Molecular calculated vibrational spectra

The possibility of directly measuring molecular stractures is an important advantage of microwave spectroscopy. In vibrational spectroscopy, isotopic substitution helps the interpretation of the spectra but the assigned structmes are only the calculated ones which offer the best match between the calculated vibrational spectrum and the observed one. It is also difficult to determine relative abundances from electronic spectroscopy because the relative intensity of the observed electronic transitions of the chromophore can be affected by the dynamics of the excited state. Both techniques are complementary vibrational spectroscopy can address the conformational preferences of large systems which microwave spectroscopy cannot... 

The appearance of additional peaks in the monolayer spectrum suggests the existence of surface vibratory modes associated with rotations and translations of the free molecule hindered by adsorption. To identify these modes, it is necessary to perform normal mode calculations of the vibrational spectrum of the adsorbed molecule. These calculations are also of interest because of the sensitivity of the frequency and intensity of the surface vibratory modes to the molecular orientation and the location and strength of its bonds to the substrate. 

The gas-phase molecular structures of CF3SF, CF3SCI (332), and of CFsSBr (307) were determined from electron diffraction experiments. Vibrational spectra and harmonic force field calculations were reported for CF3SCI (47). For CFsSBr an improved method of preparation from CF3SCI and HBr was developed, and a full normal coordinate analysis was performed and thermodynamic functions were derived on the basis of a modified assigiunent of the vibrational spectrum (42,307). 

High-pressure Raman studies have been made to follow phase transitions of MgSi03.460 462 Molecular dynamics calculations have been performed on the vibrational spectrum of CaSi03 over the melt to glass transition.463... 

The experimental and computational study of bacterial thioredoxin, an E. coli protein, at THz frequencies is presented. The absorption spectrum of the entire protein in water was studied numerically in the terahertz range (0.1 - 2 THz). In our work, the initial X-ray molecular structure of thioredoxin was optimized using the molecular dynamical (MD) simulations at room temperature and atmospheric pressure. The effect of a liquid content of a bacterial cell was taken into account explicitly via the simulation of water molecules using the TIP3P water model. Using atomic trajectories from the room-temperature MD simulations, thioredoxin s THz vibrational spectrum and the absorption coefficient were calculated in a quasi harmonic approximation. 

In the first step the positions of all atoms in the cell are optimized. Cell parameters are usually borrowed from experiment. In some cases they are optimized [84] and in some cases not [85]. Harmonic frequency calculations verify that the computed structure corresponds to the global PES minimum. In the second step the anharmonic OH stretching [83, 84] frequency is estimated using ID potential curves calculated as a function of the displacement for the hydrogen atom. In the third step classical molecular dynamics (MD) simulations are performed. The IR [85] or vibrational spectrum [82, 83] of the crystal is computed from the Fourier transform of the corresponding time correlation function (see Section 9.3.1). 

Cyclohexadecane is an interesting and instructive example. From both X-ray diffraction and vibrational spectroscopy the low-temperature crystal form has the square [4444] conformation which is also found for derivativesThis is reckoned most stable for the gas phase by molecular mechanics calculations " , and best explains the dynamic NMR results for a solution at —152 °C. What seems to be a consistent picture is perturbed by the fact that there is a high-temperature crystal form which, like the liquid at room temperature, has a vibrational spectrum that indicates the presence of little of the [4444] conformation The experimental heat of formation and that calculated for the [4444] conformation are also discrepant As yet there is no explanation for these various facts. ... 

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