Analysis of infrared and Raman spectra calculated by molecular dynamics

Conformational symmetry and vibrational dynamics of polymers

“…Let us consider the ideal polymer chain which can be geometrically constructed by applying a screw-symmetry operation to the starting chemical repeat unit. In the quadratic approximation, the vibrational potential energy of such systems, V = V(R i n ), where R i n are the i th internal coordinates of the n th residue, can be expressed in Taylor's series about the equilibrium configuration and the expansion truncated to second order when the harmonic approximation is adopted (22) Since at equilibrium the system possesses a minimum potential energy, (F) i n is equal to zero. After a suitable shifting of axes, the potential energy in harmonic approximation can be written as (23) Making use of the periodicity of the chain, it follows that (24) The kinetic energy of the infinite chain can be written in an analogous way in terms of the momenta P n conjugate to the coordinates R i n and the kinetic energy matrix G. …”

“…The MD even enables modeling of disordered systems. The forgoing techniques have been widely used in a variety of systems [21][22][23][24][25][26][27][28][29].…”

Predicting Raman Spectra of Condensed Polymer Phases from MD Simulations

“…The Raman intensity can be computed from the amplitude of molecular polarizability oscillations as the mode vibrates. The second approach is to obtain the time-varying molecular polarizability directly from a simulation trajectory and compute the power spectrum; this method has been applied only a few times, to crystalline systems. − The necessary polarizability can either be obtained either from ab initio calculations − or empirical models. , Ab initio methods such as density functional theory (DFT) are more accurate but require vastly more computational resources.…”

“…The bond polarizability constants are sometimes called electro-optical parameters in literature. − Values for bond polarizability constants can be obtained either by fitting to experimental Raman peak intensities of molecules containing the bonds of interest or by fitting molecular polarizabilities computed using DFT . The bond polarizability model has been used successfully to represent the molecular polarizability of hydrocarbons, ,,, small molecules, and silica polymorphs. , In our work, we will use the bond polarizability model to compute the Raman-activity of molecular vibrations in condensed phases.…”

Phonon Dispersion and Heat Capacity in β-Sheet Poly(L-alanine)

“…Analysis of infrared and Raman spectra calculated by the molecular dynamical method has also been recently reported. 3 As in case of poly(L-valine) 4 ( PLV), dispersion curves also provide information on the extent of coupling along the chain together with an understanding of the dependence of the frequency of a given mode upon the sequence length of ordered conformation.…”