Crystallography Laboratory B 1200-1CRYSTBLA5
The laboratories will consist of practical tasks directly related to the course of X-ray structural analysis.
Tasks 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
Learning outcomes
The following skills are expected to be acquired:
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 on the basis of 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
Additional information
Additional information (registration calendar, class conductors, localization and schedules of classes), might be available in the USOSweb system: