The following are resources in Organic
Chemistry and Medicinal Chemistry:
1. General Chemical Information
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CambridgeSoft maintains ChemFinder, a remarkably efficient Internet search
engine, which searches for information on specific compounds by name, formula,
CAS registry number, and molecular weight. Most of the hits are related to
toxic properties but the search engine turns up information that most tools
such as Yahoo miss. Chmoogle
is a complementary search engine which supports substructure searching.
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The ACD Labs Web site advertizes
its modeling software but also provides a number of services. These include
predicting the proton NMR spectrum, carbon-13 NMR spectrum, vapor pressure, octanol-water partition coefficient and IUPAC name of an
organic compound. The structure must be drawn using their ChemSketch
utility which can be downloaded for free. The structure is sent to their site
for processing and the results are returned. Special viewers which can be
downloaded are required to view the NMR spectra. The site also has a Web
version of the IUPAC Blue Book which covers most aspects of organic
nomenclature.
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If you brush up
on your French, you can use ChemExper, a Belgian site, as a complete reference to
organic nomenclature. The site also has links to chemical catalogues and
provides a utility which calculates the molecular weight and %-composition from
the molecular formula.
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Search a very
useful Queen Mary and
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Organic Chemistry Resources Worldwide
is an impressive collection of links to site related to all aspects of
synthetic organic chemistry. The "Bench" section provides information
on solvents, synthetic techniques, and methods of purification. This
comprehensive Web site is worth checking when you are looking for information
on the Web.
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The
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InChIs is a new computer-readable system for organic
nomenclature. The Web site for InchIs provides answers to questions and links to
resources. An alternate approach is SMILES which was
developed by Dave Weininger of Daylight while he was
with the EPA and
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The Landolt-Boernstein Institut at
the
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CHEMDB is an electronic database maintained
by the Department of Chemistry at the University of California-Irvine. It
focuses on chemical synthesis.
2. Structures of Organic Molecules
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Doctor Ihlenfeldt at the University of Erlangen-Nuernberg maintains a Web page dedicated to
"internet-based chemical information services" that are related to
molecular structure The Erlangen site includes the Enhanced NCI Database of over
250,000 structures. Professor Ihlenfeldt frequently
makes significant enhancements to htis Web site.
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The structures of
substrates involved in biochemical pathways are collected in the Klotho
database at
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Pictures in a .pdb format of a large selection of organic molecules are
available in a dataset maintained at Okanagan University
College A RasMol viewer is needed to view the
structures.
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ChemFinder
is a search engine which yields very useful data and structures for a large
number of organic compounds. A special browser which can be downloaded is
required to read the structures.
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A site at the Free
University of Berlin allows one to view the structures of all amino acids.
Some data are also provided.
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The Jena site provides images of amino
acids, saccharides, and nucleotides. A VRML reader is
required.
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The Indiana University Molecular Structure
Center is building a library of X-ray structures of organic and organometallic species. The search engine is difficult to
use. You want to search the entire report file for instances of the string
which you provide. A few examples of successful searches: cp and Cp fetch
structures with the cyclopentadienyl group, phenyl fetches those with a phenyl group. This is a
Java site.
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The Global Network of Manufacturers and Distributors
maintains a site which provides the entire data base (127,000 compounds!) of
the National Cancer Institute in a form which can be read by readers such as RasMol.
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The O Dictionary for
Hetero Compounds at
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The Organic Chemistry Portal, maintained by
Reto Mueller of
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The Centre de Recherches sur Macromolécules Végétales
of the French CNRS maintains GLYCO3D,
a 3D structural database of simple to complex glycosides.
3. Properties of Organic Molecules
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Information
including literature references, the Chemical Abstract reference number, an
applications is provided by The Aldrich-Sigma
WWW site is a useful source of information on all its products. The data
include chemical and physical properties, MSDS sheets, and the Chemical
Abstract reference number. Click on Product Search to access these data. You
can locate an entry by providing the compound's name or formula. Substructure
searching is also an option. This excellent coporate
Web site also provides selected Aldrich Technical Buletins
in a pdf format. Click on Tech Library to access this
information.
