From: Marcio Cyrillo - pos Message-Id: [199711281513.NAA05059@huckel.ifi.unicamp.br] Sent: Friday, November 28, 1997 10:13 AM To: hyperchem@hyper.com Subject: question about HyperChem versions Dear hyperchemists, Could someone please give me some information about HyperChem program versions that are and were available since its creation? I suspect the first version of HyperChem comercially available was 2.0. But my question is: which version is the first one that can read molecules whose names are in Windows 95 format (more than 8 characters). This information is important for me because I am writing a Windows 95 program, named HyperSpin, that automatically generates and executes scripts (.scr format) to rotate one or more dihedrals (one will not need Exel macros anymore). Since I want my software to be compatible with all HyperChem versions around I need this kind of information. Any other info about any other crucial differences are welcome as well. This software is going to be free and I want to make it available in my homepage or in HyperChem web page (if possible). I would like to thank you in advance for your help, Sincereley yours, M.C. From: Laurence Lavelle [lavelle@mbi.ucla.edu] Sent: Friday, November 28, 1997 12:29 AM To: hyperchem@hyper.com; chemistry@infomeister.osc.edu Subject: Ab initio computational time. Hi all, Happy Thanksgiving to those in USA. I would very much appreciate any estimates (hrs) on the ab initio computational time of the following system: single point calculation, 731 basis functions, UHF, MP2, direct SCF Hardware: Dual pentium 200MHz, 256K external cache, 192MB RAM OS: Windows NT Workstation 4.0 SP3. Computational package: HyperChem 5.02 Although NT uses SMP, HyperChem is not a multithread application so the "computational system" is a single pentium 200MHz. I look forward to hearing from you. Laurence Lavelle """""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" """""""""""""""""""" Laurence Lavelle, Ph.D. University of California Los Angeles Molecular Biology Institute, and Department of Chemistry & Biochemistry Laboratory of Structural Biology & Molecular Medicine Los Angeles, CA 90095-1570, USA Email:LAVELLE@MBI.UCLA.EDU Phone (Lab): (310) 206-8270 Phone (Office): (310) 825-2083 Fax: (310) 267-1957 http://www.doe-mbi.ucla.edu/people/lavelle/lavelle.html """""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" """""""""""""""""""" It will be a great day when schools have all the money they need, and the military has bake day sales. In nature's infinite book of secrecy A little I can read. From: Stavrev, Krassimir Sent: Monday, December 01, 1997 9:36 AM To: 'Marcio Cyrillo - pos Message-Id:' Subject: RE: question about HyperChem versions Marcio: The first version of HyperChem was Release 1 running on Transputers, see http://www.hyper.com/corporate/company_prof.html. HyperChem 5 supports long file names, longer than 8 characters. Regards, Krassimir --- Krassimir Stavrev, PhD, Director of Scientific Support Hypercube, Inc. Florida Science and Technology Park 1115 N.W. 4th Street Gainesville, Florida 32601 Voice:(352) 371-7744/(800) 960-1871 Fax:(352) 371-3662 -----Original Message----- From: Marcio Cyrillo - pos Message-Id: [SMTP:199711281513.NAA05059@huckel.ifi.unicamp.br] Sent: Friday, November 28, 1997 10:13 AM To: hyperchem@hyper.com Subject: question about HyperChem versions Dear hyperchemists, Could someone please give me some information about HyperChem program versions that are and were available since its creation? I suspect the first version of HyperChem comercially available was 2.0. But my question is: which version is the first one that can read molecules whose names are in Windows 95 format (more than 8 characters). This information is important for me because I am writing a Windows 95 program, named HyperSpin, that automatically generates and executes scripts (.scr format) to rotate one or more dihedrals (one will not need Exel macros anymore). Since I want my software to be compatible with all HyperChem versions around I need this kind of information. Any other info about any other crucial differences are welcome as well. This software is going to be free and I want to make it available in my homepage or in HyperChem web page (if possible). I would like to thank you in advance for your help, Sincereley yours, M.C. From: Stavrev, Krassimir [stavrev@hyper.com] Sent: Monday, December 01, 1997 11:20 AM To: 'hyperchem@hyper.com' Subject: A new FAQ Dear all, Several people have recently asked for support on how to setup a user account of HyperChem under Windows NT. Given the increasing interest in this subject, we decided to post a Web page on the NT user installation of HyperChem. It can be found in the Frequently Asked Questions section at www.hyper.com/support as FAQ # 33, http://www.hyper.com/support/faq/faq33.html . Regards, Krassimir --- Krassimir Stavrev, PhD, Director of Scientific Support Hypercube, Inc. Florida Science and Technology Park 1115 N.W. 4th Street Gainesville, Florida 32601 Voice:(352) 371-7744/(800) 960-1871 Fax:(352) 371-3662 From: Stavrev, Krassimir Sent: Monday, December 01, 1997 11:56 AM To: 'lsk@alchemy.yonsei.ac.kr' Subject: Re: File transfer error >I have a problem with file transter. >This is example. > >Transfered phenol file using hyperchem v5.0 (MOPAC z-matrix) > > >C 00000.0000 0 00000.0000 0 00000.0000 0 0 0 0 >C 00001.4052 1 00000.0000 0 00000.0000 0 1 0 0 >C 00001.4019 1 00120.9532 1 00000.0000 0 2 1 0 >C 00001.3936 1 00119.1105 1 00000.0000 1 3 2 1 >C 00001.3939 1 00120.3982 1 00000.0000 1 4 3 2 >C 00001.3911 1 00118.8884 1 00000.0000 1 1 2 3 >O 00001.3767 1 00116.4175 1 00179.9999 1 2 1 5 >H 00001.0985 1 00119.6011 1 00179.9999 1 1 2 3 >H 00001.0985 1 00120.3413 1 00000.0000 1 3 2 7 >H 00001.1001 1 00119.5731 1 00180.0000 1 4 3 2 >H 00001.0991 1 00120.0158 1 00179.9999 1 5 4 3 >H 00001.1003 1 00119.5250 1 00000.0000 1 6 1 8 >H 00000.9680 1 00107.9047 1 00000.0000 1 7 2 3 >0 > >Some molecular modeling program cannot read MOPAC z-matrix file because >of needless zero. > > ----------------------------------------------------------- > Sung Kwang Lee > > E-mail lsk@alchemy.yonsei.ac.kr > Address Dept. of Chemistry, Yonsei Univ. > Seoul, 120-749, S. Korea > Tel 82-2-361-2635 > Fax 82-2-364-7050 > WWW http://alchemy.yonsei.ac.kr/~lsk/ > --------------------------------------------------------- Sung: I agree, this zero seems useless for the MOPAC file purposes. We'll take a note on this - thanks! For the time being, you need to remove it manually. Regards, Krassimir --- Krassimir Stavrev, PhD, Director of Scientific Support Hypercube, Inc. Florida Science and Technology Park 1115 N.W. 4th Street Gainesville, Florida 32601 Voice:(352) 371-7744/(800) 960-1871 Fax:(352) 371-3662 From: Paddy Kane [94970459@tolka.dcu.ie] Sent: Tuesday, December 02, 1997 8:34 AM To: HChem Supp; HChem.User@ftp.hyper.com Subject: HyperChem: Incorrect geometries in amines , CCL Every , Darren Fayne <95970665@tolka.dcu.ie> Subject: HyperChem: Incorrect geometries in amines Date: Mon, 1 Dec 1997 22:03:35 +0000 (GMT) Sender: listadmin@hyper.com Precedence: bulk Reply-To: Paddy Kane <94970459@tolka.dcu.ie> Hi, I am a user of HyperChem, version 4. Whenever I use molecular mechanics with the MM+ force field, to geometry optimise molecules such as Phenylamine (C6H5NH2), the geometry about the N atom is planar rather than pyramidal, i.e., an atom type of N2 is used for the nitrogen atom, rather than N3 as would be expected. I get the same result with molecules such as H2C=CHNH2 or H2C=NNH2. I also get incorrect geometries if I initially use the model builder to obtain an approximate geometry for such molecule or if I use any of the other three force fields available within HyperChem. If I initially set the atom type for the nitrogen atom to be N3, I still get an planar geometry about the nitrogen atom. However, for molecules such as methylamine and cyclohexamine, i.e., where the atom bonded to the nitrogen atom is saturated, the correct geometry and atom type are obtained for the nitrogen atom. Has anyone else experienced this problem? I would be very grateful if someone could advise me of how to solve the problem. Kind rgds, Paddy. ************************************************************************ * * * * Paddy Kane email: 94970459@tolka.dcu.ie * * School of Chemical Sciences * * Dublin City University Tel: 00-353-1-7045641 * * Dublin 9 * * Ireland. Fax: 00-353-1-7045503 * * * ************************************************************************ * From: Stavrev, Krassimir [stavrev@hyper.com] Sent: Tuesday, December 02, 1997 12:21 PM To: 'Paddy Kane' Cc: 'hyperchem@hyper.com' Subject: RE: HyperChem: Incorrect geometries in amines Patrick: The structures you mentioned can be easily obtained in HyperChem by adding the missing lone pair to the nitrogen atom. In the case of cyclohexylamine, such an addition has little effect on the C-NH2 group, while in the case of aniline, the two H atoms abandon the CNH2 plane and assume pyramidal positions, with respect to the nitrogen atom, as known from experiment. Easy fix? I'm afraid not! The problem, as I understand it, has to do with the formal hybridization that is assumed for the N atom of the amino group - sp2 or sp3. If sp2, the lone pair will occupy a p-orbital which will be perpendicular to the NH2 plane. If there is a nearby pi-system to interact with (as for aniline, H2C=CHNH2, etc), the resonance between the lone pair and the pi-system will be highest when the CNH2 atoms are planar. However, such a CNH2 planar arrangement would involve bond angle distortions that would require more energy than the one that is gained through the resonance stabilization. Therefore the CNH2 