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ONIOM
The ONIOM (short for 'Our own n-layered Integrated molecular Orbital and Molecular mechanics') method is a computational approach developed by Morokuma and co-workers. ONIOM is a hybrid method that enables different ab initio, semi-empirical, or molecular mechanics methods to be applied to different parts of a molecule/system in combination to produce reliable geometry and energy at reduced computational cost. The ONIOM computational approach has been found to be particularly useful for modeling biomolecular systems as well as for transition metal complexes and catalysts. Codes that support ONIOM *Gaussian *NWChem * ORCA (quantum chemistry program) See also *QM/MM *Steric effects Steric effects arise from the spatial arrangement of atoms. When atoms come close together there is a rise in the energy of the molecule. Steric effects are nonbonding interactions that influence the shape ( conformation) and reactivity of ions ... (ONIOM to separate Steric effects vs. electronic ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
NWChem
NWChem is an ab initio computational chemistry software package which includes quantum chemical and molecular dynamics functionality. It was designed to run on high-performance parallel supercomputers as well as conventional workstation clusters. It aims to be scalable both in its ability to treat large problems efficiently, and in its usage of available parallel computing resources. NWChem has been developed by the Molecular Sciences Software group of the Theory, Modeling & Simulation program of the Environmental Molecular Sciences Laboratory (EMSL) at the Pacific Northwest National Laboratory (PNNL). The early implementation was funded by the EMSL Construction Project. NWChem is currently being redesigned and reimplemented for exascale computing platforms (NWChemEx ). Capabilities * Molecular mechanics * Molecular dynamics * Hartree–Fock (self-consistent field method) * Density functional theory * Time-dependent density functional theory * Post-Hartree–Fock met ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Gaussian (software)
Gaussian is a general purpose computational chemistry software package initially released in 1970 by John Pople and his research group at Carnegie Mellon University as Gaussian 70. It has been continuously updated since then. The name originates from Pople's use of Gaussian orbitals to speed up molecular electronic structure calculations as opposed to using Slater-type orbitals, a choice made to improve performance on the limited computing capacities of then-current computer hardware for Hartree–Fock calculations. The current version of the program is Gaussian 16. Originally available through the Quantum Chemistry Program Exchange, it was later licensed out of Carnegie Mellon University, and since 1987 has been developed and licensed by Gaussian, Inc. Standard abilities According to the most recent Gaussian manual, the package can do: *Molecular mechanics **AMBER **Universal force field (UFF) **DREIDING force field *Semi-empirical quantum chemistry method calculations **Austin ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
QM/MM
The hybrid QM/MM (quantum mechanics/molecular mechanics) approach is a molecular simulation method that combines the strengths of ''ab initio'' QM calculations (accuracy) and MM (speed) approaches, thus allowing for the study of chemical processes in solution and in proteins. The QM/MM approach was introduced in the 1976 paper of Warshel and Levitt. They, along with Martin Karplus, won the 2013 Nobel Prize in Chemistry for "the development of multiscale models for complex chemical systems". Efficiency An important advantage of QM/MM methods is their efficiency. The cost of doing classical molecular mechanics (MM) simulations in the most straightforward case scales as ''O''(''N''2), where ''N'' is the number of atoms in the system. This is mainly due to electrostatic interactions term (every particle interacts with everything else). However, use of cutoff radius, periodic pair-list updates and more recently the variations of the particle mesh Ewald (PME) method has reduced this ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Computational Chemistry
Computational chemistry is a branch of chemistry that uses computer simulation to assist in solving chemical problems. It uses methods of theoretical chemistry, incorporated into computer programs, to calculate the structures and properties of molecules, groups of molecules, and solids. It is essential because, apart from relatively recent results concerning the hydrogen molecular ion ( dihydrogen cation, see references therein for more details), the quantum many-body problem cannot be solved analytically, much less in closed form. While computational results normally complement the information obtained by chemical experiments, it can in some cases predict hitherto unobserved chemical phenomena. It is widely used in the design of new drugs and materials. Examples of such properties are structure (i.e., the expected positions of the constituent atoms), absolute and relative (interaction) energies, electronic charge density distributions, dipoles and higher multipole moments ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Ab Initio Quantum Chemistry Methods
''Ab initio'' quantum chemistry methods are computational chemistry methods based on quantum chemistry. The term was first used in quantum chemistry by Robert Parr and coworkers, including David Craig in a semiempirical study on the excited states of benzene. The background is described by Parr. ''Ab initio'' means "from first principles" or "from the beginning", implying that the only inputs into an ''ab initio'' calculation are physical constants. ''Ab initio'' quantum chemistry methods attempt to solve the electronic Schrödinger equation given the positions of the nuclei and the number of electrons in order to yield useful information such as electron densities, energies and other properties of the system. The ability to run these calculations has enabled theoretical chemists to solve a range of problems and their importance is highlighted by the awarding of the Nobel prize to John Pople and Walter Kohn. Accuracy and scaling ''Ab initio'' electronic structure method ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Semi-empirical Quantum Chemistry Method
