From owner-chemistry@ccl.net Fri Mar 2 06:13:01 2012 From: "Tom s Pe a Ruiz truiz---ujaen.es" To: CCL Subject: CCL:G: Problem producing wavefuncions for electronic density analysis Message-Id: <-46407-120302060940-30380-65ssfyq1rOmbiW1KQQZ0oQ_._server.ccl.net> X-Original-From: "Tom s Pe a Ruiz" Date: Fri, 2 Mar 2012 06:09:39 -0500 Sent to CCL by: "Tom s Pe a Ruiz" [truiz~~ujaen.es] Dear All Recently, I am trying to produce a wavefunction of a coumpound with CCD and CCSD approaches in order to perform a topological analysis of the electronic density with codes as AIM2000. I have tried to generate the wave function with the package Gaussian09, but the problem consists of I have to use the Douglas-Kross-Hess hamiltonian ("integral(dkh)") to account for relativistic corrections and Gaussian09 is not able to calculate analytical first derivatives for these methods so the calculations are aborted the at the very biggining. I WANT TO NOTE that I have already reported this problem to Gaussian Technical Support, but the answer has been that "the are no analytic first derivatives for the methods to use", that is the reason to report my problem here too. Thus, since Gaussian has a large variety of options maybe someone knows a way to produce the wavefuntion I wish to or maybe someone could tell me what other program or procedure I may use. Thank you very much. From owner-chemistry@ccl.net Fri Mar 2 08:23:00 2012 From: "partha kundu partha1kundu:+:gmail.com" To: CCL Subject: CCL: SERS calculation Message-Id: <-46408-120302054103-27906-CR2BFzwRdXc4iJNMGdDELQ#,#server.ccl.net> X-Original-From: partha kundu Content-Type: multipart/alternative; boundary=f46d043bdefc2a88bb04ba403655 Date: Fri, 2 Mar 2012 16:10:15 +0530 MIME-Version: 1.0 Sent to CCL by: partha kundu [partha1kundu^^gmail.com] --f46d043bdefc2a88bb04ba403655 Content-Type: text/plain; charset=ISO-8859-1 Dear All, I want to calculate SERS for some molecule.Can I just add some Ag atom close to the molecule, optimize its structure and calculate Raman in usual way to get its SERS, or I need to consider something special? Kindly help. Thanks in advance. Partha --f46d043bdefc2a88bb04ba403655 Content-Type: text/html; charset=ISO-8859-1
Dear All,
I want to calculate SERS for some molecule.Can I just add some Ag atom close to the molecule, optimize its structure and calculate Raman in usual way to get its SERS, or I need to consider something special? Kindly help.
Thanks in advance.
Partha --f46d043bdefc2a88bb04ba403655-- From owner-chemistry@ccl.net Fri Mar 2 08:58:00 2012 From: "=?ISO-8859-1?Q?Jo=E3o_M=2E_Damas?= jmdamas(a)itqb.unl.pt" To: CCL Subject: CCL: Simulation of Electron Diffraction Message-Id: <-46409-120302074255-5468-kUVK9JsSt7gUrbvj1Qs8pg|-|server.ccl.net> X-Original-From: =?ISO-8859-1?Q?Jo=E3o_M=2E_Damas?= Content-Type: multipart/alternative; boundary=e89a8ff245ddee835e04ba41e98a Date: Fri, 2 Mar 2012 12:42:27 +0000 MIME-Version: 1.0 Sent to CCL by: =?ISO-8859-1?Q?Jo=E3o_M=2E_Damas?= [jmdamas^^^itqb.unl.pt] --e89a8ff245ddee835e04ba41e98a Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Dear Sanjay, Phenix can be used to derive a .mtz file from the .cif structure factors. This .mtz file, and hence the electron diffraction data, can be visualized using Coot (you should have the CCP4 package installed, because you'll need refmac5). Or you can use CCP4 to convert the .mtz file into a .map file using fft, and then visualize it using PyMol. The CCP4 package is free, but you need to sign a licence. Sorry for the (very) late reply. Best, Jo=E3o On Fri, Aug 19, 2011 at 12:02 PM, Sanjay Bharathwaj computationalchemist * gmail.com wrote: > Dear Friends, > > I have couple of crystal structures in .cif format and > I wanted to simulate the electron diffraction data. > > Hence, could you please let me know if there are any freeware available > to do this job. > > I will be glad to have answers and i thank you all in advance. > > My best regards, > SB > > -- > Regards, > Dr. Sanjay Bharathwaj Kumar, > Dharmendra Institute of Technology, > India. > --=20 Jo=E3o M. Damas PhD Student Protein Modelling Group ITQB-UNL, Oeiras, Portugal Tel:+351-214469613 --e89a8ff245ddee835e04ba41e98a Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Dear Sanjay,

Phenix can be used to derive a .mtz file fr= om the .cif structure factors. This .mtz file, and hence the electron diffr= action data, can be visualized using Coot (you should have the CCP4 package= installed, because you'll need refmac5). Or you can use CCP4 to conver= t the .mtz file into a .map file using fft, and then visualize it using PyM= ol.

