The effect of cooperativity on hydrogen bonding interactions in native cellulose Iβ fromab initiomolecular dynamics simulations

2008 ◽  
Vol 34 (2) ◽  
pp. 183-191 ◽  
Author(s):  
Xianghong Qian
Keyword(s):  
Hydrogen Bonding ◽  
Native Cellulose ◽  
Hydrogen Bonding Interactions ◽  
Cellulose Iβ ◽  
Dynamics Simulations

scholarly journals Binding selectivity of inhibitors toward the first over the second bromodomain of BRD4: theoretical insights from free energy calculations and multiple short molecular dynamics simulations

RSC Advances ◽  
2021 ◽  
Vol 11 (2) ◽  
pp. 745-759
Author(s):  
Yan Wang ◽  
Shiliang Wu ◽  
Lifei Wang ◽  
Zhiyong Yang ◽  
Juan Zhao ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Free Energy ◽  
Hydrogen Bonding ◽  
Molecular Dynamics Simulations ◽  
Free Energy Calculations ◽  
Binding Selectivity ◽  
Energy Calculations ◽  
Hydrogen Bonding Interactions ◽  
Dynamics Simulations

Hydrogen bonding interactions of waters with BD1/BD2 and inhibitors play significant roles in inhibitor bindings.

scholarly journals Hydrogen bonding interactions of H2O and SiOH on a boroaluminosilicate glass corroded in aqueous solution

2020 ◽  
Vol 4 (1) ◽  
Author(s):  
Dien Ngo ◽  
Hongshen Liu ◽  
Zhe Chen ◽  
Huseyin Kaya ◽  
Tawanda J. Zimudzi ◽  
...  
Keyword(s):  
Hydrogen Bonding ◽  
Physical Processes ◽  
Sum Frequency ◽  
Glass Dissolution ◽  
Hydrogen Bonding Interactions ◽  
Hydrogen Bond Strength ◽  
Sum Frequency Generation Spectroscopy ◽  
Dynamics Simulations ◽  
Glass Surfaces ◽  
Soluble Silicon

AbstractHydrogen bonding interactions play an important role in many chemical and physical processes occurring in bulk liquids and at interfaces. In this study, hydrous species (H2O and Si-OH) on nano-porous alteration layers (gels) formed on a boroaluminosilicate glass called International Simple Glass corroded in aqueous solutions at pH 7 and pH 9, and initially saturated with soluble silicon-containing species were analyzed using linear and non-linear vibrational spectroscopy in combination with molecular dynamics simulations. The simulation results revealed various possible types of hydrogen bonds among these hydrous species in nanoconfinement environments with their populations depending on pore-size distribution. The nano-porous gels formed on corroded glass surfaces enhance hydrogen bond strength between hydrous species as revealed by attenuated total reflectance infrared spectroscopy. Sum frequency generation spectroscopy showed some significant differences in hydrogen bonding interactions on alteration layers formed at pH 7 and pH 9. The glass dissolution under the leaching conditions used in this study has been known to be ten times faster at pH 7 in comparison to that at pH 9 due to unknown reasons. The simulation and experimental results obtained in this study indicate that the water mobility in the gel formed at pH 9 could be slower than that in the gel formed at pH 7, and as a result, the leaching rate at pH 9 is slower than that at pH 7.

scholarly journals Formation of an unusual glutamine tautomer in a blue light using flavin photocycle characterizes the light-adapted state

2020 ◽  
Vol 117 (43) ◽  
pp. 26626-26632 ◽  
Author(s):  
Joshua J. Goings ◽  
Pengfei Li ◽  
Qiwen Zhu ◽  
Sharon Hammes-Schiffer
Keyword(s):  
Hydrogen Bonding ◽  
Long Range ◽  
Blue Light ◽  
Tautomeric Form ◽  
Proton Coupled Electron Transfer ◽  
Hydrogen Bonding Interactions ◽  
Forward Proton ◽  
Dynamics Simulations ◽  
Spectroscopic Signatures ◽  
Modular Nature

