From chemistry-request@server.ccl.net Thu May 24 00:54:32 2001 Received: from mailgw.barc.ernet.in ([202.54.18.131]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f4O4sTS13365 for ; Thu, 24 May 2001 00:54:30 -0400 Received: from apsara.barc.ernet.in (apsara.barc.ernet.in [192.168.1.21]) by mailgw.barc.ernet.in (8.9.3/8.9.3) with ESMTP id KAA41715 for ; Thu, 24 May 2001 10:33:42 +0530 (IST) (envelope-from tapang@apsara.barc.ernet.in) Received: from localhost (tapang@localhost) by apsara.barc.ernet.in (8.9.3/8.9.3) with ESMTP id KAA25939 for ; Thu, 24 May 2001 10:31:19 +0530 Date: Thu, 24 May 2001 10:31:19 +0530 (IST) From: "Dr.Tapan K.Ghanty" To: Subject: Alkali Metal Clusters Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi All, I was wondering if anybody know some reviews or references on Semi-empirical / Ab initio calculations of geometries and energetics of Alkali metal clusters with number of atoms more than 20 and up to 200 or so. All the replies will be summarised. With thanks in advance, Dr. Tapan K. Ghanty E-mail: tapang@apsara.barc.ernet.in Theoretical Chemistry Section Chemistry Division BARC Trombay, Mumbai 400 085 India From chemistry-request@server.ccl.net Wed May 23 20:10:06 2001 Received: from imc01.ex.nus.edu.sg ([137.132.14.60]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f4O0A5S06377 for ; Wed, 23 May 2001 20:10:06 -0400 Received: by imc01.ex.nus.edu.sg with Internet Mail Service (5.5.2653.19) id ; Thu, 24 May 2001 08:10:04 +0800 Message-ID: From: Novak Igor To: "'chemistry@ccl.net'" Subject: UVCD software Date: Thu, 24 May 2001 08:10:03 +0800 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2653.19) Content-Type: text/plain; charset="ISO-8859-1" Dear netters, I would be grateful if someone can suggest to me the software (freeware or commercial) which predict the UVCD spectra of a given molecule. Many thanks!! Yours sincerely I.Novak Dept.of Chemistry National University of Singapore Singapore 117543 chmigorn@nus.edu.sg From chemistry-request@server.ccl.net Wed May 23 18:43:35 2001 Received: from canter-n-siegel.schrodinger.com ([192.156.98.248]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f4NMhYS04738 for ; Wed, 23 May 2001 18:43:34 -0400 Received: (from announce@localhost) by canter-n-siegel.schrodinger.com (8.8.5/8.8.5) id PAA18825 for chemistry@ccl.net; Wed, 23 May 2001 15:43:31 -0700 Message-Id: <200105232243.PAA18825@canter-n-siegel.schrodinger.com> Subject: ANNC: Schrodinger Seminar on Computational Drug Design and Drug Discovery To: chemistry@ccl.net Date: Wed, 23 May 2001 15:43:30 -0700 (PDT) From: Schrodinger Announcements Reply-to: "Hege S. Beard" X-Mailer: ELM [version 2.5 PL0b2] MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear Colleague, Schrodinger, Inc. cordially invites you to a half-day seminar on setting new standards in computational drug design and drug discovery. Please join us for an informal morning with talks and discussion on topics that are of interest to you, including recent breakthroughs in structure-based drug design and virtual screening. Speakers include top scientists from well-known pharmaceutical and biopharmaceutical companies in the US. Seminars will be hosted in two locations on the East Coast and two locations on the West Coast as listed below. Seminars will run from 9:00AM - 1:00PM. Complete agendas will be posted on our website when they become available. Complementary breakfast and lunch will be served at all events. June 14 Boston, MA June 19 Princeton, NJ June 20 San Francisco, CA June 21 San Diego, CA Please take a moment