The CCP4 package is free, but you need to sign a licenc= e.

Sorry for the (very) late reply.

=
Best,
Jo=E3o

On Fri,= Aug 19, 2011 at 12:02 PM, Sanjay Bharathwaj computationalchemist * gmail.com <owner-chemistry!A!ccl.net> wrote:
Dear Friends,

I have couple of crystal structu= res in .cif format and
I wanted to simulate the electron diffraction data.

Hence, could you please let me know if there are any fr= eeware available
to do this job.

I will = be glad to have answers and i thank you all in advance.

My best regards,
SB

--
Regards,
Dr. Sanjay Bhara= thwaj Kumar,
Dharmendra Institute of Technology,
India.



-- Jo=E3o M. Damas
PhD Student
Protein Modelling Group
ITQB-UNL, Oe= iras, Portugal
Tel:+351-214469613
--e89a8ff245ddee835e04ba41e98a-- From owner-chemistry@ccl.net Fri Mar 2 09:33:00 2012 From: "Alex Allardyce aa_+_chemaxon.hu" To: CCL Subject: CCL: Program launch and Call for participants: ChemAxon European UGM - Budapest, Hungary, May 22-23, 2012 Message-Id: <-46410-120302080934-3392-SBgfL4AAwvdLnfLZmnNIzQ-x-server.ccl.net> X-Original-From: Alex Allardyce Content-Type: multipart/alternative; boundary="------------000009080400020400070709" Date: Fri, 02 Mar 2012 14:09:26 +0100 MIME-Version: 1.0 Sent to CCL by: Alex Allardyce [aa%a%chemaxon.hu] This is a multi-part message in MIME format. --------------000009080400020400070709 Content-Type: text/plain; charset=UTF-8; format=flowed Content-Transfer-Encoding: 8bit We are announcing the program and calling for participants for ChemAxon's 8th European User Group Meeting (E-UGM) which will take place on May 22-23rd in Budapest, Hungary. Highlights of the event: 1. Program is launched: http://www.chemaxon.com/events/ugm-budapest-2012/#program. 2. Presentations from industry users including; Digital Science, Epitherapeutics, Evotec, Fraunhofer-Institute, GlaxoSmithKline, Huntsman, IBDS, Imperial College London, Laboratorie d'InfoChimie, Novartis, OntoChem, TargetEx and Thomson Reuters. Titles below. 3. Preceding the meeting, on the afternoon of the 21st of May we'll host a dedicated Markush Forum, sponsored by Thomson Reuters, discussing the development of our Markush IP tools. 4. The UGM is followed by a training day (May 24th) with two different tracks: one for developers and the other for end users. 5. Following the Markush forum we will have our traditional one to one sessions at ChemAxon's offices where you interact on your issues with ChemAxon developers and management. 6. We sample the best of Hungary's wines and art at the Gala dinner at the Kiscell Museum. We look forward to welcoming you here in Budapest in May Cheers Alex Useful links: Program: http://www.chemaxon.com/events/ugm-budapest-2012/#program More information: http://www.chemaxon.com/events/ugm-budapest-2012/#overview Registration: http://www.chemaxon.com/events/ugm-budapest-2012-registration/ Developer training details: http://www.chemaxon.com/events/ugm-budapest-2012/#developer End user training details: http://www.chemaxon.com/events/ugm-budapest-2012/#appfocus UGM archives - slides, video and meeting reports from Wendy Warr and Yvonne Martin: http://www.chemaxon.com/ugm-archive/ User Presentation titles and Institutions Keynote: Kent Stewart and Alex Drijver, Abbott Labs and ChemAxon 01 Synergies between ChemAxon's chemicalize and other open resources to extract structures from patents, discern SAR, and find intersects or similarities in PubChem. - ChrisDS Consulting 02 Structure Normalization in Chemical Extraction from Patents - Digital Science 03 Comparison of virtual screening performances of Drug Profile Matching and 2D and 3D similarity based approaches 04 Integrating Instant JChem in the Discovering Organization of a Biopharmaceutical Startup - Epitherapeutics 05 Introducing JChem4SharePoint at Evotec - Evotec 06 Custom Calculators in ChemAxon Tools and Knime - Evotec 07 Exploring and Visualisation of Chemistry in patents with Marvin and Instant JChem - Fraunhofer-Institute for Algorithms and Scientific Computing (SCAI) 08 Topic area: Instant JChem global deployment - GlaxoSmithKline 09 Topic area: Compound registration as a service - GlaxoSmithKline & ChemAxon 10 Integration of Chemical space: The Case for Use Cases - Grail Entropix Ltd 11 DataCrawler - a new approach in textile dye research - Huntsman 12 The right reaction - ChemAxon in IDBS E-WorkBook - IBDS 13 Getting on the Right Track - Chemical Tracking at Imperial College - Imperial College London 14 The ScreenDB Virtual Screening Platform - Latest News. - Laboratorie d'InfoChimie 15 Moving away from ISIS software with ChemAxon's help - Novartis 16 A new system for searching legacy and eLN reaction data - Novartis Institutes for BioMedical Research 17 Chemical Ontologies for Life Sciences - OntoChem GmbH 18 Rapid virtual screening of potential PDE 4/5 inhibitors combining 2D/3D similarity search (IJC/Screen), Biological evaluation - TargetEx llc 19 Data Reduction from Patents; How Chemical Structures in Patents Are Disclosed, Indexed and Retrieved, and What Do They Mean - Thomson Reuters -- *Alex Allardyce* Marketing Dir. *ChemAxon**Ltd*. Záhony u. 7. Building HX, Budapest, 1031 Hungary http://www.chemaxon.com Tel: +361 453 0435 Fax: +361 4532659 mailto:aa-$-chemaxon.com --------------000009080400020400070709 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: 8bit We are announcing the program and calling for participants for ChemAxon's 8th European User Group Meeting (E-UGM) which will take place on May 22-23rd in Budapest, Hungary.