Blue light using flavin (BLUF) photoreceptor proteins are critical for many light-activated biological processes and are promising candidates for optogenetics because of their modular nature and long-range signaling capabilities. Although the photocycle of the Slr1694 BLUF domain has been characterized experimentally, the identity of the light-adapted state following photoexcitation of the bound flavin remains elusive. Herein hybrid quantum mechanical/molecular mechanical (QM/MM) molecular dynamics simulations of this photocycle provide a nonequilibrium dynamical picture of a possible mechanism for the formation of the light-adapted state. Photoexcitation of the flavin induces a forward proton-coupled electron transfer (PCET) process that leads to the formation of an imidic acid tautomer of Gln50. The calculations herein show that the subsequent rotation of Gln50 allows a reverse PCET process that retains this tautomeric form. In the resulting purported light-adapted state, the glutamine tautomer forms a hydrogen bond with the flavin carbonyl group. Additional ensemble-averaged QM/MM calculations of the dark-adapted and purported light-adapted states demonstrate that the light-adapted state with the imidic acid glutamine tautomer reproduces the experimentally observed spectroscopic signatures. Specifically, the calculations reproduce the red shifts in the flavin electronic absorption and carbonyl stretch infrared spectra in the light-adapted state. Further hydrogen-bonding analyses suggest the formation of hydrogen-bonding interactions between the flavin and Arg65 in the light-adapted state, providing a plausible explanation for the experimental observation of faster photoinduced PCET in this state. These characteristics of the light-adapted state may also be essential for the long-range signaling capabilities of this photoreceptor protein.

Hierarchy of π-Stacking Determines the Conformational Preference of Bis-Squaraines

2020 ◽  
Author(s):  
Abhishek Singh ◽  
Reman K. Singh ◽  
G Naresh Patwari
Keyword(s):  
Hydrogen Bonding ◽  
Rational Design ◽  
Biological Molecules ◽  
Conformational Space ◽  
X Ray Crystallography ◽  
Simple Strategy ◽  
Induced Folding ◽  
Π Stacking ◽  
Varying Length ◽  
Dynamics Simulations

The rational design of conformationally controlled foldable modules can lead to a deeper insight into the conformational space of complex biological molecules where non-covalent interactions such as hydrogen bonding and π-stacking are known to play a pivotal role. Squaramides are known to have excellent hydrogen bonding capabilities and hence, are ideal molecules for designing foldable modules that can mimic the secondary structures of bio-molecules. The π-stacking induced folding of bis-squaraines tethered using aliphatic primary and secondary-diamine linkers of varying length is explored with a simple strategy of invoking small perturbations involving the length linkers and degree of substitution. Solution phase NMR investigations in combination with molecular dynamics simulations suggest that bis-squaraines predominantly exist as extended conformations. Structures elucidated by X-ray crystallography confirmed a variety of folded and extended secondary conformations including hairpin turns and 𝛽-sheets which are determined by the hierarchy of π-stacking relative to N–H···O hydrogen bonds.

Hierarchy of π-Stacking Determines the Conformational Preference of Bis-Squaraines

2020 ◽  
Author(s):  
Abhishek Singh ◽  
Reman K. Singh ◽  
G Naresh Patwari
Keyword(s):  
Hydrogen Bonding ◽  
Rational Design ◽  
Biological Molecules ◽  
Conformational Space ◽  
X Ray Crystallography ◽  
Simple Strategy ◽  
Induced Folding ◽  
Π Stacking ◽  
Varying Length ◽  
Dynamics Simulations

The rational design of conformationally controlled foldable modules can lead to a deeper insight into the conformational space of complex biological molecules where non-covalent interactions such as hydrogen bonding and π-stacking are known to play a pivotal role. Squaramides are known to have excellent hydrogen bonding capabilities and hence, are ideal molecules for designing foldable modules that can mimic the secondary structures of bio-molecules. The π-stacking induced folding of bis-squaraines tethered using aliphatic primary and secondary-diamine linkers of varying length is explored with a simple strategy of invoking small perturbations involving the length linkers and degree of substitution. Solution phase NMR investigations in combination with molecular dynamics simulations suggest that bis-squaraines predominantly exist as extended conformations. Structures elucidated by X-ray crystallography confirmed a variety of folded and extended secondary conformations including hairpin turns and 𝛽-sheets which are determined by the hierarchy of π-stacking relative to N–H···O hydrogen bonds.

Theoretical study of hydrogen bonding interactions in substituted nitroxide radicals

2021 ◽  
Author(s):  
Thufail M. Ismail ◽  
Neetha Mohan ◽  
P. K. Sajith
Keyword(s):  
Hydrogen Bonding ◽  
Interaction Energy ◽  
Electrostatic Potential ◽  
Molecular Electrostatic Potential ◽  
Theoretical Study ◽  
Nitroxide Radicals ◽  
Hydrogen Bonding Interactions ◽  
Bonded Complexes ◽  
Hydrogen Bonded

Interaction energy (Eint) of hydrogen bonded complexes of nitroxide radicals can be assessed in terms of the deepest minimum of molecular electrostatic potential (Vmin).

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