From m.dooley@mailbox.uq.edu.au Tue Apr 22 01:37:55 1997 Received: from bunyip.cc.uq.edu.au for m.dooley@mailbox.uq.edu.au by www.ccl.net (8.8.3/950822.1) id BAA25740; Tue, 22 Apr 1997 01:03:51 -0400 (EDT) Received: from peta.ddd.uq.oz.au (peta.ddd.uq.edu.au [130.102.118.65]) by bunyip.cc.uq.edu.au (8.8.5/8.8.5) with SMTP id PAA08440 for <@bunyip.cc.uq.oz.au:chemistry@www.ccl.net>; Tue, 22 Apr 1997 15:02:57 +1000 Received: from extreme.ddd.uq.oz.au by peta.ddd.uq.oz.au via ESMTP (951211.SGI.8.6.12.PATCH1042/951211.SGI) for <@peta.ddd.uq.oz.au:chemistry@www.ccl.net> id PAA07607; Tue, 22 Apr 1997 15:02:52 -1000 Received: from chico.ddd.uq.oz.au by extreme.ddd.uq.oz.au via ESMTP (951211.SGI.8.6.12.PATCH1502/951211.SGI) for <@extreme.ddd.uq.oz.au:chemistry@www.ccl.net> id PAA06474; Tue, 22 Apr 1997 15:02:52 -0700 Received: from chico.ddd.uq.oz.au by chico.ddd.uq.oz.au via SMTP (951211.SGI.8.6.12.PATCH1042/940406.SGI.AUTO) for id PAA16247; Tue, 22 Apr 1997 15:03:14 -0700 Sender: dooley@mailbox.uq.edu.au Message-ID: <335D35A1.59E2@mailbox.uq.edu.au> Date: Tue, 22 Apr 1997 15:03:13 -0700 From: Michael Dooley X-Mailer: Mozilla 3.0 (X11; I; IRIX 5.3 IP20) MIME-Version: 1.0 To: chemistry@www.ccl.net Subject: pyridoxal phosphate AM1 optimisation Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear all, I was trying to do a simple optimisation of pyridoxal phosphate in the deprotonated phosphate form using MOPAC and AM1 for a colleague, but 2 of the phosphate oxygens kept bonding. Am I using an inappropriate semi empirical method? I'm specifying gradients precise ef am1. thanx Michael -- Michael Dooley PhD Centre for Drug Design and Development The University of Queensland Brisbane Qld 4072 Australia m.dooley@mailbox.uq.edu.au From chpajt@bath.ac.uk Tue Apr 22 03:37:56 1997 Received: from goggins.bath.ac.uk for chpajt@bath.ac.uk by www.ccl.net (8.8.3/950822.1) id DAA26153; Tue, 22 Apr 1997 03:20:43 -0400 (EDT) Received: from bath.ac.uk (actually host midge.bath.ac.uk) by goggins.bath.ac.uk with SMTP (PP); Tue, 22 Apr 1997 08:20:37 +0100 Date: Tue, 22 Apr 1997 08:20:33 +0100 (BST) From: A J Turner To: chemistry@www.ccl.net Subject: Dynamics of rare events Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi! I recently heard about the 'dynamics of rare events' where, given a knowledge of the position of a transition state, one could model a transition using dynamics. This would be especially related to high energy barriers, where conventional dynamics would take an unbelievable long time to 'get round' to crossing the barrier. Does anyone know some references for this work? Has anyone had any success with it? Thanks in advance. Alex ------------------------------------------------------------------- |Alexander J Turner |A.J.Turner@bath.ac.uk | |Post Graduate |http://www.bath.ac.uk/~chpajt/home.html| |School of Chemistry |+144 1225 8262826 ext 5137 | |University of Bath | | |Bath, Avon, U.K. |Field: QM/MM modeling | ------------------------------------------------------------------- From assfeld@host8.lctn.u-nancy.fr Tue Apr 22 05:37:55 1997 Received: from host8.lctn.u-nancy.fr for assfeld@host8.lctn.u-nancy.fr by www.ccl.net (8.8.3/950822.1) id FAA26780; Tue, 22 Apr 1997 05:11:38 -0400 (EDT) From: Received: (from assfeld@localhost) by host8.lctn.u-nancy.fr (AIX4.2/UCB 8.7/8.7) id LAA16384; Tue, 22 Apr 1997 11:12:14 +0200 (DFT) Date: Tue, 22 Apr 1997 11:12:14 +0200 (DFT) Message-Id: <199704220912.LAA16384@host8.lctn.u-nancy.fr> To: chemistry@www.ccl.net, chpajt@bath.ac.uk Subject: Re: CCL:Dynamics of rare events Hi Alex, There is a really nice paper about rare event dynamics dealing with ethylene bromination. M. Strnad, M. T. C. Martins-Costa, C. Millot, I. Tunon, M. F. Ruiz-Lopez and J.