From owner-chemistry@ccl.net Fri Oct 10 07:32:00 2014 From: "Sergio Emanuel Galembeck segalemb#%#usp.br" To: CCL Subject: CCL: Gn Methods and PCM Message-Id: <-50573-141010073047-698-7a5ueLdfayOOfFfqrdYsqA|-|server.ccl.net> X-Original-From: "Sergio Emanuel Galembeck" Date: Fri, 10 Oct 2014 07:30:45 -0400 Sent to CCL by: "Sergio Emanuel Galembeck" [segalemb .. usp.br] Dear Gustavo, First, you need to do a conformational analysis. There are some good molecular mechanics software that do that. After you need to choose a computational model to perform the geometry optimization, and another to obtain single point geometries. For those steps, my experience is to do some tests with small molecules that reproduce the main characteristics of the chemical bonds of the compound of interest. Sometimes, a not so fashionable, and not so expensive model give good results. You can find an example in J. Phys. Chem. A, 2008, 112, 4060-4066. In this paper we demonstrate that B3LYP/6-31+G(d,p) is the best model for thermochemical studies of two five membered rings. Hope this help you, Abracos, Sergio On 09/10/2014, at 19:47, Gustavo L.C. Moura gustavo.moura*ufpe.br wrote: Sent to CCL by: "Gustavo L.C. Moura" [gustavo.moura-#-ufpe.br] Dear CCL Community, I want to obtain the energies of the lowest conformers of a molecule, with the formula C18H19BrO2Se, in solution with the polarizable continuum model. My question is: Do the Gn methods give reliable results when combined with the PCM method? Thank you very much in advance. Sincerely yours, Gustavo L.C. Moura From owner-chemistry@ccl.net Fri Oct 10 10:59:00 2014 From: "GUSTAVO LAUREANO COELHO DE MOURA gustavo.moura*|*ufpe.br" To: CCL Subject: CCL: Gn Methods and PCM Message-Id: <-50574-141010104753-18883-7OQuqEKcYY1+vZFjKH8l9Q++server.ccl.net> X-Original-From: GUSTAVO LAUREANO COELHO DE MOURA Content-Type: multipart/alternative; boundary="----=_Part_130248_1103330443.1412952369403" Date: Fri, 10 Oct 2014 11:46:09 -0300 (BRT) MIME-Version: 1.0 Sent to CCL by: GUSTAVO LAUREANO COELHO DE MOURA [gustavo.moura^-^ufpe.br] ------=_Part_130248_1103330443.1412952369403 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: 7bit Dear Sergio, Thank you for your speedy answer to my question. As a matter of fact, I have already performed a conformational analysis and have already a good number of candidate low energy conformations. My own experience, running only a few test conformations with MP2, is that the relative energies I am after are overly dependent on the basis set employed. Sometimes, even the energetic order of the conformations changes with the basis set employed. That is the reason why I am considering the Gn methods. The experimentalists I am working with believe that an important component of the empirical model they proposed to explain the phenomena they are observing is intramolecular dispersion. That is the reason why I am not considering performing DFT calculations. I am still open to any suggestions. Once again thank you. Sincerely yours, Gustavo L.C. Moura ----- Mensagem original ----- De: "Sergio Emanuel Galembeck segalemb#%#usp.br" Para: "Gustavo L.C. Moura " Enviadas: Sexta-feira, 10 de outubro de 2014 8:30:45 Assunto: CCL: Gn Methods and PCM Sent to CCL by: "Sergio Emanuel Galembeck" [segalemb .. usp.br] Dear Gustavo, First, you need to do a conformational analysis. There are some good molecular mechanics software that do that. After you need to choose a computational model to perform the geometry optimization, and another to obtain single point geometries. For those steps, my experience is to do some tests with small molecules that reproduce the main characteristics of the chemical bonds of the compound of interest. Sometimes, a not so fashionable, and not so expensive model give good results. You can find an example in J. Phys. Chem. A, 2008, 112, 4060-4066. In this paper we demonstrate that B3LYP/6-31+G(d,p) is the best model for thermochemical studies of two five membered rings. Hope this help you, Abracos, Sergio On 09/10/2014, at 19:47, Gustavo L.C. Moura gustavo.moura*ufpe.br wrote: Sent to CCL by: "Gustavo L.C. Moura" [gustavo.moura-#-ufpe.br] Dear CCL Community, I want to obtain the energies of the lowest conformers of a molecule, with the formula C18H19BrO2Se, in solution with the polarizable continuum model. My question is: Do the Gn methods give reliable results when combined with the PCM method? Thank you very much in advance. Sincerely yours, Gustavo L.C. Mourahttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt------=_Part_130248_1103330443.1412952369403 Content-Type: text/html; charset=utf-8 Content-Transfer-Encoding: quoted-printable <= div style=3D'font-family: verdana,helvetica,sans-serif; font-size: 10pt; co= lor: #000000'>

Dear Sergio,

Thank you for your speedy answer to my question.

