81. Introduction To Computational Chemistry Introduction to computational chemistry. Many universities are now offering classes, which are an overview of various aspects of computational chemistry. http://www.sci.muni.cz/~physics/CC/compchem.htm

Introduction to Computational Chemistry David Young E-mail dyoung@asc.edu Division of University Computing 144 Parker Hall Auburn University Auburn, AL 36849 Table of Contents Introduction Ab Initio Semiempirical Modeling the solid state ... Further information Introduction Recent years have seen an increase in the number of people doing theoretical chemistry. Many of these newcomers are part time theoreticians, who work on other aspects of chemistry as well. This increase has been facilitated by the development of computer software which is increasingly easy to use. It is now easy enough to do computational chemistry that you do not have to know what you are doing to do a computation. As a result, many people don't understand even the most basic description of how the calculation is done and are therefore sucessufully doing a lot of work which is, frankly, garbage. Many universities are now offering classes, which are an overview of various aspects of computational chemistry. Since we have had many people wanting to start doing computations before they have had even an introductory course, this document has been written as step one in understanding what computational chemistry is about. Note that this is not intended to teach the fundamentals of chemistry, quantum mechanics or mathematics, only most basic description of how chemical computations are done. The term

82. Computational Chemistry GRID Conference computational chemistry GRID Conference University of Kentucky, Lexington October 16 17, 2001. Program. SURA and the University http://www.sura.org/events/2001/compchem/chemistry.html

Computational Chemistry GRID Conference Welcome News Programs Jefferson Lab ... Contact Computational Chemistry GRID Conference University of Kentucky, Lexington Program SURA and the University of Kentucky, with support from the Army Research Laboratory, are co-sponsoring the Computational Chemistry GRID Conference in October. This conference is designed to build connections between the developments in computational chemistry and the user community, and to provide a "bridge" between various Internet protocols that are being used to share information. This is the first Internet conference to use technology to link Mbone and H.323 technologies into a single distributed environment. The conference, on the cutting edge of both science and Internet technology, will center on applications of quantum mechanics, molecular dynamics, solid state chemistry and biochemistry. Leaders of quantum mechanics and molecular simulations will be speaking at this conference, including Dr. Keiji Morokuma (Emory) and Dr.Steven Harvey (UAB). In addition, developers of some of the most widely used quantum codes will speak: Dr. M. Frisch, Gaussian, Inc., Dr. Theresa Windus of Pacific Northwest Laboratories (NWChem) and Dr. P. Bartlett of the University of Florida (ACES II). This conference will be held October 16th and 17th at the University of Kentucky in Lexington. Talks from invited speakers will address the applications of techniques to research problems and the use of various state-of-the-art packages. Both morning and afternoon sessions will be interactive, allowing remote attendees the opportunity to interact with the speakers via the Internet. Posters are welcome. Please submit 200-300 word abstract to Sue@sura.org. Presentations are scheduled for Tuesday, October 16th, 6:30pm during the reception.

83. NWChem Home Page NWChem is a computational chemistry software capable of molecular dynamics simulations. It is designed to run on parallel computers and it is developed by the Pacific Northwest National Laboratory. http://www.emsl.pnl.gov/docs/nwchem/nwchem.html

84. Influenza - Introduction Provides information on the influenza virus and details how the drug Relenza was developed using computational chemistry. Also describes how the action of the drug prevents the flu virus replicating. http://www.omedon.co.uk/influenza

The creation of Relenza for the treatment of Influenza Introduction Viruses Influenza Neuraminidase ... Conclusion Introduction Influenza causes epidemics of disease almost every winter. In the United States, these winter influenza epidemics can cause illness in 10% to 20% of people[1] and are associated with an average of 36,000 deaths and 114,000 hospitalisations per year[1]. Relenza prevents the spread of the virus to uninfected cells in the respiratory tract. It is the first in a class of compounds known as neuraminidase inhibitors, and the first anti-viral drug to be effective against all known strains of influenza A and B. Relenza was designed using computational chemistry. The 'Flu' Influenza is a particularly common virus which has probably affected us all in some way or another. Its well known symptoms; fever, cough, aching limbs, and weariness lead to the loss of over 75 million working days per year[1]. Although this debilitating disease typically lasts for around one week it can bring about complications in the form of meningitis or pneumonia. For some, especially the elderly, influenza can prove fatal. There have been three flu pandemics in the last century, the worst being 'Spanish flu' in 1918-19 which accounted for the deaths of 30-40 million people. Closer to home during the winter of 1989 it is estimated around 20,000 deaths occurred from flu in the UK. The devastating outbreak of Spanish Flu stimulated research into the origins of the disease, but it was not until 1933 that Smith, Andrews and Laidlaw discovered the viral nature of the infection[2].

