From chemistry-request@ccl.net Fri May 14 17:52:33 2004 Received: from cougar.it.wsu.edu (cougar.it.wsu.edu [134.121.1.10]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i4EMqVkh029869 for ; Fri, 14 May 2004 17:52:32 -0500 Received: from [134.121.44.19] (tyr0.chem.wsu.edu [134.121.44.19]) by cougar.it.wsu.edu (8.12.10/8.12.10) with ESMTP id i4EMssqk483254; Fri, 14 May 2004 15:54:54 -0700 (PDT) In-Reply-To: <200405141606.i4EG6ve24347|at|www4.ctimail.com> References: <200405141606.i4EG6ve24347|at|www4.ctimail.com> Mime-Version: 1.0 (Apple Message framework v613) Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed Message-Id: Content-Transfer-Encoding: 7bit Cc: chemistry|at|ccl.net From: Kirk Peterson Subject: Re: CCL:AUG-cc-pVDZ exponent (CISD?) Date: Fri, 14 May 2004 15:54:49 -0700 To: skpang|at|ctimail.com X-Mailer: Apple Mail (2.613) X-Virus-Scanned: by amavisd-milter (http://amavis.org/) X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net X-Spam-Status: No, hits=0.0 required=7.5 tests=none autolearn=no version=2.61 X-Spam-Level: Patrick, of course the primitives corresponding to the occupied Hartree-Fock orbitals have been optimized at the HF level of theory. The diffuse s and p functions are also optimized at the HF level for the anion, but the diffuse polarization functions (as well as the regular polarization functions) were optimized at the CISD level. Note that the resulting exponents are relatively insensitive to whether CISD, MP2, CCSD(T), etc. are used. best regards, Kirk Peterson On May 14, 2004, at 9:06 AM, skpang|at|ctimail.com wrote: > Dear all, > > Are all exponents of primitive gaussian functions (s, p,d(polarization > function) and diffuse function) in AUG-cc-pVDZ optimized by CISD? > > Best regards, > > Patrick > > My e-mail address is skpang|at|ctimail.com > > > -= This is automatically added to each message by the mailing script =- > To send e-mail to subscribers of CCL put the string CCL: on your > Subject: line > and send your message to: CHEMISTRY|at|ccl.net > > Send your subscription/unsubscription requests to: > CHEMISTRY-REQUEST|at|ccl.net > HOME Page: http://www.ccl.net | Jobs Page: http://www.ccl.net/jobs > > If your mail is bouncing from CCL.NET domain send it to the maintainer: > Jan Labanowski, jlabanow|at|nd.edu (read about it on CCL Home Page) > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+- > +-+ > > > > > > From chemistry-request@ccl.net Fri May 14 17:01:44 2004 Received: from yakko.cimav.edu.mx (yakko.cimav.ecustomer.mx [148.223.46.2] (may be forged)) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i4EM1hkh028102 for ; Fri, 14 May 2004 17:01:43 -0500 Received: from yakko (localhost [127.0.0.1]) by localhost.cimav.edu.mx (Postfix) with ESMTP id 96B181B8012; Fri, 14 May 2004 16:03:57 -0600 (MDT) Received: from localhost ([127.0.0.1]) by yakko.cimav.edu.mx (MailMonitor for SMTP v1.2.2 ) ; Fri, 14 May 2004 16:03:57 -0600 (MDT) Received: from QCOSMO05 (byron.cimav.edu.mx [148.223.46.1]) by yakko.cimav.edu.mx (Postfix) with ESMTP id 9546A1B8014; Fri, 14 May 2004 16:03:55 -0600 (MDT) From: "Dr. Daniel Glossman-Mitnik" To: , , , , Subject: CCL: O3LYP functional in Gaussian 03 Date: Fri, 14 May 2004 16:04:05 -0600 Message-ID: MIME-Version: 1.0 Content-Type: multipart/related; boundary="----=_NextPart_000_0012_01C439CD.15E16B30" X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook, Build 10.0.6626 X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2800.1409 Importance: Normal Disposition-Notification-To: "Dr. Daniel Glossman-Mitnik" X-Spam-Status: No, hits=6.3 required=7.5 tests=COMBINED_FROM,HTML_60_70, HTML_FONTCOLOR_BLUE,HTML_FONTCOLOR_UNKNOWN,HTML_FONT_BIG,HTML_MESSAGE, NO_RDNS2,SUSPICIOUS_RECIPS 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. ------=_NextPart_000_0012_01C439CD.15E16B30 Content-Type: multipart/alternative; boundary="----=_NextPart_001_0013_01C439CD.15E2F1D0" ------=_NextPart_001_0013_01C439CD.15E2F1D0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Dear Phung Quan: =20 If you want to use the O3LYP functional in Gaussian03, you must include IOp(3/74=3D-24) in your route. Please note the minus sign. This = automatically=20 set the coefficients. You will need to also include the desired basis = set in order to build the model chemistry. =20 Best regards =20 Dr. Daniel Glossman-Mitnik=20 =20 *************************************************************************= *** ********************** Dr. Daniel Glossman-Mitnik =20 CIMAV - Centro de Investigaci=F3n en Materiales Avanzados, SC=20 QCOSMO - Grupo de Qu=EDmica Computacional, Simulaci=F3n y Modelado = Molecular Miguel de Cervantes 120 - Complejo Industrial Chihuahua Chihuahua, Chih. 31109 - MEXICO Tel=E9fono: (52) 614 4391151 FAX: (52) 614 4391112 E-mail: daniel.glossman-.at.-cimav.edu.mx dglossman-.at.-prodigy.net.mx =20 P=E1gina WEB: http://www.cimav.edu.mx http://www.qcosmo.org=20 *************************************************************************= *** ***********************=20 =20 ------=_NextPart_001_0013_01C439CD.15E2F1D0 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable

Dear =A0Phung = Quan:

 

If you want to = use the O3LYP functional in Gaussian03, you must include

IOp(3/74=3D-24) = in your route. Please note the minus sign. This automatically

set the = coefficients. You will need to also include the desired basis set in

order to build = the model chemistry.

 

Best = regards

 

=A0=A0=A0=A0=A0=A0= =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0= =A0=A0=A0=A0=A0=A0=A0=A0=A0 Dr. Daniel Glossman-Mitnik

 

****************= *************************************************************************= *********

  &nbs= p;         Dr. Daniel Glossman-Mitnik

 

CIMAV - Centro de Investigaci=F3n en Materiales Avanzados, SC =

QCOSMO - Grupo de Qu=EDmica Computacional, Simulaci=F3n y = Modelado Molecular

Miguel de Cervantes 120 - Complejo Industrial Chihuahua

Chihuahua, Chih. 31109 - = MEXICO

Tel=E9fono: (52) 614 4391151           =      FAX:       (52) 614 = 4391112

P=E1gina WEB:  http://www.cimav.edu.mx  &= nbsp;    http://www.qcosmo.org =

***********************************= **************************************************************** 

 

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acmez.gatech.edu (Postfix) with ESMTP id C444F4FE86 for ; Sat, 15 May 2004 14:19:06 -0400 (EDT) (envelope-from ok16[at]mail.gatech.edu) Date: Sat, 15 May 2004 14:19:06 -0400 (EDT) From: Ohyun Kwon X-X-Sender: Reply-To: Tommy Ohyun Kwon To: Subject: Summary of predicting packing patterns of organic crystals Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Spam-Status: No, hits=1.5 required=7.5 tests=FROM_ENDS_IN_NUMS autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Dear CCLers' I summarized all answers I got about following question of mine. Dear CCLers' I am interested in predicting packing patterns of organic crystals such as benzene and organic conugated oligomers. I would greatly appreciate it if anyone would kindly tell me any informantion, experience, or any program for this purpose. have a great day! Yours, Answers are; 1) the program we use in Nijmegen is Cerius^2 with the Polymorph Predictor module. Not cheap, but often used. Furthermore have a look at these two references: @ARTICLE{Lommerse2000, AUTHOR = "Lommerse, J.P.M. and Motherwell, W.D.S. and Ammon, H.L. and Dunitz, J.D. and Gavezzotti, A. and Hofmann, D.W.M. and Leusen, F.J.J. and Mooij, W.T.M. and Price, S.L. and Schweizer, B. and Schmidt, M.U. and Van Eijck, B.P. and Verwer, P. and Williams, D.E.", TITLE = "A test of crystal structure prediction of small organic molecules", JOURNAL = "Acta Cryst.", YEAR = "2000", VOLUME = "B56", PAGES = "697-714", } and @ARTICLE{Motherwell2002, AUTHOR = "Motherwell, W.D.S and Ammon, H.L. and Dunitz, J.D. and Dzyabchenko, A. and Erk, P. and Gavezzotti, A. and Hofmann, D.W.M. and Leusen, F.J.J. and Lommerse, J.P.M. and Mooij, W.T.M. and Price, S.L. and Scherega, H. and Schweizer, B. and Schmidt, M.U. and Van Eijck, B.P. and Verwer, P. and Williams, D.E.", TITLE = "Crystal Structure Prediction of Small Organic Molecules: a Second Blind Test", JOURNAL = "Acta Cryst.", YEAR = "2002", VOLUME = "B58", PAGES = "647-661", } Egon - -- egonw[at]sci.kun.nl PhD on Molecular Representation in Chemometrics Nijmegen University http://www.cac.sci.kun.nl/people/egonw/ GPG: 1024D/D6336BA6 2) I recommend that you check out the following chapter which deals with your query. P. Verwer and F. J. J. Leusen, in Reviews in Computational Chemistry, K. B. Lipkowitz and D. B. Boyd, Eds., Wiley-VCH, New