Within Thermal Scales: The Kinetic and Energetic Pull of Chemical Entropy

Abstract

Proteins in biological systems function at the interface of single molecule and bulk chemistry and thus provide novel insights into the basic physical chemistry of scaling and emergent phenomena. For example, a binary mechanical model that accounts for many energetic and mechanical aspects of muscle contraction provides a novel and testable framework for investigating the relationship between molecular mechanics and chemical thermodynamics in single molecules and small molecular ensembles. The problem addressed here is that the model and supporting experimental data require that entropic forces balance chemical reactions. While this is consistent with statistical mechanics, it is at odds with basic chemistry. Specifically, counter to a classic chemical activity analysis, the mere presence of molecules (chemical activity or mass action) does not physically push a reaction toward equilibrium; rather, the number of microstates, Omega, accessible in a chemical state pulls a reaction down an entropic funnel of increasing Omega; toward equilibrium. Here I develop an entropic model of chemical thermodynamics and kinetics and compare it with conventional chemical activity models. I show that an a priori system reaction energy landscape fully describes the chemical kinetics of both equilibrium and non-equilibrium chemical reactions, formally justifying the thermodynamic rate constants required for binary mechanical models of muscle contraction.

The Problem with Inventing Molecular Mechanisms to Fit Thermodynamic Equations of Muscle

“…Throughout scientific history (Figure 1), even in a post-thermodynamic era, corpuscular mechanics keeps returning as a prevailing hypothesis. For example, chemists continue to describe molecules in a specific chemical state as being physically pushed out of that state (mass action) by chemical forces exerted by the mere presence of molecules in that state (chemical activities) rather than being pulled by entropy [28]. In biology, a single ATP molecule is described as transferring corpuscular chemical energy to a single protein, which is directly analogous to a single phlogiston molecule transferring corpuscular heat energy to a single air molecule.…”

“…All phases are well-defined combinations of two explicit thermodynamic processes [15,37,38] System entropy 0 -k B Tln[(N bound + 1)/N unbound ] [15,19,28] Thermal Energy Heat content of molecules Heat content of system * While under certain conditions, N bound increases with binding energy. In general, none of the above corpuscular mechanisms are supported experimentally.…”

“…Moreover, muscle is one of the most efficient, clean-burning machines on the planet, yet corpuscular mechanic models have muddied our understanding of how these machines work. As a result, we have gone decades without the extraordinary physical chemical insights that a thermodynamic analysis of muscle is now providing [19,28]-insights that have great potential to advance clean energy technologies. That, too, matters.…”