Khamis Siam

Computational Chemistry Research

My research is in the area of computational chemistry. The use of computational chemistry has progressed in the last few years to impact all areas of chemistry, biological chemistry and physics.

i. Normal Mode Analysis: In order to obtain accurate normal modes of proteins, which is a prerequisite for detailed analysis of vibrational spectroscopic techniques, reliable conformation-dependent force fields are required. Empirical force fields can provide insight into the normal modes of proteins. The task of calculating normal modes for such large systems is not trivial, since it requires the calculation of second derivatives of the energy and if one were to do this at reliable basis sets, it would take thousands of hours of computer times and generate so many integrals that would stretch the capabilities of supercomputers. Hence, one would attempt to do smaller systems, such as amino acids and dipeptides and try to extend these results to larger systems. I have calculated the force field for glycine, alanine, glycine dipeptide, and alanine dipeptide. The next step is to calculate the normal modes of these molecules and using AMBER (a widely used molecular mechanics and molecular dynamics program) to reproduce the results obtained by ab initio methods. Then a calculation of the normal modes of larger systems can be done, if the comparisons of the previous calculations prove successful.

ii. Bacterial Models for Plant Reaction Centers: Bacterial photosynthesis Reaction Centers exhibit many structural and functional homologies with Reaction Centers of green plants. Bacterial Reaction Centers from Rb. Sphaeroides and Rhodopseudomonas virdis contain similar co-factors as the Reaction Centers of PSII, a special pair of bacteriachlorophylls. P870, two bateriapheophytins, two bound quinones (Ubiquinone in bacteria and Plastoquinone in green plants), and an iron bound to four histidines. Molecular dynamics calculations are done on these large systems of >10,000 atoms. Different quinones are placed in the Reaction Center and perturbed to transfer an electron. The energies are calculated and compared with experimental results.

iii. Basis Set Dependence: The quality of the results of calculations performed at the ab initio level depends largely on the kind of basis sets used. The higher order basis sets, coupled with Electron Correlation, produce results which are very close to Hartree Fock limit and also close to experimental values when corrected for vibrational amplitudes. Use of higher order basis sets is time consuming. Hence, only small molecules can be calculated at such high levels.