The structure and activation of substrate water molecules in Sr2+-substituted photosystem II

2014 ◽  
Vol 16 (38) ◽  
pp. 20834-20843 ◽  
Author(s):  
Ruchira Chatterjee ◽  
Sergey Milikisiyants ◽  
Christopher S. Coates ◽  
Faisal H. M. Koua ◽  
Jian-Ren Shen ◽  
...  
Keyword(s):  
Hydrogen Bond ◽  
Photosystem Ii ◽  
Epr Spectroscopy ◽  
Direct Evidence ◽  
Water Molecules ◽  
Hydrogen Bond Network ◽  
Spectroscopy Study ◽  
Structural Role ◽  
Bond Network

An EPR spectroscopy study with direct evidence that the Ca2+ ion plays a structural role in maintaining the hydrogen-bond network in photosystem II.

scholarly journals Energetics of the Proton Transfer Pathway for Tyrosine D in Photosystem II

2016 ◽  
Vol 69 (9) ◽  
pp. 991 ◽  
Author(s):  
Keisuke Saito ◽  
Naoki Sakashita ◽  
Hiroshi Ishikita
Keyword(s):  
Hydrogen Bond ◽  
Photosystem Ii ◽  
Proton Transfer ◽  
Electrostatic Interactions ◽  
Water Molecules ◽  
Hydrogen Bond Network ◽  
Redox States ◽  
Redox Active ◽  
Bond Network ◽  
Tyrosine D

The proton transfer pathway for redox active tyrosine D (TyrD) in photosystem II is a hydrogen-bond network that involves D2-Arg180 and a series of water molecules. Using quantum mechanical/molecular mechanical calculations, the detailed properties of the energetics and structural geometries were investigated. The potential-energy profile of all hydrogen bonds along the proton transfer pathway indicates that the overall proton transfer from TyrD is energetically downhill. D2-Arg180 plays a key role in the proton transfer pathway, providing a driving force for proton transfer, maintaining the hydrogen-bond network structure, stabilising P680•+, and thus deprotonating TyrD-OH to TyrD-O•. A hydrophobic environment near TyrD enhances the electrostatic interactions between TyrD and redox active groups, e.g. P680 and the catalytic Mn4CaO5 cluster: the redox states of those groups are linked with the protonation state of TyrD, i.e. release of the proton from TyrD. Thus, the proton transfer pathway from TyrD may ultimately contribute to the conversion of S0 into S1 in the dark in order to stabilise the Mn4CaO5 cluster when the photocycle is interrupted in S0.

(NH4)[B3PO6(OH)3]·0.5H2O

2007 ◽  
Vol 63 (11) ◽  
pp. i185-i185 ◽  
Author(s):  
Wei Liu ◽  
Jingtai Zhao
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bond ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Water Molecules ◽  
Hydrogen Bond Network ◽  
Ammonium Ions ◽  
One Dimensional ◽  
Bond Network ◽  
Solvothermal Conditions

The title compound, ammonium catena-[monoboro-monodihydrogendiborate-monohydrogenphosphate] hemihydrate, was obtained under solvothermal conditions using glycol as the solvent. The crystal structure is constructed of one-dimensional infinite borophosphate chains, which are interconnected by ammonium ions and water molecules via a complex hydrogen-bond network to form a three-dimensional structure. The water molecules of crystallization are disordered over inversion centres, and their H atoms were not located.

X-ray Absorption Spectroscopy Study of the Hydrogen Bond Network in the Bulk Water of Aqueous Solutions

2005 ◽  
Vol 109 (27) ◽  
pp. 5995-6002 ◽  
Author(s):  
Lars-Åke Näslund ◽  
David C. Edwards ◽  
Philippe Wernet ◽  
Uwe Bergmann ◽  
Hirohito Ogasawara ◽  
...  
Keyword(s):  
Hydrogen Bond ◽  
Aqueous Solutions ◽  
Absorption Spectroscopy ◽  
Bulk Water ◽  
Hydrogen Bond Network ◽  
Spectroscopy Study ◽  
X Ray ◽  
Bond Network ◽  
X Ray Absorption

scholarly journals Characterizing Hydropathy of Amino Acid Side Chain in a Protein Environment by Investigating the Structural Changes of Water Molecules Network

2021 ◽  
Vol 8 ◽  
Author(s):  
Lorenzo Di Rienzo ◽  
Mattia Miotto ◽  
Leonardo Bò ◽  
Giancarlo Ruocco ◽  
Domenico Raimondo ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Hydrogen Bond ◽  
Amino Acid ◽  
Computational Method ◽  
Side Chain ◽  
Water Molecules ◽  
Amino Acid Side Chain ◽  
Hydrogen Bond Network ◽  
Bond Network ◽  
Protein Environment

Assessing the hydropathy properties of molecules, like proteins and chemical compounds, has a crucial role in many fields of computational biology, such as drug design, biomolecular interaction, and folding prediction. Over the past decades, many descriptors were devised to evaluate the hydrophobicity of side chains. In this field, recently we likewise have developed a computational method, based on molecular dynamics data, for the investigation of the hydrophilicity and hydrophobicity features of the 20 natural amino acids, analyzing the changes occurring in the hydrogen bond network of water molecules surrounding each given compound. The local environment of each residue is complex and depends on the chemical nature of the side chain and the location in the protein. Here, we characterize the solvation properties of each amino acid side chain in the protein environment by considering its spatial reorganization in the protein local structure, so that the computational evaluation of differences in terms of hydropathy profiles in different structural and dynamical conditions can be brought to bear. A set of atomistic molecular dynamics simulations have been used to characterize the dynamic hydrogen bond network at the interface between protein and solvent, from which we map out the local hydrophobicity and hydrophilicity of amino acid residues.

