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Organic Synthesis Software
Computer-assisted organic synthesis software is a type of application software used in organic chemistry in tandem with computational chemistry to help facilitate the tasks of designing, predicting, and producing chemical reactions. CAOS aims to identify a series of chemical reactions which, from a starting compound, can produce a desired molecule. CAOS algorithms typically use two databases: a first one of known chemical reactions and a second one of known starting materials (i.e., typically molecules available commercially). Desirable synthetic plans cost less, have high yield, and avoid using hazardous reactions and intermediates. Typically cast as a planning problem, significant progress has been made in CAOS. CAOS programs M1 RetroScore powered by CAS– demo available, based on ML models trained on CAS SciFinder dat* Syntheseus �* ChemAIRS – demo available, developed bChemical.AIas a commercial suite of software. In addition to retrosynthesis, the tool has some unique ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Application Software
Application software is any computer program that is intended for end-user use not operating, administering or programming the computer. An application (app, application program, software application) is any program that can be categorized as application software. Common types of applications include word processor, media player and accounting software. The term ''application software'' refers to all applications collectively and can be used to differentiate from system and utility software. Applications may be bundled with the computer and its system software or published separately. Applications may be proprietary or open-source. The short term ''app'' (coined in 1981 or earlier) became popular with the 2008 introduction of the iOS App Store, to refer to applications for mobile devices such as smartphones and tablets. Later, with introduction of the Mac App Store (in 2010) and Windows Store (in 2011), the term was extended in popular use to include desktop a ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Molecular Design Software
Molecular design software is notable software for molecular modeling, that provides special support for developing molecular models ''de novo''. In contrast to the usual molecular modeling programs, such as for molecular dynamics and quantum chemistry, such software ''directly'' supports the aspects related to constructing molecular models, including: * Molecular graphics * interactive molecular drawing and conformational editing * building polymeric molecules, crystals, and solvated systems * partial charges development * geometry optimization * support for the different aspects of force field development Comparison of software covering the major aspects of molecular design Notes and references See also {{columns-list, colwidth=30em, * Molecule editor *Molecular modelling * Molecular modeling on GPUs * Protein design *Drug design * Force field (chemistry) * Comparison of force field implementations * Comparison of nucleic acid simulation software *Comparison of softw ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Molecular Modelling Software
A molecule is a group of two or more atoms that are held together by attractive forces known as chemical bonds; depending on context, the term may or may not include ions that satisfy this criterion. In quantum physics, organic chemistry, and biochemistry, the distinction from ions is dropped and ''molecule'' is often used when referring to polyatomic ions. A molecule may be homonuclear, that is, it consists of atoms of one chemical element, e.g. two atoms in the oxygen molecule (O2); or it may be heteronuclear, a chemical compound composed of more than one element, e.g. water (two hydrogen atoms and one oxygen atom; H2O). In the kinetic theory of gases, the term ''molecule'' is often used for any gaseous particle regardless of its composition. This relaxes the requirement that a molecule contains two or more atoms, since the noble gases are individual atoms. Atoms and complexes connected by non-covalent interactions, such as hydrogen bonds or ionic bonds, are typically ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Computational Chemistry Software
A computation is any type of arithmetic or non-arithmetic calculation that is well-defined. Common examples of computation are mathematical equation solving and the execution of computer algorithms. Mechanical or electronic devices (or, historically, people) that perform computations are known as ''computers''. Computer science is an academic field that involves the study of computation. Introduction The notion that mathematical statements should be 'well-defined' had been argued by mathematicians since at least the 1600s, but agreement on a suitable definition proved elusive. A candidate definition was proposed independently by several mathematicians in the 1930s. The best-known variant was formalised by the mathematician Alan Turing, who defined a well-defined statement or calculation as any statement that could be expressed in terms of the initialisation parameters of a Turing machine. Other (mathematically equivalent) definitions include Alonzo Church's '' lambda-definabil ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Organic Chemistry
Organic chemistry is a subdiscipline within chemistry involving the science, scientific study of the structure, properties, and reactions of organic compounds and organic matter, organic materials, i.e., matter in its various forms that contain carbon atoms.Clayden, J.; Greeves, N. and Warren, S. (2012) ''Organic Chemistry''. Oxford University Press. pp. 1–15. . Study of structure determines their structural formula. Study of properties includes Physical property, physical and Chemical property, chemical properties, and evaluation of Reactivity (chemistry), chemical reactivity to understand their behavior. The study of organic reactions includes the organic synthesis, chemical synthesis of natural products, drugs, and polymers, and study of individual organic molecules in the laboratory and via theoretical (in silico) study. The range of chemicals studied chemistry includes hydrocarbons (compounds containing only carbon and hydrogen) as well as compounds based on carbon, but a ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Valence Bond Programs
