From owner-chemistry@ccl.net Thu Jul 20 04:51:01 2006 From: "Dr. Sudhir A. Kulkarni sudhirk++vlifesciences.com" To: CCL Subject: CCL: How to visualize a lone pair Message-Id: <-32203-060720011211-29136-YlfefUi4nXjYUSk3HrxCxQ[#]server.ccl.net> X-Original-From: "Dr. Sudhir A. Kulkarni" Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Thu, 20 Jul 2006 09:59:59 +0530 MIME-Version: 1.0 Sent to CCL by: "Dr. Sudhir A. Kulkarni" [sudhirk(_)vlifesciences.com] Mateo, There are several scalar fields which allow one to visualize lone pairs using QM calculations. Look at electrostatic potential, electron localization function, laplacian of electron density of your molecules. There are several publications on this aspects using above properties. Hope this helps. Sudhir Mateusz Witkowski big_mateo-#-inbox.com wrote: >Sent to CCL by: Mateusz Witkowski [big_mateo++inbox.com] > >Hi, >I'm interested in the directionality of O,N,S lone pairs in creation of hydrogen bonds. >Is it possible to visualize a lone pair from QM results? If so, what should be done, which software should be used? >What is your general impression about hydrogen bonds with XH-A angle ~100-120deg? Is there any border between HB and purely electrostatic interaction? > >TIA >Mateo> > > > > > -- Sudhir A. Kulkarni, Ph.D. VLife Sciences Technologies Pvt. Ltd. Pride Purple Coronet, 1st Floor, Next to Sapphire Chambers, S No. 287, Hissa No. 2, Vibhag No. 39/563, Baner Road, Pune 411 045 Tel/Fax: 27291590, 27291591, 6410035 ---------------------------------------------------------------------------------------------------------------------------------------- VLife Sciences Technologies Pvt Ltd.(VLife); Mail Disclaimer: This e-mail and any files transmitted with it are confidential and the views expressed in the same are not necessarily the views of VLife, and its Directors, Management, Employees or Associates. This communication represents the originator's personal views and opinions. If you are not the intended recipient or the person responsible for delivering the e-mail to the intended recipient, be advised that you have received this e-mail by error, and that any use, dissemination, forwarding, printing, or copying of this e-mail is strictly prohibited. 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The rights to monitor all e-mail communication through our network are reserved with us. ---------------------------------------------------------------------------------------------------------------------------------------- From owner-chemistry@ccl.net Thu Jul 20 09:31:00 2006 From: "Phil Hultin hultin * cc.umanitoba.ca" To: CCL Subject: CCL:G: Gaussian03 to AIM2000 Message-Id: <-32204-060719172955-26373-1e/eNgEBYWZUY6WgOvrDVQ(-)server.ccl.net> X-Original-From: "Phil Hultin" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="us-ascii" Date: Wed, 19 Jul 2006 15:24:35 -0500 MIME-Version: 1.0 Sent to CCL by: "Phil Hultin" [hultin|*|cc.umanitoba.ca] The recovery of properties using AIM depends to a great extent on the quality of the numerical integration of the wavefunction over each atomic basin. You cannot assume that the default integration parameters will necessarily give acceptable recovery of electron population or other properties. The fact that equivalent H atoms give different results or that properties may change as the molecule is rotated or translated may be due to too coarse a grid in the integration process. Note as well that the atomic basin integration in AIM2000 is done in two phases - an analytical integration over a "beta sphere" followed by numerical integration over the volume between the beta sphere and the atomic zero-flux surface. If the beta sphere is too large it will actually cross the zero-flux surface and you will integrate part of the volume belonging to a neighboring atom. Consult Aiken and Popelier Can. J. Chem. 2000, 78, 415-426 for a discussion of the quality of AIM integrals and the use of the atomic volume-integrated Laplacian of the charge density as an "error function" for atomic basin integration. Dr. Philip G. Hultin Professor of Chemistry, University of Manitoba Winnipeg, MB R3T 2N2 hultin()cc.umanitoba.ca http://umanitoba.ca/chemistry/people/hultin -----Original Message----- > From: owner-chemistry()ccl.net [mailto:owner-chemistry()ccl.net] Sent: July 19, 2006 2:17 PM To: Hultin, Philip G. Subject: CCL:G: Gaussian03 to AIM2000 Sent to CCL by: "Shobe, David" [dshobe_._sud-chemieinc.com] This is a multi-part message in MIME format. ------_=_NextPart_001_01C6AB4E.4B8FE977 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable I have recently purchased both of these programs, and I am having trouble s= omewhere. (I had been using Gaussian98 earlier). If I generate a wfn file= with Gaussian03 and then try to calculate atomic properties in AIM2000, I = encounter the following problems 1. Equivalent hydrogens have different atomic electron populations. 2. Atomic electron populations do not add up to an integer. 3. Atomic electron populations add up to a sum significantly less than the = total number of electrons. 4. Atomic electron populations sometimes change if the molecule is translat= ed or rotated. How can I tell where the problem is, in AIM2000, or in Gaussian03's wfn fil= e generating routine, or if I'm doing something wrong? Has anyone on CCL h= ad similar problems with either Gaussian03 or AIM2000? --David Shobe, Ph.D., M.L.S. S=FCd-Chemie, Inc. phone (502) 634-7409 fax (502) 634-7724 Don't bother flaming me: I'm behind a firewall. This e-mail message may contain confidential and / or privileged informatio= n. If you are not an addressee or otherwise authorized to receive this mess= age, you should not use, copy, disclose or take any action based on this e-= mail or any information contained in the message. If you have received this= material in error, please advise the sender immediately by reply e-mail an= d delete this message.=20 Thank you. ------_=_NextPart_001_01C6AB4E.4B8FE977 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Gaussian03 to AIM2000

