Molecular dynamicdfree energy perturbation simulations of several small amides [acetamide (ACT), N-methylacetamide (NMA), and N,N-dimethylacetamide] and amines [NH3, NH2CH3, NH(CH3)2, and N(CH3)3] in aqueous solution were performed to study the effects on solvation free energies arising from N-methylation. Using pairwise additive potentials, a uniform pattern of solvation effects was always obt...

The time-dependent fluorescence of a model dye molecule in a nanoconfined solvent is used to test approximations based on the dynamic and static linear-response theories and the assumption of Gaussian statistics. Specifically, the results of nonequilibrium molecular-dynamics simulations are compared to approximate expressions involving time correlation functions obtained from equilibrium simula...

We address the response of a random heteropolymer to preferential solvation of certain monomer types at the globule-solvent interface. For each set of monomers that can comprise the molecule's surface, we represent the ensemble of allowed configurations by a Gaussian distribution of energy levels, whose mean and variance depend on the set's composition. Within such a random energy model, mean s...

The feasibility of extractive reaction of methacrylic acid from aqueous solution using a quaternary amine, tri–octyl methyl ammonium chloride (TOMAC) as an extractant, was studied. The diluents chosen in the present work belong to different chemical classes, n–butyl acetate, carbon tetrachloride, isoamyl alcohol, methyl isobutyl ketone, and toluene. The effect of initial acid concentration in t...

The free energy of solvation, DeltaGS0, in octanol of organic compounds is quantitatively predicted from the molecular structure. The model, involving only three molecular descriptors, is obtained by multiple linear regression analysis from a data set of 147 compounds containing diverse organic functions, namely, halogenated and non-halogenated alkanes, alkenes, alkynes, aromatics, alcohols, al...

Tetrahydroimidazo-[4,5,l-jk][1,4]-benzodiazepin-2-(1H)-one (TIBO) derivatives are important nonnucleoside human immunodeficiency virus-1 reverse transcriptase inhibitors (NNRTI). Several TIBO derivatives have shown high potency to inhibit reverse transcriptase (RT) and one (Tivirapine) has entered into clinical trials. The free energy of binding (FEB) is a numerical way to express the binding a...

The solvation energy and entropy at infinite dilution consist of a solute-solvent term and a solvent reorganization term representing the contributions of changes in solvent structure upon solute insertion. In the standard, homogeneous treatment of solutions, changes in solvent structure are expressed through derivatives of the homogeneous pair correlation function, which are very difficult to ...

Continuum solvent models predict a quadratic charge dependence (linear response) of the free energy of a system of charged solutes. The relation between this prediction and the structure of the solvation shell around the solutes is discussed. Studies of the derivative of the free energy with respect to the charges for different reference states are shown to be a convenient way of testing the li...

An algorithm is developed for performing calculations for the nonlocal electrostatic solvation theory of an ion in a cavity, accounting for electrostatic boundary conditions. The latter implies an induced charge distribution on the cavity surface as well as an induced volume charge distribution in the medium. This approach is validated by a variational derivation which also provides a general e...

RNA cleavage transesterification is of fundamental reaction in biology that is catalyzed by both protein and RNA enzymes. In this work, a series of RNA transesterification model reactions with a wide range of leaving groups are investigated with density-functional calculations in an aqueous solvation environment in order to study linear free energy relationships (LFERs) and their connection to ...