-L. Rivail "Molecular Dynamics simulations of elementary chemical processes in liquid water using combined density functional and molecular mechanics potentials. II. Charge separation processes." J. CHem. Phys. 106 (1997) 3643-3657. You can also have a look a the previous paper from the same issue of J. Chem. Phys. pp 3633-3642 of the same groupe of people. Hope this helps. ...Xav assfeld@lctn.u-nancy.fr From varnai@bellatrix.pcl.ox.ac.uk Tue Apr 22 06:37:58 1997 Received: from oxmail4.ox.ac.uk for varnai@bellatrix.pcl.ox.ac.uk by www.ccl.net (8.8.3/950822.1) id FAA27037; Tue, 22 Apr 1997 05:57:17 -0400 (EDT) Received: from joule.pcl.ox.ac.uk by oxmail4 with SMTP (PP) with ESMTP; Tue, 22 Apr 1997 10:57:05 +0100 Received: from bellatrix (bellatrix.pcl.ox.ac.uk [163.1.21.231]) by joule.pcl.ox.ac.uk (8.8.5/8.6.5) with SMTP id KAA05382 for <@joule.pcl:CHEMISTRY@www.ccl.net>; Tue, 22 Apr 1997 10:56:59 +0100 (BST) Received: by bellatrix (940816.SGI.8.6.9/940406.SGI.AUTO) id JAA01615; Tue, 22 Apr 1997 09:58:04 GMT Date: Tue, 22 Apr 1997 10:58:01 +0100 (BST) From: Peter Varnai To: CHEMISTRY@www.ccl.net Subject: summary:gaussian massage Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCL, I have had problems optimizing a molecule geometry in a fixed point charge cloud using the massage keyword in g94/g92. I got error message OPERATION ON FILE OUT OF RANGE... It turned out that (although it is not obvious from the manual) gaussian cannot do the job! Thank you very much for the answers to Marc LE BRET Dr. Craig Wilson Michael A. McAllister Richard Hall Doug Fox Doug Fox: The short answer is that G94 cannot do the optimization. There may be special cases where it works but the code currently assumes translational invariance which is not generally valid in this circumstance and there are points there is nothing to control the optimization to the true minimum which would have any negative point charges coincident with one of the nuclei. We are looking into treating this for a future major revision of Gaussian. Regards, Peter Varnai From hermann@handel.RZ-Berlin.MPG.DE Tue Apr 22 07:37:58 1997 Received: from handel.RZ-Berlin.MPG.DE for hermann@handel.RZ-Berlin.MPG.DE by www.ccl.net (8.8.3/950822.1) id GAA27287; Tue, 22 Apr 1997 06:55:10 -0400 (EDT) Received: by handel.RZ-Berlin.MPG.DE (AIX 3.2/UCB 5.64/4.03) id AA40758; Tue, 22 Apr 1997 12:55:01 +0200 From: hermann@handel.RZ-Berlin.MPG.DE (Klaus Hermann ) Message-Id: <9704221055.AA40758@handel.RZ-Berlin.MPG.DE> Subject: XYZ data format To: chemistry@www.ccl.net Date: Tue, 22 Apr 1997 12:55:00 +0200 (MSZ) X-Mailer: ELM [version 2.4 PL22] Content-Type: text Dear CCLers, can anyone point me to a reliable reference of the XYZ format used in structure definition input/output files of several molecular visualization packages. In need the definition for a local omplementation. -- Thanks in advance, Klaus Hermann Berlin, April 22, 1997 =========================================================================== Prof.Dr. K. Hermann Tel.: [+49]-30-8413-4812/3 (office) Abt. Theorie, Fritz-Haber-Institut [+49]-30-8413-4702 (secrt.) Faradayweg 4-6 Fax.: [+49]-30-8413-4701 D-14195 Berlin Germany e-mail: hermann@FHI-Berlin.MPG.DE WWW: http://www.fhi-berlin.mpg.de/th/member/hermann_k.html =========================================================================== From windus@ccl.net Tue Apr 22 09:37:58 1997 Received: from bedrock.ccl.net for windus@ccl.net by www.ccl.net (8.8.3/950822.1) id IAA27978; Tue, 22 Apr 1997 08:45:44 -0400 (EDT) Received: for windus@ccl.net by bedrock.ccl.net (8.8.3/950822.1) id IAA22307; Tue, 22 Apr 1997 08:45:34 -0400 (EDT) From: Theresa Windus Message-Id: <199704221245.IAA22307@bedrock.ccl.net> Subject: G94 memory requirements To: CHEMISTRY@www.ccl.net Date: Tue, 22 Apr 1997 08:45:33 -0400 (EDT) X-Mailer: ELM [version 2.4 PL23] MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Hi all, I am trying to determine the memory requirements of G94. While I can get a rough idea, I was wondering if anyone has more exacting formulas that they would share? I am interested in all types of calculations from RHF energies, gradients, and frequencies all the way up to highly correlated wavefunctions (such as QCISD(T) and MCSCF). Any help is appreciated. Theresa Windus Computational Chemistry and Materials ASC MSRC Wright Patterson AFB 937-255-2715 x218 windustl@msrc.wpafb.af.mil From assfeld@host8.lctn.u-nancy.fr Tue Apr 22 10:37:58 1997 Received: from host8.lctn.u-nancy.fr for assfeld@host8.lctn.u-nancy.fr by www.ccl.net (8.8.3/950822.1) id JAA28325; Tue, 22 Apr 1997 09:41:16 -0400 (EDT) From: Received: (from assfeld@localhost) by host8.lctn.u-nancy.fr (AIX4.2/UCB 8.7/8.7) id PAA03194 for chemistry@www.ccl.net; Tue, 22 Apr 1997 15:41:38 +0200 (DFT) Date: Tue, 22 Apr 1997 15:41:38 +0200 (DFT) Message-Id: <199704221341.PAA03194@host8.lctn.u-nancy.fr> To: chemistry@www.ccl.net Subject: NMR Chemical Shielding Anisotropy Hi, I am computing chemical shielding tensor for various molecule. Once you diagonalyze this tensor you can expressed the isotropic chemical shield as the average of the three eigenvalues (Txx, Tyy, and Tzz). You can also compute the anisotropy, which is the difference between the larger eigenvalue (generally called Tzz) and the average of the two other. Iso = 1/3 (Txx + Tyy + Tzz) Ani = Tzz - 1/2 (Txx + Tyy) Everything is fine with me when all three eigenvalues have the same signe. Problem arises when one eigenvalue is negative. For exemple, here are three eigenvalues : -76.8050 6.2091 62.8089 If you consider that Tzz = 62.8089 you'll find an anisotropy of 62.8089-(6.2091-76.8050)/2 = 98.1069 However, if you consider that Tzz = -76.8050, (In absolute value 76.8050 is larger than 62.8089.) the anisotropy = -111.3140 My question : which one is the good choice ? I already know that G94 use the first definition. Thank you in advance for your advice. I'll summarize. ...Xav assfeld@lctn.u-nancy.fr From bruno@antas.agraria.uniss.it Tue Apr 22 12:38:00 1997 Received: from ssmain.uniss.it for bruno@antas.agraria.uniss.it by www.ccl.net (8.8.3/950822.1) id MAA00168; Tue, 22 Apr 1997 12:07:53 -0400 (EDT) Received: from antas.agraria.uniss.it by ssmain.uniss.it with SMTP (1.39.111.2/16.2) id AA086055161; Tue, 22 Apr 1997 18:06:01 +0200 Date: Tue, 22 Apr 1997 18:05:53 +0100 (NFT) From: "Dr. Bruno Manunza" To: Klaus Hermann Cc: chemistry@www.ccl.net Subject: Re: CCL:XYZ data format In-Reply-To: <9704221055.AA40758@handel.RZ-Berlin.MPG.DE> Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Tue, 22 Apr 1997, Klaus Hermann wrote: > Dear CCLers, > > can anyone point me to a reliable reference of the XYZ format used in > structure definition input/output files of several molecular visualization > packages. In need the definition for a local omplementation. > > -- > Thanks in advance, Klaus Hermann Berlin, April 22, 1997 > Dear Klaus, have a look at our software page at http://antas.agraria.uniss.it hope it helps Regards Bruno Dr Bruno Manunza DISAABA (Dept. of Agricultural Environm. Sci) University of Sassari V.le Italia 39 07100 Sassari, ITALY phone: 39 79 229215 fax: 39 79 229276 e-mail: bruno@antas.agraria.uniss.it e-mail: bruno@tharros.dipchim.uniss.it e-mail: gx6bot81@cray.cineca.it web: http://antas.agraria.uniss.it From PHogue@space.honeywell.com Tue Apr 22 13:05:52 1997 Received: from fl51mail.space.honeywell.com for PHogue@space.honeywell.com by www.ccl.net (8.8.3/950822.1) id LAA29970; Tue, 22 Apr 1997 11:50:27 -0400 (EDT) Received: from fl51m03.space.honeywell.com by fl51mail.space.honeywell.com with SMTP (1.38.193.5/16.2) id AA19841; Tue, 22 Apr 1997 12:03:17 -0400 Received: by fl51m03.space.honeywell.com with SMTP (Microsoft Exchange Server Internet Mail Connector Version 4.0.994.63) id <01BC4F13.61CC6790@fl51m03.space.honeywell.com>; Tue, 22 Apr 1997 11:50:32 -0400 Message-Id: From: "Hogue, Pat (AZ76)" To: CCL Subject: Helpful Books Date: Tue, 22 Apr 1997 08:42:00 -0400 X-Mailer: Microsoft Exchange Server Internet Mail Connector Version 4.0.994.63 Encoding: 24 TEXT I would like to suggest the following reference books to those just beginning their computational careers: 1. Clark, Tim A Handbook of Computational Chemistry, John Wiley Pub., 1985. MUST READ 2. Richards, W. G. and Cooper, D. L. Ab Initio Molecular Orbital Calculations for Chemists, 2nd ed. Claendon Press, 1985. 3. Jean, Yves, Volatron, Francois, and Burdett, Jeremy An Introduction to Molecular Orbitals, Oxford Univ. Press, 1993. 4. Fleming, Ian Frontier Orbitals and Organic Chemical Reactions, John Wiley, 1976. 5. Szabo, Attila, and Ostlund, Neil Modern Quantum Chemistry, Dover, 1996. 6. Johnson, Charles and Pedersen, Lee Problems and Solutions in Quantum Chemistry and Physics, Dover, 1986. 7. FUN READING: Dewar, Michael A semiemperical Life, ACS 1992. Cheers from Pat Hogue From balajiv@ncsa.uiuc.edu Tue Apr 22 13:18:30 1997 Received: from newton.ncsa.uiuc.edu for balajiv@ncsa.uiuc.edu by www.ccl.net (8.8.3/950822.1) id LAA00065; Tue, 22 Apr 1997 11:58:07 -0400 (EDT) Received: from pecos.ncsa.uiuc.edu (pecos.ncsa.uiuc.edu [141.142.3.51]) by newton.ncsa.uiuc.edu (8.8.5/8.8.5) with ESMTP id KAA12108 for ; Tue, 22 Apr 1997 10:58:08 -0500 (CDT) Received: (from balajiv@localhost) by pecos.ncsa.uiuc.edu (8.8.5/8.8.5) id KAA27111 for chemistry@www.ccl.net; Tue, 22 Apr 1997 10:58:07 -0500 (CDT) From: "Balaji Veeraraghavan" Message-Id: <9704221058.ZM27107@pecos.ncsa.uiuc.edu> Date: Tue, 22 Apr 1997 10:58:06 -0500 X-Mailer: Z-Mail (3.2.0 06sep94) To: chemistry@www.ccl.net Subject: 2nd Announcement for GAUSSIAN-94 WORKSHOP at NCSA Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii The National Center for Supercomputing Applications and Gaussian, Inc. are pleased to announce: Quantum Chemistry for Engineers and Chemists in the Chemical Process Industry Date: June 3-6, 