group remains non-planar and the N atom is considered in a formal sp3 hybridization. The energy differences, however, between the planar and pyramidal amines are small, approximately 1/10 of the energy of a normal chemical bond (N. Allinger et al., Organic Chemistry, Worth ). How good is molecular mechanics (or even quantum mechanics!) in solving such small-energy-difference problems? MM experts can probably add more aspects to this subject. Regards, Krassimir --- Krassimir Stavrev, PhD, Director of Scientific Support Hypercube, Inc. Florida Science and Technology Park 1115 N.W. 4th Street Gainesville, Florida 32601 Voice:(352) 371-7744/(800) 960-1871 Fax:(352) 371-3662 -----Original Message----- From: Paddy Kane [SMTP:94970459@tolka.dcu.ie] Sent: Monday, December 01, 1997 5:04 PM To: HChem Supp; HChem User; CCL Every; Darren Fayne Subject: HyperChem: Incorrect geometries in amines Hi, I am a user of HyperChem, version 4. Whenever I use molecular mechanics with the MM+ force field, to geometry optimise molecules such as Phenylamine (C6H5NH2), the geometry about the N atom is planar rather than pyramidal, i.e., an atom type of N2 is used for the nitrogen atom, rather than N3 as would be expected. I get the same result with molecules such as H2C=CHNH2 or H2C=NNH2. I also get incorrect geometries if I initially use the model builder to obtain an approximate geometry for such molecule or if I use any of the other three force fields available within HyperChem. If I initially set the atom type for the nitrogen atom to be N3, I still get an planar geometry about the nitrogen atom. However, for molecules such as methylamine and cyclohexamine, i.e., where the atom bonded to the nitrogen atom is saturated, the correct geometry and atom type are obtained for the nitrogen atom. Has anyone else experienced this problem? I would be very grateful if someone could advise me of how to solve the problem. Kind rgds, Paddy. ************************************************************************ * * * * Paddy Kane email: 94970459@tolka.dcu.ie * * School of Chemical Sciences * * Dublin City University Tel: 00-353-1-7045641 * * Dublin 9 * * Ireland. Fax: 00-353-1-7045503 * * * ************************************************************************ * From: Andy Jennings [jenninaj@mh.uk.sbphrd.com] Sent: Tuesday, December 02, 1997 3:41 AM To: Paddy Kane Cc: CCL Every Subject: CCL:Re: CCL:HyperChem: Incorrect geometries in amines On Mon, 1 Dec 1997, Paddy Kane wrote: > > Hi, Hi Paddy > > I am a user of HyperChem, version 4. Whenever I use molecular mechanics > with the MM+ force field, to geometry optimise molecules such as > Phenylamine (C6H5NH2), the geometry about the N atom is planar rather than > pyramidal, i.e., an atom type of N2 is used for the nitrogen atom, rather > than N3 as would be expected. I get the same result with molecules such as > H2C=CHNH2 or H2C=NNH2. I also get incorrect geometries if I initially use > the model builder to obtain an approximate geometry for such molecule or > if I use any of the other three force fields available within HyperChem. > If I initially set the atom type for the nitrogen atom to be N3, I still > get an planar geometry about the nitrogen atom. > > However, for molecules such as methylamine and cyclohexamine, i.e., where > the atom bonded to the nitrogen atom is saturated, the correct geometry > and atom type are obtained for the nitrogen atom. > > Has anyone else experienced this problem? Unless I'm missing the point here what you see is not a problem - simply the correct answer. The nitrogen in these systems WILL be planar due to the pi systems delocalising over all conjugated atoms. This forces the nitrogen into planarity...something which won't happen with a saturated system as there is no opportunity for pi orbital delocalisation. Might I suggest reading something like 'A guidebook to mechanism in organic chemistry' by Peter Sykes which has an excellent chapter on atomic orbitals and hybridisation. Cheers, Andy > > I would be very grateful if someone could advise me of how to solve the > problem. > > Kind rgds, > Paddy. > ================================================================= Andy Jennings - SmithKline Beecham Pharmaceuticals Phone: +44 (0) 1279 627682 Fax: +44 (0) 1279 627685 ----------------------------------------------------------------- "Statistics are like a bikini. What they reveal is suggestive,but what they conceal is vital." - Aaron Levenstein ----------------------------------------------------------------- --- Administrivia: This message is automatically appended by the mail exploder: CHEMISTRY@ccl.osc.edu: Everybody | CHEMISTRY-REQUEST@ccl.osc.edu: Coordinator MAILSERV@ccl.osc.edu: HELP CHEMISTRY or HELP SEARCH | Gopher: ccl.osc.edu 73 Anon. ftp: ccl.osc.edu | CHEMISTRY-SEARCH@ccl.osc.edu -- archive search Web: http://ccl.osc.edu/chemistry.html --- From: Jochen Kuepper [jochen@pc1.uni-duesseldorf.de] Sent: Thursday, December 04, 1997 5:07 AM To: 94970459@tolka.dcu.ie; jenninaj@mh.uk.sbphrd.com Cc: chemistry@infomeister.osc.edu Subject: CCL:HyperChem: Incorrect geometries in amines :> > I am a user of HyperChem, version 4. Whenever I use molecular = mechanics :> > with the MM+ force field, to geometry optimise molecules such as :> > Phenylamine (C6H5NH2), the geometry about the N atom is planar = rather than :> > pyramidal, i.e., an atom type of N2 is used for the nitrogen atom, = rather :> > than N3 as would be expected. I get the same result with molecules = such as :> > H2C=3DCHNH2 or H2C=3DNNH2. I also get incorrect geometries if I = initially use :> > the model builder to obtain an approximate geometry for such = molecule or :> > if I use any of the other three force fields available within = HyperChem. :> > If I initially set the atom type for the nitrogen atom to be N3, I = still :> > get an planar geometry about the nitrogen atom.=20 :> >=20 :> > However, for molecules such as methylamine and cyclohexamine, = i.e., where :> > the atom bonded to the nitrogen atom is saturated, the correct = geometry :> > and atom type are obtained for the nitrogen atom.=20 :> >=20 :> > Has anyone else experienced this problem? :>=20 :> Unless I'm missing the point here what you see is not a problem - = simply :> the correct answer. The nitrogen in these systems WILL be planar due = to :> the pi systems delocalising over all conjugated atoms. This forces = the :> nitrogen into planarity...something which won't happen with a = saturated :> system as there is no opportunity for pi orbital delocalisation. = Might I :> suggest reading something like 'A guidebook to mechanism in organic :> chemistry' by Peter Sykes which has an excellent chapter on atomic :> orbitals and hybridisation. Actually Aniline (phenylamine) in _not_ planar ! There is a complete substitution structure determined/published by = Larson ! But Andy's argumentation is ok at this level of theory (Hyperchem ?-), MM, ... ? So, that's why these calculation give 'wrong' results (in any way). Jochen PS: To be sure to have calculated something wrong, you need to measure = it !!! ----------------------------------------------------------------------- Jochen K=FCpper Heinrich-Heine-Universit=E4t D=FCsseldorf = jochen@uni-duesseldorf.de Institut f=FCr Physikalische Chemie I Universit=E4tsstrasse 1, Geb 26.43.02.19 phone ++49-211-8113681 40225 D=FCsseldorf fax ++49-211-8115195 Germany http://www-public.rz.uni-duesseldorf.de/~jochen ----------------------------------------------------------------------- -------This is added Automatically by the Software-------- -- Original Sender Envelope Address: jochen@pc1.uni-duesseldorf.de -- Original Sender From: Address: jochen@pc1.uni-duesseldorf.de CHEMISTRY@ccl.osc.edu: Everybody | CHEMISTRY-REQUEST@ccl.osc.edu: Coordinator MAILSERV@ccl.osc.edu: HELP CHEMISTRY or HELP SEARCH | Gopher: ccl.osc.edu 73 Anon. ftp: ccl.osc.edu | CHEMISTRY-SEARCH@ccl.osc.edu -- archive search Web: http://ccl.osc.edu/chemistry.html From: Laurence Lavelle [lavelle@mbi.ucla.edu] Sent: Wednesday, December 03, 1997 9:06 PM To: chemistry@infomeister.osc.edu; hyperchem@hyper.com Subject: Ab initio computational time. Hi,=20 Not much of a summary as I received one response to my initial posting, which is listed below. Thanks to Dr. L=E1szl=F3 JICSINSZKY for his comments.=20 Laurence Lavelle=20 >>>> =20 Date: Thu, 27 Nov 1997 21:28:42 -0800=20 To: hyperchem@hyper.com, chemistry@infomeister.osc.edu=3D20 From: Laurence Lavelle =20 Subject: Ab initio computational time. =20 Hi all,=20 Happy Thanksgiving to those in USA.=20 I would very much appreciate any estimates (hrs) on the ab initio computational time of the following system:=20 single point calculation, 731 basis functions, UHF, MP2, direct SCF=20 Hardware: Dual pentium 200MHz, 256K external cache, 192MB RAM=20 OS: Windows NT Workstation 4.0 SP3.=20 Computational package: HyperChem 5.02=20 Although NT uses SMP, HyperChem is not a multithread application so the "computational system" is a single pentium 200MHz.=20 I look forward to hearing from you.=20 Laurence Lavelle=20 <<<<=20 >Date: Mon, 1 Dec 1997 10:26:46 -0500=20 >From: "CYCLOLAB R&D Lab." =20 >Subject: Ab initio computational time.=20 >Sender: "CYCLOLAB R&D Lab." =20 >To: Laurence Lavelle =20 >Content-Disposition: inline=20 >=20 >Hi Laurence,=20 >=20 >>single point calculation, 731 basis functions, UHF, MP2, direct SCF =20 >=20 > Once I've tried to perform an ab initio single point calculation on=20 >alfa-cyclodextrin (C36H60O30. 390 basis function with STO-3G, direct scf,=20 >grad, P100, HC 4.5). It takes about two weeks, but though the calculation=20 >did not finish, because some hw errors (the cooler of CPU went wrong), I=20 >was very close to the final step.