From chemistry-request@www.ccl.net Sat Mar 20 16:00:31 1999 Received: from ccl.net (atlantis.ccl.net [192.148.249.4]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id QAA10466 Sat, 20 Mar 1999 16:00:30 -0500 (EST) Received: from harfang.CC.UMontreal.CA (harfang.CC.UMontreal.CA [132.204.2.102]) by ccl.net (8.8.6/8.8.6/OSC 1.1) with ESMTP id QAA09308 for ; Sat, 20 Mar 1999 16:00:27 -0500 (EST) Received: from esi21.ESI.UMontreal.CA (esi21.ESI.UMontreal.CA [132.204.2.91]) by harfang.CC.UMontreal.CA (8.8.8/8.8.8) with ESMTP id QAA24058 for ; Sat, 20 Mar 1999 16:00:14 -0500 (EST) Received: (from pichem@localhost) by esi21.ESI.UMontreal.CA id QAA08409 (8.8.7/IDA-1.6 for chemistry@ccl.net); Sat, 20 Mar 1999 16:00:14 -0500 (EST) From: Piche Michelle Message-ID: <199903202100.QAA08409@esi21.ESI.UMontreal.CA> Subject: TD-DFT excitation energies To: chemistry@ccl.net Date: Sat, 20 Mar 1999 16:00:13 -0500 (EST) X-Mailer: ELM [version 2.4 PL24 ME5a] MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Here is a list of our recent publications regarding TD-DFT as a means for obtaining excitation energies : M.E. Casida, K.C. Casida, and D.R. Salahub, Int. J. Quant. Chem. 70, 933 (1998). (International Journal of Quantum Chemistry, Quantum Chemistry Symposium No. 32, Proceedings of the International Symposium on Atomic, Molecular, and Condensed Matter Theory) "Excited-state potential energy curves from time-dependent density-functional theory: A cross-section of formaldehyde's 1A1 manifold" M.E. Casida, C. Jamorski, K.C. Casida, and D.R. Salahub, J. Chem. Phys. 108, 4439 (1998). "Molecular excitation energies to high-lying bound states from time-dependent density-functional response theory: Characterization and correction of the time-dependent local density approximation ionization threshold" M.E. Casida, in Recent Developments and Applications of Modern Density Functional Theory, edited by J.M. Seminario (Elsevier, Amsterdam, 1996), p. 391. "Time-Dependent Density Functional Response Theory of Molecular Systems: Theory, Computational Methods, and Functionals" Christine Jamorski, Mark E. Casida, and Dennis R. Salahub, J. Chem. Phys. 104, 5134 (1996). "Dynamic Polarizabilities and Excitation Spectra from a Molecular Implementation of Time-Dependent Density-Functional Response Theory: N2 as a Case Study" M.E. Casida, in Recent Advances in Density Functional Methods, Part I, edited by D.P. Chong (Singapore, World Scientific, 1995), p. 155. "Time-dependent density-functional response theory for molecules'' M.E. Casida, C. Jamorski, F. Bohr, J. Guan, and D.R. Salahub, in Theoretical and Computational Modeling of NLO and Electronic Materials, edited by S.P. Karna and A.T. Yeates (ACS Press: Washington, D.C., 1996), (Proceedings of ACS Symposium, Washington, D.C., 1994), p. 145. "Optical Properties from Density-Functional Theory" e-mail comments to : Mark.Casida@UMontreal.CA From chemistry-request@www.ccl.net Sat Mar 20 18:13:06 1999 Received: from