Combined Molecular Dynamics and Coordinate Driving Method for Automatic Reaction Pathway Search of Reactions in Solution

2018 ◽  
Vol 14 (11) ◽  
pp. 5787-5796 ◽  
Author(s):  
Manyi Yang ◽  
Lijiang Yang ◽  
Guoqiang Wang ◽  
Yanzi Zhou ◽  
Daiqian Xie ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Reaction Pathway ◽  
Pathway Search

Automatic Reaction Pathway Search via Combined Molecular Dynamics and Coordinate Driving Method

2017 ◽  
Vol 121 (6) ◽  
pp. 1351-1361 ◽  
Author(s):  
Manyi Yang ◽  
Jingxiang Zou ◽  
Guoqiang Wang ◽  
Shuhua Li
Keyword(s):  
Molecular Dynamics ◽  
Reaction Pathway ◽  
Pathway Search

Crystal structures and snapshots along the reaction pathway of human phosphoserine phosphatase

2019 ◽  
Vol 75 (6) ◽  
pp. 592-604 ◽  
Author(s):  
Marie Haufroid ◽  
Manon Mirgaux ◽  
Laurence Leherte ◽  
Johan Wouters
Keyword(s):  
Molecular Dynamics ◽  
Reaction Mechanism ◽  
Crystal Structures ◽  
Reaction Pathway ◽  
Living Cells ◽  
Homocysteic Acid ◽  
Phosphoserine Phosphatase ◽  
Key Enzyme ◽  
The Subject ◽  
Dynamics Simulations

The equilibrium between phosphorylation and dephosphorylation is one of the most important processes that takes place in living cells. Human phosphoserine phosphatase (hPSP) is a key enzyme in the production of serine by the dephosphorylation of phospho-L-serine. It is directly involved in the biosynthesis of other important metabolites such as glycine and D-serine (a neuromodulator). hPSP is involved in the survival mechanism of cancer cells and has recently been found to be an essential biomarker. Here, three new high-resolution crystal structures of hPSP (1.5–2.0 Å) in complexes with phosphoserine and with serine, which are the substrate and the product of the reaction, respectively, and in complex with a noncleavable substrate analogue (homocysteic acid) are presented. New types of interactions take place between the enzyme and its ligands. Moreover, the loop involved in the open/closed state of the enzyme is fully refined in a totally unfolded conformation. This loop is further studied through molecular-dynamics simulations. Finally, all of these analyses allow a more complete reaction mechanism for this enzyme to be proposed which is consistent with previous publications on the subject.

Shock-Induced Decomposition of 1, 3, 5-triamino-2, 4, 6-trinitrobenzene: A Reactive-Force-Field Molecular Dynamics Study

MRS Advances ◽  
2016 ◽  
Vol 1 (17) ◽  
pp. 1247-1253 ◽  
Author(s):  
Subodh C. Tiwari ◽  
Ken-ichi Nomura ◽  
Rajiv Kalia ◽  
Aiichiro Nakano ◽  
Priya Vashishta
Keyword(s):  
Molecular Dynamics ◽  
Force Field ◽  
Reaction Pathway ◽  
Dynamics Simulation ◽  
Reaction Pathways ◽  
Mechanical Stimuli ◽  
Reactive Force ◽  
Reactive Force Field ◽  
Detonation Process ◽  
Induced Decomposition

ABSTRACTShock-induced detonation simulation provides critical information about high explosive (HE) materials including sensitivity, detonation velocity and reaction pathways. Here, we report a reactive force-field molecular dynamics simulation study of shock-induced decomposition of 1,3,5-triamino-2,4,6-trinitrobenzene (TATB) crystal. A flyer acts as mechanical stimuli to induce shock in the system, which initiates chemical reactions. Reaction pathway study reveals that the detonation process of TATB is distinct from those in Octahydro-1,3,5,7-tetranitro-1,3,4,7-terazocine (HMX) and 1,3,5-Trinitro-1,3,5-triazacyclohexane (RDX). Unlike the latter HE materials, N2production in TATB occurs via three different intermolecular reaction pathways. Being an oxygen deficient HE material, a large carbon rich aggregate remains after the reaction.

Multiscale Molecular Dynamics Simulations of Nanostructured Materials

2007 ◽  
Vol 539-543 ◽  
pp. 2804-2809 ◽  
Author(s):  
Kenij Tsuruta ◽  
Atsushi Uchida ◽  
Chieko Totsuji ◽  
Hiroo Totsuji
Keyword(s):  
Molecular Dynamics ◽  
Grain Boundary ◽  
Hydrogen Diffusion ◽  
Reaction Pathway ◽  
Film Formation ◽  
Rare Event ◽  
High Energy ◽  
Long Time ◽  
Cu Thin Film ◽  
Dynamics Simulations

We present some attempts to simulate nanoscale phenomena, which involve different length-scales and time-scales, using multiscale molecular-dynamics approaches. To simulate realistically an impurity-segregated nanostructure, we have developed the hybrid quantum/classical approach. The method can describe seamlessly both dynamical changes of local chemical bonding and nanoscale atomic relaxations. We apply the method to hydrogen diffusion in Si grain boundary. We find that the hydrogen is strongly trapped in (001)Σ5 twