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CHEM 137: Special topics in organic chemistry

CHEM 137 - Spring 2015 - Instructor: Trost, B.
Last Updated: 7-May-2015

This guide contains resources for students taking Chemistry 137.

Subject Librarians

Grace Baysinger
Head Librarian and Bibliographer of the Swain Chemistry and Chemical Engineering Library
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3rd ed. / Washington, DC : American Chemical Society ; Oxford ; New York : Oxford University Press, 2006.
Chemistry & ChemEng Library (Swain) » On reserve: Ask at circulation desk » QD8.5 .A25 2006
"An essential constant in this changing environment is the requirement that information remain accurate, clear, unambiguous, and ethically sound. The ACS Style Guide is the definitive source for all information needed to write, review, submit, and edit scholarly and scientific manuscripts. It is also an excellent resource for learning how to effectively communicate scientific information." (publisher's description)
Chemical information for chemists: a primer
Chemistry & ChemEng Library (Swain) » Stacks » QD8.5 .C474 2014
"While it is not difficult to find data in many cases, what advice can you get on the quality of the data retrieved? Chemical Information for Chemists could help with this problem and more. This book is a chemical information book aimed specifically at practicing chemists. Written and edited by experts in the field, it is ideal for chemists who lack a chemical information professional able to teach basic and intermediate techniques in retrieving and evaluating information using the unique entry points of the chemical literature, including structure, formula, substructure, and sequence. Aimed at students on undergraduate and graduate courses, it could also be a useful guide to new information specialists who are facing the challenging diversity of chemical literature." (publisher's description)

About Chem 137

The course covers the basic toolbox for construction of more complex structures for function, largely directed towards molecules of biological relevance. The focus will be the ability to perform structural changes efficiently in order to enable the design of the best structure for a function. The concepts of catalytic processes are at the heart of the how small molecule drug discovery is performed. Fundamentals of the pertinent catalytic processes are discussed. The inter-relationship of synthetic chemistry and pharmaceuticals is emphasized.  Prerequisite CHEM 35.


Premium collection Oxford ; New York, N.Y.: Oxford University Press, c2002-
Stanford University Libraries » Online resource » eResource
Oxford Reference Online brings together language and subject reference works from one of the world's biggest and most trusted reference publishers into a single cross-searchable resource. The Premium Collection offers a huge range of fully-indexed, extensively linked, up to date, and cross-searchable dictionary, language reference, and subject reference works published by Oxford University Press.
IUPAC compendium of chemical terminology
Version 1.0.0. [Research Triangle Park, N.C.] : International Union of Pure and Applied Chemistry, 2006.
Chemistry & ChemEng Library (Swain) » Media » QD5 .I86 2006
The Compendium is popularly referred to as the "Gold Book", in recognition of the contribution of the late Victor Gold, who initiated work on the first edition. It is one of the series of IUPAC "Colour Books" on chemical nomenclature, terminology, symbols and units, and collects together terminology definitions from IUPAC recommendations already published in Pure and Applied Chemistry and in the other Colour Books. The result is a collection of nearly 7000 terms, with authoritative definitions, spanning the whole range of chemistry.


