Models polyatomic molecules

For a RRKM calculation without any approximations, the complete vibrational/rotational Flamiltonian for the imimolecular system is used to calculate the reactant density and transition state s sum of states. No approximations are made regarding the coupling between vibration and rotation. Flowever, for many molecules the exact nature of the coupling between vibration and rotation is uncertain, particularly at high energies, and a model in which rotation and vibration are assumed separable is widely used to calculate the quantum RRKM k(E,J) [4,16]. To illustrate this model, first consider a linear polyatomic molecule which decomposes via a linear transition state. The rotational energy for tire reactant is assumed to be that for a rigid rotor, i.e. 

Figure C3.5.6 compares the result of this ansatz to the numerical result from the Wiener-Kliintchine theorem. They agree well and the ansatz exliibits the expected exponential energy-gap law (VER rate decreases exponentially with Q). The ansatz was used to detennine the VER rate with no quantum correction Q= 1), with the Bader-Beme hannonic correction [61] and with a correction based [83, M] on Egelstaff s method [62]. The Egelstaff corrected results were within a factor of five of experiment, whereas other corrections were off by orders of magnitude. This calculation represents the present state of the art in computing VER rates in such difficult systems, inasmuch as the authors used only a model potential and no adjustable parameters. However the ansatz procedure is clearly not extendible to polyatomic molecules or to diatomic molecules in polyatomic solvents.

Most of the molecules we shall be interested in are polyatomic. In polyatomic molecules, each atom is held in place by one or more chemical bonds. Each chemical bond may be modeled as a harmonic oscillator in a space defined by its potential energy as a function of the degree of stretching or compression of the bond along its axis (Fig. 4-3). The potential energy function V = kx j2 from Eq. (4-8), or W = ki/2) ri — riof in temis of internal coordinates, is a parabola open upward in the V vs. r plane, where r replaces x as the extension of the rth chemical bond. The force constant ki and the equilibrium bond distance riQ, unique to each chemical bond, are typical force field parameters. Because there are many bonds, the potential energy-bond axis space is a many-dimensional space. 

We envision a potential energy surface with minima near the equilibrium positions of the atoms comprising the molecule. The MM model is intended to mimic the many-dimensional potential energy surface of real polyatomic molecules. (MM is little used for very small molecules like diatomies.) Once the potential energy surface iias been established for an MM model by specifying the force constants for all forces operative within the molecule, the calculation can proceed. 

Applequist J, Carl JR, Fung K-K (1972) Atom dipole interaction model for molecular polarizability. Application to polyatomic molecules and determination of atom polarizabilities. J Am Chem Soc... 

When we are working with such complicated objects like polyatomic molecules and metals, we are not able to describe completely the real system, and, consequently, we are forced to construct its model, the properties of which should satisfy the following conditions (1) it should be tractable by the contemporary theoretical methods (2) it has to simulate as much as possible the behavior of the real system and (3) it must not contradict any experimental results. Thus, the model is the point where the theory and experiments meet their mutual requirements, and where they directly influence each other ( ). 

After all, even in the first case we deal with the interaction of an electron belonging to the gas particle with all the electrons of the crystal. However, this formulation of the problem already represents a second step in the successive approximations of the surface interaction. It seems that this more or less exact formulation will have to be considered until the theoretical methods are available to describe the behavior both of the polyatomic molecules and the metal crystal separately, starting from the first principles. In other words, a crude model of the metal, as described earlier, constructed without taking into account the chemical reactivity of the surface, would be in this general approach (in the contemporary state of matter) combined with a relatively precise model of the polyatomic molecule (the adequacy of which has been proved in the reactivity calculations of the homogeneous reactions). 

Molecular dynamic studies used in the interpretation of experiments, such as collision processes, require reliable potential energy surfaces (PES) of polyatomic molecules. Ab initio calculations are often not able to provide such PES, at least not for the whole range of nuclear configurations. On the other hand, these surfaces can be constructed to sufficiently good accuracy with semi-empirical models built from carefully chosen diatomic quantities. The electric dipole polarizability tensor is one of the crucial parameters for the construction of such potential energy curves (PEC) or surfaces [23-25]. The dependence of static dipole properties on the internuclear distance in diatomic molecules can be predicted from semi-empirical models [25,26]. However, the results of ab initio calculations for selected values of the internuclear distance are still needed in order to test and justify the reliability of the models. Actually, this work was initiated by F. Pirani, who pointed out the need for ab initio curves of the static dipole polarizability of diatomic molecules for a wide range of internuclear distances. 

This chapter assesses the performance of quantum chemical models with regard to the calculation of dipole moments. Several different classes of molecules, including diatomic and small polyatomic molecules, hydrocarbons, molecules with heteroatoms andhypervalent molecules are considered. The chapter concludes with assessment of the ability of quantum chemical models to calculate what are often subtle differences in dipole moments for different conformers. 

All density functional models exhibit similar behavior with regard to dipole moments in diatomic and small polyatomic molecules. Figures 10-6 (EDFl) and 10-8 (B3LYP) show clearly that, except for highly polar (ionic) molecules, limiting (6-311+G basis set) dipole moments are usually (but not always) larger than experimental values. 

Dipole moments for hydrocarbons are small (typically less than 1 debye), and provide a good test of different models to reproduce subtle effects. A small selection of data is provided in Table 10-2, for the same models used previously for diatomic and small polyatomic molecules. ... 

Table AlO-l Dipole Moments in Diatomic and Small Polyatomic Molecules. Hartree-Fock Models... 

The harmonic oscillator energies and wavefunctions comprise the simplest reasonable model for vibrational motion. Vibrations of a polyatomic molecule are often characterized in terms of individual bond-stretching and angle-bending motions each of which is, in turn, approximated harmonically. This results in a total vibrational wavefunction that is written as a product of functions one for each of the vibrational coordinates. 

Vibrational states can be described in terms of the normal mode (NM) [50, 51] or the local mode (LM) [37, 52, 53] model. In the former, vibrations in polyatomic molecules are treated as infinitesimal displacements of the nuclei in a harmonic potential, a picture that naturally includes the coupling among the bonds in a molecule. The general formula for the energies of the vibrational levels in a polyatomic molecule is given by [54]... 

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