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Ascalaph Designer
Ascalaph Designer is a computer program for general purpose molecular modelling for molecular design and simulations. It provides a graphical environment for the common programs of quantum and classical molecular modelling ORCA, NWChem, Firefly, CP2K and MDynaMix . The molecular mechanics calculations cover model building, energy optimizations and molecular dynamics. Firefly (formerly named PC GAMESS) covers a wide range of quantum chemistry methods. Ascalaph Designer is free and open-source software, released under the GNU General Public License, version 2 (GPLv2). Key features Uses See also * List of software for molecular mechanics modeling * Molecular design software * Molecule editor * Abalone Abalone ( or ; via Spanish , from Rumsen ''aulón'') is a common name for any of a group of small to very large marine gastropod molluscs in the family (biology), family Haliotidae. Other common name In biology, a common name of a taxon o ... References Exter ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Microsoft Windows
Windows is a group of several Proprietary software, proprietary graphical user interface, graphical operating system families developed and marketed by Microsoft. Each family caters to a certain sector of the computing industry. For example, Windows NT for consumers, Windows Server for servers, and Windows IoT for embedded systems. Defunct Windows families include Windows 9x, Windows Mobile, and Windows Phone. The first version of Windows was released on November 20, 1985, as a graphical operating system shell for MS-DOS in response to the growing interest in graphical user interfaces (GUIs). Windows is the most popular desktop operating system in the world, with Usage share of operating systems, 75% market share , according to StatCounter. However, Windows is not the most used operating system when including both mobile and desktop OSes, due to Android (operating system), Android's massive growth. , the most recent version of Windows is Windows 11 for consumer Personal compu ... [...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 A file format is a Computer standard, standard way that information is encoded for storage in a computer file. It specifies how bits are used t ... [...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 softwar ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
List 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] |
Acetonitrile
Acetonitrile, often abbreviated MeCN (methyl cyanide), is the chemical compound with the formula and structure . This colourless liquid is the simplest organic nitrile (hydrogen cyanide is a simpler nitrile, but the cyanide anion is not classed as organic). It is produced mainly as a byproduct of acrylonitrile manufacture. It is used as a polar aprotic solvent in organic synthesis and in the purification of butadiene. The skeleton is linear with a short distance of 1.16 Å. Acetonitrile was first prepared in 1847 by the French chemist Jean-Baptiste Dumas. Applications Acetonitrile is used mainly as a solvent in the purification of butadiene in refineries. Specifically, acetonitrile is fed into the top of a distillation column filled with hydrocarbons including butadiene, and as the acetonitrile falls down through the column, it absorbs the butadiene which is then sent from the bottom of the tower to a second separating tower. Heat is then employed in the separatin ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Ionic Liquid
An ionic liquid (IL) is a salt in the liquid state. In some contexts, the term has been restricted to salts whose melting point is below a specific temperature, such as . While ordinary liquids such as water and gasoline are predominantly made of electrically neutral molecules, ionic liquids are largely made of ions. These substances are variously called liquid electrolytes, ionic melts, ionic fluids, fused salts, liquid salts, or ionic glasses. Ionic liquids have many potential applications. They are powerful solvents and can be used as electrolytes. Salts that are liquid at near-ambient temperature are important for electric battery applications, and have been considered as sealants due to their very low vapor pressure. Any salt that melts without decomposing or vaporizing usually yields an ionic liquid. Sodium chloride (NaCl), for example, melts at into a liquid that consists largely of sodium cations () and chloride anions (). Conversely, when an ionic liquid is cooled ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Polyelectrolyte
Polyelectrolytes are polymers whose repeating units bear an electrolyte group. Polycations and polyanions are polyelectrolytes. These groups dissociate in aqueous solutions (water), making the polymers charged. Polyelectrolyte properties are thus similar to both electrolytes (salts) and polymers (high molecular weight compounds) and are sometimes called polysalts. Like salts, their solutions are electrically conductive. Like polymers, their solutions are often viscous. Charged molecular chains, commonly present in soft matter systems, play a fundamental role in determining structure, stability and the interactions of various molecular assemblies. Theoretical approaches to describing their statistical properties differ profoundly from those of their electrically neutral counterparts, while technological and industrial fields exploit their unique properties. Many biological molecules are polyelectrolytes. For instance, polypeptides, glycosaminoglycans, and DNA are polyelectrolytes ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Lipid Bilayer
