From owner-chemistry@ccl.net Wed Jul 5 10:39:51 1995 Received: from owl.und.ac.za for TSHEHLA@che.und.ac.za by www.ccl.net (8.6.10/930601.1506) id KAA09112; Wed, 5 Jul 1995 10:34:32 -0400 Received: from Charon1.CC.und.ac.za by owl.und.ac.za with SMTP (PP) id <01119-7@owl.und.ac.za>; Wed, 5 Jul 1995 16:33:01 +0200 Received: From STUD-AFF/WORKQUEUE by charon1.cc.und.ac.za via Charon-4.0A-VROOM with IPX id 100.950705162854.2528; 05 Jul 95 16:33:00 -0200 Message-ID: From: Tankiso Tshehla - PG Organization: University of Natal - Durban To: chemistry@ccl.net Date: Wed, 5 Jul 1995 16:28:42 +0200 (SAST) Subject: BSSE sign summary response Priority: normal X-mailer: Pegasus Mail v3.22 To all the netters; While I will be summarising the responses, I would like to thank all who responded. The general view is that this should not have happened, if it did may something was not correct in the beginning. Or perhaps the basis set in incomplete. The reason I posted the meassage was simply because I did not believe the results I was getting. I am glad that through the different views >from CCL I finally got the solution. I ran the massage job once more with completely new input and it worked. I suspect that one of the parameters might have been wrong. Thanks to all T M Tshehla Summary charles W Ulmer, II Ph. D. wrote: I wouldn't want to begin to answer your question without knowing more about the way in which you calculated the BSSE. ref to Nagy, P. I. C. W. II; Smith, D.A J. Chem. Phy. 1995, 102, 6812. David E. Woon wrote: You shouldn't be able to get negative BSSE from the counterpoise correction (assuming you are using full CP correction). The monomers in the dimers basis set must have lower energies than their respective monomer sets. Since it sounds like you're optimising the monomer geometries in the dimer basis, you also add a correction for that, even if the change is small. R. G. A. Bone Ph D. wrote: The only thing you can really do is to increase the size of the basis set--- substantially for a correlated level calculation. There may be other ways of compensating for BSSE at the MP2 level, other than using the CP correction; this is still an open issue. M A Zottola wrote: are you sure that: 1) The Z-matrix describing your system is correct- 2) you subtracted the sum of the counterpoise-calculated monomer energies from the the energy of the complex- 3) You are using the Mp2 energies not the HF energies for the calc. of dE I have never seen a negative correction from BSSE - indeed that observation contradicts the concept of superposition error. good luck in ferreting out an answer! all all all all From owner-chemistry@ccl.net Wed Jul 5 11:24:57 1995 Received: from CPWSCA.PSC.EDU for JOHNSONB@CPWSCA.PSC.EDU by www.ccl.net (8.6.10/930601.1506) id LAA10505; Wed, 5 Jul 1995 11:24:09 -0400 Date: Wed, 5 Jul 1995 11:24:09 -0400 (EDT) From: JOHNSONB@B.PSC.EDU To: chemistry@ccl.net CC: JOHNSONB@B.PSC.EDU Message-Id: <950705112409.40405b83@B.PSC.EDU> Subject: Molecular integrals >I am looking for a good source (book or article) that describes in detail >all the integrals (analytic forms for some) that one needs to calculate. >Can quantum chemists out there point me to a good source. For a good review of the efficient calculation of quantum chemical integrals, see P. M. W. Gill, Advan. Quantum Chem. 25, 141 (1994). Regards, Benny ------------------------------------------------------------------------------- Benny G. Johnson, Ph.D. Phone: (412) 268-1056 President Fax: (412) 268-6945 Q-Chem, Inc. E-mail: johnsonb@psc.edu 317 Whipple St. Pittsburgh, PA 15218 USA ------------------------------------------------------------------------------- From owner-chemistry@ccl.net Wed Jul 5 11:39:52 1995 Received: from www.hyper.com for polowin@hyper.hyper.com by www.ccl.net (8.6.10/930601.1506) id LAA11002; Wed, 5 Jul 1995 11:38:37 -0400 Received: from hyper.hyper.com (hyper.hyper.com [204.50.3.217]) by www.hyper.com (8.6.9/8.6.9) with SMTP id KAA11703; Wed, 5 Jul 1995 10:36:14 -0400 Received: by hyper.hyper.com (920330.SGI/920502.SGI) for @www.hyper.com:64MNR@NPD.UFPE.BR id AA16245; Wed, 5 Jul 95 10:47:14 -0400 Date: Wed, 5 Jul 95 10:47:14 -0400 From: polowin@hyper.hyper.com (Joel Polowin) Message-Id: <9507051447.AA16245@hyper.hyper.com> To: <64MNR@NPD.UFPE.BR> Subject: Re: CCL:more information about d orbitals in tin complexes Cc: chemistry@ccl.net > From: <64MNR@NPD.UFPE.BR> > Date: Tue, 04 Jul 1995 19:23:31 -0300 > Subject: CCL:more information about d orbitals in tin complexes > I forgot to discriminate that I'm working with hexacoordinate tin > complex so I need the inclusion of d orbitals. Does the new version of > Hyperchem contain PM3 parameters with these orbitals? The PM3 parameters that we provide are the set developed by James J.P. Stewart; all of its d-orbital parameters for tin are 0. I don't know if anyone's got a modified PM3 parameter set with non-0 d-orbital parameters for tin. (If so, using other parameters with HyperChem is a matter of modifying the parameter files with a text editor.) > Some time ago one of our department requested information about how to > buy this program and at moment we didn't have none information. Please, could > you send us details about it. I'll send that privately; if anyone else is interested, please contact me at the address below. Regards, Joel ------------ Joel Polowin, Ph.D. Manager, Scientific Support Email to: polowin@hyper.com Hypercube Inc, 419 Phillip St, Waterloo, Ont, Canada N2L 3X2 (519)725-4040 Info requests to: info@hyper.com Support questions to: support@hyper.com Email group: Send "subscribe hyperchem" to hyperchem-request@hyper.com WWW: http://www.hyper.com/ From owner-chemistry@ccl.net Wed Jul 5 11:56:04 1995 Received: from server.chem.ufl.edu for bartberg@server.chem.ufl.edu by www.ccl.net (8.6.10/930601.1506) id LAA11424; Wed, 5 Jul 1995 11:51:50 -0400 Received: (from bartberg@localhost) by server.chem.ufl.edu (8.6.10/8.6.9) id LAA01329; Wed, 5 Jul 1995 11:53:36 -0400 Date: Wed, 5 Jul 1995 11:53:35 -0400 (EDT) From: "Michael D. Bartberger" To: Computational Chemistry List Subject: Spin contamination Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hello all: In G92, after the value of is printed in a UHF calculation, there is a value printed after this which shows "after annihilation of the first spin contaminant." Could someone kindly explain the significance of this in terms of the "usefulness" of the energy or geometry obtained with the spin-contaminated wavefunction? The reason for my question is this: we are calculating some ground and transition states (UHF) for some (fluorinated) radical addition and cyclization reactions. I find that in many of the cases the degree of spin contamination is too high for comfort ( is around 1.0 at worst. ) However, according to G92, after annihilation of the first spin contaminant, this value drops to a quite acceptable 0.76. Now, what does that say regarding the geometries and energies I've obtained? I'm not so sure or happy about using ROHF if necessary since my understanding is that one can not do analytical second derivatives in G92 with ROHF..... with numerical second derivatives on systems of the size we are studying, the largest so far being C6F11(.) , I feel this would really cripple us, in terms of required CPU time. The lack of account of spin polarization is another matter............... I guess the main question is what is the significance of annihilation of that first spin contaminant? Is the original S^2 is "bad" but the "annihilated" S^2 is "not so bad", then what? :-) I'd greatly appreciate any responses, advice, suggestions, or flames. (Well, go easy on the flames.) =:^) I'll certainly summarize if there is interest. Best regards, Michael ________________________________________________________________________________ Michael D. Bartberger bartberg@chem.ufl.edu TEL: (904) 392-3580 Department of Chemistry bartberg@qtp.ufl.edu FAX: (904) 846-0296 University of Florida Gainesville, FL 32611 USA ________________________________________________________________________________ From owner-chemistry@ccl.net Wed Jul 5 13:24:53 1995 Received: from soochak.ncst.ernet.in for ipcakc@vigyan.iisc.ernet.in by www.ccl.net (8.6.10/930601.1506) id NAA13187; Wed, 