From chemistry-request@server.ccl.net Fri Nov 23 06:38:27 2001 Received: from exasp.biogeo.uw.edu.pl ([212.87.8.1]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id fANBcQB01740 for ; Fri, 23 Nov 2001 06:38:27 -0500 Received: (from grzesb@localhost) by exasp.biogeo.uw.edu.pl (8.11.0/8.11.0) id fANBcIR02274; Fri, 23 Nov 2001 12:38:18 +0100 Date: Fri, 23 Nov 2001 12:38:18 +0100 From: Grzegorz Bakalarski To: chemistry@ccl.net Cc: Grzegorz Bakalarski Subject: AIM in g98 problems - NO GOOD SOLUTION --- SUMMARY Message-ID: <20011123123818.A2101@exasp.biogeo.uw.edu.pl> Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Disposition: inline User-Agent: Mutt/1.2.5i Dear CCLer Few days ago I've asked about AIM in Gaussian 98, which failed for calculations performed by my collegue (she wants to get AIM derived bond orders). Unfortunately noone gave a solution for this particular problem. Few people advised to use AIM2000 package from Prof. Bader's group, but this program does not calculate explicitly bond orders. One pointed out that it is possible to estimate bond order > from electronic density at critical point (for bond) usuing formulae given by Prof. Bader (but probably my collegue would have to fit again parameters in this formulae for DFT and used basis set). One also suggested to use NBO instead of AIM. Many thanks for all who responded. Best regards, gb P.S. I also take a loot at Prof. Bader's group's page: http://www.chemistry.mcmaster.ca/faculty/bader/aim/ ******************* ***********************HERE IS SUMMARY: ******************* ******************* -----------------My query------------------------------ A collegue of mine wants to calculate bond orders in guanine molecule and its modifications. She uses g98 and AIM(BO,tight) keyword. She tried different methods and different bases but with no success (she tried b3lyp and HF with bases: STO-3G, 3-21G, 6-31G, 6-31(d), 6-31+G(d,p). The only result is that she got every possible error message (i.e. that some critical points are missing, Newton minimizer fails etc) She also tried to use some IOps (e.g IOp(6/36= ..) IOp(6/38=...) IOp(6/39=...) IOp(6/55=...) but with no success. Is there any tested set IOp's she should try? Or any other solution? Any help is welcome! gb ----------- From: y tantirungrotechai -------- Hi, The best solution is to use density(current) and output(wfn) and punch out the .wfn file. Then use it with Prof. Bader's aimpac or aim2000 developed by his former coworker. Both are free and can download from the net. What you need to add in, for example *******begin********** #p density(current) output(wfn) molecule specfication nameofoutput.wfn **********end *********** Hope this help. Yuthana Tantirungrotechai --------------- From: Matthias Lein ------ Maybe you can use the original aimpac by the Bader group. You just have to create a .wfn file with e.g. g98 and let the aimpac suite of programs do the analysis. Cheers, Matthias. ------------From: y tantirungrotechai --------------------- Hi, Check Bader's book or http://www.ch.ic.ac.uk/ectoc/echet98/pub/048/node8.htm There is an expression relating the bond order and the electron density at the bond critical point. So basically get the density at the bond critical point > from aimpac or aim2000 and use the formula as indicated. Best regards, Yuthana Tantirungrotechai ------------ From: Peeter Burk --------------------- A much better (robust) implementation of AIM analysis is in the original program suite from prof. Bader's group in McMasters University (Canada). The program was (at least some time ago) freely downloadable > from their web site (which I unfortunately do not have at a moment). Hope that helps Peeter -------------From: Steve Williams ---------------- >Do you think that in AIM2000 program