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ChemSpider,
developed by ChemZoo Corporation, has a search engine
for millions of compounds. A tabulation of physical properties such a logP is provided for each hit.
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The DuPont site provides physical
properties such as vapor pressure, dipole moment, and boiling points as well as
MSDS data sheets for intermediates which it manufactures for sale. The
compounds in the database are diacids, diesters, diamines, nitriles, and cyclic alkenes.
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LIPIDAT maintained at
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Dudley Chemical Company
provides a fairly comprehensive table of dyes and stains and the Chemicalk Abstracts Registry number of each dye. With the
registry number in hand you can use ChemFinder to track down information on the dye.
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The Facultad de Quimica y Biologia of the Universidad de Santiago de
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The olfactory
properties of organic molecules often attract students to the study of organic
chemistry. Two useful sets of links to flavor and fragrance are maintained by Leffingwell &
Associates. Information on the compounds in coffee is provided by the Coffee Research Institute.
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The chemistry
server at the Freie Universität
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SYRRES provides
the interactive PhysProp database with data for over 25,000 compounds.
The user must provide the CAS number of the compound to use the on-line free
version.
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The Bordwell
table of pKa's of many organic acids
in DMSO is now available in electronic format at a
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The NIST Special Publication 922, Polycylcin Aromatic Hydrocarbon Structure Index, is now
available on the WWW. the index developed by Lane
Sander and Stephen Wise provides for each hydrocarbon in the database its
structure with numbering on the rings and structural parameters such the
length, width, and thickness.
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The SweetDB,
maintained at the
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The Structural
Bioinformatics Group at Charité Berlin, a
consortium of the clinics operated by the Freie Universität Berlin and the Alexander von Humboldt Universität, maintains the Super Natural
Database, a searchable database of natural products and their properties.,
4. Spectra of Organic Molecules
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I have placed the
best source at the head of the list. NIMC, the National Institute of Materials
and Chemical Research in
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The NIST WebBook provides a
gateway to NIST's valuable, extensive collection of
IR and MS spectral data as well as thermodynamic and kinetic data.
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Steffen Thomas at
the
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NMRShiftDB is a
German database of compounds and their carbon-13 chemical shifts. The Web site
provides means of predicting a chemical shift. The software is based on
empirical rules drawn on the data for the compounds in the database. The
database is described in C. Steinbeck, S. Krause, and S. Kuhn, J. Chem. Inf.
Comput. Sci. 2003,
43, 1733-1739.
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Tutorials and IR,
UV, NMR, and MS spectra of selected compounds are available at the University of the West Indies
Web site. A special jcamp viewer is needed to view
many of the files. The viewer can be downloaded from the site.
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Rainer
Haessner maintains a collection of NMR exercises.
The text is in German.
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A collaborative
effort of Cambridge Isotope Lab and the Department of Chemistry at UCLA has
developed WebSpectra,
an impressive collection of problems for a course in the spectrometric
identification of organic spectra. Solutions are included. Both 1D and 2D
proton and carbon-13 spectra are included as well as IR spectra. Links to
tables of data useful in the collection of NMR spectra, e.g. parameters of NMR
solvents, are also provided.
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The students in
the winter, 2004 term of Chemistry 340 at Southern Oregon University have
assembled Organic
Spectroscopy. The Website has information relevant to the class but also
includes instructive manuals for the use of NMR, IR, and GC-MS instrumentation.
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The Canadian
Human Metabolome Project maintains the Human Metabolome Database,
a source of biological and chemical data on nearly 2,500 metabolites. The data
include assigned 1D and 2D proton and carbon-13 NMR spectra and mass spectra
for each metabolite.
5. Reactions and Mechanism
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Professor Parrill
at
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In WebReactions,
you draw with the aid of a Java Applet a chemical transformation and the search
system searches the database for literature precedents for the transformation.
