From elewars@alchemy.chem.utoronto.ca Tue Aug 31 19:53:53 1993 Date: Tue, 31 Aug 93 23:53:53 -0400 From: elewars@alchemy.chem.utoronto.ca (E. Lewars) Message-Id: <9309010353.AA01890@alchemy.chem.utoronto.ca> To: chemistry@ccl.net Subject: Cartesians vs. Z-Matrices--which to use, when? 1993 Aug 31 Subject: Cartesians or Z-matrix? I read in Gaussian news that optimizations of floppy molecules should be done with a Z-matrix (internal coordinates), while rigid molecules are best done with cartesians. Is it really true that optimizations are NOT always faster with a Z-matrix? In particular, my problem is this: I have a HF/6-31G* structure for 1 in cartesians (from another program which always uses cartesians). I want to use the HF structure as input for an MP2 opt with G92 (then do G92 MP2 freqs on the MP2 geom). 1. WILL THE MP2 OPT BE MUCH FASTER WITH A Z-MATRIX THAN WITH CARTESIANS? o If so, I will have to convert my cartesians / \ to a Z-mat, which is a pain (I use MOPAC's =======\ AIGOUT feature, since I haven't been able to see / \ from the Gaussian 92 User's Guide how to use / \ C6H4O New Z-mat), although I've had plenty of \\ // C2v practice writing Z-matrices from scratch. \\ _____ // 2. FOR AN MP2 FREQ JOB ON AN ALREADY OPTIMIZED GEOM, DOES IT MATTER (AS FAR AS SPEED GOES) 1 WHETHER I USE CARTESIANS OR A Z-MATRIX? IF IT DOES MATTER, ARE THE FACTORS TO WATCH OUT FOR THE SAME AS IN AN OPTIMIZATION--i.e. FLOPPIES WITH Z-MAT, RIGIDS WITH CATESIANS? ================================================================================= elewars@trentu.ca Errol Lewars Chem Dept Trent University Peterborough, Ontario Canada K9J 7B8 ============================================================================== From AJS1@phx.cam.ac.uk Wed Sep 1 10:12:23 1993 From: Anthony Stone Message-Id: <9309010912.AA13975@fandango.ch.cam.ac.uk> Subject: Re: 4-coord angles To: CHEMISTRY@ccl.net Date: Wed, 1 Sep 1993 10:12:23 +0000 (BST) > > The original question: > > > Given five of the six central angles in a general four-coordinate > >arrangment (2 special cases, of course, being a tetrahedron and a square > >plane), what is the forumula for the sixth (and redundant) angle in terms > >of the other five? Is there a simple invariant (sum rule?) for this system > >that I'm missing? I thought I'd see if anyone already knew the answer > >before I went through the trig myself. > > The answer appears to be that the sum of the cosines = -2. Try it. Sorry, I don't believe it. Counterexample: take the degenerate case where all four bonds coincide. All the angles are zero (or 360) so the sum of the cosines is 6. Anthony Stone University Chemical Laboratory, Internet: ajs1@phx.cam.ac.uk Lensfield Road, Phone: +44 223 336375 Cambridge CB2 1EW Fax: +44 223 336362 From ruusvuor@csc.fi Wed Sep 1 15:53:43 1993 Date: Wed, 1 Sep 1993 12:53:43 +0300 (EET) From: Raimo Uusvuori Subject: Re: Molecular Manufacturing and Chemical Design Automation News To: Ralph Merkle Message-Id: On Tue, 31 Aug 1993, Ralph Merkle wrote: > Chemical Design Automation News permanently ceased publication > with the August 1993 issue. > > Unfortunately, I had an invited article on "Molecular Manufacturing: > Adding Positional Control to Chemical Synthesis" scheduled for the > *September* issue.... C'est la vie. > > The article is now available in postscript format by anonymous FTP > from "parcftp" in file "/pub/nano/MolecularManufacturing.ps". > > Ralph C. Merkle > Xerox PARC > 3333 Coyote Hill Road > Palo Alto, CA 94304 > merkle@xerox.com > As far as I understand CDAN has not ceased publication. The August 1993 issue was accompanied by two letters. One was from CDAN saying that: "We have been working hard to find a new home for Chemical Design Automation News ..... We are pleased to inform you that your next issue will be published by Butterworth-Heinemann, publishers of Journal of Molecular Graphics. ..." Another one was NOTIFICATION OF NEW PUBLISHER from Butterworth-Heinemann: "Effective with Volume 8, Number 9, September/October 1993, CHEMICAL DESIGN AUTOMATION NEWS will be published by Butterworth-Heinemann, a of member the Reed-Elsevier group, based in Stoneham, Massachusetts, USA. ..." By the way, I was very disappointed to the August issue. There was nothing about new computer systems. Hopefully this is not a permanent editorial policy of the new publisher of CDAN, because this information has been very useful for us in the past. Raimo Uusvuori ------------------------------------------------------------------------ Raimo Uusvuori | Phone: +358-0-457 3210 Scientific Software Specialist | FAX: +358-0-457 2302 Chemistry | | Center for Scientific Computing | Street address: P.O. Box 405 | Tietotie 6, FIN-02150 ESPOO FIN-02101 ESPOO | E-mail: ruusvuor@csc.fi FINLAND | Raimo.Uusvuori@csc.fi ------------------------------------------------------------------------ From pis_diez@cpd.uva.es Wed Sep 1 11:56:05 1993 Date: Wed, 1 Sep 1993 11:56:05 UTC+0100 From: Reinaldo Pis Diez Subject: Molecular graphics package To: chemistry@ccl.net (confirm) Message-Id: Hi all!! Does anybody out there know any package (or a simple program) for handling (rotate, translate, etc) molecules and obtaining molecular graphics, preferably on a PC? Free packages are welcome. Thanx in advance, Reinaldo PD: answers can be directed to me. ****************************************************************************** Dr. Reinaldo PIS DIEZ Departamento de Fisica Teorica * Department of Theoretical Physics * Facultad de Ciencias * Faculty of Sciences * E 47011 Valladolid, Spain * E 47011 Valladolid, Spain * Phone: +34 83 42 31 47 Fax: +34 83 42 30 13 Email: pis_diez@cpd.uva.es ****************************************************************************** From bewilson@Kodak.COM Wed Sep 1 03:49:32 1993 Date: Wed, 1 Sep 93 07:49:32 -0400 Message-Id: <9309011149.AA20339@Kodak.COM> From: bewilson@Kodak.COM (Bruce E. Wilson, Eastman Chemical Company, (bewilson@kodak.com)) To: "m10!trucks@uunet.uu.net"@Kodak.COM Subject: RE: Linear Structure Notation > Can anyone direct me to documentation or specification of the SMILES linear > structure notation? (SMILES = Simplified Molecular Input Line Entry System). > In addition, is this considered the "standard", or are there new improved, > public domain notation systems more widely accepted? SMILES is _a_ standard. It is (IMO) deficient in some respects, primarily in being able to specify steriochemistry. For specifying connectivity it seems to work acceptably for the types of structures I deal with. There are several people (including myself) who have worked on extensions to SMILES, but there are no universally recognized extensions to handle specifying configurational isomers. D. Weininger J. Chem. Inf. Comput. Sci 28 (1988) 31-36. D. Weininger, A. Weininger and J.L. Weininger J. Chem. Inf. Comput. Sci 29 (1989) 97-101. D. Weininger J. Chem. Inf. Comput. Sci 30 (1990) 237-243. Bruce Wilson (bewilson@kodak.com) From frj@dou.dk Sun Sep 1 15:41:00 1993 Date: 1 Sep 93 13:41 +0200 From: Frank Jensen To: chemistry@ccl.net Message-Id: <873*frj@dou.dk> Subject: cartesian vs. z-matrix for optimization Optimizations in cartesian coordinates have for a long time had a bad reputation of being slowly convergent, and "good" z-matrices usually give much faster convergence. Actually, optimizing in cartesian coordinates is not much worse than in internal coordinates, PROVIDED that care is taken to implement the optimization algorithm "correct". In general there are two factors that determine how fast the convergence is. I here assume that the algorithm is a standart Newton-Raphson iterate, using first and second derivatives. 1) The translational and rotational degrees of freedom must be removed in the formation of the geometry step. This is automatically done when z-matrices are used, but rarely when cartesians are used. This is the main reason for the slow convergence when optimizing in cartesian! 2) The more diagonal dominant the Hessian matrix is, the faster the optimization. This is the criteria for chosing a "good" z-matrix. In cartesian cordinates the off-diagonal elements of the Hessian is roughly of the same size for all systems. With a "good" z-matrix the Hessian is almost diagonal and optimization will be faster than in cartesian. On the other hand, with a "bad" z-matrix, the optimization will be worse than in cartesians! Cyclic systems are typical examples where it is very difficult to construct a "good" z-matrix. Thus, properly implemented, optimization in cartesians give a fairly uniform convergence for a lot of different systems. A "good" set of internal coordinates will improve the convergence, but the choice of a good set is largely a matter of experience. And now for the commercial: the most recent versions of AMPAC and MOPAC is able to efficiently optimize systems in cartesian cordinates. Ignore the warning about more than 3N-6 variables (:-). Frank From jas@medinah.atc.ucarb.com Wed Sep 1 03:46:56 1993 Message-Id: <9309011246.AA27454@medinah.atc.ucarb.com> Date: Wed, 1 Sep 1993 08:46:56 -0500 To: chemistry@ccl.net From: jas@medinah.atc.ucarb.com (Jack Smith) Subject: Re: 4-coord angles (Wrong answer!) I thought I'd forward my response to Anthone Stone (and some others) to the list before I get anymore counterexamples. - Jack >>> >>> The original question: >>> >>> > Given five of the six central angles in a general four-coordinate >>> >arrangment (2 special cases, of course, being a tetrahedron and a square >>> >plane), what is the forumula for the sixth (and redundant) angle in terms >>> >of the other five? Is there a simple invariant (sum rule?) for this system >>> >that I'm missing? I thought I'd see if anyone already knew the answer >>> >before I went through the trig myself. >>> >>> The answer appears to be that the sum of the cosines = -2. Try it. >> >>Sorry, I don't believe it. Counterexample: take the degenerate case where all >>four bonds coincide. All the angles are zero (or 360) so the sum of the >>cosines is 6. Anthony: Thanks for actually trying it. Several others have also come up with counterexamples. When it worked for the square plane, a tetrahedron, and one arbitrary (distorted square plane) case, I prematurely assumed it was correct -- not exactly an inductive proof! I had about 50+ actual cases I could have tried it on -- I apparently picked one that was still close to -2. Since originally posting the question I actually started to look into a little and found a discourse on spherical triangles, but I didn't pursue it -- perhaps I shall! - Jack -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= JACK A. SMITH || Union Carbide Corp. || Phone: (304) 747-5797 Catalyst Skill Center || FAX: (304) 747-5571 P.O. Box 8361 || S. Charleston, WV 25303 || Internet: jas@medinah.atc.ucarb.com -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= From Chris_Ruggles@MSI.COM Sun Sep 1 10:07:29 1993 Message-Id: <9309011408.AA25591@schizoid.msi.com> Date: 1 Sep 1993 10:07:29 +0000 From: "Chris Ruggles" Subject: Re: Molecular Manufacturing To: "osc chemistry bbs" Subject: Time:10:05 AM OFFICE MEMO RE> Molecular Manufacturing and Date:9/1/93 Folks, Ralph Merkle writes: >Chemical Design Automation News permanently ceased publication >with the August 1993 issue. Dr. Merkle is mistaken. The following is taken verbatim from a mailing sent to all CDA News subscribers with the August issue. ---- Butterworth - Heinemann ---- 80 Montvale Avenue ---- Stoneham, MA 02180 ---- Tel: 617/438-8464 Telex: 880052 Fax: 617/279-4851 >NOTIFICATION OF NEW PUBLISHER >Effective with Volume 8, Number 9. September/October 1993, CHEMICAL >DESIGN AUTOMATION NEWS will be published by Butterworth-Heinemann, a >member of the Reed-Elsevier group, based in Stoneham, Massachusetts, >USA. >Butterworth-Heinemann is very pleased to welcome CDA NEWS. We believe >it is an excellent complement to our extensive list of journals, particularly >the JOURNAL OF MOLECULAR GRAPHICS, which is published in association >with the Molecular Graphics Society. >Readers and contributors may be assured that Butterworth-Heinemann is >committed to maintaining the quality and integrity of CHEMICAL DESIGN >AUTOMATION NEWS. >Please let me know if I can provide you wirh any additional information. >Rita S. Kessel >Publisher I hope that this helps avert the confusion. Chris Ruggles Manager, Scientific Support Molecular Simulations Incorporated From denise@wucmd.wustl.edu Wed Sep 1 04:56:31 1993 Date: Wed, 1 Sep 93 09:56:31 -0500 From: denise@wucmd.wustl.edu (Denise Beusen) Message-Id: <9309011456.AA08565@wucmd> To: CHEMISTRY@ccl.net Subject: Protein Adsorption to Surfaces I am trying to access any literature dealing with computational studies on the adsorption of proteins to solid surfaces (in particular, polymeric surfaces such as polycarbonate). Can anyone provide me with some leading references that would give me a path into the field? Thanks for your assistance. Denise D. Beusen, Ph.D. Asst. Prof. Center for Molecular Design Washington University in St. Louis 314-935-4667 denise@wucmd.wustl.edu From CLETNER@DESIRE.WRIGHT.EDU Wed Sep 1 07:24:32 1993 Date: Wed, 01 Sep 1993 12:24:32 -0500 (EST) From: CLETNER@DESIRE.WRIGHT.EDU Subject: MMP2 and MM2 ftp site To: chemistry@ccl.net Message-Id: <01H2FMSOCMJ60003CM@DESIRE.WRIGHT.EDU> Hello, Is there an ftp site where I can obtain MMP2 and/or MM2. Thanks Chuck Charles Letner Department of Biochem. and Mol. Bio. Wright State University Dayton, OH 45435 e-mail: cletner@desire.wright.edu From ncv@tci002.uibk.ac.at Wed Sep 1 21:01:06 1993 Date: Wed, 1 Sep 1993 19:01:06 +0200 From: ncv@tci002.uibk.ac.at (Nguyen Cong Vu) Message-Id: <9309011701.AA16938@tci002.uibk.ac.at> To: chemistry@ccl.net Subject: Physical Constants of Organic Compounds Needed Dear Netters, Is there any ftp site from where I get some Physical Constants of Organic Compounds (boiling points, melting points, refractivity indexes, viscosities,... of simple alcohols, aldehydes, ketones,...)? Thanks for any help. Nguyen Cong Vu ncv@tci002.uibk.ac.at From ckoelmel@iris72.biosym.com Wed Sep 1 03:58:56 1993 Date: Wed, 1 Sep 93 10:58:56 -0700 From: ckoelmel@biosym.com (Christoph Koelmel) Message-Id: <9309011758.AA23042@iris72.biosym.com> To: CHEMISTRY@ccl.net Subject: 4-coord angles. again The original question: > Given five of the six central angles in a general four-coordinate >arrangment (2 special cases, of course, being a tetrahedron and a square >plane), what is the forumula for the sixth (and redundant) angle in terms >of the other five? Is there a simple invariant (sum rule?) for this system >that I'm missing? I thought I'd see if anyone already knew the answer >before I went through the trig myself. The answer appears to be that the sum of the cosines = -2. Try it. Ok, here it goes : A,B,C,D : corners of the tetrahedron M = (A+B+C+D)/4 : center of it. a = A-M etc. The six angles are those between a and b, a and c etc. From definition of M : (a+b+c+d)*(a+b+c+d) = 0 (scalar product) => (a-b)^2 + (a-c)^2 + (a-d)^2 + (b-c)^2 + (b-d)^2 + (c-d)^2 = 4*(a^2 + b^2 + c^2 + d^2 ) => (A-B)^2 + (A-C)^2 + (A-D)^2 + (B-C)^2 + (B-D)^2 + (C-D)^2 = 4*(a^2 + b^2 + c^2 + d^2 ) (relation between length of the 6 edges and the distances between the 4 corners and the 'center'). If a,b,c,d are the