From chemistry-request@server.ccl.net Thu Nov 15 03:32:45 2001 Received: from arrhenius.che.chalmers.se ([129.16.90.200]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id fAF8WiB09235 for ; Thu, 15 Nov 2001 03:32:44 -0500 Received: from arrhenius.che.chalmers.se (arrhenius.che.chalmers.se [129.16.90.200]) by arrhenius.che.chalmers.se (8.9.3/8.9.3) with ESMTP id JAA1187936 for ; Thu, 15 Nov 2001 09:34:35 +0100 (MET) Date: Thu, 15 Nov 2001 09:34:35 +0100 From: Harald Svedung X-X-Sender: To: Subject: vinoxy Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hello! Do anyone have a good potentialfunction for the vinoxy radical? Preferably it should work all the way to dissociation. Any hints are very welcome! :-) /Harald Harald Svedung (PhD) phone: +46-31-7722816 Department of Chemistry fax: +46-31-167194 Physical Chemistry home phone:+46-31-240897, +46-709223206 Goeteborg University home e-mail: harald.svedung@svedung.pp.se SE-412 96 Goeteborg, Sweden. www.che.chalmers.se/~svedung/welcome.html From chemistry-request@server.ccl.net Thu Nov 15 10:20:35 2001 Received: from deimos.email.Arizona.EDU (IDENT:root@[128.196.133.166]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id fAFFKYB17219 for ; Thu, 15 Nov 2001 10:20:34 -0500 Received: from chad (128.196.86.119) by deimos.email.Arizona.EDU (6.0.034) id 3BF0ADC10004A065 for chemistry@ccl.net; Thu, 15 Nov 2001 08:20:23 -0700 Message-ID: <000e01c13dfa$43437fe0$7756c480@chem.arizona.edu> From: "cmrisko" To: Subject: Allyl Excited State Geometries Date: Sat, 15 Sep 2001 08:22:42 -0700 MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 6.00.2600.0000 X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2600.0000 Good day! I am in the process of studying a molecular system that has properties related to the allyl cation. Does anyone know of references that specify calculated values for ground- and excited-state geometries? I reviewed the CCL archive and could not find (or probably just missed!) past discussions relating to the geometry of this system, and literature searches to this point have turned-up very little. Thank you in advance for any assistance that you may be able to provide. I hope all is well. Chad ============================== Chad Risko Graduate Student Department of Chemistry University of Arizona ============================== From chemistry-request@server.ccl.net Thu Nov 15 10:22:45 2001 Received: from MAIL.AD.Berry.edu ([66.20.28.66]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id fAFFMhB17270 for ; Thu, 15 Nov 2001 10:22:43 -0500 Received: from [10.16.232.24] ([10.16.232.24]) by MAIL.AD.Berry.edu with Microsoft SMTPSVC(5.0.2195.2966); Thu, 15 Nov 2001 10:23:16 -0500 User-Agent: Microsoft-Outlook-Express-Macintosh-Edition/5.02.2022 Date: Thu, 15 Nov 2001 10:22:37 -0500 Subject: Re: CCL:Bonds vs No Bonds in Minimized Structures From: Gary Breton To: Message-ID: Mime-version: 1.0 Content-type: text/plain; charset="US-ASCII" Content-transfer-encoding: 7bit X-OriginalArrivalTime: 15 Nov 2001 15:23:16.0541 (UTC) FILETIME=[72E396D0:01C16DE9] I just wanted to say thank you to all that responded to my query concerning GaussView's quirkiness about drawing bonds in minimized structures (see below for the full question). All of the answers were very helpful and all relayed essentially the same message: just because a bond is not drawn does not mean there is no bond. GaussView apparently has a certain maximum bond length assigned to the N-N bond beyond which it arbitrarily decides not to draw a bond. Certainly I suspected this to be true, but, as still a relative newbie at computational chemistry, I wanted to be sure. As always, some very useful information was conveyed, especially concerning the application of Bader's AIM, Weinhold's NBO, and ELF (electron localization function) theory to determine if a bond truly exists. I look forward to employing these methods. Best regards! Gary W. Breton Chair and Associate Professor Department of Chemistry Berry College PO Box 495016 Mount Berry, GA 30149 "There's a light at the end of the tunnel, but it may be an oncoming train" ******************************************** > From: Gary Breton > Date: Wed, 14 Nov 2001 07:16:46 -0500 > To: > Subject: CCL:Bonds vs No Bonds in Minimized Structures > > Hello all, > > I have been conducting some geometry minimizations on some > 1,2-diazacyclobutane structures using Gaussian98 with the GaussView GUI. > When I minimize the parent compound (1,2-diazacyclobutane with N-H bonds) at > the RHF631G* level, everything looks fine. If, however, I minimize at the > RB3LYP6311+G** level, a similar structure to the HF minimization results, > but GaussView does NOT SHOW a bond between the two nitrogen atoms. The bond > has apparently not broken since the molecule adopts a geometry as if its > still there (i.e., in the HF minimization the N-N, C-N and C-C bond lengths > are 1.45405, 1.47272 and 1.53174, respectively, while in the B3LYP they are > 1.49052, 1.49351 and 1.53844, respectively). Furthermore, if I start with > the HF structure and further minimize at the B3LYP level, the bond again > disappears! If I start with the B3LYP structure and ADD a N-N bond and then > re-minimize, it again eliminates the bond. > > Is there any significance to the presence or absence of the bond? Why would > GaussView not put a bond into the structure? > > Thanks and best regards! > > > Gary W. Breton > Chair and Associate Professor > Department of Chemistry > Berry College > PO Box 495016 > Mount Berry, GA 30149 > > "There's a light at the > end of the tunnel, but it > may be an oncoming train" From chemistry-request@server.ccl.net Thu Nov 15 06:34:28 2001 Received: from mail.takas.lt ([212.59.31.66]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id fAFBYRB12452 for ; Thu, 15 Nov 2001 06:34:27 -0500 Received: from olegas ([212.59.14.74]) by mail.takas.lt with Microsoft SMTPSVC(5.0.2195.2966); Thu, 15 Nov 2001 13:31:24 +0200 Message-ID: <000201c16dd1$cb565630$4a0e3bd4@olegas> From: "Olegas Eicher-Lorka" To: Subject: Summary: Norm. Coord. Anal. Date: Thu, 15 Nov 2001 11:48:16 +0100 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_008F_01C16DCB.69D06BE0" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.50.4807.1700 X-MimeOLE: Produced By Microsoft MimeOLE V5.50.4807.1700 X-OriginalArrivalTime: 15 Nov 2001 11:31:25.0096 (UTC) FILETIME=[0F058A80:01C16DC9] This is a multi-part message in MIME format. ------=_NextPart_000_008F_01C16DCB.69D06BE0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Dear CCLers, We received a large number of replies few of which were useful. A number = dealt with the thorny isssue of names: I mentioned Normal Coordinate = Analysis (NCA), this is the terminology I was taught as an undergrad, = and is the terminology used in all of my text books (and the "standard" = Peterson & McIntosh BMAT suite of programs) - even the unreadable = Wilson, Decius and Cross book. I also notice that the Gaussian people = don't like the name NCA- is it a physics/maths thing? I really should have been clearer and asked for something to = "Automatically generate 3N-6 internal coordinates for NCA". I would also thank those kind people, who advised us to use = www.google.com and get "only" 20000 hits. David van der Spoel suggested this: If you mean normal mode analysis of (bio) molecules try www.gromacs.org Dr. David van der Spoel, Biomedical center, Dept. of Biochemistry Husargatan 3, Box 576, 75123 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 spoel@xray.bmc.uu.se spoel@gromacs.org http://zorn.bmc.uu.se/~spoel which looks nice (and useful), but not quite what we wanted. The same goes for this: I was browsing through CCL's own source code archives, and came across a = free normal coordinate analysis software. The URL is=20 http://www.ccl.net/cca/software/SOURCES/FORTRAN/normal_coor_anal/index.sh= tml Ha-Yeon Cheong Bowdoin College Intern Chemistry Department Kris van Alsenoy was very helpful, suggesting firstly this: why don't you try GAR2PED which starts from gausssian archive records. I can provide it. And after some clarification, giving us the following references: have a look at papers by P. Pulay and coworkers, in particular : pulay, fogarasi, pang, boggs, JACS, v101, p2550 (1979) fogarasi, zhou, taylor, pulay, JACS, v114, p 8191 (1992) Kris Van Alsenoy, Structural Chemistry Group, Department of Chemistry, University of Antwerp (UIA), Universiteitsplein 1, B-2610 Antwerp, = Belgium E-mail: alsenoy@uia.ua.ac.be / Phone: +32(03)8202366 / Fax: = +32(03)8202310 Both of which are good. But it looks like for an automatic definition of = 3N-6 internal coordinates, the first step is still Prometheus: http://www.ruhr-uni-bochum.de/www-public/goetzhbv/ftir/prometheus.html ------=_NextPart_000_008F_01C16DCB.69D06BE0 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
Dear CCLers,
 
