20 research outputs found

    Thermodynamically Dominant Hydration Structures of Ions and their Role in Ion-Specificity

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    Thermodynamic Principles of Metal Binding to Biological Systems

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    Mini-grand canonical ensemble: chemical potential in the solvation shell

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    Quantifying the statistics of occupancy of solvent molecules in the vicinity of solutes is central to our understanding of solvation phenomena. Number fluctuations in small `solvation shells' around solutes cannot be described within the macroscopic grand canonical framework using a single chemical potential that represents the solvent `bath'. In this communication, we hypothesize that molecular-sized observation volumes such as solvation shells are best described by coupling the solvation shell with a mixture of particle baths each with its own chemical potential. We confirm our hypotheses by studying the enhanced fluctuations in the occupancy statistics of hard sphere solvent particles around a distinguished hard sphere solute particle. Connections with established theories of solvation are also discussed

    Role of Internal Motions and Molecular Geometry on the NMR Relaxation of Hydrocarbons

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    The role of internal motions and molecular geometry on 1^1H NMR relaxation times T1,2T_{1,2} in hydrocarbons is investigated using MD (molecular dynamics) simulations of the autocorrelation functions for in{\it tra}molecular GR(t)G_R(t) and in{\it ter}molecular GT(t)G_T(t) 1^1H-1^1H dipole-dipole interactions arising from rotational (RR) and translational (TT) diffusion, respectively. We show that molecules with increased molecular symmetry such as neopentane, benzene, and isooctane show better agreement with traditional hard-sphere models than their corresponding straight-chain nn-alkane, and furthermore that spherically-symmetric neopentane agrees well with the Stokes-Einstein theory. The influence of internal motions on the dynamics and T1,2T_{1,2} relaxation of nn-alkanes are investigated by simulating rigid nn-alkanes and comparing with flexible (i.e. non-rigid) nn-alkanes. Internal motions cause the rotational and translational correlation-times Ο„R,T\tau_{R,T} to get significantly shorter and the relaxation times T1,2T_{1,2} to get significantly longer, especially for longer-chain nn-alkanes. Site-by-site simulations of 1^1H's along the chains indicate significant variations in Ο„R,T\tau_{R,T} and T1,2T_{1,2} across the chain, especially for longer-chain nn-alkanes. The extent of the stretched (i.e. multi-exponential) decay in the autocorrelation functions GR,T(t)G_{R,T}(t) are quantified using inverse Laplace transforms, for both rigid and flexible molecules, and on a site-by-site bases. Comparison of T1,2T_{1,2} measurements with the site-by-site simulations indicate that cross-relaxation (partially) averages-out the variations in Ο„R,T\tau_{R,T} and T1,2T_{1,2} across the chain of long-chain nn-alkanes. This work also has implications on the role of nano-pore confinement on the NMR relaxation of fluids in the organic-matter pores of kerogen and bitumen

    Local Contributions to Free Energy Changes

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    Apolar Behavior of Hydrated Calcite (10{-1}4) Surface Assists in Naphthenic Acid Adsorption

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    Water molecules bind strongly to the polar calcite surface and form a surface adsorbed layer that has properties akin to an apolar surface. This has important implications for understanding the thermodynamic driving forces underlying the adsorption of acid groups from crude oil, in particular naphthenic acid, onto calcite. Free energy calculations show that naphthenic acid binds favorably to the water mono-layer adsorbed on the calcite surface. But to bond directly to the calcite, a free energy barrier has to be overcome to expel the intervening layer of water. Further, naphthenic acids with longer alkyl chains bind with lower free energy to the calcite surface than those with shorter alkyl chains, and, for the same chain length, branching also enhances adsorption. To better understand this behavior, for a specified alkyl chain length we study adsorption at different temperatures. Consistent with experiments, we find that adsorption is enhanced at higher temperatures. Examining the enthalpic and entropic contributions to adsorption shows that adsorption of naphthenic acid is entropically favored.<br /
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