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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.
When carbon dioxide enters the active site, it subject to nucleophilic attack by the oxygen atom which carries a partial negative charge, or indeed a full negative charge if the water molecule is dissociated. The CO 2 is rapidly converted into a bicarbonate ion. [23] [(-hys) 3 Zn(H 2 O)] 2+ + CO 2 → [(-hys) 3 Zn] 2+ + HCO 3 − + H +
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]
A plastic ball-and-stick model of proline. In chemistry, the ball-and-stick model is a molecular model of a chemical substance which displays both the three-dimensional position of the atoms and the bonds between them. [1] The atoms are typically represented by spheres, connected by rods which represent the bonds.
Draw the structure in your molecule editor, and save it as a Windows Metafile (.wmf), Enhanced Metafile (.emf), or Encapsulated Postscript (.eps). Open the saved file in Inkscape. Resize the picture about 400%, then click to File→Document Properties→Fit page to selection. Select the molecule and click Path→Object to path.