From chemistry-request@ccl.net Mon Dec 13 22:55:58 2004 Received: from ultra.chem.ucsb.edu (ultra.chem.ucsb.edu [128.111.114.119]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id iBE3ttlS013085 for ; Mon, 13 Dec 2004 22:55:55 -0500 Received: by ultra.chem.ucsb.edu (Postfix) id A341B5028A; Mon, 13 Dec 2004 20:11:21 -0800 (PST) Delivered-To: grcomet-05=at=chem.ucsb.edu Received: from localhost (localhost [127.0.0.1]) by ultra.chem.ucsb.edu (Postfix) with ESMTP id 357815028E; Mon, 13 Dec 2004 20:11:21 -0800 (PST) Received: from ultra.chem.ucsb.edu ([127.0.0.1]) by localhost (ultra [127.0.0.1]) (amavisd-new, port 10024) with ESMTP id 07616-02; Mon, 13 Dec 2004 20:11:13 -0800 (PST) Received: from [128.111.114.185] (c114d185.chem.ucsb.edu [128.111.114.185]) by ultra.chem.ucsb.edu (Postfix) with ESMTP id 2528B5028A; Mon, 13 Dec 2004 20:11:13 -0800 (PST) Message-ID: <41BE67E2.8050608=at=chem.ucsb.edu> Date: Mon, 13 Dec 2004 20:11:14 -0800 From: Alec Wodtke User-Agent: Mozilla/5.0 (Windows; U; Windows NT 5.1; en-US; rv:1.7.2) Gecko/20040804 Netscape/7.2 (ax) X-Accept-Language: en-us, en MIME-Version: 1.0 To: Alec Wodtke Subject: GORDON RESEARCH CONFERENCE ON MOLECULAR ENERGY TRANSFER- Buellton CA Content-Type: multipart/alternative; boundary="------------020101070607030904030502" X-Virus-Scanned: by amavisd-new X-Spam-Status: No, hits=6.9 required=7.5 tests=HTML_50_60,HTML_MESSAGE, HTML_TAG_EXISTS_TBODY,HTML_TITLE_EMPTY,LINES_OF_YELLING,MY_HTML_OBFU, NO_RDNS2 autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net This is a multi-part message in MIME format. --------------020101070607030904030502 Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 8bit STILL TIME TO REGISTER FOR THE 2005 GORDON RESEARCH CONFERENCE ON MOLECULAR ENERGY TRANSFER (GRCOMET) There are still ~15 slots available at the Gordon Conference on Molecular Energy Transfer. www.grc.org/programs/2005/molenerg.htm . Registering by the end of this week ensures a $50.- discount. The 2005 GRCOMET will take place January 9-14 at the Rancho Santa Barbara Marriott in Buellton, CA (north of Santa Barbara). This meeting has alternated with the European conference on molecular energy transfer (COMET). Application information can be found at www.grc.org/programs/2005/molenerg.htm . A vision statement and speakers list follows. Understanding the flow of energy within and between molecules is essential to the development of a fundamental understanding of the nature of all chemical processes. Furthermore, the deepest understanding can be achieved when phenomena are dealt with at the molecular level, connecting quantum-state, time-resolved and other modern methods of experimentation to ab initio theoretical study. The Gordon Research Conference on Molecular Energy Transfer will bring scientists together concerned with a wide variety of interests spanning chemistry, physics and biology, yet unified by the idea that developing a molecular picture of chemical dynamics is a central goal of their endeavors. An important aspect of this field is the fact that nearly every forefront topic of inquiry is well represented by experimental and theoretical advances. Topics of interest to this community are remarkably diverse, as the emphasis on deriving fundamental understanding often leads to insights in real world phenomena or even development of novel technologies. The Gordon Conference will highlight a variety of areas of study in molecular energy transfer, including: energy transfer in extreme conditions; in clusters; with electrons and ions; at interfaces; simulations of natural processes; photochemistry; reaction dynamics. There will also be a special session looking at exporting basic science for societal needs, which will include talks by Kim Prather; Sir Harry Kroto and Franz Hillenkamp. Prof Yuan T. Lee will be giving a keynote lecture as part of the Thursday evening session. A full Speakers List Follows. Speakers List Ludger Woeste (Free University Berlin) "The role