85. Chemistry At UCLA, Theoretical-Computational THEORETICAL AND computational chemistry AT UCLA. The department has a rich array of research projects in theoretical and computational http://www.chem.ucla.edu/dept/TheoryComp.html

THEORETICAL AND COMPUTATIONAL CHEMISTRY AT UCLA The department has a rich array of research projects in theoretical and computational chemistry in physical chemistry and in biochemistry, inorganic chemistry and organic chemistry. Brief summaries of the faculty and research programs are given on this page. For additional information, call 310-825-3150 or e-mail chair@chem.ucla.edu. Physical Chemistry Emily A. Carter B.S., University of California, Berkeley; Ph.D., California Institute of Technology Ab initio molecular dynamics (AIMD), kinetics, and energetics for surface chemistry of semiconductors, metals, and metal-ceramic interfaces. Development of hybrid quantum mechanics methods. Pseudospectral local correlation, embedding techniques, adaptive mesh. AIMD, density functional theory-tight binding theory for transition metals. William M. Gelbart B.S., Harvard University; Ph.D., University of Chicago Theory of light scattering and optical properties of simple fluids; orientational order in flexible polymers and liquid crystals; statistical thermodynamics of surfactant solutions, micro-emulsions, and interfaces; elastic and strength properties of composite materials. Daniel Kivelson A. B., M.S., PhD. Harvard University

86. Seascape! Seascape offers computational chemistry and biology software/services including molecular dynamics calculations. http://www.seascapelearning.com

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87. Theoretical/Computational Chemistry Group http://theochem.weizmann.ac.il/

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88. Caltech Division Of Chemistry And Chemical Engineering Research areas include biochemistry, physical chemistry, advanced spectroscopy, and computational chemistry. http://www.caltech.edu/subpages/chem.html

WELCOME One of six divisions at the California Institute of Technology, Chemistry and Chemical Engineering offers unique opportunities in a broad scope of traditional and interdisciplinary research areas. This site contains information for current and prospective students and researchers. If you cannot find what you need, check our search page. Division Seminars Click here for the latest updates. State-of-the-art facilities, combined with world-class faculty. Myriad opportunites for research. A great intramural softball league in the summer. It's no wonder that Caltech is #1. Quick Links Applying to Caltech Apply for graduate, postdoctoral, or undergraduate studies. Interested in Research? Check the faculty pages for research interests, virtual lab tours, ... or DOWNLOAD PDF versions of each faculty member's research interests or the entire brochure. Faculty Positions Looking for the Chemical Engineering Web Site? Check HERE Home Caltech Home Program Classes Faculty ... Search

89. Albany Molecular Research: The Company: Departments: Medicinal Chemistry: Molecu chemistry;. For more information about AMRI s computational chemistry and related services, please use the links in the table below. http://www.albmolecular.com/company/departments/medchem/molmod/

AMRI's Computer-Aided Drug Discovery Group is capable of addressing a wide range of drug discovery problems at both the small molecule and macromolecular level. These include: lead identification and refinement; prediction of three-dimensional structures of therapeutic protein targets; identification of binding sites, structure-based design, diversity analysis, and virtual screening. Current discovery applications include database mining and virtual screening projects and, in particular, the identification of synthetic compounds with activity similar to hits obtained from screening. Cheminformatics Computational methods have been developed to capture similarities of molecules, regardless of their chemical source. These concepts are applied to search databases for molecules with biological activity similar to query compounds. Furthermore, compound partitioning techniques have successfully been used to explore "active neighborhoods" of hits obtained from screening. A major focal point is the development and application of molecular similarity concepts to identify synthetically accessible mimics of specifically active natural molecules. Computational docking techniques are employed to screen compound collections on binding sites and explore binding characteristics of hits. The information is then used, for example, to guide "hit to lead" chemistry programs. Virtual screening projects of databases consisting of a total of several hundred thousand molecules are carried out using three-dimensional structures of targets, if available, and/or hits from screening as templates. Binary QSAR methodology is applied to develop predictive models for lead identification on the basis of screening data sets.

