Enhancement of Hydrophobic Interactions and Hydrogen Bond Strength by Cooperativity: Synthesis, Modeling, and Molecular Dynamics Simulations of a Congeneric Series of Thrombin Inhibitors

2010 ◽  
Vol 53 (5) ◽  
pp. 2126-2135 ◽  
Author(s):  
Laveena Muley ◽  
Bernhard Baum ◽  
Michael Smolinski ◽  
Marek Freindorf ◽  
Andreas Heine ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Hydrogen Bond ◽  
Bond Strength ◽  
Molecular Dynamics Simulations ◽  
Hydrophobic Interactions ◽  
Thrombin Inhibitors ◽  
Hydrogen Bond Strength ◽  
Dynamics Simulations

scholarly journals Molecular Dynamics Simulations of Heterogeneous Hydrogen Bond Environment in Hydrophobic Deep Eutectic Solvents

2021 ◽  
Author(s):  
Usman Abbas ◽  
Manh Tien Nguyen ◽  
Qi Qiao ◽  
Jian Shi ◽  
Qing Shao
Keyword(s):  
Molecular Dynamics ◽  
Hydrogen Bond ◽  
Hydrogen Bonds ◽  
Molecular Dynamics Simulations ◽  
High Performance ◽  
Deep Eutectic Solvents ◽  
Decanoic Acid ◽  
Hydrogen Bond Strength ◽  
Multiple Hydrogen Bond ◽  
Dynamics Simulations

Hydrophobic deep eutectic solvents (DESs) have emerged as excellent extractants. Their performance depends on the heterogeneous hydrogen bond environment formed by multiple hydrogen bond donors and acceptors. An understanding of this heterogeneous hydrogen bond environment can be used to develop principles for designing high-performance DESs for extraction and other separation applications. We investigate the structure and dynamics of hydrogen bonds in eight hydrophobic DESs formed by decanoic acid, menthol, thymol, and Lidocaine using molecular dynamics simulations. The results show the diversity of hydrogen bonds in the eight DESs and their impact on diffusivity and molecular association. Each DES possesses four-six types of hydrogen bonds and one or two of them overwhelm the others in quantity and lifetime. The dominating hydrogen bonds determine whether the DESs are governed by intra- or inter-component associations. The component diffusivity presents an inverse relationship with the hydrogen bond strength.

Molecular Basis of Iterative C–H Oxidation by TamI, a Multifunctional P450 Monooxygenase from the Tirandamycin Biosynthetic Pathway

2020 ◽  
Author(s):  
Sean A. Newmister ◽  
Kinshuk Raj Srivastava ◽  
Rosa V. Espinoza ◽  
Kersti Caddell Haatveit ◽  
Yogan Khatri ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Molecular Basis ◽  
Hydrophobic Interactions ◽  
Cytochromes P450 ◽  
Targeted Mutagenesis ◽  
P450 Monooxygenase ◽  
Bond Functionalization ◽  
Dynamics Simulations

Biocatalysis offers an expanding and powerful strategy to construct and diversify complex molecules by C-H bond functionalization. Due to their high selectivity, enzymes have become an essential tool for C-H bond functionalization and offer complementary reactivity to small-molecule catalysts. Hemoproteins, particularly cytochromes P450, have proven effective for selective oxidation of unactivated C-H bonds. Previously, we reported the in vitro characterization of an oxidative tailoring cascade in which TamI, a multifunctional P450 functions co-dependently with the TamL flavoprotein to catalyze regio- and stereoselective hydroxylations and epoxidation to yield tirandamycin A and tirandamycin B. TamI follows a defined order including 1) C10 hydroxylation, 2) C11/C12 epoxidation, and 3) C18 hydroxylation. Here we present a structural, biochemical, and computational investigation of TamI to understand the molecular basis of its substrate binding, diverse reactivity, and specific reaction sequence. The crystal structure of TamI in complex with tirandamycin C together with molecular dynamics simulations and targeted mutagenesis suggest that hydrophobic interactions with the polyene chain of its natural substrate are critical for molecular recognition. QM/MM calculations and molecular dynamics simulations of TamI with variant substrates provided detailed information on the molecular basis of sequential reactivity, and pattern of regio- and stereo-selectivity in catalyzing the three-step oxidative cascade.<br>

Molecular Dynamics Simulations for Loading-Dependent Diffusion of CO2, SO2, CH4, and Their Binary Mixtures in ZIF-10: The Role of Hydrogen Bond

Langmuir ◽  
2017 ◽  
Vol 33 (42) ◽  
pp. 11543-11553 ◽  
Author(s):  
Li Li ◽  
Deshuai Yang ◽  
Trevor R. Fisher ◽  
Qi Qiao ◽  
Zhen Yang ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Hydrogen Bond ◽  
Molecular Dynamics Simulations ◽  
Binary Mixtures ◽  
Dynamics Simulations

scholarly journals The rupture mechanism of rubredoxin is more complex than previously thought

2020 ◽  
Vol 11 (23) ◽  
pp. 6036-6044
Author(s):  
Maximilian Scheurer ◽  
Andreas Dreuw ◽  
Martin Head-Gordon ◽  
Tim Stauch
Keyword(s):  
Molecular Dynamics ◽  
Hydrogen Bond ◽  
Molecular Dynamics Simulations ◽  
Strain Analysis ◽  
Rupture Force ◽  
Iron Sulfur ◽  
Hydrogen Bond Networks ◽  
Dynamics Simulations ◽  
Rupture Mechanism ◽  
Sulfur Bond

Using steered molecular dynamics simulations and strain analysis it is shown that, in contrast to previous assumptions, the experimentally found low rupture force of the iron–sulfur-bond in rubredoxin cannot be explained by hydrogen bond networks.

Reversible Hydrogen Bond Network Dynamics: Molecular Dynamics Simulations of Calix[4]arene-Catenanes

2011 ◽  
Vol 115 (20) ◽  
pp. 6445-6454 ◽  
Author(s):  
Thomas Schlesier ◽  
Thorsten Metzroth ◽  
Andreas Janshoff ◽  
Jürgen Gauss ◽  
Gregor Diezemann
Keyword(s):  
Molecular Dynamics ◽  
Hydrogen Bond ◽  
Molecular Dynamics Simulations ◽  
Network Dynamics ◽  
Hydrogen Bond Network ◽  
Bond Network ◽  
Dynamics Simulations
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