of charges in the dynamics of noble metal clusters." Carl Lineberger (Joint Institute for Laboratory Astrophysics/University of Colorado), "Time Resolved, Mode Specific Studies of Energy Flow in Size-Selected Cluster Anions" Joel Bowman (Emory University) "Questioning our assumptions about chemical reactions" Sharon Hammes-Schiffer (Pennsylvania State University) "Hydrogen tunneling and protein motion in enzyme reactions" David Clary (University of Oxford, UK) "Quantum simulation of bio-molecules" Ken Jordan (University of Pittsburgh) "Characterization of Clathrate-type Water Clusters." Sir Harry Kroto (University of Sussex, UK) "Mechanisms of Nanostructure Assembly" Kim Prather (University of California San Diego) "What can we learn about our environment by measuring one particle at a time?" <>Franz Hillenkamp (University of M|nster), "The molecular age in medicine and biology:The challenge of how to measure what we need to know" Hanna Reisler (University of Southern California) "Predissociation in clusters and covalently bound dimers". Richard Loomis (Washington University) "Probing the influences of intermolecular energy on rare gas-dihalogen half-collision dynamics". Mike Duncan (University of Georgia) "Energy Accommodation in Cluster Cations". Mark Johnson (Yale University) "Spectroscopic studies of strongly shared protons in water clusters" Jeremy Hutson (University of Durham, UK), "Cold molecules and their collisions". Roger Miller (University of North Carolina Chapel Hill) "Energy transfer in extreme conditions (Low Temperature). Marcel Drabbels (Ecole Polytechnique Federale de Lausanne, Switzerland), "Imaging the Energy Transfer in Liquid Helium Droplets" Gerard Meijer (Fritz Haber Institute, Berlin) "Manipulation of molecules with electric fields". John Hepburn (University of British Columbia) "Understanding radicals: reactions, spectroscopy, and photofragmentation" Xueming Yang (Dalian Institute of Chemical Physics, Peoples Republic of China), "State-to-state Inelastic and Reactive Scatterings of Rydberg H-atom with H2 molecules: The Validity of The Fermi Model" Theo Kitsopoulos (Foundation for Research and Technology - Hellas, Krete) Novel Applications of slice imaging to Molecular Photodissociation and State Resolved Chemical Reactions Anna Krylov (University of Southern California) "Accurate Thermochemistry for Open-Shell Species: Brute force or a smart shortcut?" Bret Jackson (University of Massachusetts Amherst), "Molecule-Substrate Energy Transfer during Gas-Surface Collisions." Dennis Jacobs (University of Notre Dame) "Inelastic Ion/Surface Collisions at Hyperthermal Energies" Rainer Beck (Ecole Polytechnique Federale de Lausanne, Switzerland) "Mode Specific Chemisorption of Methane on Nickel" Piergiorgio Casavecchia (University of Perugia, Italy) "Recent progress in crossed molecular beam reactive scattering" Tim Minton (Montana State University) "Hyperthermal Reactions of O(3P) with Hydrogen and Alkanes" Rex Skodje (Institute of Atomic and Molecular Science, Taiwan) "The Product State Distribution of Chemical Reactions: The Imprint of the Transition State" Floyd Davis (Cornell University) "Dynamics of C-H and C-C Bond Activation by Transition Metal Atoms and Complexes" Steve Sibener(University of Chicago) "Collisional Energy Transfer and Thin Film Dynamics at Complex Interfaces" Yuan T. Lee (Institute of Atomic and Molecular Science, Taiwan) "Intramolecular Energy Transfer and Unimolecular Dissociations - A Historical Perspective." -- Prof. Alec M. Wodtke - Chair Department of Chemistry and Biochemistry Mail Code 9510 University of California Santa Barbara, CA 93106-9510 USA +001 (805) 893 2056 (voice - Chair's Office) +001 (805) 893 8085 (voice - Laboratory Office) +001 (805) 893 4120 (fax) +001 (805) 893 7653 (confidential fax) wodtke=at=chem.ucsb.edu www2.chem.ucsb.edu/~wodtkelab/ --------------020101070607030904030502 Content-Type: text/html; charset=us-ascii Content-Transfer-Encoding: 7bit

