From av@ocirs4.unizh.ch Wed Jul 13 09:55:33 1994 Received: from rzusuntk.unizh.ch for av@ocirs4.unizh.ch by www.ccl.net (8.6.9/930601.1506) id JAA03480; Wed, 13 Jul 1994 09:14:18 -0400 Received: from ocirs4.unizh.ch by rzusuntk.unizh.ch (4.1/SMI-4.1.9) id AA22960; Wed, 13 Jul 94 15:15:15 +0200 Received: by ocirs4.unizh.ch (AIX 3.2/UCB 5.64/4.03) id AA11148; Wed, 13 Jul 1994 14:15:14 +0100 Date: Wed, 13 Jul 1994 14:15:14 +0100 From: av@ocirs4.unizh.ch (Alexander Voityuk) Message-Id: <9407131315.AA11148@ocirs4.unizh.ch> To: chemistry@ccl.net Subject: PF6- in MNDO/d MNDO/d gives other results for PF6- as presented in output by E.Fleischman from Cray Research Inc. Right output follows: GEOMETRY OPTIMIZATION FOR ENERGY MINIMUM PF6- anion Oh f HEAT OF FORMATION -520.596 KCAL/MOL TOTAL ENERGY -3022.270 EV ELECTRON ENERGY -8525.141 EV NUCLEIC ENERGY 5502.871 EV IONIZATION ENERGY 38.551 EV NET ATOMIC CHARGES AND ORBITAL POPULATIONS ATOM CHARGE S PX PY PZ DX2Y2 DXZ DZ2 DYZ DXY F -.3948 1.866 1.657 1.936 1.936 P 1.3690 .822 .573 .573 .573 .262 .189 .262 .189 .189 F -.3948 1.866 1.936 1.657 1.936 F -.3948 1.866 1.936 1.936 1.657 F -.3948 1.866 1.936 1.936 1.657 F -.3948 1.866 1.936 1.657 1.936 F -.3948 1.866 1.657 1.936 1.936 FINAL VARIABLES AND GRADIENTS I 1 X(I) 1.70144 G(I) .01141 FINAL OPTIMIZED GRADIENT NORM .01141 FINAL CARTESIAN GRADIENT NORM .00466 ATOM ATOMIC BOND LENGTH BOND ANGLE TWIST ANGLE NUMBER NUMBER (ANGSTROMS) (DEGREES) (DEGREES) I NA I NB NA I NC NB NA I NA NB NC 1 9 2 15 1.70144 * 1 3 9 1.70144 90.00000 2 1 4 9 1.70144 90.00000 90.00000 2 1 3 5 9 1.70144 90.00000 -90.00000 2 1 3 6 9 1.70144 90.00000 180.00000 2 1 3 7 9 1.70144 90.00000 180.00000 2 3 1 __________________________________________________________________________________________________________________________ A.Voityuk From elewars@alchemy.chem.utoronto.ca Wed Jul 13 11:53:00 1994 Received: from alchemy.chem.utoronto.ca for elewars@alchemy.chem.utoronto.ca by www.ccl.net (8.6.9/930601.1506) id LAA06477; Wed, 13 Jul 1994 11:27:30 -0400 Received: from localhost (elewars@localhost) by alchemy.chem.utoronto.ca (8.6.4/8.6.4) id LAA19672 for chemistry@ccl.net; Wed, 13 Jul 1994 11:27:38 -0400 Date: Wed, 13 Jul 1994 11:27:38 -0400 From: "E. Lewars" Message-Id: <199407131527.LAA19672@alchemy.chem.utoronto.ca> To: chemistry@ccl.net Subject: TRANSITION STATE OPTIMIZATION When I tried an MP2/6-31G* TS opt with G92, using as input the HF/6-31G* geom and hessian, the job failed with "wrong number of negative eigenvalues: desired= 1, actual= 0." When I tried again with a slightly different geom whowhose MP2 (not HF) freqs showed one imaginary vibration, corresponding to the desired mode, using this MP2 hessian as input, it still failed ("wrong number of...."). Does anyone have any idea what is going on here, and any suggestions? === From EWING@jcvaxa.jcu.edu Wed Jul 13 13:53:01 1994 Received: from jcvaxa for EWING@jcvaxa.jcu.edu by www.ccl.net (8.6.9/930601.1506) id NAA10931; Wed, 13 Jul 1994 13:43:03 -0400 Received: from jcvaxa.jcu.edu by jcvaxa.jcu.edu (PMDF V4.3-7 #6158) id <01HENRGCRAPC90MV68@jcvaxa.jcu.edu>; Wed, 13 Jul 1994 13:46:19 EST Date: Wed, 13 Jul 1994 13:46:18 -0500 (EST) From: "DAVID W. EWING (216) 397-4742" Subject: Summary: enforcing symmetry in MOPAC93 To: chemistry@ccl.net Message-id: <01HENRGCTZ5E90MV68@jcvaxa.jcu.edu> X-VMS-To: IN%"chemistry@ccl.net" X-VMS-Cc: EWING MIME-version: 1.0 Content-type: TEXT/PLAIN; CHARSET=US-ASCII Content-transfer-encoding: 7BIT Last week I asked the following question on CCL: We cannot seem to enforce symmetry in some of our optimizations. Sample input [and output are] given below. Any suggestions? Thank you in advance for any thoughts anyone may have on this! -------------------------------------------------------------- MNDO SYMMETRY EF DI PERFLUORO METHYL ETHER O C 1.4 1 C 1.4 0 130 1 1 2 F 1.3 1 110 1 60 0 2 1 3 F 1.3 0 110 0 180 0 2 1 3 F 1.3 0 110 0 300 0 2 1 3 F 1.3 0 110 0 60 0 3 1 2 F 1.3 0 110 0 180 0 3 1 2 F 1.3 0 110 0 300 0 3 1 2 0 0.0 0 0 0 0 0 0 0 0 2, 1, 3 4, 1, 5, 6, 7, 8, 9 4, 2, 5, 6, 7, 8, 9 --------------------------------------------------- Thank you to the many folks who responded. The problem was simply too many blank lines (only one is needed, the line of zeros counts as a blank line). There is an error in the MOPAC93 manual on p. 49. The example there shows two blank lines. Dave Ewing John Carroll University ewing@jcvaxa.jcu.edu From toukie@zui.unizh.ch Wed Jul 13 15:53:05 1994 Received: from rzusuntk.unizh.ch for toukie@zui.unizh.ch by www.ccl.net (8.6.9/930601.1506) id PAA13199; Wed, 13 Jul 1994 15:43:52 -0400 Received: by rzusuntk.unizh.ch (4.1/SMI-4.1.9) id AA01578; Wed, 13 Jul 94 21:44:51 +0200 X-Nupop-Charset: Swiss Date: Wed, 13 Jul 1994 21:44:12 +0100 (MET) From: "Hr. Dr. S. Shapiro" Sender: toukie@zui.unizh.ch Reply-To: toukie@zui.unizh.ch Message-Id: <78253.toukie@zui.unizh.ch> To: chemistry@ccl.net, toukie@zui.unizh.ch Subject: MOPAC calcn. of some reaction indices Dear Colleagues; I would like to calculate the following indices of reactivity for some phenolic derivatives: Sum of electrophilic superdelocalisabilities, Si(E) Sum of nucleophilic superdelocalisabilities, Si(N) pi-eloectron densities on oxygen, qo Sum of pi-electron charges, | From toukie@zui.unizh.ch Wed Jul 13 15:57:50 1994 Received: from rzusuntk.unizh.ch for toukie@zui.unizh.ch by www.ccl.net (8.6.9/930601.1506) id PAA13205; Wed, 13 Jul 1994 15:44:02 -0400 Received: by rzusuntk.unizh.ch (4.1/SMI-4.1.9) id AA01582; Wed, 13 Jul 94 21:44:57 +0200 X-Nupop-Charset: Swiss Date: Wed, 13 Jul 1994 21:44:18 +0100 (MET) From: "Hr. Dr. S. Shapiro" Sender: toukie@zui.unizh.ch Reply-To: toukie@zui.unizh.ch Message-Id: <78258.toukie@zui.unizh.ch> To: chemistry@ccl.net, toukie@zui.unizh.ch Subject: MOPAC calcn. of some reactivity indices Dear Colleagues; I would like to calculate the following indices of reactivity for some phenolic derivatives: Sum of electrophilic superdelocalisabilities, Si(E) Sum of nucleophilic superdelocalisabilities, Si(N) pi-electron densities on oxygen, qo Sum of pi-electron charges, |Qi| I have a reference in which the above indices were calculated for phenol using a simple HMO method, with the following results: Sum of Si(E) = 6.33502 Sum of Si(N) = 4.85500 qo = 1.94002 Sum of | From toukie@zui.unizh.ch Wed Jul 13 16:02:24 1994 Received: from rzusuntk.unizh.ch for toukie@zui.unizh.ch by www.ccl.net (8.6.9/930601.1506) id PAA13221; Wed, 13 Jul 1994 15:44:26 -0400 Received: by rzusuntk.unizh.ch (4.1/SMI-4.1.9) id AA01629; Wed, 13 Jul 94 21:45:17 +0200 X-Nupop-Charset: Swiss Date: Wed, 13 Jul 1994 21:44:35 +0100 (MET) From: "Hr. Dr. S. Shapiro" Sender: toukie@zui.unizh.ch Reply-To: toukie@zui.unizh.ch Message-Id: <78275.toukie@zui.unizh.ch> To: chemistry@ccl.net, toukie@zui.unizh.ch Subject: MOPAC calcn. of reactivity indices Dear Colleagues; I would like to perform AM1 or PM3 calculations of the following indices of reactivity for some phenolic compounds: Sum of electrophilic superdelocalisabilities, Si(E) Sum of nucleophilic superdelocalisabilities, Si(N) pi-electron densities on oxygen, qo Sum of pi-electron charges, |Qi| I have a reference giving these values for phenol calculated using a simple HMO method: Sum of Si(E) = 6.33502 Sum of Si(N) = 4.85500 qo = 1.94002 Sum of |Qi| = 0.21862 The software I have at my disposal is a DOS version of MOPAC 6.0 and Hyper- Chem 3.0 for Windows. I would like to know, firstly, if AM1 or PM3 calcu- lations of these indices of reactivity can be done using this software. If these calculations can indeed be done, then I would be most grateful if someone could explain in detail how to go about performing them. (The more explicit, the better.) Thanks to all responders in advance. Sincerely, S. Shapiro Institut fuer orale Mikrobiologie Zentrum fuer Zahn-, Mund- und Kieferheilkunde der Universitaet Zuerich Plattenstrasse 11 Postfach CH-8028 Zuerich, Switzerland Internet: toukie@zui.unizh.ch FAX-nr: ( ... +1) 261'56'83 From toukie@zui.unizh.ch Wed Jul 13 16:03:17 1994 Received: from rzusuntk.unizh.ch for toukie@zui.unizh.ch by www.ccl.net (8.6.9/930601.1506) id PAA13210; Wed, 13 Jul 1994 15:44:10 -0400 Received: by rzusuntk.unizh.ch (4.1/SMI-4.1.9) id AA01608; Wed, 13 Jul 94 21:45:07 +0200 X-Nupop-Charset: Swiss Date: Wed, 13 Jul 1994 21:44:24 +0100 (MET) From: "Hr. Dr. S. Shapiro" Sender: toukie@zui.unizh.ch Reply-To: toukie@zui.unizh.ch Message-Id: <78265.toukie@zui.unizh.ch> To: chemistry@ccl.net, toukie@zui.unizh.ch Subject: MOPAC calcn. of some reactivity indices Dear Colleages; I would like to calculate the following indices of reactivity for some phenolic derivatives using AM1 or PM3: Sum of electrophilic superdelocalisabilities, Si(E) Sum of nucleophilic superdelocalisabilities, Si(N) pi-electron densities on oxygen, qo Sum of pi-electron charges, |Qi| I have a reference giving these values for phenol using a simple HMO method: Sum of Si(E) = 6.33502 Sum of Si(N) = 4.85500 qo = 1.94002 Sum of |Qi| = 0.21862 The software I have at my disposal is a DOS version of MOPAC 6.0 and HyperChem 3.0 (Windows 3.1). I would be most grateful if someone could advise me, firstly, if it is possible to calculate the above indices of reactivity via AM1 or PM3 using either MOPAC 6.0 and/or HyperChem 3.0. If it is indeed possible to calculate these indices with the software available to me, could you please explain how I go about doing so? (The more explicit, the better.) Thanks to all responders in advance! Sincerely, S. Shapiro Institut fuer orale Mikrobiologie Zentrum fuer Zahn-, Mund- und Kieferheilkunde der Universitaet Zuerich Plattenstrasse 11 Postfach CH-8028 Zuerich, Switzerland Internet: toukie@zui.unizh.ch FAX-nr: ( ... +1) 261'56'83 