We received a large number of replies few of which = were=20 useful. A number dealt with the thorny isssue of names: I mentioned = Normal=20 Coordinate Analysis (NCA), this is the terminology I was taught as an = undergrad,=20 and is the terminology used in all of my text books (and the "standard" = Peterson=20 & McIntosh BMAT suite of programs) - even the unreadable Wilson, = Decius and=20 Cross book. I also notice that the Gaussian people don't like the = name NCA-=20 is it a physics/maths thing?
 
I really should have been clearer and asked for = something to=20 "Automatically generate 3N-6 internal coordinates for NCA".
 
I would also thank those kind people, who advised us = to use=20 www.google.com and get "only" 20000=20 hits.
 
David van der Spoel suggested this:
 
If you mean normal mode analysis of (bio) molecules try www.gromacs.org
 
Dr. David van der Spoel, Biomedical center, Dept. of=20 Biochemistry
Husargatan 3, Box 576,  75123 Uppsala, = Sweden
phone: 46=20 18 471 4205 fax: 46 18 511 755
spoel@xray.bmc.uu.se spoel@gromacs.org   http://zorn.bmc.uu.se/~spoel
which looks nice (and useful), but not quite what we = wanted.
 
The same goes for this:
 
I was browsing through CCL's own source code archives, and came = across a=20
free normal coordinate analysis software.

The URL is
http://www.ccl.net/cca/software/SOURCES/FORTRAN/normal_coor_= anal/index.shtml
 
Ha-Yeon Cheong
Bowdoin College
Intern
Chemistry = Department
 
Kris van Alsenoy was very helpful, suggesting = firstly=20 this:
 
why don't you try GAR2PED which starts from gausssian archive = records.
I=20 can provide it.
And after some clarification, giving us the = following=20 references:
 
have a look at papers by P. Pulay and coworkers, in particular = :
pulay,=20 fogarasi, pang, boggs, JACS, v101, p2550 (1979)
fogarasi, zhou, = taylor,=20 pulay, JACS, v114, p 8191 (1992)
Kris Van Alsenoy,
Structural Chemistry Group, Department of=20 Chemistry,
University of Antwerp (UIA), Universiteitsplein 1, B-2610 = Antwerp,=20 Belgium
 E-mail: alsenoy@uia.ua.ac.be / Phone:=20 +32(03)8202366 / Fax: +32(03)8202310

Both of which = are good.=20 But it looks like for an automatic definition of 3N-6 internal = coordinates, the=20 first step is still Prometheus:
 
http://www.ruhr-uni-bochum.de/www-public/goetzhbv/ftir/prometheus.= html
 
 

