Welcome to NetSci's
List of General Chemistry Programs
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The Software Section of NetSci is accessed by hundreds of scientists every week. Our goal is to make this resource as comprehensive as possible. If your software program is not included, please send e-mail with a brief description, the categories under which your program should appear, the platforms supported, and contact information.
For programs currently listed in NetSci, please check the table and description and notify us of any changes or additions.
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[ X, Y, Z]
--- A, B, C ---
ALOGPS (http://www.vcclab.org/lab/alogps) interactively calculates and compares lipophilicity and aqueous solubility of chemical compounds using six programs: CLOGP, XLOGP, IA_logP, IA_logS, LOGKOW and ALOGPS itself. The users can also download standalone version of the program (free for academic and non-for-profit organizations).
ALOGPS is offered by:
- Dr. Igor V. Tetko
- GSF - National Research Centre for Environment and Health
- Institute for Bioinformatics
- Ingolstaedter Landstrasse 1,
- D-85764 Neuherberg, Germany
- Tel./Fax: +49-89-3187-3575/x85
- e-mail: itetko@vcclab.org, itetko@gmail.com
Art of Science is a collection of EPS images prepared especially for the scientific community for import into page layout and word processing and programs including Microsoft Word. Art of Science is available from SoftShell
Babel is a program designed to interconvert a number of file formats currently used in molecular modeling. The program is available for Unix (AIX, Ultrix, Sun-OS, Convex, SGI, Cray, Linux), MS-DOS, and on Macs running at least System 7.0. Babel is capable of assigning hybridization, bond order, and connectivity when these elements are not present in the input file.
CALACO is a Windows data conversion program which can perform conversions in the following categories: Acceleration, Angle, Area, Energy, Length, Power, Pressure, Speed, Temperature, Time, Volume, and Weight. CALACO provides pop-up definitions for each unit. Sometimes a unit may be used in two different measurement systems. For example the "pound" can be a British pound, a US pound, or even an apothecaries pound that was used in pharmacy measurements and is now obsolete. If you are confused about a unit in CALACO simply click the Unit Definition button and a full definition is displayed. CALACO also has features to calculate boiling points at reduced pressures and perform density calculations. The program is available from
- Vogel Scientific Software, Inc.
1199 Leeward Ave
Lake Elmo, MN 55042-9643
Phone: 612-436-2998;
FAX: 612-436-2798;
E-mail: devogel@vogelscientific.com
Internet: http://www.vogelscientific.com
Chemistry 4-D Draw is a chemical drawing program which "understands" IUPAC nomenclature.
chemCLIPART A collection of over 150 pieces of professionally-drawn clip art, with a broad selection in the following categories: Benchtop (15), Experimental setups (11), Glassware (72), Lab wear (4), Labels (5), Molecules (18), People (6), Pipettes (9), and Symbols (12). And most glassware illustrations are modular (drawn with the same style and perspective). Combine them to create new images. Both Apple Macintosh and Windows versions are available. Artwork is supplied in vector format, full-color line art (Pict and EPS for Macintosh; Windows Metafile and EPS for PC's) so it scales and rotates with no "jaggies". Artwork is easily modifiable and is royalty-free. Occupies about 6 MBytes on your hard disk. Available from:
- Molecular Arts Corporation
Hanover Corporate Centre
1532 East Katella Avenue, Suite 1000
Anaheim, California 92805-6627 USA
Tel: (714) 634-8100
Fax: (714) 634-1999
E-mail: info@molecules.com
The CCP1GUI project has arisen as a result of demand within the UK academic community (principally through CCP1) for a free, extensible Graphical User Interface (GUI) for community codes, particularly for teaching purposes. There is also a long-standing requirement for a graphical interface for the GAMESS-UK quantum chemistry programme, which we plan to satisfy using the CCP1 developments.
The GUI has been built around the Python open-source programming language and the VTK visualisation toolkit, both of which have been ported to all the major operating system platforms. The GUI is therefore capable of running on all of these systems. Distributions of the GUI have already been successfully tested on Windows, and Suse and Redhat Linux distributions, and packages for these distributions are freely available from our ftp site.
The CCP1GUI has been released under the GNU GPL licence and is freely available to download. Downloads are available from the CCP1GUI pages on sourceforge or from the ftp site of the Quantum Chemistry Group at Daresbury Laboratory.
