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A three-dimensional interaction force mapping experiment was carried out on a muscovite mica surface in an aqueous solution using a high-resolution and low-thermal drift frequency-modulation atomic force microscope. By collecting oscillatory frequency shift versus distance curves at the mica/solution interface, complicated hydration structures on the mica surface were visualized. Reconstructed two-dimensional frequency shift maps showed dot-like or honeycomb-like patterns at different tip-sample distances with a separation of 0.2 nm with each other, which agree well to the water molecule density maps predicted by a statistical-mechanical theory. Moreover, site-specific force versus distance curves showed a good agreement with theoretically calculated site-specific force curves by a molecular dynamics simulation. It is found that the first and second hydration layers give honeycomb-like and dot-like patterns in the two-dimensional frequency shift images, respectively, corresponding to the lateral distribution function in each layer. [ABSTRACT FROM AUTHOR]

Hydration structures at biomolecular surfaces are essential for understanding the mechanisms of the various biofunctions and stability of biomolecules. Here, we demonstrate the measurement of local hydration structures using an atomic force microscopy system equipped with a low-noise deflection sensor. We applied this method to the analysis of the muscovite mica/water interface and succeeded in visualizing a hydration structure that is site-specific on a crystal. Furthermore, at the biomolecule/buffer solution interface, we found surface hydration layers that are more packed than those at the muscovite mica/water interface. [ABSTRACT FROM AUTHOR]

Three dimensional (3D) hydration structure is informative to clarify the functions of hydrated waters around a protein. We develop a new approach to calculate 3D solvation structure with reasonable computational cost. In the present method, the total solvation structure is obtained using conventional one dimensional reference interaction site model (RISM) followed by integrating the 3D fragment data, which are evaluated around each atom (site) of solute. Thanks to this strategy, time-consuming 3D fast Fourier transformation, which is required in 3D-RISM theory, can be avoided and high-parallel performance is achieved. The method is applied to small molecular systems for comparison with 3D-RISM. The obtained results by the present method and by 3D-RISM show good agreement. The hydration structures for a large protein computed by the present method are also consistent with those obtained by x-ray crystallography. [ABSTRACT FROM AUTHOR]

The partial molar volume changes in the transfer of several hydrophobic molecules, which are composed of aromatic rings and an aliphatic chain of different lengths, from carbon tetrachloride to water (ΔVhyd) are calculated using the three-dimensional interaction site model theory of molecular solvation. The theory reproduces recent experimental observations: the addition of a methyl group decreases ΔVhyd; in contrast, the addition of an aromatic ring increases ΔVhyd. The discrepancy is found to originate from the difference between chain and ring structures rather than that between aliphaticity and aromaticity. Furthermore, a general rule of the variation in ΔVhyd due to the addition of a hydrocarbon is found through the theoretical analysis. An outward addition at the trans position, which is to form chain structure, decreases ΔVhyd, while an inward addition at the cis position, which is to form ring structure, increases ΔVhyd. This is explained in terms of solvent packing rather than the so-called hydrophobic hydration. The present findings argue against the traditional idea that the hydrophobic hydration can be represented by the observed values of ΔVhyd. [ABSTRACT FROM AUTHOR]

The free energy change associated with the coil-to-native structural transition of protein G in aqueous solution is calculated by using the molecular theory of solvation, also known as the three-dimensional reference interaction site model theory, to uncover the molecular mechanism of protein folding. The free energy is decomposed into the protein intramolecular energy, the hydration energy, and the hydration entropy. The folding is accompanied with a large gain in the protein intramolecular energy. However, it is almost canceled by the correspondingly large loss in the hydration energy due to the dehydration, resulting in the total energy gain about an order of magnitude smaller than might occur in vacuum. The hydration entropy gain is found to be a substantial driving force in protein folding. It is comparable with or even larger than the total energy gain. The total energy gain coupled with the hydration entropy gain is capable of suppressing the conformational entropy loss in the folding. Based on careful analysis of the theoretical results, the authors present a challenging physical picture of protein folding where the overall folding process is driven by the water entropy effect. [ABSTRACT FROM AUTHOR]

The hydration free energy (HFE) of several proteins modeled using the all-atom force field is calculated by employing the three-dimensional reference interaction site model theory, a recently developed integral equation theory of molecular solvation. The HFE is decomposed into the energetic and entropic components under the isochoric condition. The former comprises the protein-water interaction energy and the water reorganization energy arising from the structural changes induced in water. Each component is further decomposed into the nonelectrostatic and electrostatic contributions. It is found that the HFE is governed by the nonelectrostatic hydration entropy and the electrostatic hydration energy. The nonelectrostatic hydration entropy is almost exclusively ascribed to the translational entropy loss of water upon the protein insertion. It asymptotically becomes proportional to the excluded volume (EV) for water molecules as the protein size increases. The hydration energy is determined by the protein-water interaction energy which is half compensated by the water reorganization energy. These energy terms are approximately proportional to the water-accessible surface area (ASA). The energetic and entropic contributions are balanced with each other and the HFE has no apparent linear relation with the EV and ASA. [ABSTRACT FROM AUTHOR]

