From owner-chemistry@ccl.net Thu Aug 24 02:44:00 2006 From: "Gopakumar gopakumar%%chem.kuleuven.be" To: CCL Subject: CCL: Varying amount of HF exchange Message-Id: <-32428-060823165428-17323-48W9KCwLwo8ihTM1VWrEAQ_._server.ccl.net> X-Original-From: Gopakumar Content-Type: TEXT/PLAIN; charset=US-ASCII Date: Wed, 23 Aug 2006 21:48:36 +0200 (CEST) MIME-Version: 1.0 Sent to CCL by: Gopakumar [gopakumar-$-chem.kuleuven.be] Hi all, Thank you very much for every one for the fast reply... But can any one tell me, whether these things are possible with turbomole, since we have access to that program. I will check the other options in the mean time. Thanking you again -Gopakumar On Wed, 23 Aug 2006, Gopakumar G gopakumar_._chem.kuleuven.be wrote: > Sent to CCL by: "Gopakumar G" [gopakumar_._chem.kuleuven.be] > Hello all, > > I am trying to do some DFT computations with the B3LYP functional, > varying the amount of HF exchange. Does any body know a program which will be good for this purpose. > > Thanking you all for your time > > > -Gopakumar> > > > -- G. Gopakumar, Division of Quantum Chemistry and Physical Chemistry, Department of Chemistry, University of Leuven, Celestijnenlaan 200F, B-3001 Heverlee (Leuven), Belgium. e-mail: gopakumar{=}chem.kuleuven.be Disclaimer: http://www.kuleuven.be/cwis/email_disclaimer.htm From owner-chemistry@ccl.net Thu Aug 24 04:30:01 2006 From: "Uwe Huniar uwe.huniar%x%cosmologic.de" To: CCL Subject: CCL: Varying amount of HF exchange Message-Id: <-32429-060824042303-24385-9blRTthdKrhL5CmIgEtDLQ.:.server.ccl.net> X-Original-From: Uwe Huniar Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-15 Date: Thu, 24 Aug 2006 09:20:12 +0200 MIME-Version: 1.0 Sent to CCL by: Uwe Huniar [uwe.huniar|-|cosmologic.de] HI, > But can any one tell me, whether these things are possible with turbomole, > since we have access to that program. no, you can not set the amount of HF exchange or any other parameter of the functionals in the input of Turbomole. Regards, Uwe Turbomole Support Team From owner-chemistry@ccl.net Thu Aug 24 07:57:01 2006 From: "Arturo Robertazzi robertaz,+,sissa.it" To: CCL Subject: CCL: Experimental stacking energies between nucleobases Message-Id: <-32430-060824033919-20714-KFqFRi/OvzRpJUdgUsMRBw[a]server.ccl.net> X-Original-From: Arturo Robertazzi Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed Date: Thu, 24 Aug 2006 09:39:05 +0200 (CEST) MIME-Version: 1.0 Sent to CCL by: Arturo Robertazzi [robertaz!^!sissa.it] Dear Arvydas, Unfortunately I am not aware of experimental data about the GC in water solvent, but I can tell you that the GC energy estimated in gas phase at CCSD level is about 70kj/mol, see Hobza et al. JACS, 2003, 125, 15608. If you cannot efford this level of theory for your calculations, you should try the BHandH DFT functional. We have found that full optimisation with BHandH/6-311++G(d,p) gives an energy for the GC stacked pair of 72kj/mol, see Journal computational Chemistry, 2006, 27, 491-504. For more details please contact me, Arturo Robertazzi On Tue, 22 Aug 2006, Arvydas Tamulis tamulis{:}mserv.itpa.lt wrote: > Sent to CCL by: Arvydas Tamulis [tamulis-#-mserv.itpa.lt] > > Dear Colleagues, > > Would you please to say what are experimental stabilizing stacking > interaction energies between natural nucleobases in water solvent? > I have received stacking energy equal to around 100 kcal/mol using > MP2/6-31+G* between guanine and cytosine in surrounded water cluster. > > With best regards, > Arvydas Tamulis> > > > -- Dr. Arturo Robertazzi INFM Democritos Center and International School for Advanced Studies (SISSA/ISAS) via Beirut 2-4 Trieste, 34014 Italy e-mail: robertaz _ sissa.it phone: 040-3787-571 Home-Page: www.arturorobertazzi.blogspot.com From owner-chemistry@ccl.net Thu Aug 24 11:25:00 2006 From: "Monique Brito moniquebrito**yahoo.com.br" To: CCL Subject: CCL: Experimental stacking energies between nucleobases Message-Id: <-32431-060823204023-4939-1TX1ljP7QbCSnUe4f9MR0w(a)server.ccl.net> X-Original-From: Monique Brito Content-Transfer-Encoding: 8bit Content-Type: multipart/alternative; boundary="0-958937077-1156376415=:58716" Date: Wed, 23 Aug 2006 23:40:15 +0000 (GMT) MIME-Version: 1.0 Sent to CCL by: Monique Brito [moniquebrito|,|yahoo.com.br] --0-958937077-1156376415=:58716 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Hi, Arvydas, Stacking energies are energies related with the interaction of aromatic rings, due to their pi electrons clouds. These interactions can be perpendicular, which is called T-stacking interactions; or can be parallel, which is called pi-stacking. I hope it helps you! Monique Brito "Arvydas Tamulis tamulis{:}mserv.itpa.lt" escreveu: Sent to CCL by: Arvydas Tamulis [tamulis-#-mserv.itpa.lt] Dear Colleagues, Would you please to say what are experimental stabilizing stacking interaction energies between natural nucleobases in water solvent? I have received stacking energy equal to around 100 kcal/mol using MP2/6-31+G* between guanine and cytosine in surrounded water cluster. With best regards, Arvydas Tamulishttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt--------------------------------- Você quer respostas para suas perguntas? Ou você sabe muito e quer compartilhar seu conhecimento? Experimente o Yahoo! Respostas! --0-958937077-1156376415=:58716 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Hi, Arvydas,

