From chemistry-request@ccl.net Tue Jan 11 10:32:28 2005 Received: from mail.chem.tamu.edu (mail.chem.tamu.edu [165.91.176.8]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id j0BFWRGg019521 for ; Tue, 11 Jan 2005 10:32:27 -0500 Received: by mail.chem.tamu.edu (CommuniGate Pro PIPE 4.2.8) with PIPE id 1523287; Tue, 11 Jan 2005 09:49:49 -0600 Received: from [165.91.176.164] ([165.91.176.164] verified) by mail.chem.tamu.edu (CommuniGate Pro SMTP 4.2.8) with ESMTP id 1523292; Tue, 11 Jan 2005 09:49:43 -0600 Mime-Version: 1.0 (Apple Message framework v619) In-Reply-To: <254B3BAF3C954E42A7074452D80FAF0903957268[at]edunivmail01.ad.umassmed.edu> References: <254B3BAF3C954E42A7074452D80FAF0903957268[at]edunivmail01.ad.umassmed.edu> Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed Message-Id: <6931BCE2-63E8-11D9-9F61-003065AFEB6E[at]mail.chem.tamu.edu> Content-Transfer-Encoding: 7bit From: Daniel Singleton Subject: CCL:isotope effects-quiver Date: Tue, 11 Jan 2005 09:49:43 -0600 To: "Catrina, Irina" , " " X-Mailer: Apple Mail (2.619) X-Chemistry_Department-MailScanner-Information: Chemistry_Helpdesk X-Chemistry_Department-MailScanner: Found to be clean X-MailScanner-From: singleton[at]mail.chem.tamu.edu X-Spam-Status: No, hits=2.0 required=7.5 tests=COMBINED_FROM 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 Irina, The original program was written by Keith Laidig with Martin Saunders in 1988. Those of us who run QUIVER these days probably run modified versions, as it is difficult to set up the input for the original quiver these days. In fact, setting up a QUIVER calculation used to be a real pain anyway, but these days I have the process automated so that it is very easy (when the automation works). I have ran QUIVER literally thousands of times, probably much more than anyone else, and while there are some things that people will just have to figure out for themselves, I guess I would be the person to ask when someone is really stuck. I can email anyone who requests it our modified version of the program source code as well as a series of csh and awk macros and an Excel spreadsheet that makes calculating isotope effects very fast, including allowing you to plug in a scaling factor and temperature on the fly. While this can all be very helpful, please understand that this is not a commercial program, the program and macros aren't user friendly, and they don't always work. There are always workarounds, and in my view QUIVER has some significant advantages over other approaches to predicting isotope effects, but there will be times when you will have to figure out what the program and macros are doing and adjust them to make them work. Dan Singleton On Jan 10, 2005, at 11:11 AM, Catrina, Irina wrote: > > Hi all, > I am looking for the QUIVER program (isotope effects calculation from > Gaussian output files). Could anybody tell me where I can find it? > Thank you very much. > Irina > > > > -= 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 Wed Jan 12 00:17:00 2005 Received: from web51304.mail.yahoo.com (web51304.mail.yahoo.com [206.190.38.170]) by server.ccl.net (8.12.8/8.12.8) with SMTP id j0C5GxJs004802 for ; Wed, 12 Jan 2005 00:16:59 -0500 Received: (qmail 66345 invoked by uid 60001); 12 Jan 2005 05:34:22 -0000 Comment: DomainKeys? See http://antispam.yahoo.com/domainkeys DomainKey-Signature: a=rsa-sha1; q=dns; c=nofws; s=s1024; d=yahoo.com; b=Ow9rl79LaeAPw7gQokuhOsoXeyM2Cw6AQ++E8VziIjj70L4KYYe3bQXfiBKWxOR76Rn1J1XE6JSjgDcsD8f3PfhRGTAHLSIMmUs6eoV6fkaNVxpGI/VVAhWHHk41gORelwvwN542+abPKuZu29XnjLc4KapPhdYwIxNM00nlrEs= ; Message-ID: <20050112053422.66343.qmail|at|web51304.mail.yahoo.com> Received: from [24.152.168.117] by web51304.mail.yahoo.com via HTTP; Tue, 11 Jan 2005 21:34:22 PST Date: Tue, 11 Jan 2005 21:34:22 -0800 (PST) From: Sengen Sun Subject: CCL: orbitals and reality To: chemistry|at|ccl.net In-Reply-To: <200501091027.46279.MatCha|at|HubWest.Com> MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii X-Spam-Status: No, hits=-0.5 required=7.5 tests=SMILEY autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Sorry for another posting on this subject. I am very disappointed that I have not received any disagreement to my earlier postings in the last two weeks. Instead, I have been praised by four CCL friends who exchanged personal e-mails with me. I wish to make a short comment on one of Dr. Matt Challacombe's messages. I agree well with Matt. But the current problem is much worse than one with a first year organic chemistry student. It is about problems with some scientific experts in the fields of physics and chemical physcics. I just noticed that the Nature paper also made a front