From owner-chemistry@ccl.net Mon Jul 25 05:07:55 2005 From: "CCL" To: CCL Subject: CCL: W:Course on Energy Surfaces, Excited States and Dynamics Message-Id: <-28921-050722090245-26617-eSc6C2yCCSce8pLLLmWjCA]*[server.ccl.net> X-Original-From: "Hans Lischka" Sent to CCL by: "Hans Lischka" Dear All, We are pleased to announce "COLUMBUS in RIO", a Quantum Chemistry Course on Multireference Methods, Energy Surfaces, Excited States and Dynamics. This event will be held at the Instituto Militar de Engenharia, Rio de Janeiro, Brazil from Nov. 27 - Dec. 02 , 2005. The goal of the course is to introduce participants into the concepts of multireference theory and their application to several interesting fields of chemistry and molecular physics with special emphasis on the calculation of energy surfaces of ground- and excited states, conical intersections and first steps into ab initio dynamics. This course will be held in the form of lectures and in practical application work organized in small working groups. More information can be found at http://www.univie.ac.at/columbus/rio/ Hans Lischka hans.lischka]*[univie.ac.at University of Vienna, Austria From owner-chemistry@ccl.net Mon Jul 25 06:01:04 2005 From: "CCL" To: CCL Subject: CCL: W:SMILES AND MODELLING] Message-Id: <-28922-050725060040-11901-eSc6C2yCCSce8pLLLmWjCA(-)server.ccl.net> X-Original-From: "Gyorgy Pirok" Content-Transfer-Encoding: 8bit Content-Type: text/plain; format=flowed; charset="iso-8859-1"; reply-type=original MIME-Version: 1.0 Sent to CCL by: "Gyorgy Pirok" Hi, FIRST ANSWER: Yes, SMILES are the best for storage in most cases, since they are much smaller than most of the other formats, approximately fifty times smaller than Molfiles. SMILES are not good if your molecules have special features which cannot be described in SMILES well (R-groups for instance) or if you need the 3D atom coordinates. SECOND ONE: Difficult to answer without seeing the cyclization reaction (might be difficult to answer after seeing too) THIRD ANSWER: I can recommend ChemAxon's JChem toolkit written in Java (www.chemaxon.com). It contains lots of useful software pieces for chemistry application developers. For example, try to process your cyclization reaction with the Reactor tool. The components of the JChem toolkit are compatible with the Daylight standards like SMILES and SMARTS (and with MDL formats too) and the functions are available through Java API, command line applications and Cartridge technology as well. Contact us for a FREE Academic license, then just download the toolkit and use it! I hope it helps. Best regards, György Gyorgy Pirok CTO ChemAxon Ltd. 1037 Budapest Maramaros koz 3/A Tel: +36 (1) 453-2661 Fax: +36 (1) 453-2659 -------- Original Message -------- Subject: CCL: W:SMILES AND MODELLING Date: Sun, 17 Jul 2005 12:42:01 -0400 > From: CCL To: Allardyce, Alex Sent to CCL by: "Antonio Starcevic" Dear All; We are a academic group working on a bioinformatics application written in Java, that involves certain chemistry solutions. That's the part we need some help solving. We are storing our molecules in SMILES format, and at the end our goal is to turn linear structures into cyclisized. FIRST QUESTION: are SMILES the best choice for database entries and computation of new structres??? SECOND QUESTION: if you model spontaneous cyclization from a linear compound, how can you determine which product out of all possible ones is most likely to be the real thing THIRD QUESTION: is there a software that can help us solve "second question", and could you recomend us some(it should cooperate with SMILES "Daylight toolkit" if possible) P.S. are there any Java libraries for this stuff??? Thanks for all suggestions! From owner-chemistry@ccl.net Mon Jul 25 06:27:10 2005 From: "CCL" server.ccl.net> To: CCL Subject: CCL: Natural