Water phase transitions from the perspective of hydrogen-bond network analysis

2018 ◽  
Vol 20 (44) ◽  
pp. 28308-28318 ◽  
Author(s):  
B. V. Ramírez ◽  
R. M. Benito ◽  
J. Torres-Arenas ◽  
A. L. Benavides
Keyword(s):  
Hydrogen Bond ◽  
Phase Transitions ◽  
Network Analysis ◽  
Water Phase ◽  
Hydrogen Bond Network ◽  
Hydrogen Bond Networks ◽  
Bond Network

Analysis of the water phase transitions from the perspective of hydrogen bond networks.

Exploration of hydrogen bond networks and potential energy surfaces of methanol clusters using a two-stage clustering algorithm

2017 ◽  
Vol 19 (1) ◽  
pp. 544-556 ◽  
Author(s):  
Po-Jen Hsu ◽  
Kun-Lin Ho ◽  
Sheng-Hsien Lin ◽  
Jer-Lai Kuo
Keyword(s):  
Hydrogen Bond ◽  
Potential Energy ◽  
Potential Energy Surfaces ◽  
Clustering Algorithm ◽  
Energy Surface ◽  
Hydrogen Bond Network ◽  
Two Stage ◽  
Hydrogen Bond Networks ◽  
Bond Network ◽  
Energy Surfaces

A two-stage algorithm based both on the similarity in shape and hydrogen bond network is developed to explore the potential energy surface of methanol clusters.

How does hydrogen bond network analysis reveal the golden ratio of water–glycerol mixtures?

2020 ◽  
Vol 22 (5) ◽  
pp. 2887-2907
Author(s):  
Trevor R. Fisher ◽  
Guobing Zhou ◽  
Yijun Shi ◽  
Liangliang Huang
Keyword(s):  
Molecular Dynamics ◽  
Hydrogen Bond ◽  
Network Analysis ◽  
Molecular Dynamics Simulations ◽  
Golden Ratio ◽  
Hydrogen Bond Network ◽  
Maximum Contribution ◽  
Water Glycerol ◽  
Bond Network ◽  
Dynamics Simulations

Molecular dynamics simulations reveal that the maximum contribution of H-bonds between water and glycerol occurs around 30 mol% glycerol. Such a concentration is also where several of the mixture's properties have an observed maxima or minima.

New representatives of solid acid conductors: CsmHn((HSO4),(H2PO4))m+n

2014 ◽  
Vol 70 (a1) ◽  
pp. C65-C65 ◽  
Author(s):  
Irina Makarova ◽  
Vadim Grebenev ◽  
Elena Dmitricheva ◽  
Vladimir Komornikov
Keyword(s):  
Hydrogen Bond ◽  
Phase Transitions ◽  
High Temperature ◽  
Hydrogen Bonds ◽  
Functional Materials ◽  
Proton Conductors ◽  
Hydrogen Bond Network ◽  
Outward Diffusion ◽  
Bond Network ◽  
Superprotonic Phase

Crystals - superprotonics are extensively studied with the goal of elucidating the influence of the hydrogen subsystem on the physicochemical properties and designing new functional materials. As opposed to other hydrogen-containing compounds, phase transitions in these crystals are accompanied by a hydrogen-bond network rearrangement, resulting in radical changes of their properties, in particular, in the appearance of proton conductivity about 10–1 Ω–1 cm–1. These crystals are unique in the class of proton conductors, since the superprotonic conductivity is related to the structural features of these compounds rather than to the presence of doping additives. The occurrence of high superprotonic conductivity in the Me3H(XO4)2 (Me = K, Rb, Cs, NH4; X = S, Se, P, As) crystals is associated with the formation of a qualitatively new and dynamically disordered hydrogen-bond system [1]. In K9H7(SO4)8·N2O crystals, the only known representative of the Me9H7(XO4)8·xN2O family, the occurrence of high conductivity is associated with the outward diffusion of water molecules, the hydrogen-bond network rearrangement, and the formation of channels for the possible motion of K+ ions [2]. The hydrogen-bond rearrangement and the hindered back diffusion of water to the crystal bulk stabilize the high-temperature crystal structure and ensure its supercooling to low temperatures. The new crystals of Cs3(HSO4)2(H2PO4), Cs4(HSO4)3(H2PO4) and Cs6H(HSO4)3(H2PO4)4 were grown up in the CsHSO4–CsH2PO4-H2O system - enough big, with good optic quality [3]. The thermal and optical properties of crystals as well as their conductivity have been investigated in the temperature range 295 – 445 K. It was observed superprotonic phase transitions at 409, 411 and 365 K correspondingly. The distinction in the properties of Cs3(HSO4)2(H2PO4) and Cs4(HSO4)3(H2PO4) (sp. gr. C2/c at 295 K) is related to differences in nets of hydrogen bonds formed between different-occupied XO4 tetrahedra. Cs6H(HSO4)3(H2PO4)4 srystals (sp. gr. I-43d at 295 K) have the net of hydrogen bonds which is completely different. After cooling the high-temperature superprotonic phase preserves long enough without essential decrease in conductivity. This study was supported by the Russian Foundation for Basic Research (projects 13-03-12216 and 13-02-92693).