The design of the GUI makes the most of Python's high degree of object-orientation, including advanced features such as multiple inheritance. The strong reliance on object orientation means that it is quick and easy to create interfaces to new computational chemistry codes as the need arises. The GUI already has a highly-featured interface for the GAMESS-UK program, and there are working interfaces for ChemShell and MOPAC.
chemDIAGRAM is a 2D Chemical Diagram Drawing software for Windows. Create publication-quality 2D structure diagrams easily and affordably on your PC. You get a complete palette of drawing tools: 12 bond tools (with 24+ basic styles), 12 ring tools (3-to-8-sided including aromatics, boat, and chair styles), 12 orbital tools, and 12 labeling tools. Includes advanced capabilities like "snap to" drawing guides, automatic label super- and sub-scripts, automatic white space around labels and overlapping bonds, bond customization, scale/rotate/stack structures, template support, and more. Plus, chemDIAGRAM comes with a complete graphics drawing tool set, text processor, page layout tools. Available from:
- Molecular Arts Corporation
Hanover Corporate Centre
1532 East Katella Avenue, Suite 1000
Anaheim, California 92805-6627 USA
Tel: (714) 634-8100
Fax: (714) 634-1999
E-mail: info@molecules.com
ChemDraw Pro/Std - The chemistry drawing program which provides specialized tools for drawing structures and reactions. ChemDraw is designed for chemists, so difficult to draw chemical notations are created automatically. The standard on all major desktop platforms. Find out how easy it is to use ChemDraw to produce professional quality chemical drawings! ChemDraw is available from CambridgeSoft
chemEXHIBIT Scientific Desktop Publishing software for Windows. Create publication-quality illustrations and documents and produce output from slides to over-sized posters. chemEXHIBIT includes a complete 2D chemical diagram drawing tool kit, 3D structure rendering tools, graphic drawing tools, text processor, special math and symbol libraries, page layout tools, and over 100 professional tools in an easy-to-use package. Available from:
- Molecular Arts Corporation
Hanover Corporate Centre
1532 East Katella Avenue, Suite 1000
Anaheim, California 92805-6627 USA
Tel: (714) 634-8100
Fax: (714) 634-1999
E-mail: info@molecules.com
ChemIntosh and ChemWindow, chemical structure drawing applications for the Macintosh and Windows platform. Several other application programs are also available including: Entropy, ChemIntosh Lite, C-13 NMR Module, Spell Checker Module, Structure Library, Chemical Engineering Symbols, Laboratory Glassware Collection, Icons of Science, MS Calculator, MS Palette Tool, RxnDriller, gMNR, GraphPad Prism and SciWords
ChemOffice Pro - Includes: CS ChemDraw Pro, CS Chem3D Pro and CS ChemFinder Pro. Chemical structure drawing, molecular modeling and information integration. CS has combined its products into one powerful and seamlessly integrated desktop solution for chemists daily software needs. Convert 2D structures into 3D models; organize and annotate your 2D structures and 3D models. Search and sort compounds by substructure, name, ID, and annotation. Create electronic notebooks and reaction cards that include 3D models and automatically perform chemistry calculations. FREE Net version available from CambridgeSoft's Web site! ChemOffice is available from CambridgeSoft
ChemPen and ChemPen3D, are chemical structure drawing software for Windows 3.X / 95. ChemPen is for chemists, chemistry students, teachers who need to illustrate chemical documentation quickly and with minimal hassle. ChemPen's Menu driven interface makes drawing chemical structures quick and easy. Drawings can be pasted into your favorite Windows wordprocessors. ChemPen calculates molecular weight, molecular formula and elemental composition. Features include:
- Mouse and Menu Driven Drawing Interface
- Chemical Awareness Helps Keep Drawings Chemically Accurate
- Context Sensitive Editors for Atoms, Bonds, Groups, Symbols and Labels
- Molecular Weight, Formula and Composition
- Paste Drawings into Windows Graphic Word Processors
- Display ChemPen3D drawings
- Online Help, Online Tutorial, Printed manual
ChemPen Chemical Structure Software: http://home.earthlink.net/~hiltonevans/chempen.htm
ChemPen Organic Reactions Page: http://www.geocities.com/chempen_software/reactions.htm
JNMRPen C-13 NMR Shifts Apple: http://www.geocities.com/chempen_software/jnmrpen.htm
