October 31, 2017

Equipments

Besides departmental equipment, such as NMR or mass spectrometers, the lab work is based on the following facilities.

Computational equipment:
•Several GPU workstations with GTX 980 and Titan cards
•Several Intel Workstations with 16 cores

Scientific software:
•YASARA-Dynamics-NMR programs for protein modelling, ligand docking and visualization
•Yasara, Desmond, VegaZZ – programs for molecular dynamics
•VMD, AVS/Express, AVIZO, CURVIS – programs for molecular visualizations
•Matlab – Bioinformatics and neural networks
•Gaussian, Gamess, Materials Studio, Schrodinger – programs for chemical modeling
•Discovery Studio, Vina, Dragon  – programs for docking, bio- and cheminformatics

Synthesis and characterization:
•DSC   differential scanning calorimetry – DSC-7 Perkin Elmer calorimeter under nitrogen flow at 10°C/min rate – DSC directly measures heat changes that occur in molecules during controlled increase or decrease in temperature.
•Jenapol microscope fitted with a Linkam THMS 600 hot stage  it is used to visualize LC textures, melting or crystallization phenomena of molecules during controlled increase or decrease in temperature.
•UV-Vis Perkin Elmer Lambda 19 spectrophotometer  Organic compounds, especially those with a high degree of conjugation, absorb light in the UV or visible regions of the electromagnetic spectrum. UV/VIS Spectrophotometry is used to determine the absorption or transmission of UV/VIS light (180 to 820 nm) by a sample. It can also be used to measure concentrations of absorbing materials based on developed calibration curves of the material.
•GPC   gel permeation chromatography – Waters 150-C ALC/GPC equipped with six 300×7.5 mm2  columns (Waters Styragel HT3, HT4, HT5, HT6, 500Å and 400Å) and a Jasco 875 UV detector set at 254 nm. GPC is a type of size exclusion chromatography (SEC) essential in polymer chemistry for measuring the distribution of molecular weights.
•TGA  thermogravimetric analysis  TGA measures the amount of weight change of a material, either as a function of increasing temperature, or isothermally as a function of time, in an atmosphere of nitrogen, or air.
•Fluorimeter  it is used to measure the intensity and the wavelength distribution of the light emitted as  fluorescence  from a molecule excited at a specific wavelength within the absorption band of a particular compound.
•IR  Infrared spectrometer  IR measures the wavelength and intensity of the absorption of infrared light by a sample. Because the wavelengths of infrared absorption bands are characteristic of specific types of chemical bonds, infrared spectrometers are often used to identify organic molecules.
•RX – X-ray diffraction spectra are recorded using a flat camera with a sample-to-film distance of 140 mm (Ni-filtered Cu-Ka radiation). High temperature X-ray diffraction patterns are collected using a modified Linkam THMS 600 hot stage. The Fujifilm MS 2025 imaging plate and a Fuji Bio-imaging Analyzer System, mod. BAS-1800, are used for recording and digitizing the diffraction patterns.