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Organic Chemistry Laboratory

CHEM 130 - Fall 2014 - Instructor: Vollmer-Snarr, H.
Last Updated: 14-Sep-2014

Subject Librarians

Grace Baysinger
Head Librarian and Bibliographer of the Swain Chemistry and Chemical Engineering Library
(650) 725-1039
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Subjects

Lab safety

Safety Resources

[Hamilton, Ont. : Canadian Centre for Occupational Health and Safety, 1999?-
Stanford University Libraries » Online resource » (no call number)
CCOHS Web Information Service presents a collection of databases related to occupational health and safety: Material Safety Data Sheets, CHEMINFO (safety info for important workplace chemicals), CHEMpendium (metasearch for chemical hazard information from many sources), Registry of Toxic Effects of Chemical Substances, OSH References (index to literature), Canadian enviroOSH (indexes Canadian environmental and occupational safety legislation and standards).
Hoboken, N.J. : Wiley, c2010.
Chemistry & ChemEng Library (Swain) » Safety Collection (non-circulating) » QD51 .H55 2010
This book is uniquely designed to accompany students throughout their four-year undergraduate education and beyond, progressively teaching them the skills and knowledge they need to learn their science and stay safe while working in any lab.
8th ed. Hoboken, NJ : John Wiley, c2011.
Chemistry & ChemEng Library (Swain) » Stacks » QD261 .Z83 2011
Zubrick provides students with a valuable guide to the basic techniques of the Organic Chemistry lab. The book will help students understand and practice good lab safety. It will also help students become familiar with basic instrumentation, techniques and apparatus and help them master the latest techniques such as interpretation of infrared spectroscopy.
This book offers prudent practices designed to promote safety and includes practical information on assessing hazards, managing chemicals, disposing of wastes, and more. Prudent It serves as a leading source of chemical safety guidelines for people working with laboratory chemicals: research chemists, technicians, safety officers, educators, and students.
7th ed. Washington, D.C. : American Chemical Society, Joint Board-Council Committee on Chemical Safety, c2003.
Stanford University Libraries » Online resource » (no call number)
One of the most widely used laboratory safety guidance documents available today. Contents: v. 1. Accident prevention for college and university students. v. 2. Accident prevention for faculty and administrators.

The Safety Song

A musical extravaganza on the importance and execution of laboratory safety.

Properties quick search

Finding Properties/Spectra for Known Substance

  • (Str) = can search by chemical structure. 
Milwaukee, WI : Sigma-Aldrich
Chemistry & ChemEng Library (Swain) » Reference (non-circulating) » TP247 .A4 2012/2014
Catalog offering more than 40,000 research chemicals. Search by chemical name, molecular formula, CAS Registry Number, and by substructure. Information about a compound usually includes identification information, chemical structure, physical and chemical properties, as well as links to materials safety data sheets and to spectral diagrams. (Str)
[Bethesda, MD] : National Library of Medicine, 2000?-
Medical Library (Lane) » Check Medical Library (Lane) catalog for status » (no call number)
This database allows users to search the NLM ChemIDplus database of over 370,000 chemicals. A user may enter compound identifiers such as Chemical Name, CAS Registry Number, Molecular Formula, Classification Code, Locator Code, and Structure or Substructure. New searchable features include search and display by Toxicity indicators such as Median Lethal Dose (LD50), by Physical/Chemical Properties such as LogP, and by Molecular Weight. (Str)
CRC Handbook of Chemistry and Physics
Cleveland, Ohio, CRC Press.
Green Library » InfoCenter: Ready Reference (non-circulating) » QD65 .H3 95TH 2014/2015
Continues to be the most accurate, reliable and current resource available on data needed by chemists, physicists and engineers. It provides wide coverage of data on properties of inorganic and organic compounds. Some of the most heavily used tables were recently updated and expanded including: Physical Properties of Inorganic Compounds; Enthalpy of Fusion; Bond Dissociation Energies; Table of the Isotopes; Inorganic Ion and Ligand Nomenclature; Chemical Carcinogens; and Global Temperature Trends for the past 150 years.
Bethesda, Md. : National Library of Medicine, [199-]-
Stanford University Libraries » Online resource » (no call number)
Comprehensive, peer-reviewed toxicology data for about 5,000 chemicals. Broad scope in human and animal toxicity, safety and handling, environmental fate, and more.
Rahway, N.J. : Merck & Co., 1968-
Green Library » InfoCenter: Ready Reference (non-circulating) » RS356 .M524 2001
Contains 10,955 monographs describing significant chemicals, drugs, and biological substances. The information provided includes chemical, common and generic names, trademarks and their associated companies, Chemical Abstracts Service (CAS) Registry Numbers, molecular formulas and weights, physical and toxicity data, therapeutic and commercial uses, citations to the chemical, biomedical and patent literature, and chemical structures. (Str)
Japan : AIST
Stanford University Libraries » Online resource » (no call number)
SDBS has a new URL: SDBS is an integrated spectral database system for organic compounds,which includes 6 different types of spectra under a directory of the compounds. The six spectra are: an electron impact Mass spectrum (EI-MS), a Fourier transform infrared spectrum (FT-IR), a 1H nuclear magnetic resonance (NMR) spectrum, a 13C NMR spectrum, a laser Raman spectrum, and an electron spin resonance (ESR) spectrum. It is possible to search by compound name, molecular formula, molecular weight, CAS Registry Number, number of atoms, and spectral peaks. (Str)

