Contribution of Many-Body Terms to the Energy for Small Water Clusters:  A Comparison of ab Initio Calculations and Accurate Model Potentials

Hodges, Matthew P.; Stone, Anthony J.; Xantheas, Sotiris S.

doi:10.1021/jp9716851

Cited by 207 publications

(200 citation statements)

References 43 publications

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“…In our simulations using the TIP3P model for water, the free hydrogens are nearly planar and are perfectly planar at a T ϭ 0 K structure. In simulations using the anisotropic site-site potential (ASPW4) (33) which is a refinement of the Millot-Stone potential (34, 35) with superior performance for water clusters, we found alternating out-of-plane dangling hydrogens in the confined C 180 water tetramer, as observed experimentally in gas phase. In the encapsulated pentamer, ring strain is relieved by displacing one of the water molecules out of the plane of the other oxygens, as seen in gas-phase experiments (24).…”

Section: Structures Of Encapsulated Water Clusterssupporting

confidence: 59%

“…For instance, during the catalytic cycle of cytochrome P450, cryocrystallography (10) indicates that the amide hydrogen of a threonine is exposed to a narrow cavity that becomes filled with a water molecule (10,11). As indicated by our simulations using the highly accurate ASPW4 potential (33), improved water models will certainly change details of the structures and thermodynamics of water clusters in cavities but are unlikely to alter our general conclusions about water in nonpolar cavities. The spectroscopic study of water clusters trapped in cavities should be of great interest in better characterizing water in a biologically relevant environment (40).…”

Section: Discussionmentioning

confidence: 86%

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Water clusters in nonpolar cavities

Vaitheeswaran

Yin

Rasaiah

et al. 2004

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

223

242

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We explore the structure and thermodynamics of water clusters confined in nonpolar cavities. By calculating the grand-canonical partition function term by term, we show that small nonpolar cavities can be filled at equilibrium with highly structured water clusters. The structural and thermodynamic properties of these encapsulated water clusters are similar to those observed experimentally in the gas phase. Water filling is highly sensitive to the size of the cavity and the strength of the interactions with the cavity wall. Water penetration into pores can thus be modulated by small changes in the polarity and structure of the cavity. Implications on water penetration into proteins are discussed.grand canonical ensemble ͉ hydrophobic interactions ͉ fullerenes ͉ free energy of transfer ͉ configurational-specific heat H ydrophobic literally means water repelling. So are nonpolar cavities hydrophobic, i.e., devoid of water? Answering this question profoundly impacts our understanding of the role of water in protein function. Although some weakly polar cavities created inside proteins by mutations were indeed found to be empty (1), recent studies using crystallography (2-4), NMR (5, 6), and simulations (7) show that water molecules may be present at least transiently. Evidence for a functional role of water in the nonpolar interior of proteins is also accumulating. Water has been implicated as the mediator for proton transfer through the nonpolar interior channels of the proton pumps cytochrome c oxidase (8) and bacteriorhodopsin (9), and the monooxygenase cytochrome P450 (10, 11), with water detected in trapped intermediates (9, 10), but empty channels in crystal structures of the resting enzymes.Water permeation of carbon nanotubes (12-14) and the dewetting of hydrophobic surfaces (15-17) have been studied recently, but the thermodynamic driving forces for water filling nonpolar cavities remain poorly understood. The loss of hydrogen-bond energy should render the transfer of a single water molecule into a nonpolar environment energetically unfavorable (18). Moreover, multiple water molecules confined into narrow spaces will form highly ordered structures, resulting in unfavorable entropies of transfer. However, mounting experimental evidence for water penetrating into weakly polar cavities in the protein interior (2-6, 9, 10, 19) suggests that this simple reasoning must be incomplete.To investigate the hydration of nonpolar cavities, we reverse the extensively studied process of nonpolar solvation in water (20, 21) and study instead the more poorly understood transfer of water into a nonpolar environment (18). We demonstrate that water can fill nonpolar cavities at ambient conditions, with entropy and ''weak'' van der Waals interactions playing a critical role, and that the strong water-hydrogen-bond interactions lead to the formation of unique water clusters similar in topology to the gas-phase structures detected spectroscopically (22-27).We study the stability and structure of water in nonpolar cavities of varyi...

