From chemistry-request@ccl.net Mon Apr 19 08:27:29 2004 Received: from mailfilter.college-de-france.fr (mailfilter.college-de-france.fr [193.52.22.7]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i3JDRRuR019682 for ; Mon, 19 Apr 2004 08:27:28 -0500 Received: from mail.college-de-france.fr (mail [192.168.2.3]) by mailfilter.college-de-france.fr (8.12.9/8.12.9) with ESMTP id i3JDPf5h039311 for ; Mon, 19 Apr 2004 15:25:47 +0200 (CEST) (envelope-from nicolas.saettel)at(college-de-france.fr) Received: from college-de-france.fr ([192.168.7.17]) by mail.college-de-france.fr (8.12.9/8.12.9) with ESMTP id i3JDQZCJ077434 for ; Mon, 19 Apr 2004 15:26:35 +0200 (CEST) (envelope-from nicolas.saettel)at(college-de-france.fr) Message-ID: <4083D3EE.2000309)at(college-de-france.fr> Date: Mon, 19 Apr 2004 15:28:14 +0200 From: Nicolas Saettel Organization: =?ISO-8859-1?Q?Coll=E8ge_de_France?= User-Agent: Mozilla Thunderbird 0.5 (Windows/20040207) X-Accept-Language: en-us, en, fr MIME-Version: 1.0 To: chemistry)at(ccl.net Subject: DNP in DMol <--> 6-31G** in Gaussian? Content-Type: multipart/alternative; boundary="------------080003040308040708020004" X-Spam-Status: No, hits=2.4 required=7.5 tests=HTML_30_40,HTML_MESSAGE, HTML_TITLE_EMPTY,NO_RDNS2 autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net This is a multi-part message in MIME format. --------------080003040308040708020004 Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 8bit Hi all, I would like to reproduce LDA calculations that were done using the double numerical basis set with polarization functions in DMol (DNP). Am I correct in using SVWN/6-31G** in Gaussian? Thank you in advance Nicolas Saettel -- Nicolas Saettel, Ph.D. http://nicolas.saettel.free.fr Laboratoire de Chimie des Interactions Moliculaires CNRS UPR 285 - Collhge de France http://www.college-de-france.fr/chaires/chaire10/index.htm 11, Place Marcelin Berthelot - 75005 PARIS Tel.: 01.44.27.13.63 FAX.: 01.44.27.13.56 --------------080003040308040708020004 Content-Type: text/html; charset=us-ascii Content-Transfer-Encoding: 7bit Hi all,
I would like to reproduce LDA calculations that were done using the double numerical basis set with polarization functions in DMol (DNP). Am I correct in using SVWN/6-31G** in Gaussian?
Thank you in advance
Nicolas Saettel

--
signature Nicolas Saettel, Ph.D. http://nicolas.saettel.free.fr
Laboratoire de Chimie des Interactions Moléculaires
CNRS UPR 285 - Collège de France
http://www.college-de-france.fr/chaires/chaire10/index.htm 11, Place Marcelin Berthelot - 75005 PARIS
Tel.: 01.44.27.13.63 FAX.: 01.44.27.13.56

--------------080003040308040708020004-- From chemistry-request@ccl.net Mon Apr 19 10:45:11 2004 Received: from mail2.atl.registeredsite.com (mail2.atl.registeredsite.com [64.224.219.76]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i3JFjAuR000459 for ; Mon, 19 Apr 2004 10:45:10 -0500 Received: from imta01a2.registeredsite.com (imta01a2.registeredsite.com [64.225.255.10]) by mail2.atl.registeredsite.com (8.12.8/8.12.8) with ESMTP id i3JFjqLM027188; Mon, 19 Apr 2004 15:45:52 GMT Received: from [128.230.29.245] by imta01a2.registeredsite.com with ESMTP id <20040419154552.UVVJ3344.imta01a2.registeredsite.com@[128.230.29.245]>; Mon, 19 Apr 2004 11:45:52 -0400 In-Reply-To: <4083D3EE.2000309(at)college-de-france.fr> References: <4083D3EE.2000309(at)college-de-france.fr> Mime-Version: 1.0 (Apple Message framework v613) Content-Type: text/plain; charset=ISO-8859-1; format=flowed Message-Id: Cc: Damian Gregory Allis From: Damian Gregory Allis Subject: Re: CCL:DNP in DMol <--> 6-31G** in Gaussian? Date: Mon, 19 Apr 2004 11:45:52 -0400 To: Nicolas Saettel , chemistry(at)ccl.net X-Mailer: Apple Mail (2.613) X-Spam-Status: No, hits=0.0 required=7.5 tests=none autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id i3JFjBuR000463 Greetings, Nicolas I've had quite a bit of experience using DMol3 (at NCSA) and GGA functionals for calculating inelastic neutron scattering