From sschulz@chemie.fu-berlin.de Tue Oct 3 04:22:05 1995 Received: from spider.chemie.fu-berlin.de for sschulz@chemie.fu-berlin.de by www.ccl.net (8.6.10/950822.1) id EAA06094; Tue, 3 Oct 1995 04:16:34 -0400 Message-Id: <199510030816.EAA06094@www.ccl.net> Received: by spider.chemie.fu-berlin.de (1.37.109.16/16.2) id AA150718188; Tue, 3 Oct 1995 09:16:28 +0100 From: Stefan Schulz Subject: cc-pVTZ basis set for Na To: chemistry@www.ccl.net Date: Tue, 3 Oct 95 9:16:28 MEZ X-Hpvue$Revision: 1.8 $ Mime-Version: 1.0 Content-Type: Message/rfc822 X-Vue-Mime-Level: 4 Mailer: Elm [revision: 70.85] Dear CCLers, I am currently using the cc-pVTZ basis set for the sodium atom as implemented in the MOLPRO94 package. While trying to find the original work about the cc-pVTZ basis set for the sodium atom I came across the basis set library at http://www.emsl.pnl.gov:2080/forms/basisform.html which gave me the following information: Basis Set Library Information on: cc-pVTZ Correlation Consistent Polarized Valence Triple Zeta (cc-pVTZ) Basis -------------------------------------------------------------------- Elements Contraction References H : (5s,2p,1d) -> [3s,2p,1d] T.H. Dunning, Jr. J. Chem. Phys. 90, 1007 (1989). He : (6s,2p,1d) -> [3s,2p,1d] D.E. Woon and T.H. Dunning, Jr., J. Chem. Phys. 100, 2975 (1994). Li - Ne: (10s,5p,2d,1f) -> [4s,3p,2d,1f] T.H. Dunning, Jr. J. Chem. Phys. 90, 1007 (1989). Na : (16s,10p,2d,1f)-> [5s,4p,2d,1f] D. Woon and T.H. Dunning, Jr. Mg : (15s,10p,2d,1f)-> [5s,4p,2d,1f] (to be published) Al - Ar: (15s,9p,2d,1f) -> [5s,4p,2d,1f] D.E. Woon and T.H. Dunning, Jr., J. Chem. Phys. 98, 1358 (1993). Does somebody know the cc-pVTZ Na basis set reference? Many thanks in advance, Stefan schulz =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= | | Stefan Schulz | | sschulz@chemie.fu-berlin.de | FU Berlin - Theoretical Chemistry | | Tel. ++49/30/838 5384 (2351) | Takustrasse 3 | | FAX. ++49/30/838 4792 | D-14195 Berlin | =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= From owner-chemistry@ccl.net Tue Oct 3 05:07:05 1995 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.6.10/950822.1) id FAA06553; Tue, 3 Oct 1995 05:00:35 -0400 Received: from relay-3.mail.demon.net for paul@heelisp.demon.co.uk by bedrock.ccl.net (8.6.10/950822.1) id FAA28732; Tue, 3 Oct 1995 05:00:30 -0400 Date: Tue, 3 Oct 1995 05:00:30 -0400 Received: from heelisp.demon.co.uk by relay-3.mail.demon.net id aa20953; 2 Oct 95 20:44 +0100 X-Sender: (Unverified) Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" To: CHEMISTRY@ccl.net From: Paul Heelis Subject: transition metal redox Message-ID: <9510022045.aa20953@relay-3.mail.demon.net> Dear CCl's, I am interested in using the SAM1 method and ZINDO to correlate the redox properties of various Iron II and III complexes with computed parameters such as HOMO energy, IP potential. Has anyone come across similar work or would like to suggest the best approach. Any useful