Infrared Spectroscopy of N-Methylacetamide Revisited by ab Initio Molecular Dynamics Simulations

Abstract

The density functional theory based molecular dynamics simulation method ("Car-Parrinello") was applied in a numerical study of the electronic properties, hydrogen bonding, and infrared spectroscopy of the trans and cis isomer of N-methylacetamide in aqueous solution. A detailed analysis of the electronic structure of the solvated molecules, in terms of localized Wannier functions and Born atomic charges, is presented. Two schemes for the computation of the solute infrared absorption spectrum are investigated: In the first method the spectrum is determined by Fourier transforming the time correlation function of the solute dipole as determined from the Wannier function analysis. The second method uses instead the molecular current-current correlation function computed from the Born charges and atomic velocities. The resulting spectral properties of trans- and cis-NMA are carefully compared to each other and to experimental results. We find that the two solvated isomers can be clearly distinguished by their infrared spectral profile in the 1000-2000 cm(-)(1) range.

Structures and spectral signatures of protonated water networks in bacteriorhodopsin

“…Although normalmode analysis of quasirigid molecules in the gas phase nowadays has become a standard tool, the computation of IR spectra in dynamically interacting environments, such as condensed phases or biomolecular matrices, is much more intricate, if based on electronic structure calculations (24,(29)(30)(31)(32)(33)(34). Furthermore, a peculiar challenge is posed by the strongly anharmonic and flat potential energy surfaces as typically encountered by excess protons in hydrogen-bonded networks (20) such as WLANs, which challenges the harmonic approximation.…”

Local electric dipole moments for periodic systems via density functional theory embedding

“…The atomic electric dipole moments computed following Eq. (27) are, similar to Mulliken atomic charges, 163 rather basis set dependent. Nevertheless, it can be concluded that the increase of the absolute electric dipole moment of a liquid EC molecule compared to the one of a gas phase EC molecule (all obtained with the TZVP-GTH basis set) mostly arises from distinct contributions from its carbonyl group.…”

“…(27). The atomic electric dipole moment origin was set to the same origin as the one of the corresponding molecular electric dipole moment (i.e., the center of charge of the subsystem).…”

“…Local electric dipole moments can be computed by localization of Wannier functions. [21][22][23][24][25][26][27][28][29][30] In this paper, an alternative approach to the evaluation of local electric dipole moments is presented. We rely on suba) Email: sandra.luber@chem.uzh.ch system DFT-based embedding (for the sake of brevity, in the following partly only referred to as "embedding") where the total electronic density is divided into electronic densities of subsystems.…”

“…This is also true for atomic electric dipole moments computed according to Eq. (27) where the origin was set to the center of atomic charge of the subsystem containing the atom of interest. In an analogous manner, the systems presented in Sec.…”