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The Innocentive Website
contains a set of problems in synthesis. A prize is awarded for each
"best" answer.
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The invaluable
synthetic protocols assembled by Organic
Syntheses are now available on line. A special ChemDraw plugin is required to read the files.
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Exclusive Chemistry, a
company devoted to comtinatorial chemistry, provides
a searchable access to Organic Syntheses and Chemicals Note, a
compendium of information on organic reagents.
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Chemical Applications of
Microwave Heating, a Web site on the synthetic applications of microwave
radiation, is hosted at the
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The Bioactives Cookbook site
from the Center for Chemical Methodology and Library Development at
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All issues of Aldrichima Acta, a journal produced by Sigma-Aldrich and devoted to organic
synthesis, are available in pdf format at the
Sigma-Aldrich Web site.
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Polymers
(Plastics, young man!)
§
Polymer
scientists at the
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Information on
the applications and properties of plastics is available at the Allied Signal site.
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Eastman
Chemical's Technical
Solution Wizard provides access to its database of properties of the
polymers that it produces.
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Matweb is a WWW site
dedicated to the properties of polymers. The quantitative data cover a wide
range of polymers and their properties. Free registration is required to access
the data.
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Medicinal
Chemistry
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Extensive reports
on selected drugs are available at the Druginfonet
site.
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Biobyte (formerly the Pomona College Medicinal Chemistry
Project) provides octanol/water partition coefficient
data (logP) for 140 selected compounds and a discussion on
how to calculate values of logP. Full documentation
on the clogP program is also available.
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BIAM (Banque
de Donée Automatisée
sur les Médicaments)
is an excellent Web site in French that provides an enormous amount of
information on drugs as well as the materials that are used in the formulation
of pharmaceutical products. BIAM is maintained by the Centre de Recherche en Informatique at the Ecole de Mines de Paris.
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Course material
and detailed lecture notes related to Pharmacology 241
at UCLA, a course on pharmacokinetics are available on the WWW.
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Dr. Malcolm
Andrew of De Montfort University,
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The
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The
Pharmaceutical Research and Manufacturers of America maintains
a wbsite devoted to the results of clinical studies of drugs
marketed in the
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MolSoft hosts the Molecular
Properties and Drug-likeness page that provides parameters for drugs and
potential drugs. The choice of parameters is based on Lipinski's rules.
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MolTable is a Web
page devoted to molecular descriptors used in QSAR. Descriptors have been
assembled for the NCI dataset. Other datasets are being added. The actual data
are accessed through an Web page in India.
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CHMIS-C, A Comprehensive
Herbal Medicine Information System for Cancer Drug Design, is a source of
information on potential drugs extracted from Chinese herbs. The database maintained
at the
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Combichemistry maintains a Web page devoted to Combinatorial Chemistry that provides
a good introduction to the methodology.
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Several Merck Manuals including the Merck
Manual of Diagnosis and Therapy is available in an on-line versiuon, The Merck Index is not available for free.
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The National
Library of Medicine of the NIH provides to layman extensive information on prescription
drugs and herbal remedies in its drug information
Web page of Medline Plus.
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Enormous effort
has recently been invested in the development of biomedical databases. Most of
these are proprietary. The following are available on the WWW:
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ChemBank,
a Harvard collection of data on small molecules
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a Database for Anti-HIV Compounds maintained
by the NIH
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ChemIDplus
maintained by the National Library of Medicine
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The Chemometrics
Web News maintained by the Chemometrics and QSAR
Research Group in
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ZINC, a free database of commercially
available compounds for screening, is maintained by the University of
California-San Francisco.
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The Cheminformatics
Web site has links to QSAR data sets.
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The U.S. National
Library of Medicine posts the status and results of clinical trails of drugs,
biologics, and devices at its Clinical
Trials Web site.
§
Andreas Bender
has assembled a linked list of QSAR
databases and programs found on the WWW.
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The Japanese firm
RIKEN
provides information on the antiobiotics that it
markets on its Web page.
last updated, 30 June 2009