The Calculation of Molecular Partition Functions

The partition function ratios needed for the calculation of the isotope effect on the equilibrium constant K will be calculated, as before, in the harmonic-oscillator-rigid-rotor approximation for both reactants and transition states. One obtains in terms of molecular partition functions q... 

O Neil JR (1986) Theoretical and experimental aspects of isotopic fractionation. Rev Mineral 16 1-40 Oi T (2000) Calculations of reduced partition function ratios of monomeric and dimeric boric acids and borates by the ab initio molecular orbital theory. J Nuclear Sci Tech 37 166-172 Oi T, Nomura M, Musashi M, Ossaka T, Okamoto M, Kakihana H (1989) Boron isotopic composition of some boron minerals. Geochim Cosmochim Acta 53 3189-3195 Oi T, Yanase S (2001) Calculations of reduced partition function ratios of hydrated monoborate anion by the ab initio molecular orbital theory. J Nuclear Sci Tech 38 429-432 Paneth P (2003) Chlorine kinetic isotope effects on enzymatic dehalogenations. Accounts Chem Res 36 120-126... 

Ol, T. 2000. Calculations of reduced partition function ratios of monomeric and dimeric boric acids and borates by the ab initio molecular orbital theory. Journal of Nuclear Science and Technology, 37, 166-172. 

The values of v and can be calculated if we write the equilibrium constant in terms of molecular partition functions per unit volume, qjV. [See Eq. (29.75).] Then... 

The molecular partition functions, Q, can be related to molecular properties of reactants and products. The partition function expresses the probability of encountering a molecule, so that the ratio of partition functions for the products versus the reactants of a chemical reaction expresses the relative probability of encountering products versus reactants and, therefore, the equilibrium constant. The partition function can be written as a product of independent factors at the level of various approximations, each of which is related to the molecular mass, the principal moments of inertia, the normal vibration frequency, and the electronic energy levels, respectively. When the ratio of isotopic partition function is calculated, the electronic part of the partition function cancels, at the level of the Born-Oppenheimer approximation, an approximation stating that the motion of nuclei in ordinary molecular vibrations is slow relative to the motions of electrons. 

This theory has not been very successful it does well for some substances but fails badly for others. Certain semiempirical calculations have been more successful, but such calculations lack the appeal of theories developed from first-principles. As a result, much recent interest has centered upon microscopic approaches to the study of the clusters in which the details of the structure or dynamics of the nucleation micro-clusters are considered. These microscopic studies have predominantly used two basic approaches the statistical mechanical calculation of cluster partition functions, and Monte Carlo and molecular dynamics simulations of supersaturated systems. 

We note that the calculation of At/ will depend primarily on local information about solute-solvent interactions i.c., the magnitude of A U is of molecular order. An accurate determination of this partition function is therefore possible based on the molecular details of the solution in the vicinity of the solute. The success of the test-particle method can be attributed to this property. A second feature of these relations, apparent in Eq. (4), is the evaluation of solute conformational stability in solution by separately calculating the equilibrium distribution of solute conformations for an isolated molecule and the solvent response to this distribution. This evaluation will likewise depend on primarily local interactions between the solute and solvent. For macromolecular solutes, simple physical approximations involving only partially hydrated solutes might be sufficient. 

We now return to the issue of configurational density of states. In the simulation of molecular systems, we are interested only in the calculation of their configurational properties, or more explicitly, the configurational contribution to their partition functions. This is because the kinetic component is analytic, and, hence, there is no need to measure it via simulation. For conventional MC simulations in the... 

The measurement of the solubility of drugs in polar and non-polar media is very important in the pharmaceutical field. One method proposed to describe this solubility is the partition coefficient between octanol and water. The mathematical calculation of an octanol-water partition coefficient from values for functional groups was first proposed by Hansch et al. as Hansch s n constants,1 and was later developed by Rekker as hydrophobic fragmental constants (logP).2 This method was further improved by the use of molecular connectivities.17 The prediction of logP values can be performed by either a computer program or by manual calculation. For example, approximate partition coefficients (log P) have been calculated by Rekker s method ... 

