Saturday, December 1, 2007

Clearinghouse for Chemical Information Instructional Materials

1 Major Tools or Databases
2 How and Where to Start
3 How and Where to Search: General
4 How and Where to Search: Specialized
5 Communicating in Chemistry
6 Miscellaneous

Major Tools or Databases
Chemical Abstracts and STN
Science Citation Index and Web of Knowledge
Beilstein Handbook of Organic Chemistry
Gmelin Handbook of Inorganic and Organometallic Chemistry
Landolt-Boernstein Numerical Data and Functional Relationships in Science and Technology
Cambridge Structural Database

How and Where to Start
Chemistry Guides
Current Awareness, Background Reading, and Document Delivery

How and Where to Search: General
Chemical Author or Corporate Name Searching
Chemical Subject Searching
Chemical Name and Formula Searching Aids
Chemical Structure Searching

How and Where to Search: Specialized
Chemical Synthesis or Reactions
Chemical Safety or Toxicology Information
Analytical Chemistry (Constitutional Chemistry)
Physical Property Searching
Chemical Patent Searching Aids
Cheminformatics Teaching Materials

Communicating in Chemistry
General Information about Chemical Publications or Databases
Chemical Nomenclature
Science Writing Tutorials and Courses

History, Biography, Directories, Chemical Industry Sources
How to Teach Chemical Information
Chemical Information Course Syllabi
Chemical Information Problem Sets and Exercises
Examinations for Chemical Information Courses

This page was originally created by Gary Wiggins. If you have a legitimate desire to contribute to its contents, please request an account from the sysop, Dr. David J. Wild, by e-mailing him at djwild @


CRSD: Chemical Reference Sources Database

CRSD is a Microsoft Access database, available on the World Wide Web. It contains some 2500 records of books and other reference material mostly in the [Indiana University] Chemistry Library. It is useful for finding reference material by subject when a search in [Indiana University OPAC] IUCAT is unsuccessful.

Keywords have been added to the records for better retrieval. Each record contains full information about the printed work, database, software or other item, and call number if available in the [Indiana University] Chemistry Library.


By Author/Editor
By Title
By Keyword(s)


Last updated 3/9/05 AL
Copyright 1997, The Trustees of Indiana University

Chemistry Databases on the Web (Classified List)

General (All Types of Compounds)
2D Structure Searchable
Specific Classes of Compounds
Drug-Related Databases
Disease-Related Databases
Physical Properties, Spectra, etc.
Spectral and Separations
Toxicity and Environmental Databases
Biomolecule Databases
Metabolic Pathways
Web Services-Enabled Bioscience DBs
Finding Others

Copyright 2007, The Trustees of Indiana University


SIRCh: Selected Internet Resources for Chemistry

SIRCh: Selected Internet Resources for Chemistry
1 How and Where to Start
2 How and Where to Search: General
3 How and Where to Search: Specialized Sources
4 Communication in Chemistry
5 Miscellaneous

How and Where to Start
The Publication Process
Guides to Chemical Information Sources and Databases
General Information on Computer Searching
Current Awareness, Reviews, and Document Delivery
Background Reading: Dictionaries, Encyclopedias, and Other Books

How and Where to Search: General
Chemistry Databases on the Web (Alphabetical List)
Chemistry Databases on the Web (Classified List)
Searching by Author or Organization Name and by Known Citations
Searching by Subject
Chemical Name and Formula Searching
Structure Searching

How and Where to Search: Specialized Sources
Searching for Synthesis or Reaction Information
Chemical Safety and Toxicology
Analytical Chemistry
Physical Property Information
Chemical Patent Searching

Communication in Chemistry
Chemistry Newsgroups, Discussion Lists, and Blogs
Molecular Visualization Tools and Sites
Science Writing Aids

Chemical History, Biography, Directories, and Industry Sources
Teaching and Study of Chemistry
Chemistry Courses on the Internet
Careers in Chemistry
Cheminformatics (aka, Chemoinformatics or Chemiinformatics)

This page was originally created by Gary Wiggins. If you have a legitimate desire to contribute to its contents, please request an account from the sysop, Dr. David J. Wild, by e-mailing him at djwild @


Saturday, October 20, 2007

PubChem: A Public Chemical Portal

PubChem provides information on the biological activities of small molecules. PubChem includes substance information, compound structures, and bioactivity data in three primary databases, PCSubstance, PCCompound, and PCBioAssay, respectively.