5 Jul 1995 13:14:59 -0400 From: Received: from iisc.ernet.in (iisc.iisc.ernet.in [144.16.64.3]) by soochak.ncst.ernet.in (8.6.8.1/8.6.6) with SMTP id WAA20665 for ; Wed, 5 Jul 1995 22:44:19 +0530 Received: from vigyan.UUCP by iisc.ernet.in (ERNET-IISc/SMI-4.1) id AA03157; Wed, 5 Jul 95 22:49:02+0530 Received: by vigyan.iisc.ernet.in (smail2.3) id AA01895; 5 Jul 95 21:07:34 EST (Wed) To: CHEMISTRY@ccl.net Subject: Bond-dissociation energies of Date: 5 Jul 95 21:07:34 EST (Wed) Message-Id: <9507052107.AA01895@vigyan.iisc.ernet.in> Dear netters, Could anyone of you please let me give the data of bond-dissociation energies of X-D bond where X = H,N,F,C,O and D is the Deuterium (isotope of Hydrogen) both in diatomic and polyatomic (X being Methyl, Ethyl, Isopropyl and t-buryl for C, NH_2 for N and HO for O etc...) ? Any reference on the Bond-Dissociation Energies of these molecules is most grately appreciated. Thanks in advance. V.Sreedhara Rao. e-mail : ipcakc@vigyan.iisc.ernet.in Int.net: akc@hamsadvani.serc.iisc.ernet.in From owner-chemistry@ccl.net Wed Jul 5 16:39:52 1995 Received: from sumter.awod.com for netsci@awod.com by www.ccl.net (8.6.10/930601.1506) id QAA17538; Wed, 5 Jul 1995 16:28:11 -0400 Received: from [198.81.225.121] (ppp112.awod.com [198.81.225.121]) by sumter.awod.com (8.6.11/8.6.9) with SMTP id QAA06907; Wed, 5 Jul 1995 16:24:36 -0400 X-Sender: arichon@awod.com Message-Id: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Wed, 5 Jul 1995 16:41:33 +0000 To: chemistry@ccl.net From: netsci@awod.com (Network Science) Subject: Network Science (NetSci) Cc: netsci@awod.com The premier issue of Network Science (NetSci) is now on-line. NetSci can be accessed at http://www.awod.com/netsci The July issue focuses on combinatorial chemistry and includes articles >from Sphinx/Lilly, Scios Nova and Ontogen. MDL, Chemical Design and Daylight highlight the use of tools available from their respective companies. Subsequent issues of NetSci will cover structure-based drug design, bioinformatics, 3D databases and mass screening. If you are unable to access the WWW but are interested in NetSci, please let us know and we will attempt to make an e-mail version available. <=================================================================> Molecular Solutions, Inc. 412 Carolina Blvd. Isle of Palms, SC 29451 803-886-8775, 803-886-5942(FAX) netsci@awod.com From owner-chemistry@ccl.net Wed Jul 5 16:54:52 1995 Received: from www.hyper.com for polowin@hyper.hyper.com by www.ccl.net (8.6.10/930601.1506) id QAA17822; Wed, 5 Jul 1995 16:45:22 -0400 Received: from hyper.hyper.com (hyper.hyper.com [204.50.3.217]) by www.hyper.com (8.6.9/8.6.9) with SMTP id QAA01284; Wed, 5 Jul 1995 16:33:15 -0400 Received: by hyper.hyper.com (920330.SGI/920502.SGI) for @www.hyper.com:64MNR@NPD.UFPE.BR id AA17723; Wed, 5 Jul 95 16:48:38 -0400 Date: Wed, 5 Jul 95 16:48:38 -0400 From: polowin@hyper.hyper.com (Joel Polowin) Message-Id: <9507052048.AA17723@hyper.hyper.com> To: <64MNR@NPD.UFPE.BR> Subject: Re: more information about d orbitals in tin complexes Cc: chemistry@ccl.net > From polowin Wed Jul 5 10:47:13 1995 > Subject: Re: CCL:more information about d orbitals in tin complexes > > The PM3 parameters that we provide are the set developed by James J.P. > Stewart; all of its d-orbital parameters for tin are 0. I don't know if > anyone's got a modified PM3 parameter set with non-0 d-orbital parameters > for tin. (If so, using other parameters with HyperChem is a matter of > modifying the parameter files with a text editor.) I have been corrected by one of my colleagues: PM3 fundamentally does not and cannot include d orbitals. This would require a different set of algorithms involving a MNDO/D. If parameters for d orbitals were added to the PM3 parameter files for HyperChem, they would simply be ignored. ------------ Joel Polowin, Ph.D. Manager, Scientific Support Email to: polowin@hyper.com Hypercube Inc, 419 Phillip St, Waterloo, Ont, Canada N2L 3X2 (519)725-4040 Info requests to: info@hyper.com Support questions to: support@hyper.com Email group: Send "subscribe hyperchem" to hyperchem-request@hyper.com