From ipcakc@vigyan.ernet.in Fri Aug 9 04:32:09 1993 To: CHEMISTRY@ccl.net Subject: spin-orbit coupling Date: 9 Aug 93 09:32:09 EST (Mon) From: ipcakc@vigyan.iisc.ernet.in Message-Id: <9308090932.AA19368@vigyan.iisc.ernet.in> Dear Netters I am doing some calculations on CH3I excited states. Ab initio or the Hartree-Fock Hamiltonian doesn't have the spin orbit coupling interaction. The excited state of methyl iodide is of E symmetry. I want to trace the individual surfaces of this state with the inclusion of spin-orbit coupling part. Can anyone suggest me of what I should do. Can i do an external single point calculation with the optimised structures whatever i got from ab initio programs. If anyone has any program which can handle spin-orbit coupling, please inform me. Thanking you. I summarise the responses to the netters. SUMATHY. DEPARTMENT OF INORGANIC AND PHYSICAL CHEMISTRY INDIAN INSTITUTE OF SCIENCE, BANGALORE 560 012. e-mail: ipcakc@ipc.iisc.ernet.in From henk@qsar.ritox.dgk.ruu.nl Mon Aug 9 10:20:58 1993 Date: Mon, 09 Aug 1993 11:55:10 MET From: henk@qsar.ritox.dgk.ruu.nl To: CHEMISTRY@ccl.net Message-Id: <00970C34.7FCA34E0.3271@qsar.ritox.dgk.ruu.nl> Subject: problem with thermo calculation in MOPAC6.0 Hi y'all I was wondering whether someone can help me with the following problem: I am trying to do a THERMO calculation in MOPAC 6.0 on a number of SN2 transition states of small electrophiles -- the nucleophile is methylpyridine. The problem is that MOPAC aborts at the entry of the THERMO calculation -- after the completion of the force calculation -- with an error from GMETRY: atoms 2 and 3 coincident; I am at a loss since I can't find them coincident. Here is first an example input file: AM1 force thermo(333,333) rot=1 trans=7 C 0.0000000 0 0.000000 0 0.000000 0 0 0 0 0.0000$ C 1.4041428 1 0.000000 0 0.000000 0 1 0 0 0.0000$ C 1.4003072 1 119.287010 1 0.000000 0 2 1 0 0.0000$ C 1.4787019 1 121.370646 1 -179.994867 1 3 2 1 0.0000$ H 1.1192502 1 110.230685 1 124.298609 1 4 3 2 0.0000$ H 1.1195439 1 110.032513 1 -116.501226 1 4 3 2 0.0000$ C 1.4037482 1 118.199497 1 0.000000 1 3 2 1 0.0000$ C 1.4009409 1 119.290356 1 0.039465 1 7 3 2 0.0000$ N 1.3529391 1 122.343011 1 -0.177708 1 1 2 3 0.0000$ H 1.1129259 1 121.575410 1 179.992907 1 1 2 3 0.0000$ H 1.0994832 1 119.576204 1 -179.857087 1 2 1 3 0.0000$ H 1.0990764 1 120.754405 1 -179.817318 1 7 3 2 0.0000$ H 1.1068320 1 120.886981 1 -179.548230 1 8 7 3 0.0000$ C 1.7541369 1 120.184947 1 174.172535 1 9 1 2 0.0000$ Cl 2.2544495 1 160.940606 1 -112.738292 1 14 9 1 0.0000$ H 1.1103209 1 95.126489 1 179.567668 1 14 9 1 0.0000$ H 1.1119808 1 92.361435 1 -58.682919 1 14 9 1 0.0000$ C 1.5197141 1 103.898555 1 60.979801 1 14 9 1 0.0000$ H 1.1252449 1 109.788566 1 161.861076 1 18 14 9 0.0000$ H 1.1254695 1 111.762008 1 40.940098 1 18 14 9 0.0000$ O 1.4215565 1 111.490261 1 -74.763710 1 18 14 9 0.0000$ C 1.4313250 1 113.395749 1 -81.024090 1 21 18 14 0.0000$ H 1.1243751 1 110.500290 1 45.269409 1 22 21 18 0.0000$ H 1.1244276 1 108.327156 1 -74.045942 1 22 21 18 0.0000$ C 1.5137000 1 107.132811 1 168.044051 1 22 21 18 0.0000$ H 1.1159768 1 110.998031 1 45.566693 1 25 22 21 0.0000$ H 1.1160053 1 109.647984 1 168.077404 1 25 22 21 0.0000$ Cl 1.7592365 1 112.757200 1 -73.536286 1 25 22 21 0.0000$ H 1.1177074 1 111.392507 1 3.805470 1 4 3 2 0.0000$ OK so far. Now next an 'after calculation' cartesian coordinate matrix from the resultant .OUT file: ORIENTATION OF MOLECULE IN FORCE CALCULATION NO. ATOM X Y Z 1 6 1.4089 0.0767 0.2535 2 6 2.8131 0.0767 0.2535 3 6 3.4981 1.2980 0.2535 4 6 4.9758 1.3518 0.2534 5 1 5.3410 1.9573 -0.6142 6 1 5.3421 1.8347 1.1947 7 6 2.7436 2.4818 0.2535 8 6 1.3449 2.4030 0.2544 9 7 0.6851 1.2197 0.2571 