We possess a 48-processors PC cluster (Alineos, AMD 2.5 GHz for a total of 96 GB of RAM, dual Gbit switch connecting 18 nodes) suitable to perform high level calculations (running REMD, Turbomole and Gaussian parallelized codes) on rather large molecular systems.
Conformational search and predicted IR spectra:
The structural assignment of biomolecules studying by means of IR
spectroscopy is done by comparison with high level ab initio
calculation on low lying isomers. The theoretical treatment can be done in
our Laboratory and through collaborations with theoretical groups with
whom we already worked with:
-M.P. Gaigeot (LAMBE Evry) for Car-Parrinello Molecular Dynamics
simulations,
-F. Calvo (LASIM Lyon) for exhaustive exploration of the potential energy
surface through Replica Exchange Molecular Dynamics (REMD) simulations
using Amber force field.
We have recently evaluated several theoretical methods (DFT, DFT-D, MP2 and hybrid QM/MM at the B3LYP/AM1 level) for assignment of IR spectra of gas phase biomolecules, including nucleobases, amino acids, peptides, sugars, neurotransmitters and antibiotics. Depending on the size of molecular species, these methods can be applied accordingly with a prediction error of the IR transition positions ranging roughly in between 10 and 15 cm-1 even for large molecular systems presently under investigation.
Ab-initio excited state calculations:
Excitation energies (vertical and adiabatic) and response properties are calculated with the CC2 method, which is a simplified and cost-effective variant of the coupled-cluster method with single and double excitations. These calculations are carried out with the TURBOMOLE suite of program, making use of the resolution-of-the-identity (RI) approximation for the evaluation of the electron-repulsion integrals