90. CompChemCtr Net Laboratory for computational chemistry. MC Escher. Webcobs. The following Software is available to the participants of the NetLab http://qcc.ru/~netlab/

Net Laboratory for Computational Chemistry M. C. Escher. Webcobs The following Software is available to the participants of the NetLab community through the Web-interface: ECF - clone of the methods for electronic structure and lower excitations of transition metal complexes. BF - a new non Hartree-Fock based semiempirical method with N-scaling. MOLCRYST - a package for calculating structure, thermodynamics, and phonon spectra of molecular crystals with use of atom-atomic scheme. MMPC - our in house molecular mechanics with orientation towards metal complexes. ECFMM - a hybride Molecular Mechanics - Effective Crystal Field program for transition metal complexes. GAMESS-US - ab-initio package for calculating molecular electronic structure and potential energy surfaces. MOPAC-6 - semi-empirical package for molecular electronic structure and potential energy surface calculations. Applies largely to simple organic molecules. Coming soon are: DeFT COSMOS programming language for manipulating molecular objects. If you are interested in joining us in the NetLab community and using the above software click here If you do not feel yourself ready to make calculations, but have a need in making some numerical estimates on your pet molecule, leave a note to the

91. Computational Chemistry Resources computational chemistry on the Web. Richard Bader s Atoms in Molecules . AMSOL, a semiempirical solvation model. computational chemistry at the CSC, Finland. http://chemistry.umeche.maine.edu/Fort/Goodcomp.html

Computational Chemistry on the Web Richard Bader's "Atoms in Molecules" AMSOL, a semi-empirical solvation model Beowulf clusters for chemists BioSym Corporation, Molecular Modeling Software Cambridge Scientific - Molecular Modeling and Drawing Software Computational Chemistry at the CSC, Finland Computational Chemistry Mailing List and Archive, OSC Cornell Theory Center DeFT: a density functional program by Alain St Amant GAMESS, for ab inito and semi-empirical MO calculations GAMESS for PCs; Alex Granowsky at Moscow State Hyperchem Modeling Software Journal of Computer-Aided Molecular Design Journal of Molecular Modeling MacroModel, a program for molecular mechanics and dynamics Molecular Modeling at the NIH PCMODEL, molecular mechanics software for PCs RasMol, a free graphics program for molecular visualization Chime, a browser add-in for molecular structures (free) SPARTAN, software for ab initio , semi-empirical, and DFT calculations XMol, a free molecular visualization program for UNIX computers AMBER, a molecular dynamics program Molecular Modeling at UMaine This page last modified 11:43 AM on Friday August 11th, 2000.

92. What Is Computational Chemistry? What is computational chemistry? Or if you want to see what I think about it, jump to my description of computational chemistry. http://www.chem.yorku.ca/profs/renef/whatiscc.html

What is Computational Chemistry? Some time ago there was a discussion on the Computational Chemistry List (CCL) about "what exactly is computational chemistry ?". Let's see what the experts have to say about that. Or if you want to see what I think about it, jump to my description of computational chemistry. It all started with a seemingly simple question: what is the difference between "computational chemistry" and "molecular modeling"? Any hints on a proper definition ? Any historical reason for different uses of "molecular modelling" ? And, above all, one or two l ? Alexandre Hocquet Facultad de Ciencias Fisicas Universidad de Chile Blanco Encalada, 2008 Santiago Centro, CHILE And now some of the answers from the CC community. There is a series of essays by Richard Counts in early volumes of J. Comput.- Aided Mol. Design on the "Computational Perspective", including one "Where Can I Find a Computational Chemist?", 1991, 5 (3), 273-274. Illuminating, perhaps especially to those who have been doing "molecular modeling" since before the term "computational chemistry" was invented. . . ... I have resolved the issue in my own mind as follows. Computational chemistry would be the application of numerical calculations to the study of molecular structure.

