scholarly journals Molecular Dynamics Simulations with Quantum Mechanics/Molecular Mechanics and Adaptive Neural Networks

2018 ◽  
Vol 14 (3) ◽  
pp. 1442-1455 ◽  
Author(s):  
Lin Shen ◽  
Weitao Yang
Keyword(s):  
Neural Networks ◽  
Molecular Dynamics ◽  
Quantum Mechanics ◽  
Molecular Dynamics Simulations ◽  
Molecular Mechanics ◽  
Adaptive Neural Networks ◽  
Dynamics Simulations

scholarly journals Lipase-catalyzed O-acylation of (RS)-propranolol is determined by the acyl group length

2020 ◽  
Author(s):  
Gilberto A. Zapata-Romero ◽  
Markus Doerr ◽  
Martha C. Daza
Keyword(s):  
Molecular Dynamics ◽  
Quantum Mechanics ◽  
Computational Modeling ◽  
Molecular Dynamics Simulations ◽  
Molecular Mechanics ◽  
Hydrocarbon Chain ◽  
Candida Antarctica Lipase ◽  
Ensemble Docking ◽  
Consensus Scoring ◽  
Dynamics Simulations

We employed a computational modeling approach to study the Michaelis complexes of (R)- and (S)-propranolol with serine-acylated Candida antarctica lipase B using four acyl groups: ethanoyl, butanoyl, octanoyl and hexadecanoyl. Our methodology involves sampling Michaelis complex conformations, first through ensemble docking using consensus scoring, and second by molecular dynamics simulations employing a quantum mechanics/molecular mechanics approach. The conformations are then categorized into two classes of near attack conformations, according to the distance of (a) the amino and (b) the hydroxy group of propranolol to the catalytic residues. The relative populations of these two classes of conformations was found to be consistent with the experimentally-observed exclusive chemoselectivity toward O-acylation with ethanoyl. Furthermore, we predict that increasing the length of the hydrocarbon chain of the acyl group will cause O-acylation to be unfavorable.

Theoretical investigations of a platinum–water interface using quantum-mechanics-molecular-mechanics based molecular dynamics simulations

2019 ◽  
Vol 21 (44) ◽  
pp. 24345-24353
Author(s):  
R. P. Hardikar ◽  
Unmesh Mondal ◽  
Foram M. Thakkar ◽  
Sudip Roy ◽  
Prasenjit Ghosh
Keyword(s):  
Molecular Dynamics ◽  
Quantum Mechanics ◽  
Molecular Dynamics Simulations ◽  
Molecular Mechanics ◽  
Water Layer ◽  
High Density ◽  
Interface Region ◽  
Water Interface ◽  
Theoretical Investigations ◽  
Dynamics Simulations

Formation of high density liquid in the water layer at the Pt–water interface. Significantly large single H-bond donors at the interface region.

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