PubChem Substance: Search deposited chemical substance records using names, synonyms or keywords. Links to biological property information and depositor web sites are provided. The PubChem substance database contains chemical structures, synonyms, registration IDs, description, related ... [Web sites], database cross-reference links to PubMed, protein 3D structures, and biological screening results. If the contents of a chemical sample are known, the description includes links to PubChem Compound.

PubChem Compound: Search unique chemical structures using names, synonyms or keywords. Links to available biological property information are provided for each compound. The PubChem Compound Database contains validated chemical depiction information that is provided to describe substances in PubChem Substance. Structures stored within PubChem Compound are pre-clustered and cross-referenced by identity and similarity groups. Additionally, calculated properties and descriptors are available for searching and filtering of chemical structures.Users can perform a term/keyword search in a same manner as for substance database. In addition, the PubChem compound database also provides a chemical property search.

PubChem BioAssay: Search bioassay records using terms from the bioassay description, for example "cancer cell line". Links to active compounds and bioassay results are provided. The PubChem BioAssay Database contains bioactivity screens of chemical substances described in PubChem Substance. It provides searchable descriptions of each bioassay, including descriptions of the conditions and readouts specific to a screening protocol.

Structure Search: Search PubChem's Compound database using a chemical structure as the query. PubChem Structure Search allows PubChem Compound Database to be queried using a chemical structure. Chemical structure queries may be sketched using the PubChem Sketcher. You may also specify the structural query input by PubChem Compound Identifier (CID), SMILES, SMARTS, InChI, Molecular Formula, or by upload of a supported structure file format.

The Substance/Compound database, where possible, provides links to bioassay description, literature, references, and assay data points. The BioAssay database also includes links back to the Substance/Compound database.

PubChem Help
This document provides tips and examples for searches of the three PubChem databases by text term/keyword, as well as tips for searching PubChem Compound by chemical properties.


PubChem is integrated with Entrez, NCBI's primary search engine, and also provides compound neighboring, sub/superstructure, similarity structure, bioactivity data, and other searching features.

PubChem is a component of NIH's Molecular Libraries Roadmap Initiative.

Thursday, October 18, 2007

Gerry McKiernan, Science and Technology Librarian

Gerry McKiernan
Science and Technology Librarian
152 Parks Library

515- 294-9886

Gerry McKiernan, Associate Professor and Science and Technology Librarian, currently has primary responsibilities for Instruction, Reference and Research Services and Collection Development in Chemical and Biological Engineering; Civil, Contruction, and Environmental Engineering; Environment Sciences; Industrial and Manufacturing Systems Engineering; and Mechanical Engineering.

He currently serves as a member of the editorial board and columnist for Science & Technology Libraries (Haworth) and has served as a contributing editor for Library Hi Tech News and the Journal of Internet Cataloging (Haworth). He has been a member of the editorial board of The Serials Librarian (Haworth) since Fall 2002.

He has delivered numerous presentations for local, state, national, and international conferences, programs, and workshops. These include meetings of the American Library Association, the Michigan Library Association, and the North American Serials Interest Group (NASIG); an Open Forum on Metadata Registries, WiLSWorld; as well as Internet Librarian 2003 and the Workshop on Peer Review in the Age of Open Archives (Trieste, Italy).

In 2005, McKiernan gave invited presentations at Digital Libraries à la Carte: Choices for the Future at Tilburg University, The Netherlands; and at The Role of Open Access Publishing in Science, the preconference held prior to Globalization of Information: Agriculture at the Crossroads, the XIth IAALD World Congress/USAIN Biennial Conference 2005, Lexington, Kentucky. 2005, McKiernan has also given selected presentations at the 12th ACRL National Conference, Minneapolis, Minnesota; and at the LITA National Forum 2005, San Jose, California, and the LITA National Forum 2007, Denver, Colorado.

McKiernan has been employed by the Iowa State University Library since April 1987. Prior to joining ISU, McKiernan has served as the Museum Librarian at the Carnegie Museum of Natural History, Pittsburgh, and as an Assistant Librarian with the Library of the New York Botanical Garden in the Bronx, his home town.