page in C & En News (12/24/04) without mentioning the controversies such as those mentioned in Dr. Eric Scerri's JCE paper. A CCL friend used a quoted word "triumph" to describe this situation and predicted more "triumphs" are coming of orbital observation. Unfortunately, these "triumphs" have already gone very very wrong and gone way too too far. Why is that? Do we really care? Sengen sengensun|at|yahoo.com --- Matt Challacombe wrote: > I would say also that you can compute several of > these > properties without resorting to MO's at all, I > believe. > A coorespondence does not an existence proof make! > (unless you are a first year organic chemistry major > ;) > > -M > __________________________________ Do you Yahoo!? Yahoo! Mail - now with 250MB free storage. Learn more. http://info.mail.yahoo.com/mail_250 From chemistry-request@ccl.net Tue Jan 11 13:20:28 2005 Received: from prserv.net (out1.prserv.net [32.97.166.31]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id j0BIKSrn030433 for ; Tue, 11 Jan 2005 13:20:28 -0500 Message-Id: <200501111820.j0BIKSrn030433|at|server.ccl.net> Received: from be2.prserv.net (be2.backbone.sch.us[10.254.181.62]) by attglobal.net (out1) with SMTP id <2005011118374520104qc604e>; Tue, 11 Jan 2005 18:37:45 +0000 From: jmmckel|at|attglobal.net To: chemistry|at|ccl.net Subject: Reduced Mass in Vibration Calculation Date: Tue, 11 Jan 2005 18:37:44 +0000 X-Priority: 3 MIME-Version: 1.0 Content-Type: text/plain Content-Transfer-Encoding: 7bit X-Spam-Status: No, hits=2.0 required=7.5 tests=NO_REAL_NAME,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 CCLers, Calculations of emission spectra using AM1 ground state vibration calculations in MOPAc vs Gaussian differ, and the suspect is the definition of reduced mass in the two codes. Could someone please comment on the two apparently different definitions? many thanks! John McKelvey From chemistry-request@ccl.net Wed Jan 12 14:38:02 2005 Received: from smtp1.kodak.com (smtp1.kodak.com [192.232.121.200]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id j0CJc00T009924 for ; Wed, 12 Jan 2005 14:38:01 -0500 Received: from roc-us-e1000-109.kodak.com (roc-us-e1000-109.kodak.com [192.232.121.189]) by smtp1.kodak.com (8.11.3/8.11.1) with SMTP id j0CJbxr11047 for ; Wed, 12 Jan 2005 14:37:59 -0500 (EST) Received: from (150.221.122.53) by roc-us-e1000-109.kodak.com via smtp id 55ff_710b7f60_64d2_11d9_90b0_0002b3eef5d5; Wed, 12 Jan 2005 14:44:57 -0500 (EST) To: chemistry_at_ccl.net Subject: Silver NMR shifts using PBC X-Mailer: Lotus Notes Release 5.0.5 September 22, 2000 Message-ID: From: leif.olson_at_kodak.com Date: Wed, 12 Jan 2005 14:37:55 -0500 X-MIMETrack: S/MIME Sign by Notes Client on Leif P. Olson/436438/EKC(Release 5.0.5 |September 22, 2000) at 01/12/2005 02:37:55 PM, Serialize by Notes Client on Leif P. Olson/436438/EKC(Release 5.0.5 |September 22, 2000) at 01/12/2005 02:37:55 PM, Serialize complete at 01/12/2005 02:37:55 PM, S/MIME Sign failed at 01/12/2005 02:37:55 PM: The cryptographic key was not found, Serialize by Router on KNOTES2/ISBP/EKC(652HF120|July 29, 2004) at 01/12/2005 02:37:59 PM, Serialize complete at 01/12/2005 02:37:59 PM MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="=_alternative 006BD79785256F87_=" X-Spam-Status: No, hits=1.3 required=7.5 tests=HTML_MESSAGE,MK_BAD_HTML_04, NO_REAL_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 This is a multipart message in MIME format. --=_alternative 006BD79785256F87_= Content-Type: text/plain; charset="us-ascii" Hello CCL, I want to compute the Ag-109 chemical shifts in a crystal structure, using periodic boundary conditions if possible. The idea is to determine how an X-ray structure and a CP-MAS Ag-109 spectrum compare to each other. I've done NMR computations before (and a few PBC calculations using Gaussian 03) but only a few PBC calculations using software that was actually designed primarily for the solid state. Attempted NMR calculations using Gaussian 03 with PBC did not work. After poking around the Internet and the literature a bit, it seems that a couple of programs that might do what I want are PARATEC and CPMD. But the PARATEC website states "This code is primarily intended for users who are familiar with the plane-wave pseudopotential method used in PARATEC". Hmmm. The CPMD site doesn't say anything like that, but it does seem to be designed primarily for molecular dynamics simulations. Advice on these or other programs that might be appropriate would be appreciated. Thanks, Leif Olson Eastman Kodak Research Laboratories leif.olson_at_kodak.com --=_alternative 006BD79785256F87_= Content-Type: text/html; charset="us-ascii"
Hello CCL,