Chemistry & ChemEng Library (Swain) » Media » QD921 .C36 2015
"The CSD is the world repository of small molecule crystal structures. Stanford has a license to the web version of CSD which is updated weekly. We also have a site license for the Cambridge Crystallographic Database System, Mercury, DASH, Hermes, and SuperStar. (Structure Searching)
Web version. Boca Raton, FL : Chapman & Hall/CRC
Stanford University Libraries » Online resource » eResource
Includes descriptive and numerical data on the chemical, physical and biological properties of compounds; systematic and common names of compounds; literature references; structure diagrams and their associated connection tables. CCD online includes: organic compounds (269,000 records); natural products (178,000 records); inorganic and organometallic compounds (103,000 records); drugs (44,000 records); and analytical reagents (14,000 records). (Structure searching)
Rahway, N.J. : Merck & Co., 1968-
Green Library » Information Center: Reference » RS356 .M524 2001
The Merck Index contains over 10,000 monographs with information relating to compounds of significance in research, commerce and environmental impact.  Each monograph in this authoritative reference source is a concise description of a single substance or a small group of closely related compounds. There is also a supplement of Organic Name Reactions.
Pharmaceutical Substances
Stuttgart ; New York : Thieme Chemistry, 2003-
Stanford University Libraries » Online resource » eResource
Version 3.8 features 32 new APIs and a total of 35,358 structures, 11,289 reactions and 2,606 active pharmaceutical ingredients.  Essential for research and process chemists, it includes the full synthetic route for the industrial manufacture of each drug elucidated from the patent literature; unique source of reactions that perform on an industrial scale; readily available overview of the pharmaceutical industry from a synthetic chemist’s perspective; and functionality affords insights into a therapeutic area and chemically related substances. Essential information for product managers, it includes patent information including approval date and expiration; determine market size & competition for an API – essential for development of new and generic pharmaceuticals; source of markets for synthesis intermediates; comprehensive coverage of older APIs and substances approved world-wide; and merger and acquisition tracking ensures that vendor information is up-to-date in a rapidly changing industry.  (Structure Searching)
[Norwich, N.Y.] : Knovel, 2003-
Stanford University Libraries » Online resource » eResource
Knovel provides access to over 2,000 leading reference works and databases from over 50 international publishers and professional societies through a single interface. Includes the ability to search numeric data.  Some books have interactive tables.