As a matter of fact, I have already performed a conformational analysis and have alread= y a good number of candidate low energy conformations.

My own experience, running only a few test conformations with MP2, is that the rel= ative energies I am after are overly dependent on the basis set employed. Sometim= es, even the energetic order of the conformations changes with the basis set employed. That is the reason why I am considering the Gn methods.

The experimentalists I am working with believe that an important component of the empirical mode= l they proposed to explain the phenomena they are observing is intramolecular dispersion. That is the reason why I am not considering performing DFT calculations.

I am sti= ll open to any suggestions.

Once again thank you.

Sincerely yours,

      &nbs= p;            &= nbsp;           Gu= stavo L.C. Moura



De: "Sergio Emanuel Galembeck segalemb#%#u= sp.br" <owner-chemistry*ccl.net>
Para: "Gustavo L.C. Moura = " <gustavo.moura*ufpe.br>
Enviadas: Sexta-feira, 10= de outubro de 2014 8:30:45
Assunto: CCL: Gn Methods and PCM
<= br>
Sent to CCL by: "Sergio Emanuel Galembeck" [segalemb .. usp.br]
D= ear Gustavo,

  First, you need to do a conformational anal= ysis. There are some good molecular mechanics software that do that. After = you need to choose a computational model to perform the geometry optimizati= on, and another to
obtain single point geometries. For those steps, my e= xperience is to do some tests with small molecules that reproduce the main = characteristics of the chemical bonds of the compound of interest. Sometime= s, a not so fashionable, and not so expensive model give good results. You = can find an example in
J. Phys. Chem. A, 2008, 112, 4060-4066. In this = paper we demonstrate that
B3LYP/6-31+G(d,p) is the best model for thermo= chemical studies of two five membered rings.

     &nb= sp;    Hope this help you,

       &nbs= p;             Abracos,

   &= nbsp;                    =     Sergio



On 09/10/2014, at 19:47, Gustavo L.C.= Moura gustavo.moura*ufpe.br
<owner-chemistry _ ccl.net>
wrote= :


Sent to CCL by: "Gustavo L.C. Moura" [gustavo.moura-#-ufpe.br]=
Dear CCL Community,
I want to obtain the energies of the lowest conf= ormers of a molecule, with the
formula C18H19BrO2Se,
in solution wit= h the polarizable continuum model.
My question is:
    = ;    Do the Gn methods give reliable results when combined with t= he PCM method?
Thank you very much in advance.
Sincerely yours,
&n= bsp;               Gustavo L.C. Mou= ra



-=3D This is automatically added to each message by the m= ailing script =3D-
To recover the email address of the author of the mes= sage, please change
the strange characters on the top line to the * sign= . You can also=     =  http://www.ccl.net/cgi-bin/ccl/send_ccl_message

E-mail to adm= inistrators: CHEMISTRY-REQUEST*ccl.net or use
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------=_Part_130248_1103330443.1412952369403-- From owner-chemistry@ccl.net Fri Oct 10 11:51:01 2014 From: "Abrash, Samuel sabrash%richmond.edu" To: CCL Subject: CCL: Text Recommendation Message-Id: <-50575-141010115011-5882-H1tba12xB18udf9pu/ERwA##server.ccl.net> X-Original-From: "Abrash, Samuel" Content-Language: en-US Content-Type: multipart/alternative; boundary="_000_A7C78D2AEE62DB40B9CB1ADE9D5990A201111E28F0quorrarichmon_" Date: Fri, 10 Oct 2014 15:50:01 +0000 MIME-Version: 1.0 Sent to CCL by: "Abrash, Samuel" [sabrash a richmond.edu] --_000_A7C78D2AEE62DB40B9CB1ADE9D5990A201111E28F0quorrarichmon_ Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: quoted-printable Hi Folks, First, I apologize for this being somewhat off topic. My first question is= can anyone recommend a text to teach molecular spectroscopy to college sen= iors/first year graduate students in Physical Chemistry? I am very fond of= Levine's Molecular Spectroscopy, but it is out of print, and doesn't inclu= de much on laser spectroscopies. I have been somewhat frustrated with what= I've found, and was hoping that someone would know a text I haven't come a= cross. Second, so that I don't pester this listserve with off-topic questions, doe= s any one know of a similar listserve serving either Physical Chemistry, or= just Chemistry in general? Again, sorry for the off-topic question. Sam Abrash Associate Professor Department of Chemistry University of Richmond Richmond, VA 23173 --_000_A7C78D2AEE62DB40B9CB1ADE9D5990A201111E28F0quorrarichmon_ Content-Type: text/html; charset="us-ascii" Content-Transfer-Encoding: quoted-printable