Semi-empirical quantum chemistry methods are based on the Hartree–Fock formalism, but make many approximations and obtain some parameters from empirical data. They are very important in computational chemistry for treating large molecules where the full Hartree–Fock method without the approximations is too expensive. The use of empirical parameters appears to allow some inclusion of electron correlation effects into the methods. Within the framework of Hartree–Fock calculations, some pieces of information (such as two-electron integrals) are sometimes approximated or completely omitted. In order to correct for this loss, semi-empirical methods are parametrized, that is their results are fitted by a set of parameters, normally in such a way as to produce results that best agree with experimental data, but sometimes to agree with ''ab initio'' results. Type of simplifications used Semi-empirical methods follow what are often called empirical methods where the two-electron ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Molecular Mechanics
Molecular mechanics uses classical mechanics to model molecular systems. The Born–Oppenheimer approximation is assumed valid and the potential energy of all systems is calculated as a function of the nuclear coordinates using force fields. Molecular mechanics can be used to study molecule systems ranging in size and complexity from small to large biological systems or material assemblies with many thousands to millions of atoms. All-atomistic molecular mechanics methods have the following properties: * Each atom is simulated as one particle * Each particle is assigned a radius (typically the van der Waals radius), polarizability, and a constant net charge (generally derived from quantum calculations and/or experiment) * Bonded interactions are treated as ''springs'' with an equilibrium distance equal to the experimental or calculated bond length Variants on this theme are possible. For example, many simulations have historically used a ''united-atom'' representation in whic ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Molecular Geometry
Molecular geometry is the three-dimensional space, 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 (chemistry), reactivity, Chemical polarity, polarity, Phase (matter), 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.e. they can be understood as approximately local and hence Transferability (chemistry), transferable properties. Determination The molecular geometry can be determined by various spectroscopy, spectroscopic methods and diffraction methods. Infrared spectroscopy, IR, Rotational spectroscopy, microwave and Raman spectroscopy can give information about the molecule geometry from the ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Energy Level
A 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. The energy spectrum of a system with such discrete energy levels is said to be quantized. In chemistry and atomic physics, an electron shell, or principal energy level, may be thought of as the orbit of one or more electrons around an atom's nucleus. The closest shell to the nucleus is called the " shell" (also called "K shell"), followed by the " shell" (or "L shell"), then the " shell" (or "M shell"), and so on farther and farther from the nucleus. The shells correspond with the principal ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Biomolecule
A biomolecule or biological molecule is a loosely used term for molecules present in organisms that are essential to one or more typically biological processes, such as cell division, morphogenesis, or development. Biomolecules include large macromolecules (or polyelectrolytes) such as proteins, carbohydrates, lipids, and nucleic acids, as well as small molecules such as primary metabolites, secondary metabolites and natural products. A more general name for this class of material is biological materials. Biomolecules are an important element of living organisms, those biomolecules are often endogenous, produced within the organism but organisms usually need exogenous biomolecules, for example certain nutrients, to survive. Biology and its subfields of biochemistry and molecular biology study biomolecules and their reactions. Most biomolecules are organic compounds, and just four elements—oxygen, carbon, hydrogen, and nitrogen—make up 96% of the human body's mass. B ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Coordination Complex
A coordination complex consists of a central atom or ion, which is usually metallic and is called the ''coordination centre'', and a surrounding array of bound molecules or ions, that are in turn known as ''ligands'' or complexing agents. Many metal-containing compounds, especially those that include transition metals (elements like titanium that belong to the Periodic Table's d-block), are coordination complexes. Nomenclature and terminology Coordination complexes are so pervasive that their structures and reactions are described in many ways, sometimes confusingly. The atom within a ligand that is bonded to the central metal atom or ion is called the donor atom. In a typical complex, a metal ion is bonded to several donor atoms, which can be the same or different. A polydentate (multiple bonded) ligand is a molecule or ion that bonds to the central atom through several of the ligand's atoms; ligands with 2, 3, 4 or even 6 bonds to the central atom are common. These compl ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Catalysis
Catalysis () is the process of increasing the rate of a chemical reaction by adding a substance known as a catalyst (). Catalysts are not consumed in the reaction and remain unchanged after it. If the reaction is rapid and the catalyst recycles quickly, very small amounts of catalyst often suffice; mixing, surface area, and temperature are important factors in reaction rate. Catalysts generally react with one or more reactants to form intermediates that subsequently give the final reaction product, in the process of regenerating the catalyst. Catalysis may be classified as either homogeneous, whose components are dispersed in the same phase (usually gaseous or liquid) as the reactant, or heterogeneous, whose components are not in the same phase. Enzymes and other biocatalysts are often considered as a third category. Catalysis is ubiquitous in chemical industry of all kinds. Estimates are that 90% of all commercially produced chemical products involve catalysts at some st ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
