Density vibrational frequencies

Since the stochastic Langevin force mimics collisions among solvent molecules and the biomolecule (the solute), the characteristic vibrational frequencies of a molecule in vacuum are dampened. In particular, the low-frequency vibrational modes are overdamped, and various correlation functions are smoothed (see Case [35] for a review and further references). The magnitude of such disturbances with respect to Newtonian behavior depends on 7, as can be seen from Fig. 8 showing computed spectral densities of the protein BPTI for three 7 values. Overall, this effect can certainly alter the dynamics of a system, and it remains to study these consequences in connection with biomolecular dynamics. 

Direct Mass Measurement One type of densitometer measures the natural vibration frequency and relates the amplitude to changes in density. The density sensor is a U-shaped tube held stationaiy at its node points and allowed to vibrate at its natural frequency. At the curved end of the U is an electrochemical device that periodically strikes the tube. At the other end of the U, the fluid is continuously passed through the tube. Between strikes, the tube vibrates at its natural frequency. The frequency changes directly in proportion to changes in density. A pickup device at the cui ved end of the U measures the frequency and electronically determines the fluid density. This technique is usefiil because it is not affec ted by the optical properties of the fluid. However, particulate matter in the process fluid can affect the accuracy. 

It should be noted that there is a considerable difference between rotational structure narrowing caused by pressure and that caused by motional averaging of an adiabatically broadened spectrum [158, 159]. In the limiting case of fast motion, both of them are described by perturbation theory, thus, both widths in Eq. (3.16) and Eq (3.17) are expressed as a product of the frequency dispersion and the correlation time. However, the dispersion of the rotational structure (3.7) defined by intramolecular interaction is independent of the medium density, while the dispersion of the vibrational frequency shift (5 12) in (3.21) is linear in gas density. In principle, correlation times of the frequency modulation are also different. In the first case, it is the free rotation time te that is reduced as the medium density increases, and in the second case, it is the time of collision tc p/ v) that remains unchanged. As the density increases, the rotational contribution to the width decreases due to the reduction of t , while the vibrational contribution increases due to the dispersion growth. In nitrogen, they are of comparable magnitude after the initial (static) spectrum has become ten times narrower. At 77 K the rotational relaxation contribution is no less than 20% of the observed Q-branch width. If the rest of the contribution is entirely determined by... 

Fig. 3.12. The room temperature CARS spectra of CH4 obtained in [162] at the following densities (1) 0.1 amagat of pure CH4 (2) 5 amagat CH4 (3) 5 amagat CH4 + 35 amagat Ar (4) 5 amagat CH4 + 85 amagat Ar. The position of the vibration frequency wv is indicated as well as the centre of gravity of the Q0i branch rotational structure wv + coq.

The assignment of the TR spectra were based on the known photochemistry of the aryl azides and comparison of the TR spectra vibrational frequencies to those predicted by density functional theory calculations for the likely photochemical intermediates. The good agreement between the experimental TR vibrational... 

The computational prediction of vibrational spectra is among the important areas of application for modem quantum chemical methods because it allows the interpretation of experimental spectra and can be very instrumental for the identification of unknown species. A vibrational spectrum consists of two characteristics, the frequency of the incident light at which the absorption occurs and how much of the radiation is absorbed. The first quantity can be obtained computationally by calculating the harmonic vibrational frequencies of a molecule. As outlined in Chapter 8 density functional methods do a rather good job in that area. To complete the picture, one must also consider the second quantity, i. e., accurate computational predictions of the corresponding intensities have to be provided. 

Amos, R. D., Murray, C. W., Handy, N. C., 1993, Structures and Vibrational Frequencies of FOOF and FONO Using Density Functional Theory , Chem. Phys. Lett., 202, 489. 

Finley, J. W., Stephens, P. J., 1995, Density Functional Theory Calculations of Molecular Structures and Harmonic Vibrational Frequencies Using Hybrid Density Functionals , J. Mol. Struct. (Theochem), 357, 225. 

Hay, P. J., Martin, R. L., 1998, Theoretical Studies of the Structures and Vibrational Frequencies of Actinide Compounds Using Relativistic Effective Core Potentials With Hartree-Fock and Density Functional Methods ... 

Hutter, J., Liithi, H. P., Diederich, F., 1994, Structures and Vibrational Frequencies of the Carbon Molecules C2-C18 Calculated by Density Functional Theory , J. Am. Chem. Soc., 116, 750. 

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