chemSAVER, a Windows-based screen saver, to help prolong the life of your monitor. Designed for specialists in the chemical industries and academia, chemSAVER features real-time, 3D animations of chemical structures utilizing sophisticated 3D graphics and user-definable animations and patterns. This latest version chemSAVER offers many new features including "Animated Windows Wallpaper," additional 3D visualization styles, a library of over 160 3D molecular structures and geometric objects, an illustrated 50+ page manual, customizable activation and deactivation settings, plus expanded menu access to chemSAVER's many features. Add your own molecules to the user-extensible library of 3D molecular structures for an unlimited variety of screen images. Available from:
- Molecular Arts Corporation
Hanover Corporate Centre
1532 East Katella Avenue, Suite 1000
Anaheim, California 92805-6627 USA
Tel: (714) 634-8100
Fax: (714) 634-1999
E-mail: info@molecules.com
chemSCENES - an extensive collection of over 40 unique 2D and 3D molecular wallpaper images (screen backgrounds). chemSCENES is the only collection of Windows Wallpaper designed specifically for scientists, researchers, engineers, academicians, and other specialists engaged in (or intrigued by) the chemical sciences. With chemSCENES you will have almost 3 megabytes of high-quality, computer-generated artwork. Included are monochrome, gray-scale, 16-color, and 256-color molecular images. And new with this version of chemSCENES are several ray-traced computer images. Available from:
- Molecular Arts Corporation
Hanover Corporate Centre
1532 East Katella Avenue, Suite 1000
Anaheim, California 92805-6627 USA
Tel: (714) 634-8100
Fax: (714) 634-1999
E-mail: info@molecules.com
ChemSymphony is a platform independent set of interactive JAVA applets that allows 3-D molecular structures to be easily incorporated into HTML documents. The system understands most of the common file formats. The structures can be manipulated in real time, rendered in a variety of styles, and edited by the user. Other functionality includes the ability to browse through databases of chemical structures as well as interfacing to computational programs.
ChemSymphony offers easy and attractive way for new generation of Java-enabled browsers bring molecular modeling into hypertext documents used in both research and the class room. The software is available from Netgenics at the ChemSymphony web site: http://www.chemsymphony.com. Information about the free copy of ChemSymphony v1.3 available to academics for individual academic use is located at http://www.netgenics.com/ng/press_rel.html#chemacademic
ChemWeb is a free chemistry drawing program for creation and transfer of two-dimensional chemical structures over the World-Wide Web. Download from the Bio-Rad site at http://www.chemwindow.com. ChemWeb can be used to output GIF89a formatted files for use in WWW-based documents.
ChemWindow is the most comprehensive chemistry publishing software for Windows® 95, 98, or NT® available today. It is designed for the chemist who needs to publish professional reports, complete with 2-D and 3-D chemical structures, chemical reactions, lab experiment setups, chemical engineering diagrams, data tables, and more. One of the most well-respected tools in the chemistry community, ChemWindow helps you produce great presentations for all aspects of chemistry research! ChemWindow is available from Bio-Rad.
CONVERT It is an unfortunate fact that there is little standardization in the formats in which chemical structural information is stored. There are about half a dozen popular formats in use at the present time, and users of molecular modeling software need to be able to transfer structural information from one modeling system to another. CONVERT allows them to do this. It also allows multi-structural files to be split up, and whole series of structures to be converted from one format to another. Contact:
- Peter Bladon
Interprobe Chemical Services
Gallowhill House, Larch Avenue
Kirkintilloch
Glasgow, SC G66 4HX
UK
Tel: 44-141-578-1109
Fax: 44-141-578-1109
E-mail: cbas25@strath.ac.uk
--- D, E, F ---
DeCipher is a flexible toolkit which enables detailed analysis of molecular modeling and simulation experiments. The format for data presentation is a spreadsheet which can be applied to a wide range of molecular systems and data obtained from both computer simulations and structure determination. The program is available from Accelrys.
DIVA displays structures and data in multiple views and provides visual tools to relate properties on thousands of compounds simultaneously. Available from Accelrys.