Stacking energies are energies related with the interaction of aromatic rings, due  to their pi electrons clouds. These interactions can be perpendicular, which is called T-stacking interactions; or can be parallel, which is called pi-stacking.
I hope it helps you!
Monique Brito 

"Arvydas Tamulis tamulis{:}mserv.itpa.lt" <owner-chemistry]-[ccl.net> escreveu:
Sent to CCL by: Arvydas Tamulis [tamulis-#-mserv.itpa.lt]

Dear Colleagues,

Would you please to say what are experimental stabilizing stacking
interaction energies between natural nucleobases in water solvent?
I have received stacking energy equal to around 100 kcal/mol using
MP2/6-31+G* between guanine and cytosine in surrounded water cluster.

With best regards,
Arvydas Tamulis






Você quer respostas para suas perguntas? Ou você sabe muito e quer compartilhar seu conhecimento? Experimente o Yahoo! Respostas! --0-958937077-1156376415=:58716-- From owner-chemistry@ccl.net Thu Aug 24 12:00:00 2006 From: "Shobe, David David.Shobe{=}sud-chemie.com" To: CCL Subject: CCL: Choosing thermochemical data Message-Id: <-32432-060824100523-16741-KJOdXVkl4zqCQ5ozch2dxg=-=server.ccl.net> X-Original-From: "Shobe, David" Content-class: urn:content-classes:message Content-Type: multipart/alternative; boundary="----_=_NextPart_001_01C6C780.D8D9B573" Date: Thu, 24 Aug 2006 15:26:02 +0200 MIME-Version: 1.0 Sent to CCL by: "Shobe, David" [David.Shobe#%#sud-chemie.com] This is a multi-part message in MIME format. ------_=_NextPart_001_01C6C780.D8D9B573 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable You may have heard the adage, "If you have a watch, you always know what ti= me it is. If you have 2 watches, you never know what time it is." Well, = a patron of mine is in a similar situation. He's trying to get the most co= rrect values of enthalpy and entropy of various light hydrocarbons at diffe= rent temperatures, and has consulted a number of sources. The problem is that every reference seems to have a different value (even f= or 298 K), and he doesn't know which one to pick. He's even found discrepan= cies between reference books and the original scientific papers cited by th= ese books. All of these are "trustable" sources, but they can't all be rig= ht and he needs a fairly high accuracy for calculations based on this therm= ochemical data. What advice should I give him? --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_01C6C780.D8D9B573 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Choosing thermochemical data

