From chemistry-request@ccl.net Fri Apr 9 09:09:39 2004 Received: from neptune.tranzymepharma.com (neptune.med.usherbrooke.ca [132.210.158.200]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i39E9djR011347 for ; Fri, 9 Apr 2004 09:09:39 -0500 Received: from mercure.neokimia.com (exchange.tranzymepharma.com [192.168.1.3]) by neptune.tranzymepharma.com (8.12.10/8.12.10) with ESMTP id i39E9VQg011883; Fri, 9 Apr 2004 10:09:31 -0400 Content-Class: urn:content-classes:message MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----_=_NextPart_001_01C41E3C.44E27C82" Subject: RE: CCL:FW: calculate accessible surface area for an occluded cavity X-MimeOLE: Produced By Microsoft Exchange V6.0.6249.0 Date: Fri, 9 Apr 2004 10:09:27 -0400 Message-ID: X-MS-Has-Attach: X-MS-TNEF-Correlator: Thread-Topic: CCL:FW: calculate accessible surface area for an occluded cavity thread-index: AcQdut4fxiOO4VyDRHei75ni4VS7iQAeXe+g From: "Axel Mathieu" To: Cc: X-NK-Spam-Status: Ce message n'est pas du SPAM, (Score: 3.041, Requis: 5, FVGT_u_HAS_2LETTERFLDR,HTML_60_70,HTML_FONTCOLOR_UNKNOWN,HTML_MESSAGE,J_CHICKENPOX_39,OACYS_SINGLE,RM_rb_ANCHOR,RM_rb_BREAK,RM_rb_DIV,RM_rb_FONT,RM_rb_PARA,RM_sl_Parens,TW_PD) X-NK-Spam-Version: SpamAssassin version 2.63 X-Scanned-By: MIMEDefang 2.42 This is a multi-part message in MIME format. ------_=_NextPart_001_01C41E3C.44E27C82 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable James, =20 Success? Well I only studied one protein (human StAR protein) during my = studies and have not really used STC in its original form since. = According to Pierre Lavigne's paper = (http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=3DRetrieve = = &db=3Dpubmed&dopt=3DAbstract&list_uids=3D10716177) STC performed = extremely well as compared to the experimental X-ray data.=20 =20 In our case for StAR, we were not looking to virtually high-throughput = dock small ligands into to the cavity and thus it becomes easy to modify = what we need to make STC recognize the ligand. Actually, STC worked fine = for cholesterol so long as we changed the "atom names" of the ligands in = the pdb file to match those found in proteins (ie: an ordinary carbon = was named CA to CM - the other atoms in cholesterol were fine - it is OK = if you repeat the same name if you do not have enough to CM so long as = you can recognize them if you need to). This was the only modification = to our ligand files that we had to do. Although, you clearly need a TER = line in your pdb files to indicate where the protein stops and where the = ligand starts ... =20 I would try this simple change on a few ligands to see if it works. As = I'm certain you realize, STC is only good for large systems where = significant changes in SAS are observed/hypothesized. Now that I'm = working with small molecules, I only use STC when I study the small = molecules alongside proteins ... =20 Since, I've docked some ligands into a protein with a solvent accessible = site using part of STC as a part of a multi-factorial scoring method = that I implemented in MOE - I found that there was a nice correlation = between dH and a good binding pose for our test systems. Success? It = worked beautifully for 2 known X-ray test sets resembling our target = (the best pose of the ligand, a pentapeptide in this case, was No 1 and = was within 1 Ang of the crystal!), BUT we did not perform the biological = assays for our target yet ... =20 My understanding is that STC is starting to be used more and more for = vHTS so people must have solved the non-protein ligand issue but I have = not crossed any papers for this yet. =20 Are you docking in a solvent accessible site or in a cavity? =20 I hope this helps, best regards, =20 APM =20 ------------------------------------ Axel Mathieu, Ph.D. Scientist/Molecular Modeling Tranzyme Pharma Inc.=20 =20 Tel: (819) 820-6840 Fax : (819) 820 6841=20 www.tranzymepharma.com =20 NOTICE: This e-mail contains confidential information and is intended = for the exclusive use of the addressee. Any other person is strictly = prohibited from disclosing, distributing or reproducing it. If you have = received this e-mail by mistake, please notify us immediately by = telephone or e-mail and delete all copies. -----Original Message----- From: james.metz-.at.-abbott.com [mailto:james.metz-.at.-abbott.com]=20 Sent: 8 avril, 2004 18:41 To: Axel Mathieu Cc: james.metz-.at.-abbott.com Subject: Re: CCL:FW: calculate accessible surface area for an occluded = cavity =20 Axel,=20 Have you any success using STC to predict the binding free = energy of small molecules to proteins or=20 receptors?=20 I have tried to do this, but the program seems to be highly = parameterized to deal only with peptides=20 and proteins. I could never seem to get small molecules to work = properly.=20 Regards,=20 Jim Metz=20 James T. Metz, Ph.D. Research Investigator Chemist GPRD R46Y AP10-2 Abbott Laboratories 100 Abbott Park Road Abbott Park, IL 60064-6100 U.S.A. Office (847) 936 - 0441 FAX (847) 935 - 0548 james.metz-.at.-abbott.com This communication may contain information that is legally privileged, = confidential, or exempt from disclosure. If you are not the intended = recipient, please note that any dissemination, distribution, use, or = copying of this communication is strictly prohibited. Anyone who = receives this message in error should notify the sender immediately by = telephone or return email and delete it from his or her computer.=20 =20 "Axel Mathieu" =20 Sent by: "Computational Chemistry List" =20 04/08/2004 02:04 PM=20 =20 To: "CCL" =20 cc: =20 Subject: CCL:FW: calculate accessible surface area for an = occluded cavity Qin,=20 =20 Take a look at the freeware STC (Structure-based thermodynamic = calculations - these are based on SAS) developped by the PENCE/CIHR = group in Canada = http://www.pence.ca/software/stc/html-4.3/stc.html. I used STC to = propose a cholesterol transfer mechanism for the StAR protein (it = conatins a cavity!). In case you're interested, my you'll find my paper = abstract and reference at: = = http://www.ncbi>.nlm.nih.gov/entrez/query.fcgi?cmd=3DRetrieve&db=3Dpubmed= &dopt=3DAbstract&list_uids=3D12459035=20 =20 STC can quickly report the SAS for each heavy atom of a residue and you = just have to add them up, or fill the cavity with the ligand and = calculate the difference (supposing your ligand fills the cavity) ...=20 =20 APM=20 =20 =20 -----Original Message----- From: Q [mailto:qzou-.at.-iupui.edu]=20 Sent: 7 avril, 2004 20:30 To: chemistry-.at.-ccl.net Subject: CCL:calculate accessible surface area for an occluded cavity=20 =20 Dear All,=20 I have a protein with an internal cavity that has no access to the = outside solvent. I would like to calculate the accessible surface area = of the residues inside the cavity to see how accessible they are to the = cavity. How can I do this or what programs could help to do it? How = about NACCESS? Thanks for any input.=20 =20 Qin=20 =20 ------_=_NextPart_001_01C41E3C.44E27C82 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable

James,

 

Success? Well I only studied one protein (human StAR protein) during my studies and have not really used STC in its original = form since. According to Pierre Lavigne’s paper (http://www.ncbi= .nlm.nih.gov/entrez/query.fcgi?cmd=3DRetrieve&db=3Dpubmed&dopt=3D= Abstract&list_uids=3D10716177) STC performed extremely well as compared to the experimental X-ray data. =

 

In our case for StAR, we were not looking to virtually high-throughput dock small ligands into to the cavity and thus it becomes easy to modify what we need to = make STC recognize the ligand. Actually, STC worked = fine for cholesterol so long as we changed the “atom names” of the ligands in the pdb file to match those found in = proteins (ie: an ordinary carbon was named CA to CM – = the other atoms in cholesterol were fine - it is OK if you repeat the same name if = you do not have enough to CM so long as you can recognize them if you need to). = This was the only modification to our ligand = files that we had to do. Although, you clearly need a TER line in your pdb files to indicate where the protein stops and where the ligand starts …

 

I would try this simple change on a = few ligands to see if it works. As I’m certain = you realize, STC is only good for large systems where significant changes in = SAS are observed/hypothesized. Now that I’m working with small = molecules, I only use STC when I study the small molecules alongside proteins = …

 

Since, I’ve docked some ligands into a protein with a solvent accessible = site using part of STC as a part of a multi-factorial scoring method that I = implemented in MOE – I found that there was a nice correlation between dH and a good binding = pose for our test systems. Success? It worked beautifully = for 2 known X-ray test sets resembling our target (the best pose of the ligand, a pentapeptide = in this case, was No 1 and was within 1 Ang of the = crystal!), BUT we did not perform the biological assays for our target yet = …

 

My understanding is that STC is = starting to be used more and more for vHTS so people = must have solved the non-protein ligand issue but I = have not crossed any papers for this yet.

 

Are you docking in a solvent = accessible site or in a cavity?

 

I hope this helps, best = regards,

 

APM

 

------------------------------------

= Axel Mathieu, Ph.D.

Scientist/Molecular= Modeling

Tranzyme Pharma Inc.

 

Tel:   = (819) 820-6840

Fax : (819) 820 = 6841

 <= /span>

NOTICE: This e-mail contains confidential information and is intended for the = exclusive use of the addressee. Any other person is strictly prohibited from = disclosing, distributing or reproducing it. If you have received this e-mail by = mistake, please notify us immediately by telephone or e-mail and delete all = copies.

-----Original = Message-----
From: = james.metz-.at.-abbott.com [mailto:james.metz-.at.-abbott.com]
Sent: 8 avril, 2004 18:41
To: = Axel Mathieu
Cc: = james.metz-.at.-abbott.com
Subject: Re: = CCL:FW: calculate accessible = surface area for an occluded cavity

 


Axel,

        Have you any success using STC to predict the = binding free energy of small molecules to proteins or
receptors?

        I have tried to do this, but the program seems to = be highly parameterized to deal only with peptides
and proteins.  I could never seem to get small molecules to work properly.

        Regards,
        Jim Metz


James T. Metz, Ph.D.
Research = Investigator Chemist

GPRD R46Y AP10-2
Abbott Laboratories
100 Abbott Park Road
Abbott Park, IL  60064-6100
U.S.A.

Office (847) 936 - 0441
FAX    (847) 935 - 0548

james.metz-.at.-abbott.com

This communication may contain information that is legally privileged, confidential, or exempt from disclosure.  If you are not the = intended recipient, please note that any dissemination, distribution, use, or = copying of this communication is strictly prohibited.  Anyone who receives = this message in error should notify the sender immediately by telephone or = return email and delete it from his or her computer.