=20 >=20 > The computation time increases in second order, that means, e.g. in my=20 >computer the calculation on your molecule on bases like above would take ~4=20 >times more than in case of alpha-cyclodextrin (8 weeks). The UHF+MP2 about=20 >duplicates the calculation time, i.e. -> ~16 weeks. You are using a P200=20 >machine, which approximately halves the calculation time comparing=20 with my=20 >machine (->~8 weeks), under Win'95. The HC runs ~70 % speed of HC4.5, that=20 >means, your time increases with about three weeks (->11 weeks). Some=20 >slowing factors are within NT4 (about 60 % slower than Win'95 with a native=20 >[32bit] application), i. e. my opinion is that your calculation takes at=20 >least 10 weeks but not more than 20 weeks.=20 >=20 > Not so inspiring.=20 >=20 > I would propose a solution: cut smaller parts your molecule. In that case=20 >you may calculate an approximative result, but much more faster (e.g. you=20 >may save dielectric integrals, if you have a large HD. As far as I know,=20 >the NT can handle larger than 2 GB HD partitions). Otherwise, I do not know=20 >any ab initio calculations such a big molecule. It is enough large for a=20 >Cray machine, as well.=20 >=20 >=20 > Regards, Laszlo=20 >=20 >-----------------------------------------------------------=20 >Dr. L=E1szl=F3 JICSINSZKY=20 >Head of Synth. Dept.=20 >CYCLOLAB R&D Lab. Ltd.=20 >H-1525 Budapest, P.O. Box: 435=20 >XI. Domb=F3v=E1ri =FAt 5-7=20 >email: cyclolab@compuserve.com=3D20 >Tel./Fax: (36-1)-206-51-36 or (36-1)-206-51-37=20 >-----------------------------------------------------------=20 >=20 >=20 """"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""= """"""""""""""""""""=20 Laurence Lavelle, Ph.D.=20 University of California Los Angeles=20 Molecular Biology Institute, and Department of Chemistry & Biochemistry Laboratory of Structural Biology & Molecular Medicine=20 Los Angeles, CA 90095-1570, USA =20 Email:LAVELLE@MBI.UCLA.EDU=20 Phone (Lab): (310) 206-8270=20 Phone (Office): (310) 825-2083=20 Fax: (310) 267-1957=20 http://www.doe-mbi.ucla.edu/people/lavelle/lavelle.html=3D20 """"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""= """"""""""""""""""""=20 It will be a great day when schools have all the money they need,=20 and the military has bake day sales.=20 In nature's infinite book of secrecy=20 A little I can read.=20 From: Pieter Stouten [pieter.stouten@dupontmerck.com] Sent: Thursday, December 04, 1997 9:02 AM To: chemistry@infomeister.osc.edu Subject: CCL:HyperChem: Incorrect geometries in amines On 97/12/04 at 11:07 +0100, Jochen Kuepper wrote: >Actually Aniline (phenylamine) in _not_ planar ! >There is a complete substitution structure determined/published by >Larson ! > >But Andy's argumentation is ok at this level of theory (Hyperchem ?-), >MM, ... ? > There actually is at least one forcefield (MSI's CFF96) that is used in Molecular Mechancis that does have properly puckered nitrogens. Are there any other forcefields people know of, that do describe aniline etc. properly? Thanks, Pieter Stouten DuPont Merck - Computer Aided Drug Design Group Web: http://www.halcyon.com/stouten/ -------This is added Automatically by the Software-------- -- Original Sender Envelope Address: pieter.stouten@dupontmerck.com -- Original Sender From: Address: pieter.stouten@dupontmerck.com CHEMISTRY@ccl.osc.edu: Everybody | CHEMISTRY-REQUEST@ccl.osc.edu: Coordinator MAILSERV@ccl.osc.edu: HELP CHEMISTRY or HELP SEARCH | Gopher: ccl.osc.edu 73 Anon. ftp: ccl.osc.edu | CHEMISTRY-SEARCH@ccl.osc.edu -- archive search Web: http://ccl.osc.edu/chemistry.html From: Fabrice Leclerc [leclerc@tammy.harvard.edu] Sent: Thursday, December 04, 1997 10:54 AM To: chemistry@infomeister.osc.edu Subject: CCL:HyperChem: Incorrect geometries in amines The Merck force field (MMFF94) does have properly puckered nitrogens as well. It gives a geometry very close to what you get with CFF96 (0.03A). -------This is added Automatically by the Software-------- -- Original Sender Envelope Address: leclerc@tammy.harvard.edu -- Original Sender From: Address: leclerc@tammy.harvard.edu CHEMISTRY@ccl.osc.edu: Everybody | CHEMISTRY-REQUEST@ccl.osc.edu: Coordinator MAILSERV@ccl.osc.edu: HELP CHEMISTRY or HELP SEARCH | Gopher: ccl.osc.edu 73 Anon. ftp: ccl.osc.edu | CHEMISTRY-SEARCH@ccl.osc.edu -- archive search Web: http://ccl.osc.edu/chemistry.html From: Peter Shenkin [shenkin@still3.chem.columbia.edu] Sent: Thursday, December 04, 1997 11:09 AM To: Pieter Stouten; chemistry@infomeister.osc.edu Subject: CCL:HyperChem: Incorrect geometries in amines On Dec 4, 9:01am, Pieter Stouten wrote: > Subject: CCL:HyperChem: Incorrect geometries in amines > On 97/12/04 at 11:07 +0100, Jochen Kuepper wrote: > > >Actually Aniline (phenylamine) in _not_ planar ! .. > There actually is at least one forcefield (MSI's CFF96) that is used in > Molecular Mechancis that does have properly puckered nitrogens. Are there > any other forcefields people know of, that do describe aniline etc. > properly? Hi, Pieter and CCL, MMFF makes sp2 N's non-planar by default as well; however, there is an option to make them planar. This option might be useful for comparing computational results to crystal structures for large molecules, where one would expect either thermal averaging or the refinement procedure to make these atoms "appear" planar. The so-called "MMFFs" (s for "static") option was added by Halgren because of demand by Merck's crystallographic group, if I recall properly. -P. -- *********** In memoriam, Stephane Grappelli, 1908 - 1997, RIP ************* * Peter S. Shenkin; Chemistry, Columbia U.; 3000 Broadway, Mail Code 3153 * ** NY, NY 10027; shenkin@columbia.edu; (212)854-5143; FAX: 678-9039 *** *MacroModel WWW page: http://www.columbia.edu/cu/chemistry/mmod/mmod.html * -------This is added Automatically by the Software-------- -- Original Sender Envelope Address: shenkin@still3.chem.columbia.edu -- Original Sender From: Address: shenkin@still3.chem.columbia.edu CHEMISTRY@ccl.osc.edu: Everybody | CHEMISTRY-REQUEST@ccl.osc.edu: Coordinator MAILSERV@ccl.osc.edu: HELP CHEMISTRY or HELP SEARCH | Gopher: ccl.osc.edu 73 Anon. ftp: ccl.osc.edu | CHEMISTRY-SEARCH@ccl.osc.edu -- archive search Web: http://ccl.osc.edu/chemistry.html From: Pieter Stouten [pieter.stouten@dupontmerck.com] Sent: Thursday, December 04, 1997 11:51 AM To: Peter Shenkin Cc: chemistry@infomeister.osc.edu Subject: CCL:HyperChem: Incorrect geometries in amines Hello Peter and CCL, >MMFF makes sp2 N's non-planar by default as well; however, there >is an option to make them planar. This option might be useful for >comparing computational results to crystal structures for large >molecules, where one would expect either thermal averaging or >the refinement procedure to make these atoms "appear" planar. > If by "large" you mean proteins, then there is no problem as protons are not observed (unless the structure is based on neutron diffraction data). What would the comparison tell you if you knowingly use a "wrong" force field to make the results look like crystal structures? >The so-called "MMFFs" (s for "static") option was added by Halgren >because of demand by Merck's crystallographic group, if I recall >properly. > And again we may come full circle :-). E.g. peptide bonds can to a large extent be restrained to planarity when solving crystal structures, then forcefields are fitted ("compared") to these data, the forcefields are used again in xray refinement and the world is good because all peptide links are planar. It is concerning that there is even the option to make forcefields fit the skewed crystallographic perspective (don't flame me! I was a happy crystallographer in a previous life). Cheers, Pieter *** Note my new e-mail address: pieter.stouten@dupontmerck.com *** Pieter Stouten || Nothing shocks me; Computer Aided Drug Design Group || The DuPont Merck Pharmaceutical Company || I am a scientist! P.O. Box 80500, Wilmington, DE 19880-0500 || Phone: +1 (302) 695 3515 || -- Fax: +1 (302) 695 9090 || Internet: pieter.stouten@dupontmerck.com || Indiana Jones Web: http://www.halcyon.com/stouten/ || -------This is added Automatically by the Software-------- * Original Sender Envelope Address: pieter.stouten@dupontmerck.com * Original Sender From: Address: pieter.stouten@dupontmerck.com CHEMISTRY@ccl.osc.edu: Everybody | CHEMISTRY-REQUEST@ccl.osc.edu: Coordinator MAILSERV@ccl.osc.edu: HELP CHEMISTRY or HELP SEARCH | Gopher: ccl.osc.edu 73 Anon. ftp: ccl.osc.edu | CHEMISTRY-SEARCH@ccl.osc.edu-archive search Web: http://ccl.osc.edu/chemistry.html From ccl@infomeister.osc.edu Thu Dec 4 13:43:02 1997 Received: from bedrock.osc.edu for ccl@infomeister.osc.edu by infomeister.osc.edu (8.8.3/950822.1) id MAA03898; Thu, 4 Dec 1997 12:43:57 -0500 (EST) Received: from theory.tc.cornell.edu for richard@tc.cornell.edu by bedrock.osc.edu (8.8.6/950822.1) id MAA00261; Thu, 4 Dec 1997 12:43:55 -0500 (EST) Received: from ren.tc.cornell.edu (REN.TC.CORNELL.EDU [128.84.244.22]) by theory.tc.cornell.edu (8.8.4/8.8.3/CTC-1.0) with SMTP id MAA38210; Thu, 4 Dec 1997 12:42:40 -0500 Sender: richard@TC.Cornell.EDU Message-ID: <3486EB8F.1372@tc.cornell.edu> Date: Thu, 04 Dec 1997 12:42:39 -0500 From: Richard Gillilan X-Mailer: Mozilla 2.02 (X11; I; IRIX 5.3 IP22) MIME-Version: 1.0 To: Pieter Stouten CC: chemistry@osc.edu Subject: Re: CCL:HyperChem: Incorrect geometries in amines References: Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit > There actually is at least one forcefield (MSI's CFF96) that is used in > Molecular Mechancis that does have properly puckered nitrogens. Are there > any other forcefields people know of, that do describe aniline etc. > properly? > > Thanks, > > Pieter Stouten