Royal Society of Chemistry Theoretical Chemistry Group

Graduate Student Meeting

King's College London - March 12th, 2003


The annual Theoretical Chemistry Group graduate student meeting will be held in Room 1.71, on the first floor of the Franklin-Wilkins Building, Stamford Street, London SE1 - on the Waterloo Campus of King's College London - on Wednesday March 12th from 13:30 to 17:30. (Please note the change of venue from previous years. This building is on the south side of the Thames, across Waterloo bridge from the Strand. The nearest tube station is Waterloo. A map can be found here.) The programme will consist of short talks presented by final year postgraduate students.

Programme

13:30Prof. R. M. Lynden-BellIntroduction
13:35Mark Watson (Cambridge)Linear scaling of molecular Coulomb interactions by multipole expansions
14:00Iryna Rozum (University College London)Electron collisions with CFx radicals
14:25Roma E. Oakes (Queen's University, Belfast)Interpreting Raman spectra using DFT methods
14:50Reimar Finken (Cambridge)Onsager model for a variable dielectric permittivity near an interface
15:15TEA 
15:45Ahlam El-Barbary (Sussex)Ab initio calculations of point defects in graphite: structure, energetics and spectroscopy
16:10Thomas V. Mortimer-Jones (Birmingham)Ant Colony Optimization and its application to the protein folding problem
16:35Ross C. Walker (Imperial College)"Lights, computer, action" - probing protein dynamics with QM/MM techniques and femtosecond laser spectroscopy
17:00M. Paul Gleeson (Manchester)Are QM/MM calculations useful in drug discovery?
17:30CLOSE 


All are welcome. There are no registration formalities.

Abstracts



Linear scaling of molecular Coulomb interactions by multipole expansions

Mark Watson (Cambridge)

We discuss the theory, implementation and application of multipole expansion methods in a Gaussian basis to treat the molecular Coulomb interaction with sub-quadratic cost using the electronic structure package Dalton.

Electron collisions with CFx radicals

Iryna Rozum (University College London)

The purpose of this work is to develop a full description of electron CFx radical collisions at energies up to 10 eV with particular emphasis placed on the energy range 2-5 eV as this is the typical energies of etching plasmas. We have performed calculations to obtain resonance parameters as well as elastic cross-sections and excitation cross-sections for the CF2 and CF molecular radicals in the incident electron energy range below 10 eV. Several low lying resonaces were detected and fitted. We also performed several test target calculations for CF3 for several target models using different basis sets (6-31G*, 6-311G* and Sadlej-pVTZ). Surprisingly, there are no data on vertical excitation energies of CF3 available in the literature, so this is a necessary precursor to scattering calculations.

Click here for a longer abstract (pdf).

Interpreting Raman spectra using DFT methods

Roma E. Oakes (Queen's University, Belfast)

Density functional theory has been used to simulate and interpret the Raman spectra of fatty acid methyl esters - FAMEs (general formula CH3(CH2)nCOOCH3). We show that DFT enables secure vibrational mode assignments to be made, even in the case of complex Raman spectra and that the interpretation of the vibrational data can lead to a greater understanding of the experimental observations. Even very subtle effects seen in the experimental spectra have been reproduced in the calculated data. In addition, the correlations that allow the determination of chain-length and degree of unsaturation from inspection of Raman spectra have successfully been reproduced using DFT and the underlying physical reasons for their existence have been determined.

Onsager model for a variable dielectric permittivity near an interface

Reimar Finken (Cambridge)

Using a generalisation of an Onsager type approach, we are able to predict a dielectric permittivity profile of an inhomogeneous dipolar fluid in the presence of a dielectric interface. The reaction and cavity fields are calculated semi-analytically using bispherical coordinates. An asymptotic expression for the local permittivity is derived as a function of distance from the interface.

Ab initio calculations of point defects in graphite: structure, energetics and spectroscopy

Ahlam El-Barbary (Sussex)

We determine the structure and energetics of the point defects in graphite from first principles calculations. Particularly, we highlight the previously unreported behaviour that is a consequence of the symmetry-breaking Jahn-Teller distortion of the vacancy in graphite. Also, we explain the discrepancy between the experimental and the theoretical value for the migration energy. We comment on a major Wigner energy release which is found to be associated with the break up and recombination of an intimate or un-separated Frenkel pair. For the first time, we interpret the three-fold symmetry of the STM image of the vacancy in graphite as a three-fold thermally average, activated by a barrier of 0.13 eV. Ab initio EELS spectra for the topographical defects in graphite are obtained.

Ant Colony Optimization and its application to the protein folding problem

Thomas V. Mortimer-Jones (Birmingham)

Determination of the native state of a protein from its amino acid sequence is an important goal of protein folding simulations. Location of the global minimum structure (lowest energy folding conformation), however, is a difficult optimization problem. In this talk, we introduce Ant Colony Optimization, which is a recently developed method for global optimization, based on the behaviour of real ant colonies, and describe its application to study protein folding for the coarse-grained 2-D HP lattice bead model.

"Lights, computer, action" - probing protein dynamics with QM/MM techniques and femtosecond laser spectroscopy

Ross C. Walker (Imperial College)

The dynamics and flexibility of a protein are of fundamental importance in understanding the relationship between its structure and function. By applying linear response theory coupled to CIS calculations on molecular dynamics trajectories it has been possible to recreate the reorganisation energies and UV/VIS spectral widths of LADH and Zinc-myoglobin to within 10% of experiment. The method is sensitive enough to validate molecular dynamics force fields for chromophores and ultimately to allow the calculation of free energies of reactions for protein based systems.

Click here for a longer abstract (pdf).

Are QM/MM calculations useful in drug discovery?

M. Paul Gleeson (Manchester)

Methods based upon empirical force fields are the traditional way of studying small molecule-protein interactions relevant to drug discovery. We here show that in a number of cases, drug potency depends upon the formation of a covalent intermediate, and a situation arises where the use of the QM/MM method can lead to a quantitative understanding of the relationship between drug structure and activity.