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 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.
Dihydrogen cationThe dihydrogen cation or hydrogen molecular ion is a cation (positive ion) with formula H2+. It consists of two hydrogen nuclei (protons) sharing a single electron. It is the simplest molecular ion. The ion can be formed from the ionization of a neutral hydrogen molecule (H2) by electron impact. It is commonly formed in molecular clouds in space by the action of cosmic rays. The dihydrogen cation is of great historical, theoretical, and experimental interest.
Protein designProtein design is the rational design of new protein molecules to design novel activity, behavior, or purpose, and to advance basic understanding of protein function. Proteins can be designed from scratch (de novo design) or by making calculated variants of a known protein structure and its sequence (termed protein redesign). Rational protein design approaches make protein-sequence predictions that will fold to specific structures.
Chemical substanceA chemical substance is a form of matter having constant chemical composition and characteristic properties. Chemical substances can be simple substances (substances consisting of a single chemical element), chemical compounds, or alloys. Chemical substances that cannot be separated into their simpler constituent elements by physical means are said to be 'pure'; this notion intended to set them apart from mixtures.
Molecular solidA molecular solid is a solid consisting of discrete molecules. The cohesive forces that bind the molecules together are van der Waals forces, dipole-dipole interactions, quadrupole interactions, π-π interactions, hydrogen bonding, halogen bonding, London dispersion forces, and in some molecular solids, coulombic interactions. Van der Waals, dipole interactions, quadrupole interactions, π-π interactions, hydrogen bonding, and halogen bonding (2-127 kJ mol−1) are typically much weaker than the forces holding together other solids: metallic (metallic bonding, 400-500 kJ mol−1), ionic (Coulomb’s forces, 700-900 kJ mol−1), and network solids (covalent bonds, 150-900 kJ mol−1).
Drug designDrug design, often referred to as rational drug design or simply rational design, is the inventive process of finding new medications based on the knowledge of a biological target. The drug is most commonly an organic small molecule that activates or inhibits the function of a biomolecule such as a protein, which in turn results in a therapeutic benefit to the patient. In the most basic sense, drug design involves the design of molecules that are complementary in shape and charge to the biomolecular target with which they interact and therefore will bind to it.
Molecular engineeringMolecular engineering is an emerging field of study concerned with the design and testing of molecular properties, behavior and interactions in order to assemble better materials, systems, and processes for specific functions. This approach, in which observable properties of a macroscopic system are influenced by direct alteration of a molecular structure, falls into the broader category of “bottom-up” design.
Probability density functionIn probability theory, a probability density function (PDF), density function, or density of an absolutely continuous random variable, is a function whose value at any given sample (or point) in the sample space (the set of possible values taken by the random variable) can be interpreted as providing a relative likelihood that the value of the random variable would be equal to that sample.
Van der Waals forceIn molecular physics, the van der Waals force is a distance-dependent interaction between atoms or molecules. Unlike ionic or covalent bonds, these attractions do not result from a chemical electronic bond; they are comparatively weak and therefore more susceptible to disturbance. The van der Waals force quickly vanishes at longer distances between interacting molecules. Named after Dutch physicist Johannes Diderik van der Waals, the van der Waals force plays a fundamental role in fields as diverse as supramolecular chemistry, structural biology, polymer science, nanotechnology, surface science, and condensed matter physics.
Force field (chemistry)In the context of chemistry and molecular modelling, a force field is a computational method that is used to estimate the forces between atoms within molecules and also between molecules. More precisely, the force field refers to the functional form and parameter sets used to calculate the potential energy of a system of atoms or coarse-grained particles in molecular mechanics, molecular dynamics, or Monte Carlo simulations. The parameters for a chosen energy function may be derived from experiments in physics and chemistry, calculations in quantum mechanics, or both.
Water modelIn computational chemistry, a water model is used to simulate and thermodynamically calculate water clusters, liquid water, and aqueous solutions with explicit solvent. The models are determined from quantum mechanics, molecular mechanics, experimental results, and these combinations. To imitate a specific nature of molecules, many types of models have been developed. In general, these can be classified by the following three points; (i) the number of interaction points called site, (ii) whether the model is rigid or flexible, (iii) whether the model includes polarization effects.
