From elewars@alchemy.chem.utoronto.ca Mon Jun 6 01:44:18 1994 Received: from alchemy.chem.utoronto.ca for elewars@alchemy.chem.utoronto.ca by www.ccl.net (8.6.4/930601.1506) id BAA15427; Mon, 6 Jun 1994 01:40:29 -0400 Received: from localhost (elewars@localhost) by alchemy.chem.utoronto.ca (8.6.4/8.6.4) id BAA26938 for chemistry@ccl.net; Mon, 6 Jun 1994 01:39:51 -0400 Date: Mon, 6 Jun 1994 01:39:51 -0400 From: "E. Lewars" Message-Id: <199406060539.BAA26938@alchemy.chem.utoronto.ca> To: chemistry@ccl.net Subject: Calculating effects of isotopic substitution S. Shapiro asks why H, D and T (hydrogen-1, -2, and -3) substituents all give the same results in his calculations. The answer is that the normal procedures of computational chemistry do not take isotopic masses into account. Thus the calculated bond orders of H-X and D-X will be the same (altho' in real life they are presumably slightly different). If you look under the hood of your program (e.g.MOPAC) you will see that the masses of the atomic nuclei do not figure in the calculations. This gives pretty good results in most cases, since chemistry is ruled by the electromagnetic force, which is far, far stronger than the gravitational force. The one common type of calculation that does use nuclear masses is a frequency calc, since freqs depend on force constants *and* nuclear masses. I suppose the mass effect on freqs shows up in zero point energies and so affects relative E's when one bothers to correct for ZPE. === Errol Lewars Chem Dept Trent U Peterborough Ontario Canada K9J 7B8 D-day 1:40 === From ipcakc@vigyan.iisc.ernet.in Mon Jun 6 13:23:53 1994 Received: from relay1.UU.NET for ipcakc@vigyan.iisc.ernet.in by www.ccl.net (8.6.4/930601.1506) id MAA06716; Mon, 6 Jun 1994 12:50:43 -0400 From: Received: from iisc.ernet.in (via iisc.iisc.ernet.in) by relay1.UU.NET with SMTP (5.61/UUNET-internet-primary) id AAwtdj13902; Mon, 6 Jun 94 12:50:39 -0400 Received: by iisc.ernet.in (ERNET-IISc/AT&T UNIX SYS V.3.2) id AA04514; Mon, 6 Jun 94 22:04:40 EDT Received: by vigyan.iisc.ernet.in (smail2.3) id AA09772; 6 Jun 94 21:56:31 EST (Mon) To: CHEMISTRY@ccl.net Subject: polymer chemistr list Date: 6 Jun 94 21:56:31 EST (Mon) Message-Id: <9406062156.AA09772@vigyan.iisc.ernet.in> hi netters, Is there anything like "Ploymer Chemistry List" as we have computational chemistry list? Debasis ipcakc@ipc.iisc.ernet.in From GKING@arserrc.gov Mon Jun 6 13:56:26 1994 Received: from arserrc.gov for GKING@arserrc.gov by www.ccl.net (8.6.4/930601.1506) id MAA06711; Mon, 6 Jun 1994 12:50:11 -0400 From: Received: from arserrc.gov by arserrc.gov (PMDF V4.2-11 #2923) id <01HD80PPRE1C000LSV@arserrc.gov>; Mon, 6 Jun 1994 12:49:25 EDT Date: Mon, 06 Jun 1994 12:49:24 -0400 (EDT) Subject: CCL:Amber Energies. What are they? To: chemistry@ccl.net Message-id: <01HD80PPS6Z6000LSV@arserrc.gov> X-VMS-To: IN%"chemistry@ccl.net" MIME-version: 1.0 Content-type: TEXT/PLAIN; CHARSET=US-ASCII Content-transfer-encoding: 7BIT On Fri, 3 Jun 1994 KGRAFTON@aardvark.ucs.uoknor.edu wrote: >AMBER 4.0 purports to output energies from MD runs in Kcals (pg 79 >of the manual). This energy does not seem to be kcals/mol, as a box >of 200 water molecules gives twice the energy as a box of 100 molecules. There is sometimes confusion about the energy unit "kcal/mol". Its use (as opposed to plain old kcal) allows us to work with numbers such as 6.02 as opposed to 1.e-23. Think of the unit kcal/mol as kcal/6.02e23 (i.e. the "/mol" is a scale factor, not a normalization factor). The energy reported by AMBER is the total energy of the particular system under consideration, and thus it makes sense that the energy of 200 water molecules is about twice as much as the energy of 100 water molecules. >My best guess is that since the AMBER code accepts a 'built-in' solvent >such as TIP3p water as a single 'molecule' built up of many residues, the >energies are reported in (kcal)/(mol of boxes of whatever). Is this true? No. AMBER simply reports the total energy of the system. We would run into some problems if AMBER and similar programs did try to normalize the energies per mole, since the programs would first have to answer the question "per mole of what: solute molecule, solvent molecule?" Most of us would not like our software to be so presumptuous as to try to answer this question. >Also, has anyone had any difficulty using TIP4p water in AMBER? The >pure solvent that I have run drops dramatically (~400 kcal) in energy >after about 30-40ps, and from there on fluctuates only about 1 kcal up or >down in total energy. The total energy *should* be constant. The potential and kinetic energy values should still be fluctuating, however. If not, you are either running your simulation at 0 Kelvin, or there is a genuine problem. >It seems to have formed some type of rigid >'polywater'structure. It has been suggested to me that this is caused by >the charge center being given a mass of ~12amu There