under LINUX 2.024 28min 49 sec I cannot seem to find the Win95 numbers right now but from what I remember it was around 27min30sec i.e. slightly faster than the NT version. All times are for 200 MHz PPros with 64 or 128 MB EDO-RAM (not interleaved) with 4 GB SCSI-II W or UW disks (Atlas-II and Seagate Barracuda both 7200 rpm drives) run with 4MW memory in G94. Best wishes, Peter From peon@medchem.dfh.dk Thu May 15 14:43:23 1997 Received: from danpost.uni-c.dk for peon@medchem.dfh.dk by www.ccl.net (8.8.3/950822.1) id NAA20302; Thu, 15 May 1997 13:53:29 -0400 (EDT) Received: from medchem.dfh.dk (medchem.dfh.dk [130.225.177.15]) by danpost.uni-c.dk (8.7.5/8.6) with SMTP id TAA14876; Thu, 15 May 1997 19:53:29 +0200 (METDST) Received: from [130.225.177.59] (compmac2 [130.225.177.59]) by medchem.dfh.dk (950413.SGI.8.6.12/950213.SGI.AUTOCF) via ESMTP id UAA03801; Thu, 15 May 1997 20:08:33 +0200 Message-Id: In-Reply-To: <199705151624.SAA08529@mpii-ol.ag1.mpi-sb.mpg.de> Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Thu, 15 May 1997 19:53:28 +0200 To: Oliver Kohlbacher , chemistry@www.ccl.net From: Per-Ola Norrby Subject: Re: CCL:Comparison of force fields Oliver Kohlbacher wrote: >I'm trying to compare the total energies of different conformations of >large protein complexes (preferably in water). >The only obvious possibility to get these energies seems to be the use of >a molecular mechanics force field. >But there's quite a lot of different force field out there, most of them >are optimized (according to their authors) especially for proteins. >But there must be a difference! >So, there's my question: Has anyone compared the quality of different >force fields or has knowledge of recent publications concerning this >problem? Dear Oliver, I was involved in a force field comparison a while ago, I believe it's the most recent and general study of this kind, the references are: Gundertofte, Liljefors, Norrby, Pettersson, J.Comp.Chem. 17, 429 (1996) Gundertofte, Palm, Pettersson, Stamvik, J.Comp.Chem. 12, 200 (1991) I know that Marc Nicklaus did the same kind of study for charmm (in press, I beleive), and Tom Halgren used a similar test set for MMFF in the April 1996 issue of J.Comput.Chem. However, these tests are for small molecules. I very much doubt that anybody has compared force fields calculating on macromolecules. Anyway, I believe there are much worse sources of errors than the force field in this type of study, at least as long as you stay with the dozen or so best protein force fields (Amber, CFF, CharMM, MMFF, just to mention some). My guess is that the solvation model and the conformational sampling technique will be much more important. I don't know of any comparative study here, sorry. I'd try a continuum solvation model like GB/SA, just because it's rapid, and I don't THINK anybody has shown it's generally inferior to explicit solvation. Regards, Per-Ola Norrby ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ * Per-Ola Norrby, Associate Professor * The Royal Danish School of Pharmacy, Dept. of Med. Chem. * Universitetsparken 2, DK 2100 Copenhagen, Denmark * tel. +45-35376777-506, +45-35370850 fax +45-35372209 * Internet: peon@medchem.dfh.dk, http://compchem.dfh.dk/ From scott@sciencemedia.com Thu May 15 16:43:24 1997 Received: from vmail.connectnet.com for scott@sciencemedia.com by www.ccl.net (8.8.3/950822.1) id QAA22558; Thu, 15 May 1997 16:14:48 -0400 (EDT) Received: from vader.connectnet.com (max-nc-123.connectnet.com [206.64.43.123]) by vmail.connectnet.com (2.0.0/1.0.0) with SMTP id TAA05175; Thu, 15 May 1997 19:09:43 GMT Message-Id: <2.2.32.19970515201346.00d9fa0c@pop3.sciencemedia.com> X-Sender: scott@pop3.sciencemedia.com X-Mailer: Windows Eudora Pro Version 2.2 (32) Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Thu, 15 May 1997 13:13:46 -0700 To: Oliver Kohlbacher , chemistry@www.ccl.net From: Scott Struthers Subject: Re: CCL:Comparison of force fields At 06:24 PM 5/15/97 +0200, Oliver Kohlbacher wrote: >Dear Netters, > >I'm trying to compare the total energies of different conformations of >large protein complexes (preferably in water). >The only obvious possibility to get these energies seems to be the use of >a molecular mechanics force field. This type of question comes up a lot. I doubt you are really interested in force field calculations here. What is the question you are asking? Relative stabilities (i.e. free energies) of different complex structures? If so, you should be more interested in long range electrostatics and hydrophobic contributions to the free energy. Mechanics (unless you do lots of very careful free energy perturbation stuff) will only give you reasonable structures. There will be lots of noise in the value of the energy as a function of parameters you are probably not interested in. check out solvation work by Honig, Eisenberg, etc for a start. good luck scott ---------------------------------- R. Scott Struthers, Ph.D. Co-Founder/Scientific Director ScienceMedia Inc. scott@sciencemedia.com www.sciencemedia.com From creyes@cgl.ucsf.EDU Thu May 15 17:14:37 1997 Received: from socrates.ucsf.EDU for creyes@cgl.ucsf.EDU by www.ccl.net (8.8.3/950822.1) id QAA22540; Thu, 15 May 1997 16:13:01 -0400 (EDT) Received: (from creyes@localhost) by socrates.ucsf.EDU (8.8.5/GSC4.26) id NAA28325; Thu, 15 May 1997 13:12:53 -0700 (PDT) Date: Thu, 15 May 1997 13:12:52 -0700 (PDT) From: Carolina Reyes X-Sender: creyes@socrates.ucsf.edu To: "Jerry C.C. Chan" cc: chemistry@www.ccl.net Subject: Re: CCL:G:Summary: Chemical Softness by DFT In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII PLEASE LET YOUR COLLEAGUE KNOW THAT IF S/HE IS GOING TO ACCESS EMAIL IN A LAB ENVIRONMENT, THEY NEED TO CLOSE THEIR MAIL SESSION AFTERWARD. NO ONE IS IN TOO MUCH OF A RUSH TO PROTECT THEIR PRIVATE AND RESEARCH CORRESPONDENCE. THANKS FOR YOUR ASSISTANCE IN POINTING THIS OUT TO YOUR FRIEND. On Thu, 15 May 1997, Jerry C.C. Chan wrote: > Dear CCLers, > > Thanks are due to all who response to my questions concerning > the chemical hardness. I am happy that many experienced CCLers did share > with me their valuable expertise. > > Sincere thanks, > Jerry > > > Last week I posted a question concerning the determination of > > chemical hardness (or softness) of the metal centre of a TM complexes. > > Maybe the way I asked the question was not specific enough, I just > > received two mails asking for the summary. So I try to write down my > > thinking explicitly and hope that someone in the net, who could not > > tolerate the naiveness or even mistakes of my post, would kindly comment > > on it. I will summarize. > > > > I want to determine the chemical hardness of the metal centre of a charged > > TM complexes. The method that comes to my mind is to do a HF calculation > > and get the MO spectrum. Based on the Koopmans' theorem the hardness of > > the complexes would be (E_LUMO - E_HOMO)/2. > > > > Even my thinking is correct, HF calculation seems to be unreliable for TM > > complexes and correlated methods are usually very expensive. Therefore > > last time I enquired the possibility of using DFT methods as an > > alternative although Koopman's theorem does not hold for KS orbitals. > > > > By the way, I have heard that Fukui function is somehow related to the > > chemical hardness but I don't have the recipe. > > > ++++++++++++++++++++++++++++++++ > Stefan Fau > Pascal HEBANT > Xavier Assfeld > Hogue, Pat (AZ76) > > R.G. Parr and W. Yang, "Density-Functional Theory of Atoms and > Molecules" (Oxford University Press, 1989, New York). > > Ian Fleming, "Frontier Orbitals and Organic Chemical Reactions" > > "Hardness and softness in Density Functional Theory in Chemical Hardness", > K.D. Sen Ed., Coll. Structure and Bonding 80, (Springer-Verlag, Berlin, > 1993). > > R.G. Pearson: J.Am. Chem. Soc. 85, 3533 ('63) > N.K. Ray, L. Samuels, R.G. Parr: J.Chem. Phys. 70, 3680 ('79) > M.S. Gopinathan, M.A. Whitehead: Isr. J. Chem. 19, 209 ('80) > J.P. Perdew, R.G. Parr, M. Levy, J.L. Balduz: > Phys. Rev. Lett. 49, 1691 ('82) > R.G. Parr, R.G. Pearson: J. Am. Chem. Soc 105, 7512 ('83) > R.F. Nalewajski: J. Am. Chem. Soc. 106, 944 ('84) > R.G. Parr, W. Yang: J. Am. Chem. Soc. 106, 4049 ('84) > W. Yang, W.J. Mortier: J. Am. Chem. Soc. 108, 5708 ('86) > R.G. Pearson: J. Chem. Ed. 64, 561 ('87) > A.R. Orsky, M.A. Whitehead: Can. J. Chem. 65, 1970 ('87) > M. Berkowitz, R.G. Parr: J. Chem. Phys. 88, 2554 ('88) > R.G. Parr, P.K. Chattaraj: J. Am. Chem. Soc. 113, 1854 ('91) > P.K. Chattaraj, H. Lee, R.G. Parr: J. Am. Chem. Soc. 113, 1855 ('91) > D. Datta, S.N. Singh: JCS Dalton Trans. 