Other typical solvent properties and indicators

Essential for MD simulations of nucleic acids is a proper representation of the solvent environment. This typically requires the use of an explicit solvent representation that includes counterions. Examples exist of DNA simulations performed in the absence of counterions [24], but these are rare. In most cases neutralizing salt concentrations, in which only the number of counterions required to create an electrically neutral system are included, are used. In other cases excess salt is used, and both counterions and co-ions are included [30]. Though this approach should allow for systematic smdies of the influence of salt concentration on the properties of oligonucleotides, calculations have indicated that the time required for ion distributions around DNA to properly converge are on the order of 5 ns or more [31]. This requires that preparation of nucleic acid MD simulation systems include careful consideration of both solvent placement and the addition of ions. 

The digestion and absorption of organic and inorganic nutrients, as well as all other biochemical processes in living organisms, are influenced by the unique properties of water. Water is an interactive liquid or solvent. Its chemical interactions with solutes are called hydration. Hydration involves weak associations of water molecules with other molecules or ions, such as Na+, Cl , starch, or protein. Because hydration bonding is weak and transitory, the number of water molecules associated with an ion or molecule at any particular moment is approximate and difficult to measure. However, typical indicated hydration numbers are Na", 1-2 K+, 2 Mg2+, 4-10 4r-8 Zn2+, 4-10 Fe, 10 Q- 1 and F-, 4 (Conway, 1981). 

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