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4 edition of Molecular dynamics and hydrogen bonds in water found in the catalog.

Molecular dynamics and hydrogen bonds in water

Molecular dynamics and hydrogen bonds in water

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Published by U.S. Dept. of Commerce, Technology Administration, National Institute of Standards and Technology in Gaithersburg, MD .
Written in English

    Subjects:
  • Molecular dynamics -- Mathematical models,
  • Hydrogen bonding -- Mathematical models

  • Edition Notes

    StatementRaymond D. Mountain
    SeriesNISTIR -- 6028
    ContributionsNational Institute of Standards and Technology (U.S.)
    The Physical Object
    FormatMicroform
    Pagination24 p.
    Number of Pages24
    ID Numbers
    Open LibraryOL13622450M
    OCLC/WorldCa40593705

    We find that water molecules in the first hydration shell of the halogenic anions Cl −, Br − and I − show much slower hydrogen-bond dynamics than water molecules in the pure liquid. We also observe that the first hydration shell shows very slow collective orientational dynamics, and forms a rigid, long-living by:   Molecular dynamics simulation of the ice nucleation and growth process leading to water freezing Fluctuation, relaxation and hydration in liquid water. Hydrogen-bond rearrangement dynamics. by:

    More insight into the effects of hydrophobes on water can be obtained by probing the hydrogen-bond dynamics of water sur-rounding hydrophobic molecular groups. In recent years it was demonstrated that valuable information on the hydrogen-bond dynamics of liquid water can be obtained with third-order vibra-Cited by:   Molecular dynamics simulations were carried out on a system of eight independent caffeine molecules in a periodic box of water at K, representing a solution near the solubility limit for caffeine at room temperature, using a newly-developed CHARMM-type force field for caffeine in by:

    The properties of hydrogen bond networks in ambient, supercritical, and stretched model water at temperatures between K and K and densities between g/cm 3 and 1 g/cm 3 have been investigated by molecular dynamics simulation. A flexible simple point charged pair potential model has been used and, after comparing two hydrogen bond definitions, a pure Cited by: BINANA is well suited for counting the number of ligand-receptor hydrogen bonds in a single structure and producing a visualization of those bonds in VMD, but it is not well suited for identifying and tallying the hydrogen bonds across an entire molecular-dynamics trajectory, which contains multiple frames with subtly different hydrogen-bond networks. In order to analyze and Cited by:


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Molecular dynamics and hydrogen bonds in water Download PDF EPUB FB2

The most simple water molecular, H2O, is a fascinating but poorly understood molecule. Its unique ability to attract an exceptionally large number of hydrogen bonds induces the formation of a dense "hydrogen bond network" that has the potential to modify the properties of the surrounding molecules and their reactivities.5/5(1).

The Hydrogen Bond and the Water Molecule offers a synthesis of what is known and currently being researched on the topic of hydrogen bonds and water molecules. The most simple water molecular, H2O, is a fascinating but poorly understood molecule. The dynamics of hydrogen bonds and the translational and rotational motions of water molecules in the vicinity of the polymer segments are analyzed to investigate the properties of water molecules which are highly cooperative with the surrounding polymer by: Molecular dynamics results show that DMSO typically forms two hydrogen bonds with water molecules.

Hydrogen bonds between DMSO and water molecules are longer lived than water-water hydrogen bonds. Ning Zhang, Zhuanglin Shen, Cong Chen, Gaohong He and Ce Hao, Effect of hydrogen bonding on self-diffusion in methanol/water liquid mixtures: A molecular dynamics simulation study, Journal of Molecular Liquids, /,(), ().Cited by: Hydrogen Bonding in Liquids [].

Hydrogen bonds are present in organic liquids like water, ethanol, hydrogen fluoride, and N-methylacetamide. These hydrogen bonds are partially responsible for the large enthalpies of vaporization, along with higher boiling points than hydrocarbons with comparable sizes.