 

"Axel = Mathieu" = <AMathieu-.at.-tranzyme.com>
Sent by: "Computational Chemistry List" <chemistry-request-.at.-ccl.net>

04/08/2004 02:04 PM

       
        To:       =  "CCL" <chemistry-.at.-ccl.net>
        cc:         =
        Subject:       =  CCL:FW: calculate accessible surface area for an occluded = cavity




Qin,

 <= /font>

Take a look = at the freeware STC (Structure-based thermodynamic calculations -  these are based on SAS) developped by = the PENCE/CIHR group in Canada http://www.pence.ca/software= /stc/html-4.3/stc.html. I used STC to propose a cholesterol transfer = mechanism for the StAR protein (it conatins a cavity!). In case you're interested, my you'll find my paper abstract = and reference at: http://www.ncbi>.nlm.nih.= gov/entrez/query.fcgi?cmd=3DRetrieve&db=3Dpubmed&dopt=3DAbstract&= amp;list_uids=3D12459035

 <= /font>

STC can = quickly report the SAS for each heavy atom of a residue and you just have to add them = up, or fill the cavity with the ligand and = calculate the difference (supposing your ligand fills the = cavity) …

 <= /font>

APM

 <= /font>

 <= /font>

-----Original Message-----
From: Q [mailto:qzou-.at.-iupui.edu]
Sent: 7 = avril, 2004 20:30
To: chemistry-.at.-ccl.net
Subject: CCL:calculate = accessible surface area for an occluded cavity

 

Dear All,

 I have a protein with an internal cavity = that has no access to the outside solvent. I would like to calculate the = accessible surface area of the residues inside the cavity to see how accessible = they are to the cavity. How can I do this or what programs could help to do it? = How about NACCESS? Thanks for any input.

 

Qin

 

