QM/MM Dynamics of CH3COO−−Water Hydrogen Bonds in Aqueous Solution

2010 ◽  
Vol 114 (38) ◽  
pp. 10443-10453 ◽  
Author(s):  
Apirak Payaka ◽  
Anan Tongraar ◽  
Bernd Michael Rode
Keyword(s):  
Aqueous Solution ◽  
Hydrogen Bonds ◽  
Water Hydrogen

Ab initio QM/MM dynamics of anion–water hydrogen bonds in aqueous solution

2005 ◽  
Vol 403 (4-6) ◽  
pp. 314-319 ◽  
Author(s):  
Anan Tongraar ◽  
Bernd Michael Rode
Keyword(s):  
Aqueous Solution ◽  
Hydrogen Bonds ◽  
Ab Initio ◽  
Water Hydrogen

Characterization of the F−-water and Cl−-water hydrogen bonds in aqueous solution: From “interior” (I) to “surface” (S) states

2017 ◽  
Vol 248 ◽  
pp. 271-277 ◽  
Author(s):  
Pattrawan Sripa ◽  
Anan Tongraar ◽  
Teerakiat Kerdcharoen
Keyword(s):  
Aqueous Solution ◽  
Hydrogen Bonds ◽  
S States ◽  
Water Hydrogen

Rate constants for the dissociation of amine-water hydrogen bonds and the effect of nonpolar groups in aqueous solution

1967 ◽  
Vol 89 (17) ◽  
pp. 4405-4411 ◽  
Author(s):  
Ernest. Grunwald ◽  
Earle K. Ralph
Keyword(s):  
Aqueous Solution ◽  
Hydrogen Bonds ◽  
Rate Constants ◽  
Water Hydrogen

Characteristics of CO32−–water hydrogen bonds in aqueous solution: insights from HF/MM and B3LYP/MM MD simulations

2011 ◽  
Vol 13 (37) ◽  
pp. 16851 ◽  
Author(s):  
Anan Tongraar ◽  
Pathumwadee Yotmanee ◽  
Apirak Payaka
Keyword(s):  
Aqueous Solution ◽  
Hydrogen Bonds ◽  
Md Simulations ◽  
Water Hydrogen

Combined QM/MM MD Study of HCOO−−Water Hydrogen Bonds in Aqueous Solution

2009 ◽  
Vol 113 (13) ◽  
pp. 3291-3298 ◽  
Author(s):  
Apirak Payaka ◽  
Anan Tongraar ◽  
Bernd Michael Rode
Keyword(s):  
Aqueous Solution ◽  
Hydrogen Bonds ◽  
Water Hydrogen

scholarly journals Crystal structure of the new hybrid material bis(1,4-diazoniabicyclo[2.2.2]octane) di-μ-chlorido-bis[tetrachloridobismuthate(III)] dihydrate

2015 ◽  
Vol 71 (11) ◽  
pp. 1384-1387
Author(s):  
Marwen Chouri ◽  
Habib Boughzala
Keyword(s):  
Crystal Structure ◽  
Aqueous Solution ◽  
Hydrogen Bonds ◽  
Room Temperature ◽  
Molar Ratio ◽  
Water Molecules ◽  
Site Symmetry ◽  
Two Dimensional ◽  
Slow Evaporation ◽  
Solution Ph

The title compound bis(1,4-diazoniabicyclo[2.2.2]octane) di-μ-chlorido-bis[tetrachloridobismuthate(III)] dihydrate, (C6H14N2)2[Bi2Cl10]·2H2O, was obtained by slow evaporation at room temperature of a hydrochloric aqueous solution (pH = 1) containing bismuth(III) nitrate and 1,4-diazabicyclo[2.2.2]octane (DABCO) in a 1:2 molar ratio. The structure displays a two-dimensional arrangement parallel to (100) of isolated [Bi2Cl10]4−bioctahedra (site symmetry -1) separated by layers of organic 1,4-diazoniabicyclo[2.2.2]octane dications [(DABCOH2)2+] and water molecules. O—H...Cl, N—H...O and N—H...Cl hydrogen bonds lead to additional cohesion of the structure.

scholarly journals Protein sequence optimization with a pairwise decomposable penalty for buried unsatisfied hydrogen bonds

2020 ◽  
Author(s):  
Brian Coventry ◽  
David Baker
Keyword(s):  
Aqueous Solution ◽  
Hydrogen Bonds ◽  
Protein Design ◽  
Protein Sequence ◽  
Quadratic Function ◽  
Energetic Cost ◽  
Energy Term ◽  
Sequence Optimization ◽  
Polar Groups ◽  
Sidechain Rotamers

AbstractIn aqueous solution, polar groups make hydrogen bonds with water, and hence burial of such groups in the interior of a protein is unfavorable unless the loss of hydrogen bonds with water is compensated by formation of new ones with other protein groups. Hence, buried “unsatisfied” polar groups making no hydrogen bonds are very rare in proteins. Efficiently representing the energetic cost of unsatisfied hydrogen bonds with a pairwise-decomposable energy term during protein design is challenging since whether or not a group is satisfied depends on all of its neighbors. Here we describe a method for assigning a pairwise-decomposable energy to sidechain rotamers such that following combinatorial sidechain packing, buried unsaturated polar atoms are penalized. The penalty can be any quadratic function of the number of unsatisfied polar groups, and can be computed very rapidly. We show that inclusion of this term in Rosetta sidechain packing calculations substantially reduces the number of buried unsatisfied polar groups.

scholarly journals Crystal structure of β-D,L-fructose

2015 ◽  
Vol 71 (10) ◽  
pp. o719-o720 ◽  
Author(s):  
Tomohiko Ishii ◽  
Tatsuya Senoo ◽  
Akihide Yoshihara ◽  
Kazuhiro Fukada ◽  
Genta Sakane
Keyword(s):  
Crystal Structure ◽  
Aqueous Solution ◽  
Hydrogen Bonds ◽  
Title Compound ◽  
Three Dimensional ◽  
Equimolar Mixture ◽  
Compound C ◽  
Dimensional Network ◽  
Hydroxy Groups

The title compound, C6H12O6, was crystallized from an aqueous solution of equimolar mixture of D- and L-fructose (1,3,4,5,6-pentahydroxyhexan-2-one,arabino-hexulose or levulose), and it was confirmed that D-fructose (or L-fructose) formed β-pyranose with a2C5(or5C2) conformation. In the crystal, two O—H...O hydrogen bonds between the hydroxy groups at the C-1 and C-3 positions, and at the C-4 and C-5 positions connect homochiral molecules into a column along theaaxis. The columns are linked by other O—H...O hydrogen bonds between D- and L-fructose molecules, forming a three-dimensional network.

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