to reserve a place using the form at our web site http://www.schrodinger.com/Announce/Registration/Workshop2001/fd_annc.html There is no charge for attending the meeting, but space is limited. Registration deadline is June 1, 2001. If you have any questions, please contact Hege S. Beard at hege@schrodinger.com, or by phone at 201-433-2014, ext. 101. -------------------------------------------------------------- If you do not wish to receive future e-mail announcements from Schrodinger, Inc., please send a message to remove@schrodinger.com. From chemistry-request@server.ccl.net Wed May 23 15:40:30 2001 Received: from snap02.snap.synapticcorp.com ([38.232.56.2]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f4NJeUS01539 for ; Wed, 23 May 2001 15:40:30 -0400 Received: by snap02.snap.synapticcorp.com with Internet Mail Service (5.5.2653.19) id ; Wed, 23 May 2001 15:40:25 -0400 Message-ID: <30F61AD0AD65A94E9C86F4779EAD6C5F01F52A@snap02.snap.synapticcorp.com> From: CSudol@synapticcorp.com To: CHEMISTRY@server.ccl.net Cc: MReitman@synapticcorp.com Subject: clogP salt removal Date: Wed, 23 May 2001 15:40:24 -0400 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2653.19) Content-Type: text/plain; charset="iso-8859-1" Dear Help, Is there a program which will remove salt structures from compounds prior to clogP calculation? Sincerely, Chris Sudol Synaptic Pharmaceutical From chemistry-request@server.ccl.net Thu May 24 10:13:22 2001 Received: from smtp1.dti.ne.jp ([202.216.228.36]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f4OEDMS02084 for ; Thu, 24 May 2001 10:13:22 -0400 Received: from b159504364 (PPP124.fukuoka-ip.dti.ne.jp [211.132.92.124]) by smtp1.dti.ne.jp (8.9.3/3.7W) with SMTP id XAA10846 for ; Thu, 24 May 2001 23:13:19 +0900 (JST) Message-ID: <01a001c0e45a$e8efe7c0$7c5c84d3@b159504364> From: "TELKUNI" To: Subject: Summary - The meaning of "SGG" and the use of "PW91" in G98W Date: Thu, 24 May 2001 23:07:44 +0900 MIME-Version: 1.0 Content-Type: text/plain; charset="windows-1252" Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.00.2615.200 X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2615.200 Hi All, Thanks a lot for those who gave me instructions and helpful information. Here I summarize them. And I hope it will be helpful to some others. The original question: > I am a novice user of Gaussian(G98W RevA.7) and have two questions of it. > Any answers, I will appreciate (including additional advice.) > > 1) > I had set the Route Section to calculate CO2 as "# BLYP/6-31G(d) Pop=Reg > Test", > I got the "Initial guess orbital symmetries" as follows: > > Occupied (SGG) (SGG) (SGU) (SGG) (SGU) (PIU) (PIU) (SGG) > (SGU) (PIG) (PIG) > Virtual (PIU) (PIU) (SGG) (SGU) (SGG) (?A) (?A) (SGG) > (SGG) (SGG) (SGG) (SGG) (DLTG) (?A) (DLTG) (PIG) > (PIG) (PIG) (PIG) (PIG) (PIG) (DLTU) (SGU) (SGU) > (SGU) (SGU) (SGU) (DLTU) (PIU) (PIU) (PIU) (PIU) > (PIU) (PIU) > > I don't know the true meaning of these strings PIU, SGG. With the words > "orbital symmetries", I think "PIU" means PI(pi, it's a Greek alphabet) orbital > has the "U" type symmetry, and "SGU" means that SG(sigma, also Greek > alphabet) has the "U" type symmetry. > > Is my guess correct? ... I am wondering because I can't explain "DLTU" by my > guess. > > > 2) > In the G98 User's Reference_2ndEdition, it is written that PW91 has two > meanings: > 1st) Perdew and Wang's 1991 gradient-corrected correlation functional, > 2nd) The Exchange component of Perdew and Wang's 1991functional. > > When I use the key word PW91, for example with the bias 6-31G(d) to