1: Biochemical Thermodynamics
- Page ID
- 398255
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- 1.1: Thermodynamic Variables and Equations of State
- Classical thermodynamics provides a physical framework from which we can understand the behavior of molecular systems in the biological sciences at a quantitative level. This chapter introduces some of the concepts relating to properties of a system and the surroundings that we will need to study classical thermodynamics. In this chapter we will focus on how the macroscopic properties of a system are related to and depend on the properties of the constituent atoms and molecules.
- 1.2: The First Law of Thermodynamics
- Systems can undergo a change of state from some initial state to a final state accompanied by a change in the system’s energy. In this chapter, we analyze two types of energy: heat and work. This leads to a presentation of the first law of thermodynamics that deals with the conservation of energy, stating that any changes in the total internal energy of the system must be due to exchanges of either heat or work with the surroundings.
- 1.3: Thermochemistry
- In this chapter we apply the first law of thermodynamics and the concept of enthalpy introduced in Chapter I.2 to chemical reactions. At standard state conditions we can use tabulated heats of formation to calculate the change in enthalpy for any reaction. At temperatures other than standard conditions we use the temperature dependence of the enthalpy to derive an expression for the change in enthalpy of a reaction at any temperature in relation to a reference temperature.
- 1.4: The Second Law of Thermodynamics
- The first law of thermodynamics describes the conservation of energy but does not tell us anything about the direction or spontaneity of a reaction. In this chapter we introduce the concept of entropy as derived by Rudolf Clausius and formulate the second law of thermodynamics. The second law of thermodynamics is of central importance in science and tells us the direction of spontaneous change for any process. We then calculate the change of entropy for a number of exemplary cases.
- 1.5: The Boltzmann Distribution and the Statistical Definition of Entropy
- In this chapter we introduce the statistical definition of entropy as formulated by Boltzmann. This allows us to consider entropy from the perspective of the probabilities of different configurations of the constituent interacting particles in an ensemble. This conception of entropy led to the development of modern statistical thermodynamics. For systems that can exchange thermal energy with the surroundings, the equilibrium probability distribution will be the Boltzmann distribution.
- 1.6: The Gibbs and Helmholtz Energy
- In this chapter we introduce two additional state properties: the Gibbs energy and the Helmholtz energy. These additional variables are useful for allowing us to determine the direction of spontaneous change without having to directly calculate the change in entropy of the universe from the second law. The Gibbs energy has particular importance in biochemistry. Emphasis is placed on the thermodynamics of mixtures and phase separations.
- 1.7: Equilibria in Biochemical Systems
- In this chapter we extend the concept of the Gibbs energy to mixtures. In the case of mixtures, the number of moles of the different components can change as a result of a chemical reaction or a phase transition. The partial molar Gibbs energy or chemical potential can be used to determine the spontaneity of a chemical reaction or of a phase transition. We first derive an expression for the chemical potential of gases, volatile liquids, and ideal solutions.