From rc_davis@srs.gov Mon May 3 05:37:16 1993 From: rc_davis@srs.gov (Ricardo C. Davis) Message-Id: <9305030937.ZM20814@cmas3.srs.gov> Date: Mon, 3 May 1993 09:37:16 -0400 Organization: Westinghouse Savannah River Company To: chemistry@ccl.net Subject: ACS E-mail Addresses? Do the American Chemical Society's offices in Washington, D.C. have Internet/BITnet addresses? It sure would be nice...If so, please post to the list. RCD -- Ricardo C. Davis Internet: rc_davis@srs.gov Building 773-42A, SCS-SRTC, Westinghouse Savannah River Co. P.O. Box 616, Aiken, SC 29802 (803)725-5172 From jtgolab@amoco.com Mon May 3 04:39:49 1993 Date: Mon, 3 May 1993 09:39:49 -0500 From: jtgolab@amoco.com Message-Id: <9305031439.AA16253@vacc47.nap.amoco.com> To: CHEMISTRY@ccl.net Subject: Re: gammes >In-Reply-To: flicker@engin.umich.edu I think that you mean "GAMESS" (=General and Atomic Molecular Electronic Structure Systems). Mike Schmidt is the caretaker/improver/guru of the program and I quote him here from the GAMESS manual: "This version of GAMESS is described in the Quantum Chemistry Program Exchange newsletter: M.W.Schmidt, K.K.Baldridge, J.A.Boatz, J.H.Jensen, S.Koseki, M.S.Gordon, K.A.Nguyen, T.L.Windus, S.T.Elbert QCPE Bulletin, 10, 52-54 (1990). Questions about GAMESS may be addressed to: Mike Schmidt = mike@si.fi.ameslab.gov ." Among some of the delightful features of GAMESS are the following... it runs on almost every (modern) machine known to peoplekind; it comes complete with scripts to compile it, scripts to run it, (very) good documentation, and all the source code (if you like to make modifications); and finally, help and support is very easy to obtain thru Email. :Joe jtgolab@amoco.com From sliu@mastermodel.ps.uci.edu Mon May 3 00:03:28 1993 Message-Id: <9305031503.AA10292@mastermodel.ps.uci.edu> To: chemistry@ccl.net Subject: GROMOS Date: Mon, 03 May 93 08:03:28 -0800 From: Song Liu Dear everyone: Can someone tell me where to find the source code and user manual for GROMOS? Thanks Song Liu Chemistry, UC. Irvine From feng@lisboa.ks.uiuc.edu Mon May 3 08:47:57 1993 From: Zhou Feng Message-Id: <9305031848.AA20390@lisboa.ks.uiuc.edu> Date: Mon, 3 May 93 13:47:57 -0500 To: chemistry@ccl.net Subject: attending ACS? Does anybody how could I attend the American Chemical Society? --- Feng Zhou +-------------------------------------------------------------------- |Theoretical Biophysics feng@lisboa.ks.uiuc.edu |University of Illinois Tel: (217)-244-1612 |3121 Beckman Institute Fax: (217)-244-6078 |405 N Mathews, Urbana, IL61801 NeXTmail Ok +-------------------------------------------------------------------- From jle@world.std.com Mon May 3 12:02:14 1993 Date: Mon, 3 May 1993 16:02:14 -0400 From: jle@world.std.com (Joe M Leonard) Message-Id: <199305032002.AA11033@world.std.com> To: chemistry@ccl.net Subject: Electrostatic potential questions Folks... I've seen several articles over the last few years, most recently Alkorta, Villar and Arteca, J Comp Chem 14,530(1993), demonstrating that electrostatic potentials calculated with the MNDO wavefunction were more similar to high-level ab initio results that those obtained from AM1 or PM3. Does anybody have an idea as to why this is the case (or what references I've missed that discuss such reasons)? Along these lines, what is the accepted wisdom when fitting charges to electrostatic potentials - how close to the VdW surface should points used in the fit be? Joe Leonard jle@world.std.com From kmoore@ncsc.org Mon May 3 12:17:39 1993 Date: Mon, 3 May 93 16:17:39 EDT From: Kevin Moore Message-Id: <9305032017.AA23964@duck.ncsc.org> To: chemistry@ccl.net Subject: hydrogen bonding... Hello- I am doing some ab initio calculations on a couple of molecules to determine the chemical shifts of a few protons. The results for one molecule are not coming as close to experiment as I had expected. In response to this, I was hoping to strategically position one or two waters in a manner that would satisfy the H-bonding that the system is probably doing in solution. I know that some work has been done on looking at water x-mers and related, but was wondering if there has been any work looking at secondary amines? On a more fundamental level, how would one approach the problem of best orienting one or two waters in relation to a molecule such as pyrrolidine. I have received suggestions of sticking it in a water box, minimize and then do dynamics and look at which h2o seem to stick closest to the molecule in the dynamics. Any other ideas? Is this a reasonable way to get started? I am trying to minimize the CPU time involved with generating the HF minimized structure for this type of system (the actual molecule is larger than pyrrolidine). ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ || Kevin Moore North Carolina Supercomputing Center || || Scientific Support Analyst 3021 Cornwallis Rd. || || (919) 248-1179 Research Triangle Park, NC 27709 || ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ From mmcallis@alchemy.chem.utoronto.ca Mon May 3 14:19:57 1993 Date: Mon, 3 May 93 18:19:57 -0400 From: mmcallis@alchemy.chem.utoronto.ca (Mike McAllister) Message-Id: <9305032219.AA18915@alchemy.chem.utoronto.ca> To: chemistry@ccl.net Subject: MP2 freqs Hey Netters, I hope someone can answer a fairly easy question for me: Is it customary to 'scale' MP2 frequencies and ZPVE values the same way one typically does with HF values??? If yes, what factor is normally used?? Also, a GAUSSIAN output calculates infrared intensities and reports them in units of 'KM/MOLE', anybody now what the heck KM/MOLE is????? How reliable is the calculation of intensities?? Thanks for any help in advance. Mike McAllister University of Toronto From DSMITH@uoft02.utoledo.edu Mon May 3 18:06:41 1993 Date: Mon, 03 May 1993 23:06:41 -0500 (EST) From: "DR. DOUGLAS A. SMITH, UNIVERSITY OF TOLEDO" Subject: Re: hydrogen bonding... To: kmoore@ncsc.org Message-Id: <01GXR7G52F8800663R@UOFT02.UTOLEDO.EDU> Kevin Moore writes: > I am doing some ab initio calculations on a couple of molecules to >determine the chemical shifts of a few protons. The results for one molecule >are not coming as close to experiment as I had expected. In response to >this, I was hoping to strategically position one or two waters in a manner >that would satisfy the H-bonding that the system is probably doing in >solution. I know that some work has been done on looking at water x-mers >and related, but was wondering if there has been any work looking at >secondary amines? On a more fundamental level, how would one approach the >problem of best orienting one or two waters in relation to a molecule >such as pyrrolidine. I have received suggestions of sticking it in >a water box, minimize and then do dynamics and look at which h2o seem to >stick closest to the molecule in the dynamics. Any other ideas? Is this a >reasonable way to get started? I am trying to minimize the CPU time involved >with generating the HF minimized structure for this type of system (the >actual molecule is larger than pyrrolidine). We recently published a paper (JACS 1993, 115, 2912) entitled "Theoretical Studies on Hydration of Pyrrole, Imidazole, and Protonated Imidazole in the Gas Phase and Aqueous Solution". While these compounds are not secondary amines but rather aromatic, the general approach is, I think, what you are after. We looked at these molecules at the HF/6-31G* and MP2/6-31G* levels for total geometry optimization both in gas phase and hydrated (one molecule of water per solute, position optimized either in the plane or above the plane of the solute; two molecules of water as well for imidazole). Single point calculations were carried out at the MP2/6-311++G** //MP2/6-31G* level and combined with frequency analyses and BSSE corrections at the MP2/6-31G* level to calculate the free energies of hydration. In addition, we carried out Monte Carlo simulations using Jorgensen's Boss 3.1 program for dilute aqueous solutions in order to determine the hydrogen bonding geometries and free energies. The MC results were also analyzed using radial distribution functions. To answer your question as to how to best orient one or two water molecules around such molecules, the best answer is 1) look at what is already in the literature, such as our paper or others with more relevant systems to your own, and start from the reported optimized positions; 2) take your best guess based on solid chemical intuition, then optimize both in plane and out of plane; 3) triple check everything. For instance, we tried to look at imidazole with one water in the plane making a sigma hydrogen bond and a second water in the pi region. However, all attempts led to a structure in which one water formed a sigma hydrogen bond while the second water formed a hydrogen bond to the first water. We are now writing up our results of similar studies on histamine. Last piece of advice - these are big, _expensive_ calculations if done right, which includes perturbation or correlation during the optimization, and at a basis set level sufficient to describe hydrogen bonding, i.e. at least 6-31G* or DZP, with at least one set of diffuse functions. The latter are extremely important, as shown by our results and those of others, such as Janet Del Bene. On another note, let me plug the symposium on Modeling the Hydrogen Bond, which I am chairing at the Chicago ACS meeting in August. It will run two full days, Sunday and Monday, and will include a number of big names and forefront research in this area. Doug