EduChem HS Exceptional Teaching Concepts, Inc. is developing teaching tools for chemistry and science, primarily for the secondary educational market. Under the current design, the products have the potential to be used in Colleges and Universities at the entry level as well. EduChem HS consists of five independent modules:
- Periodic Table of Elements
- Molecular Database
- Molecule Builder
- Molecule Viewer
- Orbital Viewer
EduChem HS efficiently covers the curricula of most high schools. It addresses chemistry (and science) in an integrated fashion. It promotes thinking skills and has various levels of difficulty. Extended EduChem Tutorials are included in a convenient HTML format. On-line help for all the modules is available at all times. EduChem HS is extremely user friendly with the text adapted to the high school audience.
Modules easily communicate with each other. EduChem HS adjusts to the student's level of ability through easy menu options, and through more sophisticated options and tutorials. It is flexible and teacher modifiable. It allows group use, and is networkable.
The full version of EduChem (Windows 95 and NT only), has the additional capability to:
- perform geometry optimizations
- calculate electronic properties of atoms and molecules
- display molecular orbitals and isosurfaces
- add more functionality for orbitals
- build proteins
For additional information, contact:
- Exceptional Teaching Concepts, Inc.
- 100 George St., Suite A,
- Hamilton, Ontario
- L8P 1E2 Canada
- Phone (905) 521-1579
- Fax: (905) 521-2128
- E-mail: info@etci.on.ca
Electrochemical Simulation Package (ESP)
Explorer EyeChem is a VRML program for chemistry.
Facio (http://www1.bbiq.jp/zzzfelis/Facio.html) is a freeware molecular builder which works on Windows and Linux.
--- G, H, I ---
Intelli Balancer is a chemical equation balance software, it can balance any chemical equation in a flash! It has a feature rich editor so that you can edit chemical equations easier.It support almost all kinds of chemical equations, eg: ionic equation and equation with hydrate.
--- J, K, L ---
JAVA-Based molecular editor is available from Denis M. Bayada, ICAMS, School of Chemistry, University of Leeds, Leeds LS2 9JT, ENGLAND; Tel: (44) (0)113 233 65 95; Fax: (44) (0)113 233 65 63; E-mail: denis@mi.leeds.ac.uk. The program may be freely downloaded and the Java source code modified. It is located at http://www.lists.ic.ac.uk/hypermail/chemweb/chemweb-May-1996/0019.html.
--- M, N, O ---
MacFormula & WinFormula are programs that calculate the average and exact mass from a user supplied formula. Users can also convert between grams and moles (and vice-versa) and other units. The programs also calculate the percent elemental composition. MacFormula & WinFormula are available at no charge from http://home.pacbell.net/jdeline/index.html. Author: James Deline (E-mail:jdeline@pacbell.net)
MF Calc is program that calculates all possible molecular formulae for a given mass; a useful utility for those working with Mass Spectrometry. Users can control tolerance, elements, and ranges of elements. Versions available for both Windows and Macintosh. MF Calc is available at no charge from ftp://ftp.netcom.com/pub/de/deline/. Author: James Deline (E-mail: deline@netcom.com)
Mol2Mol is a file conversion program for many of the widely used molecular data formats used in chemistry.
Molden is a package for displaying Molecular Density from the Ab Initio packages GAMESS-UK , GAMESS-US and GAUSSIAN and the Semi-Empirical packages Mopac/Ampac, it also supports a number of other programs via the Molden Format. Molden reads all the required information from the GAMESS / GAUSSIAN outputfile. Molden is capable of displaying Molecular Orbitals, the electron density and the Molecular minus Atomic density. Either the spherically averaged atomic density or the oriented ground state atomic density can be subtracted for a number of standard basis sets. Molden supports contour plots, 3-d grid plots with hidden lines and a combination of both. It can write a variety of graphics instructions; postscript, XWindows, VRML, povray, OpenGL, tekronix4014, hpgl, hp2392 and Figure. The Xwindows version of Molden is also capable of importing and displaying of chemx, PDB, and a variety of mopac/ampac files and lots of other formats. It also can animate reaction paths and molecular vibrations. It can calculate and display the true or Multipole Derived Electrostatic Potential and atomic charges can be fitted to the Electrostatic Potential calculated on a Connolly surface. Molden has a powerful Z-matrix editor which give full control over the geometry and allows you to build molecules from scratch, including polypeptides. Molden was also submitted to the QCPE (QCPE619), allthough the Xwindows version is considerably running behind on the current one.
