Thermally simulated polarization

DTA = differential thermal analysis FCC = face centered cubic FWHM = full width at half maximum ICDD = international center for diffraction data JCPDS = joint committee on powder diffraction standards EP = Lorentz and polarization PO = Preferred orientation. PT = parallel tempering PXRD = powder X-ray diffraction SA = simulated annealing SWE = short-wavelength-limit TGA = thermogravametric analysis XRPD = X-ray powder diffraction XRD = X-ray diffraction ... 

AIMD simulations appear as a promising tool for a first-principles modeling of enzymes. Indeed, they enable in situ simulations of chemical reactions furthermore, they are capable of tEiking crucial thermal effects [53] into account finally, they automatically include many of the physical effects so difficult to model in force-field based simulations, such as polarization effects, many-body forces, resonance stabilization of aromatic rings and hydration phenomena. 

Predictions by Simulation. Theoretical (WAXS) reflection intensities for each simulated structure were calculated by assuming the interior unit cell to be representative of the bulk and then applying the conventional summation of atomic scattering over lattice indices, h, k, and 1, to arrive at the set of structure factors F(hk/), which were then corrected for polarization, Lorentz scattering, and isotropic thermal motion to obtain observable intensities I (hkl) (15)... 

Now, the argument just presented relies on the unproven assumption that rotational quantum beats arising from a thermal sample of isolated molecules will wash each other out. Recently, we examined this assumption by directly simulating the decays associated with thermally averaged rotational beats.47 (Our initial motivation for this work was to try to explain the picosecond pump-probe results of Refs. 51 and 52, which results showed the existence of polarization-dependent early time transients in the decays of t-stilbene.) These theoretical simulations and subsequent picosecond-beam experiments47-50 have revealed that the manifestations of rotational coherence in thermally averaged decays can, in fact, be observed. In this section, we briefly review these results and examine some of their implications with regard to time-resolved studies of IVR. 

Undoubtedly, the realism of any simulation of a protein-solvent system will be further enhanced if all parts of the system experience thermal motion. Because water molecules interact most strongly with polar side chains and because the conformation of long polar side chains may be subject to considerable thermal disorder, flexibility of side chains, in particular, is a major aspect of protein-solvent interaction. Thermal motion of side chains could be provided for rather simply by rigid-body internal rotation of side chains about side-chain single bonds as part of the Monte Carlo process. 

Figure 3.19. Simulated s- and p-polarized IRRAS spectra of Si02 layers on Si as function of layer thickness at = 60°. Optical constants of thermal SI02 are specified according to Ref. [52] ns = 3.42.

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