He received his Masters of Science degree in Library Science from the University of Illinois-Urbana-Champaign in 1975 and his undergraduate degree in Anthropology from Lehman College of the City University of New York, The Bronx.

McKiernan currently maintains several blogs relating to alternative energy, notably The Bioeconomy Blog [] and The Bioenergy Blog [].

In addition, he maintains Friends, a blog devoted to"social networking sites for engaged library services" []

McKiernan and his wife of 26 years, Karen M. Anglin, are the parents of three daughters, Kate, Kristen, and Beth, and live in Ames, Iowa.

Women in Chemistry Oral History Project

Women in Chemistry Oral History Project, MS-650, Archives of Women in Science and Engineering, Special Collections Department, Iowa State University Library.

The Archives of Women in Science and Engineering (Iowa State University Library) is sponsoring an oral history project focused on women who have devoted their careers to the study of chemistry in the post World War II era. The project, funded by the ISU Library, the Camille and Henry Dreyfus Foundation, and private donors, will document the careers and experiences of women in chemistry and chemical engineering to illustrate the critical role of women in science.

Collection description

This collection, organized alphabetically by name, contains biographical information, photographs, published material, and oral history interview transcripts. Some transcripts are unavailable due to their being revised. Additional transcripts will be added continuously.

The master audio cassettes of each interview are restricted. Reference copies are available for researchers ... .

List of interviewees available

CHEMnetBASE: A Database of Full-Text Chemistry Handbooks

CHEMnetBase includes descriptive and numerical data on chemical, physical and biological properties of compounds; systematic and common names of compounds; literature references; structure diagrams and their associated connection tables.


CHEMnetBase includes:

  • Combined Chemical Dictionary (CCD)

    • Dictionary of Commonly Cited Compounds

    • Dictionary of Drugs (Formerly Pharmasource).

    • Dictionary of Inorganic and Organometallic Compounds

    • Dictionary of Natural Products

    • Dictionary of Organic Compounds

  • Handbook of Chemistry & Physics

  • Polymers: A Property Database

  • Properties of Organic Compounds

  • CRCPress Periodic Table Online

  • The Dictionaries available in the Combined Chemical Dictionary can be searched individually or concurrently with all other dictionaries.

    The Combined Chemical Dictionary database contains data for more than 500,000 substances.

    In general, CCD contains the following compounds:

  • The basic fundamental organic and inorganic compounds of simple structure, including the elements, inorganic binary and ternary compounds (hydrides, halides, oxides, sulfides).

  • Comprehensive coverage of virtually every known natural product including those of unknown structure.

  • All currently marketed drugs, including all those listed in generic name compilations (US Adopted Names, International Nonproprietary Names, British Approved Names, Japanese Accepted Names), as well as those undergoing clinical trials.

  • Compounds with an established use such as catalysts, solvents, starting materials, synthetic reagents, analytical reagents.

  • Important coordination compounds, e.g. amines, phosphines, alkoxy complexes, and major well-characterised bioinorganics.

  • Organometallic compounds representative of all important structural types

  • Important biochemicals and minerals.

  • Other compounds of particular interest because of their chemical, structural or biological properties, including many newly synthesised compounds of active research interest.

  • []

    Searching each CHEMnetBase resource is Free-Of-Charge. One can browse, perform searches and view search hitlists.

    A current subscription is required to view andor print full entries.

    CHEMnetBASE is only available to multi-user organizations on a site license basis; it is not available for individual subscription.


    Friday, September 28, 2007

    Kenneth R. Jolls: Professor, Chemical and Biological Engineering

    Kenneth R. Jolls
    ProfessorChemical and Biological Engineering
    2155 Sweeney Hall
    Iowa State University
    Ames, IA 50011

    Phone (515)294-5222
    Fax (515)294-2689


    A.B., Music, Duke University, 1958
    B.S., ChE, North Carolina State University, 1961
    M.S., ChE, University of Illinois, 1963
    Ph.D. ,ChE, University of Illinois, 1966

    Research Interests

    Visualizing computer-based analyses through high-performance graphics holds great promise for chemical engineering research, practice, and teaching. Visual thinking utilizes powerful intellectual pathways that have traditionally been underused by scientists and engineers. Many branches of chemical engineering analysis possess visualizable components - concepts dealing with structures, stresses, fields, and phases. Computer simulation in these areas yields results that are often more readily interpreted visually - through static or dynamic views of carefully conceived structures. My students and I are endeavoring to exploit these visual techniques as they apply to the fields of chemical thermodynamics and separations.

