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 orbitalIn chemistry, a molecular orbital (ɒrbədl) is a mathematical function describing the location and wave-like behavior of an electron in a molecule. This function can be used to calculate chemical and physical properties such as the probability of finding an electron in any specific region. The terms atomic orbital and molecular orbital were introduced by Robert S. Mulliken in 1932 to mean one-electron orbital wave functions. At an elementary level, they are used to describe the region of space in which a function has a significant amplitude.
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 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.
Energy levelA quantum mechanical system or particle that is bound—that is, confined spatially—can only take on certain discrete values of energy, called energy levels. This contrasts with classical particles, which can have any amount of energy. The term is commonly used for the energy levels of the electrons in atoms, ions, or molecules, which are bound by the electric field of the nucleus, but can also refer to energy levels of nuclei or vibrational or rotational energy levels in molecules.
Docking (molecular)In the field of molecular modeling, docking is a method which predicts the preferred orientation of one molecule to a second when a ligand and a target are bound to each other to form a stable complex. Knowledge of the preferred orientation in turn may be used to predict the strength of association or binding affinity between two molecules using, for example, scoring functions. The associations between biologically relevant molecules such as proteins, peptides, nucleic acids, carbohydrates, and lipids play a central role in signal transduction.
Molecular geometryMolecular geometry is the three-dimensional arrangement of the atoms that constitute a molecule. It includes the general shape of the molecule as well as bond lengths, bond angles, torsional angles and any other geometrical parameters that determine the position of each atom. Molecular geometry influences several properties of a substance including its reactivity, polarity, phase of matter, color, magnetism and biological activity. The angles between bonds that an atom forms depend only weakly on the rest of molecule, i.
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.
Planck constantThe Planck constant, or Planck's constant, is a fundamental physical constant of foundational importance in quantum mechanics. The constant gives the relationship between the energy of a photon and its frequency, and by the mass-energy equivalence, the relationship between mass and frequency. Specifically, a photon's energy is equal to its frequency multiplied by the Planck constant. The constant is generally denoted by . The reduced Planck constant, or Dirac constant, equal to divided by , is denoted by .
Avogadro constantThe Avogadro constant, commonly denoted N_A or L, is an SI defining constant with an exact value of 6.02214076e23reciprocal moles. It is used as a normalization factor in the amount of substance in a sample (in units of moles), defined as the number of constituent particles (usually molecules, atoms, or ions) divided by N_A. In practice, its value is often approximated as 6.02×1023 or 6.022×1023 particles per mole. The constant is named after the physicist Amedeo Avogadro (1776–1856).
Planck's lawIn physics, Planck's law (also Planck radiation law) describes the spectral density of electromagnetic radiation emitted by a black body in thermal equilibrium at a given temperature T, when there is no net flow of matter or energy between the body and its environment. At the end of the 19th century, physicists were unable to explain why the observed spectrum of black-body radiation, which by then had been accurately measured, diverged significantly at higher frequencies from that predicted by existing theories.
Boltzmann constantThe Boltzmann constant (kB or k) is the proportionality factor that relates the average relative thermal energy of particles in a gas with the thermodynamic temperature of the gas. It occurs in the definitions of the kelvin and the gas constant, and in Planck's law of black-body radiation and Boltzmann's entropy formula, and is used in calculating thermal noise in resistors. The Boltzmann constant has dimensions of energy divided by temperature, the same as entropy. It is named after the Austrian scientist Ludwig Boltzmann.
Amount of substanceIn chemistry, the amount of substance (symbol n) in a given sample of matter is defined as a ratio (n = N/NA) between the number of elementary entities (N) and the Avogadro constant (NA). The entities are usually molecules, atoms, or ions of a specified kind. The particular substance sampled may be specified using a subscript, e.g., the amount of sodium chloride (NaCl) would be denoted as nNaCl. The unit of amount of substance in the International System of Units is the mole (symbol: mol), a base unit.
Planck unitsIn particle physics and physical cosmology, Planck units are a set of units of measurement defined exclusively in terms of four universal physical constants, in such a manner that these physical constants take on the numerical value of 1 when expressed in terms of these units. Originally proposed in 1899 by German physicist Max Planck, these units are a system of natural units because their definition is based on properties of nature, more specifically the properties of free space, rather than a choice of prototype object.
Number densityThe number density (symbol: n or ρN) is an intensive quantity used to describe the degree of concentration of countable objects (particles, molecules, phonons, cells, galaxies, etc.) in physical space: three-dimensional volumetric number density, two-dimensional areal number density, or one-dimensional linear number density. Population density is an example of areal number density. The term number concentration (symbol: lowercase n, or C, to avoid confusion with amount of substance indicated by uppercase N) is sometimes used in chemistry for the same quantity, particularly when comparing with other concentrations.
Emission spectrumThe emission spectrum of a chemical element or chemical compound is the spectrum of frequencies of electromagnetic radiation emitted due to an electron making a transition from a high energy state to a lower energy state. The photon energy of the emitted photon is equal to the energy difference between the two states. There are many possible electron transitions for each atom, and each transition has a specific energy difference. This collection of different transitions, leading to different radiated wavelengths, make up an emission spectrum.
Physical constantA physical constant, sometimes fundamental physical constant or universal constant, is a physical quantity that is generally believed to be both universal in nature and have constant value in time. It is distinct from a mathematical constant, which has a fixed numerical value, but does not directly involve any physical measurement. There are many physical constants in science, some of the most widely recognized being the speed of light in vacuum c, the gravitational constant G, the Planck constant h, the electric constant ε0, and the elementary charge e.
Planck relationThe Planck relation (referred to as Planck's energy–frequency relation, the Planck–Einstein relation, Planck equation, and Planck formula, though the latter might also refer to Planck's law) is a fundamental equation in quantum mechanics which states that the energy of a photon, E, known as photon energy, is proportional to its frequency, ν: The constant of proportionality, h, is known as the Planck constant. Several equivalent forms of the relation exist, including in terms of angular frequency, ω: where .
Spread spectrumIn telecommunication, especially radio communication, spread spectrum designates techniques by which a signal (e.g., an electrical, electromagnetic, or acoustic) generated with a particular bandwidth is deliberately spread in the frequency domain, resulting in a signal with a wider bandwidth. Spread-spectrum techniques are used for the establishment of secure communications, increasing resistance to natural interference, noise, and jamming, to prevent detection, to limit power flux density (e.g.
Electromagnetic interferenceElectromagnetic interference (EMI), also called radio-frequency interference (RFI) when in the radio frequency spectrum, is a disturbance generated by an external source that affects an electrical circuit by electromagnetic induction, electrostatic coupling, or conduction. The disturbance may degrade the performance of the circuit or even stop it from functioning. In the case of a data path, these effects can range from an increase in error rate to a total loss of the data.