The lipid bilayer (or phospholipid bilayer) is a thin polar membrane made of two layers of lipid molecules. These membranes are flat sheets that form a continuous barrier around all cells. The cell membranes of almost all organisms and many viruses are made of a lipid bilayer, as are the nuclear membrane surrounding the cell nucleus, and membranes of the membrane-bound organelles in the cell. The lipid bilayer is the barrier that keeps ions, proteins and other molecules where they are needed and prevents them from diffusing into areas where they should not be. Lipid bilayers are ideally suited to this role, even though they are only a few nanometers in width, because they are impermeable to most water-soluble ( hydrophilic) molecules. Bilayers are particularly impermeable to ions, which allows cells to regulate salt concentrations and pH by transporting ions across their membranes using proteins called ion pumps. Biological bilayers are usually composed of amphiphilic ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Protein
Proteins are large biomolecules and macromolecules that comprise one or more long chains of amino acid residues. Proteins perform a vast array of functions within organisms, including catalysing metabolic reactions, DNA replication, responding to stimuli, providing structure to cells and organisms, and transporting molecules from one location to another. Proteins differ from one another primarily in their sequence of amino acids, which is dictated by the nucleotide sequence of their genes, and which usually results in protein folding into a specific 3D structure that determines its activity. A linear chain of amino acid residues is called a polypeptide. A protein contains at least one long polypeptide. Short polypeptides, containing less than 20–30 residues, are rarely considered to be proteins and are commonly called peptides. The individual amino acid residues are bonded together by peptide bonds and adjacent amino acid residues. The sequence of amino acid resid ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Nucleic Acid
Nucleic acids are biopolymers, macromolecules, essential to all known forms of life. They are composed of nucleotides, which are the monomers made of three components: a 5-carbon sugar, a phosphate group and a nitrogenous base. The two main classes of nucleic acids are deoxyribonucleic acid (DNA) and ribonucleic acid (RNA). If the sugar is ribose, the polymer is RNA; if the sugar is the ribose derivative deoxyribose, the polymer is DNA. Nucleic acids are naturally occurring chemical compounds that serve as the primary information-carrying molecules in cells and make up the genetic material. Nucleic acids are found in abundance in all living things, where they create, encode, and then store information of every living cell of every life-form on Earth. In turn, they function to transmit and express that information inside and outside the cell nucleus to the interior operations of the cell and ultimately to the next generation of each living organism. The encoded informatio ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Flexible SPC Water Model
In computational chemistry, a water model is used to simulate and thermodynamically calculate water clusters, liquid water, and aqueous solutions with explicit solvent. The models are determined from quantum mechanics, molecular mechanics, experimental results, and these combinations. To imitate a specific nature of molecules, many types of models have been developed. In general, these can be classified by the following three points; (i) the number of interaction points called ''site'', (ii) whether the model is rigid or flexible, (iii) whether the model includes polarization effects. An alternative to the explicit water models is to use an implicit solvation model, also termed a continuum model, an example of which would be the COSMO solvation model or the polarizable continuum model (PCM) or a hybrid solvation model. Simple water models The rigid models are considered the simplest water models and rely on non-bonded interactions. In these models, bonding interactions are impl ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Optimization (mathematics)
Mathematical optimization (alternatively spelled ''optimisation'') or mathematical programming is the selection of a best element, with regard to some criterion, from some set of available alternatives. It is generally divided into two subfields: discrete optimization and continuous optimization. Optimization problems of sorts arise in all quantitative disciplines from computer science and engineering to operations research and economics, and the development of solution methods has been of interest in mathematics for centuries. In the more general approach, an optimization problem consists of maximizing or minimizing a real function by systematically choosing input values from within an allowed set and computing the value of the function. The generalization of optimization theory and techniques to other formulations constitutes a large area of applied mathematics. More generally, optimization includes finding "best available" values of some objective function given a ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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