CH255J Homepage


Texts: Timothy D. W. Claridge, High-Resolution NMR Techniques in Organic Chemistry, 2nd. Ed., Pergamon, Oxford, 2009.
D. L. Pavia, G. M. Lampman, G. S. Kriz, Jr., Introduction to Spectroscopy: A Guide for Students of Organic Chemistry, 3rd. Ed., W. B. Saunders, Philadelphia, PA, 2001.
Syllabus


NMR Spectroscopy

JCAMP NMR and IR Spectral Display

1H Chemical Shift Prediction Substituent Constant Approach for Proton Chemical Shifts.

13C Chemical Shift Prediction Substituent Constant Approach for Proton Chemical Shifts.

Vicinal Spin-Spin Coupling Constant Prediction Altona-style Equations for 1H-1H 3J constants in alkanes (sp3-sp3) .

Vinyllic and Allylic Spin-Spin Coupling Constant Prediction Karplus-style Equations for 1H-1H 3J vinyl and 4J allylic constants in alkenes (sp2-sp3) .

JMM: 1st Order Multiplet Maker for spin-spin splitting multiplets (or, JMM: alternate version without frames or J estimation)

JJ: 1st Order Spin-Spin Multiplet Deconvolution for determining the J coupling constants from 1H NMR spin-spin splitting multiplets (under development)

Deconvolve: NMR Spectral Deconvolution and Peak Picking for automatic peak picking based on Fourier Transform spectral deconvolution. This applet is useful for creating the peak list for JJ based spin-spin multiplet deconvolution, above.

JD: Spin-Spin Splitting Simulation for up to six spins. [Old Java plotting version: JD(Java required) ]

Exchange: Chemical Exchange Lineshape Simulation for 2 site exchange (uses Java for plotting). If you don't want to use the Java dependent version use Exchange(Netscape) or Exchange(IE) for Internet Explorer.

Mass Spectrometry

Fragment Finder finds the possible formulas that match a given molar mass. Then the M+1 and M+2 ratios and the exact masses of each of the possible fragments is calculated.
Formula Finder finds the possible formulas that match a given molar mass and several fragments. Then the M+1 and M+2 ratios and the exact masses of each of the possible fragments is calculated.
Molar Mass Finder guesses possible molecular ion masses if your spectrum might not have a molecular ion peak. If you have the tabulated peak list as a text file from an HP ChemStation on a disk, you can download the peak list into the MolarMass applet.
Isotope Cluster calculates the isotope pattern for a given molecular formula. It includes 3rd and 4th period representative and transition metal elements.
Molar Mass calculates the molar mass and isotope pattern for a given molecule specified in Smiles format.
Tripeptide Mass Finder searchs for di- or tripeptide ions that match a given mass.
Peptide Mass Finder calculates the masses of ions for a given peptide sequence. You can also plot the isotope cluster for the ion. This applet allows for stable isotope substitution for an amino acid with variable composition for the normal and substituted form.
Solvent Cluster Ion Finder finds the formula for solvent cluster ions for the background in electrospray ionization MS.
Metal Complex Finder finds the formula for an inorganic complex.
Pentaoligonucleotide Mass Finder searchs for di- to penta- oligonucleotide ions that match a given mass to charge, m/z.
Cross-linker Finds all possible cross links, digests the proteins, and lists the monoisotopic mass of each cross-linked peptide.

Infra-Red Spectroscopy

IR Helper is a step-by-step tutorial on the interpretation of Infra-Red spectra. IR Helper is available in two versions:
IR Helper, Internet Explorer version

These are new versions. If you have problems with the new versions please e-mail twshattu@colby.edu.

Units Conversions

Here is an energy conversion application that you will find helpful, especially for converting Hartrees and eV to kJ/mol and Boltzman population ratios.

3D-Molecule Builders and Molecular Structure Calculations

Build the 3D-structure of a molecule and predict the IR-spectrum:

MM3 Molecular Mechanics
MM3 molecular mechanics: webMM3
Colby - Webmo Computational Chemistry on the WWW

Correlation Charts

NMR Correlation charts

HPLC Simulator

The HPLC Simulator uses a purely equilibrium model for chromatography to simulate the separation of two compounds. Equilibrium Constants and Partition coefficients can be set up for all complexes that form including dimers. The mobile phase can have an additive, M, that might be a cyclodextrin, an ion pairing reagent, etc. Detection can be direct or indirect, using the mobile phase additive. Caution: this JavaScript takes a long time to run. A 100 plate column requires 20 sec. on a very fast PC. This script runs using Netscape and Internet Explorer on Macs and PCs.

The Programmed HPLC Simulator is faster and allows the mobile phase additive to be programmed, i.e. pulsed, so that you can do some interesting equilibrium constant determinations. The programmed version is written in FORTRAN with a cgi interface, so columns with ~1000 or more plates run quickly.

Introduction to HPLC Simulator discusses the theory and applications of the program. Comments and suggestions will be very helpful (2/7/02).

WWW Links

Instrument Instructions

Colby Instruments Home Page: Instructions and User Manuals

NMR Specific

Fourier Tranform in Javascript (Jeff Clymer's)
SDBS Integrated Spectral Data Base System for Organic Compounds
NMRShiftDB, Spectral Database at the Max Planck Institute of Chemical Ecology
Sweet J A Mac application to calculate J-coupling constants using the Karplus and Altona Equations.
NMR Periodic Table (Bruker eNMR)
NMR Periodic Table (Rider Univ.)
NMR Tutorial (Rider Univ.)

NMR Home Page at the University of Potsdam has on-line applications for NMR Spectral Interpretation and Mass Spec interpretation, including:

Spectroscopy Problems

University of Colorado Organic Spectroscopy Problems (with answers).
UCLA Webspectra (with answers).
U. Notre Dame: A Workbook of Unknowns
The Wired Chemist

NMR Tutorials

NMR Tutorial (Rider Univ.)
Introduction to NMR UWI-Mona
Applications of 1H NMR spectroscopy (P. Hallpap, H. Händel)
Virtual Textbook of Organic Chemistry (W. Ruesch, Michigan State Univ.)
Introduction to Mass Spectrometry B. M. Tissue, U. Vermont
Introduction to Mass Spectrometry L. Breci, U. Arizona

General Spectroscopy

The National Institutes of Standards and Technology Chemical Web Book includes thermochemical and gas phase IR and mass spectral data.
IR Wizard Interactive IR Correlation Chart
MS Wizard Interactive MS Fragment Chart
Organic Compounds Database Search with search criteria based on information from Mass Spectrometry, UV/Visible absorption and functional groups.
NIST MS Search Program for Windows has a very useful MS Interpretation application.

Molecular Mechanics and Graphics

The RasMol Home page is a source for RasMol/RasMac applications and information.
Colby College Molecular Mechanics Tutorial for an Introduction to Molecular Mechanics and Molecular Mechanics Exercises for computational exercises using molecular mechanics and dynamics using MOE.

Molecular Structure

The Klotho Biochemical Compounds Declarative Database includes 3D-Chime structures of over 400 biochemical compounds.
The RCSB Protein Data Bank is a repository of X-ray and NMR 3D-structures of proteins and nucleic acids.
Molecular Structure Calculations at Colby using Density Functional Theory.

General Reference

ChemInfo at the Univ. of Indiana will help you find and learn how to use chemistry information resources on the Internet and elsewhere.


A Romanian translation of this Web site by Alexander Ovsov is available.

Many additional resources are available on the Colby Physical Chemistry course Web site.


For more information or corrections contact Tom Shattuck at twshattu@Colby.edu.


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Last modified: 12/31/2013