1541, ('91) > J. Cioslowski, S.T. Mixon: J. Am. Chem. Soc. 115, 1084 ('93) > J. Cioslowski & B.B. Stefanov: J. Chem. Phys. 99, 5151 ('93) > R.G. Pearson: Acc. Chem. Res. 26, 250 ('93) > P.K. Chattaraj, P.v.R. Schleyer: J. Am. Chem. Soc. 116, 1067 ('94) > F. Mendez, J.L. Gasquez: J. Am. Chem. Soc. 116, 9298 ('94) > W. Kohn, A.D. Becke, R.G. Parr: J. Phys. Chem. 100, 12974 ('96) > > +++++++++++++++++++++++++++++++++++++++++ > From: Liang Lou > > There is an equivalence in DFT calculations which is called Slater's > transition state method. In this method, the EA and IP are approximated by > the values of an halfly occupied orbital. For example, for IP, you put > +0.5e on the molecule and run a full SCF. Then you check the eigenvalue > for the one-particle state with an 0.5 occupation number. This gives a > good estimate of the IP. For EA, charge the molecule with -0.5e. The > formal explanation of this "transition state" method was given by Janet > (coauthor of the book "calculation of electronic structure in metals"). It > is roughly as follows. The total energy of an N-electron system in LDA can > be written as E=sum[n_k * epsilon_k] + ..., where n_k is the occupation of > the eigenstate k and epsilon_k is the corresponding eigenvalue. The > eigenvalue of the one-particle state k is simply epsilon_k=dE/dn_k. This > is an equivalence of the koopmans' theorem in LDA. The Slater's transition > state is a "finite-difference" approximation to the infinitesimal d(n_k). > The error of this method, from my experience, is in the range between > 0.1-0.3eV, approximately the same as from a small-delta SCF calculation > (e.g., dE(EA) = E(N) - E(N+1)). > > +++++++++++++++++++++++ > From: Rene Fournier > > > although Koopman's theorem does not hold for KS orbitals. > I would not worry about that. First, Koopman's theorem > is not so great anyway. It equates two theoretical constructs: > the energy difference between the GS and a HYPOTHETICAL excited > state with orbitals identical to those of the GS on one hand, > and the difference between the HOMO and LUMO HF orbital energies > on the other. > > Actually, I would say that Kohn-Sham DFT is THE IDEAL theory > for your problem. It has two useful theorems: > > (a) the negative of the KS HOMO energy is equal to the TRUE > ionization energy of the system (relates a theoretical construct > to an observable). CAVEAT: this theorem holds only in the limit > of an "exact" XC potential. [ But how could one expect exact > calculation of observables in any approximate theory anyway? > At least, in KS-DFT, the framework for exact calculations of > this kind is there. ] > > (b) the derivative of the KS-DFT energy w.r.t. number of > electrons, whether the XC is exact or approximate, is precisely > equal to the energy of the highest partly occupied orbital > (Janak's theorem) > > The hardness is most conveniently defined as being half the > second derivative of the energy w.r.t. number of electrons; > the finite difference approximation to that is (I-A)/2; and > that in turn can be approximated as (E_LUMO - E_HOMO)/2 . > Thanks to Janak's theorem, you can get some derivatives (dE/dN) > simply by looking up orbital energies. > > There is an excellent discussion of hardness and Fukui function in > Parr and Yang's book "Density-Functional Theory of Atoms and Molecules" > (Oxford University Press, 1989, New York). > > BTW, the Fukui function is the derivative of the electron > density at point r w.r.t. total number of electrons, N. If the > sum of nuclei charges is M, then: > > f(r) is roughly the density associated with the LUMO for N = M+delta > f(r) is roughly the density associated with the HOMO for N = M-delta > f(r) is roughly the average of the above two for N=M > > ++++++++++++++++++++++++++++++++++++ > From: "N. Sukumar" > > Hardness in DFT is given by the partial second derivative of the energy > functional with respect to the electron density, at constant external > potential, ie. (d^{2}E/d\{rho}^2)_v > See Parr & Yang's book and the references therein for details, including > relations to the Fukui functional (which is the mixed partial derivative > of the energy functional with respect to density annd external potential) : > Robert G. Parr & Weitao Yang, "Density Functional Theory of Atoms and > Molecules" (Oxford University Press, New York, 1989) > Jerzy Cioslowski in Florida has done some ab initio (Hartree-Fock level) > calculations (on small molecules) using the DFT definition of hardness, > without relying on the Koopman's theorem. Some references are : > J. Cioslowski & S. T. Mixon, J. Amer. Chem. Soc. 115, 1084 (1993) > J. Cioslowski & B. B. Stefanov, J. Chem. Phys. 99, 5151 (1993) > see also references therein (since the above two papers are primarily > concerned with BOND hardness). > > +++++++++++++++++++++++++++++++ > From: Oliver Warschkow > > You have asked about hardness/softness calculations. > I dont have any experiences in such calculations myself, > but there is a recent review by Kohn, Becke and Parr > (J.Phys.Chem (1996), 100, 12974) where hardness,softness > and fukui-functions in the framework of DFT are discussed. > The explicit expression given in there (eq.3.4) is > > hardness = (del mu / del N) at const. V > > where mu is the chemical potential (or fermi leve Ef) > of the system. So, it probably boils down to running a > two DFT calculations on the system with slightly > (that is fractionally) different number of electrons and > to see how the HOMO orbital energy (or Ef if you use > a Fermi-Dirac orbital occupation scheme) changes. Well, that > would be my guess how to do it. You are right in > that you are probably better off in doing DFT instead of > HF on TM systems and according to the review, concepts > like hardness,softness etc are quite natural to DFT. > > +++++++++++++++++++++++++++++ > From: "Jack A. Smith" > > I think a good reference for you would be "Density Functional Theory of > Atoms and Molecules" by Parr and Yang (Oxford Press, 1989), particularly > chapters 4 & 5. You'll see that the KS orbitals of DFT are actually more > directly related to the chemical potential, hardness, Fukui functions, etc. > than canonical HF orbitals [Grand Canonical HF, on the other hand, can be > viewed as a natural extension of HF to DFT which includes proper exchange > (see J. Linderberg, IJQC 12:supp 1, p267) but no extra correlation, and > whose orbitals allow similar interpretation as do KS orbitals]. > > -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= > From: Liang Lou > > > Thank you very much for your reply. Since I always work on closed shell > > system, I would like to know if I understand your suggestion correctly: > > > > If I have a +3 TM complexes, in G94 I can simply change the the charge > > from +3 to +3.5 and the multiplicity from 1 to 2 and then do a DFT > > calculation. No special keywords are needed. Repeat the calculation > > with the charge of +2.5. I may have difficulties to get the SCF > > convergence for these +3.5 and +2.5 systems but using vshift should be > > able to solve it (though I don't have any experience on it). > > As far as I know, Gaussian is not particularly strong for metals, > especially in the sense of the efficiency of basis sets. Other DFT program > packages could do better (with either highly optimized Gaussian bases or > Slater type bases, or numerical bases). I guess the level shifting would > result in artificial values for orbital energy near the separation of HOMO > and LUMO. When calculating electron removal energies, IP and EA, the > system always changes spin multiplicity and there are always associated > uncertainties. Usually, the orbital energy values do not change in the > first few decimal places after he total energy has converged to under, > say, 10**(-4). Therefore, higher convergence of total energy will not > affect comparing with experiment. > > > > > -------This is added Automatically by the Software-------- > -- Original Sender Envelope Address: chan@uni-muenster.de > -- Original Sender From: Address: chan@uni-muenster.de > CHEMISTRY@www.ccl.net: Everybody | CHEMISTRY-REQUEST@www.ccl.net: Coordinator > MAILSERV@www.ccl.net: HELP CHEMISTRY or HELP SEARCH | Gopher: www.ccl.net 73 > Anon. ftp: www.ccl.net | CHEMISTRY-SEARCH@www.ccl.net -- archive search > Web: http://www.ccl.net/chemistry.html > > From mn1@helix.nih.gov Thu May 15 17:43:25 1997 Received: from helix.nih.gov for mn1@helix.nih.gov by www.ccl.net (8.8.3/950822.1) id RAA26222; Thu, 15 May 1997 17:40:22 -0400 (EDT) Received: (from mn1@localhost) by helix.nih.gov (8.8.4/8.8.4) id RAA17048; Thu, 15 May 1997 17:40:20 -0400 (EDT) Date: Thu, 15 May 1997 17:40:20 -0400 (EDT) From: "M. Nicklaus" Message-Id: <199705152140.RAA17048@helix.nih.gov> To: CHEMISTRY@www.ccl.net Subject: G: Problem with PES Cc: mn1@helix.nih.gov Dear CCL'ers, I'm having a problem with a (relaxed) Potential Energy Scan (PES) in Gaussian 94. I'm trying to scan a torsion through 360 degrees in 30 degree steps. After having completed the first four steps (incl. the initial 0 deg. conformation), G94 crashed when I tried to start the remainder of the PES from the initial torsion + 120 degrees. Using the route card # B3LYP/6-31G(d) Guess=Read Opt=(MaxCycle=50,VeryTight,AddRedundant) I'm getting the following output (excerpt of relevant lines): Symbolic Z-matrix: Charge = 0 Multiplicity = 1 C 0. 0. 0. C 0. 0. 1.52722 [stuff omitted] H -6.26387 -0.66184 -2.74617 H -5.12334 -1.96537 -2.80824 Adding D( 5, 1, 10, 14) Coordinate has been modified. New value = -24.3000 Iteration 1 RMS(Cart)= 0.30206624 RMS(Int)= 0.12005164 Iteration 2 RMS(Cart)= 0.05406729 RMS(Int)= 0.11841405 Iteration 3 RMS(Cart)= 0.01164738 RMS(Int)= 0.11831192 Iteration 4 RMS(Cart)= 0.00444315 RMS(Int)= 0.11829129 Iteration 5 RMS(Cart)= 0.00124238 RMS(Int)= 0.11829285 Iteration 6 RMS(Cart)= 0.00035564 RMS(Int)= 0.11829414 Iteration 7 RMS(Cart)= 0.00012795 RMS(Int)= 0.11829411 Iteration 8 RMS(Cart)= 0.00003018 RMS(Int)= 0.11829398 Iteration 9 RMS(Cart)= 0.00001229 RMS(Int)= 0.11829397 Iteration 10 RMS(Cart)= 0.00000299 RMS(Int)= 0.11829398 Iteration 1 RMS(Cart)= 0.20954250 RMS(Int)= 0.09102181 Iteration 2 RMS(Cart)= 0.15676665 RMS(Int)= 0.11411643 Iteration 3 RMS(Cart)= 0.12440864 RMS(Int)= 0.14459828 Iteration 4 RMS(Cart)= 0.10264810 RMS(Int)= 0.17478759 Iteration 5 RMS(Cart)= 0.08696705 RMS(Int)= 0.20291573 Iteration 6 RMS(Cart)= 0.07509046 RMS(Int)= 0.22870662 Iteration 7 RMS(Cart)= 0.06575916 RMS(Int)= 0.25226946 Iteration 8 RMS(Cart)= 0.05822031 RMS(Int)= 0.27380674 Iteration 9 RMS(Cart)= 0.05199538 RMS(Int)= 0.29352946 Iteration 10 RMS(Cart)= 0.04676493 RMS(Int)= 0.31163228 Iteration 11 RMS(Cart)= 0.04230707 RMS(Int)= 0.32828769 Iteration 12 RMS(Cart)= 0.03846255 RMS(Int)= 0.34364635 [84 more "Iteration" lines omitted] Iteration 97 RMS(Cart)= 0.00025610 RMS(Int)= 0.56929323 Iteration 98 RMS(Cart)= 0.00024291 RMS(Int)= 0.56940351 Iteration 99 RMS(Cart)= 0.00023039 RMS(Int)= 0.56950812 Iteration100 RMS(Cart)= 0.00021853 RMS(Int)= 0.56960735 Curvilinear step not converged, using linear step Error imposing constraints Error termination via Lnk1e in /usr/programs/g94/l101.exe. Job cpu time: 0 days 0 hours 0 minutes 3.1 seconds. File lengths (MBytes): RWF= 1 Int= 0 D2E= 0 Chk= 9 Scr= 1 Any help with this? (BTW, G94 crashes identically w/o the MaxCycle=50 option.) Thanks in advance for all responses. Marc ------------------------------------------------------------------------ Marc C. Nicklaus National Institutes of Health E-mail: mn1@helix.nih.gov Bldg 37, Rm 5B29 Phone: (301) 402-3111 BETHESDA, MD 20892-4255 USA Fax: (301) 496-5839 http://www.nci.nih.gov/intra/lmch/MCNBIO.HTM Laboratory of Medicinal Chemistry, National Cancer Institute, & Lab. of Structural Biology, Div. of Computer Research and Technology ------------------------------------------------------------------------ From vedi0999@stallion.jsums.edu Thu May 15 21:43:26 1997 Received: from stallion.jsums.edu for vedi0999@stallion.jsums.edu by www.ccl.net (8.8.3/950822.1) id UAA27968; Thu, 15 May 1997 20:44:33 -0400 (EDT) Received: from localhost by stallion.jsums.edu (AIX 3.2/UCB 5.64/4.03) id AA29537; Thu, 15 May 1997 19:46:15 -0500 Date: Thu, 15 May 1997 19:46:15 -0500 (CDT) From: Venkateswarlu Divi Reply-To: Venkateswarlu Divi To: chemistry@www.ccl.net Subject: which solvation model ?? Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi netters, I am interested in accurate estimation of free-energies of hydration for some nucleic acid base analogs. I understand G94 has implementations of a number of SCRF models. Besides, I have used to someextent AM1-SM2 also. While AM1-SM2 seems a good choice as far as the computational cost is concerned, one cannot judge the numbers of AM1-SM2 and take them with a good degree of confidence in cases where there is no experimental data. While G94 implements, Onsagar,PCM, IPCM and SCIPCM models, I am not sure which one would give me a reliable free-energy of hydration quantity. Could anybody suggest me the best model for the intended work? If any of these models is a good choice at ab intio level, which basis set is the best choice? Any information on the recent literature that gives a comparative study and accuracy of these ab initio models would be highly appreciated! With regards divi Dr. Divi Venkateswarlu Phone : +(601) 973-3723 (O) Department of Chemistry : +(601) 956-1713 (R) Jackson State University Fax : +(601) 973-3674 1400, J.R. Lynch Street, E-mail: vedi0999@stallion.jsums.edu Jackson, MS 39217, USA URL@ : http://tiger.jsums.edu/~divi _______________________________________________________________________________ From ccl@www.ccl.net Sat May 10 07:42:14 1997 Received: from bedrock.ccl.net for ccl@www.ccl.net by www.ccl.net (8.8.3/950822.1) id GAA05378; Sat, 10 May 1997 06:56:19 -0400 (EDT) Received: from wchd18.chemie.uni-wuerzburg.de for s101264.k4.stud.uni-wuerzburg@wrzn12.rz.uni-wuerzburg.de by bedrock.ccl.net (8.8.3/950822.1) id GAA08414; Sat, 10 May 1997 06:56:16 -0400 (EDT) Received: from claessen (wex003.extern.uni-wuerzburg.de [132.187.248.3]) by wchd18.chemie.uni-wuerzburg.de (8.6.9/8.6.9) with SMTP id UAA19184; Sat, 10 May 1997 20:17:04 +0200 Message-Id: <199705101817.UAA19184@wchd18.chemie.uni-wuerzburg.de> Comments: Authenticated sender is From: "Rolf Claessen" To: chemconf@umdd.umd.edu, CHEMED-L@UWF.EDU, chemistry@ccl.net, CHMINF-L@listserv.INDIANA.EDU, CICOURSE@iubvm.ucs.indiana.edu, orgchem@extreme.chem.rpi.edu, ysn@crow-t-robot.stanford.edu Date: Sat, 10 May 1997 12:42:37 +0000 MIME-Version: 1.0 Content-type: text/plain; charset=US-ASCII Content-transfer-encoding: 7BIT Subject: Chemistry Books Online Reply-to: s101264@stud-mail.uni-wuerzburg.de Priority: normal X-mailer: Pegasus Mail for Win32 (v2.52) Status: RO Content-Length: 213 Chemistry Books Online A new topic of my index relates to chemistry books. You can get information about the books and even buy them online. http://www.geocities.com/Tokyo/5243/index.html Yours Rolf Claessen From ccl@www.ccl.net Sun May 11 11:42:28 1997 Received: from bedrock.ccl.net for ccl@www.ccl.net by www.ccl.net (8.8.3/950822.1) id LAA12907; Sun, 11 May 1997 11:28:22 -0400 (EDT) Received: from ns1.softcell.net for tim@softcell.net by bedrock.ccl.net (8.8.3/950822.1) id LAA17701; Sun, 11 May 1997 11:28:20 -0400 (EDT) From: Received: from softcell.net (1Cust126.Max76.New-York.NY.MS.UU.NET [153.35.37.254]) by ns1.softcell.net (8.8.4/8.8.4) with SMTP id HAA18536; Sun, 11 May 1997 07:28:53 -0700 Received: from softcell.net by softcell.net (8.8.5/8.6.5) with SMTP id GAA04116 for ; Sun, 11 May 1997 09:34:08 -0600 (EST) To: postmaster@softcell.net Message-ID: Date: Sun, 11 May 97 09:34:08 EST Subject: Knowledge Management Fot The Oil Industry Reply-To: tim@softcell.net X-PMFLAGS: 340788480 X-UIDL: 3671313288965eb1890m0762139 Comments: Authenticated sender is You may like to know that, on 23-25 June this year, the first-ever Knowledge Management event for the oil and gas industry in the US will be taking place in Houston, Tx. 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Kind regards, Tim Gunstone First Conferences tim@firstconf.com 85 Clerkenwell Road tel: 44 171 404 0424 London, EC1R 5AR fax: 44 171 404 7733 United Kingdom web: http://www.firstconf.com From dsmith@CTCnet.Net Wed May 14 07:43:04 1997 Received: from home.CTCnet.Net for dsmith@CTCnet.Net by www.ccl.net (8.8.3/950822.1) id HAA10234; Wed, 14 May 1997 07:32:01 -0400 (EDT) Received: from fock by home.CTCnet.Net (SMI-8.6/SMI-SVR4) id HAA10557; Wed, 14 May 1997 07:26:16 -0400 Message-Id: <3.0.1.32.19970514072205.009a4678@pop.dasgroup.com> X-Sender: dsmith@pop.dasgroup.com (Unverified) X-Mailer: Windows Eudora Light Version 3.0.1 (32) Date: Wed, 14 May 1997 07:22:05 -0400 To: CHEMISTRY@www.ccl.net From: "Douglas A. Smith Ph.D." Subject: Patent issued Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" For those of you who are interested, DASGroup has now been issued its patent on Impact Resistant Polymers based on Bisphenol-A-Polycarbonate. 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From ccl@www.ccl.net Tue May 13 04:42:51 1997 Received: from bedrock.ccl.net for ccl@www.ccl.net by www.ccl.net (8.8.3/950822.1) id DAA27662; Tue, 13 May 1997 03:56:33 -0400 (EDT) Received: from wchd18.chemie.uni-wuerzburg.de for s101264.k4.stud.uni-wuerzburg@wrzn12.rz.uni-wuerzburg.de by bedrock.ccl.net (8.8.3/950822.1) id DAA28381; Tue, 13 May 1997 03:56:31 -0400 (EDT) Received: from claessen (wex032.extern.uni-wuerzburg.de [132.187.248.32]) by wchd18.chemie.uni-wuerzburg.de (8.6.9/8.6.9) with SMTP id RAA21552; Tue, 13 May 1997 17:18:42 +0200 Message-Id: <199705131518.RAA21552@wchd18.chemie.uni-wuerzburg.de> Comments: Authenticated sender is From: "Rolf Claessen" To: chemconf@umdd.umd.edu, CHEMED-L@UWF.EDU, chemistry@ccl.net, CHMINF-L@listserv.INDIANA.EDU, CICOURSE@iubvm.ucs.indiana.edu, orgchem@extreme.chem.rpi.edu, ysn@crow-t-robot.stanford.edu Date: Tue, 13 May 1997 09:55:41 +0000 MIME-Version: 1.0 Content-type: text/plain; charset=US-ASCII Content-transfer-encoding: 7BIT Subject: Virtual Chemistry Bookshop Reply-to: s101264@stud-mail.uni-wuerzburg.de Priority: normal X-mailer: Pegasus Mail for Win32 (v2.52) Visit the first Virtual Chemistry Bookshop at Rolf Claessen's Chemistry Index http://www.geocities.com/Tokyo/5243/book_en.htm It has been made possible with the generous support of Amazon.Com. Yours Rolf Claessen Rolf Claessen University of Wuerzburg http://www.geocities.com/Tokyo/5243 s101264@stud-mail.uni-wuerzburg.de Tel. +49 931 701814 From jlye@tx.ncsu.edu Tue May 13 18:19:34 1997 Received: from ds10.tx.ncsu.edu for jlye@tx.ncsu.edu by www.ccl.net (8.8.3/950822.1) id RAA06585; Tue, 13 May 1997 17:25:03 -0400 (EDT) Received: by ds10.tx.ncsu.edu (5.65/Eos/C-U-09Sep93) id AA16262; Tue, 13 May 1997 17:23:46 -0400 From: "Jason Lye" Message-Id: <9705131723.ZM16260@unity.ncsu.edu> Date: Tue, 13 May 1997 17:23:21 -0400 X-Mailer: Z-Mail (3.2.1 15feb95) To: cache@pacificu.edu, chemistry@www.ccl.net Subject: Excited Phenolic Acidity AM1 Cc: Harold_Freeman@ncsu.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Dear Colleagues, It has been known for quite some time that the acidity of phenols is increased in the excited state. I am using CAChe MOPAC, specifically AM1, to try to estimate substituent effects on the acidity of phenolic protons in the first excited state. The phenols that I am studying undergo excited state intramolecular proton transfer, and I am assuming that I can faciliate this internal conversion process by increasing the excited state acidity of the phenolic proton. How can I use CAChe MOPAC to estimate the acidity of a proton in the first excited state? (So far, I have used CAChe ProjectLeader to calculate the partial charge on the proton, but the values that it gives are always the ground state partial charges, not the excited state partial charges, even if the molecule SCF energy was calculated using EXCITED SINGLET keywords.) I will summarise any responses. Thanks, Jason -- _______________________________________________________________________________ Jason Lye, | Dye Synthesis Research Group, | College Of Textiles, Box 8301, | "Lifes' cheap, but North Carolina State University, | the accessories will kill you!" Raleigh, N.C. 27695 - 8301 | | Ph: (919) 515-6615 | jlye@tx.ncsu.edu | _______________________________________________________________________________ From huesser@physik.unizh.ch Thu May 15 09:43:21 1997 Received: from caprice.physik.unizh.ch for huesser@physik.unizh.ch by www.ccl.net (8.8.3/950822.1) id IAB18632; Thu, 15 May 1997 08:58:24 -0400 (EDT) Received: by caprice.physik.unizh.ch (8.7.3cf2.18) id OAA71257; Thu, 15 May 1997 14:57:50 +0200 From: Peter Huesser Message-Id: <199705151257.OAA71257@caprice.physik.unizh.ch> Subject: freezing orbitals To: chemistry@www.ccl.net Date: Thu, 15 May 1997 14:57:50 +0200 (MEST) X-Mailer: ELM [version 2.4 PL23] MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Is it possible to freeze specifial atomic orbitals during an scf calculation ? Thanks in advance for any respond Peter H\"usser Email: huesser@physik.unzih.ch From mcblimts@leonis.nus.sg Tue May 6 00:41:08 1997 Received: from sable.nus.sg for mcblimts@leonis.nus.sg by