Specialization Laboratory - Theoretical and Structural Chemistry

obligatory courses

Blended learning
Classroom
Self-reading

Acquiring the skill of using the basic computational techniques in computational chemistry

Objective of Crystallography Specialization Lab is to familiarize students with refinements of problematic crystal structures and electron density models other than the spherical atomic model (IAM).

The Molecular Modelling part includes exercises involving leading-edge software for protein structure design and modelling as well as for tracing their evolutionary relationships.

Methods in Quantum Chemistry: Students carry out six exercises selected by the supervisor of their specialization work. Each exercise involves learning some theoretical material, solving problems, and passing a final colloquium. The six exercises are selected from the following set: variational method, time-independent perturbation theory, SCF method, theory of electron correlation, coupled cluster method, DFT approach, permutation and unitary group approach to many-electron systems, theory of intermolecular forces, theory of molecular properties, time-dependent perturbation theory, semi-empirical methods, theory of rovibrational spectra, theory of relativistic effects, band structure theory.

Molecular Modeling Methods with Bioinformatics: the student performs 6 exercises from the following list:

M1: Monte Carlo methods: multicanonical method, replica method, Metropolis diagram, applied to the model problem (simulation of polymer chains, LJ gas, water model)

M2: Modeling of multidomain protein structures with AlfaFold, RosettaFold and Rosetta software

M3: prediction of molecular properties using machine learning methods

M4: coarse-grained protein modeling - SURPASS program

M5: Searching sequential databases using PsiBlast and the HHPred package

M6: coarse-grained modeling of the lipid membrane

M7: Docking ligands to proteins with Rosetta software

Students selecting the Specialization Laboratory in Crystallochemistry Laboratory perform 15 obligatory exercises (C0-C14), which are passed on the basis of reports. The form of the report is given during the first classes of the given topic. For each report, the student may receive the maximum number of points defined for each class. The report should be submitted within one week after the end of the given exercise. List of classes within the Specialization Lab in the Crystallochemistry Lab.

C0: Introductory class - reduction and integration of X-ray data and the refinement of four crystal structures (20 pts)

C1: Refinement of structures with disorder (30 pts)

C2: Refinement of structures with twinning (20 pts)

C3: Refinement of neutron diffraction data (10 pts)

C4: TAAM Refinement (Transferable Aspherical Atom Model) in Olex (10 pts)

C5: Advanced methods for characterization of thermal vibrations in XRD experiments (10 pts)

C6: Refinement of the electron density distribution using a multipole model against high-resolution XRD data (10 pts)

C7: HAR refinement (10 pts)

C8: Integration and reduction of the synchrotron XRD data, structure solution, model building and refinement of protein structure.

C9: X-ray diffraction measurements under increased pressure - experiment with DMSO (20 pts)

C10: Preparation of new cocrystals - mechanochemistry + PXRD measurements (10 pts)

C11: Advanced theoretical calculations in CRYSTAL (10 pts)

C12: Solution of XRD structures with modulation (10 pts)

C13 Structures with diffuse scattering - DISCUSS program (10 pts)

C14: Independent X-ray measurement with data analysis and structural description (100 pts).

1.I.M. Gelfand, Wykłady z algebry liniowej, PWN, 1977.

2.L.Piela "Idee chemii kwantowej", Warszawa, PWN, 2003, Rozdzial 7.

3.Strony internetowe w Aneksie do powyższej książki:

http://www.chem.uw.edu.pl/ideas/index.php?option=com_content&task=view&id=23&Itemid=76

4.Dieter W. Heermann, Podstawy symulacji komputerowych w fizyce, WNT, Warszawa 1997.

5. Simulation methods for polymers, ed. by Michael Kotelyanskii & Doros N. Theodorou, Marcel Dekker, New York Basel 2004.

6. Giacovazzo, C.; Monaco, H. L.; Artioli, G.; Viterbo, D.; Milanesio, M.; Gilli, G.; Gilli, P.; Zanotti, G.; Catti, M. Fundamentals of Crystallography; 3rd ed., Ed.; 2011.

7. Müller, P.; Herbst-Irmer, R.; Spek, A. L.; Schneider, T. R.; Sawaya, M. R. Crystal Structure Refinement: A Crystallographer’s Guide to SHELXL; International Union of Crystallography Texts on Crystallography; Oxford University Press: Oxford, 2006. https://doi.org/10.1093/acprof:oso/9780198570769.001.0001.

Student acquires knowledge how to apply basic techniques of quantum chemistry to solve specific chemical problem problems

Upon completion of the Crystallography Specialization Lab, the student is able to perform X-ray measurements independently, perform data analysis, and recognize the characteristic features of problematic data including disorder, twinning, diffuse scattering, and modulated structures. Moreover, they know the basics of electron density models (IAM, TAAM, HAR) used in X-ray data refinement, their limitations and applicability.

homework appraisal and oral tests of the acquired knowledge

The grade for the Crystallochemistry Specialization Lab is based on the exercise reports (C0-C14). Students may receive a maximum of 300 points in the course. In order to pass the course the student must obtain at least 150 points, for the grade sufficient plus (3+) at least 195 points, for the grade good (4) 225 points, for the grade good plus (4+) 240, for the grade very good (5) 270, and for the grade excellent (5!) 285 points.

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