93. Computational Chemistry In The 1950s computational chemistry in the 1950s. 15 Since then, the use of symbolic algebra in computational chemistry has been slow in coming. http://www.chem.yorku.ca/profs/pritchard/PAPERS/history.html

Published in Computational Chemistry in the 1950s Huw O. Pritchard , Distinguished Research Professor Emeritus Department of Chemistry, York University, Toronto, Canada M3J 1P3 huw@yorku.ca To mark half a century of computational quantum chemistry, this account recalls some computer experiments in Manchester, 1951-1960 " ... whether we last the night or no, I'm sure it's always touch and go." Dylan Thomas, "Eli Jenkins' Prayer" Longuet-Higgins' antipathy towards computers in chemistry at that time is well known, a ), could not possibly provide the same insight into atomic and molecular structure as one could derive from an orbital picture; b hence, I suspect that this initiative came from M. G. Evans. Within a few months, Longuet-Higgins left for a Chair of Theoretical Physics in London, and shortly thereafter for one in Theoretical Chemistry in Cambridge. Meanwhile, Frank Sumner, without guidance and finding his project intractable, came to me and asked if I would help; he provided me with a big fat Programmer's Manual and we got down to it together. Lacking much progress, we soon sought help from Alan Turing and Tony Brooker in the Computing Machine Laboratory and they advised us, rightly of course, to forget the contour integrals and attack the eigenvalue problem head-on. It seemed obvious at the time that we should make use of symmetry in order to reduce the sizes of the secular determinants that we wished to solve, but this led to the determinants being unsymmetric. Brooker was writing a Lanczos algorithm to reduce a matrix to its characteristic polynomial

94. 5th Canadian Computational Chemistry Conference - Home CCCC5 is the continuation of a series of meetings held every three years intended to foster the excellence of computational chemistry in Canada. http://www.chem.utoronto.ca/symposium/cccc5/

C C C C 5 - 2003 New and important information for attendees and presenters Click Here Daily program now availible in pdf format - click here CCCC5 is the continuation of a series of meetings held every three years intended to foster the excellence of computational chemistry in Canada. One of the principal goals of the conference is to highlight the impact of computational chemistry in academia, industry and society. As in the previous incarnations of this meeting, a program covering major new directions in research and applications of the computational discipline has been put together, with a special emphasis on computational chemistry applied to biophysics and material science. For this purpose, we have prepared a program of speakers actively involved in developing new methods and applications of high performance computing in chemistry and related areas. The meeting will be held on the campus of the University of Toronto, with inexpensive rooms available in nearby hotels at special rates. Toronto is an exciting, diverse city with many attractions, ranging from excellent museums to fine dining. Since Toronto is the largest urban centre in Canada, travel to and from the city is easy and relatively inexpensive. The costs of the meeting are modest (all figures in Canadian dollars): Students/Post-docs: $100 (early) - $130 (After June 1)

95. Theoretical And Computational Group Welcome to Theoretical and computational chemistry in Crete (TCCC) or (TC3) Department of Chemistry (DoC), University of Crete http://tccc.iesl.forth.gr/

Welcome to T heoretical and C omputational C hemistry in C rete (TCCC) or Department of Chemistry (DoC) , University of Crete (UoC) and Institute of Electronic Structure and Laser - (IESL) FO undation for R esearch and T echnology H ellas (FORTH) Location Where we are People, Projects, Facilities, Publications Local Resources Announcements Courses, Seminars, Workshops TWO years of APPLIED MOLECULAR SPECTROSCOPY - EPEAEK (1998-2000) Please send your comments here, using mailto: Web site is maintained by SCF Last modifIed: Thur Dec 05 17:34:34 EET 2002

96. Arbeitsgruppe computational chemistry der Gesellschaft Österreichischer Chemiker. 1130 Ulrich Jordis. Chemiedatenbanken in Östereich. computational chemistry. http://phoenix.tuwien.ac.at/compuchem/

Arbeitsgruppe "Computational Chemistry" der Gesellschaft Österreichischer Chemiker Um aktuellen Entwicklungen Rechnung zu tragen wurden im Jahr 1999 die Arbeitsgruppen "Theoretische Chemie" und "EDV in der Chemie" zur neuen Arbeitsgruppe "Computational Chemistry" vereinigt. SAX, Univ.Doz. Dr. Alexander Institut für Chemie Universität Graz Strassoldogasse 10, A-8010 Graz Tel.: 0316/380-5513 Fax: 0316/380-9140 email : alexander.sax@kfunigraz.ac.at JORDIS, A.o. Prof. Dr. Ulrich Institut für Organische Chemie Technische Universität Wien Getreidemarkt 9, A-1060 Wien Tel.: 01/58801-15460 Fax: 01/58801-15499 email: ujordis@pop.tuwien.ac.at Zielsetzungen der Arbeitsgruppe Kontakte zu verwandten Fachgruppen (u.a. die Fachgruppen "Theoretische Chemie" und "CIC Chemie - Information - Computer" der GDCh, der ACS Division of Computers in Chemistry) Veranstaltung von Vorträgen und Fortbildungskursen Schwerpunkt Chemie Information: Literatur- Struktur- Reaktions- Fakten- und Patentdatenbanken für österreichische Chemiker: Information, Koordination (z.B. Konsortium Digitale Bibliothek) und Ausbildung

