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A water molecule in the first solvation shell of an aqua ion may exchange places with a water molecule in the bulk solvent. It is usually assumed that the rate-determining step is a dissociation reaction. [M(H 2 O) n] z+ → [M(H 2 O) n-1] z+ * + H 2 O. The * symbol signifies that this is the transition state in a chemical reaction. The rate of ...
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 +
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.
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.
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.
Spartan applies computational chemistry methods (theoretical models) to many standard tasks that provide calculated data applicable to the determination of molecular shape conformation, structure (equilibrium and transition state geometry), NMR, IR, Raman, and UV-visible spectra, molecular (and atomic) properties, reactivity, and selectivity.
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.
The Free Ion Activity Model is well-established in the literature, and shows that just micromolar amounts of the free ion kills some organisms. A recent example showed 6 micromolar killing 93% of all Daphnia in water. [245] The free zinc ion is a powerful Lewis acid up to the point of being corrosive.