CH3717 – Statistical Mechanics and Computational Chemistry

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Lecturers:        
Dr J. B. O. Mitchell and Dr T. van Mourik*
(*Module Convenor)

Aims:         
In the first part of the course, students will be introduced to Statistical Mechanics and the molecular or atomistic basis for thermodynamics will be considered. In particular, the statistical basis of entropy will be explained and the concepts underpinning the derivation of the Boltzmann distribution will be outlined. The key role of the partition function in linking microscopic properties associated with, for example, molecular rotation and vibration to macroscopic thermodynamic properties will be explored and applied to the calculation of equilibrium constants and in transition state theory.

In the second part of the course, the use of computational chemistry in the modern drug design process will be discussed, covering force field calculations, molecular dynamics, molecular docking, QSAR (Quantitative Structure Activity Relationships) and pharmacophores.

Introduction to Statistical Mechanics – Dr J. B. O. Mitchell

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Duration:
10 hours

Aims:
The aim of this course is to provide an introduction to the basic ideas of statistical mechanics, the essence of which is the description and interpretation of macroscopic thermodynamic quantities in microscopic / atomistic terms.

Objectives:
1. To understand the concepts of microstates and configurations and the idea of the predominant configuration.
2. To understand the Boltzmann Distribution Law and its significance in chemistry.
3. To know the form of and understand the meaning of partition functions, and to become familiar with molecular translational, rotational, vibrational and electronic partition functions.
4. To understand the pivotal relationship between partition functions and thermodynamic quantities and the notion of thermal averages. To understand how macroscopic thermodynamic quantities such as internal energy and entropy can be computed from partition functions.
5. To know how partition functions are defined and computed for molecules having multiple degrees of freedom.
6. To understand how partition functions are calculated for systems comprising many molecules. To consider the effect of distinguishability and indistinguishability on partition functions.
7. To know how and when thermodynamic quantities can be calculated easily from equipartition. To understand heat capacities.
8. To be able to calculate equilibrium constants from partition functions. To have an overview of transition state theory.
9. To be aware of applications of statistical mechanics and statistical thermodynamics in the sciences.

Computational Chemistry – Dr T. van Mourik

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Duration:
7 hours

Aims:
The aim of this part of the module is to become familiar with computational chemistry techniques that are used in modern drug design processes, covering force field calculations, molecular dynamics, molecular docking, QSAR and virtual screening.

Objectives:
1. Introduction to computational chemistry for medicinal chemists, covering its use in the design and development of drugs, with practical examples.
2. To learn how molecular mechanics force fields are used in modelling.
3. To learn the basic concepts of molecular dynamics, including the calculation of thermodynamic properties.
4. To learn how molecular docking is used to predict whether a drug candidate will bind to its target receptor.
5. To understand the basics of QSAR (Quantitative Structure Activity Relationships), and how it is used to correlate chemical structure with biological activity.
6. To understand what pharmacophores are and how they can be used to identify lead compounds.