Molecular dynamics simulations spectra

A.J. Ramirez-Cuesta, P.C.H. Mitchell, S.F. Parker P.M Rodger (1999). Phys. Chem. Chem, Phys., 1, 5711-5715. Dynamics of water and template molecules in the interlayer space of a layered aluminophosphate. Experimental inelastic neutron scattering spectra and molecular dynamics simulated spectra. 

Fig. 7.12 Experimental and calculated infrared spectra for liquid water. The black dots are the experimental values. The thick curve is the classical profile produced by the molecular dynamics simulation. The thin curve is obtained by applying quantum corrections. (Figure redrawn from Guilbt B 1991. A Molecular Dynamics Study of the Infrared Spectrum of Water. Journal of Chemical Physics 95 1543-1551.)...

Fig. 37. The translational power spectrum as predicted by molecular dynamics simulation ol liquid water (from Ref. 3>)...

The COSMO solvent model has been used to simulate the influence of water on the electronic spectrum of A -methylacetamide [81], and the results was compared with the results of molecular dynamics simulations (where the electronic spectrum were calculated as an average over 90 snapshots from MD simulations). Most of the hydration effects were found to come from the first solvation shell hydrogen-bonded water molecules, and the continuum model does not properly account for these effects. The rotatory strengths were not calculated directly in ref. [81]. However, the results were used to model ECD spectra of peptides via the coupled oscillator model, with satisfactory result. 

Use the SWISS-MODEL (9) to build possible protein structures for these genes dock potential broad-spectrum antibiotics candidates to the active sites with AutoDock (10) and use molecular dynamics simulations to research possible binding modes between antibiotics and target proteins (11). 

Garofalini, S. H. (1984b). Molecular dynamics simulation of the frequency spectrum of amorphous silica. J. Chem. Phys., 3189-92. 

Romero C, Jonah CD. (1989) Molecular dynamics simulation of the optical absorption spectrum of the hydrated electron. J Chem Phys 90 1877-1887. 

Lately, quantum-classical molecular-dynamics simulations of an excess electron in water performed for wide ranges of temperature and pressure suggest that the observed red shift of the optical absorption spectrum is a density effect rather than a temperature effect. Indeed, by increasing the temperature, the mean volume of the cavity occupied by the solvated electron increases due to weakening of bonds between solvent molecules the electron is less confined in the cavity, and the potential well becomes less deep. 

The situation is quite different for n- r transitions. The lone electron pair is particularly well stabilized by polar and particularly by protic solvents so it becomes energetically more difficult to excite. Figure 2.45 shows the spectrum of N-nitrosodimethylamine in different solvents. Results of calculations indicate that the negative solvatochromism of carbonyl compounds can be explained on the basis of the structural changes due to the formation of hydrogen bonds (Taylor, 1982). Molecular dynamics simulations, however, indicate that the net blue shift is primarily due to electrostatic interactions (Blair et al., 1989). A large number of water molecules around the entire formaldehyde are responsible for the total blue shift the first solvation shell only accounts for one-third of the full shift. 

Successful first-principles molecular dynamics simulations in the Car-Paxrinello framework requires low temperature for the annealed electronic parameters while maintaining approximate energy conservation of the nuclear motion, all without resorting to unduly small time steps. The most desirable situation is a finite gap between the frequency spectrum of the nuclear coordinates, as measured, say, by the velocity-velocity autocorrelation function. 

Reha D, Valdes H, Vondrasek J, Hobza P, Abu-Riziq A, Crews B, de Vries MS (2005) Stmc-ture and IR spectrum of phenylalanyl-glycyl-glycine tripetide in the gas-phase IR/UV experiments ab initio quantum chemical calculations and molecular dynamic simulations. Eur JChem 11 6803-6817... 

Fig.10.27 INS spectrum (solid line) and molecular dynamics simulation (dashed line) of acetanilide in the region below 400 cm. Reproduced from [57] with permission of the American Institute of Physics.

Since the direct simulation of vibrational relaxation in condensed phases is clearly a difficult and lengthy procedure for molecules with realistic vibrational frequencies, Shugard et al. ° proposed an alternative approach based on work of Adelman and Doll and applied it to relaxation of diatomic impurities in solid matrices. The motion of atoms near the impurity was simulated directly and the effect of more distant atoms was taken into account through a stochastic force, which was constructed from the phonon spectrum of the solid. This method still requires that the relaxation time not be too long compared to the vibrational period (i.e., that the vibrational frequency not be too high) but the calculation is much faster than a full molecular dynamics simulation since only a few degrees... 

A preliminary ab initio molecular dynamics simulation has been carried using the Car-Parrinello approach [9]. The volume of the simulation cell was kept constant at the experimental value of the moganite type PON. The cell contained 72 atoms ( P24O24N24 ) The weighted density of states of PON obtained from the ab intio molecular dynamics simulation is compared with the infrared spectrum in Fig. 4. It can be seen that the gross features of the experimental spectrum are reasonably reproduced in the simulation. 

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