From owner-chemistry@ccl.net Tue May 16 03:46:00 2006 From: "Goedele Roos groos : vub.ac.be" To: CCL Subject: CCL: basis set to calculate proton affinity Message-Id: <-31760-060516024107-13773-LZX5rjU6WeuiJitTQimYNQ|,|server.ccl.net> X-Original-From: Goedele Roos Date: Tue, 16 May 2006 08:40:27 +0200 (CEST) Sent to CCL by: Goedele Roos [groos[]vub.ac.be] dear all, I was wondering which basis set in combination with the B3LYP functional will give the protonaffinity up to 1% accuracy? Thank you in advance for help. Goedele Drs. Goedele Roos Dienst Algemene Chemie (ALGC) Vrije Universiteit Brussel (VUB) Pleinlaan 2 B-1050 Brussels Tel: 0032-2-629 35 16 Fax: 0032-2-629 33 17 From owner-chemistry@ccl.net Tue May 16 06:35:00 2006 From: "Dipankar Roy dipankarroy]_[iitb.ac.in" To: CCL Subject: CCL: basis set to calculate proton affinity Message-Id: <-31761-060516052719-2960-ITdmmYfaa4h/5em/j5HcCA**server.ccl.net> X-Original-From: "Dipankar Roy" Content-Transfer-Encoding: 8bit Content-Type: text/plain;charset=iso-8859-1 Date: Tue, 16 May 2006 14:56:55 +0530 (IST) MIME-Version: 1.0 Sent to CCL by: "Dipankar Roy" [dipankarroy .. iitb.ac.in] Hi, Try with augumented Dunning's basis sets e.g. aug-cc-pVTZ. Higher orders are also available (aug-cc-pvqz, aug-cc-pv5z) but may be highly resorce demanding based on your system. -dipankar > Sent to CCL by: Goedele Roos [groos[]vub.ac.be] > dear all, > > I was wondering which basis set in combination with the B3LYP functional > will give the protonaffinity up to 1% accuracy? > > Thank you in advance for help. > > Goedele > > Drs. Goedele Roos > Dienst Algemene Chemie (ALGC) > Vrije Universiteit Brussel (VUB) > Pleinlaan 2 > B-1050 Brussels > Tel: 0032-2-629 35 16 > Fax: 0032-2-629 33 17> > > > *********************************************** Dipankar Roy Graduate Student of Prof. R. B. Sunoj Computational Chemistry Laboratoty Dept. of Chemistry Indian Institute of Technology, Bombay India - 400076 Phone: +91-22-2576-4130(lab) *********************************************** GETTING A SIMPLE ANSWER FROM A PROFESSOR IS LIKE GETTING A THIMBLE OF WATER FROM A FIRE HYDRANT. - PROF. LEN SHAPIRO, NDSU From owner-chemistry@ccl.net Tue May 16 07:10:01 2006 From: "Marcel Swart m.swart=few.vu.nl" To: CCL Subject: CCL: basis set to calculate proton affinity Message-Id: <-31762-060516054737-5530-MGVKbZWu7TYl2TKg1fYL0w*_*server.ccl.net> X-Original-From: Marcel Swart Content-Type: multipart/alternative; boundary=Apple-Mail-5--187967735 Date: Tue, 16 May 2006 11:07:20 +0200 Mime-Version: 1.0 (Apple Message framework v750) Sent to CCL by: Marcel Swart [m.swart,,few.vu.nl] --Apple-Mail-5--187967735 Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=WINDOWS-1252; delsp=yes; format=flowed See the recent paper by Grimme, Nibbering and co-workers: Chem. Eur. J. 2005, 11, 1251 =96 1256 At least aug-cc-pVTZ is needed. On 16/05/2006, at 10:36, Goedele Roos groos : vub.ac.be wrote: > Sent to CCL by: Goedele Roos [groos[]vub.ac.be] > dear all, > > I was wondering which basis set in combination with the B3LYP =20 > functional will give the protonaffinity up to 1% accuracy? > > Thank you in advance for help. > > Goedele > > Drs. Goedele Roos > Dienst Algemene Chemie (ALGC) > Vrije Universiteit Brussel (VUB) > Pleinlaan 2 > B-1050 Brussels > Tel: 0032-2-629 35 16 > Fax: 0032-2-629 33 17 =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 ICREA researcher at Institut de Qu=EDmica Computacional Universitat de Girona Campus Montilivi 17071 Girona Catalunya (Spain) T +34-972-418359 F +34-972-418356 E marcel.swart**icrea.es W http://www.icrea.es/pag.asp?id=3DMarcel.Swart 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-5--187967735 Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset=WINDOWS-1252
See the recent paper = by Grimme, Nibbering and co-workers:

Chem. Eur. J. 2005, 11, = 1251 =96 1256

At least aug-cc-pVTZ is = needed.

On = 16/05/2006, at 10:36, Goedele Roos groos : vub.ac.be wrote:

Sent to CCL by: Goedele Roos = [groos[]vub.ac.be]
dear all,

I was = wondering which basis set in combination with the B3LYP functional will = give the protonaffinity up to 1% accuracy?

Thank you in = advance for help.