Highlights of the event:
  1. Program is launched: http://www.chemaxon.com/events/ugm-budapest-2012/#program.
  2. Presentations from industry users including; Digital Science, Epitherapeutics, Evotec, Fraunhofer-Institute, GlaxoSmithKline, Huntsman, IBDS, Imperial College London, Laboratorie d'InfoChimie, Novartis, OntoChem, TargetEx and Thomson Reuters. Titles below. 
  3. Preceding the meeting, on the afternoon of the 21st of May we'll host a dedicated Markush Forum, sponsored by Thomson Reuters, discussing the development of our Markush IP tools. 
  4. The UGM is followed by a training day (May 24th) with two different tracks: one for developers and the other for end users.
  5. Following the Markush forum we will have our traditional one to one sessions at ChemAxon's offices where you interact on your issues with ChemAxon developers and management.
  6. We sample the best of Hungary's wines and art at the Gala dinner at the Kiscell Museum.

We look forward to welcoming you here in Budapest in May

Cheers
Alex

Useful links:
Program: http://www.chemaxon.com/events/ugm-budapest-2012/#program
More information: http://www.chemaxon.com/events/ugm-budapest-2012/#overview
Registration: http://www.chemaxon.com/events/ugm-budapest-2012-registration/
Developer training details: http://www.chemaxon.com/events/ugm-budapest-2012/#developer
End user training details: http://www.chemaxon.com/events/ugm-budapest-2012/#appfocus
UGM archives - slides, video and meeting reports from Wendy Warr and Yvonne Martin: http://www.chemaxon.com/ugm-archive/

