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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 is neglected. The electronic structure is often also omitted unless it is necessary in illustrating the function of the molecule being modeled.
A water model is defined by its geometry, together with other parameters such as the atomic charges and Lennard-Jones parameters. In computational chemistry, a water model is used to simulate and thermodynamically calculate water clusters, liquid water, and aqueous solutions with explicit solvent, often using molecular dynamics or Monte Carlo methods.
Molecular modelling encompasses all methods, theoretical and computational, used to model or mimic the behaviour of molecules. [1] The methods are used in the fields of computational chemistry, drug design, computational biology and materials science to study molecular systems ranging from small chemical systems to large biological molecules and material assemblies.
In fact the low-molecular weight compounds will ignite spontaneously on contact with air and are immediately destroyed by reaction with water molecules. The use of zinc alkyls has been largely superseded by the use of the more easily handled Grignard reagents. This demonstrates yet another connection between the chemistries of zinc and magnesium.
For example, Marsh et al. (2005) used dual labeled (15 N- and 14 C) urea to demonstrate utilization of the compound by ammonia oxidizers as both an energy source (ammonia oxidation) and carbon source (chemoautotrophic carbon fixation). [36] Deuterated water is also used for tracing the fate and ages of water in a tree [37] or in an ecosystem. [38]
Some inorganic solids dissociate - or crack - into molecular species heating or upon dissolving, e.g. Aluminium chloride. In such cases it is helpful to depict both the molecular and the nonmolecular forms. Some important chemical species cannot be easily represented with simple pictures, e.g. hydrochloric acid and non-stoichiometric compounds.
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]