STILL TIME TO REGISTER FOR THE 2005 GORDON RESEARCH CONFERENCE ON MOLECULAR ENERGY TRANSFER (GRCOMET)

There are still ~15 slots available at the Gordon Conference on Molecular Energy Transfer.  www.grc.org/programs/2005/molenerg.htm. Registering by the end of this week ensures a $50.- discount.

The 2005 GRCOMET will take place January 9-14 at the Rancho Santa Barbara Marriott in Buellton, CA (north of Santa Barbara).  This meeting has alternated with the European conference on molecular energy transfer (COMET).  Application information can be found at www.grc.org/programs/2005/molenerg.htm.  A vision statement and speakers list follows.

Understanding the flow of energy within and between molecules is essential to the development of a fundamental understanding of the nature of all chemical processes. Furthermore, the deepest understanding can be achieved when phenomena are dealt with at the molecular level, connecting quantum-state, time-resolved and other modern methods of experimentation to ab initio theoretical study. The Gordon Research Conference on Molecular Energy Transfer will bring scientists together concerned with a wide variety of interests spanning chemistry, physics and biology, yet unified by the idea that developing a molecular picture of chemical dynamics is a central goal of their endeavors. An important aspect of this field is the fact that nearly every forefront topic of inquiry is well represented by experimental and theoretical advances. Topics of interest to this community are remarkably diverse, as the emphasis on deriving fundamental understanding often leads to insights in real world phenomena or even development of novel technologies.

The Gordon Conference will highlight a variety of areas of study in molecular energy transfer, including: energy transfer in extreme conditions; in clusters; with electrons and ions; at interfaces; simulations of natural processes; photochemistry; reaction dynamics.  There will also be a special session looking at exporting basic science for societal needs, which will include talks by Kim Prather; Sir Harry Kroto and Franz Hillenkamp. Prof Yuan T. Lee will be giving a keynote lecture as part of the Thursday evening session. A full Speakers List Follows.

Speakers List

Ludger Woeste (Free University Berlin) “The role of charges in the dynamics of noble metal clusters.”

Carl Lineberger (Joint Institute for Laboratory Astrophysics/University of Colorado), "Time Resolved, Mode Specific Studies of Energy Flow in Size-Selected Cluster Anions"

Joel Bowman (Emory University) "Questioning our assumptions about chemical reactions"

 
Sharon Hammes-Schiffer (Pennsylvania State University) "Hydrogen tunneling and protein motion in enzyme reactions"
 
David Clary (University of Oxford, UK) “Quantum simulation of bio-molecules”
 
Ken Jordan (University of Pittsburgh) “Characterization of Clathrate-type Water Clusters.”

Sir Harry Kroto (University of Sussex, UK) “Mechanisms of Nanostructure Assembly”

Kim Prather (University of California San Diego) “What can we learn about our environment by measuring one particle at a time?”
<>Franz Hillenkamp (University of Münster), "The molecular age in medicine and biology:The challenge of how to measure what we need to know”

Hanna Reisler (University of Southern California) “Predissociation in clusters and covalently bound dimers”.

Richard Loomis (Washington University) "Probing the influences of intermolecular energy on rare gas-dihalogen half-collision dynamics".

 
Mike Duncan (University of Georgia) "Energy Accommodation in Cluster Cations".  
Mark Johnson (Yale University) "Spectroscopic studies of strongly shared protons in water clusters"

Jeremy Hutson (University of Durham, UK), "Cold molecules and their collisions".

Roger Miller (University of North Carolina Chapel Hill) "Energy transfer in extreme conditions (Low Temperature).

Marcel Drabbels (Ecole Polytechnique Federale de Lausanne, Switzerland), "Imaging the Energy Transfer in Liquid Helium Droplets"

Gerard Meijer (Fritz Haber Institute, Berlin) "Manipulation of molecules with electric fields".