    Research Projects

    Scientific Visualization: A New Way to Teach Old Subjects
    No tool since the hand calculator has offered more pedagogical promise than computer visualization. With today's visually oriented students, there is a need for both teaching and research methods that give more emphasis to visual thinking. Chemical thermodynamics is a natural focus for these techniques because of the geometry-based models in its origin.

    Computer graphics is being used to model a variety of fundamental and state equations, data tabulations, and reaction equilibrium functions of interest to chemical engineers. One product of this research is the "Equations of State" program, an interactive teaching package for visualizing PVT surfaces and process thermodynamic paths. "Equations of State" is in use at 50 institutions worldwide and was cited in a national software competition.

    Interpreting Thermodynamic Stability and Phase Equilibrium through High-Performance Computer Graphics
    The fundamental-equation models of J. W. Gibbs are partitioned on the basis of thermodynamic stability. Criticality and phase-change are associated with this partitioning, and for fluid phases they are predictable from continuous equations of state. Stability limits in various systems are hierarchical with respect to the number of species present. Each added component imposes a new and more restrictive stability limit, and this ranking reveals itself in the topography of appropriately chosen property models.

    Work has been done to produce three-dimensional images of these structures and to show this hierarchical behavior visually. Pure-fluid models based on properties from the Peng-Robinson equation have been drawn using standard solid-modeling software, and Gibbs' tangent methods for predicting coexistence have been demonstrated.

    Creating such models for mixtures requires that one or more variables be fixed in order to yield plottable, three-dimensional figures. Isothermal A-V-x and isobaric H-S-x surfaces (for binaries) and isothermal-isobaric surfaces for ternaries are among the structures being studied. Future work will involve more complex mixtures that show liquid-liquid separation also.

    A collection of Gibbs models is available at []

    Simulation Graphics
    Software has been developed to produce graphical displays from the results of computer-modeled separations. Data from FLOWTRAN-simulated processes of absorption, distillation, and extraction are displayed in traditional stagewise formats and in other configurations that show equilibrium conditions and material and energy balances. Visualizing these operations through computer graphics provides rapid access to the results of a design and can speed both the learning and redesign processes. Current research is aimed at improving the user interface and extending the technique to other process simulators and to other display systems.

    Visualizing Thermophysical Properties from a Process Simulator
    Modern process simulators contain routines for calculating the wide variety of thermodynamic and physical properties needed for chemical process design. The ASPEN PLUS simulator offers many models for these determinations and is a rich source of data for the construction of thermodynamic diagrams.

    We are using ASPEN PLUS to generate fluid-phase equilibrium data for multicomponent systems in VLE and LLE ranges, including binary, ternary, and quaternary mixtures, with and without azeotropes. The data are used with OPEN INVENTOR rendering software on a Silicon Graphics IRIS workstation to produce fixed and movable phase diagrams. Single data sets are the basis for the original "Phase" program (reviewed by Science magazine, see above) and for a more recent version for PCs developed by Professor Walter Chapman at Rice University. Multiple data sets are the basis for a new program, "Animate," that uses B-splines to permit continuous scanning of VLE functions throughout the fourth and fifth dimensions.

    Computer Visualization of Heat and Mass Transfer
    Images of simulated flowfields involving heat and mass transfer are being assembled into presentations suitable for classroom use. Finite-element software is being used to provide pictorial representations of common transport situations usually treated through theory alone.

    Selected Recent Publications

    "Engineering, Entropy, and Art: A Tour Through the Thermodynamics of J. Willard Gibbs," Invited paper at a Symposium, Rethinking Theories and Practices of Imaging: Technology, Representation and Disciplines, Rochester Institute of Technology, April 16, 2004.

    with E. W. Cochran and P. Miller, IV, "Visualizing Hyperdimensional Functions Using NURBS: 'Animate' Software -- Thermodynamic Phase Diagrams for Mixtures," Symposium on Modern Computing, Ames, Iowa, November 1, 2003.

    "Righting What's Left," ASEE PRISM Online, Web Extra, September 2001.

