Computational Chemistry from Molecular Properties to Reactions: Learning-by-doing

The course of computer chemistry is practical in nature, meaning that it teaches students how to use the computer to predict the results of a chemical reaction. Along with the practical knowledge, the course also provides the necessary theoretical knowledge to understand the underlying principles of quantum mechanics. This knowledge is essential for students to understand the implications of their predictions and to be able to make informed decisions.

About the Course

Computer chemistry is a rapidly growing field of study, and it is becoming increasingly important in the field of chemistry. It is used to predict the results of chemical reactions, which can be used to develop new materials and products. It is also used to analyze existing materials and products to determine their properties and to optimize their performance. Computer chemistry is also used to develop new drugs and treatments for diseases.

Computer chemistry is an invaluable tool for chemists and other scientists, and it is becoming increasingly important in the field of chemistry. It is a powerful tool that can be used to predict the results of chemical reactions and to develop new materials and products. It is also used to analyze existing materials and products to determine their properties and to optimize their performance.

Course Programme

Module 1a. Introduction. Wave function of hydrogen-like atoms. General principles of description of many-electron systems. The concept of an orbital.

Module 1b. Practice. Basics of working in Linux operating system. Installation and basic principles of using quantum-chemical programs Molcas and ORCA.

Module 2. Molecular coordinate system. The concept of molecular orbital and the MO-LCAO method. Atomic basis sets.

Module 3a. Constructing a many-electron wave function from one-electron wave functions (orbitals). Basic approaches to solving the Schrödinger equation. Self-consistent field method. Restricted and unrestricted Hartree-Fock methods.

Module 3b. Practice. Calculation of the electronic energy of a hydrogen molecule. Calculation of the electronic energy of the triplet state for hydrogen and oxygen molecules. Calculation of dissociation energy of hydrogen molecule. Using graphical programs to visualize the results of quantum chemical calculations.

Module 4a. Post-Hartree-Fock methods. Perturbation theory method (MP2) and coupled cluster method (CCSD(T)).

Module 4b. Practice. Calculation of the dissociation energy of a hydrogen fluoride molecule by post-Hartree-Fock ab initio methods (MP2, CCSD(T)).

*Module 5a. Methods of overlapping configurations (configuration interaction) — CIS, CISD, CISDT, CISDTQ. Full Configuration Interaction method: Full Configuration Interaction (FCI). Multiconfigurational Self Consistent Field Method. Multiconfigurational Self Consistent Field (MCSCF). CASSCF and CASPT2 methods.

*Module 5b. Practice. Calculation of dissociation energy of hydrogen fluoride molecule by post-Hartree-Fock ab initio methods (CISDT, CISDTQ, MCSCF, CASSCF, CASPT2).

Module 6a. The concept of electron density. Fundamentals of density functional methods (DFT). Electron-electron interaction. Types of electron correlation.

Module 6b. Practice. Calculation of dissociation energies of two-atomic molecules using different density functionals.

Module 7a. Born-Oppenheimer Approximation. The concept of a potential energy surface.

Module 7b. Practice. Calculation of potential energy surface for hydrogen fluoride molecule by different ab initio and DFT methods.

Module 8a. Types of stationary points on the potential energy surface. Principles of calculation of gradients and Hesse matrices. Basic approaches to optimization of molecular geometry.

Module 8b. Practice. Calculation of gradients and Hesse matrices and optimization of various molecular systems using ORCA and Molcas programs.

Module 9.1a. Motion of nuclei near the equilibrium point. Oscillatory spectra.

Module 9.1b. Practice. Calculation of transition energies between vibrational levels for two-atom and multi-atom molecules.

Module 9.2a. Macroscopic properties of ensembles of molecules. Gibbs energy, enthalpy, entropy.

Module 9.2.b. Practice. Calculation of enthalpy, entropy and Gibbs energy.

Module 9.3.a. Methods of accounting for solvent in quantum chemical calculations.

Module 9.3.b. Calculation of Gibbs energy differences and relative stability of different isomers in the gas phase and solvent.

Module 10a. Basic principles of modeling chemical reactions. Approaches to optimization of transition states. Reaction pathway and reaction coordinate.

Module 10b. Practice. Calculation of potential energy surface scans. Optimization of transition states. Calculating the coordinate for a set of reactions in the gas phase and solvent.

*Modules marked with an asterisk are for in-depth study of the topic.

Learning Results

After completing the course you will know:

• the basic principles of describing multielectronic systems;
• the concept of atomic and molecular orbitals and how the wave function of a multi-electron system (atom or molecule) is constructed from them;
• basic ideas and principles of using the most commonly used ab initio methods based on wave function calculations;
• basic ideas and principles of using methods based on density functional;
• principles of choosing a calculation method for modeling various chemical systems and reactions;
• how vibrational motions of molecules are described;
• how thermodynamic characteristics such as enthalpy, entropy, Gibbs energy can be calculated;
• how to take into account the influence of the solvent when modeling chemical systems and reactions;
• get acquainted with the concept of potential energy surface and know how to use this concept to optimize the geometry of molecular systems, search for transition states and reaction paths.

After completing the course you will learn how to:

• perform various quantum-chemical calculations, including modeling of chemical reaction mechanisms, using commonly available quantum-chemical programs, in particular ORCA and Molcas programs;
• intelligently select a computational method for your application;
• use the Linux operating system;
• create scripts to automate calculations and process results using Bash and Python.

After taking the course you will be proficient in:

• basic quantum-chemical methods for calculations of various properties of molecular systems and modeling of chemical reaction mechanisms;
• skills of using widely available programs for quantum-chemical calculations, first of all, ORCA and Molcas software packages;
• Linux operating system skills, including the use of bash and python to automate routine tasks.