From owner-chemistry@ccl.net Thu Dec 15 07:56:00 2011 From: "Dr Ponnadurai Ramasami ramchemi[#]intnet.mu" To: CCL Subject: CCL: Call for paper- 7th CCA-REMINDER Message-Id: <-46037-111215023041-24836-WA20riSxXTvA9mMA+VdWsw^-^server.ccl.net> X-Original-From: "Dr Ponnadurai Ramasami" Content-Language: en-us Content-Type: multipart/alternative; boundary="----=_NextPart_000_002E_01CCBB1C.ED621BD0" Date: Thu, 15 Dec 2011 11:30:18 +0400 MIME-Version: 1.0 Sent to CCL by: "Dr Ponnadurai Ramasami" [ramchemi\a/intnet.mu] This is a multi-part message in MIME format. ------=_NextPart_000_002E_01CCBB1C.ED621BD0 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 7bit The 7th Workshop on Computational Chemistry and its Applications (7th CCA) will held as part of International Conference on Computational Science (ICCS 2012). Website: http://www.uom.ac.mu/Faculties/FOS/Chemistry/cca/ ICCS 2012 will be from 4th to 6th June 2012 in Omaha, Nebraska, USA. Website: http://www.iccs-meeting.org/ Dr Paul Blowers will deliver the keynote address entitled "Environmental Foresight though Computational Chemistry Approaches". Dr Paul Blowers is from the Institute of the Environment, The University of Arizona Tucson, Arizona 85721, USA. Website: http://www.environment.arizona.edu/paul-blowers TOPICS Topics will include aspects of computational chemistry such as (but are not limited to): (i) Methods: Force fields, semiempirical, ab initio, density functional theory (ii) Applications: Kinetics, reaction mechanisms, catalysis, molecular properties, conformational analysis, thermodynamics, molecular dynamics (iii) Research involving computational chemistry (iv) Computational chemistry in chemical education (v) Interdisciplinary computational research involving chemistry is specially invited INSTRUCTIONS Authors are invited to submit their papers, written in English, up to 10 pages, presenting the results of original research or innovative practical applications relevant to the workshop topics. Papers should be prepared according to the rules of Procedia Computer Science. Formatting information see for text/latex and for MSword. Papers should be submitted in pdf or word file format. Paper submissions should be done electronically, using submission system on page: http://www.iccs-meeting.org/iccs2012/papers/upload.php Be sure to select the correct workshop, i.e 7th Workshop on Computational Chemistry and Its Applications. At least one author of an accepted paper must register and present the paper at the workshop. DEADLINES Full paper submission: 9th January , 2012 http://www.iccs-meeting.org/iccs2012/papers/upload.php Notification of acceptance: 9th February, 2012 Camera-ready papers: 1st March, 2012 For more information, feel free to contact Dr Ponnadurai Ramasami 7th CCA Workshop Organiser http://www.uom.ac.mu/sites/ccuom/ (Under construction) ------=_NextPart_000_002E_01CCBB1C.ED621BD0 Content-Type: text/html; charset="us-ascii" Content-Transfer-Encoding: quoted-printable

The 7th Workshop on Computational Chemistry and its Applications = (7th CCA) will held as part of International Conference on Computational = Science (ICCS 2012).

Website: http://www.uom.ac.mu/Faculties/FOS/Chemistry/c= ca/

 

ICCS 2012 will be from 4th to 6th June 2012 in Omaha, Nebraska, USA.

Website: http://www.iccs-meeting.org/=

 

Dr Paul Blowers will deliver = the keynote address entitled "Environmental Foresight though Computational Chemistry Approaches”.

Dr = Paul Blowers is from the Institute of the Environment, The University of = Arizona Tucson, Arizona 85721, USA.

