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A water molecule drawn with a shaded electrostatic potential isosurface. The areas highlighted in red have a net positive charge density, and the blue areas have a negative charge. In some models, the surface of the molecule is approximated and shaded to represent a physical property of the molecule, such as electronic charge density. [39] [40]
In chemical graph theory and in mathematical chemistry, a molecular graph or chemical graph is a representation of the structural formula of a chemical compound in terms of graph theory. A chemical graph is a labeled graph whose vertices correspond to the atoms of the compound and edges correspond to chemical bonds .
The creation of mathematical models of molecular properties and behavior is referred to as molecular modeling, and their graphical depiction is referred to as molecular graphics. The term, "molecular model" refer to systems that contain one or more explicit atoms (although solvent atoms may be represented implicitly) and where nuclear structure ...
Theories of chemical structure were first developed by August Kekulé, Archibald Scott Couper, and Aleksandr Butlerov, among others, from about 1858. [4] These theories were first to state that chemical compounds are not a random cluster of atoms and functional groups, but rather had a definite order defined by the valency of the atoms composing the molecule, giving the molecules a three ...
[1] [2] [3] Introduced by Gilbert N. Lewis in his 1916 article The Atom and the Molecule, a Lewis structure can be drawn for any covalently bonded molecule, as well as coordination compounds. [4] Lewis structures extend the concept of the electron dot diagram by adding lines between atoms to represent shared pairs in a chemical bond.
In molecular physics, the molecular term symbol is a shorthand expression of the group representation and angular momenta that characterize the state of a molecule, i.e. its electronic quantum state which is an eigenstate of the electronic molecular Hamiltonian. It is the equivalent of the term symbol for the atomic case.
Jmol is an open-source Java-based viewer for browsing molecular structures on the web; it includes a simplified "cartoon" version of ribbons. Other graphics programs such as DeepView (example: urease) and MolMol (example: SH2 domain) also produce ribbon images. KiNG [11] is the Java-based successor to Mage (examples: α-hemolysin top view and ...
The most accurate way to solvate a system is to place explicit water molecules in the simulation box with the molecules of interest and treat the water molecules as interacting particles like those in the other molecule(s). A variety of water models exist with increasing levels of complexity, representing water as a simple hard sphere (a united ...