User Presentation titles and Institutions
Keynote: Kent Stewart and Alex Drijver, Abbott Labs and ChemAxon
01    Synergies between ChemAxon's chemicalize and other open resources to extract structures from patents, discern SAR, and find intersects or similarities in PubChem. - ChrisDS Consulting
02    Structure Normalization in Chemical Extraction from Patents - Digital Science
03    Comparison of virtual screening performances of Drug Profile Matching and 2D and 3D similarity based approaches
04    Integrating Instant JChem in the Discovering Organization of a Biopharmaceutical Startup - Epitherapeutics
05    Introducing JChem4SharePoint at Evotec - Evotec
06    Custom Calculators in ChemAxon Tools and Knime - Evotec
07    Exploring and Visualisation of Chemistry in patents with Marvin and Instant JChem - Fraunhofer-Institute for Algorithms and Scientific Computing (SCAI)
08    Topic area: Instant JChem global deployment - GlaxoSmithKline
09    Topic area: Compound registration as a service - GlaxoSmithKline & ChemAxon
10    Integration of Chemical space: The Case for Use Cases - Grail Entropix Ltd
11    DataCrawler - a new approach in textile dye research - Huntsman
12    The right reaction - ChemAxon in IDBS E-WorkBook - IBDS
13    Getting on the Right Track - Chemical Tracking at Imperial College - Imperial College London
14    The ScreenDB Virtual Screening Platform - Latest News. - Laboratorie d'InfoChimie
15    Moving away from ISIS software with ChemAxon's help - Novartis
16    A new system for searching legacy and eLN reaction data - Novartis Institutes for BioMedical Research
17    Chemical Ontologies for Life Sciences - OntoChem GmbH
18    Rapid virtual screening of potential PDE 4/5 inhibitors combining 2D/3D similarity search (IJC/Screen), Biological evaluation - TargetEx llc
19    Data Reduction from Patents; How Chemical Structures in Patents Are Disclosed, Indexed and Retrieved, and What Do They Mean - Thomson Reuters
--
Alex Allardyce
Marketing Dir.
ChemAxon Ltd.
Záhony u. 7. Building HX, Budapest, 1031 Hungary
http://www.chemaxon.com
Tel: +361 453 0435
Fax: +361 4532659

mailto:aa-$-chemaxon.com
--------------000009080400020400070709-- From owner-chemistry@ccl.net Fri Mar 2 11:05:00 2012 From: "Patrik Johansson patrikj]-[fy.chalmers.se" To: CCL Subject: CCL: SERS calculation Message-Id: <-46411-120302091809-4781-0NrimKqTNnRhLZi9CperXA!=!server.ccl.net> X-Original-From: Patrik Johansson Content-Type: multipart/alternative; boundary="------------070309010307090001030305" Date: Fri, 02 Mar 2012 15:17:43 +0100 MIME-Version: 1.0 Sent to CCL by: Patrik Johansson [patrikj||fy.chalmers.se] This is a multi-part message in MIME format. --------------070309010307090001030305 Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit Dear Partha, You can to some extent, but it all depends on the answers you would like if you also need larger Ag-clusters, include extra fields or treat the time-dependence explicitly etc Some starting points (admittedly some of it is my own work - that probably is the more simplistic and less accurate): - Morton and Jensen, JACS 2009, 131, 4090. - Sun et al., J. Raman Spec. 2008, 39, 402. - Jensen, Zhao, Schatz, JPC C 2007, 111, 4756. - Johansson, PCCP 2005, 7, 475. - Bjerneld, Single Molecules 2000, 1, 239. /Patrik --- Patrik Johansson Prof., MPA-APP (Chalmers), MPA-N2PMB (GU) Applied Physics Chalmers University of Technology SWEDEN partha kundu partha1kundu:+:gmail.com skrev 2012-03-02 11:40: > > Dear All, > I want to calculate SERS for some molecule.Can I just add some Ag atom > close to the molecule, optimize its structure and calculate Raman in > usual way to get its SERS, or I need to consider something special? > Kindly help. > Thanks in advance. > Partha --------------070309010307090001030305 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Dear Partha,

You can to some extent, but it all depends on the answers you would like if you also need larger Ag-clusters, include extra fields
or treat the time-dependence explicitly etc
Some starting points (admittedly some of it is my own work - that probably is the more simplistic and less accurate):

- Morton and Jensen, JACS 2009, 131, 4090.
- Sun et al., J. Raman Spec. 2008, 39, 402.
- Jensen, Zhao, Schatz, JPC C 2007, 111, 4756.
- Johansson, PCCP 2005, 7, 475.
- Bjerneld, Single Molecules 2000, 1, 239.

/Patrik
---
Patrik Johansson
Prof., MPA-APP (Chalmers), MPA-N2PMB (GU)
Applied Physics
Chalmers University of Technology
SWEDEN

partha kundu partha1kundu:+:gmail.com skrev 2012-03-02 11:40:

Dear All,
I want to calculate SERS for some molecule.Can I just add some Ag atom close to the molecule, optimize its structure and calculate Raman in usual way to get its SERS, or I need to consider something special? Kindly help.
Thanks in advance.
Partha
--------------070309010307090001030305-- From owner-chemistry@ccl.net Fri Mar 2 11:40:01 2012 From: "Wei Deng ddeng::chemaxon.com" To: CCL Subject: CCL: Second Call for abstracts: Hunting for hidden treasures Message-Id: <-46412-120302110748-20303-0nWL8ASXsZXBTl2Kr2RxUw[#]server.ccl.net> X-Original-From: "Wei Deng" Date: Fri, 2 Mar 2012 11:07:46 -0500 Sent to CCL by: "Wei Deng" [ddeng!^!chemaxon.com] Second Call for abstracts: Hunting for hidden treasures: chemical information in patents and other documents We are still accepting submission of abstracts for consideration for an ACS Division of Chemical Information (CINF) Symposium on information extraction and analysis from patents and other documents, at the ACS Fall 2012 meeting in Philadelphia, August 19-23, 2012. There is a huge chemical space represented in existing documents, such as patents, journal articles, other publications, internal documents, etc. Due to historical reasons and technical limitations, much of this space is not indexed or digitalized. How to extract this information and to make use of it has long been a challenging task and will be the focus of this symposium. A discussion of current developments can hopefully benefit not only scientists in the pharmaceutical industry and academia, but also individuals in cheminformatics, publishing, patent laws and governmental agency. Related research topics include, but not limited to: Chemical information extraction, such as chemical names, structure images, Markush structures (especially R-groups and homology groups) from documents. Complex Markush structure analysis, generation and representation. White space identification. Automated biological data mining from documents. Automated SAR (Structure-activity relationship) analysis. Different interpretations of chemical information by chemists, information scientists, patent attorneys and patent examiners. Global patent harmonization. Non-English document analysis. Presentations will be 25-30 minutes, including time for questions. The deadline for submitting an abstract for consideration is March 19th, 2012. Abstracts may be submitted via: http://abstracts.acs.org (Session code CINF005). Please contact the organizer, Wei Deng (David) (dengw2 -at- gmail.com or ddeng -at -chemaxon.com ), if you have any questions or to discuss a paper. From owner-chemistry@ccl.net Fri Mar 2 18:35:00 2012 From: "benoit le fevre bonoit_10%%yahoo.fr" To: CCL Subject: CCL: CBS-4M Message-Id: <-46413-120302183336-8948-45xLHN6UZ23bRGEx6JQIgg(_)server.ccl.net> X-Original-From: "benoit le fevre" Date: Fri, 2 Mar 2012 18:33:35 -0500 Sent to CCL by: "benoit le fevre" [bonoit_10 . yahoo.fr] Dear CCLer's, I wonder if you can help me to get how to do a cbs-4m calculation, i mean i need like cbs-4m worksheet (excel). Regards Benoit From owner-chemistry@ccl.net Fri Mar 2 19:09:01 2012 From: "Eric Scerri scerri+*+chem.ucla.edu" To: CCL Subject: CCL: website for forthcoming 3rd International Conference on the Periodic Table Message-Id: <-46414-120302175340-10126-45XCMy4OaN4rhleLt0nyaQ++server.ccl.net> X-Original-From: Eric Scerri Content-Type: multipart/alternative; boundary=Apple-Mail-54-234356860 Date: Fri, 2 Mar 2012 14:54:34 -0800 Mime-Version: 1.0 (Apple Message framework v936) Sent to CCL by: Eric Scerri [scerri*_*chem.ucla.edu] --Apple-Mail-54-234356860 Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes Content-Transfer-Encoding: 7bit http://3icpt-cusco2012.uglobalcusco.edu.pe/index.php?option=com_content&view=article&id=25&Itemid=28 ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- website: http://ericscerri.com/ Eric Scerri, A Very Short Introduction to the Periodic Table, Oxford University Press, 2011, http://www.oup.com/us/catalog/general/subject/Chemistry/?view=usa&ci=9780199582495 Eric Scerri, The Periodic Table, Its Story and Its Significance, Oxford University Press, 2007. http://www.oup.com/us/catalog/general/subject/Chemistry/?view=usa&ci=9780195305739 UCLA faculty website: http://faculty.chemistry.ucla.edu/institution/personnel?personnel_id=294334 --Apple-Mail-54-234356860 Content-Type: text/html; charset=US-ASCII Content-Transfer-Encoding: quoted-printable http://3icpt-cusco= 2012.uglobalcusco.edu.pe/index.php?option=3Dcom_content&view=3Darticle= &id=3D25&Itemid=3D28



Eric = Scerri, A Very Short Introduction to the Periodic Table, Oxford = University Press, 2011, http://www.oup.com/us/catalog/general/subject/Ch= emistry/?view=3Dusa&ci=3D9780199582495

=

Eric Scerri, The Periodic Table, Its Story = and Its Significance, Oxford University Press, = 2007. http://www.oup.com/us/catalog/general/subject/Ch= emistry/?view=3Dusa&ci=3D9780195305739 

UCLA faculty = website: http://faculty.chemistry.ucla.edu/institution/personnel?perso= nnel_id=3D294334







= --Apple-Mail-54-234356860--