scholarly journals Hydroxyl and Water Molecule Orientations in Trypsin

1996 ◽  
pp. 273-287
Author(s):  
Robert S. McDowell ◽  
Anthony A. Kossiakoff
Keyword(s):  
Water Molecule

Gas-Phase Clustering of NO+ with H2S and H2O

2007 ◽  
Vol 72 (8) ◽  
pp. 1122-1138 ◽  
Author(s):  
Milan Uhlár ◽  
Ivan Černušák
Keyword(s):  
Hydrogen Bonds ◽  
Water Molecule ◽  
Gas Phase ◽  
Saddle Points ◽  
Solvent Molecule ◽  
Local Minima ◽  
Additional Water ◽  
Three Body ◽  
Rain Formation ◽  
Stable Structures

The complex NO+·H2S, which is assumed to be an intermediate in acid rain formation, exhibits thermodynamic stability of ∆Hº300 = -76 kJ mol-1, or ∆Gº300 = -47 kJ mol-1. Its further transformation via H-transfer is associated with rather high barriers. One of the conceivable routes to lower the energy of the transition state is the action of additional solvent molecule(s) that can mediate proton transfer. We have studied several NO+·H2S structures with one or two additional water molecule(s) and have found stable structures (local minima), intermediates and saddle points for the three-body NO+·H2S·H2O and four-body NO+·H2S·(H2O)2 clusters. The hydrogen bonds network in the four-body cluster plays a crucial role in its conversion to thionitrous acid.

DFT study on the hydrolysis of metsulfuron-methyl: A sulfonylurea herbicide

2018 ◽  
Vol 17 (08) ◽  
pp. 1850050 ◽  
Author(s):  
Qiuhan Luo ◽  
Gang Li ◽  
Junping Xiao ◽  
Chunhui Yin ◽  
Yahui He ◽  
...  
Keyword(s):  
Free Energy ◽  
Water Molecule ◽  
Carbonyl Group ◽  
Energy Barrier ◽  
Density Functional ◽  
Free Energy Barrier ◽  
Functional Theory ◽  
Metsulfuron Methyl ◽  
Catalytic Role ◽  
Hydrolysis Of

Sulfonylureas are an important group of herbicides widely used for a range of weeds and grasses control particularly in cereals. However, some of them tend to persist for years in environments. Hydrolysis is the primary pathway for their degradation. To understand the hydrolysis behavior of sulfonylurea herbicides, the hydrolysis mechanism of metsulfuron-methyl, a typical sulfonylurea, was investigated using density functional theory (DFT) at the B3LYP/6-31[Formula: see text]G(d,p) level. The hydrolysis of metsulfuron-methyl resembles nucleophilic substitution by a water molecule attacking the carbonyl group from aryl side (pathway a) or from heterocycle side (pathway b). In the direct hydrolysis, the carbonyl group is directly attacked by one water molecule to form benzene sulfonamide or heterocyclic amine; the free energy barrier is about 52–58[Formula: see text]kcal[Formula: see text]mol[Formula: see text]. In the autocatalytic hydrolysis, with the second water molecule acting as a catalyst, the free energy barrier, which is about 43–45[Formula: see text]kcal[Formula: see text]mol[Formula: see text], is remarkably reduced by about 11[Formula: see text]kcal[Formula: see text]mol[Formula: see text]. It is obvious that water molecules play a significant catalytic role during the hydrolysis of sulfonylureas.

Local pseudosymmetry of the water molecule in BaBr2 · 2H2O, a neutron diffraction study

1991 ◽  
Vol 197 (3-4) ◽  
Author(s):  
Th. Kellersohn ◽  
B. Engelen ◽  
H. D. Lutz ◽  
H. Bartl ◽  
B. P. Schweiss ◽  
...  
Keyword(s):  
Neutron Diffraction ◽  
Water Molecule ◽  
Diffraction Study ◽  
Neutron Diffraction Study

AbstractBarium bromide dihydrate, BaBr

scholarly journals 1H NMR investigation of distal mutant deoxy myoglobins. Interpretation of proximal His contact shifts in terms of a localized distal water molecule.

