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Hydration Shell (hydration + shell)

Distribution by Scientific Domains

Chemistry	92%

Kinds of Hydration Shell

second hydration shell

Selected Abstracts

Ab Initio quantum mechanical charge field study of hydrated bicarbonate ion: Structural and dynamical properties

JOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 2 2010
Viwat Vchirawongkwin
Abstract The ab initio quantum mechanical charge field molecular dynamics (QMCF MD) formalism was applied to simulate the bicarbonate ion, HCO3,, in aqueous solution. The difference in coordination numbers obtained by summation over atoms (6.6) and for the solvent-accessible surface (5.4) indicates the sharing of some water molecules between the individual atomic hydration shells. It also proved the importance to consider the hydration of the chemically different atoms individually for the evaluation of structural and dynamical properties of the ion. The orientation of water molecules in the hydration shell was visualized by the ,,tilt surface plot. The mean residence time in the surroundings of the HCO3, ion classify it generally as a structure-breaking ion, but the analysis of the individual ion-water hydrogen bonds revealed a more complex behavior of the different coordination sites. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2010 [source]

Tl(I)-the strongest structure-breaking metal ion in water?

JOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 6 2007
A quantum mechanical/molecular mechanical simulation study
Abstract Structural and dynamical properties of the Tl(I) ion in dilute aqueous solution have been investigated by ab initio quantum mechanics in combination with molecular mechanics. The first shell plus a part of the second shell were treated by quantum mechanics at Hartree-Fock level, the rest of the system was described by an ab initio constructed potential. The radial distribution functions indicate two different bond lengths (2.79 and 3.16 Å) in the first hydration shell, in good agreement with large-angle X-ray scattering and extended X-ray absorption fine structure spectroscopy results. The average first shell coordination number was found as 5.9, and several other structural parameters such as coordination number distributions, angular distribution functions, and tilt- and ,-angle distributions were evaluated. The ion,ligand vibration spectrum and reorientational times were obtained via velocity auto correlation functions. The TlO stretching force constant is very weak with 5.0 N m,1. During the simulation, numerous water exchange processes took place between first and second hydration shell and between second shell and bulk. The mean ligand residence times for the first and second shell were determined as 1.3 and 1.5 ps, respectively, indicating Tl(I) to be a typical "structure-breaker". The calculated hydration energy of ,84 ± 16 kcal mol,1 agrees well with the experimental value of ,81 kcal mol,1. All data obtained for structure and dynamics of hydrated Tl(I) characterize this ion as a very special case among all monovalent metal ions, being the most potent "structure-breaker", but at the same time forming a distinct second hydration shell and thus having a far-reaching influence on the solvent structure. © 2007 Wiley Periodicals, Inc. J Comput Chem, 2007 [source]

Ab initio QM/MM dynamics of H3O+ in water

JOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 14 2006
Pathumwadee Intharathep
Abstract A molecular dynamics (MD) simulation based on a combined ab initio quantum mechanics/molecular mechanics (QM/MM) method has been performed to investigate the solvation structure and dynamics of H3O+ in water. The QM region is a sphere around the central H3O+ ion, and contains about 6,8 water molecules. It is treated at the Hartree-Fock (HF) level, while the rest of the system is described by means of classical pair potentials. The Eigen complex (H9O) is found to be the most prevalent species in the aqueous solution, partly due to the selection scheme of the center of the QM region. The QM/MM results show that the Eigen complex frequently converts back and forth into the Zundel (H5O) structure. Besides the three nearest-neighbor water molecules directly hydrogen-bonded to H3O+, other neighbor waters, such as a fourth water molecule which interacts preferentially with the oxygen atom of the hydronium ion, are found occasionally near the ion. Analyses of the water exchange processes and the mean residence times of water molecules in the ion's hydration shell indicate that such next-nearest neighbor water molecules participate in the rearrangement of the hydrogen bond network during fluctuative formation of the Zundel ion and, thus, contribute to the Grotthuss transport of the proton. © 2006 Wiley Periodicals, Inc. J Comput Chem, 2006 [source]