replies will be summarised. Paul Heelis North East Wales Institute, UK Heelisp@newi.ac.uk From pwalters@portal.vpharm.com Tue Oct 3 09:52:09 1995 Received: from portal.vpharm.com for pwalters@portal.vpharm.com by www.ccl.net (8.6.10/950822.1) id JAA09603; Tue, 3 Oct 1995 09:43:26 -0400 Received: by portal.vpharm.com (AIX 3.2/UCB 5.64/4.03) id AA18386; Tue, 3 Oct 1995 09:29:05 -0400 Date: Tue, 3 Oct 1995 09:29:05 -0400 (EDT) From: Pat Walters Sender: Pat Walters Reply-To: Pat Walters Subject: Bond Order Revisited To: chemistry@www.ccl.net Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; CHARSET=US-ASCII Dear Netters, I guess I wasn't clear in my request for bond order algorithms. I am not interested fractional bond orders or natural bond orders. I would like to be able to simply assign single, double and triple bonds in a molecule. Wally Reiher sent me the following excerpt from the DGEOM 95 release notes: New Features * Automatic connectivity generation and double bond assignment (even for conjugated and aromatic systems). This eliminates the need for supplying CONECT records and/or editing them to specify double bonds for most organic structures, including peptides and nucleotides. Automatic connectivity generation will be performed if CONECT records are missing. This is exactly what I want to do. Apparently the routines in DGEOM 95 are adapted from a program called PSSHOW by Eric Swanson. I would like to know if anyone knows of a paper describing how this method works. I'd also like to hear from anyone who could tell me more about PSSHOW. Any other relevant information would also be appreciated. Anything I learn will eventually end up in Babel and everyone will be able to use it. Thanks in advance, Pat ------------------------------------------------------------------ W. Patrick Walters, Ph.D. Scientist, Computational Chemistry and Molecular Modeling Vertex Pharmaceuticals, Inc., 40 Allston St., Cambridge, MA 02139 Voice: (617)576-3111 FAX: (617)576-2109 From itsigeln@chem.ucsd.edu Tue Oct 3 14:22:13 1995 Received: from UCSD.EDU for itsigeln@chem.ucsd.edu by www.ccl.net (8.6.10/950822.1) id OAA16112; Tue, 3 Oct 1995 14:15:58 -0400 Received: from chem.chem.ucsd.edu (chem.ucsd.edu [132.239.68.1]) by UCSD.EDU (8.6.12/8.6.9) with SMTP id LAA18923 for ; Tue, 3 Oct 1995 11:15:50 -0700 Received: by chem.chem.ucsd.edu (5.51) id AA01599; Tue, 3 Oct 95 11:14:17 PDT Received: by chemod0.ucsd.edu (931110.SGI) id AA01887; Tue, 3 Oct 95 11:18:34 -0700 Date: Tue, 3 Oct 95 11:18:34 -0700 From: itsigeln@chem.ucsd.edu (Igor Tsigelny) Message-Id: <9510031818.AA01887@chemod0.ucsd.edu> To: CHEMISTRY@www.ccl.net Subject: ATP GTP data Cc: itsigeln@chem.ucsd.edu Dear CCLers, I try to find information about the charges distribution in ATP, ADP and GTP, GDP. I foung the papre of Foley et al. in Biochemistry 1992, 31, 4951, where they estimated the partial atomic charges of GTP using 3-21G* and 6-31G** basis set. But