Water spectra harmonic vibration

In Section V the reorientation mechanism (A) was investigated in terms of the only (hat curved) potential well. Correspondingly, the only stochastic process characterized by the Debye relaxation time rD was discussed there. This restriction has led to a poor description of the submillimeter (10-100 cm-1) spectrum of water, since it is the second stochastic process which determines the frequency dependence (v) in this frequency range. The specific vibration mechanism (B) is applied for investigation of the submillimetre and the far-infrared spectrum in water. Here we shall demonstrate that if the harmonic oscillator model is applied, the small isotope shift of the R-band could be interpreted as a result of a small difference of the masses of the water isotopes. 

It is obvious that most of the modes are superimposed. The IR spectrum clearly shows at least four of the 12 IR active OH stretching modes resolved (see the insert in Figure 3.3) while 12 maxima can be distinguished in the region 1200-700 cm" , which could correspond to the resolution of aU the IR-active OH bending modes. Below 60 cm" several maxima are also observed, due to Cu—O and Cu—Cl vibrations. The features observed in the region 1700-1300 cm" are either due to harmonics of lower frequency vibrations or to water and carbonate impurities. 

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. 

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