I have recently purchased both of these pr= ograms, and I am having trouble somewhere.  (I had been using Gaussian= 98 earlier).  If I generate a wfn file with Gaussian03 and then try to= calculate atomic properties in AIM2000, I encounter the following problems=

1. Equivalent hydrogens have different ato= mic electron populations.
2. Atomic electron populations do not add= up to an integer.
3. Atomic electron populations add up to = a sum significantly less than the total number of electrons.
4. Atomic electron populations sometimes = change if the molecule is translated or rotated.

How can I tell where the problem is, in AI= M2000, or in Gaussian03's wfn file generating routine, or if I'm doing some= thing wrong?  Has anyone on CCL had similar problems with either Gauss= ian03 or AIM2000?

--David Shobe, Ph.D., M.L.S.
S=FCd-Chemie, Inc.
phone (502) 634-7409
fax (502) 634-7724

Don't bother flaming me: I'm behind a fire= wall.




This e-mail message may contain confidential and / or privileged informatio= n. If you are not an addressee or otherwise authorized to receive this mess= age, you should not use, copy, disclose or take any action based on this e-= mail or any information contained in the message. If you have received this= material in error, please advise the sender immediately by reply e-mail an= d delete this message.
Thank you.
------_=_NextPart_001_01C6AB4E.4B8FE977--http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt From owner-chemistry@ccl.net Thu Jul 20 10:06:00 2006 From: "Jason Thompson Thompson.Jason1 : mayo.edu" To: CCL Subject: CCL: nonbond parameters for Zn and Fe Message-Id: <-32205-060720094951-7193-mqr/KkTbtrh5iMS8c48klg .. server.ccl.net> X-Original-From: Jason Thompson Content-Type: multipart/alternative; boundary=Apple-Mail-17--997048357 Date: Thu, 20 Jul 2006 08:56:50 -0500 Mime-Version: 1.0 (Apple Message framework v752.2) Sent to CCL by: Jason Thompson [Thompson.Jason1^^^mayo.edu] --Apple-Mail-17--997048357 Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed This might be helpful for Zn: http://mayoresearch.mayo.edu/mayo/research/camdl/zinc_protein.cfm On Jul 19, 2006, at 12:07 PM, Marius Retegan marius.retegan^^^yahoo.com wrote: > Sent to CCL by: Marius Retegan [marius.retegan.~~.yahoo.com] > --0-690878600-1153318490=:88629 > Content-Type: text/plain; charset=us-ascii > > Hello > I need some help with finding the nonbonded parameters for Zn and > Fe for the Amber force field. > I would appreciate any reference or a method to derive these > parameters from other force fields. > Thank you > Marius Retegan > > --0-690878600-1153318490=:88629 > Content-Type: text/html; charset=us-ascii > >