Solvent structure and perturbations in solutions of chemical and biological importance

Finney, Jl; Soper, A. K.

doi:10.1039/cs9942300001

Cited by 186 publications

(157 citation statements)

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“…S2). Water dipoles pointing tangentially away from a nonpolar solute surface is a well-known result that has also been observed experimentally (62). For QMPFF3, a large number of water dipoles point away from the C 60 surface, compared to equal populations of dipole vectors pointing toward and away from the solute surface for SPC (Fig.…”

Section: Chemistrymentioning

confidence: 57%

Remarkable patterns of surface water ordering around polarized buckminsterfullerene

Chopra

Levitt

2011

Proc. Natl. Acad. Sci. U.S.A.

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Accurate description of water structure affects simulation of protein folding, substrate binding, macromolecular recognition, and complex formation. We study the hydration of buckminsterfullerene, the smallest hydrophobic nanosphere, by molecular dynamics simulations using a state-of-the-art quantum mechanical polarizable force field (QMPFF3), derived from quantum mechanical data at the MP2/aug-cc-pVTZ(-hp) level augmented by CCSD(T). QMPFF3 calculation of the hydrophobic effect is compared to that obtained with empirical force fields. Using a novel and highly sensitive method, we see polarization increases ordered water structure so that the imprint of the hydrophobic surface atoms on the surrounding waters is stronger and extends to long-range. We see less water order for empirical force fields. The greater order seen with QMPFF3 will affect biological processes through a stronger hydrophobic effect.B uckminsterfullerene (C 60 ), commonly known as the buckyball, has been the focus of many experimental and theoretical studies because of its promise in both biomedicine and nanomaterials (1-8). Carbon nanotubes, a nanomaterial similar to fullerenes, exhibit unique mechanical properties, electrical and heat conductivity; they are often hailed as a twenty-first century material that could revolutionize a number of industries (2). The behavior of fullerenes in water is of special interest for biosensors (9). Moreover, water-soluble buckyball derivatives could potentially be used for a wide variety of medical applications, including HIV protease inhibition, DNA photoclevage, antibacterial activity, and photocytotoxicity for cancer treatment (10).The interaction of water with hydrophobic surfaces is responsible for many biological processes, such as protein folding, substrate binding and biological self-assembly of micelles, lyotropic mesophases, and lipid membranes. The molecular surface of proteins can have extended hydrophobic patches, so that buckyballs, graphite surfaces, and carbon nanotubes provide model systems for study of water molecules near large hydrophobic surfaces. An accurate description of interactions between water and its surrounding environment is essential for understanding and simulating such processes. Molecular dynamics (MD) simulations are used to study the behavior of water molecules next to hydrophobic surfaces at atomic detail and subpicosecond time resolution. The hydration structure of nonpolar solutes of varying size has been studied extensively in the past (11-22) using empirical force fields. Work from our lab has used empirical potential energy functions with popular water models to model the effect of a single molecule of benzene, cyclohexane (18, 21), methane, and C 60 (22) on the structural details of water around these solutes. All these studies used force fields with nonpolarizable fixed point charge water models and analyzed water structure with a low-sensitivity method unable to detect the effect of solute surface "roughness" on water structure.Polarization, which allows the ef...

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Section: Chemistrymentioning

confidence: 57%

Remarkable patterns of surface water ordering around polarized buckminsterfullerene

Chopra

Levitt

2011

Proc. Natl. Acad. Sci. U.S.A.

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“…These are Ϫ3.74 and 6.67 fm, respectively. By combining neutron scattering measurements from isotopically distinct but otherwise identical samples, it is possible to extract structural information centred on the isotopically substituted atomic sites (Finney & Soper 1994). This can be illustrated as follows.…”

Section: (A) Neutron Scattering and Isotopic Substitutionmentioning

confidence: 99%

“…In the case of a binary molecular system where it is possible to perform independent isotopic substitutions on molecular groups of each of the two molecular constituents, it is possible to use this method to extract, via seven isotopic substitution experiments, three specific partial pair-distribution functions that characterize the key intermolecular interactions-solutesolute, solvent-solvent and solute-solvent (Finney & Soper 1994). In addition to the three pure partials, this combination of experiments also provides us with six other composite partial structure factors that each give different viewpoints on the structure that exists in the liquid.…”

Section: (A) Neutron Scattering and Isotopic Substitutionmentioning

confidence: 99%

“…We have three unknown quantities, the structure factors S XX (Q), S XM (Q) and S MM (Q), and we have the required three equations to solve them that differ by the known values of the scattering length imposed on the methyl hydrogen site by our selected substitutions. These equations are the basis of both the 1st-order and 2nd-order isotopic difference techniques that in favourable cases allow us to label specific atomic sites (and molecular functional groups) to then obtain a very detailed insight into the intermolecular interactions in which they are involved (Finney & Soper 1994). In the 1st-order difference experiment, only two experiments are performed and one can extract the sum of S XH (Q) and S HH (Q).…”

Section: (A) Neutron Scattering and Isotopic Substitutionmentioning

confidence: 99%

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Structure and interactions in simple solutions

Bowron

2004

Phil. Trans. R. Soc. Lond. B

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Neutron scattering with hydrogen/deuterium isotopic substitution techniques has been used to investigate the full range of structural interactions in a dilute 0.02 mol fraction solution of tertiary butanol in water, both in the absence and in the presence of a small amount of sodium chloride. Emphasis is given to the detailed pictures of the intermolecular interactions that have been derived using the empirical potential structure refinement technique. Analysis has been performed to the level of the spatial density distribution functions that illustrate the orientational dependence of the intermolecular interactions between all combinations of molecular and ionic components. The results show the key structural motifs involved in the interactions between the various components in a complex aqueous system. They underline the structural versatility of the water molecule in accommodating a range of different kinds of interactions while retaining its characteristic first-neighbour interaction geometry. Within this framework, the results highlight the complex interplay between the polar, non-polar and charged molecular interactions that exist in the system.

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“…At the same time this exposure allows for appreciation of the fundamental difficulties of these experiments, and the important progress made by the experimental community over the last 25 years to improve the quality of scattering data on liquid water, not only under ambient conditions as recently reported by our own group 40,41 , but in different thermodynamic regimes such as supercooled [42][43][44][45] or supercritical [46][47][48][49][50] , in confined geometries 51 , or in aqueous solutions of biochemical or chemical importance. 13,23,[52][53][54][55][56][57][58][59] This review also measures the progress in the simulation of liquid water structure. It is important to emphasize that the quality of a water model or simulation should be judged more broadly than the structure it produces, such as its performance for thermodynamic or phase stability properties, or to consider the intended purpose of the model to decide if more severe approximations are warranted.…”

Section: Introductionmentioning

confidence: 99%