www.ccl.net (8.8.3/950822.1) id AAA28148; Tue, 6 May 1997 00:28:26 -0400 (EDT) Received: from leonis.nus.sg (root@leonis.nus.sg [137.132.1.18]) by sable.nus.sg (8.8.4/8.6.9) with ESMTP id MAA30613 for ; Tue, 6 May 1997 12:28:15 +0800 (SST) Received: from limts.imcb.nus.sg ([137.132.42.122]) by leonis.nus.sg (8.6.10/8.6.9/CNS-3.5) with SMTP id MAA10691 for ; Tue, 6 May 1997 12:28:13 +0800 Date: Tue, 6 May 1997 12:28:13 +0800 Message-Id: <199705060428.MAA10691@leonis.nus.sg> X-Sender: mcblimts@leonis.nus.sg X-Mailer: Windows Eudora Light Version 1.5.2 Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" To: chemistry@www.ccl.net From: Lim Teck Sin Subject: information on SDF format Hi, Does anyone know if the specification for SDF format is publicly available? Is there a site which document the various formats that have been widely used by chemists? Thanks! Best Regards Teck Sin From ccl@www.ccl.net Tue May 6 04:49:21 1997 Received: from bedrock.ccl.net for ccl@www.ccl.net by www.ccl.net (8.8.3/950822.1) id EAA01618; Tue, 6 May 1997 04:33:33 -0400 (EDT) Received: from faui45.informatik.uni-erlangen.de for model97@organik.uni-erlangen.de by bedrock.ccl.net (8.8.3/950822.1) id EAA15191; Tue, 6 May 1997 04:33:28 -0400 (EDT) Received: from derioc1.organik.uni-erlangen.de (derioc1.organik.uni-erlangen.de [131.188.128.1]) by uni-erlangen.de with SMTP id KAA16918 (8.7.6/7.5c-FAU); Tue, 6 May 1997 10:30:17 +0200 (MET DST) Received: from indigo11.organik.uni-erlangen.de (indigo11.organik.uni-erlangen.de [131.188.128.69]) by organik.uni-erlangen.de with SMTP id KAA08519 (8.6.12/7.4f-FAU);; Tue, 6 May 1997 10:29:03 +0200 Date: Tue, 6 May 1997 10:29:03 +0200 (MDT) From: "Modelling '97" To: chem-com@mailbase.ac.uk, chem-mod@mailbase.ac.uk, chemistry@ccl.net, ipmdg-l@venus.co.uk, amber@cgl.ucsf.edu, c2-l@msi.com, cache@pacificu.edu, charmm-bbs@emperor.harvard.edu, hyperchem@hyper.com, mmodinfo@uoft02.utoledo.edu, quanta-l@msi.com, sybyl@extreme.chem.rpi.edu, watoc@ic.ac.uk Subject: MGMS Bursaries : Model(l)ing '97 Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII The Molceular Graphics and Modelling Society (MGMS) is pleased to announce that it will be awarding a total of eight bursaries for young scientists for the Model(l)ing '97 conference in Erlangen, Germany, from 2-5 Sept. 1997. For details of the conference see: http://www.organik.uni-erlangen.de/model97 Bursaries will be awarded to graduate students or postdocs who give a lecture or present a poster at the conference. Note that the deadline for lecture submissions (originally May 1st) has been extended to June 1st to allow applications for bursaries. The deadline for poster submissions from bursary-applicants is also June 1st, not July 1st as for other posters. The bursaries will include conference regstration, accomodation in an economy room and a contribution towards travel expenses. Applications should be via the electronic registration facility availble through the above URL and should be accompanied by a recommendation from the supervisor emeiled to model97@organik.uni-erlangen.de Decisions as to the winners of the bursaries will be announced on June 1st. ----- Model(l)ing '97 Computer Chemie Centrum - Institut f. Organische Chemie I Naegelsbachstrasse 25 - D-91052 Erlangen Deutschland / Germany Tel: 0049-9131 - 85 6581 Fax: 0049-9131 - 85 6565 E-Mail: model97@organik.uni-erlangen.de WWW: http://www.organik.uni-erlangen.de/model97/ From beroza@scripps.edu Tue May 6 20:41:33 1997 Received: from relay.scripps.edu for beroza@scripps.edu by www.ccl.net (8.8.3/950822.1) id UAA01309; Tue, 6 May 1997 20:02:27 -0400 (EDT) Received: from euler.scripps.edu (euler.scripps.edu [137.131.252.34]) by relay.scripps.edu (8.8.5/TSRI-1.5) with ESMTP id RAA21955; Tue, 6 May 1997 17:02:20 -0700 (PDT) Received: (from beroza@localhost) by euler.scripps.edu (8.8.5/TSRI-1.4) id RAA05078; Tue, 6 May 1997 17:01:49 -0700 (PDT) Date: Tue, 6 May 1997 17:01:49 -0700 (PDT) From: Paul Beroza Message-Id: <199705070001.RAA05078@euler.scripps.edu> To: CHEMISTRY@www.ccl.net, Vladislav.Vassiliev@bri.nrc.ca Subject: Re: CCL:How to calculate pKa values in large proteins?... Dr. Vassiliev wrote: > > Let's imagine I have coordinates of a real protein (for example, from > PDB) and now I would like to know the pKa values of all the residues > (Asp's, Glu's, Lys's, Arg's, His's) at a given pH. What kind of programs > could predict these pKa values? > > I would also be interested in any references concerning the approaches of > this kind of prediction. > Several research groups have investigated this problem, commonly referred to as the "multiple site titration problem". The most widespread approach is to assume that the pKa of a titrating residue is perturbed from its solution value by the electrostatic environment it experiences in the protein. The electrostatic energies involved can be calculated from continuum models using finite difference, and other, numerical methods. I've appended a list of references dealing with the subject (liberally sprinkled with references to my own work, of course). There are many more. I think the Bashford and Karplus paper is a good place to start, though more recent work uses more sophisticated models. Alternatively, Arieh Warshel has a more microscopic PDLD model (protein dipoles langevin dipoles) which has also been applied to pKa calculation in proteins. Several available computer programs can do these sorts of calculations: MEAD (from Don Bashford ftp.scripps.edu:pub/bashford) pep (my finite difference code ftp.scripps.edu:pub/beroza) DELPHI (from Barry Honig's group) UHBD (from Andy McCammon's group) polaris (from Arieh Warshel's group) Hope this helps, Paul --------------------------------------------------------------- Paul Beroza, Ph.D. The Scripps Research Institute email: beroza@scripps.edu Department of Molecular Biology phone: 619-784-9957 10550 N. Torrey Pines Rd. - TPC15 fax: 619-784-8896 La Jolla, CA 92037 URL: www.scripps.edu/~beroza --------------------------------------------------------------- @ARTICLE{Russel, AUTHOR="S. T. Russel and A. Warshel", JOURNAL="J. Mol. Biol.", TITLE="The Energetics of Ionized Groups in Bovine Pancreatic Trypsin Inhibitor", VOLUME="185", PAGES="389-404", YEAR="1985" } @ARTICLE{Bashford90, AUTHOR="D. Bashford and M. Karplus", JOURNAL="Biochemistry", TITLE=" {${\rm pK_a}$'s} of Ionizable Groups in Proteins: Atomic Detail from a Continuum Model", VOLUME="29", PAGES="10219-10225", YEAR="1990" } AUTHOR="P. Beroza and D. R. Fredkin and M. Y. Okamura and G. Feher", JOURNAL="Proc. Natl. Aca. Sci.", TITLE="Protonation of Interacting Residues in a Protein by a {M}onte {C}arlo Method: {A}pplication to Lysozyme and the Photosynthetic Reaction Center of {{\it Rhodobacter sphaeroides}}", VOLUME="88", PAGES="5804-5808", YEAR="1991" } @ARTICLE{Oberoi93, AUTHOR="H. Oberoi and N. M. Allewell", JOURNAL="Biophys. J.", TITLE="Multigrid Solution of the Nonlinear Poisson-Boltzmann Equation and Calculation of Titration Curves", VOLUME="65", PAGES="48-55", YEAR="1993" } @ARTICLE{Yang93, AUTHOR="A.-S. Yang and M. R. Gunner and R. Sampogna and K. Sharp and B. Honig", JOURNAL="Proteins", TITLE="On the Calculation of {${\rm pK_a}$'s} in Proteins", VOLUME="15", PAGES="252-265", YEAR="1993" } @ARTICLE{Antosiewicz94, AUTHOR="J. Antosiewicz and J.A. McCammon and M.K. Gilson", TITLE="Prediction of pH-dependent Properties of Proteins", JOURNAL="J. Mol. Biol.", VOLUME="238", PAGES="415-436", YEAR="1994" } @ARTICLE{You95, AUTHOR="T.J. You and D. Bashford", TITLE="Conformation and hydrogen ion titration of proteins: a continuum electrostatic model with conformational flexibility", JOURNAL="Biophys. J.", VOLUME="69", PAGES="1721-1733", YEAR="1995" } @ARTICLE{Beroza95, AUTHOR="P. Beroza and D. R. Fredkin and M. Y. Okamura and G. Feher", JOURNAL="Biophys. J.", TITLE="Electrostatic Calculations of Amino Acid Titration and Electron Transfer, {${\rm Q_A^- Q_B \rightarrow Q_A Q_B^-}$}, in the Reaction Center", VOLUME="68", PAGES="2233-2250", YEAR="1995" } @ARTICLE{Beroza96, AUTHOR= "P. Beroza and D. R. Fredkin", TITLE="Calculation of Amino Acid {${\rm pK_a}$s} in a Protein from a Continuum Electrostatic Model: Method and Sensitivity Analysis", JOURNAL="J. Comp. Chem.", VOLUME="17", PAGES="1229-1244", YEAR="1996" } @ARTICLE{Beroza96, AUTHOR= "P. Beroza and D. A. Case", TITLE="Including Side Chain Flexibility in Continuum Electrostatic Calculations of Protein Titration", JOURNAL="J. Phys. Chem.", VOLUME="100", PAGES="20156-20163", YEAR="1996" } From akutatel@du.edu Wed May 7 16:41:45 1997 Received: from odin.cair.du.edu for akutatel@du.edu by www.ccl.net (8.8.3/950822.1) id PAA01730; Wed, 7 May 1997 15:59:28 -0400 (EDT) Received: by odin.cair.du.edu; id AA32619; Wed, 7 May 1997 13:59:26 -0600 Received: by kizh.biochem.du.edu with Microsoft Mail id <01BC5AEE.60AB8120@kizh.biochem.du.edu>; Wed, 7 May 1997 13:55:53 -0600 Message-Id: <01BC5AEE.60AB8120@kizh.biochem.du.edu> From: Andrei Kutateladze To: "'CCL'" Cc: "'toukie@zui.unizh.ch'" Subject: CCL: SUMMARY: Torsional barriers for methyl group rotation Date: Wed, 7 May 1997 13:55:51 -0600 Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 7bit A couple of days ago I posted the following question: > A colleague of my is looking for reliable experimental data on >torsional barriers for methyl group rotation in various environments - >aromatic, n-alkyl, branched alkyl, ether etc. > Any references will be much appreciated. Many thanks to people who replied. Special thanks to Wolfgang Roth for quite a comprehensive refs list. Andrei Kutateladze University of Denver SUMMARY: =========================================== REPLY # 1 You may look at this http://www-public.rz.uni-duessledorf.de/~rothw/diplom/literatur.html part of my homepage where I placed the list of literature from my dissertation. Experimental methyl group torsion parameters of aromatic compounds are available fo the following molecules (to my knowledge): toluene (see Refs. 15, 29, 56 of the above mentioned website, see also J. Chem. Phys. 102 (1995) 6787, J. Chem. Phys. 102 (1995) 8718) 1-methyltetrazene (Refs. 44, 58) 3-fluortoluene (Ref. 27) 4-fluortoluene (Refs. 27, 44) (I wasn't interested in 2-fluortoluene) cis-3-cresol (Ref. 13) 3-methylindole (Ref. 59) 5-methylindole (Refs. 41, 59) 6-methylindole (Ref. 41) 3- and 4-methylbenzylradical (Ref. 28) 2-Methylpyrazine (Ref. 60) 2-Methylnaphthalene (Ref. 17) (data for 1-MN are also available) methylcyclopentadienylradical (Ref. 20) 4- and 5-methylpyrimidine (Ref. 38) 4-toluidine (Refs. 42, 54) Further molecules which have been investigated are xylenes acetone (lot of papers in J. Molec. Spect., maily from IR spectra for different torsional modes. methylglyoxale (Ref. 73) methanol (very early microwave papers in J. Chem. Phys.) CH3SH trans-beta-methylstyrene (J. Phys. Chem. 99 (1995) 4386 acetaldehyde (e.g. J. Mol. Struct. 