Online Resources

Computational Chemistry

  • Gaussian Basis Set Order Form: The Molecular Science Computing Facility of the Environmental and Molecular Sciences Laboratory (EMSL) is a part of the Pacific Northwest Laboratory located in Richland, Washington. This National Laboratory is funded by the U.S. Department of Energy. The EMSL Basis Set Order Form allows the user to extract Gaussian basis sets, formatted appropriately for a wide variety of popular computational chemistry software packages, including Gaussian and GAMESS.

  • STFC Computational Science and Engineering Software: software from UK Collaborative Computational Projects.

  • Software Archive: at the Materials Computation Center of UIUC.

  • Computational Chemistry List: is an electronic forum for chemistry researchers and educators.

  • Linux4Chemistry: provides information about computational chemistry software for the Linux operating system.

  • WebMO: WebMO is a web-based interface available in both freeware and commercial (Pro) versions that provides simple molecule building, set-up of calculations, and viewing of results. The program provides an easy-to-use interface to a variety of computational chemistry software packages, such as Gaussian, GAMESS, MOPAC, and Tinker. WebMO Pro, along with these four computational chemistry programs, is available on the North Carolina High School Computational Chemistry server.

  • Computational Chemistry for Chemistry Educators: Computational Chemistry for Chemistry Educators (CCCE) is the companion Web-based resource for the computational chemistry workshops offered through the Shodor Education Foundation’s National Computational Science Institute (NCSI). Funding for NCSI was provided (in part) by the Burroughs Wellcome Fund and the NSF. CCCE is designed to provide educators with sufficient information so they can begin to use molecular modeling tools in the chemistry classroom to improve the education of their students. Perhaps the most useful aspect of this site is the collection of computational laboratory exercises available for various software packages, including WebMO.

Chemical Properties

  • NIST Chemistry WebBook: provides access to data compiled and distributed by NIST under the Standard Reference Data Program, including Thermochemical data for over 7000 organic and small inorganic compounds, Reaction thermochemistry data for over 8000 reactions, IR spectra for over 16,000 compounds, Mass spectra for over 33,000 compounds, UV/Vis spectra for over 1600 compounds, Gas chromatography data for over 27,000 compounds, Electronic and vibrational spectra for over 5000 compounds, Constants of diatomic molecules (spectroscopic data) for over 600 compounds, Ion energetics data for over 16,000 compounds, Thermophysical property data for 74 fluids:

  • Computational Chemistry Comparison and Benchmark Database: A service of the National Institute of Standards and Technology (NIST), the Computational Chemistry Comparison and Benchmark Database (CCCBDB) provides a collection of both experimental and calculated thermochemical parameters for a selected set of molecules. These data are provided to help software developers evaluate program performance and to compare the results from different computational methods. The site also provides a useful source of data for educators and their students.

  • Merck Index: is an encyclopedia of chemicals, drugs and biologicals with over 10,000 monographs on single substances or groups of related compounds. It also includes an appendix with monographs on organic name reactions. It was published by the United States pharmaceutical company Merck & Co. from 1889 until 2013, when the title was acquired by the Royal Society of Chemistry.

  • CHEMnetBASE: is a web-based compilation of chemistry reference books produced by Chapman & Hall/CRC Press. The information is useful for quick access to chemical and physical property data and appropriate for undergraduate to professional levels. The contents of CHEMnetBASE come from well-known and well-respected reference books. Resources included are the Combined Chemical Dictionary (CCD), Dictionary of Commonly Cited Compounds, Dictionary of Drugs, Dictionary of Inorganic and Organometallic Compounds, Dictionary of Natural Products, Dictionary of Organic Compounds, the Handbook of Chemistry and Physics, Polymers: A Property Database, and Properties of Organic Compounds (POC).\   The Combined Chemical Dictionary is comprised of over 160,000 entries on compounds and their derivatives, uses, and properties from the five chemical dictionaries, each of which can also be searched separately. Now in its 87th edition, the Handbook of Chemistry and Physics, referred to as "the CRC" by many chemists, is the granddaddy of compilations of chemical data and often a chemist's first reference source as a student. Polymers: A Property Database offers information on polymers for a wide range of physical properties as well as commercial information. Properties of Organic Compounds, the online equivalent of the Handbook of Data on Organic Compounds, is a collection of property information and searchable spectral data on about 29,000 organic compounds.

