From owner-chemistry@ccl.net Wed Jun 9 05:30:00 2010 From: "Tamas Gunda tgunda2*puma.unideb.hu" To: CCL Subject: CCL: Mol2mol 5.6.2 upgrade Message-Id: <-42072-100608180226-6562-lqcYtQU6pCDssK4bWuJCYQ:-:server.ccl.net> X-Original-From: "Tamas Gunda" Content-Transfer-Encoding: 7bit Content-Type: text/plain; format=flowed; charset="iso-8859-2"; reply-type=original Date: Tue, 8 Jun 2010 23:02:17 +0200 MIME-Version: 1.0 Sent to CCL by: "Tamas Gunda" [tgunda2+*+puma.unideb.hu] Dear CCL Members, The new 5.6.2 version of the molecule file conversion, manipulation and utility program Mol2Mol is now available > from http://www.gunda.hu/mol2mol as trial or shareware version. The current version of Mol2Mol recognizes, and interconverts about 50 different file formats (including subtypes). By entering a format string practically every Cartesian or MOPAC type Z matrix formats can be out/inputted (even in polar coordinates). It can slice multiple structural files to single ones (such as PDB models or MDL SD files to single ones) and vice versa in several variations. Support for PDB Chime subformat (with 1-2-3 bonds). Many molecular utilities. Mol2mol 5.6.2 is a service edition with several fixes. It is impossible to write here all of the features of Mol2Mol, but have a look at its home page: http://www.gunda.hu/mol2mol Dr. Tamas E. Gunda University of Debrecen Hungary From owner-chemistry@ccl.net Wed Jun 9 07:09:00 2010 From: "Pierre Archirel pierre.archirel*o*lcp.u-psud.fr" To: CCL Subject: CCL:G: IRC convergence Message-Id: <-42073-100609055611-8345-bqt6tQbimxDN+2QR9EZrdg|server.ccl.net> X-Original-From: Pierre Archirel Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Wed, 09 Jun 2010 12:23:12 +0200 MIME-Version: 1.0 Sent to CCL by: Pierre Archirel [pierre.archirel]~[lcp.u-psud.fr] This is an answer to M. Tassell: I had many difficulties with the IRC of g09 and also tried many combinations of the parameters. The issue obviously appears when the top of the barrier is very flat in a wide region. The gaussian assistance suggested me the keyword IOp(1/108=-1) which suppresses the test on the gradient. This fixes your issue but you will possibly roam around the TS before finding a non zero gradient. I have also found the following bypass efficient: 1- take the nuclear hessian on the chk file and diagonalise it 2- perform a displacement (e.g. .5 A) in both directions of the TS direction 3- ask for two "downhill" calculations from these two points, in this way you avoid the top of the barrier from the beginning. 4- asking "opt" from these two points is very efficient but you cannot be sure that you follow the IRC. Other suggestions will be welcome. Pierre Archirel pierre.archirel###u-psud.fr ____________________________________________________________ ATTENTION MON ADRESSE ELECTRONIQUE A CHANGE: VOIR PLUS BAS Pierre Archirel Groupe Théosim: Théorie et Simulation Laboratoire de Chimie Physique Tel: 01 69 15 63 86 Bat 349 Fax: 01 69 15 61 88 91405 Orsay Cédex France pierre.archirel###u-psud.fr ____________________________________________________________ From owner-chemistry@ccl.net Wed Jun 9 10:18:00 2010 From: "Haibin Scopus lihb734!A!yahoo.com" To: CCL Subject: CCL: structural stability according to AIM Message-Id: <-42074-100609081602-423-bwF7yAlEZ5fuJ3+N+q68iQ=server.ccl.net> X-Original-From: Haibin Scopus Content-Type: multipart/alternative; boundary="0-656949385-1276082150=:59895" Date: Wed, 9 Jun 2010 04:15:50 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: Haibin Scopus [lihb734\a/yahoo.com] --0-656949385-1276082150=:59895 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable Dear CCLer, =A0 One paper (JPCA,102,1873) mentioned "Another citerion for structural st= ability is the distance between a BCP and a RCP. If these two critical poin= ts coalesce, they annihilate corresponding to bond rupture and concomitant = ring opening." However, this proposition didn't refer to references. Thus, = I want to know is there any paper(s) support this proposition? Thank you fo= r your help! Best wishes! =A0 Haibin Li Institute of Functional Material Chemistry, Faculty of Chemistry Northeast Normal University=20 changchun, Jilin, 130024 PR CHINA E-mail: lihb734-,-nenu.edu.cn; lihb734-,-yahoo.com http://www.nenu.edu.cn=0A=0A=0A --0-656949385-1276082150=:59895 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable
Dear CCLer,
  One paper (JPCA,102,1873) mentioned "Another citerion for struc= tural stability is the distance between a BCP and a RCP. If these two criti= cal points coalesce, they annihilate corresponding to bond rupture and conc= omitant ring opening." However, this proposition didn't refer to references= . Thus, I want to know is there any paper(s) support this proposition? Than= k you for your help! Best wishes!