1997 Location: National Center for Supercomputing Applications Urbana-Champaign, IL The National Center for Supercomputing Applications (NCSA) in conjunction with Gaussian, Inc. are pleased announce a workshop tuned to address the needs of researchers in the chemical process industry who need to add electronic structure methods to their arsenal of research tools. State of the art electronic structure methods and main stream chemical process industry (CPI) applications are converging at a rapid pace. Computational models now have the accuracy and reliability to predict physical properties at costs and time frames competitive with experimental approaches. This course will lay out the methods of electronic structure theory and describe how to extract physical properties from calculations. While this workshop is oriented to chemical engineering topics we encourage you to consider sending chemist/chemical engineer teams to gain optimal benefit. Instructors: Dr. Michael J. Frisch Gaussian, Inc. Prof. Phillip Westmoreland Univ. of Massachusetts Prof. Matthew Neurock Univ. of Virginia Dr. Douglas J. Fox Gaussian, Inc. Tentative Agenda Topics: Computational Chemistry: A CPI Perspective Introduction to Electronic Structure Theory Predicting Thermodynamics with Model Chemistries Geometry Optimization Techniques Electron Correlation Methods Density Functional Theory Methods Theoretical Methods for Optical and UV Spectra Predicting Molecular Properties Continuum Models for Solvation Case Studies: Electronic Structure Methods in Process Design : Model Assessment for Physical Properties There will be hands-on sessions each day between the morning and afternoon lectures. Additional hands-on sessions will be available until the building closes. Workshop participants will be provided with use of an SGI workstation to complete exercises, experiment and/or conduct short research topics. Each workshop participant will also be provided a copy of the lecture notes, a copy of Exploring Chemistry with Electronic Structure Methods (2nd. Ed.) and a copy of the Gaussian 94 User's Reference. For Application please contact: Workshop Coordinator Gaussian, Inc. Carnegie Office Park Bldg. 6, Suite 230 Pittsburgh, PA 15106 USA Additional information can be obtained from Telephone: (412) 279-6700 Fax: (412) 279-2118 Email: info@gaussian.com DEADLINES: Receipt of Registration Materials: May 2, 1997 This notice is sent without warranty of any kind, expressed or implied by Gaussian, Inc. or NCSA. Gaussian is a registered trademark of Gaussian, Inc. -- ----------------------------------------------------------------------- Balaji Veeraraghavan, Ph. D. Phone : 217-333-2754 Research Programmer, Chemistry Fax : 217-244-2909 NCSA email : balajiv@ncsa.uiuc.edu 4151 Beckman Institute 405 N. Mathews Avenue Urbana, IL 61801 ----------------------------------------------------------------------- From sanjoy@sscu.iisc.ernet.in Tue Apr 22 17:38:07 1997 Received: from milan.doe.ernet.in for sanjoy@sscu.iisc.ernet.in by www.ccl.net (8.8.3/950822.1) id QAA01867; Tue, 22 Apr 1997 16:42:24 -0400 (EDT) Received: from iisc.ernet.in by milan.doe.ernet.in (4.1/SMI-4.1) id AA11888; Wed, 23 Apr 97 02:17:42+050 Received: from sscu.iisc.ernet.in by iisc.ernet.in (ERNET-IISc/SMI-4.1) id CAA25841; Wed, 23 Apr 1997 02:12:02 +0530 Received: by sscu.iisc.ernet.in (ERNET-IISc/SMI-4.1) id BAA10038; Wed, 23 