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List Of Computer-assisted Organic Synthesis Software
Computer software for computer-assisted organic synthesis (CAOS) are 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. Examples of CAOS applications include: * Spaya Retrosynthesis planning tool freely accessible provided by Iktos* IBM Rxn * AiZynthFinder A freely accessible open source retrosynthetic planning tooldeveloped as a collaboration between AstraZeneca and the University of Bern. AiZyn ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Software
Software is a set of computer programs and associated documentation and data. This is in contrast to hardware, from which the system is built and which actually performs the work. At the lowest programming level, executable code consists of machine language instructions supported by an individual processor—typically a central processing unit (CPU) or a graphics processing unit (GPU). Machine language consists of groups of binary values signifying processor instructions that change the state of the computer from its preceding state. For example, an instruction may change the value stored in a particular storage location in the computer—an effect that is not directly observable to the user. An instruction may also invoke one of many input or output operations, for example displaying some text on a computer screen; causing state changes which should be visible to the user. The processor executes the instructions in the order they are provided, unless it is instructed ... [...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 software for ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Molecular Modelling Software
A molecule is a group of two or more atoms held together by attractive forces known as chemical bonds; depending on context, the term may or may not include ions which 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 not considere ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Computational Chemistry Software
Computation is any type of arithmetic or non-arithmetic calculation that follows a well-defined model (e.g., an algorithm). Mechanical or electronic devices (or, historically, people) that perform computations are known as ''computers''. An especially well-known discipline of the study of computation is computer science. Physical process of Computation Computation can be seen as a purely physical process occurring inside a closed physical system called a computer. Examples of such physical systems are digital computers, mechanical computers, quantum computers, DNA computers, molecular computers, microfluidics-based computers, analog computers, and wetware computers. This point of view has been adopted by the physics of computation, a branch of theoretical physics, as well as the field of natural computing. An even more radical point of view, pancomputationalism (inaudible word), is the postulate of digital physics that argues that the evolution of the universe is itself a ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Organic Chemistry
Organic chemistry is a subdiscipline within chemistry involving the scientific study of the structure, properties, and reactions of organic compounds and 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 and chemical properties, and evaluation of chemical reactivity to understand their behavior. The study of organic reactions includes the 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 in organic chemistry includes hydrocarbons (compounds containing only carbon and hydrogen) as well as compounds based on carbon, but also containing other elements, especially oxygen, nitrogen, sulfur, phosphorus (included in ... [...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 2.7 (released, 2014), by Jiabo Li, Brian Duke 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 Wei Wu. This allows several VB methods, i ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Computational Chemical Methods In Solid State Physics
Computational chemical methods in solid-state physics follow the same approach as they do for molecules, but with two differences. First, the translational symmetry of the solid has to be utilised, and second, it is possible to use completely delocalised basis functions such as plane waves as an alternative to the molecular atom-centered basis functions. The electronic structure of a crystal is in general described by a band structure, which defines the energies of electron orbitals for each point in the Brillouin zone. Ab initio and semi-empirical calculations yield orbital energies, therefore they can be applied to band structure calculations. Since it is time-consuming to calculate the energy for a molecule, it is even more time-consuming to calculate them for the entire list of points in the Brillouin zone. Calculations can use the Hartree–Fock method, some post-Hartree–Fock methods, particularly Møller–Plesset perturbation theory to second order (MP2) and d ... [...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'' results. Type of simplifications used Semi-empirical methods follow what are often called empirical methods where the two-electron p ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
List Of Software For Nanostructures Modeling
This is a list of 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 * 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 molecular dynamics codeMAPS- Graphical user interface to build complex systems (nanostructures, polymers, surfaces...), set up and analyze ab-initio (Quantum Espresso, VASP, Abinit, NWChem...) or classical (LAMMPS, Towhee) simulati ... [...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 dynamics, 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. What was new is that NVIDIA 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 (programming language), 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 accelerat ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Molecule Editor
A 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 generated by ... [...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 A 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, v ... Notes and references External linksSINCRIS [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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