 
Haibin Li
Institute of Functional Material Chemistry, Faculty of Chemistry
Northeast Normal University
changchun, Jilin, 130024 PR = CHINA

E-mail: lihb734-,-nenu.edu.cn; lihb734-,-yahoo.com
http://www.n= enu.edu.cn

=0A=0A --0-656949385-1276082150=:59895-- From owner-chemistry@ccl.net Wed Jun 9 13:12:00 2010 From: "Geoffrey Hutchison geoffh###pitt.edu" To: CCL Subject: CCL: IBM's Chemical Kinetics Simulation Message-Id: <-42075-100609123011-3310-qY+GdqawXwxgKC8UGqbjBQ+/-server.ccl.net> X-Original-From: Geoffrey Hutchison Content-transfer-encoding: quoted-printable Content-type: text/plain; charset=us-ascii Date: Wed, 09 Jun 2010 11:45:32 -0400 MIME-version: 1.0 (Apple Message framework v1078) Sent to CCL by: Geoffrey Hutchison [geoffh*|*pitt.edu] Many years ago, IBM had this nice, student-friendly chemical kinetics = simulation code for "Classic Mac," and Windows 3.1 / Win95. You could = input reaction mechanisms and rate constants, follow the concentrations = as a function of time, etc. http://www.almaden.ibm.com/st/computational_science/ck/?cks Now I can't get it to run on modern Macs, and I've had trouble running = it on Windows too. It's the kind of thing that I can imagine as a great = web service (not that I'm volunteering!). Does anyone have suggestions = for an undergrad chemical kinetics tool? Thanks very much, -Geoff --- Prof. Geoffrey Hutchison Department of Chemistry University of Pittsburgh tel: (412) 648-0492 email: geoffh|pitt.edu web: http://hutchison.chem.pitt.edu/ From owner-chemistry@ccl.net Wed Jun 9 15:34:00 2010 From: "Mahmoud A. A. Ibrahim m.ibrahim^compchem.net" To: CCL Subject: CCL: structural stability according to AIM Message-Id: <-42076-100609125306-18368-dooTuAfihat7FlqG4NoVUg(!)server.ccl.net> X-Original-From: "Mahmoud A. A. Ibrahim" Content-Type: multipart/alternative; boundary=0016e6d7dff59e30ab04889a3af4 Date: Wed, 9 Jun 2010 16:04:55 +0100 MIME-Version: 1.0 Sent to CCL by: "Mahmoud A. A. Ibrahim" [m.ibrahim{:}compchem.net] --0016e6d7dff59e30ab04889a3af4 Content-Type: text/plain; charset=ISO-8859-1 Dear Habini Yes, there is a relation between the distance between BCP and RCP, and the bond strength. The same criteria has been mentioned in a couple of papers. You may like to have a look on the following paper. Pakiari, A. H.; Eskandari, K., Closed shell oxygen-oxygen bonding interaction based on electron density analysis. Journal of Molecular Structure: THEOCHEM 2007, 806, (1-3), 1-7. Sincerely; M. Ibrahim On Wed, Jun 9, 2010 at 12:15 PM, Haibin Scopus lihb734!A!yahoo.com < owner-chemistry-*-ccl.net> wrote: > Dear CCLer, > One paper (JPCA,102,1873) mentioned "Another citerion for structural > stability is the distance between a BCP and a RCP. If these two critical > points coalesce, they annihilate corresponding to bond rupture and > concomitant ring opening." However, this proposition