Major Reference Works

Emphasizing synthetic strategy and practice, this online reference work features experimental procedures for stereoselective synthetic reactions applicable to drug targets and natural products. The reference details synthetic methodology, reaction mechanisms, and applications for medicinal chemistry and drug discovery; and explores strategy and interdisciplinary work, laboratory synthesis for natural products, the preparative aspects of stereoselective synthesis for drugs, natural products, and potential biologically active compounds.
Stuttgart ; New York : Thieme.
Stanford University Libraries » Online resource » eResource
"Science of Synthesis (SoS) provides a critical review of synthetic methodology developed to-date in the fields of organic and organometallic chemistry. Features include: Selection of molecular transformations by world-renowned experts with elaboration on scope and limitations; Full-text descriptions of synthetic methods with practical experimental procedures immediately applicable in the lab; Community of over 1,000 experts involved in the review and updating of methods; Logical organization of the synthetic methods for each functional group; and Intuitive search functions to allow rapid lead generation and route optimization."  Please see Science of Synthesis at Stanford to view online help, learn more about content, and see what's new. (Structure and Reaction Searching)
7th ed. [Hoboken, N.J.] : Wiley, c2010.
Stanford University Libraries » Online resource » eResource
Burger's offers easy access to broad coverage of medicinal chemistry and drug discovery for new, as well as experienced, medicinal chemists, biologists, pharmacologists, and molecular biologists. Burger's offers a comprehensive, global perspective of drug design and drug development. With expanded content, this edition of Burger’s Medicinal Chemistry and Drug Discovery includes more than 50% new material. An entire section has been dedicated to cancer research. Areas included are those at the foreground of life science including: proteomics, genomics, bioinformatics, combinatorial chemistry, high-throughput screening, blood substitutes, allosteric effectors as potential drugs, COX inhibitors, statins, high-throughput pharmacology, and much more.
Amsterdam ; New York : Elsevier, c2007.
Chemistry & ChemEng Library (Swain) » Reference » RS402 .C65 2007 V.1
Comprehensively reviews the strategies, technologies, principles and applications of modern medicinal chemistry. Provides a global and current perspective of today's drug discovery process and discusses the major therapeutic classes and targets. Includes a unique collection of case studies and personal assays reviewing the discovery and development of key drugs.
Comprehensive Organic Synthesis II
Second edition.
Stanford University Libraries » Online resource » eResource
"The second edition of Comprehensive Organic Synthesis builds upon the highly respected first edition in drawing together the new common themes that underlie the many disparate areas of organic chemistry. These themes support effective and efficient synthetic strategies, thus providing a comprehensive overview of this important discipline. Fully revised and updated, this new set forms an essential reference work for all those seeking information on the solution of synthetic problems, whether they are experienced practitioners or chemists whose major interests lie outside organic synthesis.  It contains over 170 articles across nine volumes, including detailed analysis of core topics such as bonds, oxidation, and reduction. Includes over 10,000 schemes and images. Important growth areas-including combinatorial chemistry, new technological, industrial, and green chemistry developments are covered extensively."
1st ed. Oxford, England ; New York : Pergamon Press, 1991.
Chemistry & ChemEng Library (Swain) » Reference » QD262 .C535 1991 V.1
"The development of more effective routes to known materials and the production of new materials are important goals in many areas, including electronics, agriculture, medicine and textiles. Organic synthesis is central to achieving these goals. Comprehensive Organic Synthesis draws together the common themes that underlie the many apparently disparate areas of organic chemistry which underpin synthetic strategies, thus providing a comprehensive overview of this important discipline.  The contributions have been organized to reflect the way in which synthetic chemists approach a problem. In terms of organic molecules, the work is divided into formation of carbon-carbon bonds, introduction of heteroatoms and heteroatom interconversions. Thus, Volumes 1-5 focus on carbon-carbon formation, but also include aspects of heteroatom introduction. Volumes 6-8 concentrate on interconversion of heteroatoms, but also deal with exchange of carbon-carbon bonds for carbon-heteroatom bonds. Organization of the chapters is along the theme of selectivity, which is a critical question in determining the suitability of a synthetic method. Volume 9 contains cumulative author and subject indexes.  Comprehensive Organic Synthesis will appeal to a wide audience. The set will be an essential reference work for all those seeking information on the solution of synthetic problems, whether they be experienced practitioners or chemists whose major interests lie outside organic synthesis. In addition, synthetic chemists requiring the essential facts in new areas, as well as students completely new to the field, will find Comprehensive Organic Synthesis an invaluable source, providing authoritative accounts of the essential facts and concepts."
1st ed. Amsterdam ; Boston : Elsevier, 2005.
Chemistry & ChemEng Library (Swain) » Reference » QD262 .C534 2005 V.1
By systematically treating each functional group in turn the work also identifies what is not known, thus pointing the way to new research areas. Organized by the arrangement and bonding of hetero-atoms around a central carbon atom. Each chapter is written by experts who have critically read and reviewed the literature and presented the best methods of forming every known functional group.
[Hoboken, NJ?] : John Wiley & Sons, 1999-
Stanford University Libraries » Online resource » eResource
Patai covers all aspects of the chemistry of functional groups including physical organic chemistry, analytical chemistry and techniques, reaction mechanisms, synthetic pathways, reactions and strategies plus applications in drug discovery, pharmaceuticals, biochemistry and molecular biology.  All volumes published from 1964 to 1995 are available online in the PATAI’S Chemistry of Functional Groups Backfile.
Amsterdam ; Boston : Elsevier, c2012.
Biology Library (Falconer) » Reference » QH505 .C588 2012 V.1
Comprehensive Biophysics provides definitive introductions to a broad array of topics, uniting different areas of biophysics research, from the physical techniques for studying macromolecular structure to protein folding, muscle and molecular motors, cell biophysics, bioenergetics and more. The result is this comprehensive scientific resource: a valuable tool both for helping researchers come to grips quickly with material from related biophysics fields outside their areas of expertise, and for reinforcing their existing knowledge.
[Bethesda, Md.] : John Wiley and Sons, 2011-
Stanford University Libraries » Online resource » eResource
"Comprehensive Physiology is the most authoritative and comprehensive collection of physiology information that has ever been assembled. Its starting point is more than 30,000 pages of content from the American Physiological Society's renowned Handbook of Physiology series, which is presented here for the first time in an online format. New and updated materials will be published in a quarterly serial format."


