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.
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).
Molecular physicsMolecular physics is the study of the physical properties of molecules and molecular dynamics. The field overlaps significantly with physical chemistry, chemical physics, and quantum chemistry. It is often considered as a sub-field of atomic, molecular, and optical physics. Research groups studying molecular physics are typically designated as one of these other fields. Molecular physics addresses phenomena due to both molecular structure and individual atomic processes within molecules.
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.
Newtonian fluidA Newtonian fluid is a fluid in which the viscous stresses arising from its flow are at every point linearly correlated to the local strain rate — the rate of change of its deformation over time. Stresses are proportional to the rate of change of the fluid's velocity vector. A fluid is Newtonian only if the tensors that describe the viscous stress and the strain rate are related by a constant viscosity tensor that does not depend on the stress state and velocity of the flow.
GasGas is one of the four fundamental states of matter. The others are solid, liquid, and plasma. A pure gas may be made up of individual atoms (e.g. a noble gas like neon), elemental molecules made from one type of atom (e.g. oxygen), or compound molecules made from a variety of atoms (e.g. carbon dioxide). A gas mixture, such as air, contains a variety of pure gases. What distinguishes a gas from liquids and solids is the vast separation of the individual gas particles.
Avogadro's lawAvogadro's law (sometimes referred to as Avogadro's hypothesis or Avogadro's principle) or Avogadro-Ampère's hypothesis is an experimental gas law relating the volume of a gas to the amount of substance of gas present. The law is a specific case of the ideal gas law. A modern statement is: Avogadro's law states that "equal volumes of all gases, at the same temperature and pressure, have the same number of molecules." For a given mass of an ideal gas, the volume and amount (moles) of the gas are directly proportional if the temperature and pressure are constant.
Protein–protein interactionProtein–protein interactions (PPIs) are physical contacts of high specificity established between two or more protein molecules as a result of biochemical events steered by interactions that include electrostatic forces, hydrogen bonding and the hydrophobic effect. Many are physical contacts with molecular associations between chains that occur in a cell or in a living organism in a specific biomolecular context. Proteins rarely act alone as their functions tend to be regulated.
Fluid dynamicsIn physics, physical chemistry and engineering, fluid dynamics is a subdiscipline of fluid mechanics that describes the flow of fluids—liquids and gases. It has several subdisciplines, including aerodynamics (the study of air and other gases in motion) and hydrodynamics (the study of liquids in motion). Fluid dynamics has a wide range of applications, including calculating forces and moments on aircraft, determining the mass flow rate of petroleum through pipelines, predicting weather patterns, understanding nebulae in interstellar space and modelling fission weapon detonation.
Fluid parcelIn fluid dynamics, a fluid parcel, also known as a fluid element or material element, is an infinitesimal volume of fluid, identifiable throughout its dynamic history while moving with the fluid flow. As it moves, the mass of a fluid parcel remains constant, while—in a compressible flow—its volume may change, and its shape changes due to distortion by the flow. In an incompressible flow, the volume of the fluid parcel is also a constant (isochoric flow). Material surfaces and material lines are the corresponding notions for surfaces and lines, respectively.
Van der Waals equationIn chemistry and thermodynamics, the Van der Waals equation (or Van der Waals equation of state) is an equation of state which extends the ideal gas law to include the effects of interaction between molecules of a gas, as well as accounting for the finite size of the molecules. The ideal gas law treats gas molecules as point particles that interact with their containers but not each other, meaning they neither take up space nor change kinetic energy during collisions (i.e. all collisions are perfectly elastic).
Equation of stateIn physics and chemistry, an equation of state is a thermodynamic equation relating state variables, which describe the state of matter under a given set of physical conditions, such as pressure, volume, temperature, or internal energy. Most modern equations of state are formulated in the Helmholtz free energy. Equations of state are useful in describing the properties of pure substances and mixtures in liquids, gases, and solid states as well as the state of matter in the interior of stars.
PressurePressure (symbol: p or P) is the force applied perpendicular to the surface of an object per unit area over which that force is distributed. Gauge pressure (also spelled gage pressure) is the pressure relative to the ambient pressure. Various units are used to express pressure. Some of these derive from a unit of force divided by a unit of area; the SI unit of pressure, the pascal (Pa), for example, is one newton per square metre (N/m2); similarly, the pound-force per square inch (psi, symbol lbf/in2) is the traditional unit of pressure in the imperial and US customary systems.
VolumeVolume is a measure of three-dimensional space. It is often quantified numerically using SI derived units (such as the cubic metre and litre) or by various imperial or US customary units (such as the gallon, quart, cubic inch). The definition of length (cubed) is interrelated with volume. The volume of a container is generally understood to be the capacity of the container; i.e., the amount of fluid (gas or liquid) that the container could hold, rather than the amount of space the container itself displaces.
Gas constantThe molar gas constant (also known as the gas constant, universal gas constant, or ideal gas constant) is denoted by the symbol R or . It is the molar equivalent to the Boltzmann constant, expressed in units of energy per temperature increment per amount of substance, i.e. the pressure–volume product, rather than energy per temperature increment per particle. The constant is also a combination of the constants from Boyle's law, Charles's law, Avogadro's law, and Gay-Lussac's law.
Ideal gas lawThe ideal gas law, also called the general gas equation, is the equation of state of a hypothetical ideal gas. It is a good approximation of the behavior of many gases under many conditions, although it has several limitations. It was first stated by Benoît Paul Émile Clapeyron in 1834 as a combination of the empirical Boyle's law, Charles's law, Avogadro's law, and Gay-Lussac's law. The ideal gas law is often written in an empirical form: where , and are the pressure, volume and temperature respectively; is the amount of substance; and is the ideal gas constant.
Ideal gasAn ideal gas is a theoretical gas composed of many randomly moving point particles that are not subject to interparticle interactions. The ideal gas concept is useful because it obeys the ideal gas law, a simplified equation of state, and is amenable to analysis under statistical mechanics. The requirement of zero interaction can often be relaxed if, for example, the interaction is perfectly elastic or regarded as point-like collisions.
Perfect gasIn physics and engineering, a perfect gas is a theoretical gas model that differs from real gases in specific ways that makes certain calculations easier to handle. In all perfect gas models, intermolecular forces are neglected. This means that one can neglect many complications that may arise from the Van der Waals forces. All perfect gas models are ideal gas models in the sense that they all follow the ideal gas equation of state.
Van der Waals surfaceThe Van der Waals surface of a molecule is an abstract representation or model of that molecule, illustrating where, in very rough terms, a surface might reside for the molecule based on the hard cutoffs of Van der Waals radii for individual atoms, and it represents a surface through which the molecule might be conceived as interacting with other molecules.
Intermolecular forceAn intermolecular force (IMF) (or secondary force) is the force that mediates interaction between molecules, including the electromagnetic forces of attraction or repulsion which act between atoms and other types of neighbouring particles, e.g. atoms or ions. Intermolecular forces are weak relative to intramolecular forces – the forces which hold a molecule together. For example, the covalent bond, involving sharing electron pairs between atoms, is much stronger than the forces present between neighboring molecules.