97. ARL PET Computational Chemistry And Materials Science Welcome to PETCCM. Programming Environment Training (PET) computational chemistry Materials Science (CCM). Serving ALL DoD CCM Researchers. http://www.arl.hpc.mil/PET/cta/ccm.html

DoD High Performance Computing Modernization Program Welcome to PET-CCM Serving ALL DoD CCM Researchers NEW: The PET-CCM Website has moved to http://www.osc.edu/PET/CCM/skeleton/index.html This is part of an ongoing effort to migrate all MSRC hosted PET pages to the OKC. The CCM Team: Ruth Pachter (AFRL), CTA Lead A.D. (Tony) Rollett (CMU), CCM FAPOC Nick Nystrom (PSC), CCM FAPOC alt Jean Blaudeau (HPTi), ASC on-site Mark Zottola (HPTi), ARL on-site Charles Cornwell (HPTi), ARL on-site Note: AFRL - Air Force Research Laboratory ARL - Army Research Laboratory ASC - Aeronautical Systems Center CMU - Carnegie Mellon University FAPOC - Functional Area Point of Contact HPTi - High Performance Technologies, Inc. PSC - Pittsburgh Supercomputer Center "The appearance of these hyperlinks do not constitute endorsement by the Department of Defense of these web sites or the information, products or services contained therein. For other than authorized activities such as military exchanges and Morale, Welfare and Recreation sites, the Department of Defense does not exercise any editorial control over the information you may find at these locations. These links are provided consistent with the stated purpose of this DoD Web site." Please email all comments and suggestions to web@arl.hpc.mil

98. Dictionary Of Computational Chemistry NIU Electronic Conferenceshosted by. the Trinity University Cheminformatics Site. (formerly the NIU Cheminformatics Site). Electronic computational chemistry Conferences (ECCC) http://www.shef.ac.uk/misc/personal/ch1mg/dict/

Next: Contents Dictionary of Computational Chemistry Martin Grayson Contents Introduction A AMBER - Assisted Model Building with Energy Refinement ... About this document ... Martin Grayson Tue Nov 25 13:54:09 GMT 1997

99. 2.8 Case Study Computational Chemistry 2.8 Case Study computational chemistry. Computational techniques are being used increasingly as an alternative to experiment in chemistry. http://www-unix.mcs.anl.gov/dbpp/text/node22.html

Next: 2.9 Summary Up: 2 Designing Parallel Algorithms Previous: 2.7 Case Study: Floorplan Optimization 2.8 Case Study: Computational Chemistry Our third case study, like the first, is from computational science. It is an example of an application that accesses a distributed data structure in an asynchronous fashion and that is amenable to a functional decomposition. 2.8.1 Chemistry Background Computational techniques are being used increasingly as an alternative to experiment in chemistry. In what is called ab initio quantum chemistry Plate 6 shows a molecular model for the active site region in the enzyme malate dehydrogenase, a key enzyme in the conversion of glucose to the high-energy molecule ATP. This image is taken from a simulation of the transfer of a hydride anion from the substrate, malate, to a cofactor, nicotinamide adenine diphosphate. The two isosurfaces colored blue and brown represent lower and higher electron densities, respectively, calculated by using a combined quantum and classical mechanics methodology. The green, red, blue, and white balls are carbon, oxygen, nitrogen, and hydrogen atoms, respectively. Fundamental to several methods used in quantum chemistry is the need to compute what is called the Fock matrix , a two-dimensional array representing the electronic structure of an atom or molecule. This matrix, which is represented here as

100. Hackberry.chem.niu.edu/ECCC4/ computational chemistry softwarePittsburgh Supercomputing Center Search Site Map Help Contacts, computational chemistry software. Ab initio conventional; http://hackberry.chem.niu.edu/ECCC4/

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