From owner-chemistry@ccl.net Wed Jun 24 05:17:01 2009 From: "may abdelghani may01dz,+,yahoo.fr" To: CCL Subject: CCL: transition states for fluxional molecules Message-Id: <-39601-090623163022-32690-434RaM2qmPPcJqY5UxkYmA!A!server.ccl.net> X-Original-From: may abdelghani Content-Type: multipart/alternative; boundary="0-426046375-1245785409=:26577" Date: Tue, 23 Jun 2009 19:30:09 +0000 (GMT) MIME-Version: 1.0 Sent to CCL by: may abdelghani [may01dz _ yahoo.fr] --0-426046375-1245785409=:26577 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable dear CCL'ers I study the fluxional behavior of a molecule. I find that the energy of the= transition states is fare from that of the ground one by 20 kcal/mole. I a= sk if this quantity of energy is big for such reaction: this king of reacti= on, spend small energy to "transfer" from one isomer to other, like I know. The easy exchange between the tow isomers manifest clearly on the Walsh dia= gram: no crossing between the orbital, no hug different, in energy of the f= rontier orbital, between that of reaction, TS and product structure.=20 I don=E2=80=99t know, in what extend the 20 kcal/mol is big, or, it is a bi= g cost, to spend a 20 kcal/mol of energy, to transfer from one isomer to an= other, in such a reaction. I need your help. =C2=A0=C2=A0 May abdelghani, Algeria=0A=0A=0A --0-426046375-1245785409=:26577 Content-Type: text/html; charset=utf-8 Content-Transfer-Encoding: quoted-printable
dear CCL'ers

I study the fl= uxional behavior of a molecule. I find that the energy of the transition st= ates is fare from that of the ground one by 20 kcal/mole. I ask if this qua= ntity of energy is big for such reaction: this king of reaction, spend smal= l energy to "transfer" from one isomer to other, like I know.

The easy excha= nge between the tow isomers manifest clearly on the Walsh diagram: no cross= ing between the orbital, no hug different, in energy of the frontier orbita= l, between that of reaction, TS and product structure.

I don=E2=80=99= t know, in what extend the 20 kcal/mol is big, or, it is a big cost, to spe= nd a 20 kcal/mol of energy, to transfer from one isomer to another, in such= a reaction. I need your help.  &nbs= p;

May abdelghani, Algeria

=0A=0A=0A=0A --0-426046375-1245785409=:26577-- From owner-chemistry@ccl.net Wed Jun 24 10:56:00 2009 From: "daniele tomerini dt334{}cam.ac.uk" To: CCL Subject: CCL: GULP with DREIDING potential Message-Id: <-39602-090624104810-24690-JogCPQK5nTkootXxHc970g:+:server.ccl.net> X-Original-From: "daniele tomerini" Date: Wed, 24 Jun 2009 10:48:07 -0400 Sent to CCL by: "daniele tomerini" [dt334_+_cam.ac.uk] Dear CCLers, I've been trying to use GULP with the dreiding potential to calculate properties of molecular organic crystals (paracetamol, in particular). To my disappointment, the input files I tried (with different settings) didn't give me sensible results, spanning from "not convergence" to unacceptable distortion of the structures. Has anybody experience with that, and is willing to share his input files, so that I can sort what I'm doing wrong? Thanks, Daniele From owner-chemistry@ccl.net Wed Jun 24 11:31:01 2009 From: "Jan Labanowski janl===speakeasy.net" To: CCL Subject: CCL: Reminder on COMP ACS Division Election deadline Message-Id: <-39603-090624110252-28317-Sn8pi/0nunbLS8NzEJnLuQ,server.ccl.net> X-Original-From: Jan Labanowski Content-Disposition: inline Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="iso-8859-1" Date: Wed, 24 Jun 2009 11:02:38 EDT MIME-Version: 1.0 Sent to CCL by: Jan Labanowski [janl_+_speakeasy.net] I was asked to post the following reminder: The Computers in Chemistry Division of the ACS would like to take a moment = to remind its members that the election is nearly complete, and any outstanding ballots should be cast by the deadline of July 15, 2009. Ballots went out= to all members via Survey Monkey, so please take a moment to locate the email = if you may have discarded the ballot inadvertently. If you have opted out of Surv= ey Monkey in the past, you will have to opt in to vote, but a new ballot will = have to be sent, and you will need to personally contact the assistant secretary= .=20 Please contact the assistant secretary (http://www.acscomp.org) if you need assistance locating your ballot. From owner-chemistry@ccl.net Wed Jun 24 12:25:00 2009 From: "Alcides Simao alsimao*|*gmail.com" To: CCL Subject: CCL: QSAR Message-Id: <-39604-090624113944-17531-E0jsM/jVCD+fGuMzwRm/9w a server.ccl.net> X-Original-From: Alcides Simao Content-Type: multipart/alternative; boundary=001485f81290b71bca046d193c36 Date: Wed, 24 Jun 2009 15:51:07 +0100 MIME-Version: 1.0 Sent to CCL by: Alcides Simao [alsimao ~ gmail.com] --001485f81290b71bca046d193c36 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Hello All! I would like to ask you to point me out to some (preferably free) QSAR software and relevant QSAR literature! Best, Alcides --001485f81290b71bca046d193c36 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Hello All!

