Molecular degrees of freedom

Teleman, O. Jonsson, B. Engstrdm, S. (1987) A Molecular Dynamics Simulation of a Water Model with Intramolecular Degrees of Freedom, Molecular Physics 60, 193-203... 

An interesting point is that infrared absorptions that are symmetry-forbidden and hence that do not appear in the spectrum of the gaseous molecule may appear when that molecule is adsorbed. Thus Sheppard and Yates [74] found that normally forbidden bands could be detected in the case of methane and hydrogen adsorbed on glass this meant that there was a decrease in molecular symmetry. In the case of the methane, it appeared from the band shapes that some reduction in rotational degrees of freedom had occurred. Figure XVII-16 shows the IR spectrum for a physisorbed H2 system, and Refs. 69 and 75 give the IR spectra for adsorbed N2 (on Ni) and O2 (in a zeolite), respectively. 

In an ideal molecular gas, each molecule typically has translational, rotational and vibrational degrees of freedom. The example of one free particle in a box is appropriate for the translational motion. The next example of oscillators can be used for the vibrational motion of molecules. 

Straub J E and Berne B J 1986 Energy diffusion in many dimensional Markovian systems the consequences of the competition between inter- and intra-molecular vibrational energy transfer J. Chem. Phys. 85 2999 Straub J E, Borkovec M and Berne B J 1987 Numerical simulation of rate constants for a two degree of freedom system in the weak collision limit J. Chem. Phys. 86 4296... 

The direct dissociation of diatomic molecules is the most well studied process in gas-surface dynamics, the one for which the combination of surface science and molecular beam teclmiques allied to the computation of total energies and detailed and painstaking solution of the molecular dynamics has been most successful. The result is a substantial body of knowledge concerning the importance of the various degrees of freedom (e.g. molecular rotation) to the reaction dynamics, the details of which are contained in a number of review articles [2, 36, 37, 38, 39, 40 and 41]. 

Many optical studies have employed a quasi-static cell, through which the photolytic precursor of one of the reagents and the stable molecular reagent are slowly flowed. The reaction is then initiated by laser photolysis of the precursor, and the products are detected a short time after the photolysis event. To avoid collisional relaxation of the internal degrees of freedom of the product, the products must be detected in a shorter time when compared to the time between gas-kinetic collisions, that depends inversely upon the total pressure in the cell. In some cases, for example in case of the stable NO product from the H + NO2 reaction discussed in section B2.3.3.2. the products are not removed by collisions with the walls and may have long residence times in the apparatus. Study of such reactions are better carried out with pulsed introduction of the reagents into the cell or under crossed-beam conditions. 

A very recent overview, including efforts to interface semi-empirical electronic structure with molecular mechanics treatments of some degrees of freedom is given by ... 

A quantum mechanical treatment of molecular systems usually starts with the Bom-Oppenlieimer approximation, i.e., the separation of the electronic and nuclear degrees of freedom. This is a very good approximation for well separated electronic states. The expectation value of the total energy in this case is a fiinction of the nuclear coordinates and the parameters in the electronic wavefunction, e.g., orbital coefficients. The wavefiinction parameters are most often detennined by tire variation theorem the electronic energy is made stationary (in the most important ground-state case it is minimized) with respect to them. The... 

Molecular dynamics tracks tire temporal evolution of a microscopic model system tlirough numerical integration of tire equations of motion for tire degrees of freedom considered. The main asset of molecular dynamics is tliat it provides directly a wealtli of detailed infonnation on dynamical processes. 

Election nuclear dynamics theory is a direct nonadiababc dynamics approach to molecular processes and uses an electi onic basis of atomic orbitals attached to dynamical centers, whose positions and momenta are dynamical variables. Although computationally intensive, this approach is general and has a systematic hierarchy of approximations when applied in an ab initio fashion. It can also be applied with semiempirical treatment of electronic degrees of freedom [4]. It is important to recognize that the reactants in this approach are not forced to follow a certain reaction path but for a given set of initial conditions the entire system evolves in time in a completely dynamical manner dictated by the inteiparbcle interactions. 

The time dependence of the molecular wave function is carried by the wave function parameters, which assume the role of dynamical variables [19,20]. Therefore the choice of parameterization of the wave functions for electronic and nuclear degrees of freedom becomes important. Parameter sets that exhibit continuity and nonredundancy are sought and in this connection the theory of generalized coherent states has proven useful [21]. Typical parameters include molecular orbital coefficients, expansion coefficients of a multiconfigurational wave function, and average nuclear positions and momenta. We write... 

In this chapter, we discussed the permutational symmetry properties of the total molecular wave function and its various components under the exchange of identical particles. We started by noting that most nuclear dynamics treatments carried out so far neglect the interactions between the nuclear spin and the other nuclear and electronic degrees of freedom in the system Hamiltonian. Due to... 

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