title: Comparison of basis set effects and the performance of ab initio and DFT methods for probing equilibrium fluctuations.
abstract: The electronic absorption and emission spectra of large molecules reflect the extent and timescale of electron-vibration coupling and therefore the extent and timescale of relaxation/reorganization in response to a perturbation. In this paper, we present a comparison of the calculated absorption and emission spectra of NADH in liver alcohol dehydrogenase (LADH), using quantum mechanical/molecular mechanical methods, in which we vary the QM component. Specifically, we have looked at the influence of basis set (STO-3G, 3-21G*, 6-31G*, CC-pVDZ, and 6-311G**), as well as the influence of applying the DFT TD-B3LYP and ab initio TD-HF and CIS methods to the calculation of absorption/emission spectra and the reorganization energy (Stokes shift). The ab initio TD-HF and CIS methods reproduce the experimentally determined Stokes shift and spectral profiles to a high level of agreement, while the TD-B3LYP method significantly underestimates the Stokes shift, by 45%. We comment on the origin of this problem and suggest that ab initio methods may be naturally more suited to predicting molecular behavior away from equilibrium geometries.
authors.affiliation: Biophysics and Biological Chemistry Group, Department of Chemistry, Imperial College London, London, UK. ross@rosswalker.co.uk
authors.forename: Ross C
authors.initials: RC
authors.lastname: Walker
authors.forename: Ian P
authors.initials: IP
authors.lastname: Mercer
authors.forename: Ian R
authors.initials: IR
authors.lastname: Gould
authors.forename: David R
authors.initials: DR
authors.lastname: Klug
mesh_terms: D000426:Alcohol Dehydrogenase / Q000737:chemistry*; D003198:Computer Simulation; D008099:Liver / Q000201:enzymology; D008956:Models, Chemical; D009243:NAD / Q000737:chemistry*; D011789:Quantum Theory; D013997:Time Factors
chemical_list: D009243:NAD; D000426:Alcohol Dehydrogenase