spectra and examining the deformation of rigid molecules in the solid-state, which also means doing side-by-side DMol3 and Gaussian/GAMESS comparisons of isolated molecules for structural comparisons. Generally speaking, dnp and 6-31G** (as reported in the Delley papers as well) line up the best from among all available choices. That said, I've not had an experience yet where the DMol3 geometries were closer to crystallographic distances than the Gaussian/GAMESS jobs. The standard molecular treatments of the "familiar" atom-centered QC packages simply do a better job of getting the structure right in the 7 or so systems I've worked on, so be less concerned with the DMol v.s. Gaussian/GAMESS structures and more concerned with those same comparisons to any structural data you have. The DMol3 normal mode calculations, however, do a phenomenal job of reproducing the vibrational spectra and intensities in the INS work despite having slightly worse geometries. For a useful geometry comparison, I direct you to the pagodane paper below. The BH4 paper below is biased towards frequencies only but provides another useful comparison. Unfortunately, I've not played around much with the LDA functionals, so can't provide any useful info about differences you'll see there. Allis D.G., Prinzbach H., and Hudson B.S. "Inelastic Neutron Scattering Spectra of Pagodane: Experiment and DFT Calculations." Chemical Physics Letters, 386 (2004) 356-363. Allis D.G. and Hudson B.S. "Inelastic Neutron Scattering Spectra of NaBH4 and KBH4: Reproduction of Anion Mode Shifts via Periodic DFT." Chemical Physics Letters, 385 (2004) 166-172. cheers, Damian On Apr 19, 2004, at 9:28 AM, Nicolas Saettel wrote: > Hi all, > I would like to reproduce LDA calculations that were done using the > double numerical basis set with polarization functions in DMol (DNP). > Am I correct in using SVWN/6-31G** in Gaussian? > Thank you in advance > Nicolas Saettel > > > -- > Nicolas Saettel, Ph.D. http://nicolas.saettel.free.fr > Laboratoire de Chimie des Interactions Moliculaires > CNRS UPR 285 - Collhge de France > http://www.college-de-france.fr/chaires/chaire10/index.htm 11, Place > Marcelin Berthelot - 75005 PARIS > Tel.: 01.44.27.13.63 FAX.: 01.44.27.13.56 > #8^(=)+< p.s. Damian apologizes for the delay. Locale : www.somewhereville.com Delivery : damian(at)somewhereville.com AOL IM : swville "You don't need money to be rich anyhow. Spending yourself is what it's all about." -Marillion, "Rich" From chemistry-request@ccl.net Mon Apr 19 14:31:45 2004 Received: from eved.chem.jyu.fi (eved.chem.jyu.fi [130.234.8.44]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i3JJVhuR011245 for ; Mon, 19 Apr 2004 14:31:43 -0500 Received: from [130.234.240.56] (comp56.hnet.jyu.fi [130.234.240.56]) by eved.chem.jyu.fi (8.11.6/8.11.6) with ESMTP id i3JIubd08355 for ; Mon, 19 Apr 2004 21:56:41 +0300 Mime-Version: 1.0 (Apple Message framework v613) To: CCL Message-Id: <4AD30C10-9238-11D8-B1CE-000393A3609A-.at.-cc.jyu.fi> Content-Type: multipart/alternative; boundary=Apple-Mail-1-1016732804 From: Jussi Eloranta Subject: Announcement: coherent control of chemical events (2004) Date: Mon, 19 Apr 2004 22:32:27 +0300 X-Mailer: Apple Mail (2.613) X-Spam-Status: No, hits=0.6 required=7.5 tests=HTML_MESSAGE,MK_BAD_HTML_04, MY_HTML_OBFU autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net --Apple-Mail-1-1016732804 Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=WINDOWS-1252; format=flowed Dear CCL members, I am pleased to announce the Jyv=E4skyl=E4 Summer School 2004 / = chemistry=20 program: Coherent Control of Chemical Events (CH1) Time: 14 hours during 23 =96 27 Aug 2004 Location: University of Jyv=E4skyl=E4, Jyv=E4skyl=E4, = Finland. Lecturer: Prof. David Tannor (Weizmann Institute of = Science, Israel) Course credits: ECTS 4 cr (equivalent to 2 study weeks in = Finland) Registration: http://www.jyu.fi/summerschool Contacts: Jussi Eloranta (eloranta-.at.-jyu.fi) and Juha Ruuska=20= (jss-.at.