From chemistry-request@server.ccl.net Sun Jan 13 01:44:11 2002 Received: from mail.iitk.ac.in ([203.200.95.130]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g0D6i9I05006 for ; Sun, 13 Jan 2002 01:44:10 -0500 Received: from antivirus.cc.iitk.ac.in (antivirus.cc.iitk.ac.in [172.31.1.102]) by mail.iitk.ac.in (8.9.3+Sun/8.9.3) with SMTP id MAA20770 for ; Sun, 13 Jan 2002 12:13:40 +0530 (IST) Received: (from bhaskar [172.31.1.7]) by antivirus.cc.iitk.ac.in (NAVGW 2.5.1.6) with SMTP id M2002011312420427582 for ; Sun, 13 Jan 2002 12:42:04 +0530 Date: Sun, 13 Jan 2002 12:12:42 +0530 (IST) From: "97104 Chinmoy Ranjan UG(CHM)." X-Sender: ranjan@bhaskar.cc.iitk.ac.in To: chemistry@ccl.net Subject: Gaussian query Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CClers, I want to do a population analysis for a molecule containing molybdenum using gaussian. The molecule contains around 20 atoms .(Only one Mo atom in the molecule ) What kind of calculations should I go for? If any anybody has doen any kind calculation for Molybdenenum or any other heavy atom using gaussian ? Any kind of suggestion will be highly appreciated. With regards. Chinmoy Ranjan. ****************************************************************************** CHINMOY RANJAN A-216 HALL 1 INDIAN INSTITUTE OF TECHNOLOGY KANPUR - 208016 U.P INDIA No matter what conditions you encounter in life, your right is only to the works--not to the fruits thereof. You should not be impelled to act for selfish reasons, nor should you be attached to inaction. -Bhagavad Gita ****************************************************************************** From chemistry-request@server.ccl.net Sat Jan 12 23:33:10 2002 Received: from web20603.mail.yahoo.com ([216.136.226.161]) by server.ccl.net (8.11.6/8.11.0) with SMTP id g0D4XAI01769 for ; Sat, 12 Jan 2002 23:33:10 -0500 Message-ID: <20020113043302.53444.qmail@web20603.mail.yahoo.com> Received: from [64.130.222.245] by web20603.mail.yahoo.com via HTTP; Sat, 12 Jan 2002 20:33:02 PST Date: Sat, 12 Jan 2002 20:33:02 -0800 (PST) From: Sengen Sun Subject: Mechanism of concerted cycloadditions To: chemistry@ccl.net In-Reply-To: <200107291829.f6TITWd06285@server.ccl.net> MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii I wish to continue the expression of my personal opinions on this subject. I have posted a second paper in the Pre-Print Server at http://preprint.chemweb.com/orgchem/0201002. The paper title is “Playing the Natural Puzzles of Concerted Cycloadditions: What Are the Tricks behind the Scene?” I post here the abstract as some people may be interested. My mechanistic opinions are different from those published in recent debates (J. Phys. Chem. 2001, 105, 10943-10947). I wish to see more opinions and discussions on this topic. Thanks for attention. Sengen ------- Abstract—The mystery of electron flow hides deeply inside the thermodynamic states along the IRC (intrinsic reaction coordinate) of concerted cycloaddition reactions. But the well-known experimental facts of Michael-type additions of alpha,beta-unsaturated carbonyl compounds suggest an electron-withdrawing force at the beta-position and a subsequent electron-donating force at the alpha-position. The similar electron-withdrawing and donating forces were also documented experimentally for 1,3-dipoles. These two forces are discussed as a primary driving force and a complementary driving force for thermal concerted Diels-Alder reactions and 1,3-dipolar cycloadditions. Wave functions (Hartree-Fock orbitals, Kohn-Sham orbitals, valance bond orbitals, etc.) as mathematical constructs solely depend on nuclear positions, while the kinetic electron flow is controlled by the force fields of reactants. A wave function can not confine an electron pair. Each wave function represents an open subsystem that exchanges electron resources with its environment while a reaction proceeds. The electron flowing motion and the change of wave functions along the IRC are two independent events. Their logical relationship can not be clearly established. It is because of the “non-classical” systems that mathematical constructs can not be used to describe the motions of individual electron pairs along a reaction path as we can do in classical systems. Evaluating unsymmetrical colliding structures (far away from the IRC) may provide us an opportunity to examine the nucleophilicity and electrophicility at the reacting