You may have heard the adage, "If you= have a watch, you always know what time it is.  If you have 2 watches= , you never know what time it is."   Well, a patron of mine = is in a similar situation.  He's trying to get the most correct values= of enthalpy and entropy of various light hydrocarbons at different tempera= tures, and has consulted a number of sources.

The problem is that every reference seems = to have a different value (even for 298 K), and he doesn't know which one t= o pick. He's even found discrepancies between reference books and the origi= nal scientific papers cited by these books.  All of these are "tr= ustable" sources, but they can't all be right and he needs a fairly hi= gh accuracy for calculations based on this thermochemical data.  = What advice should I give him?

--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_01C6C780.D8D9B573-- From owner-chemistry@ccl.net Thu Aug 24 13:03:00 2006 From: "Gonzalo Jimenez Oses gonzalo.jimenez:-:dq.unirioja.es" To: CCL Subject: CCL: explicit solvation and SCRF models Message-Id: <-32433-060824130155-11872-+PuBWMeW6n3BXZDYsiUzyw a server.ccl.net> X-Original-From: "Gonzalo Jimenez Oses" Date: Thu, 24 Aug 2006 13:01:54 -0400 Sent to CCL by: "Gonzalo Jimenez Oses" [gonzalo.jimenez{=}dq.unirioja.es] Hi all, A question has raised to me in the last days. When using a few explicit solvent molecules (i.e. the first solvation shell), is it more or less "correct" and/or "accurate" to use a SCRF moldel (i.e. PCM) to describe de bulk solvent effects?. I have heard somewhere that explicitly solvated solutes are more difficult to treat by means of PCM models, because of the use overlapping spheres to describe the solute cavity. I wonder if the values obtained through this methodology (which in turn seems to be more "correct" than simple SCRF models) are feasible or the solvation free energies might be somewhat over/understimated. Are there any paper related to this, apart from the well-known reviews in solvation methods? Thank u very much, I wait for your ideas. Gonzalo From owner-chemistry@ccl.net Thu Aug 24 13:37:01 2006 From: "Nathaniel Nucci nvnucci(_)mail.med.upenn.edu" To: CCL Subject: CCL:G: basis set selection for small aromatic molecule Gaussian calculations Message-Id: <-32434-060824124801-10616-l0o1/zYzWwGvVfzY6L4t+Q,+,server.ccl.net> X-Original-From: "Nathaniel Nucci" Date: Thu, 24 Aug 2006 12:48:01 -0400 Sent to CCL by: "Nathaniel Nucci" [nvnucci,mail.med.upenn.edu] Hello everyone, I am using Gaussian 98 to perform vacuum geometry optimizations and normal mode analysis on small aromatic, organic molecules, principally tyrosine derivatives but also some molecules with larger aromatic systems. Thus far, I have typically been using 6-311++G(d,p) as the largest basis set for these calculations. I've been working my way up to that basis set gradually with HF, then performing final calculations using B3LYP. My question is whether this basis set is likely to be sufficient for these systems. Are additional d functions and/or f functions for the heavy atoms necessary? Are additional p functions or d functions for the hydrogens needed? I understand that a larger basis set is better, but most of the analysis that I am doing is comparative in nature, driven toward understanding differences between these molecules as a function of chemical differences, so is this basis set sufficient for deriving reliable conclusions for such analysis? Also, I would like to perform some exited state calculations on these molecules in order to look at differences in charge distributions upon excitation. Are there additional