------_=_NextPart_001_01C41E3C.44E27C82-- From chemistry-request@ccl.net Fri Apr 9 08:44:28 2004 Received: from reformers.mr.itd.umich.edu (reformers.mr.itd.umich.edu [141.211.93.147]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i39DiSjR010530 for ; Fri, 9 Apr 2004 08:44:28 -0500 Received: from [192.168.11.5] (pcp09230223pcs.sanarb01.mi.comcast.net [69.137.220.173]) by reformers.mr.itd.umich.edu (smtp) with ESMTP id i39DiffW011995 for ; Fri, 9 Apr 2004 09:44:41 -0400 Mime-Version: 1.0 (Apple Message framework v613) In-Reply-To: References: Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed Message-Id: Content-Transfer-Encoding: 7bit From: Bruce Palfey Subject: Re: CCL:specifying the connectivity in Gaussian Date: Fri, 9 Apr 2004 09:43:24 -0400 To: CHEMISTRY-.at.-ccl.net X-Mailer: Apple Mail (2.613) Isn't this behavior the expected result for a Zwitterion in a vacuum? That is, the program is getting it right - charge separation is unfavoravble. What's missing is a solvent to stabilize charges. Bruce On Apr 8, 2004, at 8:57 PM, John Bushnell wrote: > Hi, > > If there is no barrier between the Zwitterion and the neutral > structure, then there is really no physically meaningful way to > do a full geometry optimization while maintaining the Zwitterion > if the neutral structure is lower in energy. > However, there could be a local minimum that is Zwitterionic > which is higher in energy which you might find with some careful > surface scanning (which means that there is a barrier to forming > the neutral form). > > - John > > On Thu, 8 Apr 2004, Vasile Chis wrote: > >> Dear Colleagues, >> >> I am trying to optimize a molecule (with Gaussian) with two charged >> groups, >> +NH3 and COO-, respectively. However, during the optimization, one of >> the >> amino hydrogen leaves the nitrogen and bound to one of the oxygen >> atoms of >> COO group. >> In order to preserve the two groups I imposed the same bond length >> for the >> three NH bonds, but this means a restriction which even if does not >> led to >> imaginary frequencies, however the corresponding optimized geometry >> must be >> higher in energy than that in which an NH...O hydrogen bond is >> allowed. >> The Help of the program says that there is a way of giving a specific >> connectivity for atoms, however I was not able to solve my problem. I >> will >> appreciate very much any help on this topic. >> >> Best regards and Happy Easter for everybody! >> Vasile >> >> >> ------------------------------------------- >> Dr. Vasile Chis > > > -= 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 Apr 9 06:50:03 2004 Received: from mta1.appstate.edu (mta1.appstate.edu [152.10.1.150]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i39Bo2jR006866 for ; Fri, 9 Apr 2004 06:50:03 -0500 Received: from ws1.appstate.edu (ws1.appstate.edu [152.10.1.40]) by mta1.appstate.edu (8.12.10/8.12.10) with ESMTP id i39BjSTp019419 for ; Fri, 9 Apr 2004 07:45:28 -0400 Received: from kohn.appstate.edu (cohn.chem.appstate.edu [152.10.114.100]) by appstate.edu (PMDF V6.2-X26 #30685) with ESMTP id <01L8PVQV21F6BHC468.-at-.appstate.edu> for CHEMISTRY.-at-.ccl.net; Fri, 09 Apr 2004 07:45:27 -0400 (EDT) Date: Fri, 09 Apr 2004 07:45:00 -0400 From: Steve Williams Subject: CCL: ONIOM Summary X-Sender: willsd.-at-.imap.appstate.edu To: CHEMISTRY.-at-.ccl.net Message-id: <5.1.0.14.0.20040409073628.02cd23f0.-at-.imap.appstate.edu> MIME-version: 1.0 X-Mailer: QUALCOMM Windows Eudora Version 5.1 Content-type: text/plain; format=flowed; charset=us-ascii X-MailScanner-Information: Please contact the Helpdesk @ 6266 for more information X-MailScanner-ASU-mta1: Found to be clean X-MailScanner-SpamCheck: X-MailScanner-From: willsd.-at-.appstate.edu Original Message: >I am trying to learn to do onoim calculations in g03. My test molecule is >a rather large Re(V) complex that is a +2 singlet cation. I am trying a >two layer oniom with the Re and the 6 atoms it is bound to (1 N, 4 P, 1 >Cl) as the high layer (b3lyp/lanl2dz) with the rest done at am1. I found >that the default guess did not work (stopped with an error before guess >computation began) so switched to guess=harris and got rid of that >error. I now have persistent bad file IO crashes. These usually indicate >lack of disk space, but I do not think that is the case on this machine as >I have been able to run some rather large CAS calculations, and single >layer calculations run fine (b3lyp/lanl2dz on whole complex is slow but >does run; geometry optimizations eventually converge...); none of these >large calculations required any fooling with maxdisk. I am running on a >64 bit Itanium cluster so splitting rwf file has not been needed with >other jobs. The top of my input is below: > >%mem=120MW >%nproc=4 ># opt oniom=(rb3lyp/lanl2dz:ram1) geom=connectivity guess=harris > >first try at oniom calculation for one of grant's biggies > >2 1 2 1 0 1 > C 0 9.649231 -0.243106 -0.297205 L > C 0 8.621088 -0.302810 -1.225543 L > C 0 7.252282 -0.215031 -0.805502 L > >with lots more geometry below. G03 does seem to read this file as >intended (it confirms which atoms are in the high and low layer, confirms >that the whole molecule is a +2 singlet, that the high layer is a +2 >singlet, and that the low layer is a neutral singlet. The last few lines >before G03 crashes are : > > ONIOM: Cut between C /H 120 and P 26 factor= 0.773169 0.773169 > ONIOM: saving gridpoint 17 > ONIOM: generating point 3 -- low level on real system. > Standard basis: VSTO-3G (5D, 7F) > Atomic number 75 exceeds maximum of 54 in STO -- maximum used. > There are 349 symmetry adapted basis functions of A symmetry. > Integral buffers will be 131072 words