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

What awaits you in the course?

• Lots of practice: provided during lectures and carried out as homework
• Minimal amount of theory: only to perform practical tasks meaningfully

By completing 10 modules of the course, you will learn how to use quantum chemistry methods and software to calculate the properties of chemical compounds and investigate the mechanisms of chemical reactions running the calculations either on a laptop or on supercomputers.

At the beginning of the course you will:

• get acquainted with the Linux operating system;
• install the widely used quantum chemical software packages ORCA and Molcas, which you will use to perform calculations during the course.

In the first part of the course you will learn how to:

• perform calculations using the ORCA programme;
• use density functional methods and basic ab initio quantum chemistry methods to model various molecular systems and processes, from diatomic molecules to chemical reactions;
• write simple Bash scripts to process calculation results.

In the second part of the course you will learn how to:

• perform calculations using the Molcas programme;
• use a larger number of ab initio quantum chemistry methods;
• write more complex Bash and Python scripts to automate calculations and process calculation results.

By completing the course, you will also be able to easily start using different other quantum chemistry programs such as Gaussian, NWChem, etc.

The form of education is online. Weekly classes will include watching thematic video lectures, studying additional materials and completing tests with automated verification of results. All assignments must be completed to obtain a certificate.

This course may be of interest to undergraduate, graduate and postgraduate students of higher education institutions, as well as to all those who are interested in this topic. 
For potential employees, the course will provide science-based information that will give them a competitive advantage in their own employment.

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 the hydrogen molecule. Calculation of the electronic energy of the triplet state for the hydrogen and oxygen molecules. Calculation of the dissociation energy of the 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 the hydrogen fluoride molecule using post-Hartree-Fock ab initio methods (MP2, CCSD(T)).

*Module 5a. Configuration interaction methods - CIS, CISD, CISDT, CISDTQ. Full Configuration Interaction method (FCI). Multiconfigurational Self Consistent Field (MCSCF). CASSCF and CASPT2 methods.

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

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

Module 6b. Practice. Calculation of dissociation energies of diatomic molecules using different density functionals.

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

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

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

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

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

Module 9.1b. Practice. Calculation of transition energies between vibrational levels of diatomic and polyatomic 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 for taking into account solvent effects in quantum chemical calculations.

Module 9.3.b. Calculation of the difference in Gibbs energy and the relative stability of different forms of molecules in the gas phase and solvent.

Module 10a. Basic principles of modeling chemical reactions. Approaches to the optimization of transition states. The reaction path and the reaction coordinate.

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

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

After completing the course you will know:

• the concept of atomic and molecular orbitals, how to construct the wave function of an atom or a molecule from orbitals;
• basic principles of using most common ab initio methods, i.e. methods that are based on the wave function calculation;
• basic principles of using density functional methods;
• the concept of potential energy surface and how to use this concept to optimize geometry of molecular systems, search for transition states and reaction paths;
• how to choose quantum chemical methods for modeling different chemical systems and reactions;
• how to calculate vibrational frequencies of molecules;
• how to calculate thermodynamic properties of molecular systems – enthalpy, entropy, Gibbs energy;
• how to take into account the solvent effect in quantum chemical calculations.

After completing the course you will learn how to:

• use quantum chemistry methods and software to calculate the properties of chemical compounds and investigate the mechanisms of chemical reactions;
• choose correct quantum chemistry methods for solving different problems;
• use the Linux operating system;
• write Bash and Python scripts to automate calculations and process results.

After completing the course you will be proficient in:

• application of quantum chemical methods for calculating various properties of molecular systems and modeling the mechanisms of chemical reactions;
• use of widely available quantum chemistry software;
• use of the Linux operating system;
• writing  Bash and Python scripts to automate routine tasks.

The discipline is aimed at the formation of universal competencies of students in the educational programs of the bachelor's / specialist's degree, as well as other competencies provided for by the educational program.

ПК-10 Владеет современными компьютерными технологиями, применяемыми при обработке результатов научных экспериментов и сборе, обработке, хранении и передачи информации при проведении самостоятельных научных исследований, свободно владеет ими при проведении самостоятельных научных исследований;

ПК-12 Умеет применять основные законы химии при обсуждении полученных результатов, в том числе с привлечением информационных баз данных;

ПК-4 Использует основные законы естественнонаучных дисциплин в профессиональной деятельности, применяет методы математического анализа и моделирования, теоретического и экспериментального исследования.