My unofficial implementation of MMFF94 does seem to minimize to an out-of-plane result. Looking at Halgren's papers, I do see that "aniline, N puckered" is listed in the core parameterization (Table I, paper I). Richard Gillilan Cornell Theory Center richard@tc.cornell.edu . From: Richard Gillilan [richard@TC.Cornell.EDU] Sent: Thursday, December 04, 1997 1:32 PM To: Peter Shenkin Cc: Pieter Stouten; chemistry@infomeister.osc.edu Subject: CCL:HyperChem: Incorrect geometries in amines Peter Shenkin wrote: > > The so-called "MMFFs" (s for "static") option was added by Halgren > because of demand by Merck's crystallographic group, if I recall > properly. > > -P. > Does anyone know if the MMFFs parameter set is published anywhere? Also, the original MMFF94 was not paramterized to reproduce liquid properties as well as say OPLS. Does anyone know if this problem has been addressed yet? Richard Gillilan richard@tc.cornell.edu -------This is added Automatically by the Software-------- -- Original Sender Envelope Address: richard@tc.cornell.edu -- Original Sender From: Address: richard@TC.Cornell.EDU CHEMISTRY@ccl.osc.edu: Everybody | CHEMISTRY-REQUEST@ccl.osc.edu: Coordinator MAILSERV@ccl.osc.edu: HELP CHEMISTRY or HELP SEARCH | Gopher: ccl.osc.edu 73 Anon. ftp: ccl.osc.edu | CHEMISTRY-SEARCH@ccl.osc.edu -- archive search Web: http://ccl.osc.edu/chemistry.html From: Peter Shenkin [shenkin@still3.chem.columbia.edu] Sent: Thursday, December 04, 1997 1:17 PM To: Pieter Stouten Cc: chemistry@infomeister.osc.edu Subject: CCL:HyperChem: Incorrect geometries in amines Hello again, Pieter and CCL, Yes, you make several good points. On Dec 4, 11:51am, Pieter Stouten wrote: > Subject: Re: CCL:HyperChem: Incorrect geometries in amines ... > >MMFF makes sp2 N's non-planar by default as well; however, there > >is an option to make them planar. This option might be useful for > >comparing computational results to crystal structures for large > >molecules, where one would expect either thermal averaging or > >the refinement procedure to make these atoms "appear" planar. > > > If by "large" you mean proteins, then there is no problem as protons are > not observed (unless the structure is based on neutron diffraction data). Yup. It would be interesting to know whether the nonplanarity of amide N's in proteins can be detected in neutron-diffraction studies. I suspect that there is still sufficient reliance on force-field assumptions during refinement that your accusation of circular reasoning remains valid. However, there is also the point that protein crystals are very floppy, and one might expect these non-planarities, which are small, to be time-averaged out. This discussion is similar to the question whether proteins can be adequately modeled in torsional space, given reasonable rigid values of the bond lengths and angles. That question has been extensively examined, and perhaps this amide-puckering question deserves the same kind of examination. I have personally done some conformational searches on peptides using both versions of MMFF, and in some situations it did seem to make a difference. What you'd really want to know is whether two rather different overall conformations can have their relative energetic stability seriously altered by requiring the sp2 N's to be planar. -P. -- *********** In memoriam, Stephane Grappelli, 1908 - 1997, RIP ************* * Peter S. Shenkin; Chemistry, Columbia U.; 3000 Broadway, Mail Code 3153 * ** NY, NY 10027; shenkin@columbia.edu; (212)854-5143; FAX: 678-9039 *** *MacroModel WWW page: http://www.columbia.edu/cu/chemistry/mmod/mmod.html * -------This is added Automatically by the Software-------- -- Original Sender Envelope Address: shenkin@still3.chem.columbia.edu -- Original Sender From: Address: shenkin@still3.chem.columbia.edu CHEMISTRY@ccl.osc.edu: Everybody | CHEMISTRY-REQUEST@ccl.osc.edu: Coordinator MAILSERV@ccl.osc.edu: HELP CHEMISTRY or HELP SEARCH | Gopher: ccl.osc.edu 73 Anon. ftp: ccl.osc.edu | CHEMISTRY-SEARCH@ccl.osc.edu -- archive search Web: http://ccl.osc.edu/chemistry.html From: fredvc@esalp1.dnet.dupont.com Sent: Wednesday, December 03, 1997 9:52 PM To: smtp%"jenninaj@mh.uk.sbphrd.com"@cdmhvx.dnet.dupont.com Cc: @osc.edu; fredvc@esalp1.dnet.dupont.com Subject: CCL:RE: CCL:Re: CCL:HyperChem: Incorrect geometries in amines I think the MM+ forcefield is OVERcompensating for the interaction betwen the nitrogen atom & the pi-system. If memory serves, the geometry around the N in aniline is "more planar" than in methyl amine, but not "truly planar". I would recommend checking the literature for structural studies on aniline, or running ab initio calculations [6-31G(p,d) or DZP at least] optimizing aniline & cyclohexylamine to check this. ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ FREDERIC A. VAN-CATLEDGE Scientific Computing Division || Office: (302) 695-1187 or 529-2076 Central Research & Development Dept. || The DuPont Company || FAX: (302) 695-9658 P. O. Box 80320 || Wilmington DE 19880-0320 || Internet: fredvc@esvax.dnet.dupont.com -------------------------------------------------------------------------------- Opinions expressed in this electronic message should ***> NOT <*** be taken to represent the official position(s) of the DuPont Company. *****> ANY OPINIONS EXPRESSED ARE THE PERSONAL VIEWS OF THE AUTHOR ONLY. <***** ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ --- Administrivia: This message is automatically appended by the mail exploder: CHEMISTRY@ccl.osc.edu: Everybody | CHEMISTRY-REQUEST@ccl.osc.edu: Coordinator MAILSERV@ccl.osc.edu: HELP CHEMISTRY or HELP SEARCH | Gopher: ccl.osc.edu 73 Anon. ftp: ccl.osc.edu | CHEMISTRY-SEARCH@ccl.osc.edu -- archive search Web: http://ccl.osc.edu/chemistry.html --- From: Laurence Lavelle [lavelle@mbi.ucla.edu] Sent: Thursday, December 04, 1997 2:38 PM To: hyperchem@hyper.com; chemistry@infomeister.osc.edu Subject: Gaussian 94 Windows I have a couple of questions regarding G94W: Under NT does it use SMP (i.e., is it a multithread application)? Does it interface with UNIX G94 (i.e., can one use G94W as a front end and UNIX G94 as a backend for heavy duty computations)? Since it is over a week since I asked Gaussian Inc. the same questions with no reply, perhaps someone knows. Thanks Laurence Lavelle Date: Thu, 04 Dec 1997 19:42:15 -0800 To: hyperchem@hyper.com, chemistry@infomeister.osc.edu From: Laurence Lavelle Subject: Gaussian 94 Windows Date: Thu, 04 Dec 1997 19:42:15 -0800 Gaussian Inc. just responded to my questions. Laurence Lavelle From: ryanmd@mms.sbphrd.com Sent: Friday, December 05, 1997 8:53 AM To: chemistry@infomeister.osc.edu Subject: CCL:Magnitude of uncertainty around amine geometry While getting it 'right' is of course the aim here, I wonder if anyone has an impression of the room temperature impact of these small changes. It is my impression that the non-planarity of amide (and other sp2 conjugated) nitrogens is not far from the planar geometry enthalpically, and that the surface there is quite flat. If the surface is indeed quite flat then at room temperature it could contribute significantly entropically. Stiffening up that deformation would have a measurable effect. Does anyone have a liquid simulation using the corrections Tom Halgren has talked about (in the carbon-attached hydrogen repoulsive terms) to fix the limitations Bill Jorgensen has identified in MMFF? It seems to me that this would answer much of the impact of the non-planar amide nitrogen question. Even at 0K, a flat surface with very small difference between the two states might not have much practical impact. After all, as others have pointed out, the crystal structures are averaged structures. -- M. Dominic Ryan (610)-270-6529 SmithKline Beecham Pharmaceuticals ryanmd@mms.sbphrd.com King of Prussia, PA -------This is added Automatically by the Software-------- * Original Sender Envelope Address: ryanmd@mms.sbphrd.com * Original Sender From: Address: ryanmd@mms.sbphrd.com CHEMISTRY@ccl.osc.edu: Everybody | CHEMISTRY-REQUEST@ccl.osc.edu: Coordinator MAILSERV@ccl.osc.edu: HELP CHEMISTRY or HELP SEARCH | Gopher: ccl.osc.edu 73 Anon. ftp: ccl.osc.edu | CHEMISTRY-SEARCH@ccl.osc.edu-archive search Web: http://ccl.osc.edu/chemistry.html From ccl@infomeister.osc.edu Wed Dec 3 22:39:03 1997 Received: from bedrock.osc.edu for ccl@infomeister.osc.edu by infomeister.osc.edu (8.8.3/950822.1) id VAA29566; Wed, 3 Dec 1997 21:51:55 -0500 (EST) Received: from gatekeeper.es.dupont.com for fredvc@esalp1.dnet.dupont.com by bedrock.osc.edu (8.8.6/950822.1) id VAA10139; Wed, 3 Dec 1997 21:51:50 -0500 (EST) From: Received: from ns1.es.dupont.com (ns1.es.dupont.com [138.196.90.13]) by gatekeeper.es.dupont.com with SMTP id VAA00305 for ; Wed, 3 Dec 1997 21:51:52 -0500 Received: by ns1.es.dupont.com; id AA20742; Wed, 3 Dec 97 21:46:35 -0500 Message-Id: <9712040246.AA20742@ns1.es.dupont.com> Received: from esalp1.dnet; by esds01.dnet; Wed, 3 Dec 97 21:51:51 EST Date: Wed, 3 Dec 97 21:51:51 EST To: smtp%"jenninaj@mh.uk.sbphrd.com"@cdmhvx.dnet.dupont.com Cc: mail11:;@osc.edu (@dis:chem), fredvc@esalp1.dnet.dupont.com Apparently-To: chemistry@osc.edu Subject: RE: CCL:Re: CCL:HyperChem: Incorrect geometries in amines I think the MM+ forcefield is OVERcompensating for the interaction betwen the nitrogen atom & the pi-system. If memory serves, the geometry around the N in aniline is "more planar" than in methyl amine, but not "truly planar". I would recommend checking the literature for structural studies on aniline, or running ab initio calculations [6-31G(p,d) or DZP at least] optimizing aniline & cyclohexylamine to check this. ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ FREDERIC A. VAN-CATLEDGE Scientific Computing Division || Office: (302) 695-1187 or 529-2076 Central Research & Development Dept. || The DuPont Company || FAX: (302) 695-9658 P. O. Box 80320 || Wilmington DE 19880-0320 || Internet: fredvc@esvax.dnet.dupont.com -------------------------------------------------------------------------------- Opinions expressed in this electronic message should ***> NOT <*** be taken to represent the official position(s) of the DuPont Company. *****> ANY OPINIONS EXPRESSED ARE THE PERSONAL VIEWS OF THE AUTHOR ONLY. <***** ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ From: Mr HG Kruger [kruger@eng.und.ac.za] Sent: Friday, December 05, 1997 5:42 AM To: Andy Jennings Cc: chemistry@infomeister.osc.edu; Paddy Kane Subject: CCL:HyperChem: Incorrect geometries in amines Andy, I support your view. (At least for a single aniline molecule - not sure what will happen in a crystal). > Unless I'm missing the point here what you see is not a problem - simply > the correct answer. The nitrogen in these systems WILL be planar due to > the pi systems delocalising over all conjugated atoms. This forces the > nitrogen into planarity...something which won't happen with a saturated > system as there is no opportunity for pi orbital delocalisation. Might I > suggest reading something like 'A guidebook to mechanism in organic > chemistry' by Peter Sykes which has an excellent chapter on atomic > orbitals and hybridisation. I think practical proof of the delocalised (planar) structure follows from the textbook explanation on the difference between the basicities of cyclohexaneamine (pKa 9.8) and aniline (pKa 4.6). (Thanks to my colleaque Dr JP Gerber). Best wishes Gert Kruger __________________________________________________________ Dr HG Kruger, Dept Chemistry, University of Natal, PO Box 18091, Dalbridge 4014, Durban, South Afica Tel +27-31-2602181 Fax +27-31-2603091 Email kruger@che.und.ac.za __________________________________________________________ -------This is added Automatically by the Software-------- * Original Sender Envelope Address: kruger@eng.und.ac.za * Original Sender From: Address: kruger@eng.und.ac.za CHEMISTRY@ccl.osc.edu: Everybody | CHEMISTRY-REQUEST@ccl.osc.edu: Coordinator MAILSERV@ccl.osc.edu: HELP CHEMISTRY or HELP SEARCH | Gopher: ccl.osc.edu 73 Anon. ftp: ccl.osc.edu | CHEMISTRY-SEARCH@ccl.osc.edu-archive search Web: http://ccl.osc.edu/chemistry.html From jenninaj@mh.uk.sbphrd.com Thu Dec 4 09:39:11 1997 Received: from ns01.sbphrd.com for jenninaj@mh.uk.sbphrd.com by infomeister.osc.edu (8.8.3/950822.1) id JAA02301; Thu, 4 Dec 1997 09:02:06 -0500 (EST) Received: by ns01.sbphrd.com; id JAA16369; Thu, 4 Dec 1997 09:02:07 -0500 Received: from phinet.sbphrd.com(139.136.64.5) by ns01.sbphrd.com via smap (3.2) id xma016264; Thu, 4 Dec 97 09:01:47 -0500 Received: from hbu037.ha.uk.sbphrd.com by phinet.sbphrd.com; (5.65v3.0/1.1.8.2/06Mar95-1250PM) id AA21414; Thu, 4 Dec 1997 09:01:46 -0500 Received: from hgu118.ha.uk.sbphrd.com (hgu118.ha.uk.sbphrd.com [139.136.157.118]) by hbu037.ha.uk.sbphrd.com (8.8.5/pe/sbphrd/mh/970220) with ESMTP id OAA31725 for ; Thu, 4 Dec 1997 14:01:44 GMT Received: from localhost (jenninaj@localhost) by hgu118.ha.uk.sbphrd.com (8.8.5/pe/sbphrd/clnt/970220) with SMTP id OAA08195 for ; Thu, 4 Dec 1997 14:01:43 GMT X-Authentication-Warning: hgu118.ha.uk.sbphrd.com: jenninaj owned process doing -bs Date: Thu, 4 Dec 1997 14:01:42 +0000 (GMT) From: Andy Jennings To: Comp-Chem-List Subject: Re.HyperChem: Incorrect geometries in amines..enough is enough Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Thanks for all your comments over my erroneous statement that the nitrogen in phenylamine is planar. I have now got the message...in fact I have now got many messages...can we move onto something else? Cheers, Andy PS This e-mail does _NOT_require a number of replies. ================================================================= Andy Jennings - SmithKline Beecham Pharmaceuticals Phone: +44 (0) 1279 627682 Fax: +44 (0) 1279 627685 ----------------------------------------------------------------- From: jolanala@phys.amu.edu.pl Sent: Monday, December 08, 1997 5:59 AM To: chemistry@infomeister.osc.edu; hyperchem@hyper.com Subject: Ab initio basis set Dear Netters, I would like to ask you about basis sets for iodine or anthimony. They are not included to Hyperchem 5.01 release. Could you help me in obtaining the appropriate parameters, especially for 6-31G** basis set, please? Jolanta Latosinska Sender: listadmin@hyper.com Precedence: bulk Reply-To: jolanala@phys.amu.edu.pl From: Stavrev, Krassimir Sent: Monday, December 08, 1997 9:14 AM To: 'jolanala@phys.amu.edu.pl' Subject: RE: Ab initio basis set Jolanta: Have you checked these 2 popular Web sites that provide basis sets: http://tcpc.bham.ac.uk/molpro/basisform.html and http://www.emsl.pnl.gov:2080/forms/basisform.html ? Regards, Krassimir --- Krassimir Stavrev, PhD, Director of Scientific Support Hypercube, Inc. Florida Science and Technology Park 1115 N.W. 4th Street Gainesville, Florida 32601 Voice:(352) 371-7744/(800) 960-1871 Fax:(352) 371-3662 -----Original Message----- From: jolanala@phys.amu.edu.pl [SMTP:jolanala@phys.amu.edu.pl] Sent: Monday, December 08, 1997 5:59 AM To: chemistry@infomeister.osc.edu; hyperchem@hyper.com Subject: Ab initio basis set Dear Netters, I would like to ask you about basis sets for iodine or anthimony. They are not included to Hyperchem 5.01 release. Could you help me in obtaining the appropriate parameters, especially for 6-31G** basis set, please? Jolanta Latosinska From: Ashutosh Misra [ashutosh@ti.com] Sent: Monday, December 08, 1997 12:48 PM To: chemistry@infomeister.osc.edu; hyperchem@hyper.com; jolanala@phys.amu.edu.pl Subject: re: CCL:Ab initio basis set Dear Jolanta, Attached below is the 6-31G(d) basis set for Iodine. Please consult the following papers by Glukhovtsev et al. regarding the use of all-electron iodine basis sets. (1) Glukhovtsev, M. N.; Pross, A.; McGrath, M. P.; Radom, L. J. Chem. Phys. 1995, 103, 1878. (2) Glukhovtsev, M. N.; Pross, A.; McGrath, M. P.; Radom, L. J. Chem. Phys. 1996, 104, 3407. Regards, Ashutosh --------------------------------------------------------- * I S 4 1.0 42297.957 0.0165457 6375.1354 0.1164656 1447.6218 0.4309597 390.94964 0.5667813 S 3 1.0 582.20124 -0.1144000 67.838092 0.6457644 29.640666 0.4265016 S 3 1.0 54.589064 -0.2773274 10.070202 0.8671635 4.5676679 0.2890370 S 3 1.0 8.8441340 0.3569170 2.0968138 -0.8254301 0.98611692 -0.3901444 S 2 1.0 1.5207770 0.2698431 0.27302449 -0.7625119 S 1 1.0 0.10795603 1.0000000 P 4 1.0 1997.5692 0.0239358 470.17426 0.1641003 147.12001 0.4915455 51.632190 0.4795349 P 3 1.0 158.66544 -0.0253934 21.085556 0.4791351 8.3903226 0.5879478 P 3 1.0 3.5785818 0.4341764 1.6034530 0.5290721 0.70343694 0.1113815 P 2 1.0 0.41515416 -0.3908686 0.17098833 -0.5190582 P 1 1.0 0.06856211 1.0000000 D 4 1.0 238.44881 0.0382347 69.545921 0.2205252 24.677895 0.5210939 9.0881485 0.4279063 D 3 1.0 5.9337495 0.2777183 2.2186322 0.5733560 0.80937642 0.3207317 D 1 1.0 0.266 1.000 **************************************************** Ashutosh Misra, Ph.D. Phone: 972-995-7552 Air Liquide Electronics Fax : 972-995-3204 Chemicals & Services, Inc. Pager: 972-598-1274 13546 N. Central Expressway M/S 301, Dallas, TX 75243 From: Support Sent: Monday, December 08, 1997 4:48 PM To: 'hyperchem@hyper.com' Subject: Re: CCL:Ab initio basis set Approved: goodchem123 From: "Dr. Bruno Manunza" To: jolanala@phys.amu.edu.pl Cc: chemistry@infomeister.osc.edu, hyperchem@hyper.com Subject: Re: CCL:Ab initio basis set Date: Mon, 8 Dec 1997 22:45:13 +0100 (NFT) On Mon, 8 Dec 1997 jolanala@phys.amu.edu.pl wrote: > Dear Netters, > I would like to ask you about basis sets for iodine or anthimony. > They are not included to Hyperchem 5.01 release. > Could you help me in obtaining the appropriate parameters, especially > for 6-31G** basis set, please? > Jolanta Latosinska Dear Jolanta, you'll find links to several basis sets data banks on our software links page at: http://antas.agraria.uniss.it check under Quantum Chemistry software. Hope it helps and sorrry if you already checked those links. 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: Dr. Bruno Manunza [bruno@antas.agraria.uniss.it] Sent: Monday, December 08, 1997 4:45 PM To: jolanala@phys.amu.edu.pl Cc: chemistry@infomeister.osc.edu; hyperchem@hyper.com Subject: Re: CCL:Ab initio basis set On Mon, 8 Dec 1997 jolanala@phys.amu.edu.pl wrote: > Dear Netters, > I would like to ask you about basis sets for iodine or anthimony. > They are not included to Hyperchem 5.01 release. > Could you help me in obtaining the appropriate parameters, especially > for 6-31G** basis set, please? > Jolanta Latosinska Dear Jolanta, you'll find links to several basis sets data banks on our software links page at: http://antas.agraria.uniss.it check under Quantum Chemistry software. Hope it helps and sorrry if you already checked those links. 