From owner-chemistry@ccl.net Wed May  1 10:12:00 2013
From: "Jan H Jensen jhjensen!=!chem.ku.dk" <owner-chemistry[a]server.ccl.net>
To: CCL
Subject: CCL: Computational Chemistry Highlights
Message-Id: <-48637-130501095212-5556-rJ6uWjhxiWd+5G17dcRIog[a]server.ccl.net>
X-Original-From: "Jan H Jensen" <jhjensen-,-chem.ku.dk>
Date: Wed, 1 May 2013 09:52:11 -0400


Sent to CCL by: "Jan H Jensen" [jhjensen:_:chem.ku.dk]
The April issue of Computational Chemistry Highlights is out.
http://www.compchemhighlights.org/2013_04_01_archive.html

CCH is an overlay journal that identifies the most important papers in computational and theoretical 
chemistry published in the last 1-2 years. CCH is not affiliated with any publisher: it is a free 
resource run by scientists for scientists. You can read more about it here.

Table of content for this issue features contributions from CCH editors Steven Bachrach and Jan 
Jensen:

All Five Forms of Cytosine Revealed in the Gas Phase
http://www.compchemhighlights.org/2013/04/all-five-forms-of-cytosine-revealed-in.html

Three- and four-body corrected fragment molecular orbital calculations with a novel subdividing 
fragmentation method applicable to structure-based drug design
http://www.compchemhighlights.org/2013/04/three-and-four-body-corrected-fragment.html

The Melatonin Conformer Space: Benchmark and Assessment of Wave Function and DFT Methods for 
a Paradigmatic Biological and Pharmacological Molecule
http://www.compchemhighlights.org/2013/04/the-melatonin-conformer-space-benchmark.html

Zwitterions and Unobserved Intermediates in Organocatalytic DielsAlder Reactions of Linear and 
Cross-Conjugated Trienamines
http://www.compchemhighlights.org/2013/04/zwitterions-and-unobserved.html

Interested in more? There are many ways to subscribe to CCH updates.
http://www.compchemhighlights.org/p/get-cch-updates.html


From owner-chemistry@ccl.net Wed May  1 13:06:00 2013
From: "Raul Alvarez ralvarez!A!chemcomp.com" <owner-chemistry#,#server.ccl.net>
To: CCL
Subject: CCL: FINAL Agenda - CCG's UGM & Conference - Montreal, June 25-28, 2013
Message-Id: <-48638-130501111746-30919-YsFspdSk0tyOl+WKMfqfyA#,#server.ccl.net>
X-Original-From: "Raul  Alvarez" <ralvarez- -chemcomp.com>
Date: Wed, 1 May 2013 11:17:45 -0400


Sent to CCL by: "Raul  Alvarez" [ralvarez__chemcomp.com]
The final agenda for the UGM & Conference 2013 is now available. The event will take place this June 25-28, 2013 at the St-Sulpice Hotel (http://www.lesaintsulpice.com/) in Montreal, Canada. CCGs annual UGM & Conference is a 4-day event that consist of 2 days of workshops, 2 days of scientific presentations, posters and social functions. Abstracts for presentations and more details are available at http://www.chemcomp.com/UGM-2013-North_America.htm
 
>> FINAL AGENDA <> UGM & Conference 2013
 
===============================================
TUESDAY, June 25th - Workshops
===============================================  
 
9:00-12:00   Protein Alignments and Homology Modeling 
9:00-12:00   Overview of MOE in Drug Discovery 
9:00-12:00   SVL programming in MOE 
--------------------------------------------------------------
12:00        Lunch Break
--------------------------------------------------------------
13:30-17:00  Protein Family Modeling (Kinase, Antibody and GPCRs)
13:30-17:00  Pharmacophores in Drug Discovery 
13:30-17:00  Structure-Based Drug Design and Ligand Modification 
 
===============================================
WEDNESDAY, June 26th - Workshops
===============================================  
        
9:00-12:00   Protein:Protein Interaction Analysis 
9:00-12:00   Small Molecule Analysis and Virtual Screening
9:00-12:00   Q&A - Open Discussions 
--------------------------------------------------------------
12:00        Lunch Break
--------------------------------------------------------------
13:30-17:00  Biologics Modeling and Protein Engineering
13:30-17:00  Fragment-Based Drug Discovery 
13:30-17:00  Q&A - Open Discussions
--------------------------------------------------------------
17:30        Opening Cocktail & Posters Session
 
===============================================
THURSDAY, June 27th - Scientific Presentations
===============================================
 