------=_NextPart_000_008F_01C16DCB.69D06BE0-- From chemistry-request@server.ccl.net Thu Nov 15 09:35:37 2001 Received: from postoffice.mail.cornell.edu ([132.236.56.7]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id fAFEZbB16180 for ; Thu, 15 Nov 2001 09:35:37 -0500 Received: from cornell.edu (sweet1.foodsci.cornell.edu [132.236.147.65]) by postoffice.mail.cornell.edu (8.9.3/8.9.3) with ESMTP id JAA10762; Thu, 15 Nov 2001 09:35:30 -0500 (EST) Sender: dwood@cornell.edu Message-ID: <3BF3CB2E.984AB503@cornell.edu> Date: Thu, 15 Nov 2001 09:03:26 -0500 From: "Dr. Richard L. Wood" X-Mailer: Mozilla 4.75C-SGI [en] (X11; I; IRIX 6.5 IP32) X-Accept-Language: en MIME-Version: 1.0 To: "chemistry@ccl.net" Subject: Re: CCL:Bonds vs No Bonds in Minimized Structures References: <000901c16d6b$1784c530$bbc0e380@qtp.ufl.edu> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Stefan Fau wrote: > Dear Prof. Breton, > > Dr. Robinson is right. Most viewing programs > do not analyze the electronic structure to determine > if there is a bond between two atoms. Hi all This is certainly correct. My own experience with the program Quanta confirms this. Quanta does not recognize the bond between C1 of a sugar and the O of a serine or threonine residue. Yet I know that there is a bond there so I don't get too concerned about it. Richard > -- > Richard L. Wood, Ph. D. > Physical/Computational Chemist > Post-doctoral Associate > Department of Food Science > 120 Stocking Hall > Cornell University, Ithaca, NY 14853 > From chemistry-request@server.ccl.net Thu Nov 15 11:22:27 2001 Received: from phm.utoronto.ca ([128.100.70.1]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id fAFGMRB18852 for ; Thu, 15 Nov 2001 11:22:27 -0500 Received: from phm.utoronto.ca (lpk04.phm.utoronto.ca [128.100.70.180]) by phm.utoronto.ca (8.9.3+Sun/8.9.3) with ESMTP id LAA26303; Thu, 15 Nov 2001 11:22:19 -0500 (EST) Sender: william@phm.utoronto.ca Message-ID: <3BF3EBBC.B8AE68CB@phm.utoronto.ca> Date: Thu, 15 Nov 2001 11:22:20 -0500 From: William Wei Reply-To: william@phm.utoronto.ca Organization: Faculty of Pharmacy, U of T X-Mailer: Mozilla 4.7C-SGI [en] (X11; I; IRIX64 6.5 IP30) X-Accept-Language: en MIME-Version: 1.0 To: amber@heimdal.compchem.ucsf.edu, chemistry@ccl.net Subject: Question about RESP Content-Type: multipart/alternative; boundary="------------707A7DFA2D141E481CB78ECC" --------------707A7DFA2D141E481CB78ECC Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi, Dear colleagues, I met some problems while I fitted ESP using Amber package - RESP. About the input file of RESP program, I noticed that in the samples' input file the ivary sometimes was put the value -1. But in the manual I can not find the explanation for that. Could anyone help me to understand it? Thanks. Another problem with me is about the input file of ESP's and coordinates. It seems that the input data is the ESP of all the points in the molecule volume. is that right? Does anyone use spartan? How can I get the file or data of ESP in any point from spartan? Any help and clues is very help to me and I appreciate for it. Regards. William. -- William Wei Tel: 1-416-946-7551 (Lab.) Faculty of Pharmacy Fax: 1-416-978-8511 19 Russell Street Email: william@phm.utoronto.ca Toronto, ON. M5S 2S2, Canada william.wei@utoronto.ca --------------707A7DFA2D141E481CB78ECC Content-Type: text/html; charset=us-ascii Content-Transfer-Encoding: 7bit Hi, Dear colleagues,

I met some problems while I fitted ESP using Amber package - RESP.  About the input file of RESP program, I noticed that in the samples' input file the ivary sometimes was put the value -1. But in the manual I can not find the explanation for that. Could anyone help me to understand it? Thanks.