they di dnot give the numbers of those charges. I think that those tipe of calculations were done for all these molecules (ATP, ADP, GTP , and GDP) so it will be so helpful if you can give me some references or/and data. Sincerely Igor Tsigelny ------------------------------------------------ IGOR TSIGELNY Ph.D. University of California, San Diego itsigeln@ucsd.edu From patrick@hartree1.rug.ac.be Tue Oct 3 18:52:16 1995 Received: from mserv.rug.ac.be for patrick@hartree1.rug.ac.be by www.ccl.net (8.6.10/950822.1) id SAA21772; Tue, 3 Oct 1995 18:42:37 -0400 Received: from allserv.rug.ac.be by mserv.rug.ac.be with SMTP id AA09226 (5.67b/IDA-1.5 for ); Tue, 3 Oct 1995 23:42:12 +0100 Received: from hartree1.rug.ac.be by allserv.rug.ac.be (5.x/SMI-SVR4) id AA10050; Tue, 3 Oct 1995 14:40:33 +0100 Received: by hartree1.rug.ac.be (AIX 3.2/UCB 5.64/4.03) id AA09054; Tue, 3 Oct 1995 14:39:15 +0200 Date: Tue, 3 Oct 1995 14:39:15 +0200 (DFT) From: Patrick Bultinck To: chemistry@www.ccl.net Subject: Morokuma eda, summary Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear netters, It turns out that there are not too many programs which allow for Morokuma energy decomposition analysis out there... Gamess and Monstergauss are capable, and it is on the g94 wish-list. My problem was mainly that I cannot do a direct SCF calculation with GAMESS, AND a Morokuma eda. The problem is still not really solved ! Several people mentionned the $SCF DIRSCF=.TRUE. $END line for GAMESS runs, but... I found in INPUT.DOC (GAMESS documentation) that this line is not compatible with : RUNTYP=MOROKUMA. Thanks for the effort, but it seems I am buying a 10 GB disk... Patrick P.S. Note from INPUT.DOC The present implementation has some quirks: 1. The initial guess of the monomer orbitals is always HCORE, so check your monomer energies carefully! 2. There is no restart capability. 3. The use of symmetry is turned off internally. 4. There is no direct SCF option. Two separate integral files are used, so extra disk space is needed. 5. The option applies only to ab initio RHF cases. From patrick@hartree1.rug.ac.be Tue Oct 3 19:07:16 1995 Received: from mserv.rug.ac.be for patrick@hartree1.rug.ac.be by www.ccl.net (8.6.10/950822.1) id SAA21867; Tue, 3 Oct 1995 18:46:02 -0400 Received: from allserv.rug.ac.be by mserv.rug.ac.be with SMTP id AA10133 (5.67b/IDA-1.5 for ); Tue, 3 Oct 1995 23:46:00 +0100 Received: from hartree1.rug.ac.be by allserv.rug.ac.be (5.x/SMI-SVR4) id AA09616; Tue, 3 Oct 1995 14:32:00 +0100 Received: by hartree1.rug.ac.be (AIX 3.2/UCB 5.64/4.03) id AA10071; Tue, 3 Oct 1995 14:30:30 +0200 Date: Tue, 3 Oct 1995 14:30:27 +0200 (DFT) From: Patrick Bultinck To: chemistry@www.ccl.net Subject: CCL:G:Stuttgart Pseudopotentials, summary Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII A while ago I asked about the use of Stuttgart-Pseudopotentials with programs such as GAMESS, or GAUSSIAN. The reason for this question was