distances between M and A,B,C,D then => a^2 + ... + 2abcos(a,b) + ... = 0. (relation between the cosines; if A=B=C=D, the sum of the cosines is -2, indeed ...). Is this computational chemistry or what :-) christoph koelmel ckoelmel@biosym.com From rrk@iris3.chem.fsu.edu Wed Sep 1 14:24:37 1993 Date: Wed, 1 Sep 93 18:24:37 -0400 From: rrk@iris3.chem.fsu.edu (Randal R. Ketchem) Message-Id: <9309012224.AA18053@iris3.chem.fsu.edu> To: chemistry@ccl.net Subject: Huckel Molecular Oribitals Somebody recently requested information on a Mac program that will calculate Huckel Molecular Orbitals. I asked Archie. He replied: Host ftp.edvz.univie.ac.at (131.130.1.4) Last updated 12:59 29 Aug 1993 Location: /mac/MacSciTech/chem FILE -rw-r--r-- 1189 bytes 08:00 25 May 1993 HuckelMO.ReadMe FILE -rw-r--r-- 150219 bytes 00:00 3 May 1991 HuckelMO.sea.hqx From shenkin@still3.chem.columbia.edu Wed Sep 1 14:17:42 1993 Date: Wed, 1 Sep 93 18:17:42 -0400 From: shenkin@still3.chem.columbia.edu (Peter Shenkin) Message-Id: <9309012217.AA01154@still3.chem.columbia.edu> To: chemistry@ccl.net Subject: 4-coord angles. again, and again.... > Given five of the six central angles in a general four-coordinate > arrangment (2 special cases, of course, being a tetrahedron and a square > plane), what is the forumula for the sixth (and redundant) angle in terms > of the other five? Is there a simple invariant (sum rule?) for this system > that I'm missing? I thought I'd see if anyone already knew the answer > before I went through the trig myself. I sent this question to my friend Mark Reboul, who likes this sort of thing, and he pointed out that the sixth angle is not necessarily redundant. Before I go on, here's his ID: T. Mark Reboul Sr. User Services Consultant Columbia-Presbyterian Cancer Center Computing Facility mark@cuccfa.ccc.columbia.edu He had some arguments which are more elegant than the counterexample he supplied, but I'll just state the counterexample. For simplicity we'll place the surrounding points (ligands) on the unit sphere. Let's call the points a, b, c, d, and the central point o. Suppose we have: a: (1,0,0) b: (0,1,0) c: (0,0,1) this gives three of the angles: a-o-b = a-o-c = b-o-c = 90 deg Now suppose we have: a-o-d = b-o-d = 70 deg (or any other value greater than 45 and less than or equal to 90 deg) There are then two possible locations for d, one lying at positive z and one at negative z (ie, one in the "northern hemisphere" and one in the "southern hemisphere," taking the vector o-c to point north). These two positions of d have different values of c-o-d, one less than 90 degrees, one greater. In particular, if a-o-d = b-o-d = 90 deg, then c-o-d could be either 0 deg (d falls on the "north pole," on top of c) or 180 deg (d is at the "south pole", xyz coordinates (0,0,-1). Thus the c-o-d angle is not determined by the other five. Given this picture, it is easy to construct examples with less symmetry which share the same property. -P. ************************f*u*cn*rd*ths*u*cn*gt*a*gd*jb************************ Peter S. Shenkin, Box 768 Havemeyer Hall, Dept. of Chemistry, Columbia Univ., New York, NY 10027; shenkin@still3.chem.columbia.edu; (212) 854-5143 ********************** Wagner, Beame, Screvane in '93! ********************** From daniel@gecko.biocad.com Wed Sep 1 08:14:38 1993 Message-Id: <9309012214.AA00588@gecko.biocad.com> To: CHEMISTRY@ccl.net Subject: FDAT??.cam -> 3D MOL file conversion utility needed Date: Wed, 01 Sep 93 15:14:38 -0700 From: daniel Dear Netters, I have several multi-compound crystal structure files in the FDAT file format (fdat??.cam) that I would like to convert to 3D MOL files. If anyone knows of a utility that can accomplish this conversion (preferably running on SGI systems), I would appreciate knowing how to get it. Thanks in advance. Daniel -------- Daniel