From owner-chemistry@ccl.net Fri Apr 1 02:40:00 2011 From: "neeraj misra neerajmisra^hotmail.com" To: CCL Subject: CCL: ERROR IN GAUSSIAN Message-Id: <-44264-110401023844-4755-bP80qyjeyaNQQXdqqsnzsg:server.ccl.net> X-Original-From: "neeraj misra" Date: Fri, 1 Apr 2011 02:38:43 -0400 Sent to CCL by: "neeraj misra" [neerajmisra-#-hotmail.com] DEAR CCLER'S PLEASE ADVISE ME AS TO WHY THE FOLLOWING ERROR IS COMING UP WHENEVER I OPEN A .CHK FILE IN G09W. CConnectionGFCHK::parse-GFCHK() Missing or bad data: Alpha Orbital Energies Line Number 702 OK thanks in advance NM From owner-chemistry@ccl.net Fri Apr 1 03:50:00 2011 From: "Andrew Voronkov drugdesign%yandex.ru" To: CCL Subject: CCL: Are there LigandScout users here? Message-Id: <-44265-110401034821-17481-SYDJ03d/5BHVm8EDcoDvKA^^^server.ccl.net> X-Original-From: Andrew Voronkov Content-Transfer-Encoding: 7bit Content-Type: text/plain Date: Fri, 01 Apr 2011 11:48:12 +0400 MIME-Version: 1.0 Sent to CCL by: Andrew Voronkov [drugdesign[]yandex.ru] Hello! I am interested to find other LigandScout users to be able to discuss questions related to software work, I have several questions on LigandScout 3.0. Sincerely yours, Andrey From owner-chemistry@ccl.net Fri Apr 1 08:28:00 2011 From: "huixiaokang328 huixiaokang328^163.com" To: CCL Subject: CCL: absolute hardness Message-Id: <-44266-110401081804-15375-dhAt6IgAI0wdF+GEnmc81Q**server.ccl.net> X-Original-From: huixiaokang328 Content-Type: multipart/alternative; boundary="----=_Part_150416_837832333.1301660263854" Date: Fri, 1 Apr 2011 20:17:43 +0800 (CST) MIME-Version: 1.0 Sent to CCL by: huixiaokang328 [huixiaokang328[A]163.com] ------=_Part_150416_837832333.1301660263854 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: base64 RGVhciBGbGljawpUaGFuayB5b3UgZm9yIHlvdXIga2luZGx5IGhlbHAsIGFuZCBJd2lzaCB5b3Ug YXJlIGhlYWx0aHkgYW5kIGhhcHB5LgoKU2luY2VyZWx5IHlvdXJzCgp4a2FuZwoKQXQgMjAxMS0w My0zMSAxMToyNzoxMu+8jCJXaWxsaWFtIEYuIENvbGVtYW4gd2NvbGVtYW46Kzp3ZWxsZXNsZXku ZWR1IiA8b3duZXItY2hlbWlzdHJ5QGNjbC5uZXQ+IHdyb3RlOgoKIkNDTCBTdWJzY3JpYmVycyIg PGNoZW1pc3RyeUBjY2wubmV0PiB3cml0ZXM6CkRlYXIgYWxsCiAgICAKICAgIEkgbmVlZCBzb21l 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L3NwYW4+PC9zcGFuPg== ------=_Part_150416_837832333.1301660263854-- From owner-chemistry@ccl.net Fri Apr 1 14:26:00 2011 From: "Ronald Cook cookrl]^[tda.com" To: CCL Subject: CCL: absolute hardness Message-Id: <-44267-110401142238-16973-eTV4VU/pEWHPZfJVxI97+A^-^server.ccl.net> X-Original-From: Ronald Cook Content-Type: multipart/alternative; boundary=000e0cd1582e302f7a049fdf7e8a Date: Fri, 1 Apr 2011 12:22:30 -0600 MIME-Version: 1.0 Sent to CCL by: Ronald Cook [cookrl===tda.com] --000e0cd1582e302f7a049fdf7e8a