Anomalous proton conduction behavior across a nanoporous two-dimensional conjugated aromatic polymer membrane

2020 ◽  
Vol 22 (5) ◽  
pp. 2978-2985
Author(s):  
Le Shi ◽  
Zhixuan Ying ◽  
Ao Xu ◽  
Yonghong Cheng
Keyword(s):  
Hydrogen Bond ◽  
Atomic Structure ◽  
Proton Conduction ◽  
Polymer Membrane ◽  
Water Molecules ◽  
Two Dimensional ◽  
Hydrogen Bond Network ◽  
Aromatic Polymer ◽  
Conduction Behavior ◽  
Bond Network

The unique atomic structure of 2D-CAP can induce the formation of a stable local hydrogen bond network, thus restraining the motion of involved water molecules and impeding proton penetration.

Hydration and Proton Transfer in 3M™ PEM Ionomers: An Ab Initio Study

2012 ◽  
Vol 1384 ◽  
Author(s):  
Jeffrey K. Clark ◽  
Stephen J. Paddison
Keyword(s):  
Hydrogen Bond ◽  
Proton Transfer ◽  
The State ◽  
Side Chain ◽  
Water Molecules ◽  
Side Chains ◽  
Hydrogen Bond Network ◽  
Group Separation ◽  
Proton Dissociation ◽  
Bond Network

ABSTRACTElectronic structure calculations were performed to study the effects local hydration, neighboring side chain connectivity, and protogenic group separation have in facilitating proton dissociation and transfer in fragments of 3M ionomers under conditions of low hydration. Two different types of ionomers, each consisting of a poly(tetrafluoroethylene) (PTFE) backbone, were considered: (1) perfluorosulfonic acid (PFSA) ionomeric fragments containing two pendant side chains (–O(CF2)4SO3H) of distinct separation along the PTFE backbone to model different equivalent weight ionomers and (2) single side chain fragments of three bis(sulfonyl imide)- based fragments with multiple and distinct acid groups per side chain having structural and chemical differences mediating protogenic group separation (side chains: –O(CF2)4SO2(NH)- SO2C6H4SO3H) with the sulfonic acid group located in either the meta or the ortho position on the phenyl ring and –O(CF2)4SO2(NH)SO2(CF2)3SO3H). Fully optimized structures of these fragments with and without the addition of water molecules at the B3LYP/6-311G** level revealed that both side chain connectivity and protogenic group separation, along with local hydration, are key contributors to proton dissociation and the energetics of proton transfer in these materials. Specifically, cooperative interaction between protogenic groups through hydrogen bonding and electron withdrawing –CF2– groups are critical for first proton dissociation and the state of the dissociated proton at low levels of hydration. However, the close proximity of protogenic groups in the ortho bis acid precluded second proton dissociation at low hydration as the relatively fixed protogenic group separation promoted interactions between water molecules, while the labile side chains in the PFSA ionomers allowed for greater freedom in the hydrogen bond network formed. Potential energy profiles for proton transfer were determined at the B3LYP/6-31G** level. The energetic penalty associated with proton transfer was found to be strongly dependent on the surrounding hydrogen bond network and the state of the dissociated proton(s), as well as, the separation between protogenic groups.

L-Leucylglycine 0.67-hydrate and [(4S)-2,2-dimethyl-4-(2-methylpropyl)-5-oxoimidazolidin-3-ium-1-yl]acetate

2012 ◽  
Vol 68 (12) ◽  
pp. o498-o501 ◽  
Author(s):  
Tamiko Kiyotani ◽  
Yoko Sugawara
Keyword(s):  
Aqueous Solution ◽  
Hydrogen Bond ◽  
Hydrogen Bonding ◽  
Carbonyl Group ◽  
Water Molecules ◽  
Hydrogen Bond Network ◽  
Amino Groups ◽  
Unit Cell Parameters ◽  
Cell Parameters ◽  
Bond Network

Crystals of L-leucylglycine (L-Leu–Gly) 0.67-hydrate, C8H16N2O3·0.67H2O, (I), were obtained from an aqueous solution. There are three symmetrically independent dipeptide zwitterionic molecules in (I) and they are parallel to one another. The hydrogen-bond network composed of carboxylate and amino groups and water molecules extends parallel to theabplane. Hydrophilic regions composed of main chains and hydrophobic regions composed of the isobutyl groups of the leucyl residues are aligned alternately along thecaxis. An imidazolidinone derivative was obtained from L-Leu–Gly and acetone,viz.[(4S)-2,2-dimethyl-4-(2-methylpropyl)-5-oxoimidazolidin-3-ium-1-yl]acetate, C11H20N2O3, (II), and was crystallized from a methanol–acetone solution of L-Leu–Gly. The unit-cell parameters coincide with those reported previously for L-Leu–Gly dihydrate revealing that the previously reported values should be assigned to the structure of (II). One of the imidazolidine N atoms is protonated and the ring is nearly planar, except for the protonated N atom. Protonated N atoms and deprotonated carboxy groups of neighbouring molecules form hydrogen-bonded chains. The ring carbonyl group is not involved in hydrogen bonding.

scholarly journals Fast Rotational Diffusion of Water Molecules in a 2D Hydrogen Bond Network at Cryogenic Temperatures

2018 ◽  
Vol 120 (19) ◽  
Author(s):  
T. R. Prisk ◽  
C. Hoffmann ◽  
A. I. Kolesnikov ◽  
E. Mamontov ◽  
A. A. Podlesnyak ◽  
...  
Keyword(s):  
Hydrogen Bond ◽  
Rotational Diffusion ◽  
Water Molecules ◽  
Cryogenic Temperatures ◽  
Hydrogen Bond Network ◽  
Bond Network
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