sites of reactants for many cycloaddition reactions. The electron flow may be described based on intrinsic kinetic driving forces and hindrances. The experimentally observed interacting forces and those fundamental laws of physics are the most important knowledge that should be respected in the theoretical formulation. __________________________________________________ Do You Yahoo!? Send FREE video emails in Yahoo! Mail! http://promo.yahoo.com/videomail/ From chemistry-request@server.ccl.net Sun Jan 13 16:31:34 2002 Received: from ccmsi.jsums.edu ([143.132.103.54]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g0DLVYI22807 for ; Sun, 13 Jan 2002 16:31:34 -0500 Received: from Falcon [10.30.4.199] by ccmsi.jsums.edu (SMTPD32-7.05) id ACB01600CA; Sun, 13 Jan 2002 15:31:28 -0600 Message-ID: <007601c19c79$a875c1b0$c7041e0a@ccmsi.jsums.edu> From: "Yevgeniy Podolyan" To: Subject: Second Southern School on Computational Chemistry Date: Sun, 13 Jan 2002 15:31:27 -0600 MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 6.00.2600.0000 X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2600.0000 Dear Colleague: Recently, you received an email with an invitation to participate in the Second Southern School on Computational Chemistry, which will be held at the Hampton Inn in beautiful Orange Beach, Alabama (next to Pensacola, FL) on March 22 and 23, 2002 (Friday 2 p.m. - Saturday 10 p.m.). If you have already registered and sent your abstract, thank you. If not, there is still time to do it. BUT HURRY, the last day to submit an abstract is February 1, 2002. For more information and/or to register, please visit our web site at http://ccmsi.jsums.edu/sscc Sincerely, Yevgeniy Podolyan Department of Chemistry Jackson State University Jackson, MS 39217-0510 Tel: (601) 979-4114 Fax: (601) 979-7823 e-mail: podolyan@ccmsi.jsums.edu http://ccmsi.jsums.edu/podolyan From chemistry-request@server.ccl.net Sun Jan 13 22:42:40 2002 Received: from mail.shcnc.AC.CN ([202.127.16.28]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g0E3gcI00979 for ; Sun, 13 Jan 2002 22:42:39 -0500 Received: from PC18 ([202.127.19.225]) by mail.shcnc.AC.CN (8.12.1/8.12.1) with SMTP id g0EIeoDt018753 for ; Mon, 14 Jan 2002 10:40:50 -0800 (PST) Message-Id: <200201141840.g0EIeoDt018753@mail.shcnc.AC.CN> Date: Mon, 14 Jan 2002 11:41:39 +0800 From: bxiong To: "chemistry@ccl.net" Subject: AMBER question!!! X-mailer: FoxMail 3.0 beta 2 [cn] Mime-Version: 1.0 Content-Type: text/plain; charset="GB2312" Content-Transfer-Encoding: 7bit Dear CCLs: I use the AmBER sander.MC Module and I used the Cap water, I do not know the control parameters , can someone give me a copy of the control.in ? By the way, I use the control.in and it quickly died. I do not know why.may be someone know what wrong of it, so I copy the log.out file to you to hope it useful. Here is the input file: # mc/md using sander &cntrl irest=0, ntx=1, ibelly=0, imin=0, nstlim=3100, ntpr=10, t=0.0, dt=0.0020, vlimit=20.0, ntt=1, temp0=300.0, dtemp=0.0, tautp=0.02, ntb=0, ntf=2, igb=2, ntc=2, tol=0.0005, nsnb=20, cut=9.0, scnb=2.0, scee=1.2, ntwr=50, ntwx=500, imcdo = 0, ntr=1, &end &ewald nbflag=1, skinnb = 1.0, eedmeth=4, use_pme=0, vdwmeth=0, verbose=0, &end &cmcmd imcsol = 0, imcfil = 1, imccp = 0, imcew = 0, imcrst = 0, EMCIF = 1.0, EMCNF = 0.0, IMCINT = 0 , emcofe = 1.0d0, emcofn = 1.0d0, imcfrs = 305, imclst = 306, imccur = 305, imcns = 100, imcans = 200, &end Group input for restrained atoms 5.0 RES 1 304 RES 307 328 RES 334 336 RES 527 551 END END begin time read from input coords = 0.000 ps Number of triangulated 3-point waters found: 383 NSTEP = 0 TIME(PS) = 0.000 TEMP(K) = 0.00 PRESS = 0.00 Etot = -13803.1934 EKtot = 0.0000 EPtot = -13803.1934 BOND = 663.6023 ANGLE = 1802.0128 DIHED = 1726.4369 1-4 NB = 1061.8815 1-4 EEL = 12051.2919 VDWAALS = -1983.7956 EELEC = -29124.6232 EHBOND = 0.0000 CONSTRAINT = 0.0000 ------------------------------------------------------------------------------ vlimit exceeded for step 2; vmax = 96.85260855818514 vlimit exceeded for step 3; vmax = 27.87656435858480 vlimit exceeded for step 4; vmax = 2123.093135853720 COORDINATE RESETTING CANNOT BE ACCOMPLISHED, DEVIATION IS TOO LARGE NITER, NIT, LL, I AND J ARE : 0 1 2386 4798 4799 wish you can give me some suggestion!!!! Best regards! bxiong@mail.shcnc.ac.cn Xiong Bin Shanghai Institute of Materia Medica, C.A.S. phone:021-64311833-222(office)