didn't refer to > references. Thus, I want to know is there any paper(s) support this > proposition? Thank you for your help! Best wishes! > > ------------------------------ > ------------------------------ > *Haibin Li* > Institute of Functional Material Chemistry, Faculty of Chemistry > *Northeast Normal University* > changchun, Jilin, 130024 PR CHINA > > E-mail: lihb734:nenu.edu.cn; lihb734:yahoo.com > http://www.nenu.edu.cn > > -- Mahmoud A. A. Ibrahim Current Address 7.05, School of Chemistry, The University of Manchester, Oxford Road, Manchester, M13 9PL, United Kingdom. Home Address Chemistry Department, Faculty of Science, Minia University, Minia 61519, Egypt. Contact Information Email: m.ibrahim-*-compchem.net Website: www.compchem.net Fax No.: +20862342601 --0016e6d7dff59e30ab04889a3af4 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Dear Habini
Yes, there is a relation between the distance between BCP a= nd RCP, and the bond strength. The same=A0criteria=A0has been mentioned in = a couple of papers. You may like to have a look on the following paper.
Pakiari, A. H.; Eskandari, K., Closed shell oxygen-oxygen bonding inte= raction based on electron density analysis. Journal of Molecular Structure:= THEOCHEM 2007, 806, (1-3), 1-7.
Sincerely;
M. Ibrahim<= br>
On Wed, Jun 9, 2010 at 12:15 PM, Haibin Scop= us lihb734!A!yahoo.com &= lt;owner-chemistry-*-ccl.net&g= t; wrote:
Dear= CCLer,
=A0 One paper (JPCA,102,1873) mentioned "Another citerion for str= uctural stability is the distance between a BCP and a RCP. If these two cri= tical points coalesce, they annihilate corresponding to bond rupture and co= ncomitant ring opening." However, this proposition didn't refer to= references. Thus, I want to know is there any paper(s) support this propos= ition? Thank you for your help! Best wishes!
=A0
Haibin Li
Institute of Functional Material Chemistry, Faculty of Chemistry
Northeast Normal University
changchun, Jilin, 130024 PR = CHINA

E-mail: lihb734:nenu.edu.cn; lihb734:= yahoo.com
http://www.nenu.edu.cn=




--
=A0 =A0 =A0 =A0 = =A0 =A0 =A0 =A0 =A0Mahmoud A. A. Ibrahim =A0 =A0 =A0 =A0
=A0 =A0 =A0 = =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 Current Address
=A0 =A0 =A0 =A0 =A0 =A0= =A0 =A0 7.05, School of Chemistry,
=A0 =A0 =A0 =A0 =A0 =A0 =A0The Univ= ersity of Manchester,
=A0 =A0 =A0 =A0 Oxford Road, Manchester, M13 9PL,
=A0 =A0 =A0 =A0 =A0= =A0 =A0 =A0 =A0 =A0 =A0 United Kingdom.

=A0 =A0 =A0 =A0 =A0 =A0 = =A0 =A0 =A0 =A0 =A0 =A0Home Address
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0= Chemistry Department,
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 Faculty o= f Science,
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0Minia Univers= ity,
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 Minia 61519,
=A0 = =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0Egypt.

