Hydrogen Bond Formation Between the Gate and Water Molecules Accelerates Channel Opening of the Bacterial Mechanosensitive Channel Mscl

Reline, a mixture of urea and choline chloride in 2:1 molar ratio, is one of the most frequently used deep eutectic solvents. Pure reline and its aqueous solution have large scale industrial use. Owing to the presence of active hydrogen bond formation sites, urea and choline cation can disrupt the hydrogen-bonded network in water. However, a quantitative understanding of the microscopic structural features of water in the presence of reline is still lacking. We use extensive all-atom molecular dynamics simulations to elucidate the effect of the gradual addition of co-solvents on microscopic arrangements of water molecules. We consider four aqueous solutions of reline, between the wt% 26.3 to 91.4. A disruption of the local hydrogen-bonded water structure is observed on inclusion of urea and choline chloride. The extent of deviation of water structure from tetrahedrality is quantified using the orientational order parameter. Our analyses show a monotonic increase in structural disorder as the co-solvents are added. Increment in the values are observed when highly electro-negative hetero-atoms like Nitrogen, Oxygen of urea and choline cations are counted as the partners of the central water molecules. Further insights are drawn from the characterization of the hydrogen-bonded network of the water and we observe gradual rupturing of water-water hydrogen bonds and its subsequent replacement by the water-urea hydrogen bonds. A negligible contribution from the hydrogen bonds between water and bulky choline cation has also been found. Considering all the constituents as the hydrogen bond partner we calculate the possibility of successful hydrogen bond formation with a central water molecule. This gives a clear picture of the underlying mechanism of water replacement by urea.

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Covalency in the hydrogen bond and the properties of water and ice

Proceedings of the Royal Society of London Series A - Mathematical and Physical Sciences ◽

10.1098/rspa.1958.0206 ◽

1958 ◽

Vol 247 (1251) ◽

pp. 481-492 ◽

Cited By ~ 118

Keyword(s):

Hydrogen Bond ◽

Dielectric Relaxation ◽

Bond Formation ◽

Water Molecules ◽

Dielectric Relaxation Time ◽

Hydrogen Bond Formation ◽

Self Diffusion ◽

Hexagonal Ice ◽

Polar Solutes ◽

Bulk Relaxation

Covalency in a hydrogen bond between two water molecules produces a partial charge separation and some rehybridization of the L -shell electrons of the oxygen atom partner. These changes promote the participation of the molecules in additional bond formation which, in turn, stabilizes the original bond. These interactions must be expected to impart a co-operative character to hydrogen-bond formation in liquid water, and it is postulated that the structure of this liquid is characterized by co-operatively bonded flickering clusters of ice-like material surrounded by, and alternating roles with, disordered fluid which makes up the rest of the sample. This assumption offers an explanation for a number of facts, including the essential identity of the heats of activation obtained for viscous flow, for self-diffusion, for dielectric relaxation and (probably) for bulk relaxation. It also makes possible the interpretation of the extra ice-likeness found in aqueous solutions of non-polar solutes, and of the further fact that this extra ice-likeness seems to be accompanied by a lengthening of dielectric relaxation time. When applied to ice these concepts, taken together with the discussion given by Jeffrey et al . (1956) of Wurzite-type crystals, seem to offer a straightforward explanation of the facts that a ‘diamond’ modification of ice is observed at low temperatures and that the c/a ratio in hexagonal ice becomes smaller with rising temperature. The degree of covalency which this explanation presupposes seems to require a modification of the simple Bjerrum (1951) picture of the rotational defects which have been invoked to explain the dielectric properties of ice. An alternative dielectric process seems to be possible which would involve flickering droplets of liquid-like material in ice, which might, mutatis mutandis , play a role corresponding to that of flickering clusters in the liquid phase.