Here /i j3 is the chemical potential of the ideal gas at the standard pressure. It will be seen subsequently that qi for an ideal gas depends linearly on the volume V, so fif is a function only of the temperature. It does of course depend on the distribution of energy levels of the ideal gas molecules. The form of Equation 4.59 for the chemical potential of an ideal gas component is the same as that previously derived from thermodynamics (Equation 4.47). The present approach shows how to calculate m through the evaluation of the molecular partition function. Furthermore, the... 

In earlier sections of this chapter we learned that the calculation of isotope effects on equilibrium constants of isotope exchange reactions as well as isotope effects on rate constants using transition state theory, TST, requires the evaluation of reduced isotopic partition function ratios, RPFR s, for ordinary molecular species, and for transition states. Since the procedure for transition states is basically the same as that for normal molecular species, it is the former which will be discussed first. 

Schrodinger equation. When the molecule is too large and difficult for quantum mechanical calculations, or the molecule interacts with many other molecules or an external field, we turn to the methods of molecular mechanics with empirical force fields. We compute and obtain numerical values of the partition functions, instead of precise formulas. The computation of thermodynamic properties proceeds by using a number of techniques, of which the most prominent are the molecular dynamics and the Monte Carlo methods. 

At the actual reaction temperature, the molecular partition function for all intermediates are calculated from the properties of each intermediate. 

We see that the partition function of a molecule is the product of the contributions of the translational, rotational, vibrational, and electronic partition functions, which we can calculate separately, as discussed next. We will see in Section 8.5 that any thermodynamic quantity of interest can be derived from the molecular partition function. Thus it is important to be able to evaluate q. 

It is also important to keep in mind the independent (state) variables that were specified in deriving q. That is, the partition function was derived with the number of molecules N, the volume of the system V, and the temperature T specified as the independent variables. Thus, when taking the derivative with respect to temperature, as will be needed later, it is good to keep in mind that q = q(N, V, T). The partition function for the entire system of identical molecules, with independent variables N, V, and T, is denoted by a capital Q. If the molecules are indistinguishable, as would normally be the case when calculating thermochemical properties for a given species, then the system partition function is related to the molecular partition function by... 

The partition function provides the bridge to calculating thermodynamic quantities of interest. Using the molecular partition function and formulas derived in this section, we will be able to calculate the internal energy E, the heat capacity Cp, and the entropy S of a gas from fundamental properties of the molecule, such as its mass, moments of inertia, and vibrational frequencies. Thus, if thermodynamic data are lacking for a species of interest, we usually know, or can estimate, these molecular constants, and we can calculate reasonably accurate thermodynamic quantities. In Section 8.6 we illustrate the practical application of the formulas derived here with a numerical example of the thermodynamic properties for the species CH3. 

All calculations will be done for the standard pressure of 1 bar and, unless otherwise noted, at T = 298.15 K for one mole of gas. Table 8.1 lists the calculated molecular partition function, thermal energy (energy in excess of the ground-state energy), heat capacity, and entropy. The individual contributions from translation, rotation, each of the six vibrational modes, and from the first excited electronic energy level are included. 

The translational contribution to the molecular partition function, which is calculated using Eq. 8.59, clearly makes the largest contribution. (In obtaining this value, we also made use of the ideal gas law to calculate the volume V = 0.02479 m3 of a mole of gas at this temperature and pressure.) The rotational partition function is evaluated via Eq. 8.67, and the vibrational partition function for each mode is found via Eq. 8.71. Only the very... 

The information needed to evaluate the molecular partition functions qb (13.63), may in principle be obtained from experimental spectroscopic measurements or theoretical calculations on each molecule i. Each type of energy contribution to qt (translational, rotational, vibrational, electronic) in principle requires associated quantum energy levels... 

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