simply the fact that I was told my calculations had to be incorrect because the Stuttgart PP's would NOT be compatible with GAMESS, nor GAUSSIAN. However, I tested the use of these PP's by reproducing some published results, and it turned out quite okay. The man got me scared enough, because I had submitted some material for publication, and I started fearing to have blundered. However, it turns out that I was correct ! You CAN use them with gamess, gaussian, etc. if AND ONLY IF you take care of the following (which I did for the submitted material). Most programs like Gaussian or GAMESS take Hay-Wadt and SBK type pseudopotentials without problem. It was my idea that they'd also take Stuttgart PP's then, since the functional expansions are exactly the same, and you only have to take care in the absence/presence of a term U_Lmax. The fact is that there is a LOCAL potential in the HW case, but none in the SP case (HW=Hay-Wadt, SP=Stoll-Preuss (Stuttgart)). Taking into account the fact that : 1/ the Coulombic term is the same for both types 2/ the functional expansions are the same for both types 3/ HW give values for U_l-U_Lmax terms, and SP give them for simple U_l's So the principal thing to do is to make sure that the U_l's from SP are treated as U_l's, and not some U_Lmax where U_Lmax has an expansion coeff. other than zero... Some people used the SP's by simply typing them in as U_l1, U_l2 etc., but this brings about the problem that U_l2 is not used as U_l2, but as U_l2-U_l1. Needless to say that this brings quite large trouble... So to be sure you have to ADD a U_Lmax with a zero coefficient so that U_l2 is regarded as U_l2-0 = U_l2... So if we have a look at e.g. Kaupp et al., J. Chem. Phys., 94(2), 1994, page 1360, table V, you should NOT type them in like that, instead e.g. for Ba-eda complexes you make an input file like : GAMESS $CONTRL SCFTYP=RHF RUNTYP=OPTIMIZE MPLEVL=0 EXETYP=RUN MAXIT=60 ICHARG=2 MULT=1 ECP=READ COORD=UNIQUE UNITS=ANGS PLTORB=.TRUE. $END $SYSTEM TIMLIM=6000 $END $DATA ML1 (M=Ba, L=EDA) C1 C1 6.0 2.6334798056 .7948995815 -.2986987461 N31 6 L 1 1 .0438000000 1.00000000 1.00000000 D 1 1 .8000000000 1.00000000 N2 7.0 1.4449298124 1.5568068287 .1673421777 N31 6 L 1 1 .0639000000 1.00000000 1.00000000 D 1 1 .8000000000 1.00000000 BA3 56.0 -.9055002857 -.0357795561 -.0061803598 S 4 1 7.534953 -0.109880 2 4.349914 0.521701 3 2.101075 -0.965838 4 0.431167 0.899494 S 1 1 0.207402 1.0 S 1 1 0.045686 1.0 S 1 1 0.019287 1.0 P 4 1 2.915898 -0.494299 2 2.209730 0.954769 3 1.385694 -0.287822 4 0.442754 -0.665119 P 1 1 0.193704 1.0 P 1 1 0.047209 1.0 P 1 1 0.020055 1.0 D 3 1 1.282886 -0.096560 2 0.649498 0.143954 3 0.276523 0.304285 D 2 1 0.105884 0.478247 2 0.036134 0.368057 N4 7.0 1.5653776307 -1.4378371894 -.1469127736 N31 6 L 1 1 .0639000000 1.00000000 1.00000000 D 1 1 .8000000000 1.00000000 C5 6.0 2.6835773070 -.5848300856 .3351195397 N31 6 L 1 1 .0438000000 1.00000000 1.00000000 D 1 