[3rd ed.] Berlin ; Heidelberg : Springer, c2012.
Stanford University Libraries » Online resource » eResource
The merging of different basic and clinical scientific disciplines towards the common goal of fighting cancer makes such a comprehensive reference source all the more necessary. Containing over 7,000 entries, this work includes information on all of the biomolecules, types of cancers pathways, and therapies of great importance in the field.
Encyclopedia of Biological Chemistry 2nd Edition
Second edition.
Stanford University Libraries » Online resource » eResource
Representing the current state of a dynamic and crucial field of study, the 2nd edition of this encyclopedia pulls together over 500 articles that help define and explore contemporary biochemistry.  It acknowledges that understanding every living process-from physiology, to immunology, and genetics is impossible without a grasp on the basic chemistry that provides its underpinning.  Written by experts, each article provides an up-to-date snapshot of a given topic, as well as suggestions for further readings for students and researchers wishing to go into greater depth. 
Spanning the entire spectrum of the life sciences, ELS is a monthly-updating reference work containing over 4,500 specially commissioned and peer-reviewed articles written by leaders in the field. ELS has articles on these subject areas: Biochemistry, Cell Biology, Developmental Biology, Ecology, Evolution and Diversity of Life, Genetics and Disease, Genetics and Molecular Biology, Immunology, Microbiology, Neuroscience, Plant Science, Science and Society, Structural Biology, and Virology.
Weinheim : Wiley-VCH Verlag, 2004-2005.
Stanford University Libraries » Online resource » eResource
"The Encyclopedia of Molecular Cell Biology and Molecular Medicine covers both the molecular and cellular basis of life and medicine. Since its origins, the Encyclopedia has expanded, through two print editions, to contain more than 350 articles. Each begins with a glossary of keywords, a concise definition of the subject and its importance, followed by a detailed review and bibliography."
Berlin ; London : Springer, 2008.
Stanford University Libraries » Online resource » eResource
This comprehensive encyclopedia provides concise information on the molecular pathophysiology of disease. Determining and understanding the molecular mechanisms of disease is one of the key goals of modern medical research. The studies of medical genetics, microbiology, immunology, structural biology, molecular cell biology, neuroscience and developmental biology have been brought to bear on the full range of human diseases.
2nd ed. Berlin ; New York : Springer, c2008.
Stanford University Libraries » Online resource » eResource
The two volume set combines the knowledge of classic pharmacology describing drug action as well as the more recent approach of the precise analysis of the molecular mechanisms by which drugs exert their effects.
Hoboken, N.J. : John Wiley & Sons, c2009.
Chemistry & ChemEng Library (Swain) » Reference » QP512 .W48 2009 V.1
This encyclopedia illuminates the crucial role of chemistry and chemical techniques in the life sciences. WECB is an evolving online database of information, combining the most useful features of traditional reference works and review journals in a compelling format designed to exploit the full potential of the online medium. Includes extensive linking to the primary literature and to other online resources.


Start With These Databases

Palo Alto, Calif. : Annual Reviews, Inc.
Stanford University Libraries » Online resource » eResource
Annual Reviews publishes authoritative, analytic reviews in 42 focused disciplines within the Biomedical, Physical, and Social Sciences. Annual Reviews publications are among the most highly cited in scientific literature. Updated continuously, covers 1932-present.
[Frankfurt, Germany ; New York, NY] : Elsevier
Stanford University Libraries » Online resource » eResource
Available via the web, Reaxys Xcelerate contains an extensive repository of experimentally validated data that chemists need including structures, reactions (including multi-step reactions) and physical properties. Reaxys was formed by the merger of three databases: Beilstein Handbook of Organic Chemistry, Gmelin Handbook of Inorganic and Organometallic Chemistry, and the Chemistry Patent database. (Structure and Reaction Searching)
[Columbus, Ohio : American Chemical Society, Chemical Abstracts Service]
Stanford University Libraries » Online resource » eResource
SciFinder is the most comprehensive database for coverage of chemistry & chemical engineering. It has the world's largest collection of organic and inorganic substance information. The web version of SciFinder provides integrated access to CAPlus, CAS Registry, CASREACT, CHEMLIST, and CHEMCATS which are produced by Chemical Abstracts Service, and to MEDLINE which is produced by the U.S. National Library of Medicine. Sources covered in SciFinder include 10,000 journals, patents from 63 patent authorities, book chapters, conference proceedings, dissertations, evaluated reference works, technical reports, as well as book reviews and biographical information. (Structure and Reaction Searching)
Stanford University Libraries » Online resource » eResource
Search over 12,000 core journals across the sciences, social sciences, and arts and humanities to find the high quality research. Move backward/forward in time using cited/citing reference identified by researchers. Updated weekly, includes Science Citation Index Expanded (1899-present), Social Sciences Citation Index (1898-present), Arts & Humanities Citation Index (1975-present), Conference Proceedings Citation Index- Science (1990-present), Conference Proceedings Citation Index- Social Science & Humanities (1990-present), Book Citation Index (2005-present), Index Chemicus (1993-present), and Current Chemical Reactions (1985-present; also includes Institut National de la Propriete Industrielle structure data back to 1840)). (Structure searching)
Santa Fe, N.M.: Deep Web Technologies
Stanford University Libraries » Online resource » eResource
xSearch enables Stanford students and researchers to search multiple resources at one time.  The 250+ resources in xSearch include abstracts and indexes, full-text ejournal and ebook sites, patents, technical reports, reference materials, plus more.

