The Effective Use of Technology in a Graduate

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The Effective Use of Technology in a Graduate
Molecular Modeling Class Bihter Padak, Caitlin
A. Callaghan, Nicole Labbe, and Jennifer
Wilcox Worcester Polytechnic Institute Department
of Chemical Engineering

METHODOLOGY
MOTIVATION

• The class was broken up into the following 4
  sections
• During the first quarter students were introduced
  to quantum mechanics, which serves as the
  foundation for many of the calculations involved
  in molecular modeling. Some example problems
  included, particle in a 1-d box, harmonic
  oscillator, perturbation theory, and the
  variational principle.
• In the second quarter students were introduced to
  the Gaussian software package using WebMO as an
  interface. A server was set up just for the
  class so that students could submit calculations
  from any location that the internet was
  accessible. The Learning Through an Example was
  assigned at this time.
• In the third quarter students were asked to take
  the tools of the software from step 2, to apply
  to reactions provided. At this point they
  learned kinetic tools rather than QM tools.
  These tools included the Hard Sphere Collision
  Model, Transition State Theory and RRKM. The
  Learning Through an Example Assignment was
  completed at this time.
• In the fourth quarter students were then asked to
  apply the tools learned to a project associate
  with either their graduate research project or
  their Major Qualifying Project (senior thesis).
  Images of these projects serve as the backdrop of
  this poster.

• To introduce graduate and upper-level
  undergraduates to tools that will
• allow them to bridge the gap between
  fundamental science and engineering
• applications.
• To help foster the intuitive side of an engineer
  through teaching first principle concepts, which
  provide them with a molecular-scale and
  mechanistic approach to problem solving in
  science.
• To use newly developed software, such as
  Gaussian03 and gOpenMol to assist students in
  active and hands-on learning.
• To effectively use the software without it
  dictating the nature of the course, i.e. to use
  the software purely as a supplement to learning.

Learning Through an Example Students were
expected to learn the capabilities of the
Gaussian98 software package by means of a
thorough structural, thermodynamic, and kinetic
investigation of an assigned reaction similar
to, H F2 ? HF F STEP 1. A variety of levels
of theory were employed for the investigation
involving a wide range of method and basis set
combinations B3LYP/LANL2DZ MP2/6-311G QCISD/
6-311G HF/6-31G MP2/6-311G(d,p) CCSD/6-31G
MP2/6-31G QCISD/6-31G QCISD/6-311G Students
were required to choose two more levels of theory
on their own for further analysis and to organize
the data using Excel. STEP 2. An opt freq
calculation was run at each level of theory, and
for each compound in the given reaction. Results
including the predicted geometry (e.g.
equilibrium bond lengths, angles, and dihedrals),
energy, thermal correction including the zero
point energy, vibrational frequencies, rotational
constants, dipole and/or quadrupole moments were
reported in an organized fashion using a separate
Excel spreadsheet. Using references such as the
CRC Handbook of Chemistry and Physics, NIST
webbook, and individual reference papers (e.g.
obtained via databases such as Science Direct and
SciFinder Scholar), each predicted chemical
property was compared to experiment where
experimental data is available. STEP 3.
Calculation of thermodynamic parameters such as
reaction enthalpies (?Hrxn), entropies (?Srxn),
Gibbs free energies (?Grxn), and equilibrium
constants (Keq) were determined for the given
reaction at each level of theory. STEP 4.
Calculation of kinetic parameters such as
activation energies and rate constants were
determined for the given reaction at selected
levels of theory. The following steps were
involved in determining an overall rate
expression calculation of a potential energy
surface (ab initio-derived energies were plotted
using MatLab), determination of a saddle point
corresponding to a transition structure linking
reactants to products of the reaction path of
interest, frequency calculation at the predicted
transition structure to ensure there exists one
and only one negative frequency, evaluation of
rotational, vibrational, and translational
partition functions for preexponential factor
calculation, and use of transition state theory
(TST) at varying temperatures for the final
expression. A tunneling correction by
Gonzalez-Lafont was used in conjunction with
TST. STEP 5. The rate expression for the
reaction was calculated as a function of
temperature in both directions. The equilibrium
constant was reexamined for validation. All
kinetic (k1 and k-1) and thermodynamic ( Keq )
predictions were compared to experimental values
where available. The NIST kinetic database served
as a reference for this comparison.
Examples of Students Work
D2 Cl ? DCl D
F2 H ? HF F
EVALUATION OF SUCCESS

• The results of the Learning Through an Example
  exercise has resulted in two manuscript
  submissions to the Journal of Molecular Structure
  (THEOCHEM).
• Students from the class have incorporated the
  tools learned into their research. Some examples
  are,
• -Electrochemical water-gas shift reactions on
  platinum and ruthenium catalysts
• Application fuel cell chemistry
• -Adsorption mechanisms of MTBE, Chloroform, and
  1,4-dioxane on zeolites
• Application separation of contaminants
  from groundwater using zeolites
• -Mechanism development of sulfurs role in
  poisoning palladium
• Application hydrogen separation using Pd
  membranes

CONCLUSIONS FUTURE PLANS

• Students provided helpful feedback for improving
  the class in the future
• Seek additional funding to add computational
  strength to the class server often times
  calculations were backed up even though the
  levels of theory were minimal.
• In the future provide more focus to the levels of
  theory considered in the Learning Through an
  Example assignment so that a smaller, but more
  effective list is employed.