8:30   Morning Coffee
--------------------------------------------------------------           
8:50   Opening Remarks
9:00   "Biomolecular Simulations Using Implicit Solvent Models: PB, GB and 3D-RISM"
       David A. Case, Professor, Rutgers University
9:30   "Water-based Modeling and Rational Drug Design Challenges in Optimization Projects"
       Rajiah Aldrin Denny, Principal Research Scientist, Pfizer
10:00  "Waters Role in Compound Design for Drug Discovery"
       Hongyao Zhu, Senior Principal Scientist, Pfizer
--------------------------------------------------------------
10:30  Morning Break
--------------------------------------------------------------           
11:00  "The impact of backbone flexibility on immune recognition of antigens: A computational and experimental study"
       Jaafar Haidar, Senior Scientist, Imclone Systems
11:30  "Placing Trust in Loop Prediction: Is it even Possible?"
       Christopher Corbeil, Research Scientist, Chemical Computing Group
--------------------------------------------------------------
12:00  Lunch Break
--------------------------------------------------------------
14:00  "MOE at the Bench"
       JW Feng, Scientist, Genentech
14:30  "Application of Extended Huckel Theory to Pharmacophore Discovery"
       Alain Ajamian, Director, Chemical Computing Group
15:00  "Integrated Fragment-based Drug-discovery" 
       Sabine Ruppel, Senior Scientist, Boehringer Ingelheim      
--------------------------------------------------------------
15:30  Afternoon Break
--------------------------------------------------------------           
16:00  "Protein-Family Virtual Screening with accuracy comparable to experimental HTS -- Kinases and Beyond"
       Eric Martin, Director, Computational Chemistry, Novartis
16:30  "Virtual Screening of Asymmetric Organocatalysts: Mining MOE's Lead-like and Linker Databases"
       Ghislain Deslongchamps, Professor, University of New Brunswick
--------------------------------------------------------------   
18:00  Reception
19:00  Gala Dinner
 
===============================================
FRIDAY, June 28th  Scientific Presentations
===============================================
 
8:30   Morning Coffee
--------------------------------------------------------------                        
9:00   "Rethinking Protein-ligand Interactions in Drug Discovery"
       Jos Duca, Head, Computer-Aided Drug Discovery, Novartis
9:30   "Probing Pocket Plasticity in Molecular Design"
       Matthew R. Lee, Research Advisor, Eli Lilly
--------------------------------------------------------------
10:00  Morning Break
--------------------------------------------------------------           
10:30  "Druggability (Ligandability) Assessment of Protein Targets by Dynamics Simulations in the Presence of Probe Molecules"
       Neysa Nevins, Computational Chemist, GlaxoSmithKline
11:00  "Hybrid Approaches for Predictive Modeling: Combining Docking, Ligand Similarity, and Protein Pocket Similarity"
       Ajay Jain, Professor, UCSF
11:30  "Fast Secondary Structure Similarity Searching and Alignment"
       Howard Feldman, Research Scientist, Chemical Computing Group
--------------------------------------------------------------
12:00  Lunch Break
--------------------------------------------------------------
14:00  "Computational Modeling of Lysophosphatidic Acid Receptor 1 (LPA1) and Small-molecule Inhibitors"
       John Nicholas, Director of Computational Chemistry and Computational Biology, InterMune
14:30  "Challenges in Designing Allosteric Inhibitors for ITK kinase"
       Ray Unwalla, Research Scientist, Pfizer
15:00  "ForceBalance: A Systematic, Reproducible, Statistically Driven, High-accuracy Approach to Force Field Parameterization"
       Vijay Pande, Professor, Stanford University
15:30  Closing remarks
-------------------------------------------------------------- 
15:45  Closing reception

===============================================
REGISTER [*] http://www.chemcomp.com/UGM-2013-North_America-Register.htm
===============================================

For more information please contact: 

Raul Alvarez
Senior Marketing Manager
Chemical Computing Group
ralvarez - at - chemcomp.com


From owner-chemistry@ccl.net Wed May  1 14:40:00 2013
From: "David Gallagher gallagher.da*gmail.com" <owner-chemistry(!)server.ccl.net>
To: CCL
Subject: CCL: Cocrystals: New in silico screening method
Message-Id: <-48639-130501142848-11854-jbak9LPGpz8SBICWNxwoyQ(!)server.ccl.net>
X-Original-From: David Gallagher <gallagher.da:gmail.com>
Content-Type: multipart/alternative;
 boundary="------------030601090409000708080609"
Date: Wed, 01 May 2013 11:28:41 -0700
MIME-Version: 1.0


Sent to CCL by: David Gallagher [gallagher.da||gmail.com]
This is a multi-part message in MIME format.
--------------030601090409000708080609
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
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*Cocrystals:  New /in silico/ screening method*

The formulation, design, and implementation of active pharmaceutical 
ingredients (API) is an area of great interest. Changing the structure 
and composition of a drug formulation, such as through 
cocrystallization, can have a significant influence on the properties 
and bioavailability of the API, and can offer the potential for new patents.