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Microscopic Structural Features of Water in Aqueous-Reline Mixture of Varying Composition

10.26434/chemrxiv.13490892.v1 ◽

2020 ◽

Author(s):

Soham Sarkar ◽

Atanu Maity ◽

Rajarshi Chakrabarti

Keyword(s):

Hydrogen Bond ◽

Hydrogen Bonds ◽

Choline Chloride ◽

Bond Formation ◽

Orientational Order ◽

Water Structure ◽

Structural Features ◽

Water Molecules ◽

Hydrogen Bond Formation ◽

Hydrogen Bonded

Reline, a mixture of urea and choline chloride in 2:1 molar ratio, is one of the most frequently used deep eutectic solvents. Pure reline and its aqueous solution have large scale industrial use. Owing to the presence of active hydrogen bond formation sites, urea and choline cation can disrupt the hydrogen-bonded network in water. However, a quantitative understanding of the microscopic structural features of water in the presence of reline is still lacking. We use extensive all-atom molecular dynamics simulations to elucidate the effect of the gradual addition of co-solvents on microscopic arrangements of water molecules. We consider four aqueous solutions of reline, between the wt% 26.3 to 91.4. A disruption of the local hydrogen-bonded water structure is observed on inclusion of urea and choline chloride. The extent of deviation of water structure from tetrahedrality is quantified using the orientational order parameter. Our analyses show a monotonic increase in structural disorder as the co-solvents are added. Increment in the values are observed when highly electro-negative hetero-atoms like Nitrogen, Oxygen of urea and choline cations are counted as the partners of the central water molecules. Further insights are drawn from the characterization of the hydrogen-bonded network of the water and we observe gradual rupturing of water-water hydrogen bonds and its subsequent replacement by the water-urea hydrogen bonds. A negligible contribution from the hydrogen bonds between water and bulky choline cation has also been found. Considering all the constituents as the hydrogen bond partner we calculate the possibility of successful hydrogen bond formation with a central water molecule. This gives a clear picture of the underlying mechanism of water replacement by urea.

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Adsorption and Dehydration of Water Molecules from α, β and γ Cyclodextrins — A Study by TGA Analysis and Gravimetry

Advanced Materials Research ◽

10.4028/www.scientific.net/amr.1120-1121.886 ◽

2015 ◽

Vol 1120-1121 ◽

pp. 886-890

Author(s):

Alfred A. Christy

Keyword(s):

Hydrogen Bond ◽

Hydrogen Bonding ◽

Thermogravimetric Analysis ◽

Bond Formation ◽

The Other ◽

Water Molecules ◽

Hydrogen Bond Formation ◽

Oh Groups ◽

Hydrogen Bondings ◽

Tga Analysis

The adsorption and desorption of water molecules from α, β and γ-cyclodextrins were studied by gravimetric and thermogravimetric analysis. Cyclodextrins like all the other carbohydrates have tendency to adsorb water molecules. However, their cyclic nature tends to affect the adsorption patterns. The cyclic nature of the cyclodextrins facilitates the formation of hydrogen bondings between OH groups of the neighbouring glucose units. The C2(1)-OH forms hydrogen bonding with C3(2)-OH. The extent of the hydrogen bond formation and strength of the hydrogen bond affect the way the adsorption and dehydration of water molecules from cyclodextrins take place.

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Two-dimensional hydrogen-bonded networks in 1-(diaminomethylene)thiouron-1-ium nitrate and bis[1-(diaminomethylene)thiouron-1-ium] phosphonate monohydrate

Acta Crystallographica Section C Crystal Structure Communications ◽

10.1107/s0108270109006325 ◽

2009 ◽

Vol 65 (3) ◽

pp. o118-o120 ◽

Cited By ~ 1

Author(s):

Jan Janczak ◽

Genivaldo Julio Perpétuo

Keyword(s):

