Learning outcomes of the course unit
The aim of the class is knowledge and understanding of the principles underlying physical processes and chemical reactions, by means of models, peculiarity of the Physical Chemistry. At the end of the class, the students would acquire the ability of applying the acquired knowledge and understanding to the study and to the interpretation of biochemical, biological, and pharmaceutical processes.
At the end of the class, the student, by using previously acquired knowledge of General Chemistry, Physics and Mathematics, will show rigorous knowledge about:
- Classical and statistical thermodynamics, and kinetics, applied to the chemical reactions and to the biological systems;
- transport processes, explained by means of non-equilibrium thermodynamics models, stability of the colloidal systems, and their involvement in the pharmaceutical field;
- principles of quantum mechanics as basics for spectroscopy and computational pharmaceutical chemistry.
Knowledge of General Chemistry, Physics and Mathematics.
Course contents summary
The first part of the class is devoted to the equilibrium thermodynamics with statistical thermodynamics outline and to the kinetics, also in connection with the already acquired knowledge of General Chemistry and Physics.
The second part deals with non-equilibrium thermodynamics and transport processes with reference to the biological systems and to the pharmaceutical applications.
The third part is connected with the colloidal systems and their stability, particularly as far as the pharmaceutical and food systems are concerned.
The fourth part deals with quantum chemistry, the foundation of spectroscopy and computational pharmaceutical chemistry.
Equilibrium thermodynamics applied to chemical and biological systems with a statistical thermodynamics outline. Variables and state functions. The laws of thermodynamics. The temperature and pressure dependence of thermodynamic quantities. Thermochemistry. Calorimetry.. Outline of statistical thermodynamics. The molecular interpretation of thermodynamic quantities. Molecular partition function. Maxwell’s equations. Exercises.
Changes of state: physical transformations of pure substances. Phase diagrams. Clausius-Clapeyron equation. Gas-liquid phase transition and critical phenomena. The principle of corresponding states. Gibbs phase rule
Changes of state: physical transformations of simple mixtures. Open systems and partial molar quantities. Ideal and real solutions. Raoult and Henry laws. Fugacity and activity. Water activity in foods. Regular solutions. Ideal mixing and excess functions. Phase equilibria in binary systems. Fractional distillation. Azeotropes, eutectic, partially miscible liquids, binary mixtures compounds forming. Solvent chemical potential. Colligative properties. Molecular weight measurements. Membrane equilibria. Solutions of macromolecules. Dialysis equilibrium. Donnan equilibrium.
Equilibria of chemical reactions. Gibbs free energy and equilibrium constant. Activity and ionic strength. Statistical Thermodynamic interpretation of equilibria in solution. The Bjerrum function. Distribution diagrams. Binding curves. Cooperativity.
Electrochemistry. Electrochemical cells. Electrodes. Nernst equation. Standard reduction potentials. The potentiometer. Electrolyte concentration cells. Nerve stimulus.
Bioenergetics. Active and passive processes. Transport phenomena: passive and active transport. Exergonic and endergonic reactions. Coupled reactions. High energy compounds. Scale of transfer potentials.
Non-equilibrium thermodynamics and transport processes. Force and flow. Phenomenological equations. Curie theorem. Prigogine theorem. Onsager law. Dissipation function. Steady state concept. Mobility of the ions in solution. Electrophoresis. Diffusion. Sedimentation. Viscosity.
Chemical kinetics. The rate of chemical reactions. Stoichiometry, order and , molecularity. 1st and 2nd order reactions. Half-life time. Arrhenius equation. Catalysis. Enzyme kinetics. Fast reactions.
Intermolecular forces. Van de Waals forces. Dipole and induced dipole. Potential energy. Hydrogen bond. Hydrophobic interactions. Partition coefficient.
Colloid, surface chemistry and biopolymers. Definition and classification. Surface tension. Intermolecular forces in colloidal systems. DLVO theory. Structure and classification of surfactants. Micelle formation. Solid-gas, liquid-gas, liquid-liquid, solid-liquid interfaces. Adhesion and cohesion work. Emulsions. Emulsifiers and stabilizers in foods. Microemulsions. Liquid crystals. Langmuir-Blodgett films. Biological and artificial membranes.
Quantumchemistry. The failure of classical mechanics. The quantization of energy. The rhodopsin and the vision mechanism. The wave-particle dualism. Basic assumptions of quantum mechanics. The wave function. The operators. Shrödinger equation. The particle in a box. Harmonic oscillator and diatomic molecules. Rigid rotator. Atoms and molecules.
Spectroscopy. Electromagnetic radiation. Longitudinal and transverse wave. Polarization. Addition of waves. Interaction of light with matter: absorption, emission, scattering. Rayleigh limit, Thomson limit, Lorentz limit. Electromagnetic spectrum. Energy levels and photons. Surrounding effect: colour vision. Time scale and rate of the spectroscopic transitions. Induced dipole moment: classical an quantum mechanics interpretation. Outline of UV-visible, IR, Raman spectroscopy and of circular dichroism and optical rotatory dispersion. LASER.
P. W. Atkins, J. De Paula, Chimica Fisica Biologica, vol.1 e 2, Zanichelli, Bologna, 2008
P. W. Atkins, J. De Paula, Chimica Fisica, quarta edizione italiana, Zanichelli, Bologna, 2004.
P. W. Atkins, R.S. Friedman, Meccanica Quantistica Molecolare, Zanichelli, Bologna, 2000
During lectures, done by means of computer ppt presentations, available to the students before classes in the web site of the class, general topics related to the use of chemico-physical models for studying biological, biochemical and pharmaceutical systems will be discussed. Lectures will be implemented by means of problem solving and “question time” like activities in order to maximize the understanding level of the students.
Assessment methods and criteria
In order to prove the achievement of the expected expertises, during teaching activity (three months) the students can take three written “in itinere” tests, one each month. The exam is passed if the average mark is 18/30 and no mark of the “in itinere” tests is under 16/30. Otherwise, there is a written examination on the whole syllabus during scheduled examination sections.
The “in itinere” tests and the final written examination consist of open questions and problem solving in such a way that the students can demonstrate knowledge and understanding of the class subjects.