long. > Raffenetti 1 integral format. > Two-electron integral symmetry is turned on. > 349 basis functions, 1047 primitive gaussians, 349 cartesian basis > functions > 179 alpha electrons 179 beta electrons > nuclear repulsion energy 5857.5087847753 Hartrees. > NAtoms= 130 NActive= 130 NUniq= 130 SFac= 1.00D+00 NAtFMM= 60 Big=T > FileIO operation on non-existent file. >FileIO: IOper= 2 IFilNo(1)= -516 Len= 61075 IPos= 61075 >Q=***************** > > > dumping /fiocom/, unit = 1 NFiles = 51 SizExt = 524288 WInBlk > = 2048 > defal = T LstWrd = 4567040 FType=2 FMxFil=10000 > > Number 0 501 502 503 507 > 508 511 520 > Base 4167680 432128 448512 600064 610304 > 3831808 1906688 3848192 > >Then there is good bit of related (diagnostic?) stuff. My problem was caused by ignorance of the ONIOM method: the ENTIRE molecule is treated with the low level method, and the high level subset is also treated with high level method. Since there are no AM1 parameters in G03 for Re, this means that my intended calculation was doomed from the beginning. The best I can hope for is to treat the low level with something like rhf/lanl2dz, and this will nor be a large time savings over treating the whole molecule with B3LYP/lanl2dz. Thanks for helpful suggestions from Etienne Derat and Goedele Roos. Steve Williams Steve Williams A. R. Smith Department of Chemistry Appalachian State University Boone, NC 28608 USA 828-262-2965 From chemistry-request@ccl.net Fri Apr 9 08:51:43 2004 Received: from prserv.net (asmtp2.prserv.net [32.97.166.52]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i39DpgjR010703 for ; Fri, 9 Apr 2004 08:51:42 -0500 Received: from goofy (dhcp065-029-074-207.indy.rr.com[65.29.74.207]) by prserv.net (asmtp2) with SMTP id <2004040913515425202a2a96e> (Authid: jmmckel); Fri, 9 Apr 2004 13:51:55 +0000 Message-ID: <024c01c41e42$4ba5fa20$6401a8c0@goofy> From: "John McKelvey" To: "Joseph Han" , "'Jim Kress'" Cc: References: <00da01c41dbf$517de260$1a7e40ab@alphahelix> Subject: Re: CCL:DFT functionals comparison Date: Fri, 9 Apr 2004 09:52:34 -0500 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 Don't forget Goddard's X3LYP results published in the Proceedings of the National Academy of Science,... PNAS V101, p2673-2677, 2004. It compares 18 different DFT methods in addition to X3LYP Mean average deviation for G2 set for X3LYP for HOF is .12EV. John McKelvey ----- Original Message ----- From: "Joseph Han" To: "'Jim Kress'" Cc: Sent: Thursday, April 08, 2004 6:15 PM Subject: CCL:DFT functionals comparison > Jim, > > This might help: > > Tests of second-generation and third-generation density functionals for > thermochemical kinetics > Zhao, Y; Pu, JZ; Lynch, BJ; Truhlar, DG > Source: PHYSICAL CHEMISTRY CHEMICAL PHYSICS; 2004; v.6, no.4, p.673-676 > > It covers barrier heights and atomization energies. > > They did leave out KMLYP however. We've run the same tests as described > in the paper using KMLYP with the following results. > > BH6 AE6 > MSE MUE MSE MUE > KMLYP/DIDZ w/ HLC -2.86 2.86 -0.79 0.98 > KMLYP/MG3S w/ HLC -2.92 2.92 0.18 0.45 > KMLYP/6-311+G(2df,2p) w/ HLC -2.92 2.92 0.06 0.50 > > MMUE KMLYP w/ HLC 1.80 > > These results would place KMLYP near the top compared with all the other > tested methods. The only method that does a better job predicting > barrier heights is MPW1K, but the MPW1K atomization energies have a > larger error. The KMLYP atomization energies are comparable with the > best shown in the paper. Finally, the MMUE would be the best of all the > methods evaluated. > > It is important to apply the high level correction (HLC) as specified in > the original KMLYP reference in order to obtain good AE results. > > Hope this helps. > > Joseph Han > Department of Chemical Engineering > Stanford University > 650-723-0420 > FAX: 650-725-7294 > > > -----Original Message----- > > From: Computational Chemistry List > > [mailto:chemistry-request.-at-.ccl.net] On Behalf Of Jim Kress > > Sent: Thursday, April 08, 2004 12:57 PM > > To: chemistry.-at-.ccl.net > > Subject: CCL:DFT functionals comparison > > > > > > I searched the CCL archive and could find nothing on this topic. > > > > Does anyone on the list know of (and would share) a (recent) > > comprehensive > > review of DFT functionals and the quality of their prediction > > of molecular > > properties? > > > > Thanks. > > > > Jim > > > > > > > > > > -= 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 > > > > Send your subscription/unsubscription requests to: > > CHEMISTRY-REQUEST.-at-.ccl.net > > > > If your mail is bouncing from CCL.NET domain send it to the > > maintainer: > > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ > > -+-+-+-+-+ > > > > > > > > > > > > > > -= 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 Apr 9 08:09:10 2004 Received: from helix.nih.gov (helix.nih.gov [128.231.2.3]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i39D99jR009526 for ; Fri, 9 Apr 2004 08:09:09 -0500 Received: (from hlwoodc@localhost) by helix.nih.gov (8.11.7-8.359.2.8/8.11.6) id i39D9Lu9519352; Fri, 9 Apr 2004 09:09:21 -0400 (EDT) Date: Fri, 9 Apr 2004 09:09:21 -0400 From: "Woodcock, H. Lee" To: Jim Kress cc: chemistry.