1994 ◽  
Vol 269 (47) ◽  
pp. 29629-29635
Author(s):  
G N La Mar ◽  
F Dalichow ◽  
X Zhao ◽  
Y Dou ◽  
M Ikeda-Saito ◽  
...  
Keyword(s):  
Water Molecule ◽  
1H Nmr

scholarly journals Fe(2)OG: an integrated HMM profile-based web server to predict and analyze putative non-haem iron(II)- and 2-oxoglutarate-dependent dioxygenase function in protein sequences

2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Siddhartha Kundu
Keyword(s):  
Amino Acid ◽  
Water Molecule ◽  
Active Site ◽  
Ferrous Iron ◽  
Web Server ◽  
Protein Sequences ◽  
Diverse Group ◽  
And Function ◽  
Functionally Diverse ◽  
Haem Iron

Abstract Objective Non-haem iron(II)- and 2-oxoglutarate-dependent dioxygenases (i2OGdd), are a taxonomically and functionally diverse group of enzymes. The active site comprises ferrous iron in a hexa-coordinated distorted octahedron with the apoenzyme, 2-oxoglutarate and a displaceable water molecule. Current information on novel i2OGdd members is sparse and relies on computationally-derived annotation schema. The dissimilar amino acid composition and variable active site geometry thereof, results in differing reaction chemistries amongst i2OGdd members. An additional need of researchers is a curated list of sequences with putative i2OGdd function which can be probed further for empirical data. Results This work reports the implementation of $$Fe\left(2\right)OG$$ F e 2 O G , a web server with dual functionality and an extension of previous work on i2OGdd enzymes $$\left(Fe\left(2\right)OG\equiv \{H2OGpred,DB2OG\}\right)$$ F e 2 O G ≡ { H 2 O G p r e d , D B 2 O G } . $$Fe\left(2\right)OG$$ F e 2 O G , in this form is completely revised, updated (URL, scripts, repository) and will strengthen the knowledge base of investigators on i2OGdd biochemistry and function. $$Fe\left(2\right)OG$$ F e 2 O G , utilizes the superior predictive propensity of HMM-profiles of laboratory validated i2OGdd members to predict probable active site geometries in user-defined protein sequences. $$Fe\left(2\right)OG$$ F e 2 O G , also provides researchers with a pre-compiled list of analyzed and searchable i2OGdd-like sequences, many of which may be clinically relevant. $$Fe(2)OG$$ F e ( 2 ) O G , is freely available (http://204.152.217.16/Fe2OG.html) and supersedes all previous versions, i.e., H2OGpred, DB2OG.

Water Molecule Dispositions in the Cesium Sulfate α- and β-Alums: Single-Crystal Neutron Diffraction Studies of CsM(SO4)2.12H2O (M=V, Rh)

1993 ◽  
Vol 46 (9) ◽  
pp. 1337 ◽  
Author(s):  
JK Beattie ◽  
SP Best ◽  
FH Moore ◽  
BW Skelton ◽  
AH White
Keyword(s):  
Neutron Diffraction ◽  
Water Molecule ◽  
Single Crystal ◽  
Tilt Angle ◽  
Room Temperature ◽  
Bond Angle ◽  
Sulfate Salt ◽  
Cell Dimensions ◽  
Coordinated Water ◽  
Unit Cell Dimensions

Room-temperature single-crystal neutron diffraction studies are recorded for two alums, Cs( Rh /V)(SO4)2.12H2O [cubic, Pa3, a 12.357(5) ( Rh ), 12.434(1)Ǻ (V)], residuals 0.037 and 0.068 for 328 and 164 'observed' reflections, with the intention of defining water molecule hydrogen atom orientations. Whereas the two tervalent hexaaqua cations are similar in size [ rM -O = 2.010(6)Ǻ (M = V) and 2.006(2)Ǻ (M = Rh )] the vanadium salt adopts the β alum modification while rhodium gives an α alum. Significantly, the water coordination geometry is different in the two cases with the tilt angle between the plane of the water molecule and the M-O bond vector being 1° (M = V) and 35° (M = Rh ). The tilt angle for water coordinated to rhodium in CsRh (SeO4)2.12H2O is inferred from the unit cell dimensions to be similar to that of the corresponding sulfate salt and not that which generally pertains for caesium selenate alums. Significant differences in the H-O-H bond angle are found for trigonal planar and trigonal pyramidal water coordination, suggesting that differences in the metal(III)-water interaction are a determinant of the geometry of the coordinated water molecule in the caesium sulfate/ selenate alum lattices.

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