Print spectral resources

Swain Reference Books on Spectra

Ed. 3. Milwaukee, Wis. (940 W. St. Paul Ave., Milwaukee 53233) : Aldrich Chemical Co., c1981.
Chemistry & ChemEng Library (Swain) » Reference (non-circulating) » QD96.I5 P67 1981
Includes more than 12,000 spectra classified by functional group and structural presentation.
Ed. 1. Milwaukee, Wis. : Aldrich Chemical Co., c1985-1989.
SAL3 (off-campus storage) » Stacks » QD96 .I5 P66 1985 F V.1
This three volume set includes over 18,000 spectra categorized by chemical functionality and arranged in order of increasing structural complexity.
Ed. 1 Milwaukee : Aldrich Chemical Co., c1993.
Chemistry & ChemEng Library (Swain) » Reference (non-circulating) » QC462.85 .A44 1993 F V.1
This three volume set of 12,000 high-resolution 75MHz 13C and 300MHz 1H FT-NMR spectra is arranged according to functionality.
Ed. 2. Milwaukee, Wis. (P.O. Box 355, Milwaukee 53201) : Aldrich Chemical Co., c1983.
Chemistry & ChemEng Library (Swain) » Reference (non-circulating) » QD96.N8 P68 1983 F V.1
A two volume set of more than 8,500 60MHz 1H NMR spectra.
3rd ed. Chichester ; New York : Wiley, 2001.
Chemistry & ChemEng Library (Swain) » Reference (non-circulating) » QC457 .S69 2001
This revised text but has been extended to meet the interpretive needs of Raman users as well as those working in the IR region. The result is a uniquely practical, comprehensive and detailed source for spectral interpretation. Combining in one volume, the correlation charts and tables for spectral interpretation for these two complementary techniques, this book will be of great benefit to those using or considering either technique.

Spectral Resources - Selected Textbooks

7th ed. / Hoboken, NJ : John Wiley & Sons, c2005.
Chemistry & ChemEng Library (Swain) » Stacks » QD272 .S6 S55 2005
First published over 40 years ago, this was the first text on the identification of organic compounds using spectroscopy. This text is now considered to be a classic. The key strength of this text is the extensive set of real-data problems (in Chapters 7 and 8). Even professional chemists use these spectra as reference data. Spectrometric Identification of Organic Compounds is written by and for organic chemists, and emphasizes the synergistic effect resulting from the interplay of the spectra. This book is characterized by its problem-solving approach with extensive reference charts and tables.
4., rev. and enl. ed. / Berlin ; Heidelberg : Springer. c2009.
Stanford University Libraries » Online resource » (no call number)
This fourth edition of the highly successful and concise textbook contains about 20 % new data. Now included are chapters on 19F and 31P NMR as well as references to important Raman bands. With their unique approach of presenting - in the form of texts, tables, charts, and graphs - a succinct compilation of essential reference data for the interpretation of NMR, IR, UV/Vis, and mass spectra, the authors also provide a hands-on guide for interpreting experimental spectral data and elucidating the structure of the respective compounds behind them.
8th ed. Hoboken, NJ : J. Wiley, c2004.
Chemistry & ChemEng Library (Swain) » Request at circulation desk » QD261 .S965 2004
Dedicated to qualitative organic chemistry, this book explains how to identify organic compounds through step-by-step instructions. Topics include elemental analysis, solubility, infrared, nuclear magnetic resonance and mass spectra; classification tests; and preparation of a derivative. Most directions for experiments are described in micro or mini scales. Discusses chromatography, distillations and the separation of mixtures. Questions and problems emphasize the skills required in identifying unknown samples.

Unknowns, syntheses, & reactions

Search Using Spectral Peaks

  • (Str) = can search by chemical structure
  • (Rxn) = can search by drawing chemical reaction
Japan : AIST
Stanford University Libraries » Online resource » (no call number)
SDBS has a new URL: SDBS includes 6 different types of spectra under a directory of the compounds. The six spectra are as follows, an electron impact Mass spectrum (EI-MS), a Fourier transform infrared spectrum (FT-IR), a 1H nuclear magnetic resonance (NMR) spectrum, a 13C NMR spectrum, a laser Raman spectrum, and an electron spin resonance (ESR) spectrum. It is possible to search by compound name, molecular formula, molecular weight, CAS Registry Number, number of atoms, and spectral peaks.
Web version 6.0. Boca Raton, FL : Chapman & Hall/CRC Press, c2002.
Stanford University Libraries » Online resource » (no call number)
POC is a database that contains over 30,000 of the most commonly sought organic compounds, featuring physical data, spectral data, and structures. With a high quality display and powerful search capabilities, it acts as an easy-to-use tool for identifying unknown compounds or for locating additional data and references for a known compound. Search by spectral peak, molecular formula/elements, properties, and substructure. Please download structure drawing plugin the first time you search POC. (Str)

Use Spectral Prediction Software

2.0. [Toronto, Canada] : ACD.
Stanford University Libraries » Online resource » (no call number)

The online ACD/I-lab prediction engine may be used to predict physicochemical properties, NMR spectra and chemical shifts and ADME toxicities. It also assesses prediction reliability and includes searchable content databases. (Str)

Find Key Literature References

The Dictionary of Organic Compounds includes key literature references to spectra, crystallography, synthesis, and review papers.

Locating full-text from references:

  • Enter reference into Citation Linker on the eJournals page to see if the full-text is available online
  • Search journal title in SearchWorks, Stanford Libraries Catalog, to see if the library has the print or online version
Boca Raton, FL : Chapman & Hall/CRC Press
Stanford University Libraries » Online resource » (no call number)

The Dictionary of Organic Compounds (DOC), part of CHEMnetBASE, contains chemical, structural, and bibliographic information on over 290,000 of the most important organic compounds. Data provided includes names and synonyms, formulae, chemical structures, CAS Registry numbers, physical properties, and key literature citations. Search by properties, molecular formula, and substructure.Data provided includes names and synonyms, formulae, chemical structures, CAS Registry numbers, physical properties, and key literature citations. Search by properties, molecular formula, and substructure. (Str)

Search the Two Largest Chemistry Databases

It is possible to search Reaxys and SciFinder by a chemical structure, reaction scheme, and bibliographic data.  Reaxys is the largest handbook of physical property data and includes links to articles that contain spectra.  SciFinder is the largest chemistry database and is compiling handbook type of information - properties and links to spectral diagrams - in the full display of chemical substance records.