factors that I must consider in terms of basis set for those calculations? Thanks in advance to any who can offer suggestions, advice, or good references. Nathaniel Nucci From owner-chemistry@ccl.net Thu Aug 24 14:17:01 2006 From: "Mark Zottola mzottola-#-gmail.com" To: CCL Subject: CCL:G: basis set selection for small aromatic molecule Gaussian calculations Message-Id: <-32435-060824141524-23555-Qw0ZmFsuct8Yi8MCTfh6OQ_+_server.ccl.net> X-Original-From: "Mark Zottola" Content-Type: multipart/alternative; boundary="----=_Part_159885_1677445.1156443319509" Date: Thu, 24 Aug 2006 14:15:19 -0400 MIME-Version: 1.0 Sent to CCL by: "Mark Zottola" [mzottola++gmail.com] ------=_Part_159885_1677445.1156443319509 Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit Content-Disposition: inline Nathaniel, If I may point you to some recent work of ours; Klein, R.A.; Zottola, M.A.; *Chem. Phys. Lett. **2006*, 419, 254. This evaluates the performance of MPW1PW91/6-311++(2d,p) against other B3LYP, MP2, and CCSD against 6-31+g(d,p) and a variety of Dunning basis sets. I think you will find the the MPW1PW91/6-311++g(2d,p) is a superior method for getting structures of moderately-sized molecules on a par with CCSD and higher order (DZ through QZ) Dunning sets. As to excited state calculations, I will let others better versed in that field address this question. I hope this helps! Mark On 8/24/06, Nathaniel Nucci nvnucci(_)mail.med.upenn.edu < owner-chemistry++ccl.net> wrote: > > Sent to CCL by: "Nathaniel Nucci" [nvnucci,mail.med.upenn.edu] > Hello everyone, > > I am using Gaussian 98 to perform vacuum geometry optimizations and normal > mode analysis on small aromatic, organic molecules, principally tyrosine > derivatives but also some molecules with larger aromatic systems. Thus far, > I have typically been using 6-311++G(d,p) as the largest basis set for these > calculations. I've been working my way up to that basis set gradually with > HF, then performing final calculations using B3LYP. My question is whether > this basis set is likely to be sufficient for these systems. Are additional > d functions and/or f functions for the heavy atoms necessary? Are > additional p functions or d functions for the hydrogens needed? I > understand that a larger basis set is better, but most of the analysis that > I am doing is comparative in nature, driven toward understanding differences > between these molecules as a function of chemical differences, so is this > basis set sufficient for deriving reliable conclusions for such > analysis? Also, I would like to ! > perform some exited state calculations on these molecules in order to look > at differences in charge distributions upon excitation. Are there > additional factors that I must consider in terms of basis set for those > calculations? Thanks in advance to any who can offer suggestions, advice, > or good references. > > Nathaniel Nucci> > > > ------=_Part_159885_1677445.1156443319509 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Content-Disposition: inline
Nathaniel,
 
If I may point you to some recent work of ours;

Klein, R.A.; Zottola, M.A.; Chem. Phys. Lett. 2006, 419, 254.

This evaluates the performance of MPW1PW91/6-311++(2d,p) against other= B3LYP, MP2, and CCSD against 6-31+g(d,p) and a variety of Dunning basis se= ts.  I think you will find the the MPW1PW91/6-311++g(2d,p) is a superi= or method for getting structures of moderately-sized molecules on a par wit= h CCSD and higher order (DZ through QZ) Dunning sets.
 
As to excited state calculations, I will let others better versed in t= hat field address this question.
 
