CONTENTS
 

What Is Computational Chemistry?

 

Methods of Computational Chemistry

 

Current  Modeling Project of Diatomic/Enzyme Interactions

 

Nickel-Iron Hydrogenase

 

Jaguar Software

 

Visualizing the Thiocubane Structure

 

Probability Density Animation of Thiocubane

 

Guide to gOpenMol

 

Slide Show of Ni-Fe Hydrogenase

What Is Computational Chemistry?Computational chemistry is a branch of theoretical chemistry that utilizes computers to determine a wide range of molecular properties.  Computational chemistry can be emplyed to view 3-D structures of everything from simple diatomic molecules to very large protein molecules. Calculations can be performed to determine the most likely structure for ground state and excited state geometries, heats of formation, vibrational modes, and other experimentally determined values.  Computational chemistry does not only involve using current computing methods to look at molecular orbitals, electron densities, and even reaction dynamics, but it also involves applications of cutting edge theories or building upon previous theories to create new computational methods.

Currently, I am working on using molecular modeling to explore the interaction of diatomic molecules and enzymes that work on them. This work can be viewed by clicking here.

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Methods of Computational Chemistry  There are a variety of methods for determining molecular properties.  As the size of molecules increase, determining these properties becomes more difficult very rapidly.  This happens because what one is trying to do is determine the wave function for the electron.  As more and more electrons become involved, more and more approximations are needed to solve for the wave function. Another problem that arises as the number of electrons increases, is that moving to heavier atoms requires consideration of relativistic effects, not a trivial problem! To deal with this problem, the use of electron core potentials (ECP) are often employed.  A calculation involving ECP treats only the valence electrons explicitly and utilizes a much smaller set for the core electrons. The methods discussed below are all common methods used to calculate molecular properties

ab initio calculations, also called first principle calculations use the Hamiltonian operator and only the known physical constants to determine the electronic wave functions.  This method can be very computationally time consuming and extremely demanding on large molecules.

Semiempirical methods involves the use of parameters that will give rise to the best fit to experiemtnal data.  This method is not as time consuming as ab initio calculations.  Common examples of semiempirical methods are AM1 and PM3.

Molecular Mechanics (MM) is used for larger systems.  This calculation uses Newtonian mechanics to predict the molecular properties such as geometry.  This caclulation treats the atoms as  spheres so it is not founded on quantum mechanical principle.

Density Functional Theory does not calculate the electronic wave function.  Instead, this method finds the electron probability density.

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Jaguar  Jaguar is a software program that allows its users to have easy aces to the code and also the benefit of a xterm interface.  Jaguar can be used to study a variety of chemical systems.  Jaguar can be used to optimize geometries, calculate molecular vibrations, dipole moments, electron density surfaces, and the electrostatic potential. The electrostatic potential is a measure of  the attraction of a point charge  at various regions of the molecule. To view output from Jaguar, one can use gOpenMol created by Leif Laaksonnen.   We are currently running Jaguar 4.0 on the LINUX OS. It has proved to be a valuable tool for calculations involving transition metals.

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Animation Created Using gOpenMol and Jaguar
This is an animation of the changing probability density.  Note how the delocalization of electrons increases moving farther from the nucleus of the thiocubane structure.  Sulfur atoms are yellow, iron atoms are purple.

 

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