Another problem with me is about the input file of ESP's and coordinates. It seems that the input data is the ESP of all the points in the molecule volume. is that right? Does anyone use spartan? How can I get the file or data of ESP in any point from spartan? Any help and clues is very help to me and I appreciate for it.

Regards.

William. 

-- 
William Wei                    Tel: 1-416-946-7551 (Lab.)
Faculty of Pharmacy            Fax: 1-416-978-8511
19 Russell Street              Email: william@phm.utoronto.ca
Toronto, ON. M5S 2S2, Canada          william.wei@utoronto.ca
  --------------707A7DFA2D141E481CB78ECC-- From chemistry-request@server.ccl.net Thu Nov 15 03:40:54 2001 Received: from uscmail.usc.es ([193.144.75.8]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id fAF8erB09456 for ; Thu, 15 Nov 2001 03:40:53 -0500 Received: from qfcronos (qfcronos.usc.es [193.144.74.154]) by uscmail.usc.es (8.9.1/8.9.1) with SMTP id JAA02122 for ; Thu, 15 Nov 2001 09:40:46 +0100 (MET) Message-ID: <000001c16db1$d5822640$9a4a90c1@usc.es> From: =?iso-8859-1?Q?Jes=FAs_Rodr=EDguez_Otero?= To: Subject: Athlon vs P4 for G98 Date: Wed, 14 Nov 2001 18:58:23 +0100 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_0021_01C16D3E.55F7FD00" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.00.2615.200 X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2615.200 This is a multi-part message in MIME format. ------=_NextPart_000_0021_01C16D3E.55F7FD00 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Hi=20 Anybody has benchmarks about Athlon XP DDR versus P4 RDRAM using = Gaussian98?? For the P 4, is the RDRAM clearly advantageous as contrasted with SDRAM? The economic difference is very large!! Thanks ------=_NextPart_000_0021_01C16D3E.55F7FD00 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
Hi
 
Anybody has benchmarks about Athlon XP = DDR versus=20 P4 RDRAM using Gaussian98??
 
For the P 4, is the RDRAM clearly = advantageous as=20 contrasted with SDRAM?
The economic difference is very=20 large!!
 
