Physical Theory

Overview

STAFF

NAME CONTRIBUTION
Dr A. Doherty
A.P.Doherty@qub.ac.uk Kinetics (6 hours lectures, 2 hours seminars)
Electrochemistry (5 hours lectures, 1 hour seminar and 1 tutorial)
Dr M. Huang
m.huang@qub.ac.uk Laboratory Classes
Dr P. Kavanagh
p.kavanagh@qub.ac.uk Phase Equilibria, (10 hours lectures, 3 hours seminars, 2 hours assessment); Laboratory Classes
Dr L. Moura
l.moura@qub.ac.uk Basic Thermodynamics, (8 hours lectures, 4 hours seminars and 1 tutorial)
Dr L. Stella
l.stella@qub.ac.uk Computer Workshops (6 hours)
Dr J. Thompson
jillian.thompson@qub.ac.uk Chemical Equilibria (10 hours lectures, 3 hours seminars); Laboratory Classes
Dr J. Vyle
j.vyle@qub.ac.uk Physical Chemistry Aspects of Drug Design (6 hours lectures, 3 hours seminars and 1 tutorial)

Lecture content
Chemical Equilibria (10 hours lectures, 3 hours seminars):
 1.1 Introduction to physical chemistry: review states of matter and introduction to ideal gases and ideal solutions, enthalpy and internal energy, Hess cycles, heat capacity and heat transfer.
 1.2 Chemical Equilibria: Definitions and calculations involving equilibrium constants Kc and Kp, including examples of homogeneous and heterogeneous equilibria (Ksp). Definitions and calculations involving enthalpy of solution and lattice energy. Application of Le Chatelier’s Principle to determine the effect of change in concentration, pressure, temperature and catalyst on the composition of the reaction mixture and the equilibrium constant. The Common Ion Effect.
 1.3 Acids and Bases: Definitions of conjugate acid and base; strong and weak acids and bases. Calculation of pH, pKa and pKb. The special case of water Kw and pKw Terminology in acid/base titrations, calculation of pH at the end point, and indicators. Definition of a buffered solution and calculation of its pH. Examples of polyfunctional acids and their behaviour in titrations.

Phase Equilibria (10 hours lectures, 3 hours seminars, 2 hours class test – first semester):
 2.1. Phase Change: Phase changes including melting temperature, boiling temperature, density and molar volume, lattice energy, bond dissociation energy, enthalpy of vaporisation, introduction to entropy.
 2.2. One Component Systems: Phase equilibria in single component systems using simple
P-T diagrams, the phase rule. Vapour pressure – temperature relationships: the Clapeyron and Clausius-Clapeyron Equations, the Antoine Equation.
 2.3. Two-component systems (vapour-liquid equilibria of ideal systems): Raoult’s Law, Dalton’s Law and Henry’s Law applied to ideal two component systems, volatility and relative volatility, constant pressure diagrams (x,y and T-x,y) and the Lever rule.
 2.4. Introduction to non-ideal solutions: An azeotrope being a mixture that vaporizes and condenses without a change in composition; a eutectic being a mixture that freezes and melts without change of composition.
 2.5. Colligative properties: Relative lowering of vapour pressure, boiling point elevation and boiling point depression in binary solutions containing non-volatile solutes; osmotic pressure.

Kinetics (6 hours lectures, 2 hours seminars):
 3.1. Key concepts: Elementary reactions, reaction molecularity, molecularity vs. stoichiometry, definition of reaction rates, calculating reaction rates from experimental data, writing differential rate laws, reaction orders, order vs. molecularity, reaction rate constants, initial rates method, integrated rate laws (how and why), collision and transition state theories, Arrhenius rate law and activation energy, reaction kinetics in relation to reaction mechanism. Catalysis. Methods of measuring reaction rates.
 3.2. Derivation of rate equations: Derivation of zero, 1st and 2nd rate laws, experimental data analysis and visualisation, Obtaining reaction orders and rate constants by the initial rates method. Analysing data using integrated rate laws and making predictions.
 3.3. Collision and transition state theories: The Arrhenius equation. Activation by collision and the collision theory. Measurement of activation energies.
 3.4. Classes of reaction: Simple gas phase reactions. Chain and branched chain reactions. Reactions in solution, reactions of solids, catalysed reactions.

Basic Thermodynamics, (8 hours lectures, 4 hours seminars and 1 tutorial):
 4.1. Summary review. Thermodynamics and the concepts of temperature, heat/energy flow and thermal equilibrium. Introduction to enthalpy, work, internal energy, zeroth law of thermodynamics, the first law of thermodynamics, state function, standard conditions, enthalpy of formation.
 4.2. The direction of spontaneous change. Spontaneous vs non-spontaneous change. Entropy as criterion for spontaneous change. Reversible and irreversible processes. Classical and molecular basis of entropy.
 4.3. The second law of thermodynamics. Examples and calculations using standard entropies; entropy changes with volume, temperature, phase transitions and chemical reactions.
 4.4. Absolute entropy and the third law of thermodynamics.
 4.5. Chemical equilibrium: Gibbs energy and spontaneity, energy minimum, direction of chemical change and influence of enthalpy and entropy. Variation of Gibbs energy with temperature, pressure and concentration. Gibbs energy relationship with equilibrium and the equilibrium constant. Examples and calculations.
 4.6. Gibbs energy and phase equilibria. The thermodynamics of transition. Review of one component and two component phase diagrams. Liquid-liquid equilibria, phase separation, critical solution temperature, distillation of partially miscible liquids. Examples of extractions, separations and molecular interactions.