orbital related questions Message-Id: <-28923-050722105516-8872-eSc6C2yCCSce8pLLLmWjCA<*>server.ccl.net> X-Original-From: James Kirkpatrick imperial.ac.uk> Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed MIME-Version: 1.0 Sent to CCL by: James Kirkpatrick imperial.ac.uk> Hi CCLers. I have some Natural Orbital related questions. Is there a good reason why Gaussian does not allow one to make Natural Orbital analysis of ZINDO calculations? I understand that Natural Orbitals are the eigenvectors and eigenvalues of the 1 electron density matrix, surely it is possible to calculate the 1 electron density matrix > from the CIS expansion of the wavefunction of a ZINDO calculation? On a more practical note, when I run a g03 job with the zindo keyword, at a certain point I am told: "1PDM for each excited state written to RWF 633" How do I get to this matrix? Once I get there, I assume I can just put it in mathematica and diagonalise it? The background reason for asking these questions, is that a collegue has asked me how to relate the energies obtained from a ZINDO calculation to the MO energies, am I wrong in asserting that the energies of the MOs are as relevant to a CIS calculation as the enrgies of Atomic orbitals are to the SCF calculation? But, what one can consider is the charge density, and the natural orbitals are a good way to look at that, right? Thank you very much for any tips - I would also be most grateful for any tips for good reading on the subject of CIS/ZINDO calculations . Happy weekend -- James Kirkpatrick ------------------------------------------- Centre for Electronic Materials and devices Imperial College ------------------------------------------- 020 759 47519 From owner-chemistry@ccl.net Mon Jul 25 08:21:47 2005 From: "CCL" To: CCL Subject: CCL: Drawing in Linux Message-Id: <-28924-050725072143-18921-eSc6C2yCCSce8pLLLmWjCA^^^server.ccl.net> X-Original-From: Miklos Vargyas Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=us-ascii; format=flowed MIME-Version: 1.0 Sent to CCL by: Miklos Vargyas CCL wrote: > Hello! I was wondering if anyone would know a program like ChemDraw > for Linux? > Thank you all in advance, > Fleming Hi Fleming! Sure! It is MarvinSketch from ChemAxon. As it is written in pure Java it runs on all Java capable platforms including Linux. You can download the software from http://www.chemaxon.com/marvin/. Its usage is free if it is not an integral part of an other application. Regards, Miklos Vargyas From owner-chemistry@ccl.net Mon Jul 25 12:09:49 2005 From: "CCL" To: CCL Subject: CCL: SMD Format Message-Id: <-28925-050725102021-12125-eSc6C2yCCSce8pLLLmWjCA:-:server.ccl.net> X-Original-From: Mireille Krier Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed MIME-Version: 1.0 Sent to CCL by: Mireille Krier Dear CCLers, I want to know if the SMD format (see reference below) is still used? Bebak, H.; Buse, C.; Donner, W. T.; Hoever, P.; Jacob, H.; Klaus, H.; Pesch, J.; Roemelt, J.; Schilling, P.; Woost et, a., Standard Molecular Data format (SMD format) as an integration tool in computer chemistry. J. Chem. Inf. Comput. Sci. 1989, 29, (1), 1-5. Mireille Krier -- ----------------------------------------------------------------------- Bioinformatique du médicament, Equipe 5 du Laboratoire de Pharmacochimie et de la communication cellulaire UMR 7081 ULP-CNRS Faculté de Pharmacie 74, route du Rhin - B.P. 60024 F-67401 Illkirch CEDEX, France ----------------------------------------------------------------------- From owner-chemistry@ccl.net Mon Jul 25 20:33:40 2005 From: "CCL" To: CCL Subject: CCL: Friendly Reminder: Special issue on Ecotoxicological Modeling Message-Id: <-28926-050725202458-24026-ETc9kVj+VqHwexQEb/3djg]|[server.ccl.net> X-Original-From: Kunal Roy Content-Transfer-Encoding: 8bit Content-Type: multipart/alternative; boundary="0-1670506837-1122337494=:52983" MIME-Version: 1.0 Sent to CCL by: Kunal Roy --0-1670506837-1122337494=:52983 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Dear Colleagues, Submissions to the special issue of Molecular Diversity [ISSN: 1381-1991 (print version); ISSN: 1573-501X (electronic version); Journal no. 11030; Springer Netherlands] (http://www.springeronline.com/journal/11030/) on “Ecotoxicological modeling and risk assessment using chemometric tools” (http://www.mdpi.org/modi/specialissues.htm) will fall due on September 01, 2005. Send your contribution electronically to Dr. Kunal Roy [Guest Editor] Drug Theoretics & Cheminformatics Lab, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, JADAVPUR UNIVERSITY, Kolkata 700 032 (INDIA) Phone: (O): +91-33-2867 0786; (M): +91-98315 94140 Email: kunalroy_in]|[yahoo.com http://www.geocities.com/kunalroy_in Regards, Kunal Roy ________________________________ -------------------------------- CALL FOR PAPERS Special issue of Molecular Diversity [ISSN: 1381-1991 (print version); ISSN: 1573-501X (electronic version); Journal no. 11030; Springer Netherlands] (http://www.springeronline.com/journal/11030/) on “Ecotoxicological modeling and risk assessment using chemometric tools” (http://www.mdpi.org/modi/specialissues.htm) Scope The scope of the special issue includes application of chemometric tools (like PLS, GA, NN fitting, etc.) and cheminformatics in ecotoxicological and environmental modeling and risk assessment with focus on the quantitative structure-activity relationships (QSAR) in the following subject fields: 1. Aquatic and terrestrial ecotoxicology 2. Animal toxicology 3. Persistent organic pollutants 4. Environmental fate 5. Endocrine disruptors 6. Biochemistry and Pharmacokinetics with reference to Environmental Toxicology 7. Ecotoxicological modeling of pharmaceuticals 8. Hazardous waste 9. Occupational hazards and exposure 10. Green chemistry 11. Data mining of chemical toxicity data 12. Developments in statistical theory with application to ecotoxicological modeling. Type of manuscripts: 1. Original papers (Full paper/Short Communication) 2. Reviews, in emerging areas Instructions for authors Please visit http://www.springeronline.com/journal/11030/ for detailed instructions and journal format. Please note: 1. The full text of the manuscript along with Tables, Figures and References should be submitted as single WORD file. 2. Use Times New Roman font (size 12). 3. Tables should be entered using “Insert Table” option. 4. Equations should be entered using “Equation Editor”. 5. After acceptance of the paper, .tif or .jpg files of the figures will have to be submitted All papers will be peer reviewed by at least two referees. Submission (http://www.geocities.com/kunalroy_in/call_for_paper.html) Single WORD file of the manuscript should be submitted electronically to Dr. Kunal Roy [Guest Editor] Drug Theoretics & Cheminformatics Lab, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, JADAVPUR UNIVERSITY, Kolkata 700 032 (INDIA) Phone: (O): +91-33-2867 0786; (M): +91-98315 94140 Email: kunalroy_in]|[yahoo.com http://www.geocities.com/kunalroy_in Deadline for submission September 01, 2005 Send instant messages to your online friends http://in.messenger.yahoo.com --0-1670506837-1122337494=:52983 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: 8bit
Dear Colleagues,
Submissions to the special issue of Molecular Diversity [ISSN: 1381-1991 (print
version); ISSN: 1573-501X (electronic version);
Journal no. 11030; Springer Netherlands]
(http://www.springeronline.com/journal/11030/) on “Ecotoxicological
modeling and risk assessment using chemometric
tools” (http://www.mdpi.org/modi/specialissues.htm)
will fall due on September 01,
2005.  Send your contribution electronically to
 
