Molecular dynamicsMolecular dynamics (MD) is a computer simulation method for analyzing the physical movements of atoms and molecules. The atoms and molecules are allowed to interact for a fixed period of time, giving a view of the dynamic "evolution" of the system. In the most common version, the trajectories of atoms and molecules are determined by numerically solving Newton's equations of motion for a system of interacting particles, where forces between the particles and their potential energies are often calculated using interatomic potentials or molecular mechanical force fields.
X-ray absorption spectroscopyX-ray absorption spectroscopy (XAS) is a widely used technique for determining the local geometric and/or electronic structure of matter. The experiment is usually performed at synchrotron radiation facilities, which provide intense and tunable X-ray beams. Samples can be in the gas phase, solutions, or solids. XAS data is obtained by tuning the photon energy, using a crystalline monochromator, to a range where core electrons can be excited (0.1-100 keV).
Absorption spectroscopyAbsorption spectroscopy refers to spectroscopic techniques that measure the absorption of electromagnetic radiation, as a function of frequency or wavelength, due to its interaction with a sample. The sample absorbs energy, i.e., photons, from the radiating field. The intensity of the absorption varies as a function of frequency, and this variation is the absorption spectrum. Absorption spectroscopy is performed across the electromagnetic spectrum.
Molecular biologyMolecular biology məˈlɛkjʊlər is the study of chemical and physical structure of biological macromolecules. It is a branch of biology that seeks to understand the molecular basis of biological activity in and between cells, including biomolecular synthesis, modification, mechanisms, and interactions. Molecular biology was first described as an approach focused on the underpinnings of biological phenomena—uncovering the structures of biological molecules as well as their interactions, and how these interactions explain observations of classical biology.
SpectroscopySpectroscopy is the field of study that measures and interprets the electromagnetic spectra that result from the interaction between electromagnetic radiation and matter as a function of the wavelength or frequency of the radiation. Matter waves and acoustic waves can also be considered forms of radiative energy, and recently gravitational waves have been associated with a spectral signature in the context of the Laser Interferometer Gravitational-Wave Observatory (LIGO).
X-ray spectroscopyX-ray spectroscopy is a general term for several spectroscopic techniques for characterization of materials by using x-ray radiation. When an electron from the inner shell of an atom is excited by the energy of a photon, it moves to a higher energy level. When it returns to the low energy level, the energy which it previously gained by the excitation is emitted as a photon which has a wavelength that is characteristic for the element (there could be several characteristic wavelengths per element).
Chemical reactionA chemical reaction is a process that leads to the chemical transformation of one set of chemical substances to another. Classically, chemical reactions encompass changes that only involve the positions of electrons in the forming and breaking of chemical bonds between atoms, with no change to the nuclei (no change to the elements present), and can often be described by a chemical equation. Nuclear chemistry is a sub-discipline of chemistry that involves the chemical reactions of unstable and radioactive elements where both electronic and nuclear changes can occur.
Molecular modellingMolecular modelling encompasses all methods, theoretical and computational, used to model or mimic the behaviour of molecules. The methods are used in the fields of computational chemistry, drug design, computational biology and materials science to study molecular systems ranging from small chemical systems to large biological molecules and material assemblies. The simplest calculations can be performed by hand, but inevitably computers are required to perform molecular modelling of any reasonably sized system.
Ultrafast laser spectroscopyUltrafast laser spectroscopy is a spectroscopic technique that uses ultrashort pulse lasers for the study of dynamics on extremely short time scales (attoseconds to nanoseconds). 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. Dynamics on the as to fs time scale are in general too fast to be measured electronically.
Chemical kineticsChemical kinetics, also known as reaction kinetics, is the branch of physical chemistry that is concerned with understanding the rates of chemical reactions. It is different from chemical thermodynamics, which deals with the direction in which a reaction occurs but in itself tells nothing about its rate. Chemical kinetics includes investigations of how experimental conditions influence the speed of a chemical reaction and yield information about the reaction's mechanism and transition states, as well as the construction of mathematical models that also can describe the characteristics of a chemical reaction.