mail-b.bcc.ac.uk (mail-b.bcc.ac.uk [144.82.100.22]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id SAA10875 Sat, 20 Mar 1999 18:13:05 -0500 (EST) Received: from socrates-a.ucl.ac.uk by mail-b.bcc.ac.uk with SMTP (XT-PP); Sat, 20 Mar 1999 23:12:40 +0000 From: uccatvm Message-Id: <13983.199903202312@socrates-a.ucl.ac.uk> Subject: Re: Q re multi ref CCSD(T) or MP4 To: chemistry@www.ccl.net Date: Sat, 20 Mar 1999 23:12:39 +0000 (GMT) Cc: T.vanMourik@UCL.ac.uk (Tanja van Mourik) In-Reply-To: <199903191921.OAA29428@kirk.anderson.edu> from "Mike Falcetta" at Mar 19, 99 02:21:29 pm X-Mailer: ELM [version 2.4 PL25] MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit > > I was wondering if anyone knows if multi-reference MP4(SDTQ) or CCSD(T) methods > were being developed and what the status of such work might be. > The Utrecht group has been working on MR-MP methods. A few references: Convergence behaviour of multi-reference perturbation theory: An indicator Huub J.J. van Dam, and Joop H. van Lenthe Molecular Physics, Vol. 90, No. 6, 1007-1012 (1997) The size consistency of multi-reference Moller-Plesset perturbation theory Huub J.J. van Dam, Joop H. van Lenthe, and Peter Pulay Molecular Physics, Vol. 93, No. 3, 431-439 (1998) Tanja -- ==================================================================== Tanja van Mourik phone University College London work: +44 (0)171-504-4665 Christopher Ingold Laboratories home: +44 (0)1895-259-312 20 Gordon Street e-mail London WC1H 0AJ work: T.vanMourik@ucl.ac.uk United Kingdom home: tanja@netcomuk.co.uk ==================================================================== From chemistry-request@www.ccl.net Thu Mar 18 02:52:52 1999 Received: from tiger (dragon.hzuniv.edu.cn [210.32.180.3]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id CAA09818 Thu, 18 Mar 1999 02:52:37 -0500 (EST) Received: from cuihua by tiger (SMI-8.6/SMI-SVR4) id PAA00117; Thu, 18 Mar 1999 15:51:19 +0800 Message-ID: <000901be7113$e2953860$15bb20d2@cuihua.tiger.hzuniv.edu.cn> From: "cuihua" To: Subject: stochastic boundary by MD Date: Thu, 18 Mar 1999 15:49:14 +0800 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_0006_01BE7156.DF7893A0" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 4.72.3110.5 X-MimeOLE: Produced By Microsoft MimeOLE V4.72.3110.3 This is a multi-part message in MIME format. ------=_NextPart_000_0006_01BE7156.DF7893A0 Content-Type: text/plain; charset="hz-gb-2312" Content-Transfer-Encoding: quoted-printable Dear CCL'ers, I would be grateful for any explanation to stochastic boundary for the fluctuation calculations in the frame of MD methods . Thanks in advance, Jian Chen cuihua@tiger.hzuniv.edu.cn Zhejiang University=20 ------=_NextPart_000_0006_01BE7156.DF7893A0 Content-Type: text/html; charset="hz-gb-2312" Content-Transfer-Encoding: quoted-printable
 
Dear CCL'ers,

I would be grateful for any explanation to = stochastic=20 boundary for the
fluctuation calculations in the frame of MD methods=20 .

