The Center for Collective Use “X-ray single crystal diffractometry” was established on the basis of the Institute of Organic Chemistry of NASU in 2006 in order to rationally use expensive single-crystal diffractometric complex SMART APEX II manufactured by “Bruker” (hereinafter – the Device).
The single-crystal SMART APEX II diffractometer in IOC is equipped with a tube with a molybdenum anode (λ = 0.71073 Å) which is a universal solution and allows to carry out diffraction studies of single crystals of compounds with any elemental composition from light to heavy elements. The Center’s research is aimed at studying the molecular and crystalline structure of organic, inorganic and elemental organic compounds, establishing the absolute configuration of compounds in crystals by the anomalous dispersion method. The 2D detector of the device with CCD detector 62 ˣ 62 mm is capable to register many reflexes for one scan at the same time, has high sensitivity and low level of own noise thanks to cooling of an electronic light-sensitive chip to temperatures below -50 ° C.
The maximum size of the crystal in any direction should not exceed 0.5 mm, the minimum is usually about 0.05 mm, depending on the elemental composition of the crystal, the parameters as well as volume of the unit cell, the quality of the crystal.
Only one single crystal of a substance is enough for diffraction research, however the quality of the received data and structure as a whole depends on its quality. Therefore, a specialist using a microscope visually selects several crystals of the appropriate size, after which they are fixed on special holders and tested it on the diffractometer until you find the best or high quality.
After that, it is necessary to determine the parameters of the unit cell, the type of crystal lattice, symmetry for the crystal and optimize the data collection parameters, then collect the complete set of diffraction data and process the obtained diffraction data. Later, using crystallographic programs, the molecular structure is solved and refined, and the necessary data files are prepared, which include bond lengths, angles, information about the conformation of molecules, and their packaging in the crystal.
To ensure the stability of the sample over time for unstable and sensitive to oxigen\water compounds, to prevent the destruction of crystalls, as well as to improve the quality of diffraction, it is possible to perform diffraction measurements at low temperatures (Typical data collection temperature is -100 ° C, but can be changed by agreement). It is also possible to study phase transitions for crystals. To do this, the device is equipped with a low-temperature attachment Oxford Cryosystems 700, which consumes liquid nitrogen and allows you to cool the sample to low temperatures. The minimum sample temperature is approximately -180 ° C, the flow of cooling nitrogen 5-10 l/min. The controller of the low-temperature device provides the necessary temperature stability during the experiment or provides the ability to control the rate of temperature changes in the operating temperature range. Data collection at low temperatures and phase transition studies of the samples takes place by prior arrangement. The required amount of liquid nitrogen depends on the shooting temperature and is approximately 10 liters per working day at 7 o’clock.
It is not recommended to dry the crystals in vacuum, because in the case of crystal solvates, this leads to a deterioration in the quality of the crystals or even their complete destruction when removing the solvent that was part of the crystal. We cannot guarantee that a crystal of even visually high quality will be suitable for research because cutting an oversized crystal can lead to its destruction or deterioration, the crystal can have internal defects, dislocations, be highly mosaic and disordered with very low diffraction level, etc., which makes it impossible to work. However, we can provide advice on methods of growing, transporting and storing crystals, and if necessary, help with growing crystals of the required quality (by arrangement). Low-temperature studies of samples of crystals moisture or oxygen sensitive and those that decompose over time for any reason are accepted by prior arrangement. Unstable crystalline compounds must be provided in a suitable airtight container protected from air, moisture or together with the solvent from which they are grown. Keep in mind that after opening a container in which an unstable sample is stored, it decomposes over time, so it is better to provide several separate portions of the sample in a separate container to be able to select and work with a fresh sample several times.