Apr 1997 01:51:39 +0600 Date: Wed, 23 Apr 1997 01:51:39 +0600 From: sanjoy@sscu.iisc.ernet.in (Mr.Sanjoy ) Message-Id: <199704221951.BAA10038@sscu.iisc.ernet.in> To: CHEMISTRY@www.ccl.net Subject: CCL: Phase Diagram Hi, Can anyone tell me any reference where I can get the ternary phase diagram of Sodium dodecyl sulphate (SDS)-Water-dodecanol system. Thanks in advance. Sanjoy Bandyopadhyay (sanjoy@sscu.iisc.ernet.in) From cdac.ernet.in!gadre@parcom.ernet.in Tue Apr 22 01:30 EDT 1997 Received: from sangam.ncst.ernet.in for cdac.ernet.in!gadre@parcom.ernet.in by www.ccl.net (8.8.3/950822.1) id BAA25774; Tue, 22 Apr 1997 01:30:26 -0400 (EDT) Received: from iucaa (iucaa.ernet.in [144.16.31.4]) by sangam.ncst.ernet.in (8.7.5) with SMTP id LAA29559 for ; Tue, 22 Apr 1997 11:07:05 +0530 (GMT+05:30) Received: from iucaa.iucaa.ernet.in by iucaa (5.65v3.2/SMI-4.1) id AA18884; Tue, 22 Apr 1997 10:58:06 +0500 Received: by parcom.cdac.ernet.in (4.1/SMI-4.1) id AA29268; Tue Apr 22 10:41:48 1997 (GMT + 0530) Date: Tue Apr 22 10:41:48 1997 (GMT + 0530) From: gadre@cdac.ernet.in Message-Id: <9704220511.AA29268@parcom.cdac.ernet.in> To: ccl@www.ccl.net Subject: DNA base triplexes Content-Type: text Dear Sirs : Are there any theoretical investigations regarding stabilities of DNA base triplexes ? How reliable are such results ? The experimental studies involve studies on oligomeric systems. Is it possible to relate the stabilities of isolated triplets to the results of UV melting experiments ? Another important problem is how to calculate the interaction energy of a trimer using ab initio method if applied to the supermolecule as well as fragment monomers. Any comments ? Thanks a lot. Shridhar Gadre (gadre@chem.unipune.ernet.in & gadre@parcom.ernet.in) Department of Chemistry University of Pune 411007 INDIA. From sbrozell@silicon.mps.ohio-state.edu Tue Apr 22 19:38:04 1997 Received: from silicon.mps.ohio-state.edu for sbrozell@silicon.mps.ohio-state.edu by www.ccl.net (8.8.3/950822.1) id SAA03238; Tue, 22 Apr 1997 18:52:59 -0400 (EDT) Received: (from sbrozell@localhost) by silicon.mps.ohio-state.edu (8.8.5/8.8.5) id SAA25051 for CHEMISTRY@www.ccl.net; Tue, 22 Apr 1997 18:53:01 -0400 (EDT) From: Scott Brozell Message-Id: <199704222253.SAA25051@silicon.mps.ohio-state.edu> Subject: CCL:Dynamics of rare events To: CHEMISTRY@www.ccl.net Date: Tue, 22 Apr 1997 18:52:59 -0400 (EDT) X-Mailer: ELM [version 2.4 PL13] Content-Type: text Hi, "A method for accelerating the molecular dynamics simulation of infrequent events." Arthur F. Voter, J. Chem. Phys. 106, 4665-4677 (1997). scott brozell > I recently heard about the 'dynamics of rare events' where, given a > knowledge of the position of a transition state, one could model a > transition using dynamics. This would be especially related to high > energy barriers, where conventional dynamics would take an unbelievable > long time to 'get round' to crossing the barrier. > > Does anyone know some references for this work? Has anyone had any > success with it? > > ------------------------------------------------------------------- > |Alexander J Turner |A.J.Turner@bath.ac.uk | > |Post Graduate |http://www.bath.ac.uk/~chpajt/home.html| > |School of Chemistry |+144 1225 8262826 ext 5137 | > |University of Bath | | > |Bath, Avon, U.K. |Field: QM/MM modeling | > -------------------------------------------------------------------