MD and Ab Initio Modeling of Electronic Spectra of N-methylacetamide and Peptides in Water Solutions


J. Šebek1,2, Z. Kejík1 and P. Bouř2


1Institute of Chemical Technology, Technická 5, 166 28 Praha

2Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nám. 2, 166 10, Praha


Many methods used in analytical chemistry are based on interactions of molecules with ultra-violet, visible (UV-vis) or infrared (IR) light. Spectral shapes and band positions depend not only on the structure, but also on solvent environment. We deal with modeling of absorption and circular dichroism (CD) spectra in UV-vis region and with the influence of polar solvents (water). N-methylacetamide (NMA) is the simplest molecule containing the amide chromophore R-CO-NH-R (where R and R are other groups than H) and thus it is convenient for modeling of general spectral characteristics of peptides and proteins [1]. The influence of the solvent was simulated by combining of continuum dielectric model (COSMO) with inclusion of explicit water molecules. Results of these calculations revealed three main mechanisms by which the solvent modifies the spectra: 1) via change of geometrical parameters of the amide group, 2) by the electrostatic field (in the case of polar solvent) and 3) by the hydrogen bonding and direct participation of the water orbitals.

Cluster geometries were obtained from MD simulations (TINKER software, AMBER forcefield). Cluster absorption spectra were computed ab initio in vacuum and with the COSMO model for multiple geometries. Average spectra were in a very good agreement with experimental spectrum of aqueous NMA solution. Influence of non-H bonded water molecules on the band shapes and frequencies was not significant.

Average transition dipole moments of the NMA molecule obtained ab initio were used for the predicting of the CD spectra (in the UV region) of main peptide conformations: α-helix, β-sheet and coil conformation (polyproline II-like). Rotatory strengths were obtained by a semiempical Transition Dipole Coupling (TDC) model. Computed CD spectra of α-helix and coil were in a good agreement with available experiment, for β-sheet the agreement was not so good.


[1] Bouř, P.; Michalík, D.; Kapitán, J. J. Chem. Phys. 2005, 122, 144501 1-9.