1 .8000000000 1.00000000 H6 1.0 3.5467384473 1.3297986593 -.0646853243 N31 6 S 1 1 .0360000000 1.00000000 P 1 1 1.1000000000 1.00000000 H7 1.0 2.5842143635 .7120250697 -1.3800104778 N31 6 S 1 1 .0360000000 1.00000000 P 1 1 1.1000000000 1.00000000 H8 1.0 1.6185529594 1.8582868540 1.1150402787 N31 6 S 1 1 .0360000000 1.00000000 P 1 1 1.1000000000 1.00000000 H9 1.0 1.4045807754 2.4232655108 -.3481764213 N31 6 S 1 1 .0360000000 1.00000000 P 1 1 1.1000000000 1.00000000 H10 1.0 1.7752611462 -1.7240346035 -1.0920081312 N31 6 S 1 1 .0360000000 1.00000000 P 1 1 1.1000000000 1.00000000 H11 1.0 1.5864554796 -2.3051259485 .3683577366 N31 6 S 1 1 .0360000000 1.00000000 P 1 1 1.1000000000 1.00000000 H12 1.0 3.6393250405 -1.0459146679 .1140564957 N31 6 S 1 1 .0360000000 1.00000000 P 1 1 1.1000000000 1.00000000 H13 1.0 2.6129781514 -.5066912651 1.4156027116 N31 6 S 1 1 .0360000000 1.00000000 P 1 1 1.1000000000 1.00000000 $END $ZMAT ! H6 H7 H12 H13 ! ! \ / \ / ! ! H8 C1-----C5 H11 ! ! \ / \ / ! ! N2 N4 ! ! / \ / \ ! ! H9 ION H10 ! ! IZMAT(1)=1,1,2, 1,2,3, 1,3,4, 1,4,5, 1,5,1, 1,6,1, 1,7,1, 1,8,2, 1,9,2, 1,10,4, 1,11,4, 1,12,5, 1,13,5, 2,5,1,2, 2,1,2,3, 2,2,3,4, 2,3,4,5, 2,4,5,1, 3,5,1,2,3, 3,1,2,3,4, 3,2,3,4,5, 3,3,4,5,1, 3,4,5,1,2, 2,6,1,7, 2,6,1,2, 2,7,1,2, 2,6,1,5, 2,7,1,5, 2,8,2,9, 2,8,2,1, 2,9,2,1, 2,8,2,3, 2,9,2,3, 2,10,4,11, 2,10,4,3, 2,11,4,3, 2,10,4,5, 2,11,4,5, 2,12,5,13, 2,12,5,4, 2,13,5,4, 2,12,5,1, 2,13,5,1 IJS(1)= 1,1, 2,2, 3,3, 4,4, 5,5, 6,6, 7,7, 8,8, 9,9, 10,10, 11,11, 12,12, 13,13, 14,14, 15,14, 16,14, 17,14, 18,14, 14,15, 15,15, 16,15, 17,15, 18,15, 19,16, 20,16, 21,16, 22,16, 23,16, 19,17, 20,17, 21,17, 22,17, 23,17, 24,18, 25,18, 26,18, 27,18, 28,18, 24,19, 25,19, 26,19, 27,19, 28,19, 24,20, 25,20, 26,20, 27,20, 28,20, 24,21, 25,21, 26,21, 27,21, 28,21, 29,22, 30,22, 31,22, 32,22, 33,22, 29,23, 30,23, 31,23, 32,23, 33,23, 29,24, 30,24, 31,24, 32,24, 33,24, 29,25, 30,25, 31,25, 32,25, 33,25, 34,26, 35,26, 36,26, 37,26, 38,26, 34,27, 35,27, 36,27, 37,27, 38,27, 34,28, 35,28, 36,28, 37,28, 38,28, 34,29, 35,29, 36,29, 37,29, 38,29, 39,30, 40,30, 41,30, 42,30, 43,30, 39,31, 40,31, 41,31, 42,31, 43,31, 39,32, 40,32, 41,32, 42,32, 43,32, 39,33, 40,33, 41,33, 42,33, 43,33 SIJ(1)= 1,1,1,1,1,1,1,1,1,1,1,1,1, 1.0, -0.8090, 0.3090, 0.3090, -0.8090, 0.0, -1.1180, 1.8090, -1.8090, 1.1180, 0.3090, -0.8090, 1.0, -0.8090, 0.3090, -1.8090, 1.1180, 0.0, -1.1180, 1.8090, 4.0, 1.0, 1.0, 1.0, 1.0, 0.0, 1.0, -1.0, 1.0, -1.0, 0.0, 1.0, 1.0, -1.0, -1.0, 0.0, 1.0, -1.0, -1.0, 1.0, 4.0, 1.0, 1.0, 1.0, 1.0, 0.0, 1.0, -1.0, 1.0, -1.0, 0.0, 1.0, 1.0, -1.0, -1.0, 0.0, 1.0, -1.0, -1.0, 1.0, 4.0, 1.0, 1.0, 1.0, 1.0, 0.0, 1.0, -1.0, 1.0, -1.0, 0.0, 1.0, 1.0, -1.0, -1.0, 0.0, 1.0, -1.0, -1.0, 1.0, 4.0, 1.0, 1.0, 1.0, 1.0, 0.0, 1.0, -1.0, 1.0, -1.0, 0.0, 1.0, 1.0, -1.0, -1.0, 0.0, 1.0, -1.0, -1.0, 1.0 $END $CONTRL NZVAR=43 $END $SCF DIRSCF=.TRUE. $END $ECP C1 NONE N2 NONE Ba-Stoll GEN 46 4 1 0.000000 2.0 1.000000 2 427.845816 2.0 