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: Laurence Lavelle [lavelle@mbi.ucla.edu] Sent: Monday, December 08, 1997 8:36 PM To: chemistry@infomeister.osc.edu; gamess-users@glue.umd.edu; hyperchem@hyper.com; support@wavefun.com; info@gaussian.com Subject: All-electron basis set higher than 3-21G* for Ni. Hi, I have searched various sources for an all-electron basis set higher than 3-21G* for Ni. Does one exist, if so I would appreciate knowing where to find it? Thanks Laurence Lavelle """""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" """""""""""""""""""" Laurence Lavelle, Ph.D. University of California Los Angeles Molecular Biology Institute, and Department of Chemistry & Biochemistry Laboratory of Structural Biology & Molecular Medicine Los Angeles, CA 90095-1570, USA Email:LAVELLE@MBI.UCLA.EDU Phone (Lab): (310) 206-8270 Phone (Office): (310) 825-2083 Fax: (310) 267-1957 http://www.doe-mbi.ucla.edu/people/lavelle/lavelle.html """""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" """""""""""""""""""" It will be a great day when schools have all the money they need, and the military has bake day sales. In nature's infinite book of secrecy A little I can read. From: listadmin@hyper.com Sent: Monday, December 08, 1997 8:33 PM To: HyperChem Mailing List Subject: Transition States Message-Id: <199712091354.IAA08257@ftp.hyper.com> From: Tim Bender Reply-To: tbender@ccs.carleton.ca To: HyperChem Mailing List Subject: Transition States Date: Mon, 08 Dec 1997 20:33:19 -0500 Sender: listadmin@hyper.com Precedence: bulk Hello, in an effort to reproduce the results of a paper titled "Racemization Barriers of Helicenes: A Computational Study": Janke, R.H.; Haufe, G.; Wurthwein, E.U.; Borkent, J.H.; J.A.C.S., 118, 6031-6053, 1996. I am using the transition state searching provided in hyperchem ver 5.1, and while the transition state that it predicts is the same as the above stated paper, I have one problem, I wish to plot reaction coordinate versus heat of formation for the racimization (as they do in the paper), however, it appears that hyperchem does not have the ability to store the heat of formation (DHf) value at each point of the calculation (from starting structure to transition state) so that the racimization enthalpy can be followed, is this an accurate observation? is there any way to have hyperchem store the energy value as is available throught the snapshot file when a molecular dynamics simulaiton is performed? If this is not currently available, may I suggest that it be added to the wish list ... thank you in advance? -- Tim :-) ---------------------------------------------------------------------- Tim Bender, B.Sc | To know chemistry, Student, Department of Chemistry | is to know a little Carleton University, Ottawa, Ont, Canada | piece of nature ... Email address: tbender@ccs.carleton.ca | ---------------------------------------------------------------------- FEAR - the general public has long been divided into two parts: those who think science can do anything, and those who are afraid that it will ... Dixy Lee Ray From: Stavrev, Krassimir [stavrev@hyper.com] Sent: Tuesday, December 09, 1997 10:13 AM To: 'tbender@ccs.carleton.ca' Cc: 'hyperchem@hyper.com' Subject: RE: Transition States Tim: Your observation is correct, the current version of HyperChem does not store intermediate points during a transition state search. Typically on can extract values of interest using a script like omsgs-to-file coordinates.txt notify-on-update coordinates dynamics-playback playback do-molecular-dynamics which, in this case, will playback an existing snp-file and extract the atomic coordinates from it. It would be nice to have a transition-state-search command that will have the functionality to apply notify-on-update to properties such as heat-of-formation. It is on our wishlist for the next releases of HyperChem. Regards, Krassimir --- Krassimir Stavrev, PhD, Director of Scientific Support Hypercube, Inc. Florida Science and Technology Park 1115 N.W. 4th Street Gainesville, Florida 32601 Voice:(352) 371-7744/(800) 960-1871 Fax:(352) 371-3662 -----Original Message----- From: Tim Bender Reply-To: tbender@ccs.carleton.ca To: HyperChem Mailing List Subject: Transition States Date: Mon, 08 Dec 1997 20:33:19 -0500 Sender: listadmin@hyper.com Precedence: bulk Hello, in an effort to reproduce the results of a paper titled "Racemization Barriers of Helicenes: A Computational Study": Janke, R.H.; Haufe, G.; Wurthwein, E.U.; Borkent, J.H.; J.A.C.S., 118, 6031-6053, 1996. I am using the transition state searching provided in hyperchem ver 5.1, and while the transition state that it predicts is the same as the above stated paper, I have one problem, I wish to plot reaction coordinate versus heat of formation for the racimization (as they do in the paper), however, it appears that hyperchem does not have the ability to store the heat of formation (DHf) value at each point of the calculation (from starting structure to transition state) so that the racimization enthalpy can be followed, is this an accurate observation? is there any way to have hyperchem store the energy value as is available throught the snapshot file when a molecular dynamics simulaiton is performed? If this is not currently available, may I suggest that it be added to the wish list ... thank you in advance? -- Tim :-) ---------------------------------------------------------------------- Tim Bender, B.Sc | To know chemistry, Student, Department of Chemistry | is to know a little Carleton University, Ottawa, Ont, Canada | piece of nature ... Email address: tbender@ccs.carleton.ca | ---------------------------------------------------------------------- FEAR - the general public has long been divided into two parts: those who think science can do anything, and those who are afraid that it will ... Dixy Lee Ray From: Stavrev, Krassimir [stavrev@hyper.com] Sent: Friday, December 12, 1997 9:49 AM To: cyrillo@ifi.unicamp.br Cc: 'hyperchem@hyper.com' Subject: RE: Add-on to HyperChem Marcio: Thank you very much for your note and for your willingness to share your application with other HyperChem users. =20 Please send us copies of your programs and details (read-me files) on how to use them to support@hyper.com. We usually make such products available on the Web at www.hyper.com/support under Software Archive.=20 Regards, Krassimir =20 --- Krassimir Stavrev, PhD, Director of Scientific Support Hypercube, Inc. Florida Science and Technology Park 1115 N.W. 4th Street Gainesville, Florida 32601 Voice:(352) 371-7744/(800) 960-1871 Fax:(352) 371-3662 -----Original Message----- From: M=E1rcio Cyrillo [SMTP:cyrillo@ifi.unicamp.br] Sent: Friday, December 12, 1997 9:15 AM To: support@hyper.com Cc: Marcio Cyrillo Subject: Add-on to HyperChem Dear Sir or Madam from HyperCube, =A0 =A0=A0=A0 I am very glad of being able to let you know that I have written a program in Visual Basic 5.0 (professional edition) that interfaces with HyperChem. At first I worked with HyperChem 4.0 but since we have been given the opportunity to test HyperChem 5.02 evaluation copy, I could include some features (useful ones) to work with this particularly version.=A0 =A0=A0=A0 Well, about the program: It's named HyperSpin and allows = HyperChem users to edit scripts very easily to do conformational search (I have = no idea of how ChemPlus works with that). With my software one will be = able to rotate any proper dihedral in the selected range and collect = selected energy variables that are arranged in a text file and minimize the system for one selected variable. Minimization then occurs and the system is put in the minimal conformation automatically. An auxiliary program named HyperGraph can plot energy values on-line (while you run search on HyperSpin menu in HyperChem) for molecular mechanics calculation. If one does search with two or three dihedrals, HyperChem uses recursive scripts (.scr only) to find the global minimum for the actual phase space being analyzed. A Mathematica notebook as well as xyz text file is the generated allowing 3D visualization. =A0=A0=A0 Another tool added with the pack is HyperRemote, a program that intends to help HyperChemists that want to develop applications to work together with HyperChem since it allows to see any HyperChem variable, monitor them and execute commands very easily.=20 =A0=A0=A0 Finally I have written another very simple tool named = LogViewer that allows one to monitor changes in a HyperChem logfile as soon as they occur. =A0=A0=A0 So, I still have a lot of things to talk about my programs, = but unfortunately I do not have time to write them now. Please contact me letting me know what I have to do to provide you a copy of my program so that you can test it and about the possibilty to make it available for all other hyperchemists in you web page http://www.hyper.com. =20 =A0=A0=A0 These software make part of my masterdegree thesis and so, I'll be able to distribute them free by the end of March when I will be finished with it.=A0 =A0=A0=A0 Thank you very much for your attention. Best regards,=A0 =A0 =A0=A0=A0=A0=A0=A0=A0 M=E1rcio Cyrillo. =A0 It follows a sample of some program windows: =A0 =A0 << File: ATT00098.jpg >>=20 From: Sandy Yates [prrls08@holyrood.ed.ac.uk] Sent: Friday, December 12, 1997 7:59 PM To: hyperchem@hyper.com Subject: Add-on to HyperChem Hi HC users, I have to chance to use HyperSpin from Marcio (cyrillo@ifi.unicamp.br). It is easy to install and functions very smoothly! Within a few mintutes I was able to calculate the rotamer conformational eneries for butane. This program graphed these data at my selected angular step values. This program is a delight to use. I was excited by the watching the molecules being manipulated and the energy being calculated before my eyes. This third-party HyperChem add-on is capable of plotting a wide range is parameters (dipole moment etc etc) as a function the dihedral angle. I used this program with HyperChem 5.02 under Win95. Basically there might be a few minor refinement that I could suggest, but all in all the program made it very easy visualize this type of calculation. The script necessary for the scripts used in the calculation could be edited separately as they are stored to disk. I have asked the author if he could develop the program further by allowing other type of adjustments to be included. If you have the opportunity to download this program and try it I strongly recommend that you do. I would be nice to see other such programs being developed. Personally, this program provided me with just the type of "live" graphing facilities which I was looking for. It allowed me to track the conforamtional energies. I can imagine that it would be a great teaching aid. It looks likely that HyperCude may make this add-on available from their server in their FTP support directory Sandy ----------------------------------------------------------------------- Sandy Yates / University of Edinburgh / Dept of Chemistry (Physical) Joseph Black Building / West Mains Road / EH9 3JJ Tlf: (+44) 131 650 4734 or 4799 / Fax: (+44) 131 650 4743 email: S.Yates@ed.ac.uk (aliased from: prrls08@holyrood.ed.ac.uk) From: wojcik@chem.vill.edu Sent: Monday, December 15, 1997 12:31 PM To: hyperchem@hyper.com Subject: DDE variable It is possible to use DDE to extract, for example, "ir-frequency", "ir-intensity", etc.