CH255J Homepage


NMR Spectroscopy

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

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

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 five spins.

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. Currently, this applet does not work with Netscape on a Windows system. Other combinations are OK.
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
IR Helper, Netscape 4.03 version
These are new versions. If you have problems with the new versions please e-mail

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 Builder using Distance Geometry

Build the 3D-structure of a molecule: Distance geometry is a useful computational technique for building molecular structures when a few distance constraints are known, for example from NMR nOe measurements. Distance geometry is also a powerful way to convert atom connection tables to 3-dimensional form. Distance Geometry is a Web application that does distance geometry calculations for small molecules. You can choose to use molecular mechanics to find an optimized minimum energy structure using MM2. For MM2 minimizations you can choose to use SCF-pi molecular orbital calculations for conjugated systems, MMP2. (If you don't want to identify conjugated pi systems you can just just use MM2.) This Web page can also be used to set-up complete input files for MOPAC and Gaussian94/98.
Smiles Input: A version is also available with input from Smiles format. (The Smiles input version doesn't include distance constraints. ) Smiles input with distance geometry. These Web pages now also support Netscape 4.07 as well as Internet Explorer. The Chime plugin and Java are required.
Introduction: Please see the Molecular Mechanics Tutorial for an Introduction to Distance Geometry and several example exercises.

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

NMR Specific

SDBS Integrated Spectral Data Base System for Organic Compounds
NMRShiftDB, Spectral Database at the Max Planck Institute of Chemical Ecology
Educational NMR Software List
Mestrc-J A Windows application to calculate J-coupling constants using the Karplus and Altona Equations. (See Sweet J for the Mac version).
Sweet J A Mac application to calculate J-coupling constants using the Karplus and Altona Equations. This is a local bin-hexed Mac version, for faster downloading than directly from the Web.

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

NMR Tutorials

Introduction to NMR UWI-Mona
Applications of 1H NMR spectroscopy (P. Hallpap, H. Händel)
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.

Molecular Structure

The Klotho Biochemical Compounds Declarative Database includes 3D-Chime structures of over 400 biochemical compounds.
The Protein Data Bank at Brookhaven National Labs 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.

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

For more information or corrections contact Tom Shattuck at

Colby Chemistry Home Page

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Last modified: 3/12/2004