I want to compute the Ag-109 chemical shifts in a crystal structure, using periodic boundary conditions if possible.  The idea is to determine how an X-ray structure and a CP-MAS Ag-109 spectrum compare to each other.

I've done NMR computations before (and a few PBC calculations using Gaussian 03) but only a few PBC calculations using software that was actually designed primarily for the solid state.  Attempted NMR calculations using Gaussian 03 with PBC did not work.

After poking around the Internet and the literature a bit, it seems that a couple of programs that might do what I want are PARATEC and CPMD.  But the PARATEC website states "This code is primarily intended for users who are familiar with the plane-wave pseudopotential method used in PARATEC".  Hmmm.  The CPMD site doesn't say anything like that, but it does seem to be designed primarily for molecular dynamics simulations.

Advice on these or other programs that might be appropriate would be appreciated.  

Thanks,

Leif Olson
Eastman Kodak Research Laboratories
leif.olson_at_kodak.com --=_alternative 006BD79785256F87_=-- From chemistry-request@ccl.net Tue Jan 11 19:31:06 2005 Received: from rover.icebase.net (rover.icebase.net [64.186.224.244]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id j0C0V33Z015759 for ; Tue, 11 Jan 2005 19:31:04 -0500 Received: from rover.icebase.net (localhost.localdomain [127.0.0.1]) by rover.icebase.net (8.12.10/8.12.10) with ESMTP id j0C0mGBb001115 for ; Tue, 11 Jan 2005 16:48:17 -0800 Received: (from nobody@localhost) by rover.icebase.net (8.12.10/8.12.10/Submit) id j0C0lQ8l000723; Tue, 11 Jan 2005 16:47:26 -0800 Date: Tue, 11 Jan 2005 16:47:26 -0800 From: UCSD Extension To: Subject: Medicinal Chemistry at UCSD Extension Mime-Version: 1.0 Message-ID: <20050111164723354278.1..at..rover.icebase.net> Content-Type: multipart/alternative; boundary="============_CoolerEmail_============" X-Spam-Status: No, hits=3.8 required=7.5 tests=HTML_50_60, HTML_FONTCOLOR_UNKNOWN,HTML_FONT_BIG,HTML_MESSAGE, HTML_TAG_BALANCE_HTML,IMPRONONCABLE_1,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 --============_CoolerEmail_============ Content-Transfer-Encoding: binary Content-Type: text/plain; charset="iso-8859-1"; format="flowed"; To view this email as a webpage, please use this link: Medicinal Chemistry Certificate Building a Bridge Between Biologists and Chemists ------------------------------------------------- Gain knowledge to succeed in today's challenging pharmaceutical R&D environment. With the growing drug industry in San Diego, there is an increased need for "cross-trained" scientists to facilitate effective teamwork and development. This 18-week program, developed and taught by key professionals from the pharmaceutical industry, provides a comprehensive understanding of the drug discovery and development process from a medicinal chemistry vantage point. Date: January 20 - June 2, 2005 Time: Thursdays, 3:30 - 8:30 PM Fee: $2495* Location:UCSD Extension Sorrento Mesa Complex 6925 Lusk Blvd., San Diego, CA 92121 To Apply: Enrollment is by application only. For more information go to http://bioscience.ucsd.edu/MedChemInst.html Or call 858-964-1303 *This includes the Medicinal Chemistry Specialized Certificate candidacy fee, all classroom material costs, and meals. A $50.00 nonrefundable service charge will be applied to any cancellations after December 16, 2004. Cancellations will not be accepted after January 9, 2005. http://bioscience.ucsd.edu/MedChemInst.html --- mmweiss..at..ucsd.edu ========================================================= To help you read this email properly, you can use the link below and see the message as it was intended. Make sure you copy the entire link below into your browser's address bar: ========================================================= To send this email to a friend, follow the link below: This CoolerEmail was delivered to you on behalf of UCSD Extension. To be taken off UCSD Extension's email list, or update your account information and/or send comments to UCSD Extension, please follow the link below: If you request to be taken off UCSD Extension's email list, UCSD Extension will honor your request pursuant to CoolerEmail's permission-based email terms and conditions. Powered by CoolerEmail. For more information, please visit Postal address: CoolerEmail Inc., c/o Worksource Inc, 1231 NW Hoyt Suite 301, Portland, OR 97209 --============_CoolerEmail_============ Content-Transfer-Encoding: binary Content-Type: text/html; charset="iso-8859-1" Medicinal Chemistry at UCSD Extension
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Gain knowledge to succeed in today's challenging pharmaceutical R&D environment. With the growing drug industry in San Diego, there is an increased need for "cross-trained" scientists to facilitate effective teamwork and development. This 18-week program, developed and taught by key professionals from the pharmaceutical industry, provides a comprehensive understanding of the drug discovery and development process from a medicinal chemistry vantage point.

Date: January 20 - June 2, 2005
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For more information go to http://bioscience.ucsd.edu/MedChemInst.html
Or call 858-964-1303

*This includes the Medicinal Chemistry Specialized Certificate candidacy fee, all classroom material costs, and meals. A $50.00 nonrefundable service charge will be applied to any cancellations after December 16, 2004.

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