title: Molecular dynamics with restrictions derived from optical spectra.
abstract: The information about molecular structure coded in the optical spectra must often be deciphered by complicated computational procedures. A combination of spectral modeling with the molecular dynamic simulations makes the process simpler, by implicit accounting for the inhomogeneous band broadening and Boltzmann averaging of many conformations. Ideally, geometries of studied systems can be deduced by a direct confrontation of such modeling with the experiment. In this work, the comparison is enhanced by restrictions to molecular dynamics propagations based on the Raman and Raman optical activity spectra. The methodology is introduced and tested on model systems comprising idealized H(2)O(2), H(2)O(3) molecules, and the alanine zwitterion. An additional gradient term based on the spectral overlap smoothed by Fourier transformation is constructed and added to the molecular energy during the molecular dynamics run. For systems with one prevalent conformation the method did allow to enrich the Boltzmann ensemble by a spectroscopically favored structure. For systems with multiconformational equilibria families preferential conformations can be selected. An alternative algorithm based on the comparison of the averaged spectra with the reference enabling iterative updates of the conformer probabilities provided even more distinct distributions in shorter times. It also accounts for multiconformer equilibria and provided realistic spectra and conformer distribution for the alanine.
authors.affiliation: Institute of Organic Chemistry and Biochemistry, Academy of Sciences, Flemingovo nám. 2, 16610, Prague 6, Czech Republic.
authors.forename: Jakub
authors.initials: J
authors.lastname: Kaminský
authors.forename: Jirí
authors.initials: J
authors.lastname: Sebek
authors.forename: Petr
authors.initials: P
authors.lastname: Bour