MolDraw is a MacOS based molecular graphics program from the University of Paris (Jean-Michel CENSE, Tetrahedron Computer Methodology, 2, 65-71, 1989). The program is available at the MolDraw Web Site. Contact:
- Gerard S. PICARD
Directeur de Recherche au C.N.R.S.
LABORATOIRE D'ELECTROCHIMIE ET DE CHIMIE ANALYTIQUE
Unite de Recherche associee au C.N.R.S. no 216, Equipe
"REACTIVITE EN MILIEUX IONIQUES LIQUIDES"
11 rue Pierre et Marie Curie
75231 Paris cedex 05 - FRANCE
Tel: (33) 1.43.54.53.84
Fax: (33) 1.44.27.67.50.
molekel is an advanced Interactive 3D-Graphics system for Molecular Sciences. The program is a molecular graphics package for visualizing molecular and electronic structure data from the output of various Chemistry Applications including GAUSSIAN 94/98, GAMESS-US, ADF and many others. MOLEKEL is a GLUT / OpenGL application and is available for UNIX, LINUX and WINDOWS free of charge.
The Molecular Modelling Toolkit (MMTK) is a program library for molecular modelling applications. Its aim is to provide researchers, especially those working on the development of new modelling methods, with a code basis that can be easily extended and modified to deal with standard and non-standard problems in molecular modelling.
openbabel is an open source program that converts chemical structures from one file format to another. Features include:
- A huge variety of common chemical file formats, including SDF/MOL, Sybyl mol2, PDB, SMILES, XYZ, CML
- Recognition of file type based on filename extension
- Chemical MIME support
- Partial implementation of Daylight SMARTS molecular matching syntax
- Flexible atom typer
- Flexible bond typer for perception of multiple bonds from atomic coordinates
- Gasteiger-Marsili partial charge calculation
- Hydrogen addition and deletion
- Isotope support, calculation of average and exact masses
- Automatic feature perception (rings, bonds, hybridization, aromaticity)
- Multiple conformer storage within molecules
- Command line conversion for multiple molecules in one file
- Command line interface
- Bitvector class
- 3D Vector and matrix transformations
- Molecular test suite
- Open-source/Free Software under the GNU General Public License
- Cross platform (Windows, Linux, Mac OS X, SGI, Solaris, Dreamcast...)
Openbabel is available from the SourceForge website at http://openbabel.sourceforge.net/wiki/Open_Babel_2.0.2.
Open Molecule is a Sun SPARCstation based graphics server for molecular modeling. The program is a menu based front end for computational chemistry codes which do not have graphics capabilities, a distributed 3-D graphics system used to visualize the results of complex computations generated on a supercomputer or other high-end system and a supplemental graphics facility for commercial programs. OpenMolecule can display up to nine molecules (up to 10,000 atoms each), each with their own local graphics transformation. The program runs on OpenWindows and utilizes the XGL graphics library. Contact:
- Andataco
9550 Waples Street
San Diego, CA 91921 USA
Tel: 619-453-9191
Fax: 619-453-9294
E-mail: INQUIRE%ANDATCO.UUCP@ucsd.edu
--- P, Q, R ---
Polar simulates 16 types of voltammograms with charge current and random noise.
PrestoPlot (Version 1.16) is a a freely available, windows-based 2D plotting tool. Among the many improvements and bug fixes are:
- Vector plots.
- Plot arbitrary 1D functions (including cartesian, polar and parametric plots).
- Perform interactive non-linear curve fitting of 1D data sets with an arbitrary number of fit parameters.
- Move and resize graphs using the mouse.
- Zoom and scroll graphs using the wheel mouse and middle mouse button.
Source code and executable are available at: http://lancelot.bio.cornell.edu/jason/presto.html
Prode Calculator is a programmable process calculator, with graphical interface, as well as an in-line unit-conversion calculator. It contains functions to calculate VLE/transport properties and a library of about 1000 chemicals. A free copy of Prode Calculator with a limit of 100 chemicals and thermodynamic models is available at URL: http://www.prode.com/prode.html
Qmol is a program for viewing molecular structures and animating molecular trajectories. Originally based on the molview demo program by Mark Kilgard (from his book, Programming OpenGL for the X Window System) and inspired by the Xmol program. Qmol is similar to programs like VMD , MolMol , weblab, Swiss-Pdb Viewer, MolScript, RasMol, gOpenMol and ICM, but opts for a fast, easy to use user interface with a set of features focused on the display of proteins and small molecules. It supports the following (on the Windows platform - features under *uix are unfortunately rather limited):
- Display wire frame, stick figure, ball and stick, point, space-filling, solid and flat ribbon, trace and tube molecular structures from a PDB file.
- Display of multiple molecular models (as used in NMR).
- Animate molecular trajectories stored in a DCD (i.e. CHARMm/Xplor binary trajectory) file in either big- or little-endian formats.
- Kabsch rotate all structures in a trajectory against the initial structure.
- Interactively measure bond lengths, bond angles and torsion angles.
- Dynamically adjust user selected torsion angles.
- Display atom labels.
- Display coordinate axis.
- Dynamic modification of the color scheme (including color-by-element, color-by-atom-number, color-by-residue-number, color-by-temperature and color-by-occupancy).
- Dynamic lighting.
- Adjust atomic radii (including radii-by-temperature and radii-by-occupancy).
- Print to any Windows supported printer and copy images to the Windows clip board.
- Generate AVI movies from a molecular trajectory.
- Assign secondary structure via the STRIDE program.
- Stereo view.
- Directly query the Protein Data Bank and display the resulting structure.
- Detect and display hydrogen bonds (using the energetic criterion of Kabsch and Sander).
- Use the wheel mouse to zoom in and out.
- NEW: User defined clipping plane with rendered sphere/plane intersections.
- NEW: Paste temperature and occupancy PDB fields from the windows clipboard.
Qmol is available from Jason D. Gans who is a part of David I. Shalloway's group at Cornell University (http://lancelot.bio.cornell.edu/jason/qmol.html).
Quac Pac is a suite of programs that generate high-quality charge states and charges for small molecules and proteins. It includes pKa state and tautomer enumeration to get correct protonation states, partial charges using multiple models, and electrostatic potential map construction and storage. The software runs on Linux, Windows, MacOSX, HP, IBM, SGI and SUN UNIX. Contact OpenEye at http://www.eyesopen.com
.React is a program to calculate reaction kinetics equations. The program is available in compiled form for the Macintosh, DOS, and OS/2 platforms.
--- S, T, U ---
SAMPLS is a new formulation of the Partial Least Squares
(PLS) statistical method. SAMPLS, written by Bruce Bush at Merch
Research Laboratories, can be used to develop a structure-activity
relationship for any single response based on the "distance"
between samples in the training set. SAMPLS is especially efficient
when the relationship is based on a large number of computed
molecular properties, whether topological or geometric. SAMPLS is
written in FORTRAN 77 for SGI systems. It is available from QCPE.
STRUVIR is a public domain program for preparing VRML, HPGL, POSTSCRIPT and POVRAY files for drawing inorganic crystal structures. MS Windows 95 and ALPHA-AXP Open VMS versions are available together with the FORTRAN 77 sources, a hypertext tutorial, examples, etc.
UNIMOL suite of programs is used to calculate unimolecular rate constants. The UNIMOL suite can be obtained using FTP. To run the program suite, you will also need the manual, which is some 30 pages in length. This manual can be sent electronically, most easily as a Macintosh binhex file which can then be printed out.
Note also that the program and manual make frequent reference to the text, "Theory of unimolecular and recombination reactions" by R.G. Gilbert and S.C. Smith. Blackwell Scientific Publications, Oxford and Cambridge Mass., 1990. Users have found having access to this text makes the program much easier to understand.
To access UNIMOL programs and sample data files, ftp to ftp.chem.usyd.edu.au as ftp or anonymous Change Directory to /pub/unimol and copy all of the files in the directory.
The main directory contains the program file. The subdirectory doc contains the documentation, both as a Macintosh BinHex file or as an RTF ("rich-text format") file which can be read into any word processor. These are available as manual.hqx and manual.rtf
For further details, email Dr. Robert G. Gilbert at gilbert@chem.usyd.edu.au or contact him at:
- Professor Robert G Gilbert
Sydney University Polymer centre
Chemistry School,
Sydney University. NSW 2006 Australia
phone: 61-2-351 3366
fax: 61-2-351 3329
--- V, W ---
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