  • NCMS Solvents: brings together a wealth of information on commercially available solvents, including: Health and Safety considerations involved in choosing and using solvents; Chemical and Physical data affecting the suitability of a particular solvent for a wide range of potential applications; Regulatory responsibilities, including exposure and effluent limits, hazard classification status with respect to several key statutes, and selected reporting requirements; Environmental Fate data, to indicate whether a solvent is likely to break down or persist in air or water, and what types of waste treatment techniques may apply to it.

  • CODATA Key Values for Thermodynamics: A table presenting the final results of the project to establish internationally agreed values for the thermodynamic properties of key chemical substances conducted by Committee on Data for Science and Technology (CODATA).

  • Interactive Pressure-Temperature Nomograph: a web applet from Sigma-Aldrich with properties for common solvents built in.

  • Thermodynamic Properties of Air: calculates the thermodynamic properties of air given the pressure and entropy, pressure and density, specific energy and density, entropy and enthalpy, or pressure and temperature.

Structure Databases

The following online resources contain files which can be downloaded for interactive viewing either from a stand-alone visualization software or viewed from the website as a Java applet.

  • Cambridge Structural Database: a repository for small-molecule organic and metal-organic crystal structures with over half-a-million x-ray and neutron diffraction analyses.

  • ICSD Web: the Inorganic Crystal Structure Database. This site contains a free demonstration version of the Inorganic Crystal Structure Database. This database contains a 3325 structure subset of the 76,480 inorganic structures as of 2004. The demo version can be queried and accessed by a web-interface which allows multiple methods of searching, and the resulting crystal structures can then be viewed online (with the CHIME plug-in) or downloaded for viewing with other visualization software. Also included on the site are updates of bug fixes, conditions of use and prices, tips for displaying the structures, a gallery of images, a flash movie, and instructions for installing a ICSD server.

  • American Mineralogist Crystal Structure Database. This site is an interface to a crystal structure database that includes every structure published in the American Mineralogist, the Canadian Mineralogist, and the European Journal of Mineralogy. The database is maintained under the care of the Mineralogical Society of America and the Mineralogical Association of Canada, and financed by the National Science Foundation. The site is searchable by mineral, author, chemistry, or cell parameters and symmetry.

  • Crystallography Open Database. This database is a sister to the American Mineralogist Crystal Structure Database (AMCSD) and contains all the data that is in the AMCSD as well as data that has been deposited by individuals and laboratories. The database is searchable by text, words, elements, volume, or number of elements. Crystal structure data are downloadable in CIF format, and users may upload crystal data as CIF or REF files.

  • Crystallographic Database for Minerals and Their Structural Analogues. This searchable database, maintained by the Russian Foundation of Basic Research, includes 4785 entries (2365 unique mineral names). Each mineral can be searched by name, specification, crystal chemical formula, or crystal structure characteristics. The crystal structure information includes mineral name, specification, crystal chemical formula, space group, unit cell parameters, coordinates, thermal factors and occupancy of atomic positions as well as literature references on crystal structure determination.

  • Crystal Structures. This website features interactive Java applets of a variety of crystal structures of minerals and non-minerals. The Java applet allows the user to rotate and change the size of the crystal. The site also includes links to other webpages about crystal structures.

  • Protein Data Bank: The Protein Data Bank (PDB) is a repository of structural information on large biological molecules such as proteins and nucleic acids. The structures have mostly been solved using single crystal X-ray diffraction, nuclear magnetic resonance (NMR), and cryo-electron microscopy (cryo-EM) techniques. A detailed understanding of the 3-D structure of these biomolecules can lead to an understanding of their function in a living organism. Atomic coordinates of the structures (in .pdb file format) can also be downloaded for use in computational chemistry programs.

  • Molecular Libraries: Reciprocal Net is funded by the U.S. National Science Foundation (NSF) as part of the National Science Digital Library (NSDL) project. Reciprocal Net maintains a distributed database of crystallographic information focused on smaller molecules of general interest. The structural data can be viewed in a variety of formats, and the data files can be downloaded and imported into programs such as WebMO so that calculations can be performed.\   The Mathmol library has 3-D structures for molecules that are often presented in introductory biology and chemistry textbooks. These structures can be downloaded (.pdb file format) and imported into WebMO.\   Another site that has downloadable structural files is Inorganic, organic, therapeutic drug, and biomolecular structures can be downloaded (.mol file format) and imported.

  • Bilbao Crystallographic Server: contains web-based crystallography tools the Bilbao Incommensurate Crystal Structure Database.

  • Database of Zeolite Structures: This database provides structural information on all of the Zeolite Framework Types that have been approved by the Structure Commission of the International Zeolite Association (IZA-SC). It includes descriptions and drawings of each framework type, user-controlled animated displays of each framework type, crystallographic data and simulated powder diffraction patterns for representative materials, relevant references, detailed instructions for building models, descriptions of some families of disordered zeolite structures.

Spectroscopy Databases

  • Bio-Rad Spectral Database: offers over 1.4 million high-quality IR, MS, NMR, NIR, Raman, and UV-Vis spectra (including Sadtler data), for interpretation, identification, verification, and classification of spectra.

  • is a unique web site dedicated to providing analytical chemists with on-line access to high quality FTIR and Raman spectral libraries. It replaces the free Spectra Online.

  • Spectral Database for Organic Compounds SDBS: is an integrated spectral database system for 34,000, mostly commercial organic compounds, which includes 24,700 electron impact Mass spectra (EI-MS), 52,500 Fourier transform infrared spectra (FT-IR), 15,400 1H nuclear magnetic resonance (NMR) spectra, 13,600 13C NMR spectra, 3,500 laser Raman spectra, and 2,000 electron spin resonance (ESR) spectra.

Scientific Computing


Fortran Compilers



ParaView and VisIt are two general purpose visualization tools, which support volume rendering and other advanced techniques. VTK is an open-source C++ library for 3D computer graphics, image processing and visualization, and has several interpreted interface layers including Tcl/Tk, Java, and Python. VMD is a very popular molecular visualization program.


Install Schrodinger.


Install Jmol


Installing VMD

  1. Go to the website
  2. Click on the VMD button and find your platform (preferably with Open GL). Click to begin the download.
  3. Follow the instructions to create a user account (used to determine usage and reported to the NSF or other funding agency supporting VMD development) and browse the README file (onscreen) while the program downloads.
  4. When download is complete, open a Finder window and move VMD into the Applications folder. To do this, drag the VMD icon (looks like a water molecule) over the ‘Applications’ menu on the left of the Finder window. The cursor should become a green plus sign.

Generating high-quality images

  • Make sure that in the Graphical Representations window, all your visualized components have high values for their resolution.
  • Open File Render Controls: from VMD Main window, File -> Render.
  • Changing the method from “Snapshot (VMD OpenGL window)” to basically anything else will dramatically improve the image quality. VMD User's Guide recommends “Tachyon (internal, in-memory rendering)”. The default Snapshot renderer just captures what is on the VMD OpenGL Display area. It will even include other objects that are on top of the display window at the time when you perform the rendering.
  • To use renderers other than “Snapshot (VMD OpenGL Window)” or “Tachyon (internal, in-memory rendering)”, you need to perform two steps: first generate a scene description file from VMD, and second run the separate rendering program with your desired options to generate a raster graphics file. See Chapter 8.2 Higher Quality Rendering of VMD User's Guide for more details on the different rendering programs and recommended options.
  • For example, to use Tachyon renderer with custom parameters, choose “Tachyon”, and in the Render Command text box enter: “/Applications/VMD” -aasamples 8 -rescale_lights 0.4 -add_skylight 0.7 %s -format TARGA -o %s.tga. VMD will generate a scene file suitable as input for the Tachyon rendering program, with the name specified in the Filename text box, and then run the command given in the Render Command box to actually render the image. “%s” is the file name specified in the Filename box.
  • In addition, you can manually modify the scene file in order to change settings such as the resolution, anti aliasing threshold, and re-run the rendering program from the command line to generate another image file with the modifications you just made to scene descriptions.

Add/remove bonds

When reading in a simulation snapshot, VMD will try to determine the bonds between atoms. Sometimes it will draw bonds where they should not exist and at other times it can also miss certain bonds. Use the pickbond script from VMD Script Library to add/remove bonds.

  • Save the file to your disk.
  • Open VMD Main Window -> Extensions -> Tk Console.
  • Change to the directory where you save the tcl script and invoke the script:
cd target/directory
source pickbond.tcl # read in the script
pickbond add/del/stop # add bond, remove bond, stop pickbond action
  • Change the mouse mode to Pick by pressing P or from VMD Main Window -> Mouse -> Pick.
  • Click the two atoms between which you want to create and delete a bond.

Perform periodic boundary conditions at arbitrary positions

Sometimes you will want a particular molecule to be at the center of your system while your movie file has it always at the boundary of the simulation box. Suppose the simulation box is cubic with sides of length 32.0, and the molecule of interest is at (16.0, 32.0, 0.0), you can do the following:

set sel [atomselect top "all"] # select all atoms in your top molecule
$sel moveby {0 -16 16} # move all molecules
pbc set {32.0 32.0 32.0 90.0 90.0 90.0} # set the lattice parameters of the simulation box
pbc wrap # perform periodic boundary conditions
pbc join connected # re-connect molecules

TraPPE Force Field

Below is a list of the different papers that make up the TraPPE (Transferrable Potentials for Phase Equilibria.) force field, along with some information concerning what types of molecules are treated.



  • M.G. Martin, and J.I. Siepmann, 'Transferable potentials for phase equilibria. 1. United-atom description of n-alkanes,' J. Phys. Chem. B, 102, 2569-2577 (1998).
  • M.G. Martin, and J.I. Siepmann, 'Novel configurational-bias Monte Carlo method for branched molecules. Transferable potentials for phase equilibria. 2. United-atom description of branched alkanes,' J. Phys. Chem. B, 103, 4508-4517 (1999).
  • C.D. Wick, M.G. Martin, and J.I. Siepmann, 'Transferable potentials for phase equilibria. 4. United-atom description of linear and branched alkenes and of alkylbenzenes,' J. Phys. Chem. B, 104, 8008-8016 (2000).
    • Ethene, propene, 1-butene, trans- and cis-2-butene, 2-methylpropene, 1,5-hexadiene, 1-octene, benzene, toluene, ethylbenzene, propylbenzene, isopropylbenzene, o-, m-, and p-xylene, naphthalene
  • B. Chen, J.J. Potoff, and J.I. Siepmann, 'Monte Carlo calculations for alcohols and their mixtures with alkanes. Transferable potentials for phase equilibria. 5. United-atom description of primary, secondary and tertiary alcohols,' J. Phys. Chem. B, 105, 3093-3104 (2001).
  • J.M. Stubbs, J.J. Potoff, and J.I. Siepmann, 'Transferable potentials for phase equilibria. 6. United-atom description for ethers, glycols, ketones and aldehydes,' J. Phys. Chem. B, 108, 17596-17605 (2004).
  • X.S. Zhao, B. Chen, S. Karaborni, and J.I. Siepmann, 'Vapor-liquid and vapor-solid phase equilibria for united-atom benzene models near their triple points: The importance of quadrupolar interactions,' J. Phys. Chem. B 109, 5368-5374 (2005).
    • 6-site model: 6 x CH placed at carbon sites
    • 9-site model: 6 x CH placed at carbon sites, 3 additional charge sites
      • +0.242 e on benzene plane, -0.121 e at ±0.785 A from benzene plane
      • Q = -23.9 x 10-40 C m2
  • C.D. Wick, J.M. Stubbs, N. Rai, and J.I. Siepmann, 'Transferable potentials for phase equilibria. 7. United-atom description for nitrogen, amines, amides, nitriles, pyridine and pyrimidine,' J. Phys. Chem. B, 109, 18974-18982 (2005).
  • N. Lubna, G. Kamath, J.J. Potoff, N. Rai, and J.I. Siepmann, 'Transferable potentials for phase equilibria. 8. United-atom description for thiols, sulfides, disulfides, and thiophene,' J. Phys. Chem. B, 109, 24100-24107 (2005).
  • K.A. Maerzke, N.E. Schultz, R.B. Ross, and J.I. Siepmann, 'TraPPE-UA force field for acrylates and Monte Carlo simulations for their mixtures with alkanes and alcohols,' J. Phys. Chem. B 113, 6415-6425 (2009).
  • S.J. Keasler, S.M. Charan, C.D. Wick, I.G. Econonmou, and J.I. Siepmann, 'Transferable potentials for phase equilibria-United atom description of five- and six-membered cyclic alkanes and ethers,' J. Phys. Chem. B, 116, 11234-11246 (2012).
    • Cyclopentane, tetrahydrofuran, 1,3-dioxolane, cyclohexane, oxane, 1,4-dioxane, 1,3-dioxane, 1,3,5-trioxane