Website: http://www.environment.arizona.edu/paul-blower= s

 

TOPICS

Topics will include aspects of computational chemistry such as (but are not = limited to):
(i) Methods: Force fields, semiempirical, ab initio, density = functional theory
(ii) Applications: Kinetics, reaction mechanisms, catalysis, molecular properties, conformational analysis, thermodynamics, molecular = dynamics
(iii) Research involving computational chemistry
(iv) Computational chemistry in chemical education
(v) Interdisciplinary computational research involving chemistry is = specially invited

 

INSTRUCTIONS

Authors are invited to submit their papers, written in English, up to 10 pages, presenting the results of original research or innovative practical applications relevant to the workshop topics.

Papers should be prepared according to the rules of Procedia Computer = Science.

Formatting information see for text/latex and for MSword.

Papers should be submitted in pdf or word file format.

Paper submissions should be done electronically, using submission system on = page:

http://www.iccs-meeting.org/iccs2012/papers/upload.php

Be sure to select the correct workshop, i.e 7th Workshop on Computational Chemistry and Its Applications.

At least one author of an accepted paper must register and present the = paper at the workshop.

 

DEADLINES

Full paper submission:  9th January , 2012

http://www.iccs-meeting.org/iccs2012/papers/up= load.php

Notification of acceptance: 9th February, 2012

Camera-ready papers: 1st March, 2012

 

For more information, feel free to contact

Dr Ponnadurai Ramasami

7th CCA Workshop Organiser

http://www.uom.ac.mu/sites/ccuom/ (Under construction)

 

 

------=_NextPart_000_002E_01CCBB1C.ED621BD0-- From owner-chemistry@ccl.net Thu Dec 15 12:04:00 2011 From: "Carlos T Nieto eneas|usal.es" To: CCL Subject: CCL: Energy barriers Message-Id: <-46038-111215120149-6215-eXnJ+GzxF0iBnMWOxqhyQg{:}server.ccl.net> X-Original-From: "Carlos T Nieto" Date: Thu, 15 Dec 2011 12:01:47 -0500 Sent to CCL by: "Carlos T Nieto" [eneas#%#usal.es] Hi,everybody Which range of energy do you consider as high for a reaction? Does anybody know any way to know if, lets say, 25 kJ/mol is high energy barrier at room temperature? Will be the same at -78C? Thanks!! From owner-chemistry@ccl.net Thu Dec 15 12:41:00 2011 From: "Pedro Silva pedros : ufp.edu.pt" To: CCL Subject: CCL: Energy barriers Message-Id: <-46039-111215123957-3887-hfo0lPfx8by9bTPZSb+I3w#%#server.ccl.net> X-Original-From: Pedro Silva Content-Type: text/plain; charset=ISO-8859-1 Date: Thu, 15 Dec 2011 17:39:48 +0000 MIME-Version: 1.0 Sent to CCL by: Pedro Silva [pedros%x%ufp.edu.pt] Please use the Arrhenius or Eyring equations for answer to that question. CCL is not meant to solve undergrad homework problems. Pedro S. -- Pedro J. Silva Associate Professor Universidade Fernando Pessoa Porto - Portugal http://homepage.ufp.pt/pedros/science/science.htm http://biochemicalmatters.blogspot.com From owner-chemistry@ccl.net Thu Dec 15 13:16:00 2011 From: "Arne Dieckmann adieckma^-^googlemail.com" To: CCL Subject: CCL: Energy barriers Message-Id: <-46040-111215124901-20879-zfssAWCNtI9yOb/sIkYOCA++server.ccl.net> X-Original-From: Arne Dieckmann Content-Disposition: inline Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="utf-8" Date: Thu, 15 Dec 2011 09:48:46 -0800 MIME-Version: 1.0 Sent to CCL by: Arne Dieckmann [adieckma,+,googlemail.com] Hi, every book on basic physical chemistry or kinetics will show you how to calculate a rate constant from a given barrier. Of course, rate constants are temperature dependent. Cheers, Arne On Thursday, December 15, 2011 at 9:01 AM, Carlos T Nieto eneas|usal.es wrote: > > Sent to CCL by: "Carlos T Nieto" [eneas#%#usal.es (http://usal.es)] > > Hi,everybody > > Which range of energy do you consider as high for a reaction? Does anybody know any way to know if, lets say, 25 kJ/mol is high energy barrier at room temperature? Will be the same at -78C? > > Thanks!!> > E-mail to subscribers: CHEMISTRY[A]ccl.net (mailto:CHEMISTRY[A]ccl.net) or use:> > E-mail to administrators: CHEMISTRY-REQUEST[A]ccl.net (mailto:CHEMISTRY-REQUEST[A]ccl.net) or use From owner-chemistry@ccl.net Thu Dec 15 14:06:00 2011 From: "Sergio Manzetti sergio.manzetti**gmail.com" To: CCL Subject: CCL: Energy barriers Message-Id: <-46041-111215140245-21442-bFQrZCGGMdMn51hbM5GiaQ]-[server.ccl.net> X-Original-From: Sergio Manzetti Content-Type: multipart/alternative; boundary=bcaec5016115da77a704b42620d0 Date: Thu, 15 Dec 2011 20:02:39 +0100 MIME-Version: 1.0 Sent to CCL by: Sergio Manzetti [sergio.manzetti|-|gmail.com] --bcaec5016115da77a704b42620d0 Content-Type: text/plain; charset=ISO-8859-1 Pedro, the energy barrier will vary if it is endotermic reaction. Sergio On Thu, Dec 15, 2011 at 6:39 PM, Pedro Silva pedros : ufp.edu.pt < owner-chemistry^ccl.net> wrote: > > Sent to CCL by: Pedro Silva [pedros%x%ufp.edu.pt] > Please use the Arrhenius or Eyring equations for answer to that > question. CCL is not meant to solve undergrad homework problems. > > Pedro S. > > > > -- > Pedro J. Silva > Associate Professor > Universidade Fernando Pessoa > Porto - Portugal > http://homepage.ufp.pt/pedros/science/science.htm > http://biochemicalmatters.blogspot.com> > > --bcaec5016115da77a704b42620d0 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Pedro, the energy barrier will va= ry if it is endotermic reaction.

Sergio

On Thu, Dec 15, 2011 at 6:39 PM, Pedro Silva pedros : ufp.edu.pt <owner-chemistry^ccl.net> wrote:

Sent to CCL by: Pedro Silva [pedros%x%ufp.edu.pt]
Please use the Arrhenius or Eyring equations for answer to that
question. CCL is not meant to solve undergrad homework problems.

Pedro S.



--
Pedro J. Silva
Associate Professor
Universidade Fernando Pessoa
Porto - Portugal
http://homepage.ufp.pt/pedros/science/science.htm
http:/= /biochemicalmatters.blogspot.com



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--bcaec5016115da77a704b42620d0-- From owner-chemistry@ccl.net Thu Dec 15 14:57:00 2011 From: "Carlos T Nieto eneas|usal.es" To: CCL Subject: CCL: Energy barrier reformulation Message-Id: <-46042-111215145542-6655-5cY3l86rit5A2Rgsg74OWQ ~~ server.ccl.net> X-Original-From: "Carlos T Nieto" Date: Thu, 15 Dec 2011 14:55:40 -0500 Sent to CCL by: "Carlos T Nieto" [eneas(a)usal.es] Hi again, Maybe I haven't be very specific. I'll reformulate my question... In a reaction: would you consider 25 kJ/mol an energy barrier as reversible at 298 K? I mean, it wont be higher and the reaction will take place, wouldnt it? If the reaction is carried out at 195 K, then the reaction wont take place, will it? Fortunately, I know how to calculate rate constants and, obviously, its clear i didnt recquire that help. Please dont hesitate in answer me but, Ill appreciate those that consider meaningless this topic dont answer and i apologise if anyone has been ofended. Regards From owner-chemistry@ccl.net Thu Dec 15 15:43:00 2011 From: "Pedro Silva pedros*o*ufp.edu.pt" To: CCL Subject: CCL: Energy barriers Message-Id: <-46043-111215154103-16065-n+xf6Lev23prQXSOGi/Z2A-,-server.ccl.net> X-Original-From: Pedro Silva Content-Type: text/plain; charset=ISO-8859-1 Date: Thu, 15 Dec 2011 20:40:55 +0000 MIME-Version: 1.0 Sent to CCL by: Pedro Silva [pedros++ufp.edu.pt] On Thu, Dec 15, 2011 at 7:02 PM, Sergio Manzetti sergio.manzetti**gmail.com wrote: > Pedro, the energy barrier will vary if it is endotermic reaction. > Of course energy barriers vary with temperature, since enthalpy and entropy also vary with temperature. However, temperature effects on rate constant are already incorporated in the Eyring equation, which relates the observed rate constant with the temperature and the activation Delta G. Activation Delta H and activation Delta S for the temperature of interest may be obtained from experimental values of k at different temperatures. Transforming these values to activation Delta G is straightforward, and so is the computation of the activation deltaG associated to a rate constant. Pedro PS: I'm glossing over the influence ofpossible changes of the transmission coeefficient with temperature but that factor is often assumed to be unity, anyway.. -- Pedro J. Silva Associate Professor Universidade Fernando Pessoa Porto - Portugal http://homepage.ufp.pt/pedros/science/science.htm http://biochemicalmatters.blogspot.com From owner-chemistry@ccl.net Thu Dec 15 16:18:00 2011 From: "Shirley Peng speng-$-chemcomp.com" To: CCL Subject: CCL: New version of MOE released - MOE 2011.10 Message-Id: <-46044-111215154200-16814-HszkON+GZhAiC4DVQgaY2A_._server.ccl.net> X-Original-From: "Shirley Peng" Date: Thu, 15 Dec 2011 15:41:59 -0500 Sent to CCL by: "Shirley Peng" [speng!A!chemcomp.com] We are very pleased announce the release of MOE 2011.10. Some of the new and enhanced features in MOE include: ================================================================ Non-Bonded Interaction Visualization Model - Visualize halogen bonds, H-bonds, CH-X, proton- for interactive modeling - Calculate strengths using Extended Hckel Model - Display strengths and interactions in 2D Ligand Interaction Diagrams Sequence Editor Redesign - Wrapped view, zoom, chain name/tag, etc. - Synchronized coloring (% identity, similarity, Clustal X, RMSD) - Cut and paste for loop grafting, inserting linkers, filling gaps, etc. Combinatorial Build in Pocket - Add R-groups to one or more attachment points in 3D pocket - Apply 2D and 3D filters, refine in (flexible) pocket and score - Use Builder to scan fragments for interactive ligand optimization Analysis of Solvent in Binding - Calculate within minutes a solvent binding free energy map using 3D-RISM - Calculate water, salt and hydrophobe solvation densities in complex or apo receptor - Diagnose how well alternate groups take advantage of water upon binding Macromolecular