| Competences |
| Type A | Code | Competences Specific |
| CE12 | Make numerical calculations and interpret experimental data, with special emphasis on precision and accuracy | |
| Type B | Code | Competences Transversal |
| Type C | Code | Competences Nuclear |
| Learning outcomes |
| Type A | Code | Learning outcomes |
| CE12 |
To know the theories, models and digital technologies most widely used in computational chemistry | |
| Type B | Code | Learning outcomes |
| Type C | Code | Learning outcomes |
| Contents |
| Topic | Sub-topic |
| Overview: from Angstrom to micrometer | 1) Different methods for different problems: Importance of choosing the correct approach to obtain relevant insights into chemical problems 2) Counting atoms: Typical system sizes in biochemistry, organic and inorganic chemistry, astrochemistry |
| Large systems: Force Fields methods | 1)Energy expression: Stretching, bending, torsion, non-bonding, electrostatic and cross terms. 2) Parameterization schemes: Elements with different hybridizations, radical centers, lone pairs, different functional groups, coarse graining (grouping together various atoms into one). 3) Different Force Fields: AMBER, CHARMM, GROMOS, UFF, etc. 4) Advantages and Limitations: Validation, Transition metals, System size, Molecular dynamics simulations. |
| Medium systems: Mean field wave function methods | 1) Adiabatic and Born Oppenheimer approximations 2) Hartree-Fock: Variational principle, Slater determinants, basis set approximation, Fock matrix, Self Consistent Field algorithm. 3) Semi-empirical methods: reducing the cost by minimal basis sets and neglecting or approximating integrals, fitting to experimental data, different parametrizations (AM1, PM3, MNDO, (extended-)Hückel), limits of semi-empirical methods. |
| Small systems: Electron correlation | 1) Excited Slater determinants: Singles-Doubles-Triples..., Convergence to exact wave function for infinite excitation level in infinite basis set. 2) Configuration Interaction: CI matrix, Slater-Condon rules, full CI H2 in minimal basis, size of the CI matrix, truncated CI 3) Many-body perturbation theory: Rayleigh-Schrödinger PT, choice of H(0) and physical content of the perturbation operator in MP2. Intruder states. |
| Beyond medium-sized systems: Density Functional Theory | 1) Hohenberg-Kohn theorema: correspondence between energy and density, meaning of 'functional'. 2) Orbital free DFT: Division of the energy functional in T[rho], E_ne[rho] and E_ee[rho], Thomas Fermi expressions. 3) Kohn-Sham Theory: Re-introduction of the orbitals, exact expression of T_S[rho] for non-interacting electrons with orbitals, physical content of exchange-correlation functional. 4) Exchange-correlation functionals: requirements for an exact functional, X_alpha, LDA, Gradient-corrected methods, meta-GGA. 5) Hybrid functionals: Adiabatic connection formula, Half-and-Half method, B3LYP and other popular hybrids. |
| Basis Sets | 1) Slater and Gaussian type orbitals: Advantages and drawbacks 2) Classification of the basis sets: minimal basis, double zeta, polarization and diffuse functions 3) Examples of commonly used basis sets: Pople (STO-3G, 3-21G, 6-31G, '*' and '+' extensions), Ahlrichs, correlation consistent (cc, cc-p, aug-cc), atomic natural orbitals, plane waves 4) Effective core potentials |
| Other aspects of Computational Chemistry | 1) Use of symmetry 2) Introduction of the effects of the environment. Solvent effects. 3) QM/MM methods. |
| Project: Computational Chemistry at work | Hands-on computational work. Use of computational chemistry programs and visualization of the results. Calculations on several molecules are done and their properties analyzed by means of Quantum Chemistry methods worked during the course. |
| Planning |
| Methodologies :: Tests | ||||||||||
| Competences | (*) Class hours |
Hours outside the classroom |
(**) Total hours | |||||||
| Introductory activities |
|
1 | 0 | 1 | ||||||
| IT-based practicals in computer rooms |
|
8 | 8 | 16 | ||||||
| Lecture |
|
12 | 12 | 24 | ||||||
| Problem solving, exercises in the classroom |
|
7 | 3.5 | 10.5 | ||||||
| Personal attention |
|
1 | 1 | 2 | ||||||
| Mixed tests |
|
2 | 0 | 2 | ||||||
| (*) On e-learning, hours of virtual attendance of the teacher. (**) The information in the planning table is for guidance only and does not take into account the heterogeneity of the students. | ||||||||||
| Methodologies |
| Description | |
| Introductory activities | Outline of the course. Balance between theoretical and practical sessions. In the former, we will discuss the concepts of the different computational approaches and it the second type of sessions this knowledge is put to work by resolving a chemical issue in a computational manner. |