=20 Is there a variable (that I cannot find) to extract "ir-symmetry" which is listed at the bottom of the ir frequency dialog? Similarly, is there a variable for molecule symmetry such as is listed at the end of a single point calculation? =20 Thanks! John F. W=F3jcik=20 John F. W=F3jcik Department of Chemistry Villanova University Villanova, PA 19085-1699 wojcik@rs6chem.vill.edu (610) 519-4868 From: Stavrev, Krassimir [stavrev@hyper.com] Sent: Monday, December 15, 1997 1:18 PM To: 'wojcik@chem.vill.edu' Cc: 'hyperchem@hyper.com' Subject: RE: DDE variable John: Enclosed is the full list of variables you can use with HyperChem 5 that comes from print-variable-list. Not all the calculated properties are presently on it. For example, ir-frequency is on the list, while symmetries are not. We are trying to make the variable list as big as possible. Regards, Krassimir --- Krassimir Stavrev, PhD, Director of Scientific Support Hypercube, Inc. Florida Science and Technology Park 1115 N.W. 4th Street Gainesville, Florida 32601 Voice:(352) 371-7744/(800) 960-1871 Fax:(352) 371-3662 -----Original Message----- From: wojcik@chem.vill.edu [SMTP:wojcik@chem.vill.edu] Sent: Monday, December 15, 1997 12:31 PM To: hyperchem@hyper.com Subject: DDE variable It is possible to use DDE to extract, for example, "ir-frequency", "ir-intensity", etc. Is there a variable (that I cannot find) to extract "ir-symmetry" which is listed at the bottom of the ir frequency dialog? Similarly, is there a variable for molecule symmetry such as is listed at the end of a single point calculation? Thanks! John F. Wójcik John F. Wójcik Department of Chemistry Villanova University Villanova, PA 19085-1699 wojcik@rs6chem.vill.edu (610) 519-4868 ------ =_NextPart_000_01BD095B.E4772790 Content-Type: text/plain; name="VariableList.txt" From: Richard Gillilan [richard@TC.Cornell.EDU] Sent: Thursday, December 04, 1997 12:43 PM To: Pieter Stouten Cc: chemistry@osc.edu Subject: CCL:Re: CCL:HyperChem: Incorrect geometries in amines > There actually is at least one forcefield (MSI's CFF96) that is used in > Molecular Mechancis that does have properly puckered nitrogens. Are there > any other forcefields people know of, that do describe aniline etc. > properly? > > Thanks, > > Pieter Stouten My unofficial implementation of MMFF94 does seem to minimize to an out-of-plane result. Looking at Halgren's papers, I do see that "aniline, N puckered" is listed in the core parameterization (Table I, paper I). Richard Gillilan Cornell Theory Center richard@tc.cornell.edu --- Administrivia: This message is automatically appended by the mail exploder: CHEMISTRY@ccl.osc.edu: Everybody | CHEMISTRY-REQUEST@ccl.osc.edu: Coordinator MAILSERV@ccl.osc.edu: HELP CHEMISTRY or HELP SEARCH | Gopher: ccl.osc.edu 73 Anon. ftp: ccl.osc.edu | CHEMISTRY-SEARCH@ccl.osc.edu -- archive search Web: http://ccl.osc.edu/chemistry.html --- From: Andy Jennings [jenninaj@mh.uk.sbphrd.com] Sent: Thursday, December 04, 1997 9:02 AM To: Comp-Chem-List Subject: CCL:Re.HyperChem: Incorrect geometries in amines..enough is enough Thanks for all your comments over my erroneous statement that the nitrogen in phenylamine is planar. I have now got the message...in fact I have now got many messages...can we move onto something else? Cheers, Andy PS This e-mail does _NOT_require a number of replies. ================================================================= Andy Jennings - SmithKline Beecham Pharmaceuticals Phone: +44 (0) 1279 627682 Fax: +44 (0) 1279 627685 ----------------------------------------------------------------- --- Administrivia: This message is automatically appended by the mail exploder: CHEMISTRY@ccl.osc.edu: Everybody | CHEMISTRY-REQUEST@ccl.osc.edu: Coordinator MAILSERV@ccl.osc.edu: HELP CHEMISTRY or HELP SEARCH | Gopher: ccl.osc.edu 73 Anon. ftp: ccl.osc.edu | CHEMISTRY-SEARCH@ccl.osc.edu -- archive search Web: http://ccl.osc.edu/chemistry.html --- From: Marcio Cyrillo - pos Message-Id: [199712161950.RAA02592@huckel.ifi.unicamp.br] Sent: Tuesday, December 16, 1997 2:50 PM To: hyperchem@hyper.com Subject: HyperSpin requests. Dear HyperChemists, I am very glad to receive various e-mails inquiring about HyperSpin. The e-mail Sandy Yates sent to the HC list was very kind and I hope he has not overestimated the software, since it is just an add-on to HyperChem facilities. Sandy's suggestions were very fruitful. For example it is possible now to select dihedrals directly on HyperChem workspace. He has also helped me to find out some obscure bugs. Talking now about HyperSpin: it is free of charge and I intend to keep it so for all HyperChem users under the condition of proper acknowledgments. If you publish any material using HyperSpin please cite the following: Real Time Graphical Interface Add-on to HyperChem (HyperSpin). M. Cyrillo and D.S. Galvao, to be published. I cannot distribute it now, since I am still preparing a readme textfile and fixing some small bugs. I hope This will be done in the next few days and then I will be glad to send all users that ask for it a copy of the installation program or the link to get it from my web page. System requirements: Windows 95 in any language but with English set as default language on the control panel (I hope it will work on NT as well). Resolution 800x600 or greater. HyperChem installed. Tests were done with HyperChem 3, 4 and 5.02. The full features are for HC 5.02 (Thanks to evaluation copy provided by HyperCube). In order to provide all bug reports and new releases to potencial HyperSpin users, please provide the following information: Name: e-mail: homepage: address: (full) pc model: HyperChem version: sent by e-mail to cyrillo@ifi.unicamp.br with the message subject "HyperSpin request." Thank you very much, regards, Marcio Cyrillo Attention MOPAC users: I have also another software Chem2Pac that is a interface to help HyperChem users to prepare MOPAC inputs and analyze its outputs. For example a keywords editor, a automatic data extractor from FOR006, etc. From: Marcio Cyrillo - pos Message-Id: [199712171250.KAA02714@huckel.ifi.unicamp.br] Sent: Wednesday, December 17, 1997 7:50 AM To: hyperchem@hyper.com Subject: thanks. Dear HyperChemists, Thank you very much for the mails I have received. It will be very nice to have so many users of my program. This certainly will contribute to its improvements as new suggestions will come! Notice that I will be abroad from the end of November and begining of March: From 31. Dec. to 4. Jan. I will be in Frankfurt, Germany, in some hotel with nothing to do because I will be waiting for the train to Freiburg (Albert Ludwigs Universitaet - South Germany) where I will attend a course from 5. Jan. to 25. Fev. From 26. Fev to 3. Mar. I will be waiting for my flight back to Brazil and I will be able to travel a bit.. So, If anyone wants to meet me, just let me know. I will have the two programs I mentioned in my hands (two diskettes for each) and if a pc is available I can explain how the programs work. Someone has asked me if Chem2Pac works with mopac for pc. I don't know. I have tested it with MOPAC6 (the last free of charge unix version) and I do not know how the program works with other versions since it reads MOPAC output files trought their specific format. I use FTP to transfer the inputs to the unix system and to get the outputs to be analized with C2P. I hope I will be able to read e-mails, either from cyrillo@ifi.unicamp.br or mcyrillo@yahoo.com Marry christmas and happy new year for you all! Best regards, Marcio. ps: I would like to thank Krassimir Stravrev from HyperChem staff for his help and efforts to make HyperSpin available in HyperCube web site. From: Support [support@hyper.com] Sent: Wednesday, December 17, 1997 9:55 AM To: 'hyperchem@hyper.com' Subject: downloads Dear all, We have received several requests to post the list of HyperChem script variables. The 53Kb file is now downloadable from ftp://ftp.hyper.com/support/Variable.list.txt . Alternatively, the list can be obtained by executing a one-line script, e.g. "print-variable-list list.txt". HyperSpin, a nice HyperChem interface written by Marcio Cyrillo, will also be made available for download from our Web site. I asked Marcio to provide his home Web page as an alternative download site. Please check our software archive at www.hyper.com/support in a few days. Regards, Krassimir --- Krassimir Stavrev, PhD, Director of Scientific Support Hypercube, Inc. Florida Science and Technology Park 1115 N.W. 4th Street Gainesville, Florida 32601 Voice:(352) 371-7744/(800) 960-1871 Fax:(352) 371-3662 From: Marcio Cyrillo - pos [cyrillo@ifi.unicamp.br] Sent: Thursday, December 18, 1997 7:17 AM To: hyperchem@hyper.com Subject: Script variables. Hi All, I have a good news to all HyperChem users who uses script variables in its own