Crystallography Laboratory B 1200-1CRYSTBLA5
The laboratories are divided into two parts: theoretical and practical.
a) Theoretical classes are held every week throughout the semester.
The theoretical part will be devoted to solving problems related to the topics covered in the Crystallography B lecture and issues appearing in the practical part, i.e.: crystal morphology, operations and symmetry elements of solids and molecules, point groups, illustration of point symmetry using projections, rules of coexistence of symmetry elements, unit cell and its contents, ion coordination and stoichiometry of compounds, translational symmetry, crystallographic systems, spatial lattices, Miller indices, simple crystallographic calculations, Bravais lattices, space groups and their interpretation in the International Crystallographic Tables, basics of X-ray diffraction, Bragg equation and Laue equations, reciprocal lattice, Ewald construction, factors influencing the intensity of the diffracted beam, structure factors, systematic extinctions, matrix description of symmetry, geometric parameters of molecules, properties of neutron and electron radiation.
b) The laboratories in the practical part constitute a series of 10 meetings of 4h, which begin in the 5-th week of semester to enable students to become familiar with the basic material from the lectures and from the theoretical part necessary to carry out practical tasks.
The practicals will consist of tasks directly related to the sequence of X-ray structural analysis.
These will include: crystallization methods (e.g. setting simple crystallization), choosing a crystal suitable for X-ray structural analysis (evaluation of the quality and size of crystals under a microscope), methods of placing the selected crystal on the diffractometer, assessment of the quality of the obtained X-ray scattering (e.g. assessment X-ray data resolution and verification whether the sample is monocrystalline), performing preliminary measurements to determine the parameters of the reciprocal lattice and the real network for the selected sample, determining the symmetry of the diffractograms (Laue class), analyzing systematic extinctions, demonstrating the procedure of diffraction data reduction, solving and refining the structure for selected samples using crystallographic software (SHELX / OLEX2), assessment of the quality of obtained X-ray data and the reliability of the refined structural model, interpretation of structural information stored in the CIF file format (i.e.: finding bond lengths, values of valence angles and torsion angles, description of intermolecular interactions in the crystal, description of conformations and determining the absolute configuration for the selected compound), visualization of structural data using crystallographic programs (OLEX2, Mercury), methods of utilizing crystallographic databases (in particular CSD, also PDB, ICSD), validation of data retrieved as a result of such searches.
Type of course
Mode
Prerequisites (description)
Course coordinators
Term 2025Z: | Term 2024Z: |
Learning outcomes
We expect acquisition of the following skills:
a) knowledge and understanding of the basic crystallographic terms for describing the symmetry and structure of crystals, as well as in the field of X-ray crystallography and X-ray structure determination of molecules and biomolecules
b) setting simple crystallization, working with a microscope, assessing whether a given crystalline sample is suitable for X-ray structural analysis, determining the symmetry of a diffractogram (Laue class), interpreting structural data (searching for geometric parameters, assessing quality and reliability of data), basic use of structural databases and software for visualizing such data.
Assessment criteria
The final grade is determined as the arithmetic mean of two grades a) and b) awarded on the basis of:
a) short written tests held at the beginning of each theoretical laboratory, except for the first meeting. Short tests, maximum 10 minutes long, are assessed on a scale of 1 to 10 points. The grade from the tests is awarded on the basis of the total number of points obtained in the above tests (as a percentage of the maximum number of points possible to obtain):
Points obtained (x) are converted into grades according to the scale (mlp - maximum number of points possible to get):
x> 90% max. number of points (mlp) rating 5
80%
In individual cases, the activity of students in class may be the basis to increase the grade.
b) Reports prepared by students in groups after each laboratory and 15-minute presentation containing a summary of a scientific article related to X-ray structural analysis. Short reports are rated on a scale of 1 to 10 points, a maximum of 30 points can be obtained for the presentation. The grade is issued on the basis of the total number of points obtained for the reports and the presentation (in percentage of the maximum number of points possible to obtain):
Points obtained (x) are converted into grades according to the scale (mlp - maximum number of points possible to get):
x> 90% max. number of points (mlp) rating 5
80%
In individual (ABSOLUTELY EXCEPTIONAL) cases, the activity of students in class may be the basis for increasing the grade.
Laboratory exercises are performed in teams of 2.
One report per team should be prepared after each laboratory.
Presentations are to be prepared individually by each student.
REPORTS should be delivered within a week of the laboratory's completion, at the latest by the end of the day on which the next laboratory takes place. In the case of a report submitted after the deadline, the total number of points to be earned for the given report is reduced:
by 2 points (max: 8 points) - delay by 1 week
by 4 points (max: 6 points) - delay by 2 weeks
by 6 points (max: 4 points) - delay of 3 or more weeks
Reports can be delivered in the form of a printout to the assistant's room / locker, or - preferentially - in the form of a .pdf file to the assistant's email address.
The assistant has the right (also at the students' request) to order students to correct the submitted report. As a result of such correction, the total number of points to be earned is reduced by at least 1 point.
Students have a week to make corrections.
The report can be corrected only immediately after its evaluation. It is not acceptable that the student, e.g. just before the end of term, decides to correct the report from e.g. Laboratory 1.
In the event that one person from the team clearly does not fulfill their obligations and hinders the work of the other, the assistant may commission separate reports to each member of the team.
ABSENCES
Absence from classes is considered justified if:
a) the student presents a sick leave confirmation as soon as possible
b) the student informs the assistant in advance about the planned absence justified e.g. by participation in a conference or an exam.
c) the student has not passed the admission test.
An excused absence entitles to participation in the laboratory by joining another group or, in individual cases, at a time proposed by the assistant, e.g. during the exam session.
In the absence of one member of a team, each person from this team prepares an independent report after this particular laboratory.
Ujustified absence from a laboratory results in the student being awarded 0 points for the report.
4 unjustified absences will be interpreted as resignation from the course.
In the event that one person from the team is late at the Laboratory by more than ½ h, the assistant may order the latecomer to work independently and prepare a separate report from his/her teammate.
ADMISSION TESTS
Starting from Laboratory 2, laboratories will begin with a 5-min. admission test, the purpose of which is to check whether the student has read the script and recommended literature prior to the laboratory. Obtaining 0p from the entrance ticket results in a justified absence and the need to perform this laboratory at another time, indicated by the assistant. Admission grades do NOT affect the subject grade.
Practical placement
not applicable
Bibliography
1. Z. Bojarski, M. Gigla, K. Stróż, M. Surowiec, Krystalografia. Podręcznik wspomagany komputerowo, PWN, Warszawa, 1996, 2001, 2007.
2. Z. Trzaska Durski, H. Trzaska Durska, Podstawy krystalografii, Oficyna Wydawnicza Politechniki Warszawskiej, Warszawa 2003.
3. M. van Meerssche i J. Feneau-Dupont, Krystalografia i chemia strukturalna, PWN, Warszawa 1984.
4. J. P. Glusker, M. Lewis, M. Rossi, Crystal Structure Analysis for Chemists and Biologists, VCH Publishers (1994).
5. C. Giacovazzo, H. Z. Monaco, D. Biterbo, F. Scordari, G. Gilli, G. Zanotti, M. Catti, Fundamentals of Crystallography, IUCR, Oxford University Press, 2000.
Additional information
Additional information (registration calendar, class conductors, localization and schedules of classes), might be available in the USOSweb system: