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Chemical and other reaction theories involving thermodynamical equilibrium states utilize statistical mechanical equilibrium density distributions. Here, a definition of heat-work transformation termed thermo-mechanical coherence is first made, and it is conjectured that most molecular bonds have the above heat-work transformation property, which models a chemical bond as a “centrifugal heat engine”, where the internal energy state need not correspond to any of the standard equilibrium densities. Expressions are derived for the standard Gibbs free energy, enthalpy, and entropy where the bond coordinates need not conform to a non-degenerate Boltzmann state, since bond breakdown and formation are processes that have direction, whereas equilibrium distributions are derived when the Hamiltonian is of fixed form, which is not the case for chemical reactions using localized Hamiltonians. The empirically determined Gibbs free energy from a known molecular dynamics simulation of a dimer reaction $$ 2{\rm A} \rightleftharpoons {\rm A}_{\rm 2} $$, accords rather well with the theoretical estimate. A relation connecting the rate of reaction with the equilibrium constant and other kinetic parameters is derived and could place the commonly observed linear relationship between the logarithms of the rate constant and equilibrium constant on a firmer theoretical footing. These relationships could include analogues of the Hammett correlations used extensively in physical organic chemistry, as well as others which are temperature dependent. One prediction of the principles developed here is that the equilibrium standard reaction free energy is more dependent on the height of the intermolecular potential than its depth, so that the sign of the ΔG θ can change for varying barrier height with fixed well depth, which may appear counter-intuitive. All the above developments can be tested directly in simulations and therefore provides a fertile ground for further research with significant implications on how standard states are determined in relation to the direction of chemical reaction.This work treats the molecular bond using standard thermodynamics as if it were a system, and it is anticipated that with the advent of single-molecule science and experiment, that might be one direction in which molecular statistical thermodynamics would develop.

An Energy Interconversion Principle Applied in Reaction dynamics for the determination of equilibrium standard states