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TIP3P
In computational chemistry, a water model is used to simulate and thermodynamically calculate water clusters, liquid water, and aqueous solutions with explicit solvent, often using molecular dynamics or Monte Carlo methods. The models describe intermolecular forces between water molecules and are determined from quantum mechanics Quantum mechanics is the fundamental physical Scientific theory, theory that describes the behavior of matter and of light; its unusual characteristics typically occur at and below the scale of atoms. Reprinted, Addison-Wesley, 1989, It is ..., molecular mechanics, experimental results, and these combinations. To imitate the specific nature of the intermolecular forces, many types of models have been developed. In general, these can be classified by the following three characteristics; (i) the number of interaction points or ''sites'', (ii) whether the model is rigid or flexible, and (iii) whether the model includes polarization effects. ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
CHARMM
Chemistry at Harvard Macromolecular Mechanics (CHARMM) is the name of a widely used set of force fields for molecular dynamics, and the name for the molecular dynamics simulation and analysis computer software package associated with them. The CHARMM Development Project involves a worldwide network of developers working with Martin Karplus and his group at Harvard to develop and maintain the CHARMM program. Licenses for this software are available, for a fee, to people and groups working in academia. Force fields The CHARMM force fields for proteins include: united-atom (sometimes termed ''extended atom'') CHARMM19, all-atom CHARMM22 and its dihedral potential corrected variant CHARMM22/CMAP, as well as later versions CHARMM27 and CHARMM36 and various modifications such as CHARMM36m and CHARMM36IDPSFF. In the CHARMM22 protein force field, the atomic partial charges were derived from quantum chemical calculations of the interactions between model compounds and water. Furthermor ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Molecular Dynamics
Molecular dynamics (MD) is a computer simulation method for analyzing the Motion (physics), 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 dynamics (mechanics), dynamic "evolution" of the system. In the most common version, the trajectory, trajectories of atoms and molecules are determined by Numerical integration, numerically solving Newton's laws of motion, Newton's equations of motion for a system of interacting particles, where Force (physics), forces between the particles and their potential energy, potential energies are often calculated using interatomic potentials or molecular mechanics, molecular mechanical Force field (chemistry), force fields. The method is applied mostly in chemical physics, materials science, and biophysics. Because molecular systems typically consist of a vast number of particles, it is impossible to determine the properties of such complex systems analyt ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Electrostatic Constant
Coulomb's inverse-square law, or simply Coulomb's law, is an experimental law of physics that calculates the amount of force between two electrically charged particles at rest. This electric force is conventionally called the ''electrostatic force'' or Coulomb force. Although the law was known earlier, it was first published in 1785 by French physicist Charles-Augustin de Coulomb. Coulomb's law was essential to the development of the theory of electromagnetism and maybe even its starting point, as it allowed meaningful discussions of the amount of electric charge in a particle. The law states that the magnitude, or absolute value, of the attractive or repulsive electrostatic force between two point charges is directly proportional to the product of the magnitudes of their charges and inversely proportional to the square of the distance between them. Coulomb discovered that bodies with like electrical charges repel: Coulomb also showed that oppositely charged bodies attract ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Dielectric Permittivity
In electromagnetism, the absolute permittivity, often simply called permittivity and denoted by the Greek letter (epsilon), is a measure of the electric polarizability of a dielectric material. A material with high permittivity polarizes more in response to an applied electric field than a material with low permittivity, thereby storing more energy in the material. In electrostatics, the permittivity plays an important role in determining the capacitance of a capacitor. In the simplest case, the electric displacement field resulting from an applied electric field E is \mathbf = \varepsilon\ \mathbf ~. More generally, the permittivity is a thermodynamic function of state. It can depend on the frequency, magnitude, and direction of the applied field. The SI unit for permittivity is farad per meter (F/m). The permittivity is often represented by the relative permittivity which is the ratio of the absolute permittivity and the vacuum permittivity \kappa = \varepsilon_\ma ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Density