there is easy way >to calculate BOND ORDERS????? I've downloaded the >program and cannot find how ... Should I integrate >over some basins ??? Unfortunately, the answer is no. As far as I know, the only population based AIM method for getting bond orders is in gaussian. Anything else you might want to do with aim is easier with aim2000, but it does not do bond orders. However, you can calibrate the critical density to give bond orders, as described in Bader's book. This involves choosing a scale factor such that the exponential function in Bader's book gives 1, 2, or 3 > from the critical density for ethane, ethene, and ethyne for instance. You can then get other c-c bond orders from the critical densities in your molecule. Steve ---------------- From: Eric Glendening -------- Your colleague might consider using the NBO analysis. The NBO program is straightforward to use and very efficient. It is distributed (version 3.1) with Gaussian 98. Several measures of bond order are evaluated. For example, following input ------------------------------- #b3lyp/6-31g* pop=nboread Formamide...b3lyp/6-31g* 0 1 C 0.000000 0.420333 0.000000 O 1.201750 0.236462 0.000000 N -0.940819 -0.565065 0.000000 H -0.457873 1.430460 0.000000 H -0.642312 -1.531146 0.000000 H -1.928080 -0.357560 0.000000 $nbo bndidx $end ------------------------------- prints the Wiberg bond indices. ------------------------------- Wiberg bond index matrix in the NAO basis: Atom 1 2 3 4 5 6 ---- ------ ------ ------ ------ ------ ------ 1. C 0.0000 1.7226 1.2109 0.8934 0.0065 0.0028 2. O 1.7226 0.0000 0.1920 0.0710 0.0064 0.0188 3. N 1.2109 0.1920 0.0000 0.0065 0.8013 0.8118 4. H 0.8934 0.0710 0.0065 0.0000 0.0177 0.0000 5. H 0.0065 0.0064 0.8013 0.0177 0.0000 0.0001 6. H 0.0028 0.0188 0.8118 0.0000 0.0001 0.0000 Wiberg bond index, Totals by atom: Atom 1 ---- ------ 1. C 3.8361 2. O 2.0107 3. N 3.0224 4. H 0.9885 5. H 0.8319 6. H 0.8335 ------------------------------- More information about NBO is at http://www.chem.wisc.edu/~nbo5 Eric Glendening From chemistry-request@server.ccl.net Fri Nov 23 07:16:08 2001 Received: from oxygen.chem.nthu.edu.tw ([140.114.45.223]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id fANCG8B02598 for ; Fri, 23 Nov 2001 07:16:08 -0500 Received: by oxygen.chem.nthu.edu.tw (Postfix, from userid 212) id ADBB3A216; Fri, 23 Nov 2001 20:16:04 +0800 (CST) Date: Fri, 23 Nov 2001 20:16:04 +0800 From: chem@oxygen.chem.nthu.edu.tw To: =?iso-8859-1?Q?Jes=FAs_Rodr=EDguez_Otero?= Cc: chemistry@ccl.net Subject: Re: CCL:Athlon vs P4 for G98 Message-ID: <20011123201604.A17480@OXYGEN.chem.nthu.edu.tw> References: <000001c16db1$d5822640$9a4a90c1@usc.es> Mime-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Disposition: inline Content-Transfer-Encoding: 8bit User-Agent: Mutt/1.2.5i In-Reply-To: <000001c16db1$d5822640$9a4a90c1@usc.es>; from qftjesus@usc.es on Wed, Nov 14, 2001 at 06:58:23PM +0100 On Wed, Nov 14, 2001 at 06:58:23PM +0100, Jesús Rodríguez Otero wrote: > Hi > > Anybody has benchmarks about Athlon XP DDR versus P4 RDRAM using Gaussian98?? > > For the P 4, is the RDRAM clearly advantageous as contrasted with SDRAM? > The economic difference is very large!! > We are doing a huge series of benchmark on this. All jobs are expected to finish next week. I'll post a hyperlink here then. -- Jen-Shiang Kenny Yu // jsyu@Platinum.chem.nthu.edu.tw Theoretical Chemistry Lab, Department of Chemistry, National Tsing Hua University Hsinchu 300, TAIWAN From chemistry-request@server.ccl.net Fri Nov 23 10:38:11 2001 Received: from mercury.chem.nwu.edu (hutchisn@[129.105.116.2]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id fANFcBB06953 for ; Fri, 23 Nov 2001 10:38:11 -0500 Received: from localhost (hutchisn@localhost) by mercury.chem.nwu.edu (8.11.3/8.11.3) with ESMTP id fANFc8922615; Fri, 23 Nov 2001 09:38:08 -0600 (CST) Date: Fri, 23 Nov 2001 09:38:08 -0600 (CST) From: Geoff Hutchison X-X-Sender: To: Christoph Nimptsch cc: Subject: Re: CCL:Convert MOs between G98/Jaguar and GAMESS In-Reply-To: <3.0.6.32.20011122090814.007aedd0@cpbnc01.mail.uni-tuebingen.de> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Thu, 22 Nov 2001, Christoph Nimptsch wrote: > > Hi, all! I'd like to convert MOs from G98/Jaguar calculations to GAMESS's > > $vec format. Does any one know where to find a program or scripts to do so? > > Thanks! > Have you tried Babel? It is free and can convert a number of file formats > into each other. While Babel is a nice program, it does not convert anything beyond cartesian coordinates (and atom and bond types if one of the formats uses these). It does not attempt to deal with things like total charge, spin, orbital energies, MOs/eigenvectors, etc. Now it might be nice to figure out ways to add these "on top" of Babel, but that's a different story. -- -Geoff Hutchison Marks/Ratner Groups (847) 491-3295 Northwestern Chemistry From chemistry-request@server.ccl.net Fri Nov 23 13:39:27 2001 Received: from mcmail.cis.mcmaster.ca (mattacf@[130.113.64.66]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id fANIdQB09887 for ; Fri, 23 Nov 2001 13:39:27 -0500 Received: from localhost (mattacf@localhost) by mcmail.cis.mcmaster.ca with ESMTP id NAA06056; Fri, 23 Nov 2001 13:39:12 -0500 (EST) Date: Fri, 23 Nov 2001 13:39:12 -0500 (EST) From: "C.F. Matta" To: Grzegorz Bakalarski cc: Subject: Re: CCL:AIM in g98 problems In-Reply-To: <20011123123818.A2101@exasp.biogeo.uw.edu.pl> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear Dr. Bakalarski I am sorry to answer you with some delay. I understand you would like to compute "bond orders (B.O.)" using the equation which relates it empirically to the electron density at the bond critical point Rho(b): B.O. = exp { c [ Rho(b) - c' ] }. I suggest that instead of this empirical relationship, you may perhaps whish to consider a "real physical measure" of the degree of electron sharing between two atoms (whether bonded or not). I refer to the AIM delocvalization indices (delta). This gives you directly the number of pairs shared between any two atoms in a molecule, whether they are linked by a bond path or not (Sure enough the delocalization index is much higher when there is a bond path). The delocalization index is defined in terms of the product of the overlap integrals integrated over atomic basins: Delta(atomA, AtomB) = 4 SUM(i)SUM(j) Sij(atomA) Sij(atomB) where the factor 4 arises from 2(alpha and beta electrons) x 2 (contribution AB + contribution BA, which are equal). To give you a few numerical examples: Delta (N,N)=3.005 pairs in N2 molecule, Delta (H,H) = 1.000 in H2, Delta (C,C) =1.00 and Delta (C,H) = 0.99 in ethane, Delta (C,C) =1.85 in ethylene, and Delta (C,C) = 1.39 in benzene. We have used this index extensively in the recent literature. The way to calculate it: (1) Generagte the wavefunction. (2) Perform the atomic integrations using AIMPAC (taking care to turn on the "overlap matrix" option ON during the atomic integrations. AIMPAC is available free of charge at: http://www.chemistry.mcmaster.ca/aimpac/ (3) Use the program AIMDELOC to calculate the localization and deloxcalization indices matrix. (available either directly from myself) or from the QCPE web site: http://qcpe.chem.indiana.edu/ REFERENCES: =========== (1) Definition of the delocalization and localization indeces: Fradera, X., Austen, M.A. & Bader, R.F.W. (1999) "The Lewis model and beyond". J. Phys. Chem. A, 103, 304-314. Bader, R.F.W., Streitwieser, A., Neuhaus, A., Laidig, K.E. & Speers, P. (1996) "Electron delocalization and the Fermi