calculate > the structure, should I write PW91/6-31G(d) or PW91PW91/6-31G(d) in the > Route Section? --- Answers: --- ***From: Cory Pye Yes, this is correct. DLTU stands for a delta MO with ungerade symmetry, sounds like you are doing a molecule with D_{\infty h} point group with at least d-orbitals in the basis set. A delta bond would be like a pi bond formed between side to side overlap of d-orbitals. For instance, taking the z axis to be the infinite order symmetry axis and the bond between A and B, the dxy(A) and dxy(B) would form a delta bond. ***From: Dominik Horinek Hi Telkuni, DLT == delta? Cheers, Dominik ***From: Stefan Fau Hi Telkuni, DLTU means "Delta ungerade" Stefan ***From: Adam Hixson DLTU would be Delta ungerade, which is also a character in the D infinity h point group. ***From: Shobe, Dave Your guess with the orbitals is correct: the "PI" and "SG" refer to pi and sigma orbital symmetries, and the "U" and "G" refer to orbital symmetries with respect to the center of symmetry of the molecule. You will just see (SG) and (PI) for linear noncentrosymmetric moleucles such as HCN. As for DLT, this refers to delta symmetry. This is introduced by the "(d)" part of the basis set, and refer to orbitals with two nodal planes. In 1st-row compounds only virtual orbitals should have this symmetry. Use of "f"-type polarization functions gives a pair of orbitals with PHI symmetry. Again, "U", and "G" are added when the molecule is centrosymmetric. ***From: Doug Fox The orbitals for a linear molecule are sigma(SG), pi(PI), delta (DLT), etc. For linear molecules with a center of inversion, D(inf)h, then these are further modified as to potential change of sign on inversion, G=gerade for no change and U for ungerade from German. So DLTU is a delta orbital which changes sign on inversion. If you wish both the exchange and correlation terms for PW91 you would indeed specify # PW91PW91/basis .... PW91 by itself is not recognized and you need to specify both an exchange and a correlation functional. ***From: Qadir K. Timergazin Correct. DLTU should be delta-u PW91PW91/6-31G(d) is correct, PW91/6-31G(d) just doesn't work. by PW91PW91 you specify both parts - correlation and exchange. From chemistry-request@server.ccl.net Thu May 24 10:37:53 2001 Received: from ucidoor.unitedcatalysts.com ([208.23.162.2]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f4OEbrS02574 for ; Thu, 24 May 2001 10:37:53 -0400 Received: by ucidoor.unitedcatalysts.com; (8.8.8/1.3/10May95) id KAA25559; Thu, 24 May 2001 10:37:52 -0400 (EDT) Received: from 10.1.0.50 by ucismtp02.unitedcatalysts.com (InterScan E-Mail VirusWall NT); Thu, 24 May 2001 10:38:09 -0400 (Eastern Daylight Time) Received: from lvlxch01.unitedcatalysts.com ([10.16.100.88]) by lvlmail.unitedcatalysts.com (PMDF V6.0-24 #41777) with ESMTP id <0GDU00C2AGFTXL@lvlmail.unitedcatalysts.com> for chemistry@ccl.net; Thu, 24 May 2001 10:33:29 -0400 (EDT) Received: by lvlxch01.unitedcatalysts.com with Internet Mail Service (5.5.2650.21) id ; Thu, 24 May 2001 10:38:02 -0400 Content-return: allowed Date: Thu, 24 May 2001 10:37:51 -0400 From: "Shobe, Dave" Subject: RE: CCL:CAS Registry Numbers algorithm To: "'CCL'" Message-id: <157A51F55AAAD3119CD70008C7B1629DDAAF0C@lvlxch01.unitedcatalysts.com> MIME-version: 1.0 X-Mailer: Internet Mail Service (5.5.2650.21) Content-type: text/plain; charset=iso-8859-1 Come to think of it: the algorithm might catch transposition errors, but a single-digit error such as 5555-31-7 vs. 5555-81-7 would not be detected, if the digits differ by 5 in an even position, or