Valence bond (VB) computer programs for modern valence bond calculations * CRUNCH, by Gordon A. Gallup and his group. * GAMESS (UK), includes calculation of VB wave functions by the TURTLE code, due to J.H. van Lenthe. * GAMESS (US), has links to interface VB2000, and XMVB. * MOLPRO and MOLCAS include code by David L. Cooper for generating Spin Coupled VB wave functions from CASSCF calculations. * 'VB2000'' version 3.0 (released, 2022), by Jiabo Li, Brian Duke, David W. O. de Sousa, Rodrigo S. Bitzer and Roy McWeeny allows the use of Group Function theory, whereby different groups can be handled by different methods (VB or Hartree–Fock). Many types of VB, including spin-coupled VB, and CASVB calculations are possible. It is part of the GAMESS (US) release and can be compiled into the GAMESS(US) executable. There is a more limited stand-alone program. Earlier versions were interfaced to GAUSSIAN. * XMVB (previously known as XIAMEN), by Lingchun Song, Yirong Mo, Qianer Zhang and ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Computational Chemical Methods In Solid State Physics
A computation is any type of arithmetic or non-arithmetic calculation that is well-defined. Common examples of computation are mathematical equation solving and the execution of computer algorithms. Mechanical or electronic devices (or, historically, people) that perform computations are known as ''computers''. Computer science is an academic field that involves the study of computation. Introduction The notion that mathematical statements should be 'well-defined' had been argued by mathematicians since at least the 1600s, but agreement on a suitable definition proved elusive. A candidate definition was proposed independently by several mathematicians in the 1930s. The best-known variant was formalised by the mathematician Alan Turing, who defined a well-defined statement or calculation as any statement that could be expressed in terms of the initialisation parameters of a Turing machine. Other (mathematically equivalent) definitions include Alonzo Church's '' lambda-definabili ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Semi-empirical Quantum Chemistry Methods
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 quantum chemistry methods, ''ab initio'' results. Type of simplifications used Semi-empirical methods follow what are often called empiric ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
List Of Software For Nanostructures Modeling
This is a list of notable computer programs that are used to model nanostructures at the levels of classical mechanics and quantum mechanics. * Furiousatoms - a powerful software for molecular modelling and visualization * Aionics.io - a powerful platform for nanoscale modelling * Ascalaph Designer * Atomistix ToolKit and Virtual NanoLab * CoNTub * CP2K * CST Studio Suite * Deneb – graphical user interface (GUI) for SIESTA, VASP, QE, etc., DFT calculation packages * Enalos Cloud Platform – a cloud platform containing tools for the digital construction of energy minimized nanotubes and ellipsoidal nanoparticles and the calculation of their atomistic descriptors. * Exabyte.io - a cloud-native integrated platform for nanoscale modeling, supporting simulations at multiple scales, including Density Functional Theory and Molecular Dynamics * JCMsuite – a finite element analysis software for simulating optical properties of nanostructures * LAMMPS – Open source molecu ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Molecular Modeling On GPU
Molecular modeling on GPU is the technique of using a graphics processing unit (GPU) for molecular simulations. In 2007, Nvidia introduced video cards that could be used not only to show graphics but also for scientific calculations. These cards include many arithmetic units (, up to 3,584 in Tesla P100) working in parallel. Long before this event, the computational power of video cards was purely used to accelerate graphics calculations. The new features of these cards made it possible to develop parallel programs in a high-level application programming interface (API) named CUDA. This technology substantially simplified programming by enabling programs to be written in C/ C++. More recently, OpenCL allows cross-platform GPU acceleration. Quantum chemistry calculations and molecular mechanics simulations (molecular modeling in terms of classical mechanics) are among beneficial applications of this technology. The video cards can accelerate the calculations tens of times, so a ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Molecule Editor
A notable molecule editor is a computer program for creating and modifying representations of chemical structures. Molecule editors can manipulate chemical structure representations in either a simulated two-dimensional space or three-dimensional space, via 2D computer graphics or 3D computer graphics, respectively. Two-dimensional output is used as illustrations or to query chemical databases. Three-dimensional output is used to build molecular models, usually as part of molecular modelling software packages. Database molecular editors such as Leatherface, RECAP, and Molecule Slicer allow large numbers of molecules to be modified automatically according to rules such as 'deprotonate carboxylic acids' or 'break exocyclic bonds' that can be specified by a user. Molecule editors typically support reading and writing at least one file format or line notation. Examples of each include Molfile and simplified molecular input line entry specification (SMILES), respectively. Files ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Comparison Of Software For Molecular Mechanics Modeling
This is a list of computer programs that are predominantly used for molecular mechanics calculations. See also *Car–Parrinello molecular dynamics *Comparison of force-field implementations *Comparison of nucleic acid simulation software *List of molecular graphics systems *List of protein structure prediction software *List of quantum chemistry and solid-state physics software *List of software for Monte Carlo molecular modeling *List of software for nanostructures modeling *Molecular design software *Molecular dynamics *Molecular modeling on GPUs *Molecule editor *PyMOL Notes and references External linksSINCRIS [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