WWW: http://www.hyper.com/ From owner-chemistry@ccl.net Wed Jul 5 17:04:16 1995 Received: from po7.andrew.cmu.edu for mca3+@andrew.cmu.edu by www.ccl.net (8.6.10/930601.1506) id QAA17758; Wed, 5 Jul 1995 16:40:23 -0400 Received: (from postman@localhost) by po7.andrew.cmu.edu (8.6.12/8.6.12) id QAA16044; Wed, 5 Jul 1995 16:37:32 -0400 Received: via switchmail; Wed, 5 Jul 1995 16:37:31 -0400 (EDT) Received: from unix18.andrew.cmu.edu via qmail ID ; Wed, 5 Jul 1995 16:35:39 -0400 (EDT) Received: from unix18.andrew.cmu.edu via qmail ID ; Wed, 5 Jul 1995 16:35:35 -0400 (EDT) Received: from mms.4.60.Jan.26.1995.18.43.47.sun4c.411.EzMail.2.0.CUILIB.3.45.SNAP.NOT.LINKED.unix18.andrew.cmu.edu.sun4c.411 via MS.5.6.unix18.andrew.cmu.edu.sun4c_411; Wed, 5 Jul 1995 16:35:34 -0400 (EDT) Message-ID: Date: Wed, 5 Jul 1995 16:35:34 -0400 (EDT) From: Michael F Crowley To: Outbound News Subject: CCL:ANNOUCE: Workshop Cc: Outbound News , Outbound News , Outbound News , Outbound News , Outbound News , Outbound News , Outbound News , Outbound News , Outbound News , chemistry@ccl.net, rna@net.bio.net References: <9507052027.AA03787@pscuxb.psc.edu> "METHODS OF MOLECULAR MECHANICS AND DYNAMICS OF BIOPOLYMERS" WORKSHOP Pittsburgh Supercomputing Center August 16-19, 1995 The Pittsburgh Supercomputing Center (PSC) is hosting a workshop on "Methods of Molecular Mechanics and Dynamics of Biopolymers," August 16-19, 1995. The workshop will familiarize biomedical researchers with computational methods and provide practice in applying supercomputing resources to problems of concern in molecular mechanics. Practical experience on our supercomputers will be gained in the application to: (1) the theory and practice of molecular mechanics and dynamics; (2) the development and refinement of molecular mechanics force fields; (3) the problem of conformation mapping and analysis of polypeptide structures, including the refinement of structure from measured NMR data; and (4) computation of interaction energies and free energies for protein-drug interactions and conformational thermodynamics. Workshop leaders are Dr. Charles L. Brooks III, The Scripps Research Institute and Dr. Alexander D. MacKerell Jr., University of Maryland at Baltimore. The worskhop will consist of lectures and extensive hands-on sessions. General aspects of molecular mechanics software will be discussed and a number of packages are available for use at the PSC. However, the programs CHARMM and QUANTA will be utilized most extensively in demonstrations. Hands-on sessions will be emphasized. Participants will be able to work on the examples provided or on their own experimental data. No prior supercomputing experience is necessary. This workshop is funded by a grant from the Biomedical Research Technology Program, National Center for Research Resources, National Institutes of Health. TRAVEL, MEALS AND HOTEL ACCOMMODATIONS FOR RESEARCHERS AFFILIATED WITH U.S. ACADEMIC INSTITUTIONS ARE SUPPORTED BY THIS GRANT. Enrollment is limited to 20. An application form is included. Deadline for applications is: July 10, 1995. Please direct inquires or send the following application form to blankens@psc.edu. Additional information about this workshop can be found in http://pscinfo.psc.edu/biomed/workshops95.html PITTSBURGH SUPERCOMPUTING CENTER BIOMEDICAL INITIATIVE ************************************** August 16-19, 1995 APPLICATION Name:________________________________________________________________________ Affiliation:_________________________________________________________________ Address:_____________________________________________________________________ (Business) _____________________________________________________________________________ ____________________________________________________________________________ (Home) ____________________________________________________________________________ Telephone: ____________________ ______________________ (Business) (Home) *Social Security Number: _______-_____-_______ Citizenship: ____________ Electronic Mail Address:____________________________________________________ Status: ___Graduate ___Post-doctoral Fellow ___Faculty ___Other (specify) Please indicate specifically any special housing, transportation or dietary arrangements you will need: _______________________________________________ How did you learn about this workshop? _____________________________________ REQUIREMENTS: Applicants must submit a completed application form and a cover letter. The letter should describe, in one or two paragraphs, your current research and how participating in the workshop will enhance this research. Please include a brief statement describing your level of experience with computers. Faculty members, staff and post-docs should provide a curriculum vita. Graduate students must have a letter of recommendation from a faculty member. Please return all application materials by July 10, 1995 to: Biomedical Workshop Applications Committee Pittsburgh Supercomputing Center 4400 Fifth Avenue, Suite 230C Pittsburgh, PA 15213 Direct inquiries to: Nancy Blankenstein, blankens@psc.edu or 412/268-4960. *Disclosure of Social Security Number is voluntary. PSC does not discriminate on the basis of race, color, religion, sex, age, creed, national or ethnic origin, or handicap. - ------- End of Unsent Draft ------- End of Forwarded Message From owner-chemistry@ccl.net Wed Jul 5 17:10:56 1995 Received: from phem3 for KZHANG@MIAMIU.ACS.MUOHIO.EDU by www.ccl.net (8.6.10/930601.1506) id RAA18394; Wed, 5 Jul 1995 17:05:58 -0400 Received: from MIAMIU.ACS.MUOHIO.EDU (MAILER@MIAMIU) by phem3.acs.ohio-state.edu (PMDF V4.2-13 #5888) id <01HSIOHYYW0W9CCTYV@phem3.acs.ohio-state.edu>; Wed, 5 Jul 1995 17:05:45 EDT Received: from MIAMIU (NJE origin KZHANG@MIAMIU) by MIAMIU.ACS.MUOHIO.EDU (LMail V1.2a/1.8a) with BSMTP id 8157; Wed, 5 Jul 1995 17:04:56 -0500 Date: Wed, 05 Jul 1995 17:03:21 -0500 (EST) From: Kui Zhang Subject: BSSE Correction for Protonation Energy To: Computational Chemistry List Message-id: <01HSIOI1VN989CCTYV@phem3.acs.ohio-state.edu> Content-transfer-encoding: 7BIT Dear Netters, One of our projects is the calculation of protonation energy for some interesting compounds using high level ab initio calculations. Recently I have been trying to correct calculated protonation energies with BSSE. I first used CH3NH2 as model compound to do testing calculations at HF, MP2 and MP4 levels with several basis sets. The calculations were carried out using Gaussian 92 with MASSAGE method. The following is a set of calculated values of the BSSE correction for CH3NH2: BSSE Correction (kcal/mol) HF/6-31G*//HF/6-31G* 0.60 HF/6-31+G**//HF/6-31+G** 0.84 HF/6-31+G(2d,2p)//HF/6-31+G(2d,2p) 0.31 MP2/6-31+G**//HF/6-31+G** 6.87 MP4/6-31+G**//HF/6-31+G** 7.20 MP2/6-31+G**//MP2/6-31+G** 14.15 It can be obviously seen that the MP and HF give a such huge difference that there is absolutely not comprimise between HF and MP values. The same situation was also observed in another compound similar to CH3NH2. Can any of you help me handle this problem? My question is that which method I should trust in term of the BSSE computation, MP or HF? I would greatly appreciate any direction, suggestion and comment. Thank you very much in advance. Kui Zhang Department of Chemistry Miami University Oxford, OH 45056 USA E-mail to: kzhang@miamiu.acs.muohio.edu From owner-chemistry@ccl.net Wed Jul 5 17:13:47 1995 Received: from gsusgi1.Gsu.EDU for chessyx@gsusgi1.Gsu.EDU by www.ccl.net (8.6.10/930601.1506) id QAA18054; Wed, 5 Jul 1995 16:52:20 -0400 Received: (from chessyx@localhost) by gsusgi1.Gsu.EDU (8.6.10/8.6.10) id QAA20720 for chemistry@ccl.net; Wed, 5 Jul 1995 16:52:20 -0400 Date: Wed, 5 Jul 1995 16:52:20 -0400 From: Shijie Yao Message-Id: <199507052052.QAA20720@gsusgi1.Gsu.EDU> To: chemistry@ccl.net Subject: Responses to my QM contributions in FEP Q Hi, Jeremy at jeremy@med.su.oz.au, Bear at bear@basie.pharm.arizona and interested netters; As I promised, the following is a collection of the responses to my questions on quantum mechanics contribution to FEP calculations. I sincerely thank Professor Kollman and Dr. Erin Duffy of Professor Jorgensen's group in Yale for their kindly reply. 1) >From kollman@theochem.kun.nl > >If all you want is the solvation free energy difference and you make >the assumption that any intramolecular effects are similar in >gas phase and solution, probably a reasonable assumption for the >molecules you describe, it is an excellent approximation(Jorgensen and >Ravimohan, JCP, 1985) just to do the FEP in solution...it isnt >clear from your mail what your goal is?...peter k. 2) From eduffy@laplace.csb.yale.edu > Hi - If you are using free energy perturbation, you only need > to complete the following thermodynamic cycle: > > A > r-anthracene (g) -----> r-anthracene (aq) > > | | > | (1) | (2) > | | > v v > > B > anthracene (g) -----> anthracene (aq) > > Experimentally, one measures A and B, which correspond to the > free energies of transfer of the anthrancenes from vacuum, in > this case, to water. These calculations would be difficult to > do computationally, as one would have to compute two potentials > of mean force where one moves the individual solutes from the gas > phase into the aqueous solution. Fortunately, as this is a thermodynamic > cycle, you can compute the equivalent processes (1) and (2). If > the molecules are rigid (no intramolecular degrees of freedom), then > this involves only the computation of (2), which is a gradual mutation of > substituted anthracene to the unsubstituted one (or a "reeling-in" > of that r- group to dummies). If you are including internal motion, then > the gas-phase mutation (1) is needed, such that the ddG reflects only > the differences in solvation of the monomers. By the way, I assume you're > using FEP in the context of Monte Carlo (bonus) or MD? Whatever the case, > ab initio isn't needed here, other than - perhaps - to obtain starting > geometries and/or partial charges for the monomers, if you don't have > them already. You might find the following quite helpful: > > Jorgensen, W. L. "Free Energy Calculations: A Breakthrough for Modeling > Organic Chemistry in Solution." Acc. Chem. Res., 1989, v.22, 184-189. > > Jorgensen, W. L. "Computational Insights on Intermolecular Interactions > and Binding in Solution." Chemtracts - Org. Chem., 1991, v.4, 91-119. > > Severance, D. L.; Essex, J. W.; Jorgensen, W. L. "Generalized Alteration > of Structure and Parameters: A New Method for Free-Energy Perturbations > in Systems Containing Flexible Degrees of Freedom." J. Comput. Chem., 1995, > v.16, 311-327. > If I have been unclear or have misunderstood your situation (which is > entirely possible), please do not hesitate to contact me. > > Erin Duffy > (eduffy@laplace.csb.yale.edu) 3) My Q: ----------------------------- Dear Professor Kollman, Thank you very much for your response to our question on the free energy problem we posted earleir. When we consider a thermodynamics cycle like the following to get the total free energy difference (not only solvation free energy), A E + S1(aq) -----------> ES1(aq) | | (1)| |(2) | | v v E + S2(aq) -----------> ES2(aq) B we know that the intramolecular effects for E + S1(aq) -----> ES1(aq) and also for E + S2(aq) -----> ES2(aq) are different. How should we consider the quantum mechanical contributions in such a situation? Do we also need to include the zero point vibrational energy difference to the total free energy? Thank you very much for the help and your time. Shijie Yao at chessyx@gsusgi1.gsu.edu ----------------------------- >From kollman@theochem.kun.nl Tue Jun 27 13:43:01 1995 > >I want to make sure we are communicating correctly...if the cycle >corresponds to a weak non-covalent interaction, it is not >clear that the two intramolecular effects will be different...however, >if they are, e.g., see Cieplak et al JACS, 1987 for base tautomers, >then you should run ab initio calcs for the gas phase energies to make >sure they are as accurate as possible...again, given that you have done >the qm, you can also consider the normal modes and determine not only >the zero point energy, but also the thermal energy and entropy...gas phase >of course...so I would have to be informed what you are actually >symbolizing by E, S and ES1 to give you a definitive answer of whether >the