Thanks in advance,

Jian=20 Chen
cuihua@tiger.hzuniv.edu.cn=
Zhejiang=20 University
------=_NextPart_000_0006_01BE7156.DF7893A0-- From chemistry-request@www.ccl.net Thu Mar 18 10:27:46 1999 Received: from bastion.tbc.com (bastion.tbc.com [207.243.182.3]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id KAA11407 Thu, 18 Mar 1999 10:27:45 -0500 (EST) Received: from tbc.com (hub.tbc.com [207.243.182.50]) by bastion.tbc.com (8.8.5/8.8.5) with SMTP id JAA24186 for ; Thu, 18 Mar 1999 09:00:16 -0600 (CST) Message-Id: <199903181500.JAA24186@bastion.tbc.com> Date: Thu, 18 Mar 1999 9:31 -0600 From: "David Maxwell" To: chemistry@www.ccl.net Cc: TYou@tbc.com, QChen@tbc.com, jli@tbc.com Subject: Inclusion of modelers on synthetic compound patents Dear CCL Members, What determines inclusion of molecular modelers on a synthetic compound patent? Our group is working a list of guidelines that would outline what is needed for molecular modelers to be included on a synthetic compound patent. Obviously, it should be fair to the modelers, the synthetic chemists, and other contributors. The guidelines should not just allow the modelers to claim everything that came up in a 10-minute database search. On the other hand, it should allow for inclusion of a modeler if that person came up with the scaffold or contributed significantly to modifications based on evidence from various modeling programs. Most modelers that I know don't actually go the lab and sythesize compounds. Should this be reason enough to exlude us from the compound patents, since we can't formally carry out our ideas. I don't think so, and I have to believe that other modelers would agree. Please e-mail me with any opinions you have on this topic. I will summarize. David Maxwell Senior Scientist Biophysics Group Texas Biotechnology Corp. dmaxwell@tbc.com From chemistry-request@www.ccl.net Thu Mar 18 16:27:06 1999 Received: from gate-sl1.mdli.com (ns2.mdli.com [208.200.221.3]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id QAA16050 Thu, 18 Mar 1999 16:27:05 -0500 (EST) Received: (from smap@localhost) by gate-sl1.mdli.com (8.8.8/8.8.8) id NAA09631; Thu, 18 Mar 1999 13:17:07 -0800 (PST) Received: from puffin.mdli.com(191.254.19.10) by gate-sl1.mdli.com via smap (V2.1) id xma009629; Thu, 18 Mar 99 13:17:02 -0800 Received: from shepherd.mdli.com by puffin.mdli.com (8.8.5/BCH1.0) id NAA20111; Thu, 18 Mar 1999 13:26:23 -0800 (PST) Received: by shepherd.mdli.com with Internet Mail Service (5.5.2232.9) id ; Thu, 18 Mar 1999 13:27:52 -0800 Message-ID: <8E13FBBA26A9DA119ED400A0C9AB2CE5F92476@shepherd.mdli.com> From: Dori Luzbetak To: "'ACSMEDI'" , "'MOL-DIVERSITY'" , "'CHMINF-L'" , "'chemweb'" , "'ISISFORUM-L'" , "'ISISDEV-L'" , "'COMP-CHEM-LIST (CCL)'" Subject: MDL INTRODUCES CHESHIRE FOR ISIS Date: Thu, 18 Mar 1999 13:27:47 -0800 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2232.9) Content-Type: text/plain; charset="iso-8859-1" CONTACT: Corbin Collins MDL Information Systems, Inc. (510) 895-1313, ext. 1371 corbin@mdli.com http://www.mdli.com European mirror site: http://www.mdli.co.uk MDL INTRODUCES CHESHIRE FOR ISIS, A CHEMICAL INTERPRETATION ENVIRONMENT FOR INDUSTRY-LEADING ISIS --Companies Can Create Cheminformatics Business Rules, Automate the Analysis and Manipulation of Large Volumes of Chemical Information-- SAN LEANDRO, California--March 17, 1999--MDL Information Systems, Inc. today introduced Cheshire, a sophisticated chemical representation component that tightly integrates a powerful chemical scripting language into the industry-standard ISIS (Integrated Scientific Information System) framework. Cheshire provides a software development environment for building abstract and complex business rules that automate the analysis and interpretation of chemical structures and that calculate chemical information from chemical structures. The system is designed for chemical registration, data mining, property prediction, and sophisticated chemical representation controls within custom cheminformatics applications. Cheshire runs on both client and server platforms within the ISIS family of products, and is portable to future MDL architectures. MDL will demonstrate Cheshire at the meeting of the American Chemical Society, March 22-24, booth 819, Anaheim Convention Center. Cheshire includes Cheshire Studio, an interactive prototyping environment that developers can use to build, edit, and run scripts executed by the Cheshire runtime environment, the workhorse of the Cheshire system. The Cheshire runtime environment is exposed to users and developers directly through several programs in the ISIS family of products--ISIS/Base, ISIS/Object Library, ISIS for Microsoft Excel, ISIS/Host Application Program Interface (API), ISIS Procedural Language (PL), and Chemscape. This accessibility allows Cheshire to plug-and-play with