Reaction mechanismIn chemistry, a reaction mechanism is the step by step sequence of elementary reactions by which overall chemical reaction occurs. A chemical mechanism is a theoretical conjecture that tries to describe in detail what takes place at each stage of an overall chemical reaction. The detailed steps of a reaction are not observable in most cases. The conjectured mechanism is chosen because it is thermodynamically feasible and has experimental support in isolated intermediates (see next section) or other quantitative and qualitative characteristics of the reaction.
Chemical bondA chemical bond is a lasting attraction between atoms or ions that enables the formation of molecules, crystals, and other structures. The bond may result from the electrostatic force between oppositely charged ions as in ionic bonds, or through the sharing of electrons as in covalent bonds. The strength of chemical bonds varies considerably; there are "strong bonds" or "primary bonds" such as covalent, ionic and metallic bonds, and "weak bonds" or "secondary bonds" such as dipole–dipole interactions, the London dispersion force, and hydrogen bonding.
Structural biologyStructural biology is a field that is many centuries old which, as defined by the Journal of Structural Biology, deals with structural analysis of living material (formed, composed of, and/or maintained and refined by living cells) at every level of organization. Early structural biologists throughout the 19th and early 20th centuries were primarily only able to study structures to the limit of the naked eye's visual acuity and through magnifying glasses and light microscopes.
Structural bioinformaticsStructural bioinformatics is the branch of bioinformatics that is related to the analysis and prediction of the three-dimensional structure of biological macromolecules such as proteins, RNA, and DNA. It deals with generalizations about macromolecular 3D structures such as comparisons of overall folds and local motifs, principles of molecular folding, evolution, binding interactions, and structure/function relationships, working both from experimentally solved structures and from computational models.
Bond energyIn chemistry, bond energy (BE), also called the mean bond enthalpy or average bond enthalpy is a measure of bond strength in a chemical bond. IUPAC defines bond energy as the average value of the gas-phase bond-dissociation energy (usually at a temperature of 298.15 K) for all bonds of the same type within the same chemical species. The bond dissociation energy (enthalpy) is also referred to as bond disruption energy, bond energy, bond strength, or binding energy (abbreviation: BDE, BE, or D).
Reaction rateThe reaction rate or rate of reaction is the speed at which a chemical reaction takes place, defined as proportional to the increase in the concentration of a product per unit time and to the decrease in the concentration of a reactant per unit time. Reaction rates can vary dramatically. For example, the oxidative rusting of iron under Earth's atmosphere is a slow reaction that can take many years, but the combustion of cellulose in a fire is a reaction that takes place in fractions of a second.
Molecular graphicsMolecular graphics is the discipline and philosophy of studying molecules and their properties through graphical representation. IUPAC limits the definition to representations on a "graphical display device". Ever since Dalton's atoms and Kekulé's benzene, there has been a rich history of hand-drawn atoms and molecules, and these representations have had an important influence on modern molecular graphics. Colour molecular graphics are often used on chemistry journal covers artistically.
X-ray crystallographyX-ray crystallography 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.
Molecular design softwareMolecular design software is notable software for molecular modeling, that provides special support for developing molecular models de novo. In contrast to the usual molecular modeling programs, such as for molecular dynamics and quantum chemistry, such software directly supports the aspects related to constructing molecular models, including: Molecular graphics interactive molecular drawing and conformational editing building polymeric molecules, crystals, and solvated systems partial charges development g
X-ray fluorescenceX-ray fluorescence (XRF) is the emission of characteristic "secondary" (or fluorescent) X-rays from a material that has been excited by being bombarded with high-energy X-rays or gamma rays. The phenomenon is widely used for elemental analysis and chemical analysis, particularly in the investigation of metals, glass, ceramics and building materials, and for research in geochemistry, forensic science, archaeology and art objects such as paintings.