Patent databases

[Philadelphia] : Institute for Scientific Informtion, [1999?]-
Stanford University Libraries » Online resource » eResource
"Using information from 41 patent-issuing authorities, DII facilitates rapid, precise patent searching, letting you conduct patent and citation searches of inventions in chemical, electrical, electronic, and mechanical engineering. Descriptive titles and indexing have been added. Find “equivalent” patents published in a language you can read. Also contains both citing and cited patents and literature references, allowing users to move both forward and backward in time from a selected patent. Updated weekly, covers 1963-present." (Structure Searching)
[Place of publication not identified] : European Patent Office.
Stanford University Libraries » Online resource » eResource
"Espacenet's worldwide database enables you to search for information about published patent applications from over 90 different countries and regions. Espacenet offers free access to more than 80 million patent documents worldwide--most of them patent applications rather than granted patents--from 1836 to today. Patent applications normally represent the first publication of a new idea, appearing ahead of journal articles and before new products reach the market. It is possible to print and download full-text documents."

Additional Databases

[New York?] : Thomson Reuters.
Stanford University Libraries » Online resource » eResource
Biosis is a comprehensive source for life sciences and biomedical research from nearly 6,000 life sciences journals plus abstracts from meetings, books and patents. Search options include using taxonomy, MeSH, CAS registry numbers, Sequence Databank Numbers, and Major Concepts. Updated weekly, covers 1926--present. Cited reference searching finds more recent works that cite an earlier document of interest
Bethesda, MD : National Center for Biotechnology Information, [1997]-
Stanford University Libraries » Online resource » eResource
"PubMed comprises over 22 million citations for biomedical literature from MEDLINE, life science journals, and online books. PubMed citations and abstracts include the fields of biomedicine and health, covering portions of the life sciences, behavioral sciences, chemical sciences, and bioengineering. PubMed also provides access to additional relevant web sites and links to the other NCBI molecular biology resources. PubMed is a free resource that is developed and maintained by the National Center for Biotechnology Information (NCBI), at the U.S. National Library of Medicine (NLM), located at the National Institutes of Health (NIH)."


Featured books

Use SearchWorks to find books in the library catalog.    Use xSearch to find book chapters.

Chemistry & ChemEng Library (Swain) » Reference » QD262 .S354 2014/5
Not available online yet in the Reference Library for Science of Synthesis.  We have vols 1-3 in print.
Cambridge : Royal Society of Chemistry, 2011.
Stanford University Libraries » Online resource » eResource
Weinheim : Wiley-VCH, c2008.
Chemistry & ChemEng Library (Swain) » Stacks » RM301.42 .M65 2008

New Books on Drug Design

New Books on Pharmaceutical Chemistry

  1. edited by Xijun Wang ; associate editors, Aihua Zhang, Hui Sun.. 2015

  2. Pierangelo Metrangolo, Giuseppe Resnati, editors ; with contributions by H. Ajani [and more].. 2015

  3. edited by Andrew Davis and Simon E. Ward. 2015

  4. edited by Brian Cox, Martin Gosling. 2015

  5. by Carmen Avendaño and J. Carlos Menéndez. 2015



Color atlases from Thieme

  1. Diethelm Wallwiener [and eight others].. 2015

  2. [edited by] Jamie Ullman, P.B. Raksin ; medical illustrator, Jennifer Pryll. 2015

  3. Werner Platzer ; illustrations by Gerhard Spitzer. 2015

  4. Helga Fritsch, Wolfgang Kuehnel. 2015


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