Chemical Thermodynamics of Molecular Aggregates (Lecture Notes)

Vocabulary flashcards covering core terms from the lecture notes on chemical thermodynamics of molecular aggregates.

Chemical thermodynamics of molecular aggregates

The study of thermodynamic properties and processes for aggregates (solutions, micelles, lipid membranes, polymers, proteins) to connect microscopic structure and interactions with macroscopic behavior.

Solvation free energy (Dµ)

The free energy change when transferring a solute from vacuum into a solvent; reflects how the solvent environment stabilizes or destabilizes the solute.

Solubility (S)

Equilibrium concentration of a solute in a solvent; related to Dµ via Dµ = −RT ln S with a chosen standard state.

Chemical potential (µ)

Partial molar Gibbs free energy; drives partitioning, mass transfer, and reactions; equal across phases at equilibrium.

Ideal term (µid)

The concentration-dependent part of µ, typically µid = RT ln(c/w) for a given standard state w.

Excess term (µex)

The non-ideal contribution to chemical potential arising from interactions with the solvent/environment beyond the ideal solution.

Activity (a)

Effective concentration relative to a standard state, a = c/w; used to describe real solutions.

Activity coefficient (g)

Ratio g = a/c that measures deviation from ideal behavior; g = 1 in ideal dilute solutions.

Standard state (w)

Reference state used for activities and chemical potentials (e.g., 1 M, 1 atm) to define µ and related quantities.

Partition coefficient (K)

Ratio of a species’ concentrations between two phases at equilibrium; determined by equal chemical potentials in each phase.

Gibbs free energy (G)

G = U − TS + pV; a state function that governs spontaneity at constant T and p; spontaneous changes satisfy dG ≤ 0.

Helmholtz free energy (A)

A = U − TS; a state function useful when temperature and volume are held constant; spontaneous changes satisfy dA ≤ 0.

Internal energy (U)

Total energy content of a system; a state function with changes given by dU = dq + dw.

First law of thermodynamics

Energy conservation: dU = dq + dw; energy can be transferred as heat or work but U is conserved as a state function.

Second law of thermodynamics

Entropy of an isolated system does not decrease; for reversible paths dS = dqrev/T; entropy is a state function.

Entropy (S)

A state function representing energy dispersal; increases in spontaneous processes; defined via reversible paths.

Reversible process

A quasi-static process maintaining equilibrium at every step; yields maximum work and satisfies pex = psystem.

Spontaneous process

A process that occurs with dG ≤ 0 at fixed T and p (not necessarily reversible); can proceed without external input.

Temperature (T)

A measure of hotness; defined via the zeroth law and thermal equilibrium; a key variable in thermodynamics.

Pressure (p)

Force per area; boundary conditions with surroundings determine mechanical equilibrium and work in pV processes.

Aggregation number (n)

Number of monomer units in an aggregate; influences intra-solute energy (Es) and solvation energy (Dµ).

Cosolvent effect

Addition of solvents like urea or DMSO that modify solvation free energy and can inhibit or promote aggregation.

All-atom MD

All-atom molecular dynamics simulations that resolve every atom to study structure and solvation energetics (e.g., Dµ).

Solvation free energy in polymers

Dµ for solvent (e.g., water) in a polymer; determines dissolution, diffusion, and polymer–solvent interactions.

Hydration

Solvation of a solute by water; hydration number indicates how many water molecules are associated; tunable by density/temperature.

Supercritical water

Water above its critical point with tunable density and solvent power; can alter reaction pathways and solvation behavior.

Separation membrane

Polymer-based membrane used for separation; performance depends on diffusion, partition, and permeability.

Permeability (P)

Rate of transport of a species through a membrane; P ≈ K × D, linking partitioning (K) and diffusion (D).