Experiment 4: Computational Molecular Modeling (WebMO)

WebMO on Sunbird

All of the calculations for this experiment and future experiments will be completed using Gaussian09 using WebMO.  It can be accessed via the UW Chemistry Departmental Cluster.  You must know your username and password which you will recieve approximately 1 week prior to your scheduled lab date.  It is critical that your web browser and Java installations are up-to-date in order for your WebMO experience to be relatively smooth.

Day 1 Pre-Lab Requirements:

Before the first day you are schedule to work on Experiment 4,  you will need to have completed/confirmed the following:

  • Confirmed that you receieved your username and password via email.
  • Logged into WebMO on the departmental cluster successfully.
  • Viewed and taken notes on lectures 1 and 2 on molecular modeling.  You are encouraged to log into WebMO and build the molecules as shown in lecture 2.  These videos were recorded using an older version of WebMO, but the interface and images have changed only slightly.
  • Read Chapter 4 in the lab manual.

Lecture 1 – Molecular Modeling (56:20)

Lecture 2 – Molecular Modeling (1:10:39)

Lecture note-taking slides


Day 2 Pre-Lab Requirements:

Before the second day you are scheduled to work on Experiment 4, you need to watch lecture 3 on molecular modeling.


Lecture 3 – Molecular Modeling (37:48)

Required/Recommended Course Software:

Mozilla Firefox Latest Version

Google Chrome

ChemDraw Pro 15 Free Download



1H-NMR & 13C-NMR FID Data & Example MestreNova Workup Videos (no audio, old file structure)

Chem 344 MestReNova Guide

4′-hydroxyacetophenone 1H-NMR and 13C-NMR fid data

Folder 1 in the zip file is the 1H-NMR spectral data and folder 2 in the zip file is the 13C-NMR spectral data.

4′-hydroxyacetophenone 1H-NMR and 13C-NMR Sample Spectra (Not available for submission for credit)


Molecular Modeling Lecture Calculations:

All of the following calculations were completed using WebMO with Gaussian09 at a B3LYP/6-31G(d) level.

Water C2v Opt + Vib


Water C2v NBO

water p orbital lone pair

Anisole Cs Opt + Vib


Anisole Cs NBO

anisole O-atom lone pair

Anisole Dihedral Scan

anisole coordinate scan

Urea C2v (Planar) Opt + Vib

planar urea C2v

Urea C2 (Non-planar) Opt + Vib

nonplanar urea C2

Urea C2 (Non-planar) NBO

pi1 molecular orbital urea

O-protonated urea C1 Opt + Vib

O-atom protonated urea

O-protonated urea C1 NBO

O-atom protonated urea pi 1 orbital

N-protonated urea Cs Opt + Vib

N-atom protonated urea

N-protonated urea Cs NBO

N-protonated urea pi1 orbital


Frequently Asked Questions:

Q1)  Why do I need to optimize a structure?  What does the program do when optimizing?

A1)  Put very simply, optimzing the structure allows Gaussian09 to calculate a good geometry for the molecule.  An optimized geometry should give reasonable energies, orbital occupancies, and other properties that you may wish to calculate.  In the process of optimizing, Gaussian will adjust the paramters of the molecule (distances, angles, and dihedral angles) until the energy of the structure settles into a local minimum on the potential energy surfcace.  If you are starting from a good guess of a starting structure, these changes will be relatively subtle and the calculation time will be small.


Q2)  How can I tell if my output is reasonable?

A2)  This is one of the hardest questions to answer and is a question that computational chemists ask every time they look at the output files of a calculation.

  1. Make sure the calculation has finished properly.  WebMO will display a status of Complete for all successfully complete jobs.
  2. Confirm that the level of theory, basis set, and job type are the desired ones.
  3. Use your chemical intution and determine whether or not the structure looks reasonable.
  4. If you are looking for a reactant, product, or intermediate check to see that all of the molecules vibrational frequencies are positive values.  If you are looking for a transition state, check to see that exactly one vibrational frequency is negative or imaginary.


Q3) How can I predict whether or not VSEPR will adequately predict a molecular geometry?

A3) Valence-Shell Electron Pair Repulsion Theory (VSEPR) is a useful tool for predicting molecular geometries.  As we saw for water (see the LP orbitals in the NBO job above) it can often get the rightmolecular geometry (bent) even when it fails to predict the correct electron geometry.  Unlike the two equivalent lone pairs predicted by VSEPR, a quick molecular orbital calculation of water reveals two distinct lone pairs, one of which is in a p orbital.  Furthermore, as we saw with anisole, VSEPR fails to predict a reasonable bond angle for th Me-O-Ph angle which is far closer to 120 ° than 109.5 ° VSEPR alone would suggest.  This can make it confusing and difficult to know when VSEPR is likely to give the wrong electron geometry and when it is likely to give the wrong electron and molecular geometry.

A reasonable guidline is to assume that VSEPR will often give a good prediction for the molecular geometry when steric repulsion of lone and bond pairs of electrons is the major or only factor involved.  If conjugation of orbitals, orbital mixing, hyrogen bonding, or any other factor impacts the geometry, VSEPR may not do very well.

Importantly, VSEPR will fail to predict the proper electron geometry for all atoms that possess two or more lone pairs.

oseltamivir (Tamiflu)


Opt + Vib


Shown above is the molecule oseltamivir optimized at B3LYP/6-31G(d) with no imaginary vibrational frequencies.  This molecule is interesting in that it showcases the successes and limitations of VSEPR geometry prediction within the same molecule.  If you click on the optimized structure, WebMO will allow you to measure the bond angles and dihedral angles throughout the molecule.

VSEPR works well to predict the molecular geometries of the carbon atoms.  The amine nitrogen atom appears to be well predicted by VSEPR and displays a trigonal pyramidal shape.  The amide nitrogen atom has a lone pair in conjugation with the neighboring carbonyl group π bond.  The C-N-C bond angle that results is 121.5 ° and the nitrogen-atom is nearly trigonal planar.  Likewise the geometry of both oxygen atoms which have bonds to two different atoms are poorly described by VSEPR.  The ether oxygen atom has a C-O-C angle of about 114.0 ° and the ester oxygen atom attached to the ethyl group has a C-O-C angle of about 115.8 °.

Q4) What are symmetry point groups and what do I need to know about them for Chem 344?

A4)  Symmetry point groups are geometric designations that identify all of the symmetry elements within a structure of that group.  It is not critical for Chem 344 that you understand the point group symmetry elements or are able to assign point groups.  A lengthy description can be found on wikipedia, but shown below are point groups that you’ll encouter a lot in this course.

Point Group Example(s) Key Characteristics
C1 (R)-2-butanol



Molecules in this point group lack internal mirror planes or symmetric points.  It is the most common point group.
Cs anisole

anisole symmetry


Molecules in this point group contain an internal mirror plane.  This occurs when the molecules is planar and any atoms out of plane are matched by atoms out of plane on the other face of the molecule.
C2v water

water with symmetry elements



These molecules contain an internal mirror plane like the CS point group, but also contain a second mirror plane perpendicular to the first cutting the molecule in equal halves.


Linear molecules with different atoms in each half of the molecule fit into this point group
D6h benzene


The image displaying the symmetry elements for benzene appears really complicated.  Essentially this it is a D6h structure which means that it is planar with a six mirror planes that are perpendicular to the molecular plane.  Each atom has a counterpart opposite it from the center of the molecule.