Goedele

Drs. Goedele Roos
Dienst Algemene Chemie (ALGC)
Vrije Universiteit Brussel (VUB)
Pleinlaan 2
B-1050 = Brussels
Tel: 0032-2-629 35 16
Fax: 0032-2-629 33 = 17
dr. Marcel Swart

ICREA researcher=A0Institut de Qu=EDmica = Computacional
Universitat de Girona

Campus = Montilivi
17071 Girona
Catalunya (Spain)

= --Apple-Mail-5--187967735-- From owner-chemistry@ccl.net Tue May 16 13:03:00 2006 From: "Nalaka Kodituwakku nalaka-.-aps.anl.gov" To: CCL Subject: CCL: Gaussian 03 CIS output problem Message-Id: <-31763-060515182018-13932-1YqYHK+1Y694T8tyZJ7QZg[A]server.ccl.net> X-Original-From: "Nalaka Kodituwakku" Date: Mon, 15 May 2006 18:20:13 -0400 Sent to CCL by: "Nalaka Kodituwakku" [nalaka!A!aps.anl.gov] I do an electronic excitation calculation on CuPc. inthe output file i get this " Ground to excited state transition densities written to RWF 633" What does this mean how do i get this information? Thank you, Nalaka. From owner-chemistry@ccl.net Tue May 16 13:37:00 2006 From: "Spencer Snyder Ericksen spencer_ericksen _ hotmail.com" To: CCL Subject: CCL: polypeptide tethers to span protein subunits Message-Id: <-31764-060516130608-28910-ONy0kkO/oLyKBxBsU+uX9A.:.server.ccl.net> X-Original-From: "Spencer Snyder Ericksen" Date: Tue, 16 May 2006 13:06:07 -0400 Sent to CCL by: "Spencer Snyder Ericksen" [spencer_ericksen,,hotmail.com] I'm interested in constructing concatenated monomers of a heteropentameric ion channel. I'm linking tandem monomers using polypeptides of different sequence and length. Using a homology model, Ive tested these linkers to span two fixed monomers within a fixed pentameric assembly by comparing the molecular mechanics energy of certain isomeric arrangements (after many cycles of simulated annealing and optimization in vacuo). When the linker length is too short for a given arrangement, the strain energy increases abruptly. I then deem the linker a poor choice for application. Sometimes, however, when examining different adjacent arrangements of the tandem (clockwise vs. counterclockwise) within the pentamer, I see little difference in relative strain energies (MM) for the systems. These arrangements present significantly different distances for spanning, yet there is no discernible difference in molecular mechanical strain in the configurations. In wet-lab experiments, we see almost no expression of the CCW arrangement. If my calculations are informative, then I conclude that either the dimerization is kinetically controlled such that the CW arrangement is simply more accessible and/or the CW arrangement is favored due to sterically selective dimerization prior to pentameric assembly. Am I leaving something out? It seems that linker length may depend upon the polypeptides free RMS end-to-end distance and or persistence length. I cant seem to find tables in literature for such values for various polypeptide sequences. Could you point me to some? Also, I thought that the relative strain in different configurations would tell me about the influence of the linker on assembly. Is it likely that the neglected entropic contribution to relative free energies of the arrangements is very important here? I am mostly concerned about the ability for a polymer to span two bodies fixed at different positions. Is there a better way to explore this potential theoretically? From owner-chemistry@ccl.net Tue May 16 20:54:01 2006 From: "Young Leh youngleh#gmail.com" To: CCL Subject: CCL:G: Gaussian03 and Periodic Bondary Condition Message-Id: <-31765-060516203213-20029-SCGD2TGrDVTtUWtLMgZpKg__server.ccl.net> X-Original-From: "Young Leh" Date: Tue, 16 May 2006 20:32:12 -0400 Sent to CCL by: "Young Leh" [youngleh- -gmail.com] Dear CCLer, > From the Gaussian website, it looks like Gaussian03 is able to perform periodic caculations. But I can not find further explanation on how to achieve this. I need some information like how to specify the input and what the keyword(s) are? Could somebody please help? Regards, Young Leh From owner-chemistry@ccl.net Tue May 16 21:32:00 2006 From: "Nuno A. G. Bandeira nuno.bandeira-#-ist.utl.pt" To: CCL Subject: CCL:G: Gaussian03 and Periodic Bondary Condition Message-Id: <-31766-060516213056-10678-AIwzPg531ro+fQfej27yzA^server.ccl.net> X-Original-From: "Nuno A. G. Bandeira" Date: Tue, 16 May 2006 21:30:50 -0400 Sent to CCL by: "Nuno A. G. Bandeira" [nuno.bandeira,+,ist.utl.pt] Young Leh younglehgmail.com wrote: > Sent to CCL by: "Young Leh" [youngleh- -gmail.com] > Dear CCLer, > > >> From the Gaussian website, it looks like Gaussian03 is able to perform periodic caculations. But I can not find further explanation on how to achieve this. I need some information like how to specify the input and what the keyword(s) are? Periodic calculations are automatic in Gaussian so long as you specify the translation vectors in the coordinate section. Read this : http://www.gaussian.com/g_ur/m_molspec.htm A printed version of the manual would help you. -- Nuno A. G. Bandeira, AMRSC Graduate researcher and molecular sculptor Inorganic and Theoretical Chemistry Group, Faculty of Science University of Lisbon - C8 building, Campo Grande, 1749-016 Lisbon,Portugal http://cqb.fc.ul.pt/intheochem/nuno.html Doctoral student (~) IST,Lisbon --