-cc.jyu.fi) Course outline: Introduction to wavepacket dynamics (4 hours of lectures) 1. Introduction to the time dependent Schr=F6dinger equation 2. Gaussian wavepackets 3. The Wigner representation 4. Wavepacket correlation functions and spectra Passive control of chemical reactions (4 hours of lectures) 1. Time dependent perturbation theory 2. Femtosecond pump and probe experiments 3. Absorption and resonance Raman spectroscopy 4. Rabi solution, FVH representation, dressed states Active Control of Chemical Reactions (6 hours of lectures) 1. Pump-dump control of reaction products 2. Optimal control of chemical reactions 3. STIRAP and local optimization 4. Interfering pathway control 5. Pulse shaping, learning algorithms, and mechanism Additional homework and related reading will be distributed during the=20= lectures. Jussi Eloranta (eloranta-.at.-jyu.fi) Department of Chemistry University of Jyv=E4skyl=E4 Finland --Apple-Mail-1-1016732804 Content-Transfer-Encoding: quoted-printable Content-Type: text/enriched; charset=WINDOWS-1252 Dear CCL members, I am pleased to announce the Jyv=E4skyl=E4 Summer School 2004 / = chemistry program: Times Coherent Control of Chemical Events (CH1) Time: 14 hours during 23 =96 27 Aug 2004 Location: University of Jyv=E4skyl=E4, Jyv=E4skyl=E4, = Finland.=20 Lecturer: Prof. David Tannor (Weizmann Institute of = Science, Israel) Course credits: ECTS 4 cr (equivalent to 2 study weeks in = Finland) Registration: = 0000,0000,FFFFhttp://www.jyu.fi/summersch= ool Contacts: Jussi Eloranta = (0000,0000,FFFFeloranta-.at.-jyu.fi) and Juha Ruuska (jss-.at.-cc.jyu.fi) Course outline: Times TimesIntroduction to wavepacket dynamics (4 hours of lectures) 1. Introduction to the time dependent Schr=F6dinger equation 2. Gaussian wavepackets 3. The Wigner representation=20 4. Wavepacket correlation functions and spectra Passive control of chemical reactions (4 hours of lectures) 1. Time dependent perturbation theory 2. Femtosecond pump and probe experiments 3. Absorption and resonance Raman spectroscopy 4. Rabi solution, FVH representation, dressed states Active Control of Chemical Reactions (6 hours of lectures) 1. Pump-dump control of reaction products 2. Optimal control of chemical reactions 3. STIRAP and local optimization 4. Interfering pathway control 5. Pulse shaping, learning algorithms, and mechanism Times Additional homework and related reading will be distributed during the lectures. =20 Jussi Eloranta (eloranta-.at.-jyu.fi) Department of Chemistry University of Jyv=E4skyl=E4 Finland = --Apple-Mail-1-1016732804-- From chemistry-request@ccl.net Mon Apr 19 15:40:32 2004 Received: from postoffice6.mail.cornell.edu (postoffice6.mail.cornell.edu [132.236.56.21]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i3JKeWuR013724 for ; Mon, 19 Apr 2004 15:40:32 -0500 Received: from webmail.cornell.edu (hermes8.mail.cornell.edu [132.236.56.35]) by postoffice6.mail.cornell.edu (8.12.10/8.12.6) with SMTP id i3JKfNZZ015639 for ; Mon, 19 Apr 2004 16:41:23 -0400 (EDT) Received: from 129.123.250.158 (SquirrelMail authenticated user rlw28) by webmail.cornell.edu with HTTP; Mon, 19 Apr 2004 16:41:22 -0400 (EDT) Message-ID: <4316.129.123.250.158.1082407282.squirrel(at)webmail.cornell.edu> Date: Mon, 19 Apr 2004 16:41:22 -0400 (EDT) Subject: converting an sdf database into a chemfinder database From: "Richard L. Wood" To: chemistry(at)ccl.net User-Agent: SquirrelMail/1.4.2 MIME-Version: 1.0 Content-Type: text/plain;charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-Priority: 3 Importance: Normal X-Spam-Status: No, hits=2.0 required=7.5 tests=FROM_ENDS_IN_NUMS, PRIORITY_NO_NAME autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Hi all I'm wondering if there is anyway to convert an sdf database into something that Chemfinder can read easily. Chemfinder is supposed to be able to import sdf databases, but the file I have must not be formatted correctly, because chemfinder can't read it. Thanks in advance, Richard