Content-Type: text/plain; charset=ISO-8859-1 Before you get too far in your calculations, you should probably read the references I have provided below. While the theoretical basis for Absolute Electronegativity and Absolute Hardness is well grounded, the calculations are not as straight forward as some would have you believe. Most moderate to high level QM calculations will give you a pretty good value for the ionization potential (I) (or the HOMO energy if you are using the Koopman's theorem approach). However, the electron affinity (A) is another matter. The "natural" way to calculate I and A for use in hardness calculations is from total electronic energy calculations on the N-1, N and N+1 electron systems using the geometry of the neutral molecule. I is then I=E(N-1)-E(N) and A is E(N)-E(N-1). The Koopmans approach assigns I as -HOMO energy and A as -LUMO energy. The problem arises when negative electon affinities are encountered as a result of the DFT calculations. The values you get for A are often dicated by the size of the diffuse orbitals used in the calculation The cautions about using electron affinities calculated using standand DFT methods and some work arounds are described in Proft et al. Faraday Discussions 135, 151 (2007), Tozer and Proft, J Phys Chem A109, 8923 (2005), Puiatu et al., Physical Chemistry Chemical Physics 10, 1394 (2008), Puiatu et al., Physical Chemistry Chemical Physics 11, 9013 (2009) Ronald Cook Principal Scientist TDA Research, Inc. On Wed, Mar 30, 2011 at 8:16 PM, Kang Xiaohui huixiaokang328() 163.com < owner-chemistry%ccl.net> wrote: > > Sent to CCL by: "Kang Xiaohui" [huixiaokang328!^!163.com] > Dear all > > I need some information on the molecular absolute hardness in my study, > but I don't know how to calculate it and which data I need to compute in > gaussion 09. Therefore, I need a detail computational process, formulas or > examples on gaining the molecular absolute hardness. > Any help will be appreciated, I am looking forward to your timely reply > > Sincerely yours> > > -- Ronald L Cook Principal Scientist TDA Research, Inc. cookrl%tda.com 303-940-2302 --000e0cd1582e302f7a049fdf7e8a Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Before you get too far in your calculations, you should probably read the r= eferences I have provided below.=A0 While the theoretical basis for Absolut= e Electronegativity and Absolute Hardness is well grounded, the calculation= s are not as straight forward as some would have you believe.=A0 Most moder= ate to high level QM calculations will give you a pretty good value for the= ionization potential (I) (or the HOMO energy if you are using the Koopman&= #39;s theorem approach).=A0

