Orientational dynamics orientation

There is, of course, a mass of rather direct evidence on orientation at the liquid-vapor interface, much of which is at least implicit in this chapter and in Chapter IV. The methods of statistical mechanics are applicable to the calculation of surface orientation of assymmetric molecules, usually by introducing an angular dependence to the inter-molecular potential function (see Refs. 67, 68, 77 as examples). Widom has applied a mean-held approximation to a lattice model to predict the tendency of AB molecules to adsorb and orient perpendicular to the interface between phases of AA and BB [78]. In the case of water, a molecular dynamics calculation concluded that the surface dipole density corresponded to a tendency for surface-OH groups to point toward the vapor phase [79]. 

Because of the generality of the symmetry principle that underlies the nonlinear optical spectroscopy of surfaces and interfaces, the approach has found application to a remarkably wide range of material systems. These include not only the conventional case of solid surfaces in ultrahigh vacuum, but also gas/solid, liquid/solid, gas/liquid and liquid/liquid interfaces. The infonnation attainable from the measurements ranges from adsorbate coverage and orientation to interface vibrational and electronic spectroscopy to surface dynamics on the femtosecond time scale. 

The practical goal of EPR is to measure a stationary or time-dependent EPR signal of the species under scrutiny and subsequently to detemiine magnetic interactions that govern the shape and dynamics of the EPR response of the spin system. The infomiation obtained from a thorough analysis of the EPR signal, however, may comprise not only the parameters enlisted in the previous chapter but also a wide range of other physical parameters, for example reaction rates or orientation order parameters. 

The polarization dependence of the photon absorbance in metal surface systems also brings about the so-called surface selection rule, which states that only vibrational modes with dynamic moments having components perpendicular to the surface plane can be detected by RAIRS [22, 23 and 24]. This rule may in some instances limit the usefidness of the reflection tecluiique for adsorbate identification because of the reduction in the number of modes visible in the IR spectra, but more often becomes an advantage thanks to the simplification of the data. Furthenuore, the relative intensities of different vibrational modes can be used to estimate the orientation of the surface moieties. This has been particularly useful in the study of self-... 

The anisotropy of the product rotational state distribution, or the polarization of the rotational angular momentum, is most conveniently parametrized tluough multipole moments of the distribution [45]. Odd multipoles, such as the dipole, describe the orientation of the angidar momentum /, i.e. which way the tips of the / vectors preferentially point. Even multipoles, such as the quadnipole, describe the aligmnent of /, i.e. the spatial distribution of the / vectors, regarded as a collection of double-headed arrows. Orr-Ewing and Zare [47] have discussed in detail the measurement of orientation and aligmnent in products of chemical reactions and what can be learned about the reaction dynamics from these measurements. 

Grr-Ewing A J and Zare R N 1995 Orientation and alignment of the products of bimolecular reactions The Chemicai Dynamics and Kinetics of Smaii Radicais vol 2, ed K Liu and A Wagner (Singapore World Scientific) pp 936-1063... 

Brochard F, Pieranski P and Guyon E 1972 Dynamics of the orientation of a nematic-liquid-crystal film in a variable magnetic field Phys.Rev.Lett 2S 1681-3... 

The END trajectories for the simultaneous dynamics of classical nuclei and quantum electrons will yield deflection functions. For collision processes with nonspherical targets and projectiles, one obtains one deflection function per orientation, which in turn yields the semiclassical phase shift and thus the scattering amplitude and the semiclassical differential cross-section... 

Nelson, M., Humphrey, W., Gursoy, A., Dalke, A., Kale, L., Skeel, R.D., Schul-ten, K. NAMD - A parallel, object-oriented molecular dynamics program. Int. J. Supercomputing Applications and High Performance Computing 10 (1996) 251-268. 

In many cases the dynamical system consists of fast degrees of freedom, labeled x, and slow degrees of freedom, labeled y. An example is that of a fluid containing polyatomic molecules. The internal vibrations of the molecules are often very fast compared to their translational and orientational motions. Although this and other systems, like proteins, have already been treated using RESPA,[17, 34, 22, 23, 24, 25, 26] another example, and the one we focus on here, is that of a system of very light particles (of mass m) dissolved in a bath of very heavy particles (mass M).[14] The positions of the heavy particles are denoted y and the positions of the light particles rire denoted by X. In this case the total Liouvillian of the system is ... 

K. Schulten. NAMD—a parallel, object-oriented molecular dynamics program. Inti. J. Supercomput. Applies. High Performance Computing, 10 251-268, 1996. 

The key to these more efficient treatments is a natural canonical formulation of the rigid body dynamics in terms of rotation matrices. The orientational term of the Lagrangian in these variables can be written simply as... 

The explicit definition of water molecules seems to be the best way to represent the bulk properties of the solvent correctly. If only a thin layer of explicitly defined solvent molecules is used (due to hmited computational resources), difficulties may rise to reproduce the bulk behavior of water, especially near the border with the vacuum. Even with the definition of a full solvent environment the results depend on the model used for this purpose. In the relative simple case of TIP3P and SPC, which are widely and successfully used, the atoms of the water molecule have fixed charges and fixed relative orientation. Even without internal motions and the charge polarization ability, TIP3P reproduces the bulk properties of water quite well. For a further discussion of other available solvent models, readers are referred to Chapter VII, Section 1.3.2 of the Handbook. Unfortunately, the more sophisticated the water models are (to reproduce the physical properties and thermodynamics of this outstanding solvent correctly), the more impractical they are for being used within molecular dynamics simulations. 

Consider a quantity of some liquid, say, a drop of water, that is composed of N individual molecules. To describe the geometry of this system if we assume the molecules are rigid, each molecule must be described by six numbers three to give its position and three to describe its rotational orientation. This 6N-dimensional space is called phase space. Dynamical calculations must additionally maintain a list of velocities. 

Molecular dynamics studies can be done to examine how the path and orientation of approaching reactants lead to a chemical reaction. These studies require an accurate potential energy surface, which is most often an analytic... 

Molecular mechanics methods have been used particularly for simulating surface-liquid interactions. Molecular mechanics calculations are called effective potential function calculations in the solid-state literature. Monte Carlo methods are useful for determining what orientation the solvent will take near a surface. Molecular dynamics can be used to model surface reactions and adsorption if the force held is parameterized correctly. 

J. I. Steiafeld, J. S. Francisco, and W. L. Hase, Chemical Kinetics and Dynamics, Prentice Hall, Englewood Chffs, N.J., 1989. Oriented more toward gas-phase reactions and iacludes more advanced microscopic iaterpretations from the perspective called chemical physics. 

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