York, 1998, Vol. 12, pp. 327-365. Computer Simulation to Predict Possible Crystal Polymorphs. Good luck. Donald B. Boyd, Ph.D. Editor Emeritus, Reviews in Computational Chemistry http://chem.iupui.edu/rcc/rcc.html Research Professor of Chemistry Department of Chemistry Indiana University-Purdue University at Indianapolis Indianapolis, Indiana 46202-3274, U.S.A. E-mail boyd[at]chem.iupui.edu 3) see the following for scripts in existing programs, programs, or references. Donovan - Predicting Crystalline Packing Arrangements of Molecules That Form Hydrogen-Bonded Tapes Chin, D. N.; Palmore, G. T. R.; Whitesides, G. M.; J. Am. Chem. Soc.; 1999; 121(10); 2115-2122. 4) I think that there is a program by Accelerys called the "polymorph predictor" or something like this that makes ab initio calculations to predict the structure of small molecules. I hope this will help. Patty 5) A good tutorial/review on that topic was written by Paul Verwer and Frank Leusen in Reviews in Computational Chemistry, VCH Publishers, Volume 12, 1998. Kenny Tommy Ohyun Kwon, Ph.D School of Chemistry and Biochemistry Georgia Institute of Technology Atlanta Georgia, 30332 Email: ohyun.kwon[at]chemistry.gatech.edu From chemistry-request@ccl.net Sat May 15 09:12:58 2004 Received: from mxv2.wvu.edu (mxv2.wvu.edu [157.182.140.123]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i4FECwIH003927 for ; Sat, 15 May 2004 09:12:58 -0500 Received: from GWIA.HSC.WVU.EDU (gateway.hsc.wvu.edu [157.182.102.90]) by mxv2.wvu.edu (8.12.10/8.12.10) with ESMTP id i4FEFMMt010418 for ; Sat, 15 May 2004 10:15:24 -0400 (EDT) (envelope-from pgannett|at|hsc.wvu.edu) Received: from HSC-DOM5-MTA by GWIA.HSC.WVU.EDU with Novell_GroupWise; Sat, 15 May 2004 10:16:04 -0400 Message-Id: X-Mailer: Novell GroupWise Internet Agent 6.5.2 Beta Date: Sat, 15 May 2004 10:15:55 -0400 From: "Peter Gannett" To: , Cc: , Subject: Re: CCL:The pi-pi stacking of hetero-aromatic ring Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Content-Disposition: inline All: Stacking (pi-pi?) has been elicited as being of considerable importance in driving the conformation of DNA. See: Sarai,A.; Mazur,J.; Nissinov,R.; Jernigan,R.L. 'Origin of DNA Helical Structure and Its Sequence Dependence', Biochemistry 27:8498-8502 (1988) I think the property is real and, at least in heterocyclic systems, of considerable importance. Pete Gannett >>> Arvydas Tamulis 5/14/2004 8:50:06 AM >>> Dear Per-Ola Norrby, Your notice is very interesting also for me because we recently optimized geometry of supramolecule of artificial photosynthetic system containing sensibilizator molecule: N,N,N',N'-tetramethyl-naphthalene-1,4-diamine and lipid molecule (we done optimization by HF 6-31G). To my great suprise N,N,N',N'-tetramethyl-naphthalene-1,4-diamine and lipid molecules arranged almost perpendicular. Seems your notice confirms our received optimization result. While I still am not sure for my obtained result because it was done by HF 6-31G. I have plans to repeat optimization using DFT PBE 6-31++G* where exist possibility to include fine effects of quantum mechanical dispersion van-der-Waals interactions. I hope that finally I will get compromise result where coulomb interactions are competiting with fine quantum mechanical dispersion (pi-pi stacking) attraction forces. Concluding of my opinion: if one use very good DFT potential or multiconfigurational methods where are accounting specific quantum mechanical dispersion