Douglas A. Smith Assistant Professor of Chemistry The University of Toledo Toledo, OH 43606-3390 voice 419-537-2116 fax 419-537-4033 email dsmith@uoft02.utoledo.edu P.S. reprints of our article are available by request - email or US mail. From imtvi06@cc.csic.es Mon May 3 23:29:48 1993 Date: Tue, 4 May 1993 5:28:05 UTC+0100 From: Luis Montero Subject: Electrostatic potential questions To: chemistry-request@ccl.net (confirm) Message-Id: <326*/S=imtvi06/OU=cc/O=csic/PRMD=iris/ADMD=mensatex/C=es/@MHS> Dear netters: The interesting finding of Arteca's paper is, from my point of view a casual quality of MNDO. Let us take into account that this method took a consistent approximate hamiltonian (Pople's NDDO, 1965-67) and parametrized it to give fair results for a fixed set of molecules which experimental geometries and heats of atomization were accurately determined. This work have been done for each element. It gave no meaning to different terms in hamiltonians, if you take them separately, but a certainly confident result for tarjet proper- ties (geometries and heats of formation, known the experimental heats of formation of gaseous elements) of the molecules. Electrostatic fields depend on molecular eigenfunctions, and they could be good from these grounds. AM1 and PM3 (truly AM1, beacuse PM3 is a reparameterization) introduced some terms in the distance matrix dependent term after the SCF procedure. It was, in the pure molecular SCF, the core-core interaction term of the Born Oppen- heimer approximation. Many theoreticians of semiempirical methods attribute to this term some of the frequent wrong results. In fact, this distance matrix dependent term is theoreticaly consistent, but it is used for introducing corrections to the approximate SCF results when geometrical quantities are calculated. AM1 used a variable set of "forza bruta" (Dewar's words) gaussian terms in this part of the calculation to improve results for certain non pure- ly bonding cases as hydrogen bridges and cyclic CH structures. It, consequen- tly, afected parameters in the SCF hamiltonian. Probably, these extrange inclusion in the full SCF procedure affected more the quality of molecular eigenfunctions than the former parameterization of MNDO. I have some non published results where it is clearly seen the lowest quality of molecular wave functions by PM3, being molecular geometries OK. Best regards, Luis Montero Universidad de La Habana (silicon%ceniai.cu@igc.apc.org) CSIC, Madrid (imtvi06@cc.csic.es) From imtvi06@cc.csic.es Mon May 3 23:29:48 1993 Date: Tue, 4 May 1993 5:28:05 UTC+0100 From: Luis Montero Subject: Electrostatic potential questions To: chemistry-request@ccl.net (confirm) Message-Id: <326*/S=imtvi06/OU=cc/O=csic/PRMD=iris/ADMD=mensatex/C=es/@MHS> Dear netters: The interesting finding of Arteca's paper is, from my point of view a casual quality of MNDO. Let us take into account that this method took a consistent approximate hamiltonian (Pople's NDDO, 1965-67) and parametrized it to give fair results for a fixed set of molecules which experimental geometries and heats of atomization were accurately determined. This work have been done for each element. It gave no meaning to different terms in hamiltonians, if you take them separately, but a certainly confident result for tarjet proper- ties (geometries and heats of formation, known the experimental heats of formation of gaseous elements) of the molecules. Electrostatic fields depend on molecular eigenfunctions, and they could be good from these grounds. AM1 and PM3 (truly AM1, beacuse PM3 is a reparameterization) introduced some terms in the distance matrix dependent term after the SCF procedure. It was, in the pure molecular SCF, the core-core interaction term of the Born Oppen- heimer approximation. Many theoreticians of semiempirical methods attribute to this term some of the frequent wrong results. In fact, this distance matrix dependent term is theoreticaly consistent, but it is used for introducing corrections to the approximate SCF results when geometrical quantities are calculated. AM1 used a variable set of "forza bruta" (Dewar's words) gaussian terms in this part of the calculation to improve results for certain non pure- ly bonding cases as hydrogen bridges and cyclic CH structures. It, consequen- tly, afected parameters in the SCF hamiltonian. Probably, these extrange inclusion in the full SCF procedure affected more the quality of molecular eigenfunctions than the former parameterization of MNDO. I have some non published results where it is clearly seen the lowest quality of molecular wave functions by PM3, being molecular geometries OK. Best regards, Luis Montero Universidad de La Habana (silicon%ceniai.cu@igc.apc.org) CSIC, Madrid (imtvi06@cc.csic.es)