-at-.ccl.net Subject: Re: CCL:DFT functionals comparison In-Reply-To: <000801c41da3$a5997970$0901a8c0@mmserver> Message-ID: References: <000801c41da3$a5997970$0901a8c0@mmserver> MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Thu, 8 Apr 2004, Jim Kress wrote: >I searched the CCL archive and could find nothing on this topic. > >Does anyone on the list know of (and would share) a (recent) comprehensive >review of DFT functionals and the quality of their prediction of molecular >properties? This is a good review of DFT functionals as they compares to Electron affinities..... Atomic and molecular electron affinities: Photoelectron experiments and theoretical computations Rienstra-Kiracofe JC, Tschumper GS, Schaefer HF, Nandi S, Ellison GB CHEMICAL REVIEWS 102 (1): 231-282 JAN 2002 From chemistry-request@ccl.net Fri Apr 9 03:47:34 2004 Received: from av7-2-sn1.fre.skanova.net (av7-2-sn1.fre.skanova.net [81.228.11.114]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i398lXjR000935 for ; Fri, 9 Apr 2004 03:47:33 -0500 Received: by av7-2-sn1.fre.skanova.net (Postfix, from userid 502) id C37E537E66; Fri, 9 Apr 2004 10:47:44 +0200 (CEST) Received: from smtp3-2-sn1.fre.skanova.net (smtp3-2-sn1.fre.skanova.net [81.228.11.164]) by av7-2-sn1.fre.skanova.net (Postfix) with ESMTP id B225937E47; Fri, 9 Apr 2004 10:47:44 +0200 (CEST) Received: from [192.168.0.100] (h93n1fls32o916.telia.com [213.65.165.93]) by smtp3-2-sn1.fre.skanova.net (Postfix) with ESMTP id E430437E58; Fri, 9 Apr 2004 10:47:34 +0200 (CEST) Mime-Version: 1.0 X-Sender: u42123287.-at-.m1.421.telia.com (Unverified) Message-Id: In-Reply-To: <5.0.0.25.2.20040408091543.02280f98.-at-.phys.ubbcluj.ro> References: <5.0.0.25.2.20040408091543.02280f98.-at-.phys.ubbcluj.ro> Date: Fri, 9 Apr 2004 10:45:05 +0200 To: Vasile Chis , chemistry.-at-.ccl.net From: Per-Ola Norrby Subject: Re: CCL:specifying the connectivity in Gaussian Content-Type: text/plain; charset="us-ascii" ; format="flowed" Dear Vasile, Many researchers have looked at the amino acid zwitterions. They usually are not minima in the gas phase. You HAVE to use a solvation model to run this calculation properly. Even if you can enforce the structure in the gas phase, the results are meaningless. I'm including some references to our publications in the area; there are plenty of others. Best regards, Per-Ola # "An NMR and ab Initio Quantum Chemical Study of Acid-Base Equilibria for Conformationally Constrained Acidic alpha-Amino Acids in Aqueous Solution" Peter Aadal Nielsen, Jerzy W. Jaroszewski, Per-Ola Norrby, and Tommy Liljefors, J. Am. Chem. Soc. 2001, 123, 2003-2006. # "Quantum Mechanical Conformational Analysis of beta-Alanine Zwitterion in Aqueous Solution" Peter Aadal Nielsen, Per-Ola Norrby, Tommy Liljefors, Nadia Rega, and Vincenzo Barone, J. Am. Chem. Soc. 2000, 122, 3151-3155 # "An ab initio study of the trimethylamine - formic acid and the trimethylammonium ion - formate anion complexes, their monohydrates and their interactions with a dielectric continuum " Tommy Liljefors and Per-Ola Norrby, J. Am. Chem. Soc. 1997, 119, 1052-1058 >Dear Colleagues, > >I am trying to optimize a molecule (with Gaussian) with two charged >groups, +NH3 and COO-, respectively. However, during the >optimization, one of the amino hydrogen leaves the nitrogen and >bound to one of the oxygen atoms of COO group. >In order to preserve the two groups I imposed the same bond length >for the three NH bonds, but this means a restriction which even if >does not led to imaginary frequencies, however the corresponding >optimized geometry must be higher in energy than that in which an >NH...O hydrogen bond is allowed. >The Help of the program says that there is a way of giving a >specific connectivity for atoms, however I was not able to solve my >problem. I will appreciate very much any help on this topic. > >Best regards and Happy Easter for everybody! >Vasile > > >------------------------------------------- >Dr. Vasile Chis >"Babes-Bolyai" University >Dept. of Physics >Kogalniceanu 1, >RO-400084 Cluj-Napoca >Romania >Tel: +40 (0)264 405300 ext 5153 >Fax: +40 (0)264 591906 >e-mail: vchis.-at-.phys.ubbcluj.ro >http://www.phys.ubbcluj.ro/~vchis >--------------------------------------------- > > > >-= 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) >-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ -- 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 From chemistry-request@ccl.net Fri Apr 9 11:06:36 2004 Received: from uucp0.ash.ops.us.uu.net (uucp0.ash.ops.us.uu.net [198.5.241.21]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i39G6ajR016192 for ; Fri, 9 Apr 2004 11:06:36 -0500 Received: from uucp0.ash.ops.us.uu.net by uucp0.ash.ops.us.uu.net with SMTP (peer crosschecked as: uucp0.ash.ops.us.uu.net [198.5.241.21]) id QQqjrc28164 for ; Fri, 9 Apr 2004 16:06:49 GMT Received: from m10.UUCP by uucp0.ash.ops.us.uu.net with UUCP/RMAIL ; Fri, 9 Apr 2004 16:06:49 +0000 Received: from svega.gaussian.com by m10.gaussian.com; Fri, 9 Apr 2004 11:58:41 -0400 Received: (from frisch@localhost) by svega.gaussian.com (980427.SGI.8.8.8/980728.SGI.AUTOCF) id LAA77630 for chemistry..at..ccl.net; Fri, 9 Apr 2004 11:58:40 -0400 (EDT) From: frisch..at..gaussian.com (Mike Frisch) Message-Id: <200404091558.LAA77630..at..svega.gaussian.com> Subject: Re: CCL:ONIOM Summary To: chemistry..at..ccl.net Date: Fri, 9 Apr 2004 11:58:40 -0400 (EDT) In-Reply-To: <5.1.0.14.0.20040409073628.02cd23f0..at..imap.appstate.edu> from "Steve Williams" at Apr 9, 2004 07:45:00 am X-Mailer: ELM [version 2.4 PL25] MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Steve Williams writes: > > My problem was caused by ignorance of the ONIOM method: the ENTIRE molecule > is treated with the low level method, and the high level subset is also > treated with high level method. Since there are no AM1 parameters in G03 > for Re, this means that my intended calculation was doomed from the > beginning. The best I can hope for is to treat the low level with > something like rhf/lanl2dz, and this will nor be a large time savings over > treating the whole molecule with B3LYP/lanl2dz. Actually, you can do the low level with LSDA/LANL2MB/Auto, which