[Frankfurt, Germany ; New York, NY] : Elsevier
Stanford University Libraries » Online resource » (no call number)

Reaxys Xcelerate is a fully integrated electronic chemistry database that contains organic, inorganic and organometallic substance, property, and reaction data for small molecules housed previously in the Beilstein, Gmelin, and Chemistry Patent databases. Includes coverage from 1771-present for 400 journals. Coverage also includes English language-only patents from the major chemistry patent classes of the U.S., European, and World Patent Offices. Reaxys Xcelerate is a premium version of Reaxys that allows faster analysis of results using visualization tools, automate synthesis planning, and use flexible reporting outputs for sharing their results and annotations with colleagues. (Str, Rxn)

[Columbus, Ohio : American Chemical Society, Chemical Abstracts Service]
Stanford University Libraries » Online resource » (no call number)

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 61 patent authorities, book chapters, conference proceedings, dissertations, evaluated reference works, technical reports, as well as book reviews and biographical information. (Str, Rxn)

Check Synthesis, Reaction, & Reference Materials

Frankfurt/ Main : Beilstein Institute, 1988.
SAL3 (off-campus storage) » Stacks » QD251 .B4 B44 1988

The Beilstein Dictionary (German/English) was compiled by the scientific staff of the Beilstein Institute to facilitate the use of Basic Series and Supplementary Series I to IV by those Handbook users whose native language is not German. With a total of about 2,100 entries, it contains most German words occurring in the Beilstein Handbook, as well as common abbreviations, alphabetically listed with their English equivalents.

Hoboken, N.J. : John Wiley, c2009.
Stanford University Libraries » Online resource » (no call number)

With its coverage of 701 organic name reactions and reagents, this online reference is the largest, most up-to-date work of its kind. It offers students and professional chemists a valuable resource for conducting experiments and performing a broad range of applications, from pharmaceuticals to plastics to pesticides. Each reaction listing is clearly organized into uniform sections that allow readers to quickly gather the information they need to conduct their own experimental procedures.

[New York] : John Wiley & Sons, c2001-
Stanford University Libraries » Online resource » (no call number)

e-EROS combines the complete text of the encyclopedia with the sophistication of a database including all the chemical reactions and structures. It contains a database of around 50,000 reactions and around 3250 of the most frequently consulted reagents and is fully searchable by structure and substructure, reagent, reaction type, experimental conditions, etc. and allows sophisticated full text searches. Offers systematic and exhaustive coverage of reagents used in organic synthesis. Kept up-to-date by regularly adding new reagents and catalysts, and by updating existing articles. The A to Z listing covers classical reagents, new "designer" reagents and catalysts. (Str)

New York : John Wiley & Sons, 1942-
Chemistry & ChemEng Library (Swain) » Reference (non-circulating) » QD251 .O7 V.84 2014

Currently containing over 140,000 reactions, Organic Reactions is a comprehensive collection of important synthetic reactions, together with a critical discussion of the reaction and tables that organize all published examples of the topic reactions. Chapters that focus on reactions of current interest are solicited by the board of editors from leading chemists worldwide. The publication process entails a comprehensive peer-review process, ensuring the high quality and attention to detail for which this series is noted. Comprehensive coverage of all examples of a given reaction is provided in tabular form. In addition to providing reaction scope, stereochemical aspects, and side reactions, a selection of representative experimental conditions are given. Online access covers Vol. 25, 1977-present. (Str)

New York : John Wiley & Sons, Inc., 1921-
Chemistry & ChemEng Library (Swain) » Reference (non-circulating) » QD262 .O723 V.90 2013

Collective Vols in Swain Reference QD262
Organic Syntheses describes checked and edited experimental procedures, spanning a broad range of synthetic methodologies, and provides chemists with a compendium of new or little known experimental procedures which lead to useful compounds or that illustrate important new developments in methodology. For every procedure, safety warnings are presented along with detailed descriptions for the preparation, purification, and identification of the compound in question. Additionally, special reaction conditions are detailed, along with the source of reagents, helpful waste disposal guidelines, discussions of results, references to the primary literature, and an appendix of nomenclature and registry numbers. The print version was published in Annual volumes and Collective Volumes. Online access covers, Vol. 1, 1921-present. (Str)