Hi Folks,

 

First, I apologize for this being somewhat off topic= .  My first question is can anyone recommend a text to teach molecular= spectroscopy to college seniors/first year graduate students in Physical C= hemistry?  I am very fond of Levine’s Molecular Spectroscopy, but it is out of print, and doesn’t include much on la= ser spectroscopies.  I have been somewhat frustrated with what I’= ;ve found, and was hoping that someone would know a text I haven’t co= me across.

 

Second, so that I don’t pester this listserve = with off-topic questions, does any one know of a similar listserve serving = either Physical Chemistry, or just Chemistry in general?

 

Again, sorry for the off-topic question.<= /p>

 

Sam Abrash

Associate Professor

Department of Chemistry

University of Richmond

Richmond, VA

23173

--_000_A7C78D2AEE62DB40B9CB1ADE9D5990A201111E28F0quorrarichmon_-- From owner-chemistry@ccl.net Fri Oct 10 13:52:01 2014 From: "=?iso-8859-1?Q?V=EDctor_Lua=F1a?= Cabal victor- -fluor.quimica.uniovi.es" To: CCL Subject: CCL: Text Recommendation Message-Id: <-50576-141010134611-8241-SPM4mjXR834iPft0VlhFHA===server.ccl.net> X-Original-From: =?iso-8859-1?Q?V=EDctor_Lua=F1a?= Cabal Content-disposition: inline Content-transfer-encoding: 8BIT Content-type: text/plain; charset=iso-8859-1 Date: Fri, 10 Oct 2014 19:36:24 +0200 MIME-version: 1.0 Sent to CCL by: =?iso-8859-1?Q?V=EDctor_Lua=F1a?= Cabal [victor ~~ fluor.quimica.uniovi.es] On Fri, Oct 10, 2014 at 03:50:01PM +0000, Abrash, Samuel sabrash%richmond.edu wrote: > Hi Folks, > > First, I apologize for this being somewhat off topic. My first question is can anyone recommend a text to teach molecular spectroscopy to college seniors/first year graduate students in Physical Chemistry? I am very fond of Levine's Molecular Spectroscopy, but it is out of print, and doesn't include much on laser spectroscopies. I have been somewhat frustrated with what I've found, and was hoping that someone would know a text I haven't come across. Molecular spectroscopy by Jeanne L. McHale, from Univ. Idaho was written exactly out of frustration for the Levine being out of print. My copy is from 1999, though ;-) Good luck, Víctor Luaña From owner-chemistry@ccl.net Fri Oct 10 14:29:00 2014 From: "Joy Ku joyku[*]stanford.edu" To: CCL Subject: CCL: Survey on credible practice of modeling and simulation in healthcare Message-Id: <-50577-141010135732-10609-+wta3vKQSdlotI0qAQ4SXw^_^server.ccl.net> X-Original-From: "Joy Ku" Date: Fri, 10 Oct 2014 13:57:30 -0400 Sent to CCL by: "Joy Ku" [joyku**stanford.edu] To help increase the use of modeling and simulation in healthcare, the interagency Committee on Credible Practice of Modeling & Simulation in Healthcare is conducting a survey on good practices for computational modeling and simulation. Please consider taking a few minutes to contribute to this important effort. More details are below. Thanks, Joy ------------------------------------------------------------------ With this invitation, we are asking you to complete a survey aimed to establish good practice guidelines in order to realize credibility of computational modeling and simulation (M&S) in healthcare. The survey can be found at: https://stanforduniversity.qualtrics.com/SE/?SID=SV_4MeRluojMgdVR7n The survey site will be available until February 15, 2015. We sincerely appreciate your participation in this survey, which should take no longer than 10 minutes. Your participation is voluntary and your responses will be anonymous. You have been identified as a potential stakeholder in the M&S community. Your support will be instrumental in developing broadly applicable best practices in M&S, for their ultimate utilization in healthcare. This survey is an initiative of the Committee on Credible Practice of Modeling & Simulation in Healthcare, to understand global and multidisciplinary perspectives in best practices to establish credibility of computational medicine. The Committee was formed as part of interactions within the Interagency Modeling and Analysis Group (IMAG) and Multiscale Modeling Consortium, which