scripts or applications. One of the components of HyperSpin package named HyperRemote is able to access all HyperChem variables in a easy way as you will see soon. You can choose them in menus like HyperChem menus e.g. you have inside a "File" menu the options: File Variables, File Commands and Menu File Activators. Choosing one of these options, all the related script messages appear in a list box. Then by clicking or double clicking one message you can read the variable or execute the command and see the HyperChem response... This was specially disigned to all interface developers. I hope you'll enjoy! Comming soon, very soon. Regards, Marcio. From: Paul H. Schlesinger [paul@cellbio.wustl.edu] Sent: Wednesday, December 17, 1997 11:53 PM To: HyperChem list Subject: keyloak I remember this issue from the past but not the solution since I was using WIN95 then and it was not important to me. When I put the hyperchem key lock on my parallel prot it disables printing from NT4. Hyperchem runs fine but it cannot print either. Can you suggest a solution? Paul From: Stavrev, Krassimir Sent: Thursday, December 18, 1997 6:15 PM To: 'paul@cellbio.wustl.edu' Subject: RE: keylok Paul: It could be your printer driver - try the latest PD 5.33 I'm sending you attached. Run the sysdrvr.exe and then install the driver from the Win_nt folder that will appear. See also our FAQ # 24 and 27 pages at www.hyper.com/support . Let me know if the problem persist. <> Regards, Krassimir --- Krassimir Stavrev, PhD, Director of Scientific Support Hypercube, Inc. Florida Science and Technology Park 1115 N.W. 4th Street Gainesville, Florida 32601 Voice:(352) 371-7744/(800) 960-1871 Fax:(352) 371-3662 From: "Paul H. Schlesinger" To: HyperChem list Subject: keyloak Date: Thu, 18 Dec 1997 04:52:46 +0000 I remember this issue from the past but not the solution since I was using WIN95 then and it was not important to me. When I put the hyperchem key lock on my parallel prot it disables printing from NT4. Hyperchem runs fine but it cannot print either. Can you suggest a solution? Paul From: jsalb@ix.netcom.com Sent: Thursday, December 18, 1997 11:03 PM To: hyperchem@hyper.com Subject: Launch .hin files from Explorer? Does anyone know what the proper NT 4.0 registry entries are to automatically launch a .hin file from Explorer? Associating the .hin extension with chem.exe launches HyperChem but doesn't load the selected .hin file. Jesse Salb From: Marcio Cyrillo - pos Message-Id: [199712191227.KAA05445@huckel.ifi.unicamp.br] Sent: Friday, December 19, 1997 7:28 AM To: hyperchem@hyper.com Subject: HyperSpin done! Dear all, Good news! HyperSpin is done including a readme file to help users getting started. I'll send the copy first to HyperCube and then to all users that have sent me the request. I need two more hours two prepare the files... see you, Marcio Cyrillo From: Gerardo Burton [burton@qo.fcen.uba.ar] Sent: Friday, December 19, 1997 12:17 PM To: Jesse Salb Cc: Hyperchem Subject: RE: Launch .hin files from Explorer? Hi Jesse, Maybe you tried this already, but this is how it is set in my machine: in Explorer View/Options choose "File types". Look for the hin file, choose Edit and then New action. There it should read, Action: open, Application used..: ..your path..\chem.exe . In my machine (Pentium Pro, NT 4.0) it works OK, although all this was set during installation, however I can't recall if it did work OK before I installed the patch (upgrade to 5.02). Good luck Gerardo -----Original Message----- De: Jesse Salb Para: hyperchem@hyper.com Fecha: viernes 19 de diciembre de 1997 12:36 Asunto: Launch .hin files from Explorer? > >Does anyone know what the proper NT 4.0 registry entries are to >automatically launch a .hin file from Explorer? Associating the .hin >extension with chem.exe launches HyperChem but doesn't load the selected >.hin file. >Jesse Salb From: Marcio Cyrillo - pos Message-Id: [199712221302.LAA03851@dfa01.ifi.unicamp.br] Sent: Monday, December 22, 1997 8:03 AM To: hyperchem@hyper.com Subject: HyperSpin download problems Dear all, Unfortunately our server (ifi.unicamp.br) was down this weekend and it seems to be down until now. I am sure they are solving the problem right now or will when they come to work. As Laszlo said, it seems that my server "is having a Christmas Holiday" With the server down I cannot even send you mails with the file attached, I have tried several times last Sunday but they all returned with problems. Well, I hope you will soon be able to download it. Krassimir Stavrev also said that HC staff would probably put the software in their page this week. I hope you will understand. Regards, Marcio. From: Marcio Cyrillo - pos Message-Id: [199712221730.PAA04001@dfa01.ifi.unicamp.br] Sent: Monday, December 22, 1997 12:30 PM To: hyperchem@hyper.com Subject: server ok. Dear all, The server where you can download HyperSpin: www.ifi.unicamp.br/~cyrillo/hyperspin/hspin.html seems to be up now. Regards, Marcio From: Stavrev, Krassimir Sent: Monday, December 22, 1997 3:14 PM To: 'Marcio Cyrillo - pos' Cc: 'hyperchem@hyper.com' Subject: RE: HyperSpin Marcio: HyperSpin is now downloadable from www.hyper.com/support/software/Other/other_index.html. Thank you, again, for making these nice and useful interfaces available to HyperChem users! Happy holidays! Regards, Krassimir --- Krassimir Stavrev, PhD, Director of Scientific Support Hypercube, Inc. Florida Science and Technology Park 1115 N.W. 4th Street Gainesville, Florida 32601 Voice:(352) 371-7744/(800) 960-1871 Fax:(352) 371-3662 -----Original Message----- From: Marcio Cyrillo - pos [SMTP:cyrillo@ifi.unicamp.br] Sent: Friday, December 19, 1997 12:14 PM To: support@hyper.com Subject: HyperSpin Dear Krassimir, HyperSpin is done. I couldn't contact you before since our network was down this morning. Can you get the zip now? use the following link: www.ifi.unicamp.br/~cyrillo/hyperspin/hspin.zmt Let me know. Regards, Marcio From: malahov@mem1.ilc.msu.su Sent: Thursday, December 25, 1997 2:45 PM To: hyperchem@hyper.com Subject: ESA calculation Dear Chemists ! I am interested in excited state absorption (ESA) spectra calculations. Prof. Zerner told me that ZINDO with PSDCI can perform such type calculation. So is it possible to calculate the ESA spectra with the help ZINDO included into HYPERCHEM. As I know HYPERCHEM can perform only single excited CI, but I am not sure. If it really possible I would like to buy this software. Best regards Phd. st. Dmitry Malakhov International Laser Center of Moscow State University, Moscow, Russia. E-mail to: mal@mem2.ilc.msu.su or malakhoff@hotmail.com From: Stavrev, Krassimir Sent: Monday, December 29, 1997 11:26 AM To: 'hyperchem@hyper.com' Cc: 'malakhoff@hotmail.com' Subject: RE: ESA calculation Dmitry: It is possible to calculate ESA (excited state absorption) spectra provided one can get the desired excited state reference. INDO/S is especially suitable model for this as it derives its parameters from the atomic spectroscopy and it was shown to do a very good job on molecules as well. We have published a work on the ESA spectrum of Mn2+ in ZnS, see K.K. Stavrev and M.C. Zerner, J. Chem. Phys. 102 (1995) 34. Mn2+ is a d5 ion with a well resolved sextet ground state (in weak and moderately strong crystal fields). The excited states are quartets and doublets. The lowest excited state 4T1(a) lies about 2.5 eV above the ground state and the emission from it to the 6A1 ground state is spin- and symmetry forbidden in Td. Therefore, ESA spectra become available from this long-living (~1 ms) excited state to the higher lying states. We were able to reproduce the ESA spectrum in conjunction with the expected Jahn-Teller motion for the excited state structures. We have done a similar work on the spectroscopy of VCl4, Chem. Phys. Lett. 263 (1996) 667. Note that in these cases CI-singles was enough to get the reference state, but this is not always so - for example, one would need CISD (CI singles and doubles) to fully describe the doublet states of Mn2+ from a sextet SCF reference. Most of the above work uses ROHF (restricted open-shell Hartree-Fock) supplemented by CIS to get the proper reference state. HyperChem explores RHF as a SCF method in the Zindo/S implementation. The Zindo/S parameters are obtained using CIS (singly excited configuration interactions) and they are expected to give best performance at this (CIS) level of theory. There are many exceptions to this rule, however, see, for example, our work in IJQC 22 (1995) 155; 63 (1997) 781; 65 (1997) 877. A review article on the INDO/S model in Theoretical Inorganic Spectroscopy, Solomon & Lever, Eds., is under way. If you wish, I'll let you know the exact reference of this paper when it becomes available. Regards, Krassimir --- Krassimir Stavrev, PhD, Director of Scientific Support Hypercube, Inc. Florida Science and Technology Park 1115 N.W. 4th Street Gainesville, Florida 32601 Voice:(352) 371-7744/(800) 960-1871 Fax:(352) 371-3662 -----Original Message----- From: malahov@mem1.ilc.msu.su [SMTP:malahov@mem1.ilc.msu.su] Sent: Thursday, December 25, 1997 2:45 PM To: hyperchem@hyper.com Subject: ESA calculation Dear Chemists ! I am interested in excited state absorption (ESA) spectra calculations. Prof. Zerner told me that ZINDO with PSDCI can perform such type calculation. So is it possible to calculate the ESA spectra with the help ZINDO included into HYPERCHEM. As I know HYPERCHEM can perform only single excited CI, but I am not sure. If it really possible I would like to buy this software. Best regards Phd. st. Dmitry Malakhov International Laser Center of Moscow State University, Moscow, Russia. E-mail to: mal@mem2.ilc.msu.su or malakhoff@hotmail.com