    "Scientific Visualization for Teaching Chemical Thermodynamics," Proceedings, Conference of the International Visual Literacy Association, Ames, Iowa, October 2000.

    with J. S. Berger, "A View from the Right Hemisphere," Proceedings, Annual AIChE Meeting, Dallas, Texas, November 1999.

    with K. S. Tian, "Fluid-phase Equilibria from a Chemical Process Simulator," ASEE Annual Conference, Milwaukee, Wisconsin, June 15-18, 1997, session 2513.

    "Visualization in Classical Thermodynamics," Proceedings, Annual Meeting of the Accreditation Board for Engineering and Technology, San Diego, California, October 1996.

    Review of Envisioning Information, by E. R. Tufte, AIChE Journal 39(2):367 (1993).

    with M. C. Schmitz, and D. C. Coy, "Seeing is Believing: A New Look at an Old Subject," The Chemical Engineer, No. 497, May 30, 1991, p. 42.

    "Gibbs and the art of thermodynamics," Proceedings of the Gibbs Symposium (Yale University), G. D. Mostow and D. G. Caldi (eds.), Amer. Math. Soc., 293 (1990).

    International Experience

    Representative for the ISU Chemical Engineering Department's Foreign Study Program at the University of Oviedo, Spain.

    Honors and Awards

    "Thermodynamics through the Eyes of a Musician," Profile article, Chemical Engineering Progress, Sept. 2005, p. 100.

    Eyestone Distinguished Lecturer, College of Engineering, Kansas State University, 2005

    Consultant to the United States Postal Service for the design of a 2005 postage stamp honoring J. Willard Gibbs [College of Engineering Feature]
    Faculty Citation, Iowa State University Alumni Association, October 2000

    Original software "Phase" reviewed by Science magazine: "An Eye for the Abstract," October 15, 1999, page 430

    Responsible Care National Catalyst Award, Chemical Manufacturers Association, 1996

    CACHE Award for the use of computers for teaching, American Society for Engineering Education 1996

    Featured Educator, biographical article in Chemical Engineering Education, 28:1 (Winter 1994)

    Award for Outstanding Engineering Software, Zenith Masters of Innovation II Competition, 1990

    Excellence in Teaching Award, Iowa State University, 1989

    Cited for accomplishment in computer graphics, MOVIE.BYU Image Contest, 1989

    Superior Engineering Teacher Award, Iowa State University, September 1978.

    Other Information

    Kenneth Jolls was director of the Research Instrumentation Laboratory at the Polytechnic Institute of Brooklyn in New York City, 1966-1970. He taught evening and extension courses in applied electronics for non-EE scientists. During the summers of 1969 and 1970 these courses were given as College Teacher Programs with support from the National Science Foundation.

    The "Phase" software has been re-released under the name "ThermoGraphics" in a collaboration with Professor Walter Chapman, Dept. of Chemical Engineering, Rice University. It was a runner-up in the year 2000 competition for Premier Engineering Courseware sponsored by NEEDS, National Engineering Education Delivery System.



    Kenneth Jolls is a part-time professional musician. He is a jazz vibraphone player with experience in arranging and conducting as well as performing. His first degree (Duke University, 1958) was in music.

    Attended music school under Band Service Scholarship at Indiana University and graduated with an AB degree in music (theory) from Duke (1958). Experience in arranging for marching band and dance band both at Indiana and Duke. Leader of the Duke Ambassadors dance orchestra, 1957-58, and toured abroad with that organization.
    Leader of the "Quarter Notes" combo that won the North Carolina Collegiate Jazz Festival, Chapel Hill, NC, spring 1956 (cited in Metronome magazine).

    University Carillonneur, Duke University, Durham, NC, 1956-59. Studied with Anton Brees.
    Played for Bob Hope, Road Show, University of Illinois, 1964.
    Percussionist for the Iowa State University Symphony Orchestra, 1972-77.
    Played in stage bands for Sonny and Cher and for Helen Reddy, road concerts at Iowa State University, 1973-74.
    Marimba soloist with the Iowa State University Wind Ensemble, February 1976.
    Featured vibraphone soloist with the Drake University Percussion Ensemble, Des Moines, IA, December 1977.