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Section: Structures Of Encapsulated Water Clusterssupporting

confidence: 59%

Section: Discussionmentioning

confidence: 86%

Water clusters in nonpolar cavities

Vaitheeswaran

Yin

Rasaiah

et al. 2004

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

223

242

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“…On the other hand, a number of water models have been developed specifically targeting cluster energies during the optimization. For example, DPP2, 35 ASP-W4, 80 and TTM series of models 34,81 were developed for this purpose. However, these models, when used for bulk phase simulation, do not give satisfactory results.…”

Section: Water Clustersmentioning

confidence: 99%

Six-site polarizable model of water based on the classical Drude oscillator

Lopes

Roux

et al. 2013

The Journal of Chemical Physics

111

151

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A polarizable water model, SWM6, was developed and optimized for liquid phase simulations under ambient conditions. Building upon the previously developed SWM4-NDP model, additional sites representing oxygen lone-pairs were introduced. The geometry of the sites is assumed to be rigid. Considering the large number of adjustable parameters, simulated annealing together with polynomial fitting was used to facilitate model optimization. The new water model was shown to yield the correct self-diffusion coefficient after taking the system size effect into account, and the dimer geometry is better reproduced than in the SWM4 models. Moreover, the experimental oxygen-oxygen radial distribution is better reproduced, indicating that the new model more accurately describes the local hydrogen bonding structure of bulk phase water. This was further validated by its ability to reproduce the experimental nuclear magnetic shielding and related chemical shift of the water hydrogen in the bulk phase, a property sensitive to the local hydrogen bonding structure. In addition, comparison of the liquid properties of the SWM6 model is made with those of a number of widely used additive and polarizable models. Overall, improved balance between the description of monomer, dimer, clustered, and bulk phase water is obtained with the new model compared to its SWM4-NDP polarizable predecessor, though application of the model requires an approximately twofold increase on computational resources.

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“…[5][6][7][8][9][10][11] Vibrational spectroscopic studies 26 as well as some of the early ab initio studies 27 suggested an open-chain conformer with nearly linear hydrogen bonds as the most stable structure of a water trimer. Some of the other experimental [28][29][30] and theoretical [31][32][33][34][35][36][37][38][39] studies show a cyclic structure with C 1 symmetry, with two external hydrogen atoms on one side of the O-O-O plane and a third one on the other side of the plane, to be the most stable. In such a structure, each monomer behaves as a donor as well as an acceptor.…”

Section: Introductionmentioning

confidence: 99%

Structure and Stability of Water Clusters (H₂O)_n, n = 8−20: An Ab Initio Investigation

Maheshwary¹,

Patel²,

et al. 2001

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Extensive ab initio calculations have been performed using the 6-31G(d,p) and 6-311++G(2d,2p) basis sets for several possible structures of water clusters (H 2 O) n , n ) 8-20. It is found that the most stable geometries arise from a fusion of tetrameric or pentameric rings. As a result, (H 2 O) n , n ) 8, 12, 16, and 20, are found to be cuboids, while (H 2 O) 10 and (H 2 O) 15 are fused pentameric structures. For the other water clusters (n ) 9, 11, 13, 14, and 17-19) under investigation, the most stable geometries can be thought of as arising from either the cuboid or the fused pentamers or a combination thereof. The stability of some of the clusters, namely, n ) 8-16, has also been studied using density functional theory. An attempt has been made to estimate the basis set superposition error and zero-point energy correction for such clusters at the HartreeFock (HF) level using the 6-311++G(2d,2p) basis set. To ensure that a minimum on the potential-energy surface has been located, frequency calculations have been carried out at the HF level using the 6-31G(d,p) and 6-311++G(2d,2p) basis sets for some of the clusters. Molecular electrostatic potential topography mapping has been employed for understanding the reactivity as well as the binding patterns of some of the structurally interesting clusters.

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Contribution of Many-Body Terms to the Energy for Small Water Clusters: A Comparison of ab Initio Calculations and Accurate Model Potentials

Cited by 207 publications

References 43 publications

Water clusters in nonpolar cavities

Water clusters in nonpolar cavities

Six-site polarizable model of water based on the classical Drude oscillator

Structure and Stability of Water Clusters (H₂O)_n, n = 8−20: An Ab Initio Investigation

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Contribution of Many-Body Terms to the Energy for Small Water Clusters: A Comparison of ab Initio Calculations and Accurate Model Potentials

Cited by 207 publications

References 43 publications

Water clusters in nonpolar cavities

Water clusters in nonpolar cavities

Six-site polarizable model of water based on the classical Drude oscillator

Structure and Stability of Water Clusters (H2O)n, n = 8−20: An Ab Initio Investigation

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Product

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Structure and Stability of Water Clusters (H₂O)_n, n = 8−20: An Ab Initio Investigation