10 1 0.8262 -0.8715 0.2534 11 1 3.3558 -0.8795 0.2511 12 1 3.2380 3.4634 0.2505 13 1 0.7242 3.3194 0.2469 14 6 -1.0611 1.1584 0.1029 15 17 -3.1355 1.4067 -0.7443 16 1 -1.2047 2.2577 0.1624 17 1 -1.0023 0.6351 -0.8765 18 6 -1.5067 0.3575 1.3152 19 1 -2.6024 0.5301 1.5041 20 1 -0.9289 0.6416 2.2383 21 8 -1.2305 -1.0277 1.1545 22 6 -2.2068 -1.7139 0.3642 23 1 -2.4567 -1.1192 -0.5567 24 1 -3.1377 -1.8390 0.9825 25 6 -1.6359 -3.0764 0.0343 26 1 -1.1851 -3.5507 0.9383 27 1 -2.4371 -3.7259 -0.3919 28 17 -0.3586 -3.0048 -1.1733 29 1 5.4210 0.3289 0.1843 As far as I can see, atoms 2 and three are separated in space; however, MOPAC aborts after the force calculation, at the entry point for the thermo calculation, with the following error message: ATOMS 2 AND 3 ARE COINCIDENT THIS IS A FATAL ERROR, RUN STOPPED IN GMETRY Am I missing something trivial? I hope someone out there can help me. Many thanks in advance. Henk Verhaar - henk@qsar.ritox.dgk.ruu.nl Research Institute of Toxicology - Utrecht University, the Netherlands From ramon@ce.ifisicam.unam.mx Mon Aug 9 08:41:47 1993 Message-Id: <199308091942.AA28427@oscsunb.ccl.net> From: Ramon Garduno Subject: Question about ProLogP To: chemistry@ccl.net (POST MSGS) Date: Mon, 9 Aug 93 13:41:47 CDT Hello, Does anybody out there know about a program called ProLogP by Compu Drug USA Inc. ? If so, will you be willing to share their address?. Or better yet, does anybody know of any other sources where I can calculate LogP?. Many thanks, -- ________________________________________________________________________ Dr. Ramon Garduno-Juarez Research Professor in Biophysics INSTITUTO DE FISICA, UNAM || bitnet: rgard@unamvm1 Lab. de Cuernavaca || email: ramon@ifisicam.unam.mx Apdo. Postal 139-B || 62191 Cuernavaca, Morelos || FAX: (73)173077 MEXICO || (73)111603 ______________________________ EOF _____________________________________ From dave@carbon.chem.csiro.au Tue Aug 10 04:58:52 1993 Message-Id: <199308092358.AA10211@shark.mel.dit.csiro.au> Date: Tue, 10 Aug 93 09:58:52 EST From: (Dr.) Dave Winkler Subject: Re: Todd Wipke comments on SECS To: chemistry@ccl.net Thanks to Todd Wipke for correcting my comments re SECS. He is correct in that we used the system in the early 80s and we did not have a reliable network. I am pleasantly surprised that SECS is still being used and developed. I would certainly like to obtain more information on its current capabilities and the types of synthetic problems it has been applied to. Who is currently marketing it? Cheers, Dave __________________________________________________________________________ Dr. David A. Winkler Voice: 61-3-542-2244 Principal Research Scientist Fax: 61-3-543-8160 CSIRO Division of Chemicals and Polymers Private Bag 10 Clayton, Australia. "Life is what happens to you while you're making other plans" From ramon@ce.ifisicam.unam.mx Mon Aug 9 15:22:07 1993 Message-Id: <199308100223.AA03575@oscsunb.ccl.net> From: Ramon Garduno Subject: Cremer-Pople puckering To: chemistry@ccl.net (POST MSGS) Date: Mon, 9 Aug 93 20:22:07 CDT Dear netters: Does anybody out there knows where I can find a program written by Larry Madsen that calculates the Cremer-Pople (JACS (1975) V97:1354-1358) puckering parameters for glucopyranoses?. May be there are other versions that someone would like to share. Cheers, -- ________________________________________________________________________ Dr. Ramon Garduno-Juarez Research Professor in Biophysics INSTITUTO DE FISICA, UNAM || bitnet: rgard@unamvm1 Lab. de Cuernavaca || email: ramon@ifisicam.unam.mx Apdo. Postal 139-B || 62191 Cuernavaca, Morelos || FAX: (73)173077 MEXICO || (73)111603 ______________________________ EOF _____________________________________