Dr. Kunal Roy [Guest Editor]
Drug Theoretics & Cheminformatics Lab,
Division of Medicinal and Pharmaceutical
Chemistry,
Department of Pharmaceutical Technology,
JADAVPUR UNIVERSITY, Kolkata 700 032 (INDIA)
Phone: (O): +91-33-2867 0786; (M): +91-98315
94140
Regards,
 
Kunal Roy
________________________________
--------------------------------
CALL FOR PAPERS
 
Special issue of Molecular Diversity [ISSN:
1381-1991 (print version);
ISSN: 1573-501X (electronic version); Journal no.
11030; Springer Netherlands]
(http://www.springeronline.com/journal/11030/) on
“Ecotoxicological modeling and risk assessment
using chemometric tools”
(http://www.mdpi.org/modi/specialissues.htm)
 
 
Scope
The scope of the special issue includes
application of chemometric tools (like PLS, GA, NN
fitting, etc.) and cheminformatics in ecotoxicological
and environmental modeling and risk assessment
with focus on the quantitative structure-activity
relationships (QSAR) in the following subject
fields:
 
1.         Aquatic and terrestrial ecotoxicology
2.         Animal toxicology
3.            Persistent organic pollutants
4.            Environmental fate
5.            Endocrine disruptors
6.            Biochemistry and Pharmacokinetics
with reference to Environmental Toxicology
7.            Ecotoxicological modeling of
pharmaceuticals
8.            Hazardous waste
9.            Occupational hazards and exposure
10.       Green chemistry
11.       Data mining of chemical toxicity data
12.            Developments in statistical theory
with application to ecotoxicological modeling.       
 
Type of manuscripts:
1.         Original papers (Full paper/Short
Communication)
2.            Reviews, in emerging areas
 
Instructions for authors
Please visit
http://www.springeronline.com/journal/11030/ for
detailed instructions and journal format.
 
Please note:
1.         The full text of the manuscript along
with Tables, Figures and References should be
submitted as single WORD file.
2.         Use Times New Roman font (size 12).
3.         Tables should be entered using “Insert
Table” option.
4.            Equations should be entered using
“Equation Editor”.
5.         After acceptance of the paper, .tif or
.jpg files of the figures will have to be            
submitted
 
All papers will be peer reviewed by at least two
referees.
Single WORD file of the manuscript should be
submitted electronically to
Dr. Kunal Roy [Guest Editor]
Drug Theoretics & Cheminformatics Lab,
Division of Medicinal and Pharmaceutical
Chemistry,
Department of Pharmaceutical Technology,
JADAVPUR UNIVERSITY, Kolkata 700 032 (INDIA)
Phone: (O): +91-33-2867 0786; (M): +91-98315
94140
 