*Coformer screening*
Fast screening for likely cocrystal coformers can now be performed with 
the/a priori /method (COSMO-RS) implemented in COSMOlogic's software 
package, COSMOtherm.  Based on Density Functional (DFT) models and 
statistical thermodynamics, the methodology is fast enough to screen 
large batches of candidate molecules in minutes or hours on a laptop 
computer.

*Solubility screening*
Solubility influences the formation of crystals, cocrystals and 
solvates, as well as the pharmacokinetics through dissolution during 
drug release.  COSMOtherm provides the ability to predict solubilities 
of pure compounds and cocrystals/mixtures in a virtually unlimited range 
of solvents and solvent mixtures.

COSMOtherm will be demonstrated at the next American Chemical Society 
meeting at Indianapolis in September 2013.  For further information 
visit: http://www.cacheresearch.com/cocrystal.html

--------------030601090409000708080609
Content-Type: text/html; charset=ISO-8859-1
Content-Transfer-Encoding: 7bit

<html>
  <head>

    <meta http-equiv="content-type" content="text/html; charset=ISO-8859-1">
  </head>
  <body text="#000000" bgcolor="#FFFFFF">
    <font face="Arial"><b>Cocrystals:&nbsp; New <i>in silico</i> screening
        method</b><br>
      <br>
      The formulation, design, and implementation of active
      pharmaceutical ingredients (API) is an area of great interest.
      Changing the structure and composition of a drug formulation, such
      as through cocrystallization, can have a significant influence on
      the properties and bioavailability of the API, and can offer the
      potential for new patents.<br>
      <br>
      <b>Coformer screening</b><br>
      Fast screening for likely cocrystal coformers can now be performed
      with the<i> a priori </i>method (COSMO-RS) implemented in
      COSMOlogic's software package, COSMOtherm.&nbsp; Based on Density
      Functional (DFT) models and statistical thermodynamics, the
      methodology is fast enough to screen large batches of candidate
      molecules in minutes or hours on a laptop computer.<br>
      <br>
      <b>Solubility screening</b><br>
      Solubility influences the formation of crystals, cocrystals and
      solvates, as well as the pharmacokinetics through dissolution
      during drug release.&nbsp; COSMOtherm provides the ability to predict
      solubilities of pure compounds and cocrystals/mixtures in a
      virtually unlimited range of solvents and solvent mixtures.<br>
      <br>
      COSMOtherm will be demonstrated at the next American Chemical
      Society meeting at </font><font face="Arial"><font face="Arial">Indianapolis

      </font> in September 2013.&nbsp; For further information visit:&nbsp; <a
        href="http://www.cacheresearch.com/cocrystal.html">http://www.cacheresearch.com/cocrystal.html</a>
    </font>
  </body>
</html>

--------------030601090409000708080609--


From owner-chemistry@ccl.net Wed May  1 21:17:01 2013
From: "Karina Mu oz karina.munozbe- -usach.cl" <owner-chemistry++server.ccl.net>
To: CCL
Subject: CCL: ADF electronic configuration problem
Message-Id: <-48640-130501204834-31814-JtA0oc4p6NXAzzogeimbEw++server.ccl.net>
X-Original-From: "Karina  Mu  oz" <karina.munozbe::usach.cl>
Date: Wed, 1 May 2013 20:48:33 -0400


Sent to CCL by: "Karina  Mu  oz" [karina.munozbe- -usach.cl]
Dear CCl subscribers,

I am working with a molecule that has six vanadium (IV) centres, all having one unpaired d1 electron. I want to optimize the same fragment, but putting one of the vanadium centres with an oxidation state of (V), in which case it will present non unpaired electrons (d0 external configuration).
Anybody knows which keyword is useful to do this ? 
Is not the same case in which I can use de SpinFlip keyword, which works to change the spin of the electron of the centre of interest.

Thank you in advance

Best regards

Karina