Parish | BioCAD Corporation | daniel@biocad.com | 415/903-3924 From gjt@nitrogen.lanl.gov Wed Sep 1 12:11:44 1993 Date: Wed, 1 Sep 93 18:11:44 MDT From: gjt@nitrogen.LANL.GOV (Gregory J. Tawa (T-12)) Message-Id: <9309020011.AA01481@nitrogen.lanl.gov> To: CHEMISTRY@ccl.net Subject: acetamide molecule To who it may concern, Does anyone know where I can find the geometry of an acetamide molecule, e.g., bond lengths and angles? Gregory J. Tawa K723 Theoretical Chemistry and Physics Group (T-12) Phone : 505-667-0324 Los Alamos National Laboratory E-mail : gjt@nitrogen.lanl.gov Los Alamos, N.M. 87545 From abuljan@socompa.cecun.ucn.cl Wed Sep 1 21:49:52 1993 Date: Wed, 1 Sep 1993 20:49:52 +0100 From: abuljan@socompa.cecun.ucn.cl (Facultad de Ciencias) Message-Id: <9309011949.AA07198@socompa.cecun.ucn.cl> To: chemistry@ccl.net Subject: EHMACC for IBM RS/6000 Hi Netters! I'm currently looking for a package QCPE-571 (The EHMACC,EHPC and EHPP) running in IBM RS/6000 (with AIX 3.2) If somebody has one available and is willing to share it, please contact us. ANTONIO BULJAN .H. Universidad Catolica del Norte Antofagasta, CHILE e-mail: ABULJAN@SOCOMPA.CECUN.UCN.CL or ABULJAN@UCANORTE.BITNET From kcross@cas.org Wed Sep 1 16:46:23 1993 Date: Wed, 1 Sep 93 20:46:23 -0400 From: kcross@cas.org (Kevin P. Cross Ext. 3192) Message-Id: <9309012046.AA24192@cas.org> Subject: ACS COMP Call for Papers (San Diego) To: chemistry@ccl.net SYMPOSIUM ANNOUNCEMENT AND CALL FOR PAPERS Scientific Visualization and Multimedia American Chemical Society Meeting San Diego, CA March 13-18, 1994 Purpose: To highlight recent applications of scientific visualization or multi-media methods towards solving chemical problems of commercial or academic interest. Emphasis will be placed on molecular modeling and computational chemistry. Format: The organizers particularly encourage presentations illustrating the application of visualization and multi-media methods to solve specific chemical structure problems. Presentations which describe general methods for appropriately applying visualization methods are also welcome. Users of commercial products describing visualization of their research are welcome. Sponsor: The Computers in Chemistry Division of the American Chemical Society. The symposium will be part of the COMP division program at the Spring (March 13-18) 1994 meeting of the American Chemical Society in San Diego, CA. This is an invited symposium but their are a limited number of openings for additional speakers available. Please submit a draft of proposed to topics to one of the organizers by September 30th. Organizers: Kevin P. Cross James W. Cooper Weige Xue Chemical Abstracts Service IBM Research Division Autodesk P.O. Box 3012 T. J. Watson Research Center 2320 Marinship Way 2540 Olentangy River Road Yorktown Heights, New York Sausalito, CA Columbus, OH 43210 10598 94565 kcross@cas.org jmcnmr@watson.ibm.com weigex@autodesk.com From RDJ3@ENH.NIST.GOV Wed Sep 1 18:40:22 1993 Date: Wed, 01 Sep 1993 22:40:22 -0400 (EDT) From: RDJ3@ENH.NIST.GOV Subject: 4-coord angles ?a solution? To: chemistry@ccl.net Message-Id: <01H2G8CC6OKO0007SD@ENH.NIST.GOV> Here is a solution for the general four vector problem. Note that there are two solutions for the sixth angle given the other five. Hope this helps. Four vectors labeled 1, 2, 3, and 4, and the angles between them: a between 1 and 2 b between 1 and 3 c between 1 and 4 d between 2 and 3 e between 2 and 4 f between 3 and 4 want angle f as a function of the other five angles work with cosines of angles, ca through cf define p = sqrt( (ca*ca + ce*ce + cc*cc - 2*cc*ce*ca - 1)* (ca*ca + cb*cb + cd*cd - 2*cd*cb*ca - 1) ) q = ca*(ce*cb + cc*cd) - cc*cb - ce*cd then the two solutions for cos(f) are cf = ( p+q)/(ca*ca-1) cf = (-p+q)/(ca*ca-1) - Russ Johnson rdj3@enh.nist.gov