intramolecular calcs are worth doing and at what QM level...peter k 4) >From eduffy@laplace.csb.yale.edu >Hi - While it is true that the unsubstituted and substituted > anthracene molecules undoubtedly have different zero-point > energies, and while it is also probable that those zero- > point energies are different in solution than they are in the > gas phase, you can't do the QM calculation in the condensed > phase. To get the difference in the intramolecular parts, > you do the mutation in the gas phase as well as in solution > and then compute the ddG: > > dG(r) > r-anthracene (g) -----> r-anthracene (sol) > > | | > | dG(gas) | dG(sol) > | | > v v > dG(u) > anthracene (g) -----> anthracene (sol) > > ddG = dG(r) - dG(u) = dG(gas) - dG(sol) > > This has been done routinely in the Jorgensen group for > all types of organic solutes, including substituted benzenes. > In fact, you might check out the following: > >Jorgensen, W. L.; Nguyen, T. B. "Monte Carlo Simulations of the >Hydration of Substituted Benzenes with OPLS Potential Functions." >J. Comput. Chem., 1993, v.13, 195-205. > > It has occurred to me that perhaps you are intending to take > a QM/MM approach to this problem? Please let me know if > this is the case. > > Anyway, I hope this has helped. Please do not hesitate to > contact me again. - Erin 5) >From: kollman@theochem.kun.nl (Peter Kollman) > >Hi, Shijie... >are the bonds formed the same in S1 and S2...if so, you may not have >to calc intramolecular...see paper by S. Rao et al, Nature, 1987 on >the tetrahedral intermediate in the serine proteases... --------------- END ------------------- Shijie Yao at chessyx@gsusgi1.gsu.edu From owner-chemistry@ccl.net Wed Jul 5 20:09:54 1995 Received: from schroeder.newcastle.edu.au for tony@schroeder.newcastle.edu.au by www.ccl.net (8.6.10/930601.1506) id TAA21295; Wed, 5 Jul 1995 19:55:28 -0400 Received: by schroeder.newcastle.edu.au (AIX 3.2/UCB 5.64/4.03) id AA21712; Thu, 6 Jul 1995 09:53:23 GMT Date: Thu, 6 Jul 1995 09:53:23 +0000 (CUT) From: Tony Dyson To: Computational Chemistry List Subject: CCL: Periodic AM1 calculations? Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII I am attempting to model the chemisorption of small hydrocarbon molecules, such as ethyne, on vicinal Si(001). I don't have the computational resources available in order to perform any kind of ab initio study of this system, due to the large size of the unit cell required to model a surface step. Cluster calculations with AM1 have proven frustrating, because of course the edge effects far outweigh any effects of the surface step itself. At present I am in the process of trying out "Siligen" atoms to terminate the bonds at the edges of the cluster, as proposed by Redondo et al. J. Vac. Sci. Technol. 19 (1981) 498. (See also Lutrus et al. Phys. Rev. B 48 (1993) 15086; Wu & Carter, Phys. Rev. B 45 (1992) 9065.) However, what would be preferable is to perform a calculation taking into account the 2-dimensional periodicity of the system. In the past our group has done this with our own SLAB-MINDO method, eg Craig & Smith, Surf. Sci. 276 (1992) 174; Surf. Sci. 225 (1990) 225, and more recently with the CRYSTAL program of Dovesi and co-workers. The MINDO formalism has unfortunately passed its "use-by date" due to the availability of much more accurate models, while the computational and storage demands of CRYSTAL calculations (with reasonable basis sets) are too great for successful application to this problem. It has come to my attention that there is a periodic implementation of the AM1 scheme contained within MOPAC 93. Do any of the CCL contributors have experience with this version of MOPAC? I would like to find out whether 2-dimensional periodicity is implemented or whether the technique is restricted to full 3-dimensional periodicity. Thank you, Tony Dyson ================================================================ Mr. Anthony J. Dyson tony@schroeder.newcastle.edu.au Dept. of Physics phone: +49 21 5425 University of Newcastle fax: +49 21 6907 Callaghan, Australia, 2308 ================================================================