shouldn't be any problem with a mass of 12amu. Regards, Greg ==================================================================== Gregory King Internet: gking@arserrc.gov Eastern Reg. Res. Ctr., ARS, USDA Voice: (1) 215 233 6675 600 East Mermaid Lane Fax: (1) 215 233 6559 Philadelphia, PA 19118-2551 ==================================================================== From mjh25920@ggr.co.uk Mon Jun 6 14:23:52 1994 Received: from gate.ggr.co.uk for mjh25920@ggr.co.uk by www.ccl.net (8.6.4/930601.1506) id NAA07122; Mon, 6 Jun 1994 13:28:06 -0400 Received: from mailhub.ggr.co.uk by gate.ggr.co.uk; Mon, 6 Jun 1994 18:26:16 +0100 Received: from uk6x49.ggr.co.uk by mailhub.ggr.co.uk; Mon, 6 Jun 1994 18:22:34 +0100 Received: by uk6x49.ggr.co.uk (8.6.8.1/imd110593) id SAA08662; Mon, 6 Jun 1994 18:26:15 GMT Date: Mon, 6 Jun 1994 18:26:14 +0000 (GMT) From: Martin Hargreaves Subject: Conference To: chemistry@ccl.net Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hello, This message is not from myself, but sent on behalf of Dr. Mike Hann. Queries regarding the message should be sent to him (mmh1203@ggr.co.uk) and not me. Queries regarding the conference should be sent to the address at the bottom of the enclosed message. Regards, Martin. ------ The Chemical Information Explosion ********************************** Chaos, Chemists and Computers ============================= A 2- day conference to be held on September 12th and 13th at the University of Reading, organised by a joint committee on the Molecular Graphics and Modelling Society, the Chemical Structures Association, the UKQSAR Group and the Computer Applications Subject Group of the Royal Society of Chemistry. THe purpose of the meeting is to bring together scientists from different disciplines who are interested in the problems posed by the chemical information explosion. There will be a poster session and a software/hardware exhibition. Topics to be covered include: 1. Chemical and Biological Data Collection and storage. 2. Getting Information from Public and Private Data. 3. Getting what we want - Can Technology bridge the gap. Speaker include: o Dick Hyde (Wellcome) o Derek Reynolds (Glaxo) o Jeff Morris (Zeneca) o John Trigg (Kodak) o Bill Town (Derwent) o Kate Harvey (Scinet) o Ian Nabney (Logica) o Dave Livingston (SB) o Ray Dessy (Virginia Tech) o Dave Bawden (City University) o Henry Rzepa (Imperial College) o Andy Morffew (IBM) o Syd Hall (Australia) o Jane McIntyre (Chapman and Hall) The conference will begin at 9.30 September 12th and finish aon Tuesday September 13th. All lectures, the poster session and the commercial exhibition will be held in the Chemistry Department of the University of Reading. The University of Reading is situated in a pleasant park close to the M4, Heathrow and public transport. Accomodation will be provided in Windsor Hall, a few minutes walk away from the lecture venue. Enquiries to Mike Drew, Department of Chemistry, University of Reading, RG6 2AD. FAX 0734 311610, Email scsdrew@reading.ac.uk ------ Martin Hargreaves | mjh25920@ggr.co.uk Computational Chemist | ch11mh@surrey.ac.uk Glaxo R & D | No problem is so large that & Surrey University | we can't fit it in somewhere From MARLA@chemf.rutgers.edu Mon Jun 6 17:24:00 1994 Received: from chemf.rutgers.edu for MARLA@chemf.rutgers.edu by www.ccl.net (8.6.4/930601.1506) id QAA11780; Mon, 6 Jun 1994 16:48:29 -0400 Date: Mon, 6 Jun 94 15:50 EST From: Marla Babcock Subject: Nucl Acid Struct Analysis Prog Release To: chemistry@ccl.net Message-id: <0723C5628BFF601AAC@chemf.rutgers.edu> X-Organization: Department of Chemistry at Rutgers University X-Envelope-to: chemistry@ccl.net X-VMS-To: IN%"chemistry@ccl.net" ANNOUNCING THE RELEASE OF A PROGRAM WHICH ANALYSES NUCLEIC ACID CRYSTALLOGRAPHIC COORDINATE DATA ACCORDINATE TO THE EMBO GUIDELINES OF 1988. Several years ago, the European Molecular Biology Organization published guidelines defining how nucleic acid duplex structures can be examined. The guidelines defined three rotational and three translational parameters between the bases comprising a base pair as well as from one base pair to the next. There are five programs readily distributed in order to perform the calculations. We are releasing a sixth which was created to be able to handle not only the calculations of normal duplexes, but also comparably examine mispaired bases, hoogstein base pairs, looped out bases, a single base adjacent to a base pair, intercalated drugs for which a coordinate frame has been defined, etc. The nucleic acid structure analysis program is written in Fortran and runs in a UNIX or VMS environment (please specify preference). The program calculates all of the rotational and translational parameters for complementary base pairs, neighboring base pairs in Cartesian and helical coordinate frames, and base to base Cartesian and helical parameters along each strand. A simple interactive user interface allows