provide a platform to facilitate discussions between federal agencies in the United States and investigators within the United States and worldwide. Please feel free to forward this invitation to others that may have an interest in providing their insight. Thank you for your support. If you have any questions, please feel free to contact me by phone, +1 (216) 445 9523, or by e-mail, erdemira:-:ccf.org. Regards, Ahmet Ahmet Erdemir, PhD on behalf of Committee on Credible Practice of Modeling & Simulation in Healthcare From owner-chemistry@ccl.net Fri Oct 10 22:19:01 2014 From: "Guenter Grethe ggrethe^att.net" To: CCL Subject: CCL: 2015 CINF scholarships - Reminder Message-Id: <-50578-141010184213-16126-ub8ZRJS4zlK+L27sMx39rQ|*|server.ccl.net> X-Original-From: "Guenter Grethe" Date: Fri, 10 Oct 2014 18:42:12 -0400 Sent to CCL by: "Guenter Grethe" [ggrethe(0)att.net] This is a reminder that the deadline for applying for the 2015 CINF scholarships sponsored by InfoChem and Springer is October 17, 2014. CINF Scholarship for Scientific Excellence Co-sponsored by InfoChem and Springer The international scholarship program of the Division of Chemical Information (CINF) of the American Chemical Society (ACS) co-sponsored by InfoChem (www.infochem.de) and Springer (www.springer.com) is designed to reward students in chemical information and related sciences for scientific excellence and to foster their involvement in CINF. Up to three scholarships valued at $1,000 each will be awarded at the 249th ACS National Meeting in Denver, CO, March 22 26, 2015. Student applicants must be enrolled at a certified college or university; postdoctoral fellows are also invited to apply. They will present a poster during the Welcoming Reception of the Division on Sunday evening at the National Meeting. Additionally, they will have the option to show their poster at the Sci-Mix session on Monday night. Abstracts for the poster must be submitted electronically through MAPS, the abstract submission system of ACS. To apply, please inform the Chair of the selection committee, Guenter Grethe at ggrethe(_)att.net, that you are applying for a scholarship. Submit your abstract at http://maps.acs.org using your ACS ID. If you do not have an ACS ID, follow the registration instructions and submit your abstract in the CINF program in the session CINF Scholarship for Scientific Excellence. MAPS will be open for abstract submissions from August 25, 2014, to October 17, 2014. Additionally, please send me a 2,000-word abstract in electronic form by January 31,2015, describing the work to be presented. Any questions related to applying for one of the scholarships should be directed to the same e-mail address. Winners will be chosen based on contents, presentation and relevance of the poster and they will be announced during the Sunday reception. The contents shall reflect upon the students work and describe research in the field of cheminformatics and related sciences. Guenter Grethe About InfoChem InfoChem GmbH based in Munich, Germany, is a market leader in structure and reaction handling and retrieval. Founded in 1989, InfoChem focuses on the production and marketing of new chemical information products, including structural and reaction databases, and the development of software tools required for these applications. The main software tools provided are the InfoChem Fast Search Engine (ICFSE), the InfoChem Chemistry Cartridge for Oracle (ICCARTRIDGE) and the widely used InfoChem reaction classification algorithm CLASSIFY. InfoChem distributes one of the largest structural and reaction files worldwide, currently containing 7 million organic compounds and facts and 4 million reactions covering the chemical literature published since 1974 (SPRESI). In addition, InfoChem provides tools for the automatic recognition and extraction of chemical entities and their conversion into chemical structures as well as the semantic enrichment of chemical science documents. Springer GmbH (Berlin) has held a majority interest in InfoChem since 1991. For more infromation go to www.infochem.de.