    Conducted the orchestras for the Union Board Theater productions of "Hair" and "Jesus Christ Superstar," VEISHEA, Iowa State University, 1978, 1980.
    Occasional percussionist with the Des Moines Symphony, 1975-1980.
    Jazz recitals in Berkeley, CA; Chicago, IL; Ames, IA; and New Orleans, LA, and at the Universities of Delaware and West Virginia, 1982-present.
    Hosted visits to Iowa State University by Gary Burton (March 1987) and Marian McPartland (February 1991).
    Performed for members of the Baltimore Symphony (March 1990), the Philadelphia Orchestra (May 1990), and the Leningrad Philharmonic (October 1990), in post-concert sessions sponsored by the Ames International Orchestra Festival Association.
    Cited as an outstanding carillonneur (at Duke University) in a letter to the editor by Richard Cummings, Smithsonian magazine, January 1995.

    Orchestra conductor, Stars Over VEISHEA production of "Bye Bye Birdie," C. Y. Stephens Auditorium, Iowa State University, April 1997.
    Lecture/demonstration on the jazz photographs of William Gottlieb, "Arts at Lunch," The Octagon, Ames, Iowa, December 10, 1999. Also in "Jazz Greats," The Tribune, Ames, Iowa, December 18, 1999, D1.
    Soloist in the Monday Celebrity Series, ISU Department of Music, April 29, 2002, April 28, 2003.
    "Good Vibrations" at the Cornelia Street Cafe, Greenwich Village, New York City, Jan. 5, 2003.

    Soloist with the Kansas State University jazz group under the direction of Prof. Wayne Goins, Manhattan, KS, April 2005.


    Thursday, September 27, 2007

    eMolecules: Open-Access Chemical Structure Search Engine

    eMolecules is the world's leading Open-access Chemical Structure Search Engine. [Its] ... mission is to discover, curate, and index all of the world’s public chemical information and make it globally available. Headquartered in San Diego, California, eMolecules has ... become the world's largest and most popular chemical structure search engine, distinguished by fast results, ease of use, and extensive reference information."

    eMolecules provides

    Ability to search by drawing chemical structures or substructures using common industry tools — ISIS/Draw, ChemDraw, ChemSketch and JME

    Access to more than 6 million chemical structures

    Chemical data from more than 140 suppliers, with regular updates

    Information about 3 million commercially available screening compounds and hundreds of thousands of building blocks and intermediates
    Online price quotes from select chemical suppliers

    links to public data for spectra, physical properties and biological data, notably the NIST WebBook, DrugBank, and PubChem


    Monday, September 24, 2007

    Biographical Snapshots of Famous Women and Minority Chemists

    The primary objective of this Only@JCE Online column is to provide information about chemists who have made important contributions to chemistry. A short biographical "snapshot" of each chemist provides basic information about the person's chemical work, gender, ethnicity, and cultural background.

    Latest Additions (July 2005)

    Complete Listing is Available at


    Barbara A. Burke / Chemistry Department / California State Polytechnic University, Pomona / 3801 West Temple Avenue / Pomona, CA 91768 / (Phone) 909-869-3664 / 909-869-4616 (FAX)



    Saturday, September 22, 2007

    National Chemistry Week Facebook Group

    The National Chemistry Week Facebook Group is intended to serve as a forum in which interested individuals can contribute and discuss activities related to the celebration.


    This is an ad hoc group and is not formally affiliated with the American Chemical Society or its Office of Community Activities.

    The Facebook Group is an Global Group and Is Open To All.

    Launch of the National Chemistry Week Blog

    • The National Chemistry Week blog was formally established on September 22 2007.

      "National Chemistry Week (NCW) is a community-based program of the Office of Community Activities. This annual event unites ... American Chemistry Society local section[s], businesses, schools, and individuals in communicating the importance of chemistry to our quality of life."

      The theme for National Chemisty Week in 2007 is "The Many Faces of Chemistry" and will serve as a framework for blog postings. In 2007, National Chemistry Week will be celebrated October 21-27.[]

      Over the coming weeks, there will be a variety of postings relating to
      • Biosketches of notable Iowa State University Chem/ChemE/MatSci/FoodSci/Biochem/Etc. faculty
      • Chemistry-related databases
      • Highlights of Special Collections chemistry-related resources
      • Major chemistry-related publishers/journals
      • Major professional chemistry-related association and societies
      • Profiles of ISU Science and Technology Librarians and their respective chemistry-related responsibilities
      • SciFinder Scholar