for one to specify what file is examined and which parameters to calculate. The program was designed so that the user needs to spend a minimal time reading the documentation in order for the program to run. Full disclosure of the mathematics has been made and published so that the user can readily understand what their parameters mean. The mathematics are unique for this type of calculation and aviod many of the problems previously encountered. In particular, the calculations are performed by a single rotation not sequential rotations avoiding the use of a midway coordinate frame for rotational parameter calculations. This ensures that the magnitude of the rotational parameters is strand free and direction free. Because a single rotation is used, the equations for each rotational parameter are equivalent, therefore, a 5 degree rotation about the X axis is equivalent to a 5 degree rotation about either the Y or the Z axis. This is not always true of other mathematical formulations presently being used. The mathematics used for calculating the complementary base parameters is identical to the math used to calculate the neighboring base/base pair parameters except that different axes are involved. This is not generally the case of the other available programs. In addition, since the calculations are bases upon local considerations, the value of the parameter depends on only the bases involved and are independent of adjacent bases. This allows for more accurate comparison of parameters from one structure to another. Copies of the code can be acquired by e-mailing me at: Marla@Rutchm.Rutgers.edu. Dr. Marla Babcock Dept of Chemistry Rutgers University P.O. Box 939 Piscataway, N.J. U.S.A 08855 Useful References: A users guide to the programs is provided in the paper: Babcock, M.S., Pednault, E.P.D, and Olson, W.K., "Nucleic Acid Structure Analysis: A Users Guide to a Collection of New Analysis Programs," Journal of Biomolecular Structure and Dynamics, Vol. 11, No. 3, pp 597-628, 1993. The issues surrounding the definition of nucleic acid structure parameters and how we address these issues are discussed in: Babcock, M.S., and Olson, W.K., "A New Program for the Analysis of Nucleic Acid Structure Interpretation," in Computation of Biomolecular Structures: Achievements, Problems, and Perspectives, Soumpasis, D.M., and Jovin, T.M., Eds., Springer-Verlag, Heidelberg, pp 65-85, 1993. The mathematical definitions of the nucleic acid structure parameters and the methods used to calculate them are presented in: Babcock, M.S., Pednault, E.P.D, and Olson, W.K., "Nucleic Acid Structure Analysis: Mathematics for Local Cartesian and Helical Structure Parameters That are Truly Comparable Between Structures," Journal of Molecular Biology, Vol. 237, pp 125-156, 1994. In order to take into account base-stacking effects and other physical constraints, the mathematical definitions we have developed contain parameters called "pivot points", which are the points about which the bases in a structure buckle, propeller twist, and open. The statistical analyses that were performed to determine the optimum positions of the pivot points are presented in: Babcock, M.S., and Olson, W.K., "The Effect of Mathematics and Coordinate System on Comparability and 'Dependencies' of Nucleic Acid Structure Parameters," Journal of Molecular Biology, Vol. 237, pp 98-125, 1994. From david@wucmd.wustl.edu Mon Jun 6 18:24:14 1994 Received: from wugate.wustl.edu for david@wucmd.wustl.edu by www.ccl.net (8.6.4/930601.1506) id RAA12357; Mon, 6 Jun 1994 17:41:01 -0400 Received: by wugate.wustl.edu (5.67b/WUSTL-0.3) with SMTP id AA15295; Mon, 6 Jun 1994 16:41:00 -0500 Received: by wucmd (920330.SGI/911001.SGI) for @wugate.wustl.edu:chemistry@ccl.net id AA19197; Mon, 6 Jun 94 14:24:02 -0500 Date: Mon, 6 Jun 1994 14:21:49 -0500 (CDT) From: David Chalmers Subject: Modelling electrochemical oxidations To: chemistry@ccl.net Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hello all, I would like to investigate some electrochemical oxidations of small organic molecules (ideally) using Mopac or perhaps another semiempirical method. I would like to be able to predict the difficulty of oxidation in a series of similar molecules. I would also like to be able to predict the site of oxidation in molecules that can be oxidized at several positions. Can anybody point me towards literature that describes this sort of study? If anybody has experience...are semiempirical methods good enough...or do you need to go to ab initio to get even qualitative results? Thanks David -------------------------------------------------------------------------------- David Chalmers david@wucmd.wustl.edu Washington University CMD: +1 314 935 4672 Center for Molecular Design Lab: +1 314 362 2515 Lopata Hall, Box 1099 Fax: +1 314 935 4979 One Brookings Drive St. Louis, MO 63130, USA -------------------------------------------------------------------------------