The hydrophobic effects on partial molar volume (PMV) are investigated as a PMV change in the transfer of a benzenelike nonpolar solute from the nonpolar solvent to water, using an integral equation theory of liquids. The volume change is divided into two effects. One is the “packing” effect in the transfer from the nonpolar solvent to hypothetical “nonpolar water” without hydrogen bonding networks. The other is the “iceberg” effect in the transfer from nonpolar water to water. The results indicate that the packing effect is negative and a half compensated by the positive iceberg effect. The packing effect is explained by the difference in the solvent compressibility. Further investigation shows that the sign and magnitude of the volume change depend on the solute size and the solvent compressibility. The finding gives a significant implication that the exposure of a hydrophobic residue caused by protein denaturation can either increase or decrease the PMV of protein depending on the size of the residue and the fluctuation of its surroundings. [ABSTRACT FROM AUTHOR]

Statistical mechanical expressions for the partial molar volume (PMV) and the partial molar compressibility (PMC) of a solute molecule with internal degrees of freedom are derived. The equilibrium PMV is expressed simply by the conformational ensemble average of PMV. The equilibrium PMC consists of two terms: the conformational ensemble average of PMC and the mean square fluctuation of PMV along conformational axis. As an illustrative application of the theory, the equilibrium PMV and PMC of butane in aqueous solution are calculated from the relations, in which the thermodynamic quantities of each conformer appearing in the relations are obtained by the reference interaction site model theory. The conformational ensemble average of PMC is the predominant contribution to the equilibrium PMC in this particular example. Possibility of shedding light on the protein conformation in terms of PMV and PMC is discussed. © 2003 American Institute of Physics. [ABSTRACT FROM AUTHOR]

A Kirkwood-Buff equation for the partial molar volumes of polyatomic molecules in solutions is derived based on the reference interaction site model (RISM) theory of molecular liquids. The partial molar volume of the twenty amino acids in aqueous solution at infinite dilution are calculated using the equation, and the results are discussed in comparison with the experimental data. The results indicate that ionizations of the C- and N-terminus groups give negative contributions to the volume ranging from -3.2 cm[sup 3]/mol to -9.7 cm[sup 3]/mol depending on the amino acid. Ionization of the dissociable residues also give negative contribution which ranges from -3.0 cm[sup 3]/mol to -6.0 cm[sup 3]/mol. On the other hand, contribution of the fractional charges on atoms to the volume is not necessarily negative, but rather slightly positive with few exceptions. It is clarified that contribution from an atom group to the volume is largely dependent on the situation where the group is placed. Therefore, it is concluded that the conventional way of determining the partial molar volume from group contributions is not reliable. The theoretical results for the partial molar volume exhibit a systematic deviation from corresponding experimental data, which increases nearly proportionally with increasing temperature and with the number of atoms in the amino acids. In order to account for the deviation, a concept of the "ideal fluctuation volume" is proposed, which is the ideal gas contribution to the volume, originating from the intramolecular fluctuation of solute. © 2000 American Institute of Physics. [ABSTRACT FROM AUTHOR]

In the Comment on our paper [J. Chem. Phys. 123, 167103 (2005), preceding paper], Graziano argues based on the scaled particle theory that the partial molar volume change in the transfer of a hydrophobic solute from “hypothetical nonpolar water” to water can be explained simply by the difference in the effective size of solvent molecules. Opposing to the argument, we clarify using the reference interaction site model theory that the attractive interactions represented by the hydrogen bonding play an essential role for the volume change, and that the explanation given by Graziano replaces the real physics by a fake model based on an “effective” molecular diameter. We also make a general argument against the use of hard-sphere models when one considers the properties of hydration. [ABSTRACT FROM AUTHOR]

An integral equation for rigid-body molecules with respect to site-density distribution function under arbitrary external fields is derived by the density-functional theory. Using a grand canonical partition function of molecular systems, we extend original Percus’ idea to molecular fluids. The extended Percus’ idea provides a relation between the site–site pair distribution function and site–density distribution function under an external field composed of the site–site interaction potentials of a molecule fixed at the origin. The site–density integral equation combined with the extended Percus’ relation to molecular fluids gives a closure relation of reference interaction site model equation. The site–site pair distribution functions of homonuclear diatomic Lennard-Jones fluids obtained by the integral equation agree well with those of Monte Carlo simulation. © 2001 American Institute of Physics. [ABSTRACT FROM AUTHOR]

We calculate the partial molar volume (PMV) of 20 amino acids in aqueous solution at infinite dilution by using the Kirkwood-Buff equation and the three-dimensional reference interaction site model (3D-RISM) integral equation theory for molecular liquids. As compared to the conventional, one-dimensional (1D-RISM) approach, the results exhibit drastic improvement for the quantitative agreement with experiments. The deviation from the experimental data seen for the relatively large amino acids is discussed in terms of the "ideal fluctuation volume" introduced in the previous study based on the 1D-RISM. Robustness of the new approach is further demonstrated by applying it to the PMV of polyglutamic acids in aqueous solution. The method provides reasonable account for the PMV increase with the chain length, both in α-helical and extended structures, whereas the 1D-RISM approach gives an unnatural decrease of the PMV for the α helix with a complete turn of the backbone. © 2001 American Institute of Physics. [ABSTRACT FROM AUTHOR]