forces, the stacking should be tilted by some angle depending on the competition of coulomb attraction-repulsion forces and quantum mechanical dispersion attraction forces. With best regards, Arvydas Tamulis ******************************************************************* Arvydas Tamulis Doctor of Natural Sciences, senior research fellow Institute of Theoretical Physics and Astronomy, Vilnius University, Theoretical Molecular Electronics and Spintronics Research Group, A. Gostauto 12, Vilnius 2600, Lithuania e-mails: tamulis|at|itpa.lt or arvydas_tamulis|at|yahoo.com WEBsite: http://www.itpa.lt/~tamulis/ fax: +370-5-2125361 Phones: +370-5-2625036 or +370-5-2620861 Home address: Didlaukio 27-40, Vilnius 2057, Lithuania Mobile phone: +370-69919397 ******************************************************************* On Thu, 13 May 2004, Per-Ola Norrby wrote: > Sei-Hwan Kim wrote: > > >Dear CCLers > > > >I am looking for a reference to the pi-pi stacking of hetero-aromatic ring. > > ( face to edge, offset, face to face ) > > I'd like to comment on a serious misnomer here. The > interaction between two aromatic rings is frequently called pi-pi > stacking, which implies an attractive interaction between the > pi-clouds. In the wast majority of experimental cases, there is no > such attraction, two negative pi-clouds repel each other! Only in > the case of strong lowering of a LUMO and/or raising of a HOMO does > two pi-faces attract each other (like in oxidized donor stacks, or > possibly in the case of nitrobenzene with aniline). It was shown a > few decades ago (by Liljefors and Pettersson) that the attractive > interactions of two benzene rings with each other (face to edge or > offset) can be represented by simple electrostatic effects. The > hydrogens are slightly positive, the carbons slightly negative (about > 0.15, a C-H dipole of 0.6 D). In all stable situations, the > hydrogens of one ring are situated over the face of another ring. > Inclusion of this effect is the reason why most current molecular > mechanics programs give good results for aromatic interaction. See, > for example, Houk's computational study of the Wilcox torsional > balance a few years ago. > > Thus, I'd propose reserving the term "pi-pi stacking" for the > very rare cases where two very different aromatic rings are in a > perfect face to face arrangement, and use the more correct "CH-pi > interaction" for the more common cases of benzene-like molecules > interacting with each other. > > /Per-Ola > -- > Per-Ola Norrby, Assoc. Professor, http://organisk.kemi.dtu.dk/PON/ > Technical University of Denmark, Department of Chemistry > Building 201, Kemitorvet, DK-2800 Kgs. Lyngby, Denmark > Email: pon|at|kemi.dtu.dk tel +45-45252123, fax +45-45933968 > > > > Send your subscription/unsubscription requests to: CHEMISTRY-REQUEST|at|ccl.net > HOME Page: http://www.ccl.net | Jobs Page: http://www.ccl.net/jobs > > > > > > -= This is automatically added to each message by the mailing script =- To send e-mail to subscribers of CCL put the string CCL: on your Subject: line and send your message to: CHEMISTRY|at|ccl.net Send your subscription/unsubscription requests to: CHEMISTRY-REQUEST|at|ccl.net HOME Page: http://www.ccl.net | Jobs Page: http://www.ccl.net/jobs If your mail is bouncing from CCL.NET domain send it to the maintainer: Jan Labanowski, jlabanow|at|nd.edu (read about it on CCL Home Page) -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+