Computational Chemistry

Course information:

All the information you need for this course will be accessible from this site.

Need some help!

Check the recommended texts for this course:

• Introduction to Computational Chemistry by Frank Jensen, John Wiley and Sons, Chichester, 2017, and is available as an e-version online through the library here
• Computational Chemistry by Jeremy Harvey, Oxford Chemistry Primers series, Oxford University Press, Oxford, UK, 2018
• Molecular Quantum Mechanics, Peter Atkins and Ronald Friedman, Oxford University Press, 4th or 5th edition.

Maths a bit rusty?

• Engineering Mathematics: a Foundation for Electronic, Electrical, Communications and Systems Engineers 4th edition or later, by Anthony Croft, Robert Davison, Martin Hargreaves and James Flint, Pearson, 2012, and is available as an e-version online through the library here
• Maths for Chemists has been developed by students for students, can be found here.
• see also the maths resources in Chem 203

Lecture 1: Revision and the Hydrogenic Atom

Based on student feedback this lecture will be given in a flipped format. You should download and read the Revision notes summarising chem203 quantum mechanics and read the Lecture 1 notes on the Hydrogenic Atom, for this lecture. We will spend the lecture doing the problems given at the end of the lecture notes.

1. revision:pdf
2. notes:pdf
3. problem answers:pdf
4. resources related to this lecture optional
   • check out this utube video introducing computational chemistry
   • wiki on associated Legendre polynomials
   • wiki on spherical harmonics
   • here is a nice explanation of integrating in spherical polar coordinates
   • the Orbitron a website showing 3D orbital surfaces and equations
   • wiki on associated Leguarre functions
5. extra reading related to this lecture advised
   • Chem 203 Lecture 7
   • Chem 203 Lecture 8
   • Chapter 2: Particle in a Box from Molecular Quantum Mechanics
   • Chapter 3: Particle on a Ring from Molecular Quantum Mechanics
   • Chapter 3: The Radial Schrodinger Equation from Molecular Quantum Mechanics
   • Chapter 3: Atomic Orbitals from Molecular Quantum Mechanics

Lecture 2: The Schrodinger Equation

1. notes:pdf
2. problem answers:pdf
3. resources related to this lecture optional
   • additional notes:pdf
   • my mini-videos:
     • The Schrödinger equation and operators 8min
     • The mathematics of these operators 15min
     • The wavefunction 7min
     • The Hartree equation 5min
4. extra reading related to this lecture advised
   • you can ignore the material on spin-orbit interactions, we will not be covering it
   • Chapter 7: The Structure of Helium from Molecular Quantum Mechanics
   • Chapter 7: Many Electron Atoms from Molecular Quantum Mechanics
   • Chapter 7: Slater Atomic Orbitals from Molecular Quantum Mechanics

Lecture 3: Hartree-Fock Theory

1. notes:pdf
2. additional notes on some of the equations:pdf
3. resources related to this lecture optional
   • fermions as fundamental particles wiki
   • mini-video set up for HF theory 3 min
4. extra reading related to this lecture, this is difficult stuff, these texts are for those who are very interested!
   • Essentials of Computational Cheistry by Christopher Cramer, Chapter 4: Foundations of Molecular Orbital Theory.
   • Molecular Quanutum Mechanics by Peter Atkins and Ronald Friedman, Mathematical background 4 (for determinants), Chapter 7 : Atomic spectra and atomic structure and Chapter 8: An introduction to Molecular Structure
   • Modern Quantum Chemistry : Introduction to Advanced Electronic Structure Theory by Attila Szabo and Neil Ostlund, Chapter 2 and Chapter 3
   • Atkins Physical Chemistry, by Peter Atkins and Julio De Paula , Chapter 10 sections 10.1-10.5 The Structure and Spectra of Hydrogenic Atoms and The structures of many-electron atoms.

Lecture 4: Density Functional Theory

1. notes:pdf
2. problem answers:pdf
3. resources related to this lecture optional
   • paper for D3 dispersion correction doi
   • paper for BJ damping correction doi
   • paper illustrating large scale study of functionals doi
   • paper illustrating use a reference database for benchmarking DFT doi
   • paper on how much exchange to include doi

Lecture 5: Basis Sets 1

1. notes:pdf
2. problem answers:pdf
3. resources related to this lecture optional
   • underpinning basis sets is the area of mathematics called linear algebra, one of my PG students found these utube video explanations very useful
   • article reporting def2 basis set Accurate Coulomb-fitting basis sets for H to Rn, F. Wigend Phys. Chem. Chem. Phys., 2006, 8, p1057
   • Nobel prize in chemistry 1998 to John Pople for his development of computational methods in quantum chemistry.

Lecture 6: Basis Sets 2

1. notes:pdf
2. problem answers:pdf
3. resources related to this lecture optional
   • take a look at the Basis Set Exchange to get an idea of basis sets and PPs
   • review article on Atomic orbital basis sets, F. Jensen, WIREs Comput Mol Sci 2013, 3 p273
   • Best-Practice Protocols for choosing a method and basis set doi

Tutorial

1. questions we will be covering: pdf
2. model answers to the questions: pdf

Lecture 7: Properties

1. notes:pdf
2. this lecture we will look at some "real" examples of the use of quantum chemistry, please download and take a look at both of these papers before the lecture, you don't need to understand them! But it will help you follow the discussion if you have some awareness of the papers beforehand:
   • natural products paper: Stictamycin, an Aromatic Polyketide Antibiotic Isolated from a New Zealand Lichen-Sourced Streptomyces Species, P. Hou, V. Woolner, J. Bracegirdle, P. A. Hunt, R. Keyzers, J. Owen, J. Nat. Prod., 2023, 86, 3, 526 doi
   • how can ionic liquids accelerate a non-polar reaction?, Unravelling ionic liquid solvent effects for a non-polar Cope rearrangement reaction G. Smith, S. Koutsoukos, B. Lancaster, J. Becker, T. Welton and P. A. Hunt Physical Chemistry Chemical Physics, 2024, 12453-12466, doi
   • for those who want something a bit more quantitative: Frank Jenson Chapter 11 Molecular Properties

Lecture 8: Overview of the area of Computational Chemistry and Molecular Dynamics

1. notes:pdf
2. problem answers:pdf
3. resources related to this lecture optional
   • paper from my group on partial charge methods doi
   • paper from my group showing how computational chemistry can be used doi