probably is quite a bit cheaper than B3LYP/LANL2DZ. Mike Frisch From chemistry-request@ccl.net Fri Apr 9 15:07:09 2004 Received: from mail.vu.nl (mail.vu.nl [130.37.129.161]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i39K78jR021198 for ; Fri, 9 Apr 2004 15:07:09 -0500 Received: from few.vu.nl (126-128.vu.surfnetthuis.nl [145.98.126.128]) by mail.vu.nl (8.11.6/8.11.6) with ESMTP id i39K7II25682; Fri, 9 Apr 2004 22:07:18 +0200 Date: Fri, 9 Apr 2004 22:07:18 +0200 Subject: Re: CCL:DFT functionals comparison Content-Type: multipart/alternative; boundary=Apple-Mail-8-154823257 Mime-Version: 1.0 (Apple Message framework v553) Cc: To: "Jim Kress" From: Marcel Swart In-Reply-To: <000801c41da3$a5997970$0901a8c0@mmserver> Message-Id: <80B353B6-8A61-11D8-B69E-000393AEC93C[at]few.vu.nl> X-Mailer: Apple Mail (2.553) X-MailScanner-Information: Please contact servicedesk[at]it.vu.nl for more information X-MailScanner: Found to be clean X-MailScanner-SpamCheck: geen spam, spamfilter (score=-4.9, vereist 5, autolearn=not spam, BAYES_00 -4.90) --Apple-Mail-8-154823257 Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=WINDOWS-1252; format=flowed On Thursday, Apr 8, 2004, at 21:56 Europe/Amsterdam, Jim Kress wrote: > I searched the CCL archive and could find nothing on this topic. > > Does anyone on the list know of (and would share) a (recent)=20 > comprehensive > review of DFT functionals and the quality of their prediction of=20 > molecular > properties? Two recent papers from experts in the field may be useful to you: - Staroverov, Scuseria, Tao and Perdew, J.Chem.Phys. 119(23) (2003)=20 12129-12137 they compare their latest TPSS(h) functional with HF, LSDA, BLYP,=20 BPW91, BP86, PW91, PBE, HCTH, OLYP, B3LYP, B3PW91, B3P86, PBE0, VSXC, PKZB - Boese, Martin and Handy, J.Chem.Phys. 119(6) (2003) 3005-3014 they compare HF, LSDA, PKZB, PBE, mPW1K, PW91PW91, BP86, mPW91PW91,=20= BLYP, BPW91, PBE0, OLYP, B98, B3LYP, B97-2, VSXC, HCTH-x, B97-1, t-HCTH(h) I've made a small contribution myself, by comparing the accuracy of=20 geometries of several standard GGA's and LDA using Slater type basis sets, and the=20 influence of core-electrons and relativistic corrections on it: - Swart and Snijders, Theor.Chem.Acc. 110 (2003) 34-41 =96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96= =96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96 dr. Marcel Swart Organische en Anorganische Chemie (until May 1, 2004) Theoretische Chemie (after May 1, 2004) Vrije Universiteit Amsterdam Faculteit der Exacte Wetenschappen De Boelelaan 1083 1081 HV Amsterdam The Netherlands E m.swart[at]few.vu.nl W http://go.to/m.swart =96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96= =96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96 --Apple-Mail-8-154823257 Content-Transfer-Encoding: quoted-printable Content-Type: text/enriched; charset=WINDOWS-1252 On Thursday, Apr 8, 2004, at 21:56 Europe/Amsterdam, Jim Kress wrote: I searched the CCL archive and could find nothing on this topic. Does anyone on the list know of (and would share) a (recent) comprehensive review of DFT functionals and the quality of their prediction of molecular properties? Two recent papers from experts in the field may be useful to you: - Staroverov, Scuseria, Tao and Perdew, J.Chem.Phys. 119(23) (2003) 12129-12137 they compare their latest TPSS(h) functional with HF, LSDA, BLYP, BPW91, BP86, PW91, PBE, HCTH, OLYP, B3LYP, B3PW91, B3P86, PBE0, VSXC, PKZB - Boese, Martin and Handy, J.Chem.Phys. 119(6) (2003) 3005-3014 they compare HF, LSDA, PKZB, PBE, mPW1K, PW91PW91, BP86, mPW91PW91, BLYP, BPW91, PBE0, OLYP, B98, B3LYP, B97-2, VSXC, HCTH-x, B97-1, t-HCTH(h) I've made a small contribution myself, by comparing the accuracy of geometries of several standard GGA's and LDA using Slater type basis sets, and the influence of core-electrons and relativistic corrections on it: - Swart and Snijders, Theor.Chem.Acc. 110 (2003) 34-41 = Helvetica=96=96=96=96=96=96=96=96=96=96=96=96=96= =96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96= =96=96=96=96=96=96 dr. Marcel Swart Organische en Anorganische Chemie (until May 1, 2004) Theoretische Chemie (after May 1, 2004) Vrije Universiteit Amsterdam Faculteit der Exacte Wetenschappen De Boelelaan 1083 1081 HV Amsterdam The Netherlands E m.swart[at]few.vu.nl W http://go.to/m.swart =96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96= =96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96 --Apple-Mail-8-154823257-- From chemistry-request@ccl.net Fri Apr 9 11:48:32 2004 Received: from pat.cryst.bbk.ac.uk (pat-ext.cryst.bbk.ac.uk [193.61.32.113]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i39GmWjR017235 for ; Fri, 9 Apr 2004 11:48:32 -0500 Received: from mail.cryst.bbk.ac.uk (chem239.chem.ucl.ac.uk [128.40.76.239]) by pat.cryst.bbk.ac.uk (8.12.8/8.12.8) with ESMTP id i39Gmcog029229 for ; Fri, 9 Apr 2004 17:48:42 +0100 Message-ID: <4076D2D8.5000805~at~mail.cryst.bbk.ac.uk> Date: Fri, 09 Apr 2004 17:44:08 +0100 From: Ricardo Grau-Crespo User-Agent: Mozilla/5.0 (Windows; U; Windows NT 5.0; en-US; rv:1.4) Gecko/20030624 Netscape/7.1 (ax) X-Accept-Language: en-us, en MIME-Version: 1.0 To: chemistry~at~ccl.net Subject: high-temp energy surfaces in magnetic systems Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit X-cryst-bbk-ac-uk-MailScanner-Information: Please contact CCSG more information (http://www.cryst.bbk.ac.uk/CCSG/) X-cryst-bbk-ac-uk-MailScanner: Found to be clean X-cryst-bbk-ac-uk-MailScanner-SpamCheck: not spam, SpamAssassin (score=-4.9, required 9, autolearn=not spam, BAYES_00 -4.90) Dear all, The energy hypersurface (energy as a function of the position of the