 
John Hepburn (University of British Columbia) “Understanding radicals: reactions, spectroscopy, and photofragmentation”

Xueming Yang (Dalian Institute of Chemical Physics, Peoples Republic of China), "State-to-state Inelastic and Reactive Scatterings of Rydberg H-atom with H2 molecules: The Validity of The Fermi Model"

 
Theo Kitsopoulos (Foundation for Research and Technology - Hellas, Krete) Novel Applications of slice imaging to Molecular Photodissociation and State Resolved Chemical Reactions
 
Anna Krylov (University of Southern California) "Accurate Thermochemistry for Open-Shell Species: Brute force or a smart shortcut?"

Bret Jackson (University of Massachusetts Amherst), “Molecule-Substrate Energy Transfer during Gas-Surface Collisions.”

Dennis Jacobs (University of Notre Dame) “Inelastic Ion/Surface Collisions at Hyperthermal Energies”

Rainer Beck (Ecole Polytechnique Federale de Lausanne, Switzerland) "Mode Specific Chemisorption of Methane on Nickel"

 
Piergiorgio Casavecchia (University of Perugia, Italy) "Recent progress in crossed molecular beam reactive scattering"

Tim Minton (Montana State University) “Hyperthermal Reactions of O(3P) with Hydrogen and Alkanes”

 
Rex Skodje (Institute of Atomic and Molecular Science, Taiwan) “The Product State Distribution of Chemical Reactions: The Imprint of the Transition State”

Floyd Davis (Cornell University) "Dynamics of C-H and C-C Bond Activation by Transition Metal Atoms and Complexes"

Steve Sibener(University of Chicago) “Collisional Energy Transfer and Thin Film Dynamics at Complex Interfaces”

Yuan T. Lee (Institute of Atomic and Molecular Science, Taiwan) "Intramolecular Energy Transfer and Unimolecular Dissociations - A Historical Perspective."

 
-- 
Prof. Alec M. Wodtke - Chair
Department of Chemistry and Biochemistry
Mail Code 9510
University of California
Santa Barbara, CA 93106-9510
USA

+001 (805) 893 2056 (voice - Chair's Office)
+001 (805) 893 8085 (voice - Laboratory Office)
+001 (805) 893 4120 (fax)
+001 (805) 893 7653 (confidential fax)

wodtke=at=chem.ucsb.edu
www2.chem.ucsb.edu/~wodtkelab/
--------------020101070607030904030502-- From chemistry-request@ccl.net Mon Dec 13 19:26:53 2004 Received: from lulu.it.northwestern.edu (lulu.it.northwestern.edu [129.105.16.54]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id iBE0QqlS001576 for ; Mon, 13 Dec 2004 19:26:52 -0500 Received: (from mailnull@localhost) by lulu.it.northwestern.edu (8.12.10/8.12.10) id iBE0gRni015998 for ; Mon, 13 Dec 2004 18:42:27 -0600 (CST) Received: from chunhui (cheme-86.chem-eng.northwestern.edu [129.105.205.86]) by lulu.it.northwestern.edu via smap (V2.0) id xma015796; Mon, 13 Dec 04 18:42:19 -0600 From: "Lily" To: Subject: explicit connectivity for PDB structure in Gaussian Date: Mon, 13 Dec 2004 18:42:12 -0600 Message-ID: <000101c4e175$c38d7f30$56cd6981@chunhui> MIME-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 7bit X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook, Build 10.0.2627 Importance: Normal X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2900.2180 X-Spam-Status: No, hits=0.0 required=7.5 tests=none autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Hi, I read a PDB structure into Gaussian and found that the bond order for binding ligand is not right. I guess it is because the initial structure is not good enough for proximity criteria in Gaussian. Then I wonder how to make sure the bond order for both enzyme and substrate is right and since it is a big system, it is hard to check manually. I really appreciate if you could let me how to get the right connectivity either changing parameter set up or using other package. (Prefer free available) Thanks a lot, Lily