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University of Alaska Fairbanks
Department of Chemistry and Biochemistry

Updated 7-1-2026
John Keller
 email: jwkeller-at-alaska.edu

Tutorial for WebMO demo site users, and WebMO in general

                                    The WebMO working demo at Hope College, MI, is open to all users.

What is WebMO? This is a web application installed on a web server somewhere, which provides a graphical interface to Gaussian, ORCA, MOPAC, xTB and other quantum mechanics (QM) programs. These are large (and often expensive) programs that run on dedicated compute servers networked to the WebMO server. Based on the user's input, WebMO constructs an input file and sends it to the selected QM program. It then monitors the calculation in real time and displays the results on the user's web browser. WebMO has become an important part of undergraduate chemistry education worldwide. See also WebMO FAQ.

                                                  The WebMO Demo Server

WebMO code was originally written by J.R. Schmidt, then a student at Hope College in Michigan, and Will Polik, a Hope College chemistry professor. The demo server resides at Hope College. It has a rather severe 30-sec cpu time limit, but this still allows useful calculations on small molecules and ions.

                                The WebMO "Configure Gaussian Job Options" page

Which calculations can be carried out? The four most important are:
►Molecular energy. Takes the atomic geometry in the workspace, plus the stated total charge, and derives an approximate solution to the Schrödinger Equation (HΨ=EΨ). The total energy, dipole moment, and partial atomic charges are displayed on the View Job page.
►Geometry Optimization. Changes bond lengths, bond angles, and other geometric parameters of the starting geometry in a stepwise fashion, searching for the geometry with the lowest energy content.
►Vibrational Frequencies. A molecule's bonds are stretchy; they vibrate even at absolute zero. The program calculates the force constant of each bond and combines these into 3N-6 molecular vibrational modes, where N is the number of atoms in the molecule.
►Molecular Orbitals. Same calculation as "Molecular Energy", except that the molecular orbitals (ψ's) are displayed, and other functions such as the total electron density distribution.

What are the different theories available in Gaussian? The Theory drop-down menu shows several, which are various mathematical approaches to solving the Schrödinger Equation. Hartree-Fock is the original orbital method developed in 1926 for atoms by Douglas Hartree of Cambridge University and Vladimir Fock of the Leningrad Institute of Physics and Technology. H-F has been largely supplanted by the more accurate density functional theory; various DFT methods are listed in the 2nd group. Within that group, the B3LYP method is by far the most widely used today; choose that one.

Basis Sets: What are they and which one is best?  Molecular orbitals are created mathematically as linear combinations of atomic orbitals on the constituent atoms. The basis set describes what kind, and how many, atomic orbitals will be used. The Minimal basis set contains just the familiar s- and p- orbitals. Obtaining more accurate results requires using more atomic functions on each atom such as Routine 6-31G(d), which adds d-orbitals, or Standard 6-31G(d,p), which adds p-orbitals on hydrogen.

Charge  = the total charge. For example, 0 for H2O; -1 for nitrate NO3-; +1 for ammonium NH4+.
Multiplicity = 2n, where n = number of unpaired electrons. For example, 1 for CO (singlet); 2 for NO (doublet). An unpaired electron has two possible spin states, "up" and "down". In an even-electron species such as CO each electron is paired with a second one of opposite spin; this hides the spins in a "singlet" state.

                            Quick how-to. Log on and optimize the geometry of H2O.

► Click this link to go to the WebMO demo server. Login as guest,  password guest.
► Click the New Job tab, Create New Job.
► Draw H2O as follows: click the Build tool (topmost on the left-hand toolbar). Touch the letter O on your keyboard, then left-click in the workspace to place an O atom. Now do Clean-Up, Comprehensive-Idealized, or click the "broom icon" in the left toolbar (8th from the top). Click the > arrow at the bottom right to continue to the next page.
► On the Choose Computational Engine page, choose Gaussian;  Select Server, webmo.net. Click the > arrow.
► On the Configure Gaussian page, in the Calculation box choose Geometry Optimization; Theory, = B3LYP;  Basis Set = 6-31G(d);  Charge = 0;  and Multiplicity = Singlet.  Submit the job by clicking the > arrow. (See the above discussion about these options.)
► The Job Manager will say Queued, then Running, then after a few seconds, Complete.

To see the results, click the job name or magnifying glass icon. Check out the following info on the View Job page:
► WebMO does not list bond lengths, angles, etc. Rather, you must use the Adjust tool (4th from the top) to click 2 atoms (bond length), 3 atoms (bond angle), or 4 atoms (torsion angle), with the values being displayed in bold type at bottom left of the screen. The experimental bond angle of water is 104.5°. The calculated value is low by about 1°.
► In the Geometry Sequence Energies box, notice that this optimization required  3 steps to find the minimum energy - click the magnifying glass icon to see an energy-vs-step plot. Energies in Gaussian are given in Hartrees, where 1 Hartree = 627.51 kcal/mol. Thus the final geometry is 7.31 kcal/mol (or 0.01166 Hartree) more stable than the initial structure built by WebMO.

                                             
                             Calculate and view the vibrations of H2O.

► On the WebMO demo server, optimize the geometry of H2O as above.
► Then, in the Job Manager, open the finished job by clicking the job name. Click the "New Job Using this Geometry" button. Click the > arrow.
► On the Choose Computational Engine page, choose Gaussian;  Select Server, buchner.chem.hope.edu. Click the > arrow.
► On the Configure Gaussian page, in the Calculation box choose Vibrational Frequencies, with other entries the same as above.  Submit the job by clicking the > arrow.
► The Job Manager will say Queued, then Running, then after a few seconds, Complete.

To see the results, click the job name or magnifying glass icon. Check out the following info on the View Job page:
► Scroll to the box labeled Vibrational Modes. All molecules (except linear ones) have 3N - 6 vibrational modes, where N = # atoms, therefore you will see 3 modes for H2O: one bending, and two O-H stretching. Click a film icon at the far right to view an animation of each vibration.
► In the Overview section, notice that several thermodynamic quantities are displayed, including G, H, and S. Entropy content depends on how "floppy" the molecule is, which requires doing the vibrational frequencies calculation. Recall that G = H-TS. Is that true for this calculation (T = 298.16 K)?

 

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