I would like to ask you to point me out to some (preferably free) QSAR software and relevant QSAR literature!

Best,

Alcides
--001485f81290b71bca046d193c36-- From owner-chemistry@ccl.net Wed Jun 24 18:44:00 2009 From: "Troy Wymore wymore:+:psc.edu" To: CCL Subject: CCL: PSC/NRBSC Workshop on QC/MM Methods and Applications Message-Id: <-39605-090624183830-12493-Zv9rANGh3iGFFqKRrWpOxQ%server.ccl.net> X-Original-From: "Troy Wymore" Date: Wed, 24 Jun 2009 18:38:26 -0400 Sent to CCL by: "Troy Wymore" [wymore]~[psc.edu] The National Resource for Biomedical Supercomputing at the Pittsburgh Supercomputing Center will host a workshop entitled: "Methods and Applications of Hybrid Quantum Chemical/Molecular Mechanical Simulations of Biomolecular Systems" August 11-14, 2009 Pittsburgh, PA The deadline for registration is July 7, 2009. Website: http://shannon.psc.edu/mediawiki/index.php/QCMM_Workshop_2009 The workshop will present computational approaches for the simulation of enzymatic reactions. Lectures will be held on the relevant theoretical background including the applicability of Quantum Chemical (QC) methods for large molecules, re-parameterization of Semiempirical Molecular Orbital (SMO) methods for specific reactions, molecular mechanics (MM) force fields, hybrid QC/MM potential energy functions and simulation techniques on high performance computers. In-depth tutorials will be presented primarily with the use of the freely available pDynamo package developed in the lab of Dr. Martin J. Field and will also include developing SMO parameters for quantitatively accurate enzyme reaction simulations, the issues involved in constructing a QC/MM model with either SMO or DFT methods and the various methods for generating energy profiles of bio-molecular reactions to determine mechanisms and structure-function relationships. Experience with pDynamo is helpful but not a prerequisite for attendance. The workshop is designed for graduate students, post-doctoral researchers and faculty in computational biophysics and physical organic chemistry who have experience with computational chemistry methods and seek to enhance their capabilities to include the modeling of enzymatic reactions. Participants are encouraged to discuss and work on bio-molecular systems from their own research during the workshop. Space is limited. This workshop is funded by a grant from the NIH National Center for Research Resources. These grants provide tuition and hotel costs, supercomputing time, and workshop materials for US academic participants. All participants are responsible for paying their own travel expenses. Complimentary continental breakfasts and lunches will be provided the days of the workshop. Registration is now open. http://www.nrbsc.org/education/workshops/register.php