I hope this helps!
 
 
Mark

 
On 8/24/06, = Nathaniel Nucci nvnucci(_)mail.med.upenn.edu <owner-chemistry++ccl.net> wrote:
Sent to CCL by: "Nathaniel&= nbsp; Nucci" [nvnucci,mail.= med.upenn.edu ]
Hello everyone,

I am using Gaussian 98 to perform vacuum ge= ometry optimizations and normal mode analysis on small aromatic, organic mo= lecules, principally tyrosine derivatives but also some molecules with larg= er aromatic systems.  Thus far, I have typically been using 6-311= ++G(d,p) as the largest basis set for these calculations.  I've b= een working my way up to that basis set gradually with HF, then performing = final calculations using B3LYP.  My question is whether this basi= s set is likely to be sufficient for these systems.  Are addition= al d functions and/or f functions for the heavy atoms necessary?  = ;Are additional p functions or d functions for the hydrogens needed? &= nbsp;I understand that a larger basis set is better, but most of the analys= is that I am doing is comparative in nature, driven toward understanding di= fferences between these molecules as a function of chemical differences, so= is this basis set sufficient for deriving reliable conclusions for such an= alysis?  Also, I would like to !
perform some exited state calculations on these molecules in order to l= ook at differences in charge distributions upon excitation.  Are = there additional factors that I must consider in terms of basis set for tho= se calculations?  Thanks in advance to any who can offer suggesti= ons, advice, or good references.

Nathaniel Nucci



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------=_Part_159885_1677445.1156443319509-- From owner-chemistry@ccl.net Thu Aug 24 21:27:01 2006 From: "Raji Raji raji###anal.chem.tohoku.ac.jp" To: CCL Subject: CCL:G: explicit solvation and SCRF models Message-Id: <-32436-060824212558-10976-4NiNhHzTSUH3+3fzsRnv8w*o*server.ccl.net> X-Original-From: "Raji Raji" Date: Thu, 24 Aug 2006 21:25:57 -0400 Sent to CCL by: "Raji Raji" [raji|anal.chem.tohoku.ac.jp] Dear Dr.Gonzalo, First of all I dont know what kind of property you want to calculate using explicit solvent molecules. But please do find in the following papers, the solvent effect on the electronic g-tensors. It explains the advantage of the explicit solvent molecules in combination with PCM and COSMO methods. 1) Explicit solvent molecules and PCM (gaussian) : Zilvinas Rinkevicius, Lyudmyla Telyatnyk, and Olav Vahtras, J. Chem. Phys., Vol. 121, No. 11, 2004, 5051-5060. 2)Explicit solvent molecules and COSMO (ORCA) : Sebastian Sinnecker, Arivazhagan Rajendran, Andreas Klamt, Michael Diedenhofen, and Frank Neese, J. Phys. Chem. A 2006, 110, 2235-2245. > from the above two papers, the better and almost accurate (when compare to the experimental results) results where obtained using the combined treatment of explicit solvent molecules and COSMO solvation model. Also PCM works well. Hope this helps. Best Regards, Raji. --------------------------------------------------------------------------- Sent to CCL by: "Gonzalo Jimenez Oses" [gonzalo.jimenez{=}dq.unirioja.es] Hi all, A question has raised to me in the last days. When using a few explicit solvent molecules (i.e. the first solvation shell), is it more or less "correct" and/or "accurate" to use a SCRF moldel (i.e. PCM) to describe de bulk solvent effects?. I have heard somewhere that explicitly solvated solutes are more difficult to treat by means of PCM models, because of the use overlapping spheres to describe the solute cavity. I wonder if the values obtained through this methodology (which in turn seems to be more "correct" than simple SCRF models) are feasible or the solvation free energies might be somewhat over/understimated. Are there any paper related to this, apart from the well-known reviews in solvation methods? Thank u very much, I wait for your ideas. Gonzalo