Correction of Vibrational Broadening in Molecular Dynamics Clusters with the Normal Mode Optimization Method

Abstract

Vibrational properties of solutions are frequently simulated with clusters of a solute and a few solvent molecules obtained during molecular dynamics (MD) simulations. The raw cluster geometries, however, often provide unrealistic vibrational band broadening, for both ab initio and empirical force fields. In this work, partial optimization in normal-mode coordinates is used on empirical basis to reduce the broadening. The origin of the error is discussed on a simplified two-dimensional system, which indicates that the problem is caused by the anharmonic MD potential, mode coupling, and neglect of quantum effects. Then the procedure of partial geometry optimization on Raman and Raman optical activity (ROA) spectra is applied and analyzed for the solvated lactamide molecule. Comparison to experiment demonstrates that the normal-mode partial optimization technique with a suitable frequency limit can significantly reduce the broadening error. For lactamide, experimental and simulated vibrational bandwidths are compared; the most realistic theoretical spectra are obtained for partially optimized clusters with the vibrational wavenumber cutoff of about 200 cm(-1).

On the magnetic circular dichroism of benzene. A density-functional study

“…After an equilibration stage and 0.1 ns molecular dynamics (1 fs integration time, NVT ensemble, OPLSAA 55 force field) benzene/methane clusters were created by removing solvent molecules that were farther away than 6, 8, and 15 Å from benzene. Geometry of the cluster was partially optimized in vibrational normal modes coordinates 56 with the 300 cm 1 threshold for vibrational frequencies, 57 and subjected to TDDFT computations as for the free molecule. An analogous computation was performed in benzene placed in a cubic box of water (37.12 Å box size, OPLSAAL (benzene) and TIP3P 58 (water) force fields, 6 Å cluster size only).…”

Establishing the link between fibril formation and Raman optical activity spectra of insulin

“…The fragments were capped by methyl groups and subjected to partial optimization in vibrational normal mode coordinates, 41 fixing the limiting normal frequency 42 to 100 cm À1 . This lower value allowed for a more extensive relaxation of the geometries and provided slightly better spectra (Fig.…”

Temperature Dependence of NMR Parameters Calculated from Path Integral Molecular Dynamics Simulations

“…More precisely, when the energy of the excited states is larger than the Boltzmann thermal energy (E >> k B T), application of MD is inappropriate because the system stays in the ground state. [26][27] At room temperature (k B T ~ 209 cm -1 at 300 K), for example, this situation occurs for most high-frequency vibrational molecular motions, such as C-H stretching (E ~ 3000 cm -1 ). On the other hand, averaging of the solvent positions and low-frequency molecular motions (e.g., semi-free rotation of covalent bonds) can be done with MD.…”