if they differ by an even number in the 5th position. The ISBN algorithm doesn't have this problem since 11 is prime. However any error the 11th digit would be completely undetectable. You could fix this I suppose by only using digit multipliers that are prime relative to the base. Thus an improved(?) CAS RN algorithm would take 1234-31-? and calculate 1*1+3*3+4*7+3*9+2*11+1*13. However, now the multiplers for adjacent digits would differ by 2 or 4 instead of 1, and a transposition of the type 5555-38-7 vs. 5555-83-7 would not be detected since 3*8+3=27 and 3*3+8=17. --David Shobe -----Original Message----- From: Jacobo Cruces Colado [mailto:qocruces@usc.es] Sent: Thursday, May 24, 2001 9:36 AM To: Shobe, Dave Subject: Re: CCL:CAS Registry Numbers algorithm >The algorithm described will catch transposition errors, since in xxabx-xx-x >the "ab" will contribute (k)b + (k+1)a and in xxbax-xx-x the "ba" will >contribute (k)a + (k+1)b. ("k" here representing the position of the 2nd of >the transposed digits). For these to make equal contributions to the >checksum, (k)b + (k+1)a = (k)a + (k+1)b implies a = b. However, the CAS RN people advices the algorithm to be defective. Apparently, about 17% of the CAS RN could be misschecked. It should be possible to make a hypothetic algorithm for these numbers which avoids any problem of this kind? From chemistry-request@server.ccl.net Thu May 24 12:28:04 2001 Received: from exegrnnts005.seattleu.edu ([206.81.198.91]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f4OGS3S04485 for ; Thu, 24 May 2001 12:28:04 -0400 Received: by exegrnnts005.seattleu.edu with Internet Mail Service (5.5.2653.19) id ; Thu, 24 May 2001 09:27:53 -0700 Message-ID: <2CB090FC30192549B04101547F33E93F0362FFA9@exegrnnts005.seattleu.edu> From: "Jackels, Susan" To: "'chemistry@ccl.net'" Subject: 56th ACS Northwest Regional Meeting -- Symposia Date: Thu, 24 May 2001 09:27:52 -0700 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2653.19) Content-Type: text/plain; charset="iso-8859-1" Dear ccl'ers, If you are interested in attending a meeting in Seattle in June, check the following web site: http://www.chem.plu.edu/norm Click on the program and abstract book to see the several symposia of interest to computational chemists. Thanks. Sue Jackels General Co-chair NORM 2001 From chemistry-request@server.ccl.net Thu May 24 20:05:53 2001 Received: from iris.sipp.ac.cn ([202.127.25.14]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f4P05lS12177 for ; Thu, 24 May 2001 20:05:52 -0400 Received: from iris.sipp.ac.cn [202.127.25.100] by iris.sipp.ac.cn with ESMTP (SMTPD32-6.04) id A171FC4C00D2; Fri, 25 May 2001 08:04:01 +0800 Sender: swift@ccl.net Message-ID: <3B0E748B.B93C5A85@iris.sipp.ac.cn> Date: Fri, 25 May 2001 08:04:43 -0700 From: xmao Organization: iris.sipp.ac.cn X-Mailer: Mozilla 4.7C-SGI [en] (X11; I; IRIX 6.3 IP32) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: question about ZPE calculation using GAMESS Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear everyone: I am a novice about GAMESS. I am using GAMESS to get the ZPE. I first optimized the molecule(runtyp=optimize), then use the final structure (the last one from molden animation) as the input for the ZPE calculation(runtyp=hessian), but in the output, it says this is not a stationary point on the PES, I wonder what it means.Does it mean that I do not get the minima. By the way, I also wonder if the values of E, H, G, CV, CP,S in the output have been calibrated with the ZPE, if not, how I can do that. Thanks in advance. Regards, mao xiang