However, the electron affinity (A) is another matter.=A0 The "natu= ral" way to calculate I and A for use in hardness calculations is from= total electronic energy calculations on the N-1, N and N+1 electron system= s using the geometry of the neutral molecule. I is then I=3DE(N-1)-E(N) and= A is E(N)-E(N-1). The Koopmans approach assigns I as -HOMO energy=A0 and A= as -LUMO energy.=A0 The problem arises when negative electon affinities ar= e encountered as a result of the DFT calculations.=A0 The values you get fo= r A are often dicated by the size of the diffuse orbitals used in the calcu= lation

The cautions about using electron affinities calculated using standand = DFT methods and some work arounds are described in Proft et al. Faraday Dis= cussions 135, 151 (2007), Tozer and Proft,=A0 J Phys Chem A109, 8923 (2005)= , Puiatu et al., Physical Chemistry Chemical Physics 10, 1394 (2008),=A0 = =A0 Puiatu et al., Physical Chemistry Chemical Physics 11, 9013 (2009)

Ronald Cook
Principal Scientist
TDA Research, Inc.


On Wed, Mar 30, 2011 at 8:16 PM, Kang Xiaohui h= uixiaokang328() 163.com &l= t;owner-chemistry%ccl.net>= ; wrote:

Sent to CCL by: "Kang =A0Xiaohui" [huixiaokang328!^!163.com]
Dear all

=A0 =A0I need some information on the molecular absolute hardness in my st= udy, but I don't know how to calculate it and which data I =A0need to c= ompute in gaussion 09. Therefore, I need a detail computational process, fo= rmulas or examples on gaining the molecular absolute hardness.
=A0 =A0Any help will be appreciated, I am looking forward to your timely r= eply

=A0 =A0Sincerely yours



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--
Ronald L Cook
Princi= pal Scientist
TDA Research, Inc.
cookrl%tda.com
303-940-2302

--000e0cd1582e302f7a049fdf7e8a-- From owner-chemistry@ccl.net Fri Apr 1 15:44:00 2011 From: "Adrian Stevens adrian.stevens,+,accelrys.com" To: CCL Subject: CCL: New Discovery Studio 3.0 webinars Message-Id: <-44268-110401104014-8435-jwvEbD6l3T/tDrEyjlHlaA~~server.ccl.net> X-Original-From: "Adrian Stevens" Date: Fri, 1 Apr 2011 10:40:08 -0400 Sent to CCL by: "Adrian Stevens" [adrian.stevens],[accelrys.com] As part of the release of Discovery Studio 3.0, Accelrys is very pleased to announce the extension of our webinar series to now include customer and software partner-led presentations. Learn more: http://accelrys.com/events/webinars/discovery-studio-30/index.php The next three confirmed webinars in the series are as follows: 1. "The Antibody Humanization Process by CDR Grafting" presented by: Leonardo Borras, Head, Protein Engineering, ESBATech LLC April 7th 4pm British Summer Time (BST) 2. "Integration of Molecular Discoverys GRID within Discovery Studio 3.0" presented by: Simon Cross Senior Scientist & Product Manager, Molecular Discovery Ltd. Noj Malcolm Lead Scientist, Accelrys Adrian Stevens Sr. Product Marketing Manager, Accelrys April 14th 10.30-11.30am BST REGISTER April 14th 9.00am PDT REGISTER 3. "Integration of Cresset's FieldStere within Discovery Studio 3.0" presented by Tim Cheeseright Director Products, Cresset Noj Malcolm Lead Scientist, Accelrys Adrian Stevens Sr. Product Marketing Manager, Accelrys May 5th 10.30-11.30am BST REGISTER May 5th 8.30am PDT REGISTER To learn more, or register to attend any of these webinars, please visit http://accelrys.com/events/webinars/discovery-studio-30/index.php Best regards, Adrian Stevens Sr. Product Marketing Manager, Discovery Studio From owner-chemistry@ccl.net Fri Apr 1 20:10:00 2011 From: "Eliac Brown Eliacbrown]^[yahoo.com" To: CCL Subject: CCL: Script - Dipole moment Message-Id: <-44269-110401200848-20416-DbkfCvGELU+8KEzi7UlWSQ++server.ccl.net> X-Original-From: "Eliac Brown" Date: Fri, 1 Apr 2011 20:08:46 -0400 Sent to CCL by: "Eliac Brown" [Eliacbrown|*|yahoo.com] Dear all I was wondering if anyone could support me with a software or script can be used to calculate the dipole moment of small molecules in the pdbqt formate. 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this.Is there any references that can be helpful? Any suggestions will be appreciated! Many thanks in advance. > Dear CCLers: > I'm new to Gaussian,so I try to reproduce some example at Gaussian's > website.But I'm confused about one.In the "Antiferromagnetic coupling" > example of gauss03--www.gaussian.com/g_tech/antiferr_g03.htm--it tries to > reorder the orbitals,and choose some orbitals changed to .What I'm > confused is the criterion that it choose the orbitals to be reordered.Why >they choose these orbitals to be reordered. >yes, that's indeed a confusing method. A much better (simpler and 100% >reliable) method is to take fragment orbitals and generate an >appropriate guess wavefunction. See Appendix II of the AOMix manual >(http://www.sg-chem.net/aomix/AOMix-manual.pdf) for details. >Best regards, > Serge Gorelsky