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Computer Resources for Organic Spectroscopy: Websites & Software for Organic Chem Students, Study notes of Chemistry

A list of computer resources for organic chemistry students, including spectroscopy databases, tutorials, problem sets, and drawing software. Most of these resources are free and accessible to students in chm 334. They offer various functionalities such as searching for spectra by name, formula, or physical properties, predicting nmr and ms data, and visualizing molecular structures in 2d and 3d.

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SpecComp Resources.doc Page 1 of 2 Last modified 8/26/08 3 :54 PM
CHM 334 Computer Resources for Organic Spectroscopy
This is a list of a few of the many computer resources that help organic chemists search for and
manage data on computers. Most of what is here is free and available to students in CHM 334.
Spectra Databases and Search Sites:
SDBS The National Institute of Advanced Industrual Science and Technology (Japan). A large
database of IR, MS and NMR spectra searchable by name, formula or spectral peak
http://riodb01.ibase.aist.go.jp/sdbs/cgi-bin/direct_frame_top.cgi
Colby College Organic Compounds Database A database of compound property and spectral
information that is searchable by many physical properties: mp, bp, refractive index, Mass Spec or
functional groups (from IR data)
www.colby.edu/chemistry/cmp/cmp.html
SigmaAldrich.com The largest supplier of chemicals. Many chemicals available in the online catalog
also have physical data as well as NMR and often IR spectra available in the listing.
www.sigmaaldrich.com/catalog/search/AdvancedSearchPage
NIST WebBook The National Institute of Standards and Technology has a database of thousands
of organic compounds including IR, UV/Vis, Mass Spec. You can search by name, formula or
molecular weight. http://webbook.nist.gov/chemistry/
ChemExper Chemical Directory Search by name, get IR spectra: www.chemexper.com
Spectroscopy Tutorials and Problem Sets:
CU Boulder Spec Problems: orgchem.colorado.edu/hndbksupport/spect.html
Organic Structure Elucidation Workbook spec problems from Notre Dame U. chemistry
www.nd.edu/~smithgrp/structure (sorry, no answers)
WebSpectra Good practice spec. problems. www.chem.ucla.edu/~webspectra/
Organic Chemistry OnLine Tutorial and good practice problems:
www.chem.uic.edu/web1/OCOL-II/WIN/SPEC.HTM
Spectral Animations Molecules and IR spectra. Click on an absorption band and see the
corresponding vibrational mode in the molecule (Windows only)
www.chem.umass.edu/~nermmw/Spectra/irspectra/index.htm
IR Tutor Great IR tutorial showing detailed IR assignments with animated vibrational modes. The
CD is distributed with the Solomons Organic Chemistry textbook (from CHM 227-8). Also installed in
the CHM334 directory on the Chem Library computers. Run it and explore.
Spectroscopic Tools NMR, IR, MS tutorial and peak look-up site
www.chem.uni-potsdam.de/tools/index.html
Pavia et al. Textbook website:
www.brookscole.com/chemistry_d/templates/student_resources/0030340632_gilbert/links.html
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CHM 334 Computer Resources for Organic Spectroscopy

This is a list of a few of the many computer resources that help organic chemists search for and manage data on computers. Most of what is here is free and available to students in CHM 334.

Spectra Databases and Search Sites:

SDBS The National Institute of Advanced Industrual Science and Technology (Japan). A large database of IR, MS and NMR spectra searchable by name, formula or spectral peak http://riodb01.ibase.aist.go.jp/sdbs/cgi-bin/direct_frame_top.cgi

Colby College Organic Compounds Database A database of compound property and spectral information that is searchable by many physical properties: mp, bp, refractive index, Mass Spec or functional groups (from IR data) www.colby.edu/chemistry/cmp/cmp.html

SigmaAldrich.com The largest supplier of chemicals. Many chemicals available in the online catalog also have physical data as well as NMR and often IR spectra available in the listing. www.sigmaaldrich.com/catalog/search/AdvancedSearchPage