Thanks
 
 
------=_NextPart_000_0021_01C16D3E.55F7FD00-- From chemistry-request@server.ccl.net Wed Nov 14 21:55:11 2001 Received: from eyou.com ([61.136.62.74]) by server.ccl.net (8.11.6/8.11.0) with SMTP id fAF2tAB05281 for ; Wed, 14 Nov 2001 21:55:10 -0500 Received: (qmail 81146 invoked by alias); 15 Nov 2001 10:55:03 +0800 Received: from unknown (HELO eyou.com) (172.16.2.1) by 172.16.1.2 with SMTP; 15 Nov 2001 10:55:03 +0800 Received: (qmail 47229 invoked by uid 65534); 15 Nov 2001 10:55:03 +0800 Date: 15 Nov 2001 10:55:03 +0800 Message-ID: <20011115105503.47228.qmail@eyou.com> From: "Ace Breakpoint" To: chemistry@ccl.net Reply-To: "Ace Breakpoint" Subject: A Beginnger's question: Ligand Properties and Reactive Site Hi, everyone: My field is organometallic chemistry. My question is: I have the structure of a organic ligand and I performed an ab initio calculation on it. Can I prognosticate the reactive site, i. e. which atom of the ligand will coordinate to the metal center through pi-bond and feedback bond? Is the key factor 1) electron populations, 2) charge desity, 3) HOMO/LUMO or something else? Would the professionals give me some advice or literatures? Thank you all very much. Ace Breakpoint --http://www.eyou.com --稳定可靠的免费电子信箱 语音邮件 移动书签 日历服务 网络存储...亿邮未尽 From chemistry-request@server.ccl.net Thu Nov 15 16:07:32 2001 Received: from postal.sdsc.edu (IDENT:JMBZb9m2lcIqgGwszj29advezCp1QXfl@[132.249.20.114]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id fAFL7VB26500 for ; Thu, 15 Nov 2001 16:07:31 -0500 Received: from koa.sdsc.edu (IDENT:TxSUa3f52pxj3OeV0siGdNRMaElWPpDr@koa.sdsc.edu [132.249.23.116]) by postal.sdsc.edu (8.11.6/8.11.6/SDSCserver-20) with ESMTP id fAFL7Oj15673; Thu, 15 Nov 2001 13:07:24 -0800 (PST) Received: from localhost by koa.sdsc.edu (SGI-8.9.3/1.11-IRIXclient) with ESMTP id NAA62553; Thu, 15 Nov 2001 13:07:23 -0800 (PST) Date: Thu, 15 Nov 2001 13:07:23 -0800 From: Wibke Sudholt To: William Wei cc: Subject: Re: CCL:Question about RESP In-Reply-To: <3BF3EBBC.B8AE68CB@phm.utoronto.ca> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hello, I do not know Amber and the newest version of Spartan, but maybe you can use the Spartan interface to Gaussian or Gaussian itself to create such an ESP file (see http://www.gaussian.com/keyword.htm, keywords cube and prop). Hopefully, this helps! Best regards, Wibke Sudholt University of California, San Diego wibke@sdsc.edu On Thu, 15 Nov 2001, William Wei wrote: > Hi, Dear colleagues, > > I met some problems while I fitted ESP using Amber package - RESP. > About the input file of RESP program, I noticed that in the samples' > input file the ivary sometimes was put the value -1. But in the manual I > can not find the explanation for that. Could anyone help me to > understand it? Thanks. > > Another problem with me is about the input file of ESP's and > coordinates. It seems that the input data is the ESP of all the points > in the molecule volume. is that right? Does anyone use spartan? How can > I get the file or data of ESP in any point from spartan? Any help and > clues is very help to me and I appreciate for it. > > Regards. > > William. > > -- > William Wei Tel: 1-416-946-7551 (Lab.) > Faculty of Pharmacy Fax: 1-416-978-8511 > 19 Russell Street Email: william@phm.utoronto.ca > Toronto, ON. M5S 2S2, Canada william.wei@utoronto.ca > > > From chemistry-request@server.ccl.net Thu Nov 15 19:38:05 2001 Received: from mail.shcnc.AC.CN ([202.127.16.28]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id fAG0c4B01760 for ; Thu, 15 Nov 2001 19:38:04 -0500 Received: from pc7 ([202.127.19.247]) by mail.shcnc.AC.CN (8.12.1/8.12.1) with SMTP id fAGFaV84009831 for ; Fri, 16 Nov 2001 07:36:31 -0800 (PST) Message-Id: <200111161536.fAGFaV84009831@mail.shcnc.AC.CN> Date: Fri, 16 Nov 2001 8:40:44 +0800 From: llshen To: "CHEMISTRY@ccl.net" Subject: helix bending in MD simulation X-mailer: FoxMail 3.0 beta 2 [cn] Mime-Version: 1.0 Content-Type: text/plain; charset="GB2312" Content-Transfer-Encoding: 7bit Dear CCLers: There is helix bending (unfloding on two residues) happened on the protein I simulated. Different structure prediction methods show that the helix is robust and conserved. Is there any person met same problems? And is there any simulation skills/analysis tools to find out the mechanical reason of the bending? BTW, I used paralleled EGO for MD simulation . THX! Lingling Shen