existing discovery systems and support the breadth of scientific applications used within the pharmaceutical, chemical, and biotech industries. Cheshire enables high-level functions that can operate on entire collections of atoms and bonds, not just individual atoms and bonds. For the developer, this high-level abstraction makes the scripting language intuitive and easy to program. For the end user, the abstraction enables high-level operations such as exploring molecular fingerprints to aid in structure-activity relationship studies. Cheshire's scripting language is modeled on Javascript, allowing the use of familiar programming constructs such as objects, methods, and properties. Cheshire comes standard with a library of sample scripts, including a part of the chemical representation conversion rules MDL uses when building databases such as the Available Chemicals Directory. The system also comes with valuable example utilities, including an ISIS/Base add-in that provides scientists working in ISIS/Base off-the-shelf access to Cheshire capabilities. Users can extend ISIS/Base immediately with a sophisticated chemical interpretation component to calculate physicochemical data from structures, which helps scientists analyze chemical structures that would otherwise require tedious manual inspection. "In our view, Cheshire is based on a set of abstract concepts including 'collections' and 'mappings' within an object-oriented framework," said Dr Upali Bandara, business analyst, ZDW Scientific Information, BASF Aktiengesellschaft. "The combination of these concepts with the rich dictionary of basic operations allows Cheshire to cover all the business rules we need in the process of structure registration. The Cheshire Studio will help us to do the programming and testing in a remarkably efficient way." "Cheshire fits into multiple discovery environments where different scientists and programmers can use it to automate tasks related to in-depth chemical structure processing in numerous ways," said Rudy Potenzone, senior vice president of product development at MDL. "The system's robust chemical intelligence and its sophisticated methods for analyzing and interpreting chemistry not only enhance core ISIS products but interoperate easily in a variety of ways with other MDL systems. We designed Cheshire to help research organizations build a comprehensive and integrated discovery informatics framework." The ISIS Family and Complementary Systems For the past seven years, ISIS solutions have provided an information management architecture that supports the registration, retrieval, display, and analysis of all types of scientific information. Pharmaceutical, biotech, agrochemical, and chemical industries worldwide use ISIS applications, which support compound-discovery research and development. Cheshire works with * ISIS/Draw, a chemically intelligent drawing program * ISIS/Base, a forms-based desktop database management system and/or client for querying and accessing corporate data sources through ISIS/Host * ISIS/Object Library, an OLE interface to ISIS on the client * ISIS/Host API, a programmable interface to the ISIS/Host integration engine on the server * ISIS/PL, a programming language within ISIS on the client and the server * ISIS for Microsoft Excel, a data analysis tool that combines the spreadsheet environment of Excel with the chemical structure handling capabilities of ISIS * Chemscape, a Web-based system that provides complete ISIS structure and data searching capabilities from within Web browsers Cheshire also integrates with other MDL products, including * Reagent Selector, MDL's new system for selecting and obtaining reagents * Central Library, MDL's solution for combinatorial chemistry * The Spotfire product suite, systems for the interactive visualization of large data sets and chemical structures About MDL MDL Information Systems, Inc. is the recognized leader in discovery informatics for the life science and chemical industries. MDL software, content, and services provide the enterprise framework for identifying successful new products. A wholly owned subsidiary of Elsevier Science, MDL has offices worldwide with headquarters in San Leandro, California. ### Chemscape and MDL are registered trademarks and Available Chemicals Directory, Central Library, Cheshire, ISIS, ISIS/Object Library, and Reagent Selector are trademarks of MDL Information Systems, Inc. Microsoft is a registered trademark of the Microsoft Corporation. Spotfire is a registered trademark of Spotfire, Inc. All other product names may be registered trademarks or trademarks of their respective holders. Dori Luzbetak Web Communications Manager Marketing Communications MDL Information Systems, Inc. 14600 Catalina Street San Leandro, CA 94577 (510) 895-1313 x1652 (510) 614-3608 - FAX dori@mdli.com