  • N. Rai, and J.I. Siepmann, 'Transferable potentials for phase equilibria. 9. Explicit-hydrogen description of benzene and 5-membered and 6-membered heterocyclic aromatic compounds,' J. Phys. Chem. B, 111, 10790-10799 (2007).
    • Benzene, pyridine, pyrimidine, pyrazine, pyridazine, thiophene, furan, pyrrole, thiazole, oxazole, isoxazole, imidazole, pyrazole
  • N. Rai, D. Bhatt, J.I. Siepmann, and L.E. Fried, 'Monte Carlo simulations of 1,3,5-triamino-2,4,6-trinitrobenzene (TATB): Pressure and temperature effects for the solid phase and vapor-liquid phase equilibria,' J. Chem. Phys. 129, art. no. 194510/8 pages (2008).
  • N. Rai, and J.I. Siepmann, 'Transferable potentials for phase equilibria. 10. Explicit-hydrogen description of substituted benzenes and polycyclic aromatic compounds,' J. Phys. Chem. B, 117, 273-288 (2013).


  • B. Chen, J.J. Potoff, and J.I. Siepmann, 'Adiabatic nuclear and electronic sampling Monte Carlo simulations in the Gibbs ensemble: Application to polarizable force fields for water,' J. Phys. Chem. B 104, 2378-2390 (2000).



  • S.T. Cui, J.I. Siepmann, H.D. Cochran, and P.T. Cummings, 'Intermolecular potentials and vapor-liquid phase equilibria of perfluorinated alkanes,' Fluid Phase Equil. 146, 51-61 (1998).
  • L. Zhang and J.I. Siepmann, 'Pressure dependence of the vapor-liquid-liquid phase behavior of ternary mixtures consisting of n-alkanes, n-perfluoroalkanes and carbon dioxide,' J. Phys. Chem. B 109, 2911-2919 (2005).
  • N. Rai, and J.I. Siepmann, 'High-Level Electronic Structure Calculations for Methane/Perfluoromethane Dimers. Development of the TraPPE-EH Force Field for Hydrofluorocarbons,' (2009). ppt


  • P. Bai, M. Tsapatsis, and J.I. Siepmann, 'TraPPE-zeo: Transferable potentials for phase equilibria force field for all-silica zeolites,' J. Phys. Chem. C 117, 24375-24387 (2013).
    • Rigid framework assumption, so tight fitting systems such as benzene, xylenes in MFI can be problematic.
    • Adsorption and diffusion of any types of molecules on all-silica zeolites of any framework type. Tested: non-polar: methane, ethane, n-heptane, 2-methylpropane, 2-methylpentane, 3-methylpentane, 2,2-dimethylbutane adsorption in MFI; propane adsorption in TON; quadrupolar: carbon dioxide adsorption in MFI; polar and hydrogen-bonding: methanol, ethanol, water adsorption in MFI; methanol adsorption in FAU; diffusion: methane, water in MFI.
  • An ad-hoc extension to Ca2+-exchanged aluminosilicates is developed for a simulation challenge: P. Bai, P. Ghosh, J. Sung, D. Kohen, J.I. Siepmann, and R.Q. Snurr, 'A computational study of the adsorption of n-perfluorohexane in zeolite BCR-704,' Fluid Phase Equil. 360, online (2013).

Configurational-Bias Algorithms

Configurational-Bias Monte Carlo (CBMC)

Allows for the efficient sampling of the conformational space of linear chain molecules in condensed phases

Coupled-Decoupled Configurational-Bias Monte Carlo (CD-CBMC)

Allows for the efficient sampling of the conformational space of branched chain molecules

  • M.G. Martin, and J.I. Siepmann, 'Novel configurational-bias Monte Carlo method for branched molecules. Transferable potentials for phase equilibria. 2. United-atom description of branched alkanes', J. Phys. Chem. B. 103, 4508-4517 (1999).

Self-Adapting Fixed-Endpoint Configurantional-Bias Monte Carlo (SAFE-CBMC)

Allows for the efficient sampling of the conformational space of cyclic molecules and high-molecular-weight polymers

  • C.D. Wick, and J.I. Siepmann, 'Self-adapting fixed-endpoint configurational-bias Monte Carlo method for the regrowth of interior segments of chain molecules with strong intramolecular interactions', Macromolecules. 33, 7207-7218 (2000).

Aggregation-Volume-Bias Monte Carlo (AVBMC)

Allows for the efficient sampling of the spatial distribution of aggregating (hydrogen-bonding) molecules

Adiabatic Nuclear Electronic Sampling Monte Carlo (ANES-MC)

Allows for the efficient sampling of polarizable force fields

  • B. Chen, and J.I. Siepmann, 'Monte Carlo algorithms for simulating systems with adiabatic separation of electronic and nuclear degrees of freedom', Theor. Chem. Acc.. 103, 87-104 (1999).
  • B. Chen, J.J. Potoff, and J.I. Siepmann, 'Adiabatic nuclear and electronic sampling Monte Carlo simulations in the Gibbs ensemble: Application to polarizable force fields for water', J. Phys. Chem. B. 104, 2378-2390 (2000).

Aggregation-Volume-Bias Monte Carlo with Self-Adaptive Umbrella Sampling and Histogram Reweighting (AVUS-HR)

Allows for the exceedingly efficient sampling of nucleation phenomena

  • B. Chen, J.I. Siepmann, and M.L. Klein, 'Simulating vapor-liquid nucleation of water: A combined histogram-reweighting and aggregation-volume-bias Monte Carlo investigation for fixed-charge and polarizable models', J. Phys. Chem. A. 109, 1137-1145 (2005).

Plotting Data


Creating the default settings for new graphs

Open xmgrace, make the desired changes to the various settings, save the file as ~/.grace/templates/Default.agr. A template appropriate for publication can be downloaded here. Note that in order to change the actual page dimensions, you need to go to View -> Page setup, and in the Page section, change Size to "Custom" and the Dimensions unit to be "in", put 3.25 x 3.25 (requirement for half-page figure) or 7 x 7 (for full-page figure). This will fix the size on the output devices (X11, PDF, PNG, or actual printers). The resolution on the computer screen (X11) is set in the Resolution (dpi) text box, and the resolutions for other types of devices are set in File -> Print setup -> Resolution (dpi). Unfortunately, the resolution setting and the default print device are not saved in the template file, but see below.

Setting the default printer to print to .png files with 300dpi

Create the file ~/.grace/gracerc.user and enter the following text:

DEVICE "X11" DPI 192

Special symbols

Italic, bold

italic: \1italic
bold: \2bold
italic and bold: \3xyz

Subscript, superscript

subscript: 3\s10\N
x-squared: x\S2\N

\N returns the font position to normal.

Special symbols

Angstrom symbol: \cE\C

For other characters, look at this list: ascii table with low and high characters. Just use the character from the left column between \c and \C to produce the one from the right column. I highlighted the most interesting characters (for a scientist).

Greek letters

theta: \xq\0
rho: \xr\0

\0 returns the font type to normal.

The \c, \C, and \x options are listed as deprecated in the xmgrace manual. The new method to insert special characters in xmgrace is:

  • Press ctrl-e while positioned in a text-edit field to bring up the font dialog box.
  • Select the desired font from the drop-down list. You probably want to use Symbol because it contains many of the commonly used special characters.
  • Click on the character you want to insert

This will put something like


into the text box.


Ternary diagram

You basically need to calculate the (x,y) coordinates for all your data points as well as the three vertices of the triangle. This template file will produce something like this