Time resolved crystallography utilizes X-ray crystallography imaging to visualize reactions in four dimensions (x, y, z and time). This enables the studies of dynamical changes that occur in for example enzymes during their catalysis. The time dimension is incorporated by triggering the reaction of interest in the crystal prior to X-ray exposure, and then collecting the diffraction patterns at different time delays. In order to study these dynamical properties of macromolecules three criteria must be met;
This has led to the development of several techniques that can be divided into two groups, the pump-probe method and diffusion-trapping methods.
In the pump-probe method the reaction is first triggered (pump) by photolysis (most often laser light) and then a diffraction pattern is collected by an X-ray pulse (probe) at a specific time delay. This makes it possible to obtain many images at different time delays after reaction triggering, and thereby building up a chronological series of images describing the events during reaction. To obtain a reasonable signal to noise ratio this pump-probe cycle has to be performed many times for each spatial rotation of the crystal, and many times for the same time delay. Therefore, the reaction that one wishes to study with pump-probe must be able to relax back to its original conformation after triggering, enabling many measurements on the same sample. The time resolution of the observed phenomena is dictated by the time width of the probing pulse (full width at half maximum). All processes that happen on a faster time scale than that are going to be averaged out by the convolution of the probe pulse intensity in time with the intensity of the actual x-ray reflectivity of the sample.
Diffusion-trapping methods utilizes diffusion techniques to get the substrates into the crystal and thereafter different trapping techniques are applied to get the intermediate of interest to accumulate in the crystal prior to collection of the diffraction pattern. These trapping methods could involve changes in pH,use of inhibitor or lowering the temperature in order to slow down the turnover rate or maybe even stop the reaction completely at a specific step. Just starting the reaction and then flash-freeze it, thereby quenching it at a specific time step, is also a possible method. One drawback with diffusion-trapping methods is that they can only be used to study intermediates that can be trapped, thereby limiting the time resolution one can obtain through the methods as compared to the pump-probe method.
Crystallography is the experimental science of determining the arrangement of atoms in crystalline solids. The word "crystallography" is derived from the Greek words crystallon "cold drop, frozen drop", with its meaning extending to all solids with some degree of transparency, and graphein "to write". In July 2012, the United Nations recognised the importance of the science of crystallography by proclaiming that 2014 would be the International Year of Crystallography.
Structural biology is a branch of molecular biology, biochemistry, and biophysics concerned with the molecular structure of biological macromolecules, how they acquire the structures they have, and how alterations in their structures affect their function. This subject is of great interest to biologists because macromolecules carry out most of the functions of cells, and it is only by coiling into specific three-dimensional shapes that they are able to perform these functions. This architecture, the "tertiary structure" of molecules, depends in a complicated way on each molecule's basic composition, or "primary structure."
X-ray crystallography (XRC) is the experimental science determining the atomic and molecular structure of a crystal, in which the crystalline structure causes a beam of incident X-rays to diffract into many specific directions. By measuring the angles and intensities of these diffracted beams, a crystallographer can produce a three-dimensional picture of the density of electrons within the crystal. From this electron density, the mean positions of the atoms in the crystal can be determined, as well as their chemical bonds, their crystallographic disorder, and various other information.
Solid-state chemistry, also sometimes referred as materials chemistry, is the study of the synthesis, structure, and properties of solid phase materials, particularly, but not necessarily exclusively of, non-molecular solids. It therefore has a strong overlap with solid-state physics, mineralogy, crystallography, ceramics, metallurgy, thermodynamics, materials science and electronics with a focus on the synthesis of novel materials and their characterisation. Solids can be classified as crystalline or amorphous on basis of the nature of order present in the arrangement of their constituent particles.
Surface science is the study of physical and chemical phenomena that occur at the interface of two phases, including solid–liquid interfaces, solid–gas interfaces, solid–vacuum interfaces, and liquid–gas interfaces. It includes the fields of surface chemistry and surface physics. Some related practical applications are classed as surface engineering. The science encompasses concepts such as heterogeneous catalysis, semiconductor device fabrication, fuel cells, self-assembled monolayers, and adhesives. Surface science is closely related to interface and colloid science. Interfacial chemistry and physics are common subjects for both. The methods are different. In addition, interface and colloid science studies macroscopic phenomena that occur in heterogeneous systems due to peculiarities of interfaces.
X-ray scattering techniques are a family of non-destructive analytical techniques which reveal information about the crystal structure, chemical composition, and physical properties of materials and thin films. These techniques are based on observing the scattered intensity of an X-ray beam hitting a sample as a function of incident and scattered angle, polarization, and wavelength or energy.
Femtochemistry is the area of physical chemistry that studies chemical reactions on extremely short timescales in order to study the very act of atoms within molecules (reactants) rearranging themselves to form new molecules (products). In a 1988 issue of the journal Science, Ahmed Hassan Zewail published an article using this term for the first time, stating "Real-time femtochemistry, that is, chemistry on the femtosecond timescale...". Later in 1999, Zewail received the Nobel Prize in Chemistry for his pioneering work in this field showing that it is possible to see how atoms in a molecule move during a chemical reaction with flashes of laser light.
In physics, the phase problem is the problem of loss of information concerning the phase that can occur when making a physical measurement. The name comes from the field of X-ray crystallography, where the phase problem has to be solved for the determination of a structure from diffraction data. The phase problem is also met in the fields of imaging and signal processing. Various approaches of phase retrieval have been developed over the years.
Electron crystallography is a method to determine the arrangement of atoms in solids using a transmission electron microscope (TEM).
Ultrafast laser spectroscopy is a spectroscopic technique that uses ultrashort pulse lasers for the study of dynamics on extremely short time scales. Different methods are used to examine the dynamics of charge carriers, atoms, and molecules. Many different procedures have been developed spanning different time scales and photon energy ranges; some common methods are listed below.
In biochemistry, a conformational change is a change in the shape of a macromolecule, often induced by environmental factors.
Fiber diffraction is a subarea of scattering, an area in which molecular structure is determined from scattering data. In fiber diffraction the scattering pattern does not change, as the sample is rotated about a unique axis. Such uniaxial symmetry is frequent with filaments or fibers consisting of biological or man-made macromolecules. In crystallography fiber symmetry is an aggravation regarding the determination of crystal structure, because reflexions are smeared and may overlap in the fiber diffraction pattern. Materials science considers fiber symmetry a simplification, because almost the complete obtainable structure information is in a single two-dimensional (2D) diffraction pattern exposed on photographic film or on a 2D detector. 2 instead of 3 co-ordinate directions suffice to describe fiber diffraction.
Multi-wavelength anomalous diffraction is a technique used in X-ray crystallography that facilitates the determination of the three-dimensional structure of biological macromolecules via solution of the phase problem.
A crystallographic database is a database specifically designed to store information about the structure of molecules and crystals. Crystals are solids having, in all three dimensions of space, a regularly repeating arrangement of atoms, ions, or molecules. They are characterized by symmetry, morphology, and directionally dependent physical properties. A crystal structure describes the arrangement of atoms, ions, or molecules in a crystal.
Protein crystallization is the process of formation of a regular array of individual protein molecules stabilized by crystal contacts. If the crystal is sufficiently ordered, it will diffract. Some proteins naturally form crystalline arrays, like aquaporin in the lens of the eye.
Nuclear magnetic resonance crystallography is a method which utilizes primarily NMR spectroscopy to determine the structure of solid materials on the atomic scale. Thus, solid-state NMR spectroscopy would be used primarily, possibly supplemented by quantum chemistry calculations, powder diffraction etc. If suitable crystals can be grown, any crystallographic method would generally be preferred to determine the crystal structure comprising in case of organic compounds the molecular structures and molecular packing. The main interest in NMR crystallography is in microcrystalline materials which are amenable to this method but not to X-ray, neutron and electron diffraction. This is largely because interactions of comparably short range are measured in NMR crystallography.
Operando spectroscopy is an analytical methodology wherein the spectroscopic characterization of materials undergoing reaction is coupled simultaneously with measurement of catalytic activity and selectivity. The primary concern of this methodology is to establish structure-reactivity/selectivity relationships of catalysts and thereby yield information about mechanisms. Other uses include those in engineering improvements to existing catalytic materials and processes and in developing new ones.
Precession electron diffraction (PED) is a specialized method to collect electron diffraction patterns in a transmission electron microscope (TEM). By rotating (precessing) a tilted incident electron beam around the central axis of the microscope, a PED pattern is formed by integration over a collection of diffraction conditions. This produces a quasi-kinematical diffraction pattern that is more suitable as input into direct methods algorithms to determine the crystal structure of the sample.
Serial femtosecond crystallography (SFX) is a form of X-ray crystallography developed for use at X-ray free-electron lasers (XFELs). Single pulses at free-electron lasers are bright enough to generate resolvable Bragg diffraction from sub-micron crystals. However, these pulses also destroy the crystals, meaning that a full data set involves collecting diffraction from many crystals. This method of data collection is referred to as serial, referencing a row of crystals streaming across the X-ray beam, one at a time.