System Preparation - Correct common problems in protein structures automatically - Browse alternate conformations, cap termini, build missing loops - Optimize hydrogen bond network by flipping residues and adjusting states GPCR Family Database and Alignment Tools - Identify and annotate transmembrane regions of GPCRs - Add alignment constraints to improve GPCR sequence alignments - Augment a database of GPCR crystal structures with in-house data =================================================================== Read/download the official MOE 2011.10 press release is at www.chemcomp.com/press_releases/2011-12-15.htm =================================================================== MOE MAIN APPLICATION AREAS: Structure-Based Design |Fragment-Based Design | Pharmacophore Discovery Protein and Antibody Modeling | Cheminformatics & QSAR | Medicinal Chemistry A MOE overview can be found at: http://www.chemcomp.com/software.htm If youre interested in evaluating MOE 2011.10 please go to: http://www.chemcomp.com/software-info.htm. ---------------------------------------------------------------------------- For additional information please contact: Raul Alvarez | Sr. Marketing Manager | ralvarez=chemcomp.com ---------------------------------------------------------------------------- From owner-chemistry@ccl.net Thu Dec 15 16:53:00 2011 From: "Pedro Silva pedros]-[ufp.edu.pt" To: CCL Subject: CCL: Energy barrier reformulation Message-Id: <-46045-111215155102-17578-aBQdCsXLxfYbbUO7dtoXLQ::server.ccl.net> X-Original-From: Pedro Silva Content-Type: text/plain; charset=ISO-8859-1 Date: Thu, 15 Dec 2011 20:50:54 +0000 MIME-Version: 1.0 Sent to CCL by: Pedro Silva [pedros^ufp.edu.pt] On Thu, Dec 15, 2011 at 7:55 PM, Carlos T Nieto eneas|usal.es wrote: > > Sent to CCL by: "Carlos T Nieto" [eneas(a)usal.es] > > Fortunately, I know how to calculate rate constants and, obviously, its clear i didnt recquire that help. > Again, if you know the equations, you can just compute the rate constant at 298 K and at 195 K, and see for yourself if those values are large enough. Compare them to ANY rate constant in a Physical Chemistry book, and you will know the answer. Believe me: the answer is SO obvious that any one who has taken any introductory course on Organic Chemistry and still remembers how to transform kJ/mol to kcal/mol can do it (at 298 K ) without a calculator. -- Pedro J. Silva Associate Professor Universidade Fernando Pessoa Porto - Portugal http://homepage.ufp.pt/pedros/science/science.htm http://biochemicalmatters.blogspot.com From owner-chemistry@ccl.net Thu Dec 15 21:36:00 2011 From: "Arne Dieckmann adieckma!^!googlemail.com" To: CCL Subject: CCL: Energy barrier reformulation Message-Id: <-46046-111215160802-15229-aNtca1aanmyfriURJUlwgA|server.ccl.net> X-Original-From: Arne Dieckmann Content-Disposition: inline Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="utf-8" Date: Thu, 15 Dec 2011 13:07:47 -0800 MIME-Version: 1.0 Sent to CCL by: Arne Dieckmann [adieckma : googlemail.com] Hi again, please read a good book on physical chemistry and kinetics, this will save everybody a lot of time. Reversibility does not only depend on barrier height with respect to precursors, but also with respect to products. Up to now, everybody has been quite polite - take your chance to keep it that way. Arne - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Arne Dieckmann Houk Research Lab University of California, Los Angeles email: adieckma+*+googlemail.com On Thursday, December 15, 2011 at 11:55 AM, Carlos T Nieto eneas|usal.es wrote: > > Sent to CCL by: "Carlos T Nieto" [eneas(a)usal.es (http://usal.es)] > > Hi again, > > Maybe I haven't be very specific. I'll reformulate my question... > > In a reaction: would you consider 25 kJ/mol an energy barrier as reversible at 298 K? I mean, it wont be higher and the reaction will take place, wouldnt it? If the reaction is carried out at 195 K, then the reaction wont take place, will it? > > Fortunately, I know how to calculate rate constants and, obviously, its clear i didnt recquire that help. > > Please dont hesitate in answer me but, Ill appreciate those that consider meaningless this topic dont answer and i apologise if anyone has been ofended. > > Regards> > E-mail to subscribers: CHEMISTRY+*+ccl.net (mailto:CHEMISTRY+*+ccl.net) or use:> > E-mail to administrators: CHEMISTRY-REQUEST+*+ccl.net (mailto:CHEMISTRY-REQUEST+*+ccl.net) or use