scholarly journals Hydrogen bond network analysis reveals the pathway for the proton transfer in the E-channel of T. thermophilus Complex I

2020 ◽  
Vol 1861 (10) ◽  
pp. 148240 ◽  
Author(s):  
Umesh Khaniya ◽  
Chitrak Gupta ◽  
Xiuhong Cai ◽  
Junjun Mao ◽  
Divya Kaur ◽  
...  
Keyword(s):  
Hydrogen Bond ◽  
Network Analysis ◽  
Proton Transfer ◽  
Complex I ◽  
Hydrogen Bond Network ◽  
Bond Network

Hydrogen bond network structures of protonated short-chain alcohol clusters

2018 ◽  
Vol 20 (22) ◽  
pp. 14971-14991 ◽  
Author(s):  
Asuka Fujii ◽  
Natsuko Sugawara ◽  
Po-Jen Hsu ◽  
Takuto Shimamori ◽  
Ying-Cheng Li ◽  
...  
Keyword(s):  
Hydrogen Bond ◽  
Short Chain ◽  
Network Structures ◽  
Hydrogen Bond Network ◽  
Chain Alcohol ◽  
Hydrogen Bond Networks ◽  
Physical Essence ◽  
Short Chain Alcohol ◽  
Bond Network

Protonated alcohol clusters enable extraction of the physical essence of the nature of hydrogen bond networks.

Performance of the MM/GBSA scoring using a binding site hydrogen bond network-based frame selection: the protein kinase case

2014 ◽  
Vol 16 (27) ◽  
pp. 14047-14058 ◽  
Author(s):  
Francisco Adasme-Carreño ◽  
Camila Muñoz-Gutierrez ◽  
Julio Caballero ◽  
Jans H. Alzate-Morales
Keyword(s):  
Hydrogen Bond ◽  
Protein Kinase ◽  
Network Analysis ◽  
Binding Site ◽  
Case Studies ◽  
Hydrogen Bond Network ◽  
Frame Selection ◽  
Bond Network

Conformational clustering using hydrogen bond network analysis improved the MM/GBSA scoring for some protein-kinase–ligand systems used as case studies.

Two polymorphs of bis(2-carbamoylguanidinium) fluorophosphonate dihydrate

2012 ◽  
Vol 68 (2) ◽  
pp. o71-o75 ◽  
Author(s):  
Jan Fábry ◽  
Michaela Fridrichová ◽  
Michal Dušek ◽  
Karla Fejfarová ◽  
Radmila Krupková
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonds ◽  
Water Molecule ◽  
Three Dimensional ◽  
Mirror Plane ◽  
Water Molecules ◽  
Hydrogen Bond Network ◽  
Hydrogen Bond Networks ◽  
Bond Network ◽  
Graph Set

Two polymorphs of bis(2-carbamoylguanidinium) fluorophosphonate dihydrate, 2C2H7N4O+·FO3P2−·2H2O, are presented. Polymorph (I), crystallizing in the space groupPnma, is slightly less densely packed than polymorph (II), which crystallizes inPbca. In (I), the fluorophosphonate anion is situated on a crystallographic mirror plane and the O atom of the water molecule is disordered over two positions, in contrast with its H atoms. The hydrogen-bond patterns in both polymorphs share similar features. There are O—H...O and N—H...O hydrogen bonds in both structures. The water molecules donate their H atoms to the O atoms of the fluorophosphonates exclusively. The water molecules and the fluorophosphonates participate in the formation ofR44(10) graph-set motifs. These motifs extend along theaaxis in each structure. The water molecules are also acceptors of either one [in (I) and (II)] or two [in (II)] N—H...O hydrogen bonds. The water molecules are significant building elements in the formation of a three-dimensional hydrogen-bond network in both structures. Despite these similarities, there are substantial differences between the hydrogen-bond networks of (I) and (II). The N—H...O and O—H...O hydrogen bonds in (I) are stronger and weaker, respectively, than those in (II). Moreover, in (I), the shortest N—H...O hydrogen bonds are shorter than the shortest O—H...O hydrogen bonds, which is an unusual feature. The properties of the hydrogen-bond network in (II) can be related to an unusually long P—O bond length for an unhydrogenated fluorophosphonate anion that is present in this structure. In both structures, the N—H...F interactions are far weaker than the N—H...O hydrogen bonds. It follows from the structure analysis that (II) seems to be thermodynamically more stable than (I).

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