350 (1995) 83) methyl-subtituted stilbenes (work of Spangler and coworkers, e.g. J. Phys. Chem. 99 (1995) 9316) methylacetylene ... I decided to cut the list here because I have approximately 100 to 150 references to experimental and theoretical papers dealing with internal rotation maily of the methyl group. I don't have informations about ether because this molecules are not accessible to medium or high resolution laser induced fluorescence. If You/Your colleague is interested in the whole list which is an Excel 4.0 file, please send me an email. Regards Wolfgang Roth ====================== REPLY # 2 Andrei, The following reference might be useful: Cohen, N.; Benson, S. W. In "The chemistry of Alkanes and Cycloalkanes"; Patai, S.; Rappoport, Z., Ed.; John Wiley, 1992; Chapter 6. Regards, Ashutosh (Misra Ashutosh, ashutosh@jove.acs.unt.edu) ======================= REPLY # 3 Dear Andrei Kutateladze, There is a table of about twenty or so methyl barriers in a book on thermodynamics: "Thermodynamics of Organic Compounds in the Gas State", Volume I, Michael Frenkel, K.N. Marsh, R. C. Wilhoit, G. J. Kabo, G. N. Roganov page 26. A recent paper in JCP deals with internal rotation treated by ab innitio methods, and some of references there may lead to experimental data. Russ Dr. Russell D. Johnson III Research Chemist Physical and Chemical Properties Division National Institute of Standards and Technology Gaithersburg, MD 20899 email: russell.johnson@nist.gov From huber@library.ucsb.edu Wed May 7 19:02:40 1997 Received: from ariz.library.ucsb.edu for huber@library.ucsb.edu by www.ccl.net (8.8.3/950822.1) id RAA17178; Wed, 7 May 1997 17:43:58 -0400 (EDT) Received: by ariz.library.ucsb.edu (5.65/DEC-Ultrix/4.3) id AA24882; Wed, 7 May 1997 14:43:55 -0700 Date: Wed, 7 May 1997 14:43:55 -0700 (PDT) From: Chuck Huber To: chemistry@www.ccl.net Subject: Chemical Structure Association Award (fwd) Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII The following message is being posted to multiple listservs; please pardon any duplication. ======================================================= CHEMICAL STRUCTURE ASSOCIATION AWARD FOR US STUDENT The Chemical Structure Association (CSA) is an international organisation which aims to bring together people whose work involves the handling of information about chemical structures. Members of the CSA are interested in all aspects of chemical structure information, including molecular modelling, combinatorial chemistry, computer systems for handling chemical structural information, chemical databases, online systems, use of the Internet to access chemical information, and manual and CD-ROM reference tools. The CSA is offering an Award of 210 US dollars to assist a US student to attend the Fall ACS meeting in Las Vegas. Students may be undergraduate or postgraduate, and should be specialising in some aspect of chemical structure information handling. Applicants must be students at the time of application for the award, but need not necessarily be a student at the time of the meeting. The value of the award is equivalent to the full registration fee for the meeting. Applications for the award should be sent, together with a supporting reference, by 1 June 1997 (deadline extended) to: Chuck Huber, Chairman of CINF Awards Committee, Davidson Library University of California Santa Barbara, CA 93106 e-mail: huber@ariz.library.ucsb.edu Chuck Huber Davidson Library University of California Santa Barbara huber@library.ucsb.edu From ccl@www.ccl.net Thu May 8 15:41:52 1997 Received: from bedrock.ccl.net for ccl@www.ccl.net by www.ccl.net (8.8.3/950822.1) id PAA21290; Thu, 8 May 1997 15:26:34 -0400 (EDT) Received: from alpha.strubix.com for cfisher@strubix.com by bedrock.ccl.net (8.8.3/950822.1) id PAA03318; Thu, 8 May 1997 15:26:20 -0400 (EDT) Received: from alpha.strubix.com ([127.0.0.1]) by alpha.strubix.com (Netscape Mail Server v1.1) with SMTP id AAA4171 for ; Thu, 8 May 1997 12:26:01 -0700 From: cfisher@strubix.com (Cindy Fisher) Message-Id: <9705081226.ZM4168@alpha.strubix.com> Date: Thu, 8 May 1997 12:26:00 -0700 X-Mailer: Z-Mail (3.2.3 08feb96 MediaMail) To: chemistry@ccl.net Subject: PROTEP program Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Does anyone know how to get a copy of the program PROTEP? Cindy -- Cindy Fisher Structural Bioinformatics, Inc. cfisher@strubix.com From kless@chem.ucla.edu Thu May 1 08:13:28 1997 Date: Wed, 30 Apr 1997 11:29:34 -0700 (PDT) From: Achim Kless To: michael nolan Subject: Re: CCL:mn complexes Dear Michael, > I have a really bad problem and I cannot do anything about it. > Here it is: > I am trying to run ab-initio calculations on Mn(CO)3 and Cr(CO)3, using > GAMESS-UK. > I have tried the following methods (I also give if ti was succesful or > not): > > 1) RHF/3-21G (3-21G on all atoms) > for Mn(CO)3 this is successful, for Cr(CO)3 I get excessive number of > iterations and an oscillation of the energy. > > 3) RHF with minimal basis ECP on all atoms for Mn(CO)3 and Cr(CO)3. > This gives a ludicrously low energy (about -70a.u.), oscillations in the > energy and excessive number of iterations > > 5) RHF, min. basis ECP and ECPDZ on Mn, 3-21G and 6-31G on C and O try out the basis sets from A. Schaefer, C. Huber, and R. Ahlrichs. They are suitable especially for the middle-transition metals. See: Fully Optimized Contracted Gaussian Basis Sets of Triple Zeta Valence Quality for Atoms Li to Kr. A. Schaefer, C. Huber, and R. Ahlrichs; J. Chem. Phys. 100, 5829 (1994). Regarding ECPs check out the Pseudopotentials from M. Dolg, H. Stoll, H. Preuss. (http://www.theochem.uni-stuttgart.de) best regards, Achim --------------------------- Dr. Achim Kless UCLA, Dept. Chemistry and Biochemistry This was very helpful, I found these bais sets useful and also Dunning's double-zeta basis sets. ******************************************************************************* answer 2: From her10531@argon.chem.tu-berlin.de Thu May 1 08:13:36 1997 Date: Wed, 30 Apr 1997 19:51:16 +0200 From: Rolad Hertwig To: michael nolan Subject: Re: CCL:mn complexes Micheal, welcome to the world of transition metal quantum chemistry! I will try to give you some hints, but in addition you should get in touch with people ( I mean personally), who have experience in the field, if your thesis advisor has not. > 1) RHF/3-21G (3-21G on all atoms) > for Mn(CO)3 this is successful, for Cr(CO)3 I get excessive number of > iterations and an oscillation of the energy. Oscillation is not unusual in organo-metallic complexes. Play around with SCF accelerators, like damping, diis, and shifting of virtual orbitals. There is no general recipe to avoid this. Also, change your starting geometry. Avoid too small bond lengths. Exploit symmetry, and specify electronic occupations explicitly as far as this is possible (I have little experience with GAMESS). > 3) RHF with minimal basis ECP on all atoms for Mn(CO)3 and Cr(CO)3. > This gives a ludicrously low energy (about -70a.u.), oscillations in the > energy and excessive number of iterations ECPs emulate the shielding of core electrons. Since these electrons are not treated explicitly, they do not contribute to the total energy, therefore you get small total energies. Do not compare total energies calculated with ECPs with those resuting from all electron calcs. > Does anyone have any ideas for how I can use ECPs (we are limited to about > 1.2GB) or anything else to get these calculations to run (we do not yet > have DFT). Okay, ECPs are not t h e solution to your problems as long as you do not have to worry about relativistic effects (Not crucial for 3d TMs). If you use them, be sure to use the basis set that comes along with them, since it has been specifically designed for that certain ECP. You do not necessarily need more than 1 GB of disk space, unless you are going to use correlated post-HF methods. DFT would be suitable for your case, since HF is rather inappropriate. However it is not te worst to start with. I hope I could give you some general clues, but it is not easy to do this via email for the problems you have. I would really recommend, you rip some money out of yor advisor's pockets and travel somewhere for a couple of weaks to learn the trade. Good luck! Roland ----------------------------------------------------------------------- Roland H. Hertwig Institut fuer Organische Chemie, TU-Berlin ******************************************************************************** answer 3: From Philippe.Maitre@cth.u-psud.fr Thu May 1 08:13:45 1997 Date: Wed, 30 Apr 1997 18:55:26 +0200 From: Philippe Maitre To: Maiden@RedBrick.DCU.IE Subject: your Mn and Cr complexes, Dear Michael, I have had similar problems and I guess I could help you. You said "I assume the fact that Mn(CO)3 is positively charged has nothing to do with it (it is a closed shell)". I do not agree. The typical problem of SCF convergence with Transition Metal is that you have a near generacy of several d orbitals for low-coordination complexes. This