| IT-based practicals in computer rooms | Work on a chemical problem using computational chemistry programs and other software. The students have a guide delivered by the professor. - Optimization of structures and calculation of molecular energies and other properties. - Use of the data obtained to answer the questions proposed by the professor in the guide. - Prepararation of a complete written report, one per group (couple), and delivery to the professor within the deadline established at the beginning of the course. |
| Lecture | Presentation and discussion of the main facts about Computational Chemistry, with visual support and multiple reference to information sources available to the student. Discussion of practical examples based on calculations. The students will be asked to do previous work (guided by the professor) outside the room (book chapter readings or similar) to profit as much as possible the work with the group, which will be highly dynamic and participative (discussion, question-answer, etc.). |
| Problem solving, exercises in the classroom | The professor will propose exercices to solve in the room to assess the degree of understanding. Discussion of exercises and clarification of previously taught concepts (even outside the room) will be a part of the session. |
| Personal attention | During the practical sessions, students can raise all the doubts they have on the contents of the program, both related to the practical sessions and the theoretical lectures. |
| Personalized attention |
| Description |
| During the practical sessions, students will work in groups of two persons. Doubts on the strategy to be followed to resolve the problem will be addressed by the teacher on an individual basis as much as possible. |
| Assessment |
| Methodologies | Competences | Description | Weight | ||||
| IT-based practicals in computer rooms |
|
Hand over a full report about the practical work done in the PC room (one per group). The individual work and involvement during the practicals will be considered in the final evaluation. | 50% | ||||
| Mixed tests |
|
A written exam will be used to evaluate the students understanding of the computational strategies discussed during the lectures. | 50% | ||||
| Others |
| Other comments and second exam session | |||
|
The course is entirely taught in English. All the activities in the rrom will be done in this language, although the written exam can be answered in the language chosen by the student (Catalan, Spanish or English). The minimum mark required (to pass the course) in the written exam is 5 over 10 in any of both calls.The mark of the exam will be combined with that of the practical work (in-person work with computers + written report) as indicated in the Assessment section. In the second call, the overall assessment is the same as in the 1st call (exam + practical work). During exams, it is forbidden the use of mobile phones, tables, computers and any other device, unless allowance by the professor. All electronic devices must be switched off and out of the reach of the students. Demostratively fraudulent actions by a student in the exam or in any other assessed activity (cheating) will be punished with failing grade of the activity or even the whole course. Independently, such serious facts can be prosecuted if the faculty asks for a resolution from the rector. |
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| Sources of information |
| Basic |
Frank Jensen, Introduction to computational chemistry , 3rd, 2006
Cristopher Cramer, Essentials of computational chemistry : theories and models , , 2004
Wolfram Koch, Max C. Holthausen, A chemist's guido to density functional theory, Second Edition, 2001 |
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| Complementary |
Juan Andrés, Joan Bertran (eds), Theoretical and computational chemistry : foundations, methods and techniques, , 2007
Ira N. Levine, Quantum Chemistry, , 2001 |
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| Recommendations |
| Subjects that are recommended to be taken simultaneously | ||
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| Subjects that it is recommended to have taken before | ||||
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| Other comments | |
| The End of Degree Work. in case it is carried out in the Quantum Chemistry Group of the faculty, will be related to the concepts developed in this optional course. So, it is highly recommended to enrol it in this case. |
(*)The teaching guide is the document in which the URV publishes the information about all its courses. It is a public document and cannot be modified. Only in exceptional cases can it be revised by the competent agent or duly revised so that it is in line with current legislation.