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.
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.
Computational chemistryComputational chemistry is a branch of chemistry that uses computer simulation to assist in solving chemical problems. It uses methods of theoretical chemistry, incorporated into computer programs, to calculate the structures and properties of molecules, groups of molecules, and solids. It is essential because, apart from relatively recent results concerning the hydrogen molecular ion (dihydrogen cation, see references therein for more details), the quantum many-body problem cannot be solved analytically, much less in closed form.
Density functional theoryDensity-functional theory (DFT) is a computational quantum mechanical modelling method used in physics, chemistry and materials science to investigate the electronic structure (or nuclear structure) (principally the ground state) of many-body systems, in particular atoms, molecules, and the condensed phases. Using this theory, the properties of a many-electron system can be determined by using functionals, i.e. functions of another function. In the case of DFT, these are functionals of the spatially dependent electron density.
Quantum mechanicsQuantum mechanics is a fundamental theory in physics that provides a description of the physical properties of nature at the scale of atoms and subatomic particles. It is the foundation of all quantum physics including quantum chemistry, quantum field theory, quantum technology, and quantum information science. Classical physics, the collection of theories that existed before the advent of quantum mechanics, describes many aspects of nature at an ordinary (macroscopic) scale, but is not sufficient for describing them at small (atomic and subatomic) scales.
Statistical mechanicsIn physics, statistical mechanics is a mathematical framework that applies statistical methods and probability theory to large assemblies of microscopic entities. It does not assume or postulate any natural laws, but explains the macroscopic behavior of nature from the behavior of such ensembles. Sometimes called statistical physics or statistical thermodynamics, its applications include many problems in the fields of physics, biology, chemistry, and neuroscience.
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
Materials scienceMaterials science is an interdisciplinary field of researching and discovering materials. Materials engineering is an engineering field of finding uses for materials in other fields and industries. The intellectual origins of materials science stem from the Age of Enlightenment, when researchers began to use analytical thinking from chemistry, physics, and engineering to understand ancient, phenomenological observations in metallurgy and mineralogy. Materials science still incorporates elements of physics, chemistry, and engineering.
Ensemble (mathematical physics)In physics, specifically statistical mechanics, an ensemble (also statistical ensemble) is an idealization consisting of a large number of virtual copies (sometimes infinitely many) of a system, considered all at once, each of which represents a possible state that the real system might be in. In other words, a statistical ensemble is a set of systems of particles used in statistical mechanics to describe a single system. The concept of an ensemble was introduced by J. Willard Gibbs in 1902.
Classical mechanicsClassical mechanics is a physical theory describing the motion of macroscopic objects, from projectiles to parts of machinery and astronomical objects, such as spacecraft, planets, stars, and galaxies. For objects governed by classical mechanics, if the present state is known, it is possible to predict how it will move in the future (determinism), and how it has moved in the past (reversibility). The "classical" in "classical mechanics" does not refer classical antiquity, as it might in, say, classical architecture.
Interpretations of quantum mechanicsAn interpretation of quantum mechanics is an attempt to explain how the mathematical theory of quantum mechanics might correspond to experienced reality. Although quantum mechanics has held up to rigorous and extremely precise tests in an extraordinarily broad range of experiments, there exist a number of contending schools of thought over their interpretation. These views on interpretation differ on such fundamental questions as whether quantum mechanics is deterministic or stochastic, local or non-local, which elements of quantum mechanics can be considered real, and what the nature of measurement is, among other matters.
Mathematical formulation of quantum mechanicsThe mathematical formulations of quantum mechanics are those mathematical formalisms that permit a rigorous description of quantum mechanics. This mathematical formalism uses mainly a part of functional analysis, especially Hilbert spaces, which are a kind of linear space. Such are distinguished from mathematical formalisms for physics theories developed prior to the early 1900s by the use of abstract mathematical structures, such as infinite-dimensional Hilbert spaces (L2 space mainly), and operators on these spaces.
Quantum statistical mechanicsQuantum statistical mechanics is statistical mechanics applied to quantum mechanical systems. In quantum mechanics a statistical ensemble (probability distribution over possible quantum states) is described by a density operator S, which is a non-negative, self-adjoint, trace-class operator of trace 1 on the Hilbert space H describing the quantum system. This can be shown under various mathematical formalisms for quantum mechanics. One such formalism is provided by quantum logic.
Covalent bondA covalent bond is a chemical bond that involves the sharing of electrons to form electron pairs between atoms. These electron pairs are known as shared pairs or bonding pairs. The stable balance of attractive and repulsive forces between atoms, when they share electrons, is known as covalent bonding. For many molecules, the sharing of electrons allows each atom to attain the equivalent of a full valence shell, corresponding to a stable electronic configuration. In organic chemistry, covalent bonding is much more common than ionic bonding.
Partition function (statistical mechanics)In physics, a partition function describes the statistical properties of a system in thermodynamic equilibrium. Partition functions are functions of the thermodynamic state variables, such as the temperature and volume. Most of the aggregate thermodynamic variables of the system, such as the total energy, free energy, entropy, and pressure, can be expressed in terms of the partition function or its derivatives. The partition function is dimensionless.
Microstate (statistical mechanics)In statistical mechanics, a microstate is a specific configuration of a system that describes the precise positions and momenta of all the individual particles or components that make up the system. Each microstate has a certain probability of occurring during the course of the system's thermal fluctuations. In contrast, the macrostate of a system refers to its macroscopic properties, such as its temperature, pressure, volume and density.
Coordinate covalent bondIn coordination chemistry, a coordinate covalent bond, also known as a dative bond, dipolar bond, or coordinate bond is a kind of two-center, two-electron covalent bond in which the two electrons derive from the same atom. The bonding of metal ions to ligands involves this kind of interaction. This type of interaction is central to Lewis acid–base theory. Coordinate bonds are commonly found in coordination compounds. Coordinate covalent bonding is ubiquitous.
Introduction to quantum mechanicsQuantum mechanics is the study of matter and its interactions with energy on the scale of atomic and subatomic particles. By contrast, classical physics explains matter and energy only on a scale familiar to human experience, including the behavior of astronomical bodies such as the moon. Classical physics is still used in much of modern science and technology. However, towards the end of the 19th century, scientists discovered phenomena in both the large (macro) and the small (micro) worlds that classical physics could not explain.
Measurement in quantum mechanicsIn quantum physics, a measurement is the testing or manipulation of a physical system to yield a numerical result. A fundamental feature of quantum theory is that the predictions it makes are probabilistic. The procedure for finding a probability involves combining a quantum state, which mathematically describes a quantum system, with a mathematical representation of the measurement to be performed on that system. The formula for this calculation is known as the Born rule.
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.
