MolData

ORGANIC CHEMISTRY

The following are resources in Organic Chemistry and Medicinal Chemistry:

1.     General Chemical Information

o    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.

o    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.

o    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.

o    Search a very useful Queen Mary and Westfield site maintained by Gerry Moss for the full texts of the IUPAC documents dealing with organic nomenclature, conventions, and symbols.

o    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.

o    The National Center for Biotechnology Information of the National Institutes of Health maintains the PubChem database, a searchable database of nearly one million compounds.

o    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 Pomona College.

o    The Landolt-Boernstein Institut at the University of Hamburg produces the most comprehensive complilation of data covering all areas of science. The Landolt-Boernstein Substance/Property Index generates for a compound not only detailed citations for information in the L-B database but also descriptors such as the CAS registry number and the molecular formula.

o    CHEMDB,  a Web site maintained by the Department of Chemistry at the University of California-Irvine, provides a range of resources: selected databases of drugs, interactive modules focusing on synthesis, and a modeling toolkit.  The modeling toolkit includes Babel, COSMOS, and modules that convert a SMILES string to a 2D or 3D structure.

2.     Structures of Organic Molecules

o    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.

o    CrystalEye, a project of the University of Cambridge, provides crystallographic structures mined from WWW resources and converts the data to CML.  The Web site has a search engine based on SMILES and a Java display window.  It is possible to capture the original cif file.

o    The structures of substrates involved in biochemical pathways are collected in the Klotho database at Washington University. Rasmol or an equivalent 3D viewer is needed to view the .pdb files which are provided.

o    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.

o    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.

o    A site at the Free University of Berlin allows one to view the structures of all amino acids. Some data are also provided.

o    The Jena site provides images of amino acids, saccharides, and nucleotides. A VRML reader is required.

o    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.

o    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.

o    The O Dictionary for Hetero Compounds at Uppsala University is a collection of the structures of monatomic to polyatomic small molecules abstracted from the Brookhaven protein database, e.g. chloride anion and 1-deazaadenosine. HICUP, the Hetero-Compound Information Center at Uppsala has its own link to the same database.

o    The Organic Chemistry Portal, maintained by Reto Mueller of Liestal, Switzerland, provides a wide array of onformation on organic compounds. Free tools predict NMR chemical shifts and logP.

o    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

o    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.

o    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.

o    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.

o    LIPIDAT maintained at Ohio State University is a relational database of chemical and physical proerties of lipids. Extensive information on phase transitions is included

o    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.

o    The Facultad de Quimica y Biologia of the Universidad de Santiago de Chile has assembled CARBHYD , a comprehensive set of valuable links covering carbohydrate chemistry and biochemistry..

o    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.

o    The chemistry server at the Freie Universität Berlin offers a short but useful page on terpenes with spectra and properties.

o    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.

o    The Bordwell table of pKa's of many organic acids in DMSO is now available in electronic format at a University of Wisconsin site. Gas-phase and aqueous-phase data re also provided. Professor Evans at Harvard provides a pdf document with additional pKa's in water and DMSO.

o    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.

o    The SweetDB, maintained at the German Cancer Research Center in Heidelberg, is a database devoted to the structures and spectra (NMR and MS) of all classes of carbohydrates.

o    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

o    I have placed the best source at the head of the list. NIMC, the National Institute of Materials and Chemical Research in Ibaraki, Japan, maintains SDBS, the Spectral Data Base System. SDBS is an extensive integrated library of IR, Raman, MS, and NMR spectra. Use the flexible search engine to obtain spectra.

o    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.

o    Steffen Thomas at the University of Potsdam has assembled an extensive database of MS and NMR data as well as means to predict NMR spectra.

o    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.

o    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.

o    Rainer Haessner maintains a collection of NMR exercises. The text is in German.

o    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.

o    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.

o    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

o    Professor Parrill at Michigan State University has written a useful set of on-line tutorials in organic chemistry which include an integrated road map to organic reactions and a discussion of the conformation of cycloalkanes.

o    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.

o    The Innocentive Website contains a set of problems in synthesis. A prize is awarded for each "best" answer.

o    The invaluable synthetic protocols assembled by Organic Syntheses are now available on line. A special ChemDraw plugin is required to read the files.

o    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.

o    Chemical Applications of Microwave Heating, a Web site on the synthetic applications of microwave radiation, is hosted at the University of Edinburgh.

o    The Bioactives Cookbook site from the Center for Chemical Methodology and Library Development at Boston University provides synthetic routes for the molecules in its database.

o    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.

o    Francis Carey and Richard Sundberg maintain the Organic Chemistry Portal which provides detailed information on organic transformations and synthetic methods.  Their page provides references to instructive monographs and links to the current organic primary literature.

 

6.     Polymers  (Plastics, young man!)

o     Polymer scientists at the University of Southern Mississippi have assembled the Macrogalleria, an instructive survey of polymer science which will be useful to the novice as well as the student who needs comprehensive coverage of the uses, properties, and synthesis of polymers.

o    All Information on the applications and properties of plastics is available at the Allied Signal site.

o    All Eastman Chemical's Technical Solution Wizard provides access to its database of properties of the polymers that it produces.

o    PoLyInfo (Polymer Database) is a Japanese site that provides extensive data on a wide range of polymers.

o    All 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.

 

7.     Medicinal Chemistry

o    Extensive reports on selected drugs are available at the Druginfonet site.

o    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.

o    The Great Molecular Crapshot is a blog that addresses aspects of drug discovery and QSAR with provocative, thoughtful essays. 

o    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.

o    Course material and detailed lecture notes related to Pharmacology 241 at UCLA, a course on pharmacokinetics are available on the WWW.

o    Dr. Malcolm Andrew of De Montfort University, Leicester, England maintains Pharmscape, a Web page dedicated to the university's program in pharmacology and medicinal chemistry. The page on Drug Discovery provides a tour of the process of drug development with several instructive examples. Links are provided on this page to pages dedicated to toxicology, dosage, and formulation.

o    The University of Alberta maintains DrugBank, an on-line pharmacopoeia with infomation on over 4100 drugs.

o    The European Bioinformatics Institute hosts ChEMBL, a database devoted to drugs and bioactive molecules.  Information includes structures and parameters related to the Rule of Five.

o    The Pharmaceutical Research and Manufacturers of America maintains a wbsite devoted to the results of clinical studies of drugs marketed in the US.

o    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.

o    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.

o    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 University of Michigan, is in effect a Materia Medica Sinica.

o    Combichemistry maintains a Web page devoted to Combinatorial Chemistry that provides a good introduction to the methodology.

o    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.

o    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.

o    CarlsbadOne is a WWW application developed by Translational Informatics Division of the University of New Mexico which integrates bioactivity databases for the exploration of structure activity relations (SAR).

o    Enormous effort has recently been invested in the development of biomedical databases. Most of these are proprietary. The following are available on the WWW:

§  ChemBank, a Harvard collection of data on small molecules

§  a Database for Anti-HIV Compounds maintained by the NIH

§  ChemIDplus maintained by the National Library of Medicine

§  The Chemometrics Web News maintained by the Chemometrics and QSAR Research Group in Milano, Italy provides reference data sets which can be used in the development of QSAR equations.

§  ZINC, a free database of commercially available compounds for screening, is maintained by the University of California-San Francisco.

§  The Cheminformatics Web site has links to QSAR data sets.

§  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.

§  The Japanese firm RIKEN provides information on the antibiotics that it markets on its Web page.

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last updated, 25 March 2014