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Fragment Molecular Orbital
The fragment molecular orbital method (FMO) is a computational method that can compute very large molecular systems with thousands of atoms using ab initio quantum-chemical wave functions. History of FMO and related methods The fragment molecular orbital method (FMO) was developed by K. Kitaura and coworkers in 1999. FMO is deeply interconnected with the energy decomposition analysis (EDA) by Kitaura and Morokuma, developed in 1976. The main use of FMO is to compute very large molecular systems by dividing them into fragments and performing ab initio or density functional quantum-mechanical calculations of fragments and their dimers, whereby the Coulomb field from the whole system is included. The latter feature allows fragment calculations without using caps. The mutually consistent field (MCF) method had introduced the idea of self-consistent fragment calculations in their embedding potential, which was later used with some modifications in various methods including FMO. Ther ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Drug Design
Drug 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. Drug design frequently but not necessarily relies on computer modeling techniques. This type of modeling is sometimes referred to as computer-aided drug design. Finally, drug design that relies on the knowledge of the three-dimensional structure of the biomolecular target is known as structure-based drug design. In addition to small molecules, biopharmaceuticals including peptides and especially therapeutic antibodies a ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Generalized Valence Bond
The generalized valence bond (GVB) is a method in valence bond theory that uses flexible orbitals in the general way used by modern valence bond theory. The method was developed by the group of William A. Goddard, III around 1970. Theory The generalized Coulson–Fischer theory for the hydrogen molecule, discussed in Modern valence bond theory, is used to describe every electron pair in a molecule. The orbitals for each electron pair are expanded in terms of the full basis set and are non-orthogonal. Orbitals from different pairs are forced to be orthogonal - the strong orthogonality condition. This condition simplifies the calculation but can lead to some difficulties. Calculations GVB code in some programs, particularly GAMESS (US) General Atomic and Molecular Electronic Structure System (GAMESS (US)) is computer software for computational chemistry program. The original code started on October 1, 1977 as a National Resources for Computations in Chemistry project. In 1981, t . ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Unrestricted Hartree–Fock
Unrestricted Hartree–Fock (UHF) theory is the most common molecular orbital method for open shell molecules where the number of electrons of each spin are not equal. While restricted Hartree–Fock theory uses a single molecular orbital twice, one multiplied by the α spin function and the other multiplied by the β spin function in the Slater determinant, unrestricted Hartree–Fock theory uses different molecular orbitals for the α and β electrons. This has been called a ''different orbitals for different spins'' (DODS) method. The result is a pair of coupled Roothaan equations, known as the Pople–Nesbet–Berthier equations. :\mathbf^\alpha\ \mathbf^\alpha\ = \mathbf \mathbf^\alpha\ \mathbf^\alpha\ :\mathbf^\beta\ \mathbf^\beta\ = \mathbf \mathbf^\beta\ \mathbf^\beta\ Where \mathbf^\alpha\ and \mathbf^\beta\ are the Fock matrices for the \alpha\ and \beta\ orbitals, \mathbf^\alpha\ and \mathbf^\beta\ are the matrices of coefficients for the ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Restricted Open-shell Hartree–Fock
Restricted open-shell Hartree–Fock (ROHF) is a variant of Hartree–Fock method for open shell molecules. It uses doubly occupied molecular orbitals as far as possible and then singly occupied orbitals for the unpaired electrons. This is the simple picture for open shell molecules but it is difficult to implement. The foundations of the ROHF method were first formulated by Clemens C. J. Roothaan in a celebrated paper and then extended by various authors, see e.g. for in-depth discussions. As with restricted Hartree–Fock theory for closed shell molecules, it leads to Roothaan equations written in the form of a generalized eigenvalue problem :\mathbf \mathbf = \mathbf \mathbf \mathbf Where F is the so-called Fock matrix (which is a function of C), C is a matrix of coefficients, S is the overlap matrix of the basis functions, and \epsilon is the (diagonal, by convention) matrix of orbital energies. Unlike restricted Hartree–Fock theory for closed shell molecules, the form of t ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
GAMESS (US)
General Atomic and Molecular Electronic Structure System (GAMESS (US)) is computer software for computational chemistry program. The original code started on October 1, 1977 as a National Resources for Computations in Chemistry project. In 1981, the code base split into GAMESS (US) and GAMESS (UK) variants, which now differ significantly. GAMESS (US) is maintained by the members of the Gordon Research Group at Iowa State University. GAMESS (US) source code is available as source-available freeware, but is not open-source software, due to license restrictions. Abilities GAMESS (US) can perform several general computational chemistry calculations, including Hartree–Fock method, density functional theory (DFT), generalized valence bond (GVB), and multi-configurational self-consistent field (MCSCF). Correlation corrections after these SCF calculations can be estimated by configuration interaction (CI), second order Møller–Plesset perturbation theory (MP2), and coupled clust ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
DFTB
The Density Functional Based Tight Binding method is an approximation to density functional theory, which reduces the Kohn-Sham equations to a form of tight binding related to the Harris functional. The original approximation limits interactions to a non-self-consistent two center hamiltonian between confined atomic states. In the late 1990s a second-order expansion of the Kohn-Sham equations, Kohn-Sham energy enabled a charge self-consistent treatment of systems where Mulliken population analysis, Mulliken charges of the atoms are solved self-consistently. This expansion has been continued to the 3rd order in charge fluctuations and with respect to spin fluctuations. Unlike empirical tight binding the (single particle) wavefunction of the resulting system is available, since the integrals used to produce the matrix elem elements are calculated using a set of atomic basis functions. References Electronic structure methods Electronic band structures Quantum chemistry Th ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Polarizable Continuum Model
The polarizable continuum model (PCM) is a commonly used method in computational chemistry to model solvation effects. If it is necessary to consider each solvent molecule as a separate molecule, the computational cost of modeling a solvent-mediated chemical reaction would grow prohibitively high. Modeling the solvent as a polarizable continuum, rather than individual molecules, makes ''ab initio'' computation feasible. Two types of PCMs have been popularly used: the dielectric PCM (D-PCM) in which the continuum is polarizable (see dielectrics) and the conductor-like PCM (C-PCM) in which the continuum is conductor-like similar to COSMO Solvation Model.Jacopo Tomasi, Benedetta Mennucci, and Roberto Cammi (2005). "Quantum Mechanical Continuum Solvation Models." Chem. Rev. 105(8): 2999-309/ref> The molecular Gibbs free energy, free energy of solvation is computed as the sum of three terms: :''G''sol = ''G''es + ''G''dr + ''G''cav ::''G''es = electrostatic ::''G''dr = dispersion-re ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Coupled Cluster
Coupled cluster (CC) is a numerical technique used for describing many-body systems. Its most common use is as one of several post-Hartree–Fock ab initio quantum chemistry methods in the field of computational chemistry, but it is also used in nuclear physics. Coupled cluster essentially takes the basic Hartree–Fock molecular orbital method and constructs multi-electron wavefunctions using the exponential cluster operator to account for electron correlation. Some of the most accurate calculations for small to medium-sized molecules use this method. The method was initially developed by Fritz Coester and Hermann Kümmel in the 1950s for studying nuclear-physics phenomena, but became more frequently used when in 1966 Jiří Čížek (and later together with Josef Paldus) reformulated the method for electron correlation in atoms and molecules. It is now one of the most prevalent methods in quantum chemistry that includes electronic correlation. CC theory is simply the pertur ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
