|
Empirical Valence Bond
In theoretical chemistry, the Empirical Valence Bond (EVB) approach is an approximation for calculating free-energies of a chemical reaction in condensed-phase. It was first developed by Israeli chemist Arieh Warshel, and was inspired by the way Marcus theory uses potential surfaces to calculate the probability of electron transfer. Where most methods for reaction free-energy calculations require at least some part of the modeled system to be treated using quantum mechanics, EVB uses a calibrated Hamiltonian to approximate the potential energy surface of a reaction. For a simple 1-step reaction, that typically means that a reaction is modeled using 2 states. These states are valence bond descriptions of the reactants and products of the reaction. The function that gives the ground energy then becomes: E_g = \frac \biggl(H_ + H_ - \sqrt \biggr) where and are the valence bond descriptions of the reactant and product state respectively, and is the coupling parameter. The a ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Theoretical Chemistry
Theoretical chemistry is the branch of chemistry which develops theoretical generalizations that are part of the theoretical arsenal of modern chemistry: for example, the concepts of chemical bonding, chemical reaction, valence, the surface of potential energy, molecular orbitals, orbital interactions, and molecule activation. Overview Theoretical chemistry unites principles and concepts common to all branches of chemistry. Within the framework of theoretical chemistry, there is a systematization of chemical laws, principles and rules, their refinement and detailing, the construction of a hierarchy. The central place in theoretical chemistry is occupied by the doctrine of the interconnection of the structure and properties of molecular systems. It uses mathematical and physical methods to explain the structures and dynamics of chemical systems and to correlate, understand, and predict their thermodynamic and kinetic properties. In the most general sense, it is explanation of ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Ground State
The ground state of a quantum-mechanical system is its stationary state of lowest energy; the energy of the ground state is known as the zero-point energy of the system. An excited state is any state with energy greater than the ground state. In quantum field theory, the ground state is usually called the vacuum state or the vacuum. If more than one ground state exists, they are said to be degenerate. Many systems have degenerate ground states. Degeneracy occurs whenever there exists a unitary operator that acts non-trivially on a ground state and commutes with the Hamiltonian of the system. According to the third law of thermodynamics, a system at absolute zero temperature exists in its ground state; thus, its entropy is determined by the degeneracy of the ground state. Many systems, such as a perfect crystal lattice, have a unique ground state and therefore have zero entropy at absolute zero. It is also possible for the highest excited state to have absolute zero temper ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Gregory A
Gregory may refer to: People and fictional characters * Gregory (given name), including a list of people and fictional characters with the given name * Gregory (surname), a surname Places Australia *Gregory, Queensland, a town in the Shire of Burke **Electoral district of Gregory, Queensland, Australia *Gregory, Western Australia. United States *Gregory, South Dakota *Gregory, Tennessee *Gregory, Texas Outer space *Gregory (lunar crater) *Gregory (crater on Venus) Other uses * "Gregory" (''The Americans''), the third episode of the first season of the television series ''The Americans'' See also * Greg (other) * Greggory * Gregoire (other) * Gregor (other) * Gregores (other) * Gregorian (other) * Gregory County (other) * Gregory Highway, Queensland * Gregory National Park, Northern Territory * Gregory River in the Shire of Burke, Queensland * Justice Gregory (other) Justice Gregory may refer to: * George G ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Electron Equivalent
Redox (reduction–oxidation, , ) is a type of chemical reaction in which the oxidation states of substrate change. Oxidation is the loss of electrons or an increase in the oxidation state, while reduction is the gain of electrons or a decrease in the oxidation state. There are two classes of redox reactions: * ''Electron-transfer'' – Only one (usually) electron flows from the reducing agent to the oxidant. This type of redox reaction is often discussed in terms of redox couples and electrode potentials. * ''Atom transfer'' – An atom transfers from one substrate to another. For example, in the rusting of iron, the oxidation state of iron atoms increases as the iron converts to an oxide, and simultaneously the oxidation state of oxygen decreases as it accepts electrons released by the iron. Although oxidation reactions are commonly associated with the formation of oxides, other chemical species can serve the same function. In hydrogenation, C=C (and other) bonds ar ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
RAPTOR (Rapid Approach For Proton Transport And Other Reactions)
Raptor or RAPTOR may refer to: Animals The word "raptor" refers to several groups of bird-like dinosaurs which primarily capture and subdue/kill prey with their talons. * Raptor (bird) or bird of prey, a bird that primarily hunts and feeds on vertebrates * Raptor- or -raptor, a taxonomic affix used in to describe dromeosaurs or similar animals * Dromaeosauridae, a family of dinosaurs including ''Velociraptor'', informally known as raptors Arts and entertainment Film and television * ''Raptor'' (film), a 2001 film * Raptor, a fictional spacecraft in ''Battlestar Galactica'' Gaming * '' Raptor: Call of the Shadows'', a 1994 video game * Raptor heavy fighter, a fictional craft in the ''Wing Commander'' game * Lord Raptor, a ''Darkstalkers'' character In print * ''Raptor'' (novel), a 1993 novel by Gary Jennings * Raptor (Gary Wilton, Jr.), a Marvel Comics character * Raptor (Damon Ryder), a Marvel Comics character * Raptor (Brenda Drago), a Marvel Comics character Roller coas ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Q (software)