Recently, a panel of experts, nominated by IUPAC, proposed the following tentative definition for the hydrogen bond: “The hydrogen bond is an attractive interaction between a group X-H and an atom or group of atoms Y in the same or different molecule(s), where there is evidence of bond formation” (Arunan, ).The energy of H-bond (~5 Kcal/mole of H-bonds) is Cited by: three-dimensional network of hydrogen bonds (HBs) encom-passingabroaddistributionofO–H OHBanglesanddistances.

Therefore, the concept of a ‘‘broken’’ HB is an arbitrary one. This ambiguity is often evident in molecular dynamics (MD) simulations of water, where, to define an ‘‘intact’’ or “broken”.

Hydrogen bonding enhances the anharmonicity of the potential energy surface. resulting in strengthened mechanical coupling of different vibrational modes. Anharmonic mode coupling is crucial for the line shape of vibrational absorp. tion bands, hydrogen bond dynamics, and for vibrational energy transfer.

The linear‐ and angular‐momentum autocorrelation functions in liquid CO have been studied using computer‐simulated molecular dynamics. The structure of these functions appears to be determined by the corresponding autocorrelation functions of the direction of the linear and angular momentum.

Molecular Dynamics Investigation of the Influence of the Hydrogen Bond Networks in Ethanol/Water Mixtures on Dielectric Spectra.

The Journal of Physical Chemistry B(4), Cited by:   HYDROGEN bonds play a crucial role in the behaviour of water 1–4; their spatial patterns and fluctuations characterize the structure and dynamics of the liquid 5– processes of breaking Cited by: Among these CO 2 molecules, those form hydrogen bonds with hydroxyl groups are classified as hydrogen bonds CO 2 molecules and the others are classified as physi-sorption CO 2 molecules.

Fig. 10 illustrates the percentage of CO 2 molecules which are involved in 0, 1 or 2 hydrogen bonds as a function of pressure on different silica by: 3. The formation and persistence of hydrogen bonds are inherently dynamic processes.

In this research the technique of molecular dynamics is used to examine the evolution of hydrogen bonds as a function of initial conditions such as temperature, internal energy, and geometry.

Clusters of water molecules serve as the prototypical hydrogen-bonded system. An analysis of the structural and dynamical hydrogen bonding interactions at the lipid water interface from a 10 ns molecular dynamics simulation of a hydrated dimyristoylphosphatidylcholine (DMPC) lipid bilayer is presented.

We find that the average number of hydrogen bonds per lipid oxygen atom varies depending on its position within the. The hydrogen bond represents an important interaction between molecules, and the dynamics of hydrogen bonds in water create an ever-present question associated with the process of chemical and biological : Kindle.

Understanding the more detailed molecular dynamics of liquid water has long relied on numerical simulations of empirical models. By revealing a specific intermolecular motion, namely, stretching of Cited by: return to a hydrogen-bonding partner within fs.

The results from experiment and simulation demonstrate that NHBs are in-trinsically unstable and that dangling hydrogen bonds are an insignificant species in liquid water. femtosecond 2D IR spectroscopy molecular dynamics liquids O n average, molecules in liquid water are tetrahedrallyCited by: probe hydrogen bond dynamics indirectly and can be in-terpreted in only a qualitative way [5].

While limited to classical models, the method of molecular dynamics can be used to explore hydrogen bond dynamics at the mi-croscopic level [6]. Factors controlling the dynamics can be determined from trajectory calculations of correlation functions.

Molecular dynamics simulations are employed to investigate the effects of temperature and size on the hydrogen-bond dynamics of interior molecules and surface molecules in a water nanocluster. The flexible three-centred (F3C) water model is invoked in the by: 4.

the temperature dependence of the hydrogen bond lifetime is much weaker than that of the transport properties. Even if these features are well established, the dynamics of hydrogen bonds remains difficult to access directly. However, it is essential for a full understanding of the physics of liquid water at a molecular by: We discuss the analysis of molecular dynamics calculations where we simulate the kinetics of the breaking and forming of hydrogen bonds in distinctly different environments: liquid water and concentrated aqueous solution of DMSO.

In our analysis, we consider reactive flux correlation functions computed for a variet. A couple of hydrogen bonds are their formation and break is also shown (red lines). Water molecules undergo large rotations (;large-angle jumps).

Follow also the vibrations of the hydrogen atoms.