From AHOLDER@VAX1.UMKC.EDU Wed Jul 13 18:53:04 1994 Received: from vax1.umkc.edu for AHOLDER@VAX1.UMKC.EDU by www.ccl.net (8.6.9/930601.1506) id SAA16003; Wed, 13 Jul 1994 18:10:38 -0400 From: Received: from VAX1.UMKC.EDU by VAX1.UMKC.EDU (PMDF V4.2-11 #4431) id <01HENYNIGOOGA76JFI@VAX1.UMKC.EDU>; Wed, 13 Jul 1994 17:11:25 CST Date: Wed, 13 Jul 1994 17:11:25 -0600 (CST) Subject: SAM1 results for PF6- annion To: CHEMISTRY@ccl.net Message-id: <01HENYNIGOOIA76JFI@VAX1.UMKC.EDU> X-VMS-To: IN%"CHEMISTRY@ccl.net" MIME-version: 1.0 Content-transfer-encoding: 7BIT Dear Netters, Following are the SAM1 results for the PF6- anion. SAM1 does include d-orbitals for heavier main group elements as well as for the transition metals. It should be kept in mind that semiempirical methods are best applied to predict TRENDS, so basing the feasibility of a study on one molecule is sometimes not a good idea. Andy Holder -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= DR. ANDREW HOLDER Assistant Professor of Computational/Organic Chemistry Department of Chemistry || Internet Addr: aholder@vax1.umkc.edu Univ. of Missouri - Kansas City || Phone Number: (816) 235-2293 Spencer Chemistry, Room 315 || FAX Number: (816) 235-5502 Kansas City, Missouri 64110 || -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= SUMMARY OF SAM1 CALCULATION 13-Jul-94 AMPAC Version 5.0 Presented by: Semichem, Inc. 7128 Summit Shawnee, KS 66216 (913) 268-3271 (913) 268-3445 (fax) F 6 P PF6- (Oh) by Jie GRADIENT (COMPONENT) TEST WAS SATISFIED IN BFGS OR DFP SCF FIELD WAS ACHIEVED HEAT OF FORMATION = -547.840570 KCAL ELECTRONIC ENERGY = -8574.411317 EV CORE-CORE REPULSION = 5677.742587 EV GRADIENT NORM = 0.000405 DIPOLE = 0.000000 DEBYE NO. OF FILLED LEVELS = 24 CHARGE ON SYSTEM = -1 IONISATION POTENTIAL = 9.533478 EV MOLECULAR POINT GROUP = OH 0.100000 MOLECULAR WEIGHT = 144.964 COMPUTATION TIME = 2.67 SECONDS FINAL GEOMETRY OBTAINED CHARGE SAM1 PRECISE CHARGE=-1 GRAD BONDS T=200 PF6- (Oh) by Jie P 0.000000 0 0.000000 0 0.000000 0 0 0 0 2.1500 F 1.595033 1 0.000000 0 0.000000 0 1 0 0 -0.5250 F 1.595033 1 90.000000 1 0.000000 0 1 2 0 -0.5250 F 1.595033 1 90.000000 1 90.000000 1 1 2 3 -0.5250 F 1.595033 1 90.000000 1 90.000000 1 1 2 4 -0.5250 F 1.595033 1 90.000000 1 90.000000 1 1 2 5 -0.5250 F 1.595033 1 90.000000 1 180.000000 1 1 3 2 -0.5250 0 0.000000 0 0.000000 0 0.000000 0 0 0 0 From aditya!raman@uunet.uu.net Wed Jul 13 19:53:05 1994 Received: from relay3.UU.NET for aditya!raman@uunet.uu.net by www.ccl.net (8.6.9/930601.1506) id TAA16409; Wed, 13 Jul 1994 19:43:19 -0400 Received: from uucp7.UU.NET by relay3.UU.NET with SMTP (relay) id QQwyla06202; Wed, 13 Jul 1994 19:44:15 -0400 Received: from aditya.UUCP by uucp7.UU.NET with UUCP/RMAIL ; Wed, 13 Jul 1994 19:44:31 -0400 Received: by aditya (920330.SGI/911001.SGI) for uunet!ccl.net!CHEMISTRY id AA24282; Wed, 13 Jul 94 16:44:56 -0700 Date: Wed, 13 Jul 94 16:44:56 -0700 From: aditya!raman@uunet.uu.net (K. Ramnarayan) Message-Id: <9407132344.AA24282@aditya> To: uunet!ccl.net!CHEMISTRY@uunet.uu.net Subject: Program stereo from Brookhaven. Dear Netters: Is there a unix version of the program stereo.f distributed by Brookhaven Protein Databank. Thank you for your reply. raman%aditya@uunet.uu.net