| Abstract
| - Transport properties (translational and rotational) of water in the two grooves of the B-DNA duplex areknown to be different from those in the bulk. Here, we use a recently developed theoretical scheme to computethe entropies of water molecules in both of the grooves of DNA and compare them with that in the bulk. Thescheme requires as input both translational and rotational velocity autocorrelation function (CV(t) and Cω(t),respectively) data. These velocity autocorrelation functions were computed from an atomistic MD simulationof a B-DNA duplex (36 base pairs long) in explicit water (TIP3P). The average values of the entropy ofwater at 300 K in both of the grooves of DNA (the TS value in the major groove is 6.71 kcal/mol and thatin the minor groove is 6.41 kcal/mol) are found to be significantly lower than that in bulk water (the TS valueis 7.27 kcal/mol). Thus, the entropic contribution to the free energy change (TΔS) of transferring a minorgroove water molecule to the bulk is 0.86 kcal/mol and of transferring a major groove water to the bulk is0.56 kcal/mol at 300 K, which is to be compared with 1.44 kcal/mol for melting of ice at 273 K. We alsocalculate the energy of interaction of each water molecule with the rest of the atoms in the system and hencecalculate the chemical potential (Helmholtz free energy per water molecule, A = E − TS) in the differentdomains. The identical free energy value of water molecules in the different domains proves the robustnessof the scheme. We propose that the configurational entropy of water in the grooves can be used as a measureof the mobility (or microviscosity) of water molecules in a given domain.
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