Density (volumetric mass density or specific mass) is the ratio of a substance's mass to its volume. The symbol most often used for density is ''ρ'' (the lower case Greek letter rho), although the Latin letter ''D'' (or ''d'') can also be used: \rho = \frac, where ''ρ'' is the density, ''m'' is the mass, and ''V'' is the volume. In some cases (for instance, in the United States oil and gas industry), density is loosely defined as its weight per unit volume, although this is scientifically inaccurate this quantity is more specifically called specific weight. For a pure substance, the density is equal to its mass concentration. Different materials usually have different densities, and density may be relevant to buoyancy, purity and packaging. Osmium is the densest known element at standard conditions for temperature and pressure. To simplify comparisons of density across different systems of units, it is sometimes replaced by the dimensionless quantity "relative den ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Polarization Density
In classical electromagnetism, polarization density (or electric polarization, or simply polarization) is the vector field that expresses the volumetric density of permanent or induced electric dipole moments in a dielectric material. When a dielectric is placed in an external electric field, its molecules gain electric dipole moment and the dielectric is said to be polarized. Electric polarization of a given dielectric material sample is defined as the quotient of electric dipole moment (a vector quantity, expressed as coulombs*meters (C*m) in SI units) to volume (meters cubed). Polarization density is denoted mathematically by P; in SI units, it is expressed in coulombs per square meter (C/m2). Polarization density also describes how a material responds to an applied electric field as well as the way the material changes the electric field, and can be used to calculate the forces that result from those interactions. It can be compared to magnetization, which is the measure of ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Journal Of Physical Chemistry
''The Journal of Physical Chemistry A'' is a scientific journal which reports research on the chemistry of molecules - including their dynamics, spectroscopy, kinetics, structure, bonding, and quantum chemistry. It is published weekly by the American Chemical Society. Before 1997 the title was simply ''Journal of Physical Chemistry''. Owing to the ever-growing amount of research in the area, in 1997 the journal was split into ''Journal of Physical Chemistry A'' (molecular theoretical and experimental physical chemistry) and '' The Journal of Physical Chemistry B'' (solid state, soft matter, liquids, etc.). Beginning in 2007, the latter underwent a further split, with '' The Journal of Physical Chemistry C'' now being dedicated to nanotechnology, molecular electronics, and related subjects. According to the ''Journal Citation Reports'', the journal have an impact factor of 2.7 for 2023. Editors-in-chief *1896–1932 Wilder Dwight Bancroft, Joseph E. Trevor *1933–1951 S. C. ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Farad
The farad (symbol: F) is the unit of electrical capacitance, the ability of a body to store an electrical charge, in the International System of Units, International System of Units (SI), equivalent to 1 coulomb per volt (C/V). It is named after the English physicist Michael Faraday (1791–1867). In SI base units 1 F = 1 kilogram, kg−1⋅meter, m−2⋅second, s4⋅ampere, A2. Definition The capacitance of a capacitor is one farad when one coulomb of charge changes the potential between the plates by one volt. Equally, one farad can be described as the capacitance which stores a one-coulomb charge across a potential difference of one volt. The relationship between capacitance, charge, and potential difference is linear. For example, if the potential difference across a capacitor is halved, the quantity of charge stored by that capacitor will also be halved. For most applications, the farad is an impractically large unit of capacitance. Most electrical and electron ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Polarizability
Polarizability usually refers to the tendency of matter, when subjected to an electric field, to acquire an electric dipole moment in proportion to that applied field. It is a property of particles with an electric charge. When subject to an electric field, the negatively charged electrons and positively charged atomic nuclei are subject to opposite forces and undergo Electric dipole moment, charge separation. Polarizability is responsible for a material's dielectric constant and, at high (optical) frequencies, its refractive index. The polarizability of an atom or molecule is defined as the ratio of its induced dipole moment to the local electric field; in a crystalline solid, one considers the dipole moment per unit cell. Note that the local electric field seen by a molecule is generally different from the macroscopic electric field that would be measured externally. This discrepancy is taken into account by the Clausius–Mossotti relation (below) which connects the bulk behavi ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Debye
The debye ( , ; symbol: D) is a CGS unit (a non- SI metric unit) of electric dipole momentTwo equal and opposite charges separated by some distance constitute an electric dipole. This dipole possesses an electric dipole moment whose value is given as charge times length of separation. The dipole itself is a vector whose direction coincides with the position vector of the positive charge with respect to the negative charge: : p = ''q''r. named in honour of the physicist Peter J. W. Debye. It is defined as statcoulomb-centimetres.The statcoulomb is also known as the franklin or electrostatic unit of charge. : 1 statC = 1 Fr = 1 esu = 1 cm3/2⋅g1/2⋅s−1. Historically the debye was defined as the dipole moment resulting from two charges of opposite sign but an equal magnitude of 10−10 statcoulomb10−10 statcoulomb corresponds to approximately 0.2083 units of elementary charge. (generally called e.s.u. (electrostatic unit) in ol ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