Q is a computer software package for molecular dynamics (MD) simulation (current release: Q6). Unlike other MD codes, it has specialized since its conception (Marelius et al. 1998) on three specific types of free energy calculations. These calculations are based on the methods: '' empirical valence bond'' (EVB), ''free energy perturbation'' (FEP), and ''linear interaction energy'' (LIE), as well as, more recently, also path integral calculations using the bisection quantum classical path (BQCP) approach. The methods in which the program specializes can return quantitative calculations of the energy balance which occurs in proteins and nucleic acids. It can provide insight into key problems in biochemistry such as, energetic details on parts of the translation mechanism in mitochondrial ribosomes (Lind et al. 2013), or details in enzymatic reactions (Mones et al. 2013), among others. The program is similar to GROMACS in being force-field agnostic, meaning that it provides no f ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Molaris (software)
Molaris may refer to: * Molaris (software), a software using the empirical valence bond In theoretical chemistry, the Empirical Valence Bond (EVB) approach is an approximation for calculating free-energies of a chemical reaction in condensed-phase. It was first developed by Israeli chemist Arieh Warshel, and was inspired by the way ... approach to calculate free energies of enzymatic reactions * Dens molaris, a Latin expression for designing the molar (tooth) * ''Chomatodus molaris'', a prehistoric fish in genus '' Chomatodus'' *'' Scopula molaris'', a moth in the family ''Geomitridae'' {{disambiguation ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Umbrella Sampling
Umbrella sampling is a technique in computational physics and chemistry, used to improve sampling of a system (or different systems) where ergodicity is hindered by the form of the system's energy landscape. It was first suggested by Torrie and Valleau in 1977. It is a particular physical application of the more general importance sampling in statistics. Systems in which an energy barrier separates two regions of configuration space may suffer from poor sampling. In Metropolis Monte Carlo runs, the low probability of overcoming the potential barrier can leave inaccessible configurations poorly sampled—or even entirely unsampled—by the simulation. An easily visualised example occurs with a solid at its melting point: considering the state of the system with an order parameter ''Q'', both liquid (low ''Q'') and solid (high ''Q'') phases are low in energy, but are separated by a free energy barrier at intermediate values of ''Q''. This prevents the simulation from adequately sa ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Free Energy Perturbation
Free energy perturbation (FEP) is a method based on statistical mechanics that is used in computational chemistry for computing free energy differences from molecular dynamics or Metropolis Monte Carlo simulations. The FEP method was introduced by Robert W. Zwanzig in 1954. According to the free-energy perturbation method, the free energy difference for going from state A to state B is obtained from the following equation, known as the ''Zwanzig equation'': :\Delta F(\mathbf \rightarrow \mathbf) = F_\mathbf - F_\mathbf = -k_\mathrm T \ln \left \langle \exp \left ( - \frac \right ) \right \rangle _\mathbf where ''T'' is the temperature, ''k''B is Boltzmann's constant, and the angular brackets denote an average over a simulation run for state A. In practice, one runs a normal simulation for state A, but each time a new configuration is accepted, the energy for state B is also computed. The difference between states A and B may be in the atom types involved, in which case the Δ''F ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Monte Carlo Molecular Modeling
Monte Carlo molecular modelling is the application of Monte Carlo methods to molecular problems. These problems can also be modelled by the molecular dynamics method. The difference is that this approach relies on equilibrium statistical mechanics rather than molecular dynamics. Instead of trying to reproduce the dynamics of a system, it generates states according to appropriate Boltzmann distribution. Thus, it is the application of the Metropolis Monte Carlo simulation to molecular systems. It is therefore also a particular subset of the more general Monte Carlo method in statistical physics. It employs a Markov chain procedure in order to determine a new state for a system from a previous one. According to its stochastic nature, this new state is accepted at random. Each trial usually counts as a move. The avoidance of dynamics restricts the method to studies of static quantities only, but the freedom to choose moves makes the method very flexible. These moves must only satisfy a ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Molecular Dynamics
Molecular 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. 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 analytically; MD simulation circumvents this problem by using numerical methods. However, long MD simulations are mathematically ill-conditioned, generating cumulative errors in ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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. Force fields are interatomic potentials and utilize the same concept as force fields in classical physics, with the difference that the force field parameters in chemistry describe the energy landscape, from which the acting forces on every particle are derived as a gradient of the potential energy with respect to the particle coordinates. ''All-atom'' force fields provide parameters for every type of atom in ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
