AGENDA

Lecture 1: 8/26/2019 (Course Introduction)

Energy is the capacity to supply heat or do work. Two ways to transfer energy: Heat (Originate from difference in temperatures (i.e., average kinetic energy of molecules)) and Work (moving an object against a resistance (e.g., expansion work of a gas)). Mechanical work: \(w=Fd\), Expansion (PV) Work: w=PΔV (under constant pressure). Energy is fluid (but not a real fluid) that can be converted where Kinetic energy can be interconverted with Potential Energy.

Assumed Knowledge

• Temperature Conversion and Dimensional Analysis

Lecture 2: 8/28/2019 (Molecular Interactions)

Both Heat and Work are path functions (depends on the path taken from point A to B). Energy (internal) is a state function (depends on the difference from point A to B). Internal



Assumed Knowledge

• Hydrogen Bonding, Covalent vs Ionic Bonding, Van der Waals Interactions

Lecture 3: 8/30/2019 (pH and Ionization of Biological Molecules)



Assumed Knowledge

• pH Scale, Acid Strength (pKa)

No Lecture: 9/2/2019 (Labor Day Holiday)

Lecture 4: 9/4/2019 (Buffers)

Path vs. State variables. Physical and chemistry process (changes) have associated “heats”. Breaking a bond always require energy.

Lecture 5: 9/6/2019 (Amino Acids)

Enthalpy is a potential that is one driving force for pushing a reaction (chemical or physical). Since only differences of enthalpies matter, there is no absolute enthalpy values. There

Lecture 6: 9/9/2019 (Peptides)

Definition of Standard States. Definition of Heat of Reaction. Hess’s "Law of Obvious properties of a State Function." Defined in terms of Enthalpy. Definition: (Standard) Heat of Formation. Mathematical Application of Hess’s Law: \[\Delta H˚_{rxn} = \sum n• \Delta H^°_f (products) – \sum n•\Delta H^°_f (reactants)\] Enthalpy can drive a reaction (chemical or physical) and so can entropy. Entropy works by a “desire” to be more probable. Not a desire to be more disordered. Gibbs “Free” energy combines both in one function: ΔG = ΔH - TΔS. Like Enthalpy, Entropy is extensive and a state variable.

Lecture 7: 9/11/2019 (Properties of Peptides)

Definition of Standard States. Definition of Heat of Reaction. Hess’s "Law of Obvious properties of a State Function." Defined in terms of Enthalpy. Definition: (Standard) Heat of Formation. Mathematical Application of Hess’s Law: \[\Delta H˚_{rxn} = \sum n• \Delta H^°_f (products) – \sum n•\Delta H^°_f (reactants)\] Enthalpy can drive a reaction (chemical or physical) and so can entropy. Entropy works by a “desire” to be more probable. Not a desire to be more disordered. Gibbs “Free” energy combines both in one function: ΔG = ΔH - TΔS. Like Enthalpy, Entropy is extensive and a state variable.

Lecture 8: 9/13/2019 (Thermodynamics)

Macrostates: A configuration you can observed- not caring about distinguishability of components of the ensemble. Microstates: A configuration that addresses the distinguishability of components of the ensemble. Entropy can be defined in terms of the weight of microstates for a specific configuration: \(S = k_B \ln \Omega\). Entropy works by a “desire” to be more probable. Not a desire to be more random. Spontaneous reactions in isolated systems require entropy to increase.

Lecture 9: 1/28/2019 (Thermodynamics)

Gibbs “Free” energy combines both in one function. Can backtrack entropy to the increase of available states. Then the drive for entropy is just the drive to be more probable: Higher mass species have higher entropy (PIB), Species with more atoms have higher entropy (#vibrations), and species with more flexibility have higher entropy (weaker spring constant in HO). Third Law of thermodynamics assigns a zero to entropy. Can do Hess-like problems to identify entropies of reaction.

• Example Midterm 1 Questions
• Example Midterm 1 Solutions

Lecture 10: 1/30/2019 (Thermodynamics)

We can reconfigure the 2nd law: \(ΔS_{\text{entire isolated system}}>0\) into \(ΔG_{sys} = ΔH_{sys} - TΔS_{sys} <0\). This is an applicable criterion for spontaneity under constant pressure and constant temperature: (1) Reactions can be enthalpically driven, (2) Reactions can be entropically driven, (3) Reactions can be both enthalpically and entropically driven (4) or neither. Reactions that are neither are not spontaneous. Increasing temperature, increased entropic contribution to Gibbs Energy. Spontaneous if |TΔS| < |ΔH| if enthalpically driven only. Spontaneous if TΔS > ΔH if entropically driven only.

• Example Midterm 1 Questions
• Example Midterm 1 Solutions

Lecture 11: 2/1/2019 (States of Matter)

Physical Phenomena are guided by thermodynamics too. There are four fundamental forces of Nature, but electrostatic is “the beast” for chemistry. Three common states of matter (to chemists). Properties of each state is directly a consequence of the intermolecular forces at play Solids are Resistant to deformation and condensed phase. Gases are Compressible, expandable and not-condensed phase. Liquids have Definite volume and indefinite shape and condensed phase and have Fluidity, Diffusion and Surface tension.

Lecture 12: 2/4/2019 (States of Matter)

Intermolecular Forces dictate Bulk properties. Liquids have definite volume and indefinite shape and condensed phase. Other properties of liquids include: fluidity, diffusion, and surface Tension. Introduce the concept of a Potential Energy Surface (curve). Discussed four types of IMFs: (1) Permanent - Permanent Charge Distribution IMFs, (2) Permanent - Induced Charge Distribution IMFs, (3) Instantaneous - Induced Charge Distribution IMFs, and (4) Repulsive Forces. The potentials of these IMFs typically depend on both distance and orientation of the interacting molecules.

Exam 1 (Wednesday): 2/6/2019 (Lectures 1 - 12)

• Example Midterm 1 Questions
• Example Midterm 1 Solutions

Final Exam: 12/20/2019 @ 8:00 p.m.-9:50 p.m. (Friday)

• Example Midterm 1 Questions
• Example Midterm 2 Questions
• Example Final Conceptual Questions