Journal ArticleDOI
Structure and Dynamics of Water Dangling OH Bonds in Hydrophobic Hydration Shells. Comparison of Simulation and Experiment
Jill Tomlinson-Phillips,Joel G. Davis,Dor Ben-Amotz,Daniel Spångberg,Ljupčo Pejov,Kersti Hermansson +5 more
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TLDR
Simulation results indicate that hydration shell dangling OH groups preferentially point toward the central carbon atom of neopentane to a degree that increases with the lifetime of the dangling OH.Abstract:
Molecular dynamics and electric field strength simulations are performed in order to quantify the structural, dynamic, and vibrational properties of non-H-bonded (dangling) OH groups in the hydration shell of neopentane, as well as in bulk water. The results are found to be in good agreement with the experimentally observed high-frequency (∼3660 cm(-1)) OH band arising from the hydration shell of neopentanol dissolved in HOD/D(2)O, obtained by analyzing variable concentration Raman spectra using multivariate curve resolution (Raman-MCR). The simulation results further indicate that hydration shell dangling OH groups preferentially point toward the central carbon atom of neopentane to a degree that increases with the lifetime of the dangling OH.read more
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Water structural transformation at molecular hydrophobic interfaces
TL;DR: Combined polarized, isotopic and temperature-dependent Raman scattering measurements with multivariate curve resolution (Raman-MCR) that explore hydrophobic hydration by mapping the vibrational spectroscopic features arising from the hydrophilic shells of linear alcohols ranging from methanol to heptanol show clear evidence that at low temperatures the hydration shells have a hydrophobically enhanced water structure with greater tetrahedral order and fewer weak hydrogen bonds than the surrounding bulk water.
Journal ArticleDOI
Characterization of the Local Structure in Liquid Water by Various Order Parameters.
Elise Duboué-Dijon,Damien Laage +1 more
TL;DR: This work considers a series of popular order parameters and analyzes molecular dynamics simulations of water, in the bulk and in the hydration shell of a hydrophobic solute, at 298 and 260 K to confirm the absence of any iceberg-type structure.
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On the cooperative formation of non-hydrogen-bonded water at molecular hydrophobic interfaces
TL;DR: It is shown that interfacial dangling OH structures are entropically stabilized and their formation is cooperative (the probability that a non-hydrogen-bonded OH group will form depends nonlinearly on the hydrophobic surface area), exposing an important difference between the chemical properties of molecular and macroscopic oil/water interfaces.
Journal ArticleDOI
Micelle Structure and Hydrophobic Hydration.
TL;DR: These findings imply that the hydrophobic core of a micelle is surrounded by a highly corrugated surface containing hydrated non-polar cavities whose depth increases with increasing surfactant chain length, thus bearing a greater resemblance to soluble proteins than previously recognized.
Journal ArticleDOI
Application of Raman multivariate curve resolution to solvation-shell spectroscopy.
TL;DR: The results illustrate the quantitative capabilities of Raman-MCR as a solvation-shell spectroscopy, including fundamental limitations arising from “intensity” and “rotational” ambiguities.
References
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Comparison of simple potential functions for simulating liquid water
TL;DR: In this article, the authors compared the Bernal Fowler (BF), SPC, ST2, TIPS2, TIP3P, and TIP4P potential functions for liquid water in the NPT ensemble at 25°C and 1 atm.
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GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable molecular simulation
TL;DR: A new implementation of the molecular simulation toolkit GROMACS is presented which now both achieves extremely high performance on single processors from algorithmic optimizations and hand-coded routines and simultaneously scales very well on parallel machines.
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GROMACS: Fast, flexible, and free
David van der Spoel,Erik Lindahl,Berk Hess,Gerrit Groenhof,Alan E. Mark,Herman J. C. Berendsen +5 more
TL;DR: The software suite GROMACS (Groningen MAchine for Chemical Simulation) that was developed at the University of Groningen, The Netherlands, in the early 1990s is described, which is a very fast program for molecular dynamics simulation.
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Development and Testing of the OPLS All-Atom Force Field on Conformational Energetics and Properties of Organic Liquids
TL;DR: In this article, the parametrization and testing of the OPLS all-atom force field for organic molecules and peptides are described, and the parameters for both torsional and non-bonded energy properties have been derived, while the bond stretching and angle bending parameters have been adopted mostly from the AMBER force field.
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GROMACS: A message-passing parallel molecular dynamics implementation
TL;DR: A parallel message-passing implementation of a molecular dynamics program that is useful for bio(macro)molecules in aqueous environment is described and can handle rectangular periodic boundary conditions with temperature and pressure scaling.