hole." J. Am. Chem. Soc., 118, 4959-4965. (2) Program to calculate the delocalization and localization indices: Matta, C. F. (2001) "AIMDELOC01 (QCPE0802): Program to calculate AIM localization and delocalization indeces". Quantum Chemistry Program Exchange, Indiana University. (http://qcpe.chem.indiana.edu/ ) (3) Recent example of application of the delocalization indeces in organometallic chemistry: Bader, R.F.W. & Matta, C.F. (2001) Bonding to titanium. Inorg. Chem., 40, 5603-5611. Best wishes. Cherif ___________________________________________________________________________ Cherif F. Matta tel. (905) 525-9140 ext. 22502 Chemistry Department fax (905) 522-2509 McMaster University Hamilton, Ontario, CANADA L8S 4M1. ___________________________________________________________________________ On Fri, 23 Nov 2001, Grzegorz Bakalarski wrote: > Dear CCLer > > Few days ago I've asked about AIM in Gaussian 98, which failed for > calculations performed by my collegue (she wants to get AIM derived > bond orders). > Unfortunately noone gave a solution for this particular problem. > Few people advised to use AIM2000 package from Prof. Bader's group, > but this program does not calculate explicitly bond orders. > One pointed out that it is possible to estimate bond order > > from electronic density at critical point (for bond) usuing > formulae given by Prof. Bader (but probably my collegue > would have to fit again parameters in this formulae for DFT > and used basis set). > One also suggested to use NBO instead of AIM. > Many thanks for all who responded. > > Best regards, > > gb > > P.S. I also take a loot at Prof. Bader's group's page: > http://www.chemistry.mcmaster.ca/faculty/bader/aim/ > > ******************* > ***********************HERE IS SUMMARY: ******************* > ******************* > > -----------------My query------------------------------ > A collegue of mine wants to calculate bond orders in > guanine molecule and its modifications. She uses g98 > and AIM(BO,tight) keyword. She tried different methods and different > bases but with no success (she tried b3lyp and HF with > bases: STO-3G, 3-21G, 6-31G, 6-31(d), 6-31+G(d,p). > The only result is that she got every possible error > message (i.e. that some critical points are missing, > Newton minimizer fails etc) She also tried to use > some IOps (e.g IOp(6/36= ..) IOp(6/38=...) IOp(6/39=...) > IOp(6/55=...) but with no success. > Is there any tested set IOp's she should try? Or any other > solution? > Any help is welcome! > > gb > > ----------- From: y tantirungrotechai -------- > Hi, > The best solution is to use density(current) and > output(wfn) and punch out the .wfn file. Then use it > with Prof. Bader's aimpac or aim2000 developed by his > former coworker. Both are free and can download from > the net. > > What you need to add in, for example > *******begin********** > #p density(current) output(wfn) > > molecule specfication > > nameofoutput.wfn > > **********end *********** > > Hope this help. > Yuthana Tantirungrotechai > > > > --------------- From: Matthias Lein ------ > Maybe you can use the original aimpac by the Bader group. You just have > to create a .wfn file with e.g. g98 and let the aimpac suite of programs > do the analysis. > > Cheers, > Matthias. > > > ------------From: y tantirungrotechai --------------------- > Hi, > Check Bader's book or > http://www.ch.ic.ac.uk/ectoc/echet98/pub/048/node8.htm > There is an expression relating the bond order and the > electron density at the bond critical point. So > basically get the density at the bond critical point > > from aimpac or aim2000 and use the formula as > indicated. > > Best regards, > Yuthana Tantirungrotechai > > > > > ------------ From: Peeter Burk --------------------- > A much better (robust) implementation of AIM analysis is in the original > program suite from prof. Bader's group in McMasters University > (Canada). The program was (at least some time ago) freely downloadable > > from their web site (which I unfortunately do not have at a moment). > > Hope that helps > Peeter > > > > -------------From: Steve Williams ---------------- > >Do you think that in AIM2000 program there is easy way > >to calculate BOND ORDERS????? I've downloaded the > >program and cannot find how ... Should I integrate > >over some basins ??? > > Unfortunately, the answer is no. As far as I know, the only population > based AIM method for getting bond orders is in gaussian. Anything else you > might want to do with aim is easier with aim2000, but it does not do bond > orders. However, you can calibrate the critical density to give bond > orders, as described in Bader's book. This involves choosing a scale > factor such that the exponential function in Bader's book gives 1, 2, or 3 > > from the critical density for ethane, ethene, and ethyne for instance. You > can then get other c-c bond orders from the critical densities in your > molecule. > Steve > > > ---------------- From: Eric Glendening -------- > Your colleague might consider using the NBO analysis. The NBO program > is straightforward to use and very efficient. It is distributed > (version 3.1) with Gaussian 98. Several measures of bond order > are evaluated. For example, following input > > ------------------------------- > #b3lyp/6-31g* pop=nboread > > Formamide...b3lyp/6-31g* > > 0 1 > C 0.000000 0.420333 0.000000 > O 1.201750 0.236462 0.000000 > N -0.940819 -0.565065 0.000000 > H -0.457873 1.430460 0.000000 > H -0.642312 -1.531146 0.000000 > H -1.928080 -0.357560 0.000000 > > $nbo bndidx $end > > ------------------------------- > > prints the Wiberg bond indices. > > ------------------------------- > > Wiberg bond index matrix in the NAO basis: > > Atom 1 2 3 4 5 6 > ---- ------ ------ ------ ------ ------ ------ > 1. C 0.0000 1.7226 1.2109 0.8934 0.0065 0.0028 > 2. O 1.7226 0.0000 0.1920 0.0710 0.0064 0.0188 > 3. N 1.2109 0.1920 0.0000 0.0065 0.8013 0.8118 > 4. H 0.8934 0.0710 0.0065 0.0000 0.0177 0.0000 > 5. H 0.0065 0.0064 0.8013 0.0177 0.0000 0.0001 > 6. H 0.0028 0.0188 0.8118 0.0000 0.0001 0.0000 > > > Wiberg bond index, Totals by atom: > > Atom 1 > ---- ------ > 1. C 3.8361 > 2. O 2.0107 > 3. N 3.0224 > 4. H 0.9885 > 5. H 0.8319 > 6. H 0.8335 > > ------------------------------- > > More information about NBO is at http://www.chem.wisc.edu/~nbo5 > > Eric Glendening > > > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH > CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net 70 > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net > > > > > > From chemistry-request@server.ccl.net Fri Nov 23 14:19:39 2001 Received: from mail.rpi.edu (root@[128.113.22.40]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id fANJJdB10641 for ; Fri, 23 Nov 2001 14:19:39 -0500 Received: from webmail.rpi.edu (webmail.rpi.edu [128.113.26.21]) by mail.rpi.edu (8.11.3/8.11.3) with ESMTP id fANJJVZ89848; Fri, 23 Nov 2001 14:19:31 -0500 Message-Id: <200111231919.fANJJVZ89848@mail.rpi.edu> Content-Type: text/plain Content-Disposition: inline To: grzesb@asp.biogeo.uw.edu.pl From: "Dr. N. SUKUMAR" Organization: Rensselaer Polytechnic Institute Cc: chemistry@ccl.net X-Originating-Ip: 63.20.207.134 Mime-Version: 1.0 Reply-To: "Dr. N. SUKUMAR" Date: Fri, 23 Nov 2001 14:19:30 EST X-Mailer: EMUmail 4.00 Subject: Re: CCL:AIM in g98 problems - NO GOOD SOLUTION --- SUMMARY Aren't bond orders a somewhat arbitrary concept? The simplest -- and also cheapest -- way of estimating bond orders I know of is simply to use a distance criterion and parametrize for different bonds. Some molecular modeling