9.526986 204.417530 2.0 4.487510 2 293.605864 2.0 8.315930 294.193316 2.0 4.292217 2 112.550402 2.0 5.916108 181.782621 2.0 2.874842 1 -33.473174 2.0 3.589465 N4 NONE C5 NONE H6 NONE H7 NONE H8 NONE H9 NONE H10 NONE H11 NONE H12 NONE H13 NONE $GUESS GUESS=HUCKEL $END $END $STATPT DXMAX=1.5 NSTEP=40 OPTTOL=0.0001 $END ********** *GAUSSIAN* ********** %MEM=1000000 # TEST SP POP=NPA MAXDISK=40000000/GEN 6D PSEUDO=CARDS GFPRINT UNITS=Ang ML1 (M=Ba, L=EDA) 2 1 C1 2.6216857355 .7973931210 -.2922796495 N2 1.4238076271 1.5538839828 .1631000267 BA3 -.8981949406 -.0354891759 -.0061334046 N4 1.5440441018 -1.4366057110 -.1429074401 C5 2.6721399081 -.5882422073 .3285123723 H6 3.5292002566 1.3332287519 -.0415861826 H7 2.5836568533 .7253298596 -1.3743639422 H8 1.5895760616 1.8595042521 1.1094609931 H9 1.3843877919 2.4164258136 -.3561710333 H10 1.7463579453 -1.7275873045 -1.0867720648 H11 1.5657001569 -2.2999001921 .3761579618 H12 3.6224556106 -1.0506909736 .0906232509 H13 2.6136562009 -.5199967763 1.4099325420 C 0 S 6 1.00 3047.524880 .1834737130E-02 457.3695180 .1403732280E-01 103.9486850 .6884262220E-01 29.21015530 .2321844430 9.286662960 .4679413480 3.163926960 .3623119850 SP 3 1.00 7.868272350 -.1193324200 .6899906660E-01 1.881288540 -.1608541520 .3164239610 .5442492580 1.143456440 .7443082910 SP 1 1.00 .1687144782 1.000000000 1.000000000 SP 1 1.00 .4380000000E-01 1.000000000 1.000000000 D 1 1.00 .8000000000 1.000000000 **** N 0 S 6 1.00 4173.511460 .1834772160E-02 627.4579110 .1399462700E-01 142.9020930 .6858655180E-01 40.23432930 .2322408730 12.82021290 .4690699480 4.390437010 .3604551990 SP 3 1.00 11.62636186 -.1149611820 .6757974390E-01 2.716279807 -.1691174790 .3239072960 .7722183966 1.145851950 .7408951400 SP 1 1.00 .2120314975 1.000000000 1.000000000 SP 1 1.00 .6390000000E-01 1.000000000 1.000000000 D 1 1.00 .8000000000 1.000000000 **** BA 0 S 4 1.00 7.534953000 -.1098800000 4.349914000 .5217010000 2.101075000 -.9658380000 .4311670000 .8994940000 S 1 1.00 .2074020000 1.000000000 S 1 1.00 .4568600000E-01 1.000000000 S 1 1.00 .1928700000E-01 1.000000000 P 4 1.00 2.915898000 -.4942990000 2.209730000 .9547690000 1.385694000 -.2878220000 .4427540000 -.6651190000 P 1 1.00 .1937040000 1.000000000 P 1 1.00 .4720900000E-01 1.000000000 P 1 1.00 .2005500000E-01 1.000000000 D 3 1.00 1.282886000 -.9656000000E-01 .6494980000 .1439540000 .2765230000 .3042850000 D 2 1.00 .1058840000 .4782470000 .3613400000E-01 .3680570000 **** H 0 S 3 1.00 18.73113696 .3349460434E-01 2.825394365 .2347269535 .6401216923 .8137573262 S 1 1.00 .1612777588 1.000000000 S 1 1.00 .3600000000E-01 1.000000000 P 1 1.00 1.100000000 1.000000000 **** BA 0 Stoll-Preuss 4 46 L=4 COMPONENT 1 2 1.00000000 .00000000 L=0 COMPONENT 2 2 9.52698600 427.84581600 2 4.48751000 204.41753000 L=1 COMPONENT 2 2 8.31593000 293.60586400 2 4.29221700 294.19331600 L=2 COMPONENT 2 2 5.91610800 112.55040200 2 2.87484200 181.78262100 L=3 COMPONENT 1 2 3.58946500 -33.47317400