Deadline for submission
September 01, 2005

Send instant messages to your online friends http://in.messenger.yahoo.com --0-1670506837-1122337494=:52983-- From owner-chemistry@ccl.net Mon Jul 25 21:18:21 2005 From: "CCL" To: CCL Subject: CCL: Friendly Reminder: Special issue on Ecotoxicological Modeling Message-Id: <-28927-050725201449-23490-ETc9kVj+VqHwexQEb/3djg-.-server.ccl.net> X-Original-From: Kunal Roy Content-Transfer-Encoding: 8bit Content-Type: multipart/alternative; boundary="0-409386221-1122333283=:24619" MIME-Version: 1.0 Sent to CCL by: Kunal Roy --0-409386221-1122333283=:24619 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Dear Colleagues,Submissions to the special issue of Molecular Diversity [ISSN: 1381-1991 (print version); ISSN: 1573-501X (electronic version); Journal no. 11030; Springer Netherlands] (http://www.springeronline.com/journal/11030/) on “Ecotoxicological modeling and risk assessment using chemometric tools” (http://www.mdpi.org/modi/specialissues.htm) will fall due on September 01, 2005. Send your contribution electronically to Dr. Kunal Roy [Guest Editor]Drug Theoretics & Cheminformatics Lab, Division of Medicinal and Pharmaceutical Chemistry,Department of Pharmaceutical Technology, JADAVPUR UNIVERSITY, Kolkata 700 032 (INDIA) Phone: (O): +91-33-2867 0786; (M): +91-98315 94140Email: kunalroy_in-.-yahoo.com http://www.geocities.com/kunalroy_in Regards, Kunal Roy________________________________________________________________________________________________________________----------------------------------------------------------------------------------------------------------------CALL FOR PAPERS Special issue of Molecular Diversity [ISSN: 1381-1991 (print version); ISSN: 1573-501X (electronic version); Journal no. 11030; Springer Netherlands] (http://www.springeronline.com/journal/11030/) on “Ecotoxicological modeling and risk assessment using chemometric tools” (http://www.mdpi.org/modi/specialissues.htm) ScopeThe scope of the special issue includes application of chemometric tools (like PLS, GA, NN fitting, etc.) and cheminformatics in ecotoxicological and environmental modeling and risk assessment with focus on the quantitative structure-activity relationships (QSAR) in the following subject fields: 1. Aquatic and terrestrial ecotoxicology2. Animal toxicology3. Persistent organic pollutants 4. Environmental fate5. Endocrine disruptors6. Biochemistry and Pharmacokinetics with reference to Environmental Toxicology7. Ecotoxicological modeling of pharmaceuticals8. Hazardous waste9. Occupational hazards and exposure10. Green chemistry11. Data mining of chemical toxicity data12. Developments in statistical theory with application to ecotoxicological modeling. Type of manuscripts:1. Original papers (Full paper/Short Communication)2. Reviews, in emerging areas Instructions for authorsPlease visit http://www.springeronline.com/journal/11030/ for detailed instructions and journal format. Please note:1. The full text of the manuscript along with Tables, Figures and References should be submitted as single WORD file. 2. Use Times New Roman font (size 12). 3. Tables should be entered using “Insert Table” option.4. Equations should be entered using “Equation Editor”.5. After acceptance of the paper, .tif or .jpg files of the figures will have to be submitted All papers will be peer reviewed by at least two referees. Submission (http://www.geocities.com/kunalroy_in/call_for_paper.html) Single WORD file of the manuscript should be submitted electronically toDr. Kunal Roy [Guest Editor]Drug Theoretics & Cheminformatics Lab, Division of Medicinal and Pharmaceutical Chemistry,Department of Pharmaceutical Technology, JADAVPUR UNIVERSITY, Kolkata 700 032 (INDIA) Phone: (O): +91-33-2867 0786; (M): +91-98315 94140Email: kunalroy_in-.-yahoo.com http://www.geocities.com/kunalroy_in Deadline for submissionSeptember 01, 2005 Dr. Kunal Roy, MPharm, PhD, AICTE Career Awardee (2003-04) Senior Lecturer, Drug Theoretics and Cheminformatics Lab, Division of Medicinal and Pharmaceutical Chemistry Department of Pharmaceutical Technology JADAVPUR UNIVERSITY, Kolkata 700 032 (INDIA) Phone (O): 91-33-2867 0786; (R): 91-33-2435 6547; Mobile: 91-98315 94140 Email : kroy-.-pharma.jdvu.ac.in, kunalroy_in-.-yahoo.com, krjupt-.-yahoo.co.in, URL : http://www.geocities.com/kunalroy_in Send instant messages to your online friends http://in.messenger.yahoo.com --0-409386221-1122333283=:24619 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: 8bit 

Dear Colleagues,

Submissions to the special issue of Molecular Diversity [ISSN: 1381-1991 (print 
version); ISSN: 1573-501X (electronic version); 
Journal no. 11030; Springer Netherlands] 
(http://www.springeronline.com/journal/11030/) on “Ecotoxicological 
modeling and risk assessment using chemometric 
tools” (http://www.mdpi.org/modi/specialissues.htm) 
will fall due on September 01, 
2005.  Send your contribution electronically to

 

Dr. Kunal Roy [Guest Editor]