nuclei) is normally considered in molecular dynamics as a function that is independent of temperature. This is obviously just an approximation. In particular, for atoms with non-zero magnetic moments (say, for example, a ferromagnetic material) it is clear that the energy surface is not the same at low temperatures (in the ferromagnetic state) as at high temperatures (paramagnetic state). In these magnetic systems, if one wants to use 0 K ab initio calculations to obtain approximates 'high-temperature' energy surfaces (for example, in order to fit interatomic potentials to be used in high temperature MD), one normally has to choose between: 1. spin polarized calculations - which introduce the error associated to the ordering of the frozen magnetic moments (such order is not present at high temperatures), or 2. non spin polarized calculations - which introduce an error because of the wrong electronic configurations of the magnetic atoms. I would like to know which approximation is better, that is, which of these errors is less significant for the HT energy surface. Is there a general answer for this question? I would appreciate any comment or suggestion. Thank you very much, Ricardo. -- Ricardo Grau-Crespo PhD Student - University of London Christopher Ingold Laboratories, room 205 20 Gordon Street, London WC1H 0AJ United Kingdom Tel : +44(0) 20 7679 7465 Fax : +44(0) 20 7631 6803 Web : http://img.cryst.bbk.ac.uk/www/graucrespo/homepage.htm ------------------------------------------------------------- From chemistry-request@ccl.net Fri Apr 9 14:46:46 2004 Received: from mail.vu.nl (mail.vu.nl [130.37.129.161]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i39JkjjR020764 for ; Fri, 9 Apr 2004 14:46:46 -0500 Received: from few.vu.nl (126-128.vu.surfnetthuis.nl [145.98.126.128]) by mail.vu.nl (8.11.6/8.11.6) with ESMTP id i39JklI22854; Fri, 9 Apr 2004 21:46:51 +0200 Date: Fri, 9 Apr 2004 21:46:46 +0200 Subject: Re: CCL:Suitable basis set for organometallic compound Content-Type: multipart/alternative; boundary=Apple-Mail-6-153591482 Mime-Version: 1.0 (Apple Message framework v553) Cc: "CCL" To: "Kwanyong Seo" From: Marcel Swart In-Reply-To: <001201c41d74$d3338f80$e325f88f@ilsun> Message-Id: X-Mailer: Apple Mail (2.553) X-MailScanner-Information: Please contact servicedesk[at]it.vu.nl for more information X-MailScanner: Found to be clean X-MailScanner-SpamCheck: geen spam, spamfilter (score=-4.8, vereist 5, autolearn=not spam, BAYES_00 -4.90, HTML_MESSAGE 0.10) --Apple-Mail-6-153591482 Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=WINDOWS-1252; format=flowed On Thursday, Apr 8, 2004, at 16:21 Europe/Amsterdam, Kwanyong Seo wrote: > 1. If=A0we=A0use two=A0types of basis set in one calculation. How can = we=20 > write the=A0basis set=A0in > =A0=A0 G03=A0input. (For example: When we calculate the Fe(CO)5 = molecule, we=20 > use 6-31G basis set for carbon and > =A0=A0 Oxygen atom, and we use ECP basis set for iron atom) Most conveniently this is done using the following link, where you can=20= specify which atoms you want to look at, and for which program: http://www.emsl.pnl.gov/forms/basisform.html [note, there should probably be no difference between G94 and G03] Also note the following paper, which reports on p. 4658 a comparison=20 between LanL2DZ, CEP-121G, and 6-311+G** basis sets for iron complexes; LanL2DZ can not be trusted=20= they say, and a difference of ca. 4 kcal/mol is found between CEP-121G and 6-311+G**. Takashi Kamachi and Kazunari Yoshizawa* J AM CHEM SOC 125 (15): 4652-4661 =96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96= =96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96 dr. Marcel Swart Organische en Anorganische Chemie (until May 1, 2004) Theoretische Chemie (after May 1, 2004) Vrije Universiteit Amsterdam Faculteit der Exacte Wetenschappen De Boelelaan 1083 1081 HV Amsterdam The Netherlands E m.swart[at]few.vu.nl W http://go.to/m.swart =96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96= =96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96 --Apple-Mail-6-153591482 Content-Transfer-Encoding: quoted-printable Content-Type: text/enriched; charset=WINDOWS-1252 On Thursday, Apr 8, 2004, at 16:21 Europe/Amsterdam, Kwanyong Seo wrote: 1. If=A0we=A0use two=A0types of basis set in one calculation. How can we write the=A0basis set=A0in =A0=A0 G03=A0input. (For example: When we calculate the Fe(CO)5 molecule, we use 6-31G basis set for carbon and =A0=A0 Oxygen atom, and we use ECP basis set for iron = atom) Most conveniently this is done using the following link, where you can specify which atoms you want to look at, and for which program: http://www.emsl.pnl.gov/forms/basisform.html [note, there should probably be no difference between G94 and G03] Also note the following paper, which reports on p. 4658 a comparison between LanL2DZ, CEP-121G, and 6-311+G** basis sets for iron complexes; LanL2DZ can not be trusted they say, and a difference of ca. 4 kcal/mol is found between CEP-121G and 6-311+G**. HelveticaTakashi Kamachi and Kazunari Yoshizawa* Lucida SansJ AM CHEM SOC 125 (15): 4652-4661=20 Lucida Sans = Helvetica=96=96=96=96=96=96=96=96=96= =96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96= =96=96=96=96=96=96=96=96=96=96 dr. Marcel Swart Organische en Anorganische Chemie (until May 1, 2004) Theoretische Chemie (after May 1, 2004) Vrije Universiteit Amsterdam Faculteit der Exacte Wetenschappen De Boelelaan 1083 1081 HV Amsterdam The Netherlands E m.swart[at]few.vu.nl W http://go.to/m.swart =96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96= =96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96 --Apple-Mail-6-153591482--