Molecular partition function classical

This is the entire classical molecular partition function for a monatomic gas without electronic excitation. 

The classical molecular partition function for dilute diatomic and polyatomic gases without electronic excitation contains three factors. The translational factor is the same as given by the formula in Eq. (27.4-12), since the translational motion of a molecule is the same as that of an atom ... 

The derivation of the rotational factor in the classical molecular partition function of a diatomic molecule is a little more complicated, and is carried out in the following example ... 

The translational factor of the classical molecular partition function is proportional to the quantum mechanical translational factor ... 

As previously stated, the classical molecular partition function has units of kg s raised to some power, so a divisor with units must be included to make the argument of the logarithm dimensionless. If a divisor of lkgm s is used, values are obtained for the entropy and the Helmholtz energy that differ from the experimental values. However, when the classical canonical translational partition function is divided by h A and Stirling s approximation is used for ln(iV ), the same formulas are obtained as Chapter 26. For a dilute monatomic gas the corrected classical formula is... 

Note the subscript C to indicate classical (or high temperature). In Equation 4.81 the p s are momenta and the q s the associated coordinates (not to be confused with q s previously used to symbolize molecular partition functions). In Cartesian coordinates dpjdqj = dpxidpyidpzidxidy1dzi with xi, yi, zi, the coordinates of atom... 

Another way of writing the molecular partition function is to use the classical expression for Wtrans in an integral form. By classical mechanics, Tftrans for each molecule is given by... 

The derived density of states for the translations, rotations, and vibrations can be used in Eq. (6.41) to obtain the corresponding classical partition functions. This will yield an accurate translational partition function at all temperatures of chemical interest because the translational energy level spacings are so dense. It will also yield accurate rotational partition functions at room temperature because molecular rotational constants are typically between 0.01 and 1 cm k However, at the low temperatures achieved in molecular beams, the accuracy of the classical rotational partition function (especially for molecules with high rotational constants, such as formaldehyde or H2 (Bg = 60.8 cm )) is insufficient. The energy level spacing of vibrations (ca. 2000 cm ) are considerably larger than the room temperature of 207 cm " so that even at room temperature, the vibrational partition function must be evaluated by summation in Eq. (6.40). 

Now we will move onto indistinguishable particles but in the approximation of the classical hmiting case. The canonical partition function is given by expression [5.25] using the molecular partition functions. By applying equation [5.32], we calculate for the internal energy ... 

There are several model theories that treat a liquid like a disordered solid. In the cell modefi each atom of a monatomic fluid such as liquid argon is assumed to be confined in a cell whose walls are made up of its nearest neighbors. In the simplest version, this cell is approximated as a spherical cavity inside which the potential energy of the moving atom is constant and outside of which the potential energy is infinite. Because each atom moves independently, the classical canonical partition function can be written as a product of molecular partition functions. The classical canonical partition function is... 

There are three approaches that may be used in deriving mathematical expressions for an adsorption isotherm. The first utilizes kinetic expressions for the rates of adsorption and desorption. At equilibrium these two rates must be equal. A second approach involves the use of statistical thermodynamics to obtain a pseudo equilibrium constant for the process in terms of the partition functions of vacant sites, adsorbed molecules, and gas phase molecules. A third approach using classical thermodynamics is also possible. Because it provides a useful physical picture of the molecular processes involved, we will adopt the kinetic approach in our derivations. 

In the remainder of this chapter, we review the fundamentals that underlie the theoretical developments in this book. We outline, in sequence, the concept of density of states and partition function, the most basic approaches to calculating free energies and the essential strategies for improving the efficiency of these calculations. The ideas discussed here are, most likely, known to the reader. They can also be found in classical books on statistical mechanics [132-134] and molecular simulations [135, 136]. Thus, we do not attempt to be exhaustive. On the contrary, we present the material in a way that is most directly relevant to the topics covered in the book. 

Only for a special class of compound with appropriate planar symmetry is it possible to distinguish between (a) electrons, associated with atomic cores and (7r) electrons delocalized over the molecular surface. The Hiickel approximation is allowed for this limited class only. Since a — 7r separation is nowhere perfect and always somewhat artificial, there is the temptation to extend the Hiickel method also to situations where more pronounced a — ix interaction is expected. It is immediately obvious that a different partitioning would be required for such an extension. The standard HMO partitioning that operates on symmetry grounds, treats only the 7r-electrons quantum mechanically and all a-electrons as part of the classical molecular frame. The alternative is an arbitrary distinction between valence electrons and atomic cores. Schemes have been devised [98, 99] to handle situations where the molecular valence shell consists of either a + n or only a electrons. In either case, the partitioning introduces extra complications. The mathematics of the situation [100] dictates that any abstraction produce disjoint sectors, of which no more than one may be non-classical. In view if the BO approximation already invoked, only the valence sector could be quantum mechanical9. In this case the classical remainder is a set of atomic cores in some unspecified excited state, called the valence state. One complication that arises is that wave functions of the valence electrons depend parametrically on the valence state. 

The molecular modelling of systems consisting of many molecules is the field of statistical mechanics, sometimes called statistical thermodynamics [28,29], Basically, the idea is to go from a molecular model to partition functions, and then, from these, to predict thermodynamic observables and dynamic and structural quantities. As in classical thermodynamics, in statistical mechanics it is essential to define which state variables are fixed and which quantities are allowed to fluctuate, i.e. it is essential to specify the macroscopic boundary conditions. In the present context, there are a few types of molecular systems of interest, which are linked to so-called ensembles. 

Classical molecular dynamics (MD) implementing predetermined potentials, either empirical or derived from independent electronic structure calculations, has been used extensively to investigate condensed-matter systems. An important aspect in any MD simulation is how to describe or approximate the interatomic interactions. Usually, the potentials that describe these interactions are determined a priori and the full interaction is partitioned into two-, three-, and many-body contributions, long- and short-range terms, etc., for which suitable analytical functional forms are devised. Despite the many successes with classical MD, the requirement to devise fixed potentials results in several serious problems... 

Following Fey nman s original work, several authors pmsued extensions of the effective potential idea to construct variational approximations for the quantum partition function (see, e g., Refs. 7,8). The importance of the path centroid variable in quantum activated rate processes was also explored and revealed, which gave rise to path integral quantum transition state theory and even more general approaches. The Centroid Molecular Dynamics (CMD) method for quantum dynamics simulation was also formulated. In the CMD method, the position centroid evolves classically on the efiective centroid potential. Various analysis and numerical tests for realistic systems have shown that CMD captures the main quantum effects for several processes in condensed matter such as transport phenomena. 

The approach with the partitioning of the system into a QM and a classical molecular mechanical (MM) part, thus usually termed hybrid QM/MM procedure, provides a reasonable reduction of the computational effort by restricting the time-consuming QM calculation of forces to the most relevant part of the liquid system. The main error sources in this approach are a too small choice of the QM region, an inadequate level of theory for the QM calculation, the choice of suitable potentials for the MM part of the system, and smooth transitions of particles between QM and MM region. In conventional QM/MM procedures, the whole system is first evaluated at MM level and then corrected by the QM data. This means that classical potential functions (with all their problems and difficulty of construction) are needed for all components of the system. A recently developed methodology can reduce the need for such potentials to the solvent only, as will be outlined below. 

The key to a treatment of molecular clusters in situations of thermal equilibrium are the N-particle partition functions. Specifically, the classical two-particle partition function, Z2(T), is given by [183, 184, 377]... 

For the vibrational term qivib, a classical high-T continuum approximation is seldom valid, and evaluation of the discrete sum over states is therefore required over the quantum vibrational distribution. (As pointed out in Sidebar 5.13, accurate treatment of molecular vibrations is crucial for accurate assessment of entropic contributions to AGrxn.) A simple quantum mechanical model of molecular vibrations is provided by the harmonic oscillator approximation for each of the 3N — 6 normal modes of vibration of a nonlinear polyatomic molecule of N atoms (cf. Sidebar 3.8). In this case, the quantum partition function can be evaluated analytically as... 

There are two basic approaches to the computer simulation of liquid crystals, the Monte Carlo method and the method known as molecular dynamics. We will first discuss the basis of the Monte Carlo method. As is the case with both these methods, a small number (of the order hundreds) of molecules is considered and the difficulties introduced by this restriction are, at least in part, removed by the use of artful boundary conditions which will be discussed below. This relatively small assembly of molecules is treated by a method based on the canonical partition function approach. That is to say, the energy which appears in the Boltzman factor is the total energy of the assembly and such factors are assumed summed over an ensemble of assemblies. The summation ranges over all the coordinates and momenta which describe the assemblies. As a classical approach is taken to the problem, the summation is replaced by an integration over all these coordinates though, in the final computation, a return to a summation has to be made. If one wishes to find the probable value of some particular physical quantity, A, which is a function of the coordinates just referred to, then statistical mechanics teaches that this quantity is given by... 

The partition function of a solute-solvent system for a given electronic state, where for the N solutes we use as (classical) molecular coordinates the center of mass position rG, the eulerian angles 0, , molecular frame and the internal coordinates Xjn providing the atom positions in the molecular frame, is [27,28]... 

A further complication associated with the application of molecular mechanics calculations to relative stabilities is that strain energy differences correspond to A (AH) between conformers with similar chromophores (electronic effects) and an innocent environment (counter ions and solvent molecules), whereas relative stabilities are based on A (AG). The entropy term, TAS, can be calculated by partition functions, and the individual terms of AS include vibrational (5vib), translational (5 trans) and rotational (Arot) components, and in addition to these classical terms, a statistical contribution (5stat). These terms can be calculated using Eqs. 3.40-3.43tl21]. 

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