Hydrogen Bond ◽

Organic Molecule ◽

Bond Formation ◽

Double Layers ◽

Water Molecules ◽

Hydrogen Bond Formation ◽

Hydrogen Bonding Interactions ◽

Counter Ions ◽

Oppositely Charged ◽

Nitrate Anions

Crystals of the title compounds, C2H7N4S+·NO3−, (I), and 2C2H7N4S+·HPO32−·H2O, (II), are built up from 1-(diaminomethylene)thiouron-1-ium cations and nitrate anions in (I), and from phosphonate anions and water molecules in (II). In both crystals, the cations and anions are linked togetherviaN—H...O hydrogen bonds. The 1-(diaminomethylene)thiouron-1-ium cations exhibit a twisted conformation. Both arms of the cations are planar and are turned in opposite directions around the C—N bond involving the central N atom. Hydrogen-bonding interactions join oppositely charged units into layers in the nitrate salt and into double layers in the phosphonate monohydrate salt. In addition, the structures are stabilized by π–π interactions between the delocalized π bonds of the cations. The significance of this study lies in the illustration of the differences between the supramolecular aggregations in the nitrate and phosphonate salts of a small organic molecule. The different geometries of the counter-ions and their different potential for hydrogen-bond formation results in markedly different hydrogen-bond arrangements.

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Vapochromism induced by intermolecular electron transfer coupled with hydrogen-bond formation in zinc dithiolene complex

Journal of Materials Chemistry C ◽

10.1039/d0tc04280c ◽

2020 ◽

Vol 8 (42) ◽

pp. 14939-14947

Author(s):

So Yokomori ◽

Shun Dekura ◽

Tomoko Fujino ◽

Mitsuaki Kawamura ◽

Taisuke Ozaki ◽

...

Keyword(s):

Hydrogen Bond ◽

Electron Transfer ◽

Bond Formation ◽

Intermolecular Electron Transfer ◽

Hydrogen Bond Formation ◽

Complex Crystal

A novel vapochromic mechanism by intermolecular electron transfer coupled with hydrogen-bond formation was realized in a zinc dithiolene complex crystal.

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Diverse mechanisms of carbon-hydrogen bond formation through binuclear reductive elimination reactions

Journal of the American Chemical Society ◽

10.1021/ja00366a044 ◽

1982 ◽

Vol 104 (2) ◽

pp. 619-621 ◽

Cited By ~ 31

Author(s):

Mario J. Nappa ◽

Roberto Santi ◽

Steven P. Diefenbach ◽

Jack Halpern

Keyword(s):

Hydrogen Bond ◽

Bond Formation ◽

Reductive Elimination ◽

Hydrogen Bond Formation ◽

Elimination Reactions

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Theoretical analysis of the (HNO)2, (HNO···HNS), and (HNS)2 dimers — A case of red and blue shifts of N–H stretching frequency

Canadian Journal of Chemistry ◽

10.1139/v10-048 ◽

2010 ◽

Vol 88 (8) ◽

pp. 849-857 ◽

Cited By ~ 2

Author(s):

Nguyen Tien Trung ◽

Tran Thanh Hue ◽

Minh Tho Nguyen

Keyword(s):

Hydrogen Bond ◽

Quantum Chemical ◽

Bond Formation ◽

Blue Shift ◽

Proton Donor ◽

Basis Sets ◽

Coupled Cluster ◽

Hydrogen Bond Formation ◽

Length Contraction ◽

Moller Plesset

The hydrogen-bonded interactions in the simple (HNZ)2 dimers, with Z = O and S, were investigated using quantum chemical calculations with the second-order Møller–Plesset perturbation (MP2), coupled-cluster with single, double (CCSD), and triple excitations (CCSD(T)) methods in conjunction with the 6-311++G(2d,2p), aug-cc-pVDZ, and aug-cc-pVTZ basis sets. Six-membered cyclic structures were found to be stable complexes for the dimers (HNO)2, (HNS)2, and (HNO–HNS). The pair (HNS)2 has the largest complexation energy (–11 kJ/mol), and (HNO)2 the smallest one (–9 kJ/mol). A bond length contraction and a frequency blue shift of the N–H bond simultaneously occur upon hydrogen bond formation of the N–H···S type, which has rarely been observed before. The stronger the intramolecular hyperconjugation and the lower the polarization of the X–H bond involved as proton donor in the hydrogen bond, the more predominant is the formation of a blue-shifting hydrogen bond.

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