Partition function perturbation calculation

Free energy calculations rely on the following thermodynamic perturbation theory [6-8]. Consider a system A described by the energy function = 17 + T. 17 = 17 (r ) is the potential energy, which depends on the coordinates = (Fi, r, , r ), and T is the kinetic energy, which (in a Cartesian coordinate system) depends on the velocities v. For concreteness, the system could be made up of a biomolecule in solution. We limit ourselves (mostly) to a classical mechanical description for simplicity and reasons of space. In the canonical thermodynamic ensemble (constant N, volume V, temperature T), the classical partition function Z is proportional to the configurational integral Q, which in a Cartesian coordinate system is... 

In the following, the MO applications will be demonstrated with two selected equilibrium reactions, most important in radical chemistry disproportionation and dimerization. The examples presented will concern MO approaches of different levels of sophistication ab initio calculations with the evaluation of partition functions, semiempirical treatments, and simple procedures employing the HMO method or perturbation theory. 

Fickett in "Detonation Properties of Condensed Explosives Calculated with an Equation of State Based on Intermolecular Potentials , Los Alamos Scientific Lab Rept LA-2712 (1962), pp 34-38, discusses perturbation theories as applied to a system of deton products consisting of two phases one, solid carbon in some form, and the other, a fluid mixt of the remaining product species. He divides these theories into two classes conformal solution theory, and what he chooses to call n-fluid theory. Both theories stem from a common approach, namely, perturbation from a pure fluid whose props are assumed known. They differ mainly in the choice of expansion variables. The conformal solution method begins with the assumption that all of the intermolecular interaction potentials have the same functional form. To obtain the equation of state of the mixt, some reference fluid obeying a common reduced equation of state is chosen, and the mixt partition function is expanded about that of the reference fluid... 

The calculation above for the conditional probability is hard to perform because it is equivalent to the computation of a partition function. However, similarly to tricks in equilibrium statistical mechanics (the free-energy perturbation method [23]), we can compute the ratios of the conditional probabilities for slightly different Hamiltonians. For example, we may compare the diffusion of different ions a sodium ion and a potassium ion permeating through the gramicidin channel [Koneshan Siva and Ron Elber, Protein, Structure Function, and Genetics, in press]. 

Decide whether entropic effects are likely to be important (for example if charged species are released to the solvent) and, if so, decide on whether a quantum chemical approach (calculating the partition function within a harmonic-oscillator approximation) may be used or whether a molecular dynamics-based approach (e.g., free-energy perturbation theory) should be used to properly sample phase space. 

Today, there are two principal ways to develop an equation of state for polymer solutions first, to start with an expression for the canonical partition function utilizing concepts similar to those used by van der Waals (e.g., Prigogine, Flory et al., Patterson, Simha and Somcynsky, Sanchez and Lacombe, Dee and Walsh,Donohue and Prausnitz, Chien et al. ), and second, which is more sophisticated, to use statistical thermodynamics perturbation theory for freely-jointed tangent-sphere chain-like fluids (e.g., Hall and coworkers,Chapman et al., Song et al. ). A comprehensive review about equations of state for molten polymers and polymer solutions was given by Lambert et al. Here, only some resulting equations will be summarized under the aspect of calculating solvent activities in polymer solutions. 

The centroid path integral method described above enable us to conveniently determine KIEs by directly computing the ratio of the quantum partition functions for two different isotopes through free energy perturbation (FEP) theory. The use of mass perturbation in free-particle bisection sampling scheme results in a major improvement in computation accuracy for KIE calculations such that secondary kinetic isotope effects and heavy atom isotope effects can be reliably obtained. The PI-FEP/UM method is the only practical approach to yield computed secondary KIEs sufficiently accurate to be compared with experiments. ... 

If we except the Density Functional Theory and Coupled Clusters treatments (see, for example, reference [1] and references therein), the Configuration Interaction (Cl) and the Many-Body-Perturbation-Theory (MBPT) [2] approaches are the most widely-used methods to deal with the correlation problem in computational chemistry. The MBPT approach based on an HF-SCF (Hartree-Fock Self-Consistent Field) single reference taking RHF (Restricted Hartree-Fock) [3] or UHF (Unrestricted Hartree-Fock ) orbitals [4-6] has been particularly developed, at various order of perturbation n, leading to the widespread MPw or UMPw treatments when a Moller-Plesset (MP) partition of the electronic Hamiltonian is considered [7]. The implementation of such methods in various codes and the large distribution of some of them as black boxes make the MPn theories a common way for the non-specialist to tentatively include, with more or less relevancy, correlation effects in the calculations. 

The basic theoretical framework for understanding the rates of these processes is Fermi s golden rule. The solute-solvent Hamiltonian is partitioned into three terms one for selected vibrational modes of the solute, including the vibrational mode that is initially excited, one for all other degrees of freedom (the bath), and one for the interaction between these two sets of variables. One then calculates rate constants for transitions between eigenstates of the first term, taking the interaction term to lowest order in perturbation theory. The rate constants are related to Fourier transforms of quantum time-correlation functions of bath variables. The most common... 

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