Chemical and Biochemical Thermodynamics

Biochemical reactions balance the atoms of all elements except for hydrogen, or of metals when they are bound reversibly and their ionic concentrations are held constant. Thus a system of biochemical reactions can be represented by an apparent conservation matrix or an apparent stoichiometric number matrix. The adjective apparent is used because hydrogen ions are omitted in the apparent conservation matrix since they are not conserved. Hydrogen ions are also omitted in the apparent stoichiometric number matrix since they do not appear in biochemical reactions. The conservation and stoichiometric number matrices for a system of biochemical reactions can be derived from the conservation matrix 

The corresponding conservation equations are less familiar, but they contain the same information as a set of independent chemical reactions. The conservation equations for a system containing Ns species are given by 

Equation 5.1-1 for a reaction system can be written in matrix form as 

Consider a gaseous reaction system in which the only reaction is 

When stoichiometric numbers are taken to be signed quantities, this chemical equation can be written as 

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Even the most complicated aspects of thermodynamics are based ultimately on three rather simple and straightforward laws. These laws and their extensions sometimes run counter to our intuition. However, once truly understood, the basic principles of thermodynamics become powerful devices for sorting out complicated chemical and biochemical problems. At this milestone in our scientific development, thermodynamic thinking becomes an enjoyable and satisfying activity. 

J. J. Christensen. Metal-Ligand Heats and Related Thermodynamic Quantities by Titration Calorimetry. In Thermochemistry and Its Applications to Chemical and Biochemical Systems M. A. V. Ribeiro da Silva, Ed. NATO ASI Series C, Riedel Dordrecht, 1984 253-273. 

Thermodynamic studies of systems at equilibrium permit one to gain insights regarding mechanisms of chemical and biochemical reactions. Thermodynamic consider-... 

The application of cubic autocatalysis to model chemical and biochemical schemes in thermodynamically closed systems is dealt with in the following references. 

Chemical and biochemical physics, kinetics, and thermodynamics new perspectives / Paul Edwin Stott, Gennady Efremovich Zaikov and Viktor Fedorovich Kablov (editors), p. cm. 

Hence, any chemical and biochemical transformations of practical importance occur usually far from thermodynamic equilibrium— that is, far from the region of applicability of the relations of linear nonequflib rium thermodynamics. As a result, thermodynamic analysis of these pro cesses is considerably complicated and usually requires the application of direct kinetic methods for describing the system evolution in terms of differential equations. 

A major objective of any fieid of pure or applied science is to summarize a large amount of experimental information with a few basic principles. The hope, then, is that any new experimental measurement or phenomenon can be easily understood in terms of the established principles, and that prediction.s based on these principles will be accurate. This book demonstrates how a collection of general experimental observaiions can be used to establish the principle.s of an area of science called thermodynamics, and then shows how these principles can be used to study a wide variety of physical, chemical, and biochemical phenomena. 

Thennodynamics-Texibooks. 2. Chemical engineering-Tcxtbooks. 3. Biochemical engincering-Textbooks. 1. Sandler, Stanley I., 1940- Chemical and engineering thermodynamics. II. Title. 

This chapter has reviewed theoretical and practical aspects of thermodynamic perturbation and thermodynamic integration, two popular methods of extracting free energies from molecular simulations. These methods find broad application in molecular simulation studies of chemical and biochemical systems. The fundamental importance of free energy in physical and chemical processes will inspire further development and refinement of these techniques. With the increasing performance of new computer architectures,these free energy techniques will become even more powerful and versatile tools. 

The Gibbs free energy is a remarkable thermodynamic quantity. Because so many chemical reactions are carried out under conditions of near-constant pressure and temperature, chemists, biochemists, and engineers use the sign and magnitude of AG as exceptionally useful tools in the design of chemical and biochemical reactions. We will see examples of the usefulness of AG throughout the remainder of this chapter and this text... 

Ellegaard, M. D. 2011. Molecular Thermodynamics Using Fluctuation Solution Theory. Ph.D. Thesis, Department of Chemical and Biochemical Engineering, Technical University of Denmark. 

Interactions between soluble polymer and either colloidal particles, surfactant micelles, or proteins control the behavior and viability of a large number of chemical and biochemical products and processes. Considerable scientific interest also centers on these interactions because of their profound and, sometimes, unexpected effects on the thermodynamics and dynamics of the dispersions or solutions, known collectively as complex fluids. Syntheses of novel block copolymers, improved scattering and optical techniques for characterization, and predictions emerging from sophisticated statistical mechanical approaches provide additional stimulus. Thus, the area is vigorous academically and industrially as evidenced by the broad and international participation in this volume. 

Lukanina, J. K. Khvatov, A. V. Kolesnikova, N. N. Popov, A. A. Structure and properties of biodegradable polymer composite materials. Progress in chemical and biochemical physics, kinetics and thermodynamics, 2008,209-218. 

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