Anisotropy of spin relaxation of water protons in cartilage and tendon

NMR IN BIOMEDICINE, Issue 3 2010
Konstantin I. Momot
Abstract Transverse spin relaxation rates of water protons in articular cartilage and tendon depend on the orientation of the tissue relative to the applied static magnetic field. This complicates the interpretation of magnetic resonance images of these tissues. At the same time, relaxation data can provide information about their organisation and microstructure. We present a theoretical analysis of the anisotropy of spin relaxation of water protons observed in fully hydrated cartilage. We demonstrate that the anisotropy of transverse relaxation is due almost entirely to intramolecular dipolar coupling modulated by a specific mode of slow molecular motion: the diffusion of water molecules in the hydration shell of a collagen fibre around the fibre, such that the molecular director remains perpendicular to the fibre. The theoretical anisotropy arising from this mechanism follows the ,magic-angle' dependence observed in magnetic-resonance measurements of cartilage and tendon and is in good agreement with the available experimental results. We discuss the implications of the theoretical findings for MRI of ordered collagenous tissues. Copyright © 2009 John Wiley & Sons, Ltd. [source]

Molecular shapes from small-angle X-ray scattering: extension of the theory to higher scattering angles

ACTA CRYSTALLOGRAPHICA SECTION A, Issue 2 2009
V. L. Shneerson
A low-resolution shape of a molecule in solution may be deduced from measured small-angle X-ray scattering I(q) data by exploiting a Hankel transform relation between the coefficients of a multipole expansion of the scattered amplitude and corresponding coefficients of the electron density. In the past, the radial part of the Hankel transform has been evaluated with the aid of a truncated series expansion of a spherical Bessel function. It is shown that series truncation may be avoided by analytically performing the radial integral over an entire Bessel function. The angular part of the integral involving a spherical harmonic kernel is performed by quadrature. Such a calculation also allows a convenient incorporation of a molecular hydration shell of constant density intermediate between that of the protein and the solvent. Within this framework, we determine the multipole coefficients of the shape function by optimization of the agreement with experimental data by simulated annealing. [source]

Evaporation of solvent molecules by ultrafast heating: effect on conformation of solvated protein

RAPID COMMUNICATIONS IN MASS SPECTROMETRY, Issue 3 2010
Saravana Prakash Thirumuruganandham
Using molecular dynamics simulation, we compare two cases of ultrafast heating of a small water droplet containing a solvated protein (echistatin). If the water temperature after irradiation is above the critical temperature, explosive boiling liberates the protein within some 10,ps of its hydration shell, while its temperature remains relatively low. By comparing with the case where the water shell is heated to the same final temperature, but without complete evaporation, we demonstrate that the protein conformation is governed by the hydration shell rather than by the protein temperature. Copyright © 2010 John Wiley & Sons, Ltd. [source]

Structural plasticity of peanut lectin: an X-ray analysis involving variation in pH, ligand binding and crystal structure

ACTA CRYSTALLOGRAPHICA SECTION D, Issue 2 2004
S. Kundhavai Natchiar
Until recently, it has only been possible to grow crystals of peanut lectin when complexed with sugar ligands. It is now shown that it is possible to grow peanut lectin crystals at acidic pH in the presence of oligopeptides corresponding to a loop in the lectin molecule. Crystals have also been prepared in the presence of these peptides as well as lactose. Low-pH crystal forms of the lectin,lactose complex similar to those obtained at neutral pH have also been grown. Thus, crystals of peanut lectin grown under different environmental conditions, at two pH values with and without sugar bound to the lectin, are now available. They have been used to explore the plasticity and hydration of the molecule. A detailed comparison between different structures shows that the lectin molecule is sturdy and that the effect of changes in pH, ligand binding and environment on it is small. The region involving the curved front ,-sheet and the loops around the second hydrophobic core is comparatively rigid. The back ,-sheet involved in quaternary association, which exhibits considerable variability, is substantially flexible, as is the sugar-binding region. The numbers of invariant water molecules in the hydration shell are small and they are mainly involved in metal coordination or in stabilizing unusual structural features. Small consistent movements occur in the combining site upon sugar binding, although the site is essentially preformed. [source]

Molecular Mechanism of the Hydration of Candida antarctica Lipase B in the Gas Phase: Water Adsorption Isotherms and Molecular Dynamics Simulations