= =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 Contact Information
=A0 =A0 =A0= =A0 =A0 Email: m.ibrahim-*-compche= m.net
=A0 =A0 =A0 =A0 =A0 =A0 =A0Website: ww= w.compchem.net
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 Fax No.: +208623= 42601
--0016e6d7dff59e30ab04889a3af4-- From owner-chemistry@ccl.net Wed Jun 9 16:09:00 2010 From: "D. Boyd dboyd]^[iupui.edu" To: CCL Subject: CCL: 2010 Gordon Research Conference on Computational Chemistry ... Message-Id: <-42077-100609144659-28058-0JCig4MW94ZBbZC5m6SY/g[A]server.ccl.net> X-Original-From: "D. Boyd" Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=ISO-8859-1; format=flowed; delsp=yes Date: Wed, 9 Jun 2010 14:46:16 -0400 Mime-Version: 1.0 (Apple Message framework v936) Sent to CCL by: "D. Boyd" [dboyd .. iupui.edu] Prof. Dr. Walter Thiel (Max-Planck-Institut fur Kohlenforschung, =20 Mulheim, Germany) is chairing the 2010 Gordon Research Conference on =20 Computational Chemistry. This biennial conference is convening August =20= 29 - September 3, 2010 at the conference center in Les Diablerets, =20 Switzerland. The program includes the following invited speakers: Keynote Lecture: Martin Karplus (Harvard University, Cambridge, USA) "How proteins work: insights from simulations" Wilfred van Gunsteren (ETH Z=FCrich, Switzerland) "Computer simulation of polypeptide folding equilibria: factors =20 determining success or failure" Discussion Leader: Christian Ochsenfeld (University of Munich, Germany) Gustavo Scuseria (Rice University, Houston, USA) "New models for mixing wavefunctions with density functional theory" Stefan Grimme (University of M=FCnster, Germany) "Dispersion corrected density functionals for general chemistry =20 applications" Joost VandeVondele (University of Z=FCrich, Switzerland) "Applications of hybrid density functionals in large condensed phase =20 systems" Discussion Leader: Jay Ponder (Washington University Medical School, =20 St. Louis, USA) Helmut Grubmueller (Max-Planck-Institut f=FCr biophysikalische Chemie, =20= Gottingen, Germany) "Forces and non-equilibrium dynamics in biomolecular nanomachines" David Case (Rutgers University, Piscataway, USA) "Recent developments in molecular mechanics force fields for proteins =20= and nucleic acids" Discussion Leader: Hans-Martin Senn (University of Glasgow, UK) Qiang Cui (University of Wisconsin, Madison, USA) "Electrostatics in multi-resolution QM/MM and coarse-grained =20 simulations" Ursula Rothlisberger (EPF Lausanne, Switzerland) "Rhodopsin revisited: QM, QM/MM and MM simulations on rhodopsin et al." Florian Mueller-Plathe (Technical University Darmstadt, Germany) "Multiscale simulation of soft matter: status and perspectives" Discussion Leader: Holger Gohlke (University of D=FCsseldorf, Germany) Mike Gilson (University of California at San Diego, USA) "Affinity, entropy, and mechanical stress in molecular recognition" Matthias Rarey (University of Hamburg, Germany) "Structure-based molecular design: pragmatic approaches to docking, =20 scoring, and the analysis of complexes" Discussion Leader: Bill Swope (IBM Research, San Jose, USA) Weitao Yang (Duke University, Durham, USA) "Free energy and mechanism of reactions in solution and in enzymes =20 with ab initio QM/MM methods" Chris Chipot (CNRS and Universit=E9 Nancy, France) "Gliding on multidimensional free-energy landscapes using time-=20 dependent biases on collective variables" Discussion Leader: Alice Gl=E4ttli (BASF, Ludwigshafen, Germany) Jed Pitera (IBM Research, San Jose, USA) "Simulating nanostructured polymers for industrial applications" Jan Schoneboom (BASF, Ludwigshafen, Germany) "Quantum chemical calculations for material design in organic =20 photovoltaics" Discussion Leader: Vincenzo Barone (University of Pisa, Italy) Todd Martinez (Stanford University, USA) "Quantum chemistry and first principles dynamics of proteins and =20 ligand-protein interactions using graphical processing units" Frank Neese (University of Bonn, Germany) "Recent developments and applications in local coupled cluster =20 approaches based on pair natural orbitals" Andreas Dreuw (University of Frankfurt, Germany) "Excited states of large molecules: a challenge to modern electronic =20 structure theory" Discussion Leader: Julia Rice (IBM Research, San Jose, USA) Karsten Reuter (Technical University Munich, Germany) "Towards a first-principles chemical engineering" Adrian Mulholland (University of Bristol, UK) "Combined quantum mechanics/molecular mechanics (QM/MM) methods in =20 computational enzymology" The deadline for applying is August 8. To apply to participate in the =20= conference, please go to = http://www.grc.org/programs.aspx?year=3D2010&program=3Dcompchem Thanks. Donald B. Boyd, Ph.D. Research Professor of Chemistry Editor Emeritus, Reviews in Computational Chemistry Department of Chemistry and Chemical Biology Indiana University-Purdue University at Indianapolis= From owner-chemistry@ccl.net Wed Jun 9 17:21:00 2010 From: "James Eilers jeilers%x%siue.edu" To: CCL Subject: CCL: IBM's Chemical Kinetics Simulation Message-Id: <-42078-100609153052-14953-eJ9s/Mp8/sWLLLm7VN7KNw++server.ccl.net> X-Original-From: James Eilers Content-Type: multipart/alternative; boundary=Apple-Mail-5--697339269 Date: Wed, 9 Jun 2010 14:01:27 -0500 Mime-Version: 1.0 (Apple Message framework v624) Sent to CCL by: James Eilers [jeilers{:}siue.edu] --Apple-Mail-5--697339269 Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII; format=flowed Take a look at Berkeley Madonna. http://www.berkeleymadonna.com/ It does a lot of additional things that you won't use, but I use it for undergrad P-Chem with some success. On Jun 9, 2010, at 10:45 AM, Geoffrey Hutchison geoffh###pitt.edu wrote: > > Sent to CCL by: Geoffrey Hutchison [geoffh*|*pitt.edu] > Many years ago, IBM had this nice, student-friendly chemical kinetics > simulation code for "Classic Mac," and Windows 3.1 / Win95. You could > input reaction mechanisms and rate constants, follow the > concentrations as a function of time, etc. > http://www.almaden.ibm.com/st/computational_science/ck/?cks > > Now I can't get it to run on modern Macs, and I've had trouble running > it on Windows too. It's the kind of thing that I can imagine as a > great web service (not that I'm volunteering!). Does anyone have > suggestions for an undergrad chemical kinetics tool? > > Thanks very much, > -Geoff > > --- > Prof. Geoffrey Hutchison > Department of Chemistry > University of Pittsburgh > tel: (412) 648-0492 > email: geoffh!^!pitt.edu > web: http://hutchison.chem.pitt.edu/ > > > > - This is automatically added to each message by the mailing script =- > To recover the email address of the author of the message, please > change> > > James E. Eilers Professor Chemistry Department Southern Illinois University Edwardsville (618)650-3559 --Apple-Mail-5--697339269 Content-Transfer-Encoding: 7bit Content-Type: text/enriched; charset=US-ASCII Take a look at Berkeley Madonna. http://www.berkeleymadonna.com/ It does a lot of additional things that you won't use, but I use it for undergrad P-Chem with some success. On Jun 9, 2010, at 10:45 AM, Geoffrey Hutchison geoffh###pitt.edu wrote: Sent to CCL by: Geoffrey Hutchison [geoffh*|*pitt.edu] Many years ago, IBM had this nice, student-friendly chemical kinetics simulation code for "Classic Mac," and Windows 3.1 / Win95. You could input reaction mechanisms and rate constants, follow the concentrations as a function of time, etc. http://www.almaden.ibm.com/st/computational_science/ck/?cks Now I can't get it to run on modern Macs, and I've had trouble running it on Windows too. It's the kind of thing that I can imagine as a great web service (not that I'm volunteering!). Does anyone have suggestions for an undergrad chemical kinetics tool? Thanks very much, -Geoff --- Prof. Geoffrey Hutchison Department of Chemistry University of Pittsburgh tel: (412) 648-0492 email: geoffh!^!pitt.edu web: http://hutchison.chem.pitt.edu/ - This is automatically added to each message by the mailing script =-http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txtHelveticaJames E. Eilers Professor Chemistry Department Southern Illinois University Edwardsville (618)650-3559 --Apple-Mail-5--697339269--