Electrochemistry (5 hours lectures, 1 hour seminar and 1 tutorial) :
 5.1. Introduction to Electrochemistry: Equilibrium vs. Dynamic Electrochemistry classification; Units / dimensions electronic charge, coulombs; Review of Faraday’s Law; What is an electrode? Redox reactions at electrodes; Charge separation at interfaces and interfacial electric potential; Spontaneous vs. non-spontaneous charge separation; “Kinds” of electrodes; Electrode potentials = ΔG / -nF; Nernst equations for different “kinds” of electrodes; Effects of temperature and concentration on electrode potentials; Importance of the Standard Hydrogen Electrode.
 5.2 Electrochemical Cells: Electrochemical series; Electrochemical cells, net cell reactions, cell diagrams; Calculating cell potentials, ΔG overall and K, equilibrium constant; Calculating solubility of salts from cell potential measurements; Calculating cell potentials from thermodynamic data; H2/O2 fuel cell description / performance; Cell thermodynamics, potentials vs. ΔS (entropy changes) relationship.

Physical Chemistry Aspects of Drug Design (6 hours lectures, 3 hours seminars and 1 tutorial):
 6.1 Introduction to the physical properties of drugs and their targets: Recognising hydrogen bond donors and acceptors in biomolecules and in API’s (especially β-lactam antibiotics); binding affinities and selectivity; screening potential drug molecules using Lipinski’s Rule; prodrug activation strategies.
 6.2 Basic Pharmacodynamics and Pharmacokinetics: Quantitative dose response curves and rates of elimination.

Laboratory Classes (21 hours):
 Students will be divided into groups. Each group will carry out 7 different experiments (3 hrs each):
 P1 The Catalysed Decomposition of Hydrogen Peroxide in Aqueous Solution;
 P2 Buffers and pH Measurement;
 P3 Phase Transfer and Solubility of I3-;
 P4 Concentration Cells and Electrode Potentials;
 P5 Enthalpy and Entropy of Vaporisation;
 P6 Determination of the Activation Energy of a Reaction;
 P7 Visualisation of 3D structure of a medicinal chemistry compound.
 Both an individual COSHH assessment and pre-lab assessment as well as an individual post-lab report will be submitted for each experiment as indicated on Canvas.

Computer Workshops (6 hours):
 Students will attend two computer-based workshops
 Using Excel for calculation and graphing
 Using Excel for statistical analysis

Learning Objectives

On completion of this module a learner should be able to:
 Explain and use equations to describe chemical systems at equilibrium.
 Describe the general principles of phase equilibria as applied to single and binary component systems.
 Understand and apply the basic rules of chemical kinetics.
 Describe and apply the general principles of the first and second laws of thermodynamics.
 Describe equilibria of electrochemical cells and discuss applications of electrochemical theory.
 Explain the chemistry of drug design and interaction.
 Improved practical skills:
 General chemical and engineering laboratory skills including estimation of experimental error.
 Increased awareness of laboratory health and safety requirements.
 Use of Excel for calculations and graphing.
 Use of ChemDraw for presentation of chemical structures.
 Gained transferrable skills:
 Basic thermodynamic, kinetic and electrochemistry knowledge, basic laboratory skills, use of ChemDraw, Excel and estimation of error in experimental results.

Skills

Skills associated with module:
Thermodynamic and kinetic problem solving (including numerical), Excel-based calculations, graphing. General chemical and engineering laboratory skills including statistical analysis.
In addition,
Communication – spoken during practicals, tutorials and seminars and written in lab reports, tutorials, class tests and exam.
Numeracy – basic algebra and calculus.
Improved independent learning and time management.
Problem-solving –solving problems in exams, tutorials, seminars and practicals.
Safe handling of chemical materials, taking into account their physical and chemical properties, including any specific hazards associated with their use. Accurate measurement and recording of data and appreciation of error.
Standard laboratory procedures involved in physical chemistry.

Assessment

Assessment:
Examination 60 % (3hr)
Practicals and workshops 25 % (throughout both semesters)
Class test 10 % (week 12, first semester,
feedback by week 18)
Tutorials 5 % (2nd semester only)

Course Requirements:
Practical and laboratory attendance and report submission 80 %.
Examination and coursework (comprising class test, tutorials, workshops and practicals) must both be passed - 40% veto.