7th ed. Weinheim, Germany : Wiley-VCH ; New York : J. Wiley & Sons, 2009-
Stanford University Libraries » Online resource » (no call number)

This state-of-the-art reference work details the science and technology in all areas of industrial chemistry. Subject areas include: inorganic and organic chemicals, advanced materials, pharmaceuticals, polymers and plastics, metals and alloys, biotechnology and biotechnological products, food chemistry, process engineering and unit operations, analytical methods, environmental protection, etc.

Software

Prediction Software on the Web

2.0. [Toronto, Canada] : ACD.
Stanford University Libraries » Online resource » (no call number)
The online ACD/I-lab prediction engine may be used to predict physicochemical properties, NMR spectra and chemical shifts and ADME toxicities. It also assesses prediction reliability and includes searchable content databases.  Also see: iLab Flyer

Desktop Software

  • Access software from a cluster computer (in libraries, residence halls, academic computing areas)
  • Use software via website and Citrix plugin.  Go to http://cdserver.stanford.edu  Login with SUNet ID and open Chemistry folder
  • Install software on your computer. 
Cambridge, MA : CambridgeSoft
Stanford University Libraries » Online resource » (no call number)
Stanford has campus-wide site license to ChemBioOffice Ultra for Windows and ChemBioDraw Ultra for Macs. A tutorial on how to draw substances and how to do spectral predictions using ChemBioDraw Ultra is on the Sample Searches & Tutorials page of this guide for Chem 130 students. More documentation and training materials are also available. Please note: Access to training materials are limited to current students, faculty, and staff at Stanford.

Instructions to Download & Install ChemBioDraw Ultra

1. Account Verification: go to http://sitelicense.cambridgesoft.com/sitelicense.cfm?sid=188 and enter Stanford domain email address. 

2.  Create Account/login to CambridgeSoft website and then view "Services" on middle right side of page.

    a. Download software: click on "My Site License"

    b. Get Registration Code: click on "My Downloads."  (Please contact Grace Baysinger (graceb@stanford.edu) if you do not see a Registration Code.)

3.  Copy and paste Registration Code and activate software during installation process.

Step-by-Step Instructions Plus Screenshots on How to Download and Install ChemBioDraw Ultra

Downloading and Installing ChemBioOffice Ultra

Sample searches & tutorials

Help for Finding Properties of a Known Substance

Finding Physical Properties and Spectral Diagrams for a Known Chemical Substance - Sample Search

Help for Identifying Unknowns

Overview of Tasks and Resources for Identifying Unknowns
Chem 130 Lecture Outline for Identifying Unknowns
1. Simplified Flow Chart for Chem 130 Students
2. Converting Lab Data to Search Strategies
2a. Converting Lab Data to Search Strategies - Worksheet
3a. Sample Search - SDBS
3b. Sample Search - POC
3c. Sample Search - Reaxys
3d. Sample Search - SciFinder

Help for Identifying Unknowns continued

Appendix A. Types of Searches Grouped by Name of Resource
Appendix B. Types of Searches Grouped by Physical Properties, Spectra, and Chemical Reactions
Appendix C. Displaying Results - Information Available in a Resource
Appendix D. Troubleshooting

Tutorials

SDBS Tutorial
Properties of Organic Compounds Tutorial
ACD Labs NMR Prediction Software Tutorial
ChemBioDraw Ultra Tutorial - revised Winter 2013
Dictionary of Organic Compunds Tutorial
Reaxys Tutorial

Lab reports

3rd ed. / Washington, DC : American Chemical Society ; Oxford ; New York : Oxford University Press, 2006.
Chemistry & ChemEng Library (Swain) » Request 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)