Hydrogen-Bond Kinetics in the Solvation Shell of a Polypeptide

Xu, Huafeng; Berne, B. J.

doi:10.1021/jp012749h

Cited by 237 publications

(265 citation statements)

References 21 publications

Supporting

Mentioning

248

Contrasting

Unclassified

Order By: Relevance

“…In recent work on the kinetic behavior of the hydrogen bonding network, the relationship between diffusion and hydrogen bonding is described as a cooperative effort between adjacent water molecules. 34, 35 For a hydrogen bond to break, there must be another water molecule available to form a new hydrogen bond. Without the impetus to hydrogen bond to a different water molecule, it is unlikely that the first hydrogen bond will be broken.…”

Section: Discussionmentioning

confidence: 99%

Molecular Dynamics Simulations of Sodium Dodecyl Sulfate Micelle in Water: The Behavior of Water

et al. 2002

View full text Add to dashboard Cite

Using a 5 ns explicit atom molecular dynamics simulation of a 60 monomer sodium dodecyl sulfate micellar system containing 7579 TIP3P water molecules, the behavior of water in different electrostatic environments was examined. Structural evaluation of the system revealed that penetration of water molecules into the micelle was restricted to the headgroup region, leaving a 12 Å water-free hydrocarbon core. Water molecules near the headgroup exhibit a distortion of the water-water hydrogen bonding network due to headgroup oxygenwater hydrogen bond formation. The dynamic implications of this distortion are manifested in the decay of the dipole autocorrelation function, Φ(t) and translational diffusion coefficient. We observe that while the translational diffusion coefficient of water molecules in the first solvation shell of the micelle is reduced by less than a half of its value in bulk water, the slow component of the reorientational correlation function is slowed by one or two orders of magnitude.

show abstract

Section: Discussionmentioning

confidence: 99%

Molecular Dynamics Simulations of Sodium Dodecyl Sulfate Micelle in Water: The Behavior of Water

et al. 2002

View full text Add to dashboard Cite

show abstract

“…Because of the presence of straight pores and porous network, water diffusion in CC2 and CC17 is faster than in CC3 and CC16; consequently, the c(t) in the former is lower, thus leading to faster relaxation of HBs. Based on c(t HB ) = e À1 , 41 the lifetimes t HB are estimated to be 3.0, 3.3, 3.5 and 3.6 ps for CC2, CC17, CC3 and CC16, respectively. Compared with the bulk phase (1.4 ps), the t HB in the membranes are 1-2 times longer; nevertheless, they are close to that in ZIF-8 (3.5 ps), implying a similar confinement environment.…”

Section: Water Dynamics and Structure In Pocsmentioning

confidence: 99%

Porous organic cage membranes for water desalination: a simulation exploration

Kong

Jiang

2017

Phys. Chem. Chem. Phys.

View full text Add to dashboard Cite

Porous organic cages (POCs) have emerged as a new class of porous materials and received considerable interest for their potential applications. Herein we report the first proof-of-concept simulation study on POC membranes for water desalination. Among the five POC membranes, CC2 is the best for water desalination with performance superior to other membranes reported in the literature. The membrane flexibility is revealed to have a weak effect on water permeation. To provide further microscopic understanding, the permeation duration, diffusion and hydrogen bonding of water in the POC membranes are quantitatively analyzed. From this simulation study, the key factors governing water permeation in the POC membranes are unraveled and CC2 is identified to be an interesting candidate for water desalination.

show abstract

“…We have found it useful to consider that the rate of relaxation is linearly proportional to n adj . This involves two major assumptions: first, that the relaxation of hydrogen bonds occurs with the facilitation of adjacent waters that are not hydrogen-bonded to the tagged water of interest 28,31 and second that the rate of such facilitation is directly proportional to the mean local density of adjacent waters that are not involved in hydrogen-bonding with the water of interest. The first assumption is a well-accepted principle in hydrogen-bond dynamics.…”

Section: B Scaled Retarded Unitsmentioning

confidence: 99%

Structure and Dynamics of the Solvation of Bovine Pancreatic Trypsin Inhibitor in Explicit Water: A Comparative Study of the Effects of Solvent and Protein Polarizability

et al. 2005

Self Cite

View full text Add to dashboard Cite

To isolate the effects of the inclusion of polarizability in the force field model on the structure and dynamics of the solvating water in differing electrostatic environments of proteins, we present the results of molecular dynamics simulations of the bovine pancreatic trypsin inhibitor (BPTI) in water with force fields that explicitly include polarization for both the protein and the water. We use three model potentials for water and two model potentials for the protein. Two of the water models and one of the protein models are polarizable. A total of six systems were simulated representing all combinations of these polarizable and nonpolarizable protein and water force fields. We find that all six systems behave in a similar manner in regions of the protein that are weakly electrostatic (either hydrophobic or weakly hydrophilic). However, in the vicinity of regions of the protein with relatively strong electrostatic fields (near positively or negatively charged residues), we observe that the water structure and dynamics are dependent on both the model of the protein and the model of the water. We find that a large part of the dynamical dependence can be described by small changes in the local environments of each region that limit the local density of non-hydrogen-bonded waters, precisely the water molecules that facilitate the dynamical relaxation of the water-water hydrogen bonds. We introduce a simple method for rescaling for this effect. When this is done, we are able to effectively isolate the influence of polarizability on the dynamics. We find that the solvating water's relaxation is most affected when both the protein and the water models are polarizable. However, when only one model (or neither) is polarizable, the relaxation is similar regardless of the models used.

show abstract

Hydrogen-Bond Kinetics in the Solvation Shell of a Polypeptide

Cited by 237 publications

References 21 publications

Molecular Dynamics Simulations of Sodium Dodecyl Sulfate Micelle in Water: The Behavior of Water

Molecular Dynamics Simulations of Sodium Dodecyl Sulfate Micelle in Water: The Behavior of Water

Porous organic cage membranes for water desalination: a simulation exploration

Structure and Dynamics of the Solvation of Bovine Pancreatic Trypsin Inhibitor in Explicit Water: A Comparative Study of the Effects of Solvent and Protein Polarizability

Contact Info

Product

Resources

About