NIST WebBook The National Institute of Standards and Technology has a database of thousands of organic compounds including IR, UV/Vis, Mass Spec. You can search by name, formula or molecular weight. http://webbook.nist.gov/chemistry/

ChemExper Chemical Directory Search by name, get IR spectra: www.chemexper.com

Spectroscopy Tutorials and Problem Sets:

CU Boulder Spec Problems: orgchem.colorado.edu/hndbksupport/spect.html

Organic Structure Elucidation Workbook spec problems from Notre Dame U. chemistry www.nd.edu/~smithgrp/structure (sorry, no answers)

WebSpectra Good practice spec. problems. www.chem.ucla.edu/~webspectra/

Organic Chemistry OnLine Tutorial and good practice problems: www.chem.uic.edu/web1/OCOL-II/WIN/SPEC.HTM

Spectral Animations Molecules and IR spectra. Click on an absorption band and see the corresponding vibrational mode in the molecule (Windows only) www.chem.umass.edu/~nermmw/Spectra/irspectra/index.htm

IR Tutor Great IR tutorial showing detailed IR assignments with animated vibrational modes. The CD is distributed with the Solomons Organic Chemistry textbook (from CHM 227-8). Also installed in the CHM334 directory on the Chem Library computers. Run it and explore.

Spectroscopic Tools NMR, IR, MS tutorial and peak look-up site www.chem.uni-potsdam.de/tools/index.html

Pavia et al. Textbook website: www.brookscole.com/chemistry_d/templates/student_resources/0030340632_gilbert/links.html

SpecCompResources.doc Page 2 of 2 Last modified 8/26/08 3:54 PM

DRAWING SOFTWARE: For drawing and viewing 2D and 3D molecular models.

ISIS/Draw A free program for drawing chemical structures (2D). Very useful if your handwriting is bad and your benzene rings look like gnomes with bad haircuts. Download (requires registration): www.mdl.com/downloads/downloadable or it is available on the Class server in the Chem Library.

ChemDraw The industry standard 2D chemical structure drawing program. It’s expensive, but it does a lot including converting names structure and structures names, stereochemistry, predicting proton and carbon NMR, Mass Spec data etc. Free Demo: www.cambridgesoft.com/software/ChemDraw/

Chime This is a plug-in which allows a WebBrowser to view chemical structures found on web sites. It can be installed on Windows computers from: www.umass.edu/microbio/chime/getchime.htm

Mercury This is a program available for many different computer types which allows visualization of 3D molecular models. If you find a file whose name ends in .pdb, .cif, .mol or .mol2, then Mercury will open it and let you spin the model around in space. www.ccdc.cam.ac.uk/products/csd_system/mercury

A FEW OTHER SITES:

WEB-sters’ Organic Chemistry A lot of O-chem links. Many defunct http://chemconnections.llnl.gov/Websters/spectroscopy.html

Organic Syntheses Online Complete online Organic Syntheses. Reliable organic preparations that have been checked independently and work on a large scale. www.orgsyn.org/

Protein Data Bank Web repository of protein crystal structures www.rcsb.org/pdb/

Organic Chemistry Resources Worldwide O-Chem stuff www.organicworldwide.net/

VSIRI Searchable MSDS database. For when you really need toxicity/hazard info for that chemical you just spilled and lit on fire… http://www2.hazard.com/msds/

The Carcinogenic Potency Database Any of your samples here? http://potency.berkeley.edu/cpdb.html

Ensembl Genome Site Explore your favorite genome www.ensembl.org/index.html

JCE Organic The Journal of Chemical Education Organic Chemistry page http://jchemed.chem.wisc.edu/JCEDLib/ChemInfo/Organic/

The Orbitron A gallery of atomic orbitals and molecular orbitals from U of Sheffield http://winter.group.shef.ac.uk/orbitron/

The Versatile Unit Converter www.mypage.bluewin.ch/berthod/vuc

If messing with organic molecules seems too much, try starting off with simpler models: www.antonraves.nl