CHEMBIOCHEM, Issue 18 2009
Ricardo J. F. Branco Dr.
Abstract Hydration is a major determinant of activity and selectivity of enzymes in organic solvents or in gas phase. The molecular mechanism of the hydration of Candida antarctica lipase B (CALB) and its dependence on the thermodynamic activity of water (aw) was studied by molecular dynamics simulations and compared to experimentally determined water sorption isotherms. Hydration occurred in two phases. At low water activity, single water molecules bound to specific water binding sites at the protein surface. As the water activity increased, water networks gradually developed. The number of protein-bound water molecules increased linearly with aw, until at aw=0.5 a spanning water network was formed consisting of 311 water molecules, which covered the hydrophilic surface of CALB, with the exception of the hydrophobic substrate-binding site. At higher water activity, the thickness of the hydration shell increased up to 10 Å close to aw=1. Above a limit of 1600 protein-bound water molecules the hydration shell becomes unstable and the formation of pure water droplets occurs in these oversaturated simulation conditions. While the structure and the overall flexibility of CALB was independent of the hydration state, the flexibility of individual loops was sensitive to hydration: some loops, such as those part of the substrate-binding site, became more flexible, while other parts of the protein became more rigid upon hydration. However, the molecular mechanism of how flexibility is related to activity and selectivity is still elusive. [source]

The Jahn,Teller Effect of the TiIII Ion in Aqueous Solution: Extended Ab Initio QM/MM Molecular Dynamics Simulations,

CHEMPHYSCHEM, Issue 10 2004
Chinapong Kritayakornupong Dr.
Abstract Combined ab initio quantum mechanical/molecular mechanical (QM/MM) molecular dynamics simulations, including only the first and the first and second hydration shells in the QM region, were performed for TiIIIin aqueous solution. The hydration structure of TiIIIis discussed in terms of radial distribution functions, coordination-number distributions and several angle distributions. Dynamical properties, such as librational and vibrational motions and TiIIIO vibrations, were evaluated. A fast dynamical Jahn,Teller effect of TiIII(aq) was observed in the QM/MM simulations, in particular when the second hydration shell was included into the QM region. The results justify the computational effort required for the inclusion of the second hydration shell into the QM region and show the importance of this effort for obtaining accurate hydration-shell geometries, dynamical properties, and details of the Jahn,Teller effect. [source]

Computational study of the solvation of protoporphyrin IX and its Fe2+ complex

INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 13 2008
Teobaldo Cuya Guizado
Abstract Molecular dynamics (MD) simulations of a well known hydrophobic structure, the heme (ferroprotoporphyrin IX) and its precursor in the heme synthesis, protoporphyrin IX (PPIX) are presented. The objective of the present study is to determine the stability of both structures in an aqueous medium, as well as the structure-solvent relation, hydration shells, and discuss their implications for biological processes. The density functional theory (DFT) is used for the electronic and structural characterization of both PPIX and its Fe2+ complex. A classical approach based on the Gromacs package is used for the MD. The radial distribution function g(r) is used to examine the allocation of water molecules around different regions of the porphyrins. The calculations demonstrate the heterogeneous character of the porphyrins with respect to the affinity with water molecules, the general hydrophobic character of the porphyrin ring bonded or not to the ion Fe, the hydrophilic character of the carboxylic oxygen that is unchanged upon iron binding, and the low hydrophilicity of Fe2+ in the heme. © 2008 Wiley Periodicals, Inc. Int J Quantum Chem, 2008 [source]

Ab Initio quantum mechanical charge field study of hydrated bicarbonate ion: Structural and dynamical properties

Adsorption of Insulin Peptide on Charged Single-Walled Carbon Nanotubes: Significant Role of Ordered Water Molecules

CHEMPHYSCHEM, Issue 8 2009
Jia-Wei Shen
Abstract Ordered hydration shells: The more ordered hydration shells outside the charged CNT surfaces prevent more compact adsorption of the peptide in the charged CNT systems (see picture), but peptide binding strengths on the charged CNT surfaces are stronger due to the electrostatic interaction. Studies of adsorption dynamics and stability for peptides/proteins on single-walled carbon nanotubes (SWNTs) are of great importance for a better understanding of the properties and nature of nanotube-based biosystems. Herein, the dynamics and mechanism of the adsorption of the insulin chain B peptide on different charged SWNTs are investigated by explicit solvent molecular dynamics simulations. The results show that all types of surfaces effectively attract the model peptide. Water molecules play a significant role in peptide adsorption on the surfaces of charged carbon nanotubes (CNTs). Compared to peptide adsorption on neutral CNT surfaces, the more ordered hydration shells outside the tube prevent more compact adsorption of the peptide in charged CNT systems. This shield effect leads to a smaller conformational change and van der Waals interaction between the peptide and surfaces, but peptide binding strengths on charged CNT surfaces are stronger than those on the neutral CNT surface due to the strong electrostatic interaction. The result of these simulations implies the possibility of improving the binding strength of peptides/proteins on CNT surfaces, as well as keeping the integrity of the peptide/protein conformation in peptide/protein,CNT complexes by charging the CNTs. [source]