Drug Theoretics & Cheminformatics Lab, 

Division of Medicinal and Pharmaceutical 
Chemistry,

Department of Pharmaceutical Technology, 

JADAVPUR UNIVERSITY, Kolkata 700 032 (INDIA) 

Phone: (O): +91-33-2867 0786; (M): +91-98315 
94140

Email: kunalroy_in-.-yahoo.com 

http://www.geocities.com/kunalroy_in 

Regards,

 

Kunal Roy
________________________________________________________________________________________________________________
----------------------------------------------------------------------------------------------------------------
CALL FOR PAPERS
 

Special issue of Molecular Diversity [ISSN: 
1381-1991 (print version); 

ISSN: 1573-501X (electronic version); Journal no. 
11030; Springer Netherlands] 
(http://www.springeronline.com/journal/11030/) on 

“Ecotoxicological modeling and risk assessment 
using chemometric tools” 
(http://www.mdpi.org/modi/specialissues.htm)

 

 
Scope
The scope of the special issue includes 
application of chemometric tools (like PLS, GA, NN 
fitting, etc.) and cheminformatics in ecotoxicological 
and environmental modeling and risk assessment 
with focus on the quantitative structure-activity 
relationships (QSAR) in the following subject 
fields:

 

1.         Aquatic and terrestrial ecotoxicology

2.         Animal toxicology

3.            Persistent organic pollutants 

4.            Environmental fate

5.            Endocrine disruptors

6.            Biochemistry and Pharmacokinetics 
with reference to Environmental Toxicology

7.            Ecotoxicological modeling of 
pharmaceuticals

8.            Hazardous waste

9.            Occupational hazards and exposure

10.       Green chemistry

11.       Data mining of chemical toxicity data

12.            Developments in statistical theory 
with application to ecotoxicological modeling.        

 

Type of manuscripts:

1.         Original papers (Full paper/Short 
Communication)

2.            Reviews, in emerging areas

 
Instructions for authors
Please visit 
http://www.springeronline.com/journal/11030/ for 
detailed instructions and journal format.

 

Please note:

1.         The full text of the manuscript along 
with Tables, Figures and References should be 
submitted as single WORD file. 

2.         Use Times New Roman font (size 12). 

3.         Tables should be entered using “Insert 
Table” option.

4.            Equations should be entered using 
“Equation Editor”.

5.         After acceptance of the paper, .tif or 
.jpg files of the figures will have to be             
submitted

 

All papers will be peer reviewed by at least two 
referees.

 
Submission 
(http://www.geocities.com/kunalroy_in/call_for_paper.html)
 

Single WORD file of the manuscript should be 
submitted electronically to

Dr. Kunal Roy [Guest Editor]

Drug Theoretics & Cheminformatics Lab, 

Division of Medicinal and Pharmaceutical 
Chemistry,

Department of Pharmaceutical Technology, 

JADAVPUR UNIVERSITY, Kolkata 700 032 (INDIA) 

Phone: (O): +91-33-2867 0786; (M): +91-98315 
94140

Email: kunalroy_in-.-yahoo.com 

http://www.geocities.com/kunalroy_in

 
Deadline for submission
September 01, 2005


Dr. Kunal Roy, MPharm, PhD, AICTE Career Awardee (2003-04)
Senior Lecturer, Drug Theoretics and Cheminformatics Lab, Division of Medicinal and Pharmaceutical Chemistry
Department of Pharmaceutical Technology
JADAVPUR UNIVERSITY, Kolkata 700 032 (INDIA)
Phone (O): 91-33-2867 0786; (R): 91-33-2435 6547; Mobile: 91-98315 94140
Email : kroy-.-pharma.jdvu.ac.in, kunalroy_in-.-yahoo.com, krjupt-.-yahoo.co.in, URL : http://www.geocities.com/kunalroy_in

Send instant messages to your online friends http://in.messenger.yahoo.com --0-409386221-1122333283=:24619--