software do just this. But calculating bond orders ab initio? I'm afraid that really depends on how you define bond orders. More elaborate ways have been employed in the literature to calculate bond orders, but really it depends on whose definition you accept (see, e.g. J.S. Murray, N.Sukumar, S.Ranganathan and P.Politzer, “A Computational Analysis of the Electrostatic Potentials and Relative Bond Strengths of Hydrazine and some of its 1,1-Dimethyl Derivatives” Intl. J. Quantum Chem. 38, 611-629, 1990). I personally think that the bond order concept today provides no more useful information than bond length or bond dissociation energy, both of which can be unambiguously defined. AIM can be used to determine the existence or absence of a bond path between atoms in a molecule. It does not distinguish multiple bonds. Dr. N. Sukumar Rensselaer Department of Chemistry From chemistry-request@server.ccl.net Fri Nov 23 20:31:34 2001 Received: from carbon.chem.ucla.edu ([128.97.35.55]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id fAO1VYB20122 for ; Fri, 23 Nov 2001 20:31:34 -0500 Received: from [128.97.45.113] ([128.97.45.113]) by carbon.chem.ucla.edu (8.11.4/8.11.4) with ESMTP id fAO1VXC25293 for ; Fri, 23 Nov 2001 17:31:33 -0800 (PST) Mime-Version: 1.0 Message-Id: Date: Fri, 23 Nov 2001 17:31:29 -0800 To: chemistry@ccl.net From: Eric Scerri Subject: A question on C.I. Content-Type: multipart/alternative; boundary="============_-1205557004==_ma============" --============_-1205557004==_ma============ Content-Type: text/plain; charset="us-ascii" ; format="flowed" A question on C.I. Under what circumstances would one still maintain that a CI calculation can be associated with a particular configuration? Would the coefficient in front of that particular matrix need to be 0.9 or something in that region? What would be a good source to examine such coefficients for the atoms in the periodic table for most stable configurations short of actually doing CI calculations? Is there a web page that allows one to do CI for atoms in a similar way to the Hartree-Fock sites such as the one designed by Froese Fischer? regards, eric -- Dr. Eric Scerri , UCLA, Department of Chemistry & Biochemistry, 607 Charles E. Young Drive East, Los Angeles, CA 90095-1569 USA E-mail : scerri@chem.ucla.edu tel: 310 206 7443 fax: 310 206 2061 Web Page: http://www.chem.ucla.edu/dept/Faculty/scerri/index.html Editor of Foundations of Chemistry http://www.wkap.nl/journalhome.htm/1386-4238 Also see International Society for the Philosophy of Chemistry http://www.georgetown.edu/earleyj/ISPC.html --============_-1205557004==_ma============ Content-Type: text/html; charset="us-ascii" A question on C.I.
A question on C.I.

Under what circumstances would one still maintain that a CI
calculation can be associated with a particular configuration?  Would
the coefficient in front of that particular matrix need to be 0.9 or
something in that region?

What would be a good source to examine such coefficients for the atoms in the periodic table for most stable configurations short of actually doing CI calculations?  Is there a web page that allows one to do CI for atoms in a similar way to the Hartree-Fock sites such
as the one designed by Froese Fischer?
 
regards,
eric

--

Dr. Eric Scerri ,
UCLA,
Department of Chemistry & Biochemistry,
607 Charles E. Young Drive East,
Los Angeles,  CA 90095-1569
USA

E-mail :   scerri@chem.ucla.edu
tel:  310 206 7443
fax:  310 206 2061
Web Page:    http://www.chem.ucla.edu/dept/Faculty/scerri/index.html

Editor  of  Foundations of Chemistry
http://www.wkap.nl/journalhome.htm/1386-4238

Also see International Society for the Philosophy of Chemistry
http://www.georgetown.edu/earleyj/ISPC.html
--============_-1205557004==_ma============--