leads to a near degeneracy of electronic configurations, which therby leads to a near degeneracy of determinants. And that's your problem in your iteration. This problem can be further complicated, sometimes, by pseudo potential. I do not have any experience with Gamess-UK, but with a Gaussian92 or Gaussian94, the internal guess of orbitals (either generated by diagonalizing HCORE or by using the extended Huckel approach) is extremely bad when using Pseudo-potential. Do not ask me why, I do not know. Just one more thing : this bad initial guess obtained when using a pseudo potential does not mean at all that the pseudo potentials are bad. There is a simple trick to converge an scf calculation with low-coordinationtransition metal system. You take a piece of paper and you find out the orbital energy level. For ML3 systems, you can look at "Orbital interaction in chemistry" by Albright, Burdett and Whangbo. Then, you find out a spin state (with the same numebr of electrons or not) which leads to a large energy difference between the Ground state electronic configuration and the first electronic one (i.e. where there is a large gap between the HOMO and the LUMO). Run an ROHF or RHF if this is a closed shell on this guy. This will converge easily. One it's done, reuse the converged orbitals of this calculation to calculate your system of interest. Good Luck, If you have any problem, do not hesitate to contact me. But please, give me a geometry and a spin state. Philippe Maitre Laboratoire de chimie theorique Batiment 490 Universite de Paris XI 91405 Orsay , FRANCE ************************************************************************* answer 4: From tcundari@msuvx2.memphis.edu Thu May 1 08:13:52 1997 Date: Wed, 30 Apr 1997 11:57:30 -0600 From: Tom Cundari To: michael nolan Subject: Re: CCL:mn complexes Dear Michael, Noticed you said something about an RHF calc. What is the multiplicity of Cr(CO)3 and Mn(CO)3 fragments you are trying to converge on? Are you using symmetry? Another trick you can try with ECPs is to do a quick first calc on the 2nd row analogue (Mo for Cr, Tc for Mn) and if this converges use this wavefunction to start off a subsequent calculation of the first row metal. 2nd row transition metals often behave better in the SCF since their bonding is more covalent and hence the ligand fields are typically larger. At any rate, with ECPs the number of electrons should be the same and the symmetry props of the MOs should be similar. Good luck. Tom Tom Cundari Associate Professor Department of Chemistry University of Memphis (under T in the ACS Grad Directory!) ***************************************************************************** answer 5: From: chemistry-request (SMTPMAIL.chemistr) at PROFGATE Date: 4/30/97 9:57AM To: Michelle Pietsch at BVL60PO *To: C=us; A= ; P=Internet; DD.RFC-822=chemistry(a)www.ccl.net at X.400 Subject: CCL:mn complexes ------------------------------------------------------------------------------- Michael, To force convergence, increase the value of LEVEL (keyword for GAMESS-UK). You may increase this value until you force convergence. Once the wave function is converging, decrease the value for LEVEL little by little until it is at its default value. Using a large value for LEVEL will force convergence but it may converge in the wrong state. After convergence, print out your molecular orbitals and make sure that the correct orbitals are occupied. If the correct orbitals are not occupied, use the SWAP command to exchange occupied and virtuals until the correct orbitals are occupied. Always check to make sure that you have the correct orbitals occupied after using the SWAP command. You may want to examine the molecular orbitals before convergence and make any SWAPs at that time. I have found this procedure to work well for systems containing Cr and other metals. You should be able to use ECPs and any basis set. However, increasing the number of valence functions will increase the difficulty of convergence. Best of Luck, Mickey ******************************************************************************* answer 6: From bianco@lord.Colorado.EDU Thu May 1 08:14:04 1997 Date: Wed, 30 Apr 1997 09:13:44 -0600 (MDT) From: Roberto Bianco To: michael nolan Subject: Re: CCL:mn complexes Hi Michael, looking at the Metal-C distance of 1.8 angstrom you give below, my guess is that the atomic centers are too far apart for the wavefunction to converge. I would try with initial, artificially shorter Metal-C distances (say 1.2-1.4 A) to achieve convergence, and then let the geometry relax (optimize) through small steps, such that the "memory" of the converged wavefunction is not lost in the process. Roberto -- Roberto Bianco / Department of Chemistry & Biochemistry University of Colorado / Campus Box 215 / Boulder, CO 80309 / USA bianco@lord.colorado.edu / phone +(303) 492-3504 / fax +(303) 492-5894 ************************************************************************** answer 7: From E.A.Moore@open.ac.uk Fri May 9 09:55:50 1997 Date: 1 May 1997 10:08:10 +0100 From: "E.A.Moore (Elaine Moore)" To: michael nolan Subject: Mn and Co complexes Transition metal complexes are vey tricky. You can try 1) Altering the guess option 2) Putting damping on to converge and then feeding the resulting orbitals back in with the damping off 3) reordering the orbitals ECP energies will be smaller because of the missing core electrons. Elaine A. Moore e.a.moore@open.ac.uk ***************************************************************************** Michael Der Kobold hat gesprochen ****************************************************************************** Michael Nolan (nearly BSc.) Dublin City University (quantum chem.) 41 Woodview Chemistry + German Year 4 Lucan Co. Dublin Ireland / Republic of Ireland / ROI / Eire Email: Maiden@redbrick.dcu.ie ****************************************************************************** From fiona@rsc.anu.edu.au Fri May 9 06:41:59 1997 Received: from anugpo.anu.edu.au for fiona@rsc.anu.edu.au by www.ccl.net (8.8.3/950822.1) id GAA17038; Fri, 9 May 1997 06:10:50 -0400 (EDT) Received: from rsc (rsc.anu.edu.au [150.203.35.129]) by anugpo.anu.edu.au (8.8.5/8.8.5) with SMTP id UAA18157 for ; Fri, 9 May 1997 20:10:36 +1000 (EST) Received: from [150.203.37.11] by rsc (SMI-8.6/SMI-SVR4) id UAA16833; Fri, 9 May 1997 20:16:39 +1000 Date: Fri, 9 May 1997 20:16:39 +1000 Message-Id: <199705091016.UAA16833@rsc> Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" To: chemistry@www.ccl.net From: fiona@rsc.anu.edu.au (Dr Fiona Bettens) Subject: Anisotropic Hyperfine Summary Dear Netters, My original query was: >Is anyone aware of any software that will either take the >molecular-orbital expansion coefficients produced in an ab initio >calculation or do the ab initio calculation itself to calculate the >expectation values of the anisotropic hyperfine tensor. By this I >mean the tensor that represents the coupling of the electronic >mangnetic dipole with the nuclear magnetic dipole. I am interested in >transition metal complexes with more than one unpaired electron, this >complicates matters somewhat. I suspect MELDF does what I want, but >it is difficult to find documentation on exactly how it does it. ******************* ******************* The anisotropic hfs is proportional to the efg at the nucleus produced by a hypothetical charge density representing the spin density. Therefore in G94 the input card #P cisd/6-31g** scf=direct density=all IOP(6/26=4,6/17=2) prop=efg is sufficient to generate the anisotropic hf tensor for all nuclei, subject to the appropiate proportionality factors (available from a standard textbook). Sincerely Rod Macrae ******************* ******************* First note that in my reply I am \underline{not} talking about the nuclear quadrupole splitting, which is evaluated by calculating the true efg at the nucleus (i.e. not a spin property) and multiplying it by a nuclear term extracted from a spin hamiltonian treatment of the nuclear component of the interaction. However, this does give a guide as to how to think about the nucleus-electron dipole-dipole hyperfine interaction. The expression will contain an operator (describing the angular and radial properties of the interaction) evaluated at the nucleus. This will be multiplied by a factor in which the nuclear part of the interaction, expressed in terms of a spin hamiltonian, will be embedded. The efg operator takes the form $(3 \cos^{2}\theta_{J}-1)/r^{3}$. (I will write mathematical expressions in Latex form so that you can print them out and look at them if you want.) The nuclear quadrupole coupling has electronic component $V_{zz} = {\langle} \psi_{e} | {\cal V}_{zz} | \psi_{e} {\rangle}$. In the case of the dipolar hyperfine interaction the angular expression in terms of the nuclear-electronic spin hamiltonian is given by (Atkins 14.11.2): \begin{displaymath} \hat{\cal H}_{hf} = \mu_{0} g_{e} \gamma_{e} \gamma_{N} \frac{({\bf s}\cdot{\bf I} - 3 {\bf s}\cdot \hat{\bf r} \hat{\bf r} \cdot {\bf I})}{r^{3}}. \end{displaymath} At this point what generally happens is that a \underline{high field approximation} is made (aligned spins), and all spin components other than the z components disappear. What this explicitly means is that the Zeeman interaction is much larger than the hyperfine interaction, and only the largest terms in the expansion of the dipole-dipole interaction - see e.g. Abragam p. 104 - need be considered (as a perturbation of the Zeeman interaction). It is this procedure that leads to a dipole-dipole coupling proportional to $\frac{1}{r^{3}} (1 - 3 \cos^{2}\theta ) I_Z s_Z$, and therefore essentially proportional to an "electric field gradient" constructed from the spin density (rather than the charge density) distribution. This is the conceptual procedure behind my previous answer. I don't know offhand if 1) this approximation procedure is less valid for I > 1/2, or 2) there is a commercially-available program which performs the calculation using the full expression. (If you find one, I'd very much appreciate it if you'd tell me.) Sincerely Rod Sources: Atkins, Quantum Mechanics, Lucken, Nuclear Quadrupolar Interactions, Abragam, Principles of Nuclear Magnetism. R. M. Macrae, Muon Science Laboratory Institute of Physical and Chemical Research (RIKEN) e-mail: macrae@rikaxp.riken.go.jp (normal) and : macrae@rikmtl.riken.go.jp (MIME-encoded) Tel : (81) 484 62 1111 ext 3336 Fax : (81) 484 62 4648 ******************* ******************* The properties package in MELDF deals with some basic expectaction values, e.g. del(A)s, the del operator on center A evaluated over the spin density. For the anisotropic components of the hyperfine interaction it needs operators like xx/r**5, xy/r**5, yy/r**5, etc. also evaluated over the spin operator. The latter values are combined to form the anisotropic hyperfine (3x3) matrix in the molecular axis system, using a convention that requires the trace of this matrix to have a zero trace. Some of the components are defined as follows: A(xx) = (3/2)*(x2-y2)/r5 - (0.5)*(z2-r2)/r5 A(yy) = -(3/2)*(x2-yy)/r5 - (0.5)*(z2-r2)/r5 A(zz) = (z2-r2)/r5 Ernest Davidson and I have written a chapter in a book on the general topic of computing hyperfine parameters. It's in Theoretical Models of Chemical Bonding, Part 3, Spinger Verlag, 1991. David Feller | Environmental Molecular Sciences Laboratory | Battelle Pacific Northwest National Lab | Mail Stop K1-90 | e-mail:d3e102@emsl.pnl.gov 906 Battelle Blvd | Fax: (509)-375-6631 Richland, WA 99352 | ******************* ******************* The folks at Gaussian should have responded by now, but they haven't, and I've given up on them. But I think that G94 really does calculate the EFG tensor properly. IOp(6/17=2) selects the spin density, rather than the charge density, and IOp(6/26=4) causes only the electronic component of the integrals to be calculated, which is what we want. I have used the EFG to calculate the anisotropic coupling for the methyl radical as was done by Adamo, Barone, and Fortunelli in J. Chem. Phys. 102 (1995) 384, and I can reproduce their values almost exactly ( I think they used a slightly different B3LYP functional ). I then calculated the couplings for an organometallic ion that I've been working on, and I get values that are within 4-18% of experiment (which, incidentally, is the same margin of error as reported by Adamo, et al. for the methyl radical). This looks pretty good, but I'm trying to improve the results. The formula I used is: g B g_n B_n dE T_ii = ----------- -- a^3 h 10^13 dq_i where g and g_n are the electron and nuclear g factors, B and B_n are the corresponding magnetons, a is the bohr radius, and since the tensor is already diagonalized, only the _ii elements are there. G94 reports dE/dq_i in atomic units, which means (1/bohr^3), and I've converted this to MHz for T_ii with the terms in the denominator (there is a factor of 10^7 in the denominator, too, from the permeability constant). Dale Braden Department of Chemistry University of Oregon Eugene, OR 97403-1253 genghis@darkwing.uoregon.edu ******************* ******************* Here is Dan Chipman's response to my query about the problem with the x and y components of the spin operators, spin contamination, etc. Dale Braden ---------- Forwarded message ---------- Dale, It does indeed appear that G94 will do what you want by setting the options you specify. Even so, I would suggest that you make a check by trying to reproduce some number in the literature. I have found that the G94 manual is not always in concordance what what actually happens in the code. The x,y,z indices on the S_x, S_y, and S_z spin operators refer to the components relative to the applied magnetic field, which are generally unrelated to the X,Y,Z coordinates of atoms in the molecule-fixed frame. Usually, S_x and S_y only produce small second-order effects in the hyperfine interaction. For the normal first-order effects, one only need consider S_z. For a good discussion of this, look at the old but good textbook "Introduction to Magnetic Resonance" by Carrington and MacLachlan. "Averaging over spin density" is a somewhat different concept than what you indicate. It means taking the difference between values obtained from the sum of all alpha-spin orbitals and the sum of all beta-spin orbitals. Averaging over the total density, on the other hand, means adding the alpha and beta contributions instead of subtracting them. Unfortunately, taking account of spin contamination is a difficult problem. There is no simple "renormalization" correction that would take care of it. Some people suggest projecting the incorrect spin terms out of the wave function, but that is not really satisfactory either. For isotropic hyperfine interactions, neither unrestricted-Hartree Fock nor any of its spin-projected variants is reliable. However, anisotropic hyperfine interactions are often dominated by the singly-occupied molecular orbital in which case UHF, PUHF, etc. may all work fairly well. That is, when the contribution of the SOMO is dominant, one need not worry about spin contamination effects. If spin contamination is a problem, then one can either resort to spin-restricted approaches, as I usually do, or to correlated methods based on UHF such as UQCISD adn UQCISD(T) that automatically remove most of the spin contamination. Unfortunately, these latter methods are quite expensive. Dan ******************* ******************* I have received several requests about the computation of ESR anisotropic coupling constants by Gaussian94. Since this seems a general question I directly post this message for the whole CCL community. These constants are nothing else than field gradients computed with the spin rather than the total electronic density and not including the nuclear contribution. Furthermore the resulting tensor must be put in the zero-trace form. In gaussian94 it is possible to force these options by setting in the keyword list the following items: PROP IOP(6/17=2,6/26=4) Here follows an input and the relevant part of the output for a STO-3G computation of H2NO ---------------------------------------------------------------------- #UHF/PROP IOP(6/17=2) IOP(6/26=4) H2NO 0 2 X X 1 1.0 N 2 1.0 1 90.0 H 3 NH 2 90.0 1 THETA H 3 NH 2 90.0 1 -THETA O 3 NO 2 ALPHA 1 180.0 NH=1.0179 NO=1.2778 THETA=58.9235 ALPHA=110.0 ---------------------------------------------------------------------- Fermi contact analysis (atomic units). 1 1 N .042923 2 H -.005038 3 H -.005038 4 O .098025 ********************************************************************** Electrostatic Properties Using The SCF Density ********************************************************************** Warning! Using spin rather than total density! --- Only the electronic contributions will be computed --- ----------------------------------------------------- Center ---- Electric Field Gradient ---- XX YY ZZ ----------------------------------------------------- 1 Atom .119043 -.295145 -.363285 2 Atom .002506 .031422 .029384 3 Atom .002506 .031422 .029384 4 Atom 2.130337 -1.663300 -1.698867 ----------------------------------------------------- ----------------------------------------------------- Center ---- Electric Field Gradient ---- ( tensor representation ) 3XX-RR 3YY-RR 3ZZ-RR ----------------------------------------------------- 1 Atom .298838 -.115349 -.183489 2 Atom -.018598 .010318 .008280 3 Atom -.018598 .010318 .008280 4 Atom 2.540947 -1.252690 -1.288257 ----------------------------------------------------- these are the principal values of anisotropic coupling constants ---------------------------------------------------------------------- Since the directions of principal moments are often significant and transforma- tion to more conventional units can be performed once for ever, I have modified the links 601 and 602 of gaussian to obtain the following output for the same input ---------------------------------------------------------------------- ---------------------------------------------------------------------- Isotropic Fermi Contact Couplings ---------------------------------------------------------------------- Atom a.u. MegaHertz Gauss 10(-4) cm-1 1 N(14) .04292 13.86856 4.94865 4.62605 2 H -.00504 -22.51979 -8.03562 -7.51179 3 H -.00504 -22.51979 -8.03562 -7.51179 4 O(17) .09802 -59.42481 -21.20426 -19.82198 ---------------------------------------------------------------------- ********************************************************************** Electrostatic Properties Using The SCF Density ********************************************************************** Warning! Using spin rather than total density! --- Only the electronic contributions will be computed --- Atomic Center 1 is at -.021142 .543231 .000000 Atomic Center 2 is at .158563 1.036966 .871810 Atomic Center 3 is at .158563 1.036966 -.871810 Atomic Center 4 is at -.021142 -.734569 .000000 ----------------------------------------------------- Center ---- Spin Dipole Couplings ---- 3XX-RR 3YY-RR 3ZZ-RR ----------------------------------------------------- 1 Atom .298838 -.115349 -.183489 2 Atom -.018598 .010318 .008280 3 Atom -.018598 .010318 .008280 4 Atom 2.540947 -1.252690 -1.288257 ----------------------------------------------------- Center ---- Spin Dipole Couplings ---- XY XZ YZ ----------------------------------------------------- 1 Atom -.074772 .000000 .000000 2 Atom .004800 .007098 .035617 3 Atom .004800 -.007098 -.035617 4 Atom -.099769 .000000 .000000 ---------------------------------------------------------------------- Anisotropic Spin Dipole Couplings in Principal Axis System ---------------------------------------------------------------------- Atom a.u. MegaHertz Gauss 10(-4) cm-1 Axes Baa -.1835 -7.077 -2.525 -2.361 .0000 .0000 1.0000 1 N(14) Bbb -.1284 -4.953 -1.767 -1.652 .1724 .9850 .0000 Bcc .3119 12.030 4.293 4.013 .9850 -.1724 .0000 1/R**3 -.5394 -20.803 -7.423 -6.939 Baa -.0268 -14.276 -5.094 -4.762 -.2361 -.6571 .7158 2 H Bbb -.0193 -10.278 -3.667 -3.428 .9631 -.2560 .0828 Bcc .0460 24.554 8.762 8.190 .1288 .7090 .6933 1/R**3 .0633 33.780 12.053 11.268 Baa -.0268 -14.276 -5.094 -4.762 .2361 .6571 .7158 3 H Bbb -.0193 -10.278 -3.667 -3.428 .9631 -.2560 -.0828 Bcc .0460 24.554 8.762 8.190 .1288 .7090 -.6933 1/R**3 .0633 33.780 12.053 11.268 Baa -1.2883 93.221 33.264 31.095 .0000 .0000 1.0000 4 O(17) Bbb -1.2553 90.837 32.413 30.300 .0263 .9997 .0000 Bcc 2.5436 -184.059 -65.677 -61.395 .9997 -.0263 .0000 1/R**3 -1.2318 89.138 31.807 29.733 ---------------------------------------------------------------------- ---------------------------------------------------------------------- Vincenzo Barone | Professor of Theoretical Chemistry | Dipartimento di Chimica | tel. +39-81-5476503 Universita' Federico II | fax +39-81-5527771 via Mezzocannone 4 | e-mail ENZO@CHEMNA.DICHI.UNINA.IT I-80134 Napoli | Italy | ______________________________________________________________________ Below is a LaTeX summary of my findings to the original question: **************************************************** \documentstyle{article} \begin{document} \title{Calculation of the Anisotropic Dipolar Coupling Constants} \author{Fiona L. Bettens and Ryan P. A. Bettens} \date{26th March 1997} \maketitle \section{Macroscopic Hamiltonian} The anisotropic hyperfine coupling constants, $A_{\tau\upsilon}$, are phenomenological constants utilized in a ``so called'' spin Hamiltonian, below (see [\ref{bib:car67}] for example). This Hamiltonian is written for one nucleus of nonzero spin, $I_{\upsilon}$, \begin{equation} \hat{\cal H}_{\rm macro} = \mbox{\bf I}^{\dagger} \mbox{\bf A} \mbox{\bf S} = \sum_{\tau\upsilon} A_{\tau\upsilon} \hat{I}_{\tau} \hat{S}_{\upsilon} \end{equation} \noindent where the $\tau$ and $\upsilon$ represent the spaced fixed $X$, $Y$ and $Z$ axes and the operators $\hat{S}_{\upsilon}$ and $\hat{I}_{\tau}$ represent the components of {\it total} electronic spin and nuclear spin respectively. The spin Hamiltonian matrix is set up using the product basis, \begin{equation} |S, M_{S}; I, M_{I}\rangle = |S, M_{S}\rangle |I, M_{I}\rangle . \label{macro2} \end{equation} \section{Microscopic Hamiltonian} The Hamiltonian describing the {\it classical} interaction energy between a nuclear magnetic dipole and the magnetic dipoles of $n$ electrons is [\ref{bib:bev71}], \begin{equation} \hat{\cal H}_{\rm micro} = -\frac{\mu_{0}}{4\pi}g\beta g_{N}\beta_{N} \sum_{i=1}^{n} \left\{ \frac{{\bf I}\cdot{\bf s_{i}}}{{r_{i}}^{3}} - \frac{3({\bf I}\cdot{\bf r_{i}})({\bf s_{i}}\cdot{\bf r_{i}})} {{r_{i}}^{5}} \right\} \label{micro1} \end{equation} \noindent where the dimensionless constants $g$ and $g_{N}$ are the electronic and nuclear $g$ factors respectively; $\beta$ and $\beta_{N}$ are electronic Bohr and nuclear magnetons. The vectors {\bf I}, ${\bf s_{i}}$ and ${\bf r_{i}}$ represent the nuclear spin, electronic spin for electron $i$, and electronic position for electron $i$ with respect to the nucleus, operators. When Eq.\ (\ref{micro1}) is expanded the microscopic Hamiltonian becomes, \begin{equation} \hat{\cal H}_{\rm micro} = -\frac{\mu_{0}}{4\pi}g\beta g_{N}\beta_{N} \sum_{i=1}^{n} \left( \frac{1}{{r_{i}}^{3}}\right) \sum_{\tau,\upsilon}I_{\tau}s_{i\upsilon} \left( \frac{{r_{i}}^{2}\delta_{\tau\upsilon} - 3\tau_{i}\upsilon_{i}} {{r_{i}}^{2}} \right) . \label{micro2} \end{equation} If we consider here a single determinant electronic wavefunction, $\Psi_{q}$, {\it i.e.}, one for a given electronic configuration and labeled here with a $q$, then we can form a product basis with the nuclear spin eigenfunctions which corresponded to the eigenkets given in Eq.\ (\ref{macro2}). The resulting basis vectors are given by, \begin{equation} |q, M_{S}; I, M_{I}\rangle = |q, M_{S}\rangle |I, M_{I}\rangle . \label{micro3} \end{equation} \noindent The basis functions corresponding to these kets are operated upon by the microscopic Hamiltonian, Eq.\ (\ref{micro2}). \section{Equating the Expectation Values} In order to determine the anisotropic hyperfine coupling constants, $A_{\tau\upsilon}$, we compare identical matrix elements of the macroscopic and microscopic Hamiltonian matrices and equate like terms. Here we concern ourselves with only those terms diagonal in $S$ and $I$. Thus we have, \begin{eqnarray} & & \sum_{\tau\upsilon}A_{\tau\upsilon}\langle S, {M_{S}}'; I, {M_{I}}'| I_{\tau}S_{\upsilon} |S, {M_{S}}; I, {M_{I}}\rangle \nonumber \\ & = & -\frac{\mu_{0}}{4\pi}g\beta g_{N}\beta_{N} \sum_{i=1}^{n} \langle q, {M_{S}}'; I, {M_{I}}'| \left( \frac{1}{{r_{i}}^{3}}\right) \nonumber \\ & & \times \sum_{\tau,\upsilon}I_{\tau}s_{i\upsilon} \left( \frac{{r_{i}}^{2}\delta_{\tau\upsilon} - 3\tau_{i}\upsilon_{i}} {{r_{i}}^{2}} \right) |q, M_{S}; I, M_{I}\rangle \label{equate1} \end{eqnarray} \noindent so equating terms we obtain, \begin{equation} \langle S, {M_{S}}'|S_{\upsilon}|S, M_{S}\rangle A_{\tau\upsilon} = k \langle q, {M_{S}}'| \sum_{i=1}^{n} \left( \frac{1}{{r_{i}}^{3}}\right) \sum_{\tau,\upsilon}s_{i\upsilon} \left( \frac{{r_{i}}^{2}\delta_{\tau\upsilon} - 3\tau_{i}\upsilon_{i}} {{r_{i}}^{2}} \right) |q, M_{S}\rangle \label{equate2} \end{equation} \noindent where, \begin{equation} k = -\frac{\mu_{0}}{4\pi}g\beta g_{N}\beta_{N} \label{equate3} \end{equation} \noindent and we have facilitated this comparison by choosing eigenkets for nuclear spin states which have nonzero $M_{I}$, and, of course, a nonzero $I$. The nuclear dipole-electronic dipole interaction is described by the one electron operator given in Eq.\ (\ref{micro1}). When evaluating the expectation value of such an operator when the determinantal wavefunctions representing the bras and kets do not differ, {\it i.e.}, when $q$ and $M_{S}$ are the same in each bra and ket, the following expression can be shown to hold [\ref{bib:sza82}]. \begin{eqnarray} |q\rangle & = & |\cdots lm\cdots\rangle \label{oneelec1} \\ \langle q|\hat{{\cal O}}_{1}|q\rangle & = & \sum_{l}^{n}\langle l|h|l\rangle \label{oneelec2} \end{eqnarray} \noindent where $\hat{{\cal O}}_{1}$ is the one electron operator and is given by, \begin{equation} \hat{{\cal O}}_{1} = \sum_{i=1}^{n}h(i) . \label{oneelec3} \end{equation} \noindent and the $l$ and $m$ labels denote the spinorbitals $\chi_{l}$ and $\chi_{m}$. From Eq.\ (\ref{oneelec1}) - (\ref{oneelec3}), we obtain for Eq.\ (\ref{equate2}) [\ref{bib:bev71}], \begin{equation} A_{\tau \upsilon} = \frac{k}{2\langle S_{Z}\rangle} \sum_{\mu,\nu}^{N}\rho_{\mu\nu} \langle \mu | {r_{i}}^{- 5}({r_{i}}^{2}\delta_{\tau \upsilon} - 3\tau_{i} \upsilon_{i}) |\nu\rangle \label{equate4} \end{equation} \noindent where $\mu$ and $\nu$ are basis functions and the double sum is taken over all of them. The $\rho_{\mu\nu}$ is known as the spin density matrix and is given by the difference in the alpha and beta density matrices. \begin{eqnarray} \rho_{\mu\nu} & = & {P_{\mu\nu}}^{\alpha} - {P_{\mu\nu}}^{\beta} \\ {P_{\mu\nu}}^{\alpha} & = & \sum_{i=1}^{p}{c_{\mu i}}^{\alpha} {c_{\nu i}}^{\alpha} \\ {P_{\mu\nu}}^{\beta} & = & \sum_{i=1}^{q}{c_{\mu i}}^{\beta} {c_{\nu i}}^{\beta} \end{eqnarray} \noindent where the alpha and beta sums are over the $p$ occupied alpha orbitals and the $q$ occupied beta orbitals respectively. The $c_{\mu i}$ are the molecular orbital expansion coefficients for basis functions $\mu$ and MO $i$. Eq.\ (\ref{equate4}) is known as averaging the given orbital operator over spin density. It should be noted that the spin density matrix is intrinsicly different to the charge density matrix, which is the sum of the alpha and beta density matrices. It is of interest that elements of the electric field gradient are calculated in the same way as above except the average is taken over charge density. \section*{Bibliography} \begin{enumerate} \item \label{bib:car67} A. Carrington and A. D. McLachlan, {\it Introduction to Magnetic Resonance} (Harper and Row, New York, 1967). \item \label{bib:bev71} D. L. Beveridge and J. W. McIver, Jr., J. Chem. Phys. {\bf 54}, 4681, (1971). \item \label{bib:sza82} A. Szabo and N. S. Ostlund, {\it Modern Quantum Chemistry: Introduction to Advanced Electronic Structure Theory} (MacMillian, New York, 1983). \end{enumerate} \end{document} Fiona Bettens The Australian National University, Email: Fiona@rsc.anu.edu.au Department of Chemistry, Fax: 61 6 249 0760 Canberra, ACT, 0200, AUSTRALIA From ccl@www.ccl.net Fri May 9 12:53:10 1997 Received: from bedrock.ccl.net for ccl@www.ccl.net by www.ccl.net (8.8.3/950822.1) id MAA23263; Fri, 9 May 1997 12:20:28 -0400 (EDT) Received: from cliff.acs.oakland.edu for bbesler@ouchem.chem.oakland.edu by bedrock.ccl.net (8.8.3/950822.1) id MAA25930; Fri, 9 May 1997 12:20:28 -0400 (EDT) Received: from ouchem.chem.oakland.edu (ouchem.chem.oakland.edu [141.210.108.5]) by cliff.acs.oakland.edu (8.8.5/8.7.3) with SMTP id MAA15279 for ; Fri, 9 May 1997 12:21:15 -0400 (EDT) Received: by ouchem.chem.oakland.edu; id AA14132; Fri, 9 May 1997 12:21:03 -0400 From: "Brent H. Besler" Message-Id: <9705091621.AA14132@ouchem.chem.oakland.edu> Subject: Non-DEC Alpha systems To: chemistry@ccl.net Date: Fri, 9 May 1997 12:21:03 -0500 (EDT) X-Mailer: ELM [version 2.4 PL21] Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Our University has a site license for DEC Unix and DEC compilers which covers non-DEC supplied Alpha systems. It is possible to purchase an Alpha system with 512 MB of RAM, 4GB of hard disk space, and 2 MB of static RAM cache from Microway for under $15,000. Has anyone had positive or negative experiences with the Microway systems? Also, I notice that DEC allows up to 8 MB of static RAM cache on their 500 Mhz Alphas. The motherboard diagram on www.microway.com indicated the Microway system could take 8 MB of cache. Does anyone have experience with the speed difference in the 500 Mhz Alpha with various cache sizes?