Thermodynamics: Key Concepts and Applications
Fundamental Principles
Under what thermodynamic condition is the change in enthalpy equal to the heat transferred into a system? Constant pressure.
The entropy is associated with what qualitative feature of a system? Disorder.
List two general categories of energy storage at the atomic and molecular level, for subsequent access by cellular biochemistry:
- (1) Chemical reactions [bond formation and breaking]
- (2) Chemical bonding and interactions [molecular recognition]
True or false: Temperature is an extensive quantity. False, it’s intensive.
What is the defining feature of an ideal monatomic (“perfect”) gas? The constituent atoms do not interact with each other.
State the first law of thermodynamics in words: Conservation of energy.
List the three physical quantities that are related to each other through the first law of thermodynamics: Internal (system) energy; heat transfer; work.
An experimental process in which a system can exchange energy with a heat bath is referred to as Isothermal.
What is an alternative terminology for mechanical work in thermodynamics? “PV work.”
What thermodynamic quantity is used as an effective calorimetric measure of the stored potential energy of a molecular system? Heat capacity at constant pressure, Cp.
Molecular Interactions and Forces
In an empirical force field for a protein, what type of function is used to approximate the region of the potential well for interacting covalently bonded atoms along the protein backbone? Harmonic oscillator.
What is the weakest form of intermolecular interaction? Van der Waals interaction.
What is the name given to the normalization factor for the Boltzmann distribution? Partition function.
The difference between the ground state of a molecule and its first excited state is known as the energy gap.
True or false: The van der Waals interaction potential between two carbon atoms in an amino acid depends on the dihedral angle between the planes formed by adjacent covalent bonds. False.
What type of chemical bonding plays a key role in defining protein secondary structure? Hydrogen bonding.
True or false: The effective charges of the atoms in a protein structure are uniquely defined by their underlying quantum mechanical interactions. False.
Which of Newton’s laws of motion is used to compute the force on an atom from an empirical potential energy surface? Newton’s Second Law; Force = mass x acceleration.
(a) What is the approximate value of ε for water [unitless in the form of Coulomb’s law we will use, from the text]? This effect is not as strong in the interior of a protein. (b) What is the approximate value of ε in the interior of a protein? (a) ε ~ 80 in water solvent; (b) ε ~ 2-4 in the interior of the protein.
Statistical Thermodynamics
What is the mathematical expression for computing the probability P(M,N)? P(M,N) = W(M,N) x pN x (1-p)M-N
As the number of events in a statistical trial increases, do unlikely outcomes become more or less rare? More rare.
What is the name of the continuous mathematical function that can be used to approximate the discrete expression for the probability P in question #1? Gaussian Distribution.
The number of different molecular configurations that are consistent with the parameters defining the state of a system is known as the multiplicity.
True or false: The most likely thermodynamic state of a system corresponds to one for which entropy is minimized. False.
According to the third law of thermodynamics discussed in class, at T = 0 K (-273.15 C), the entropy S = 0. Apply the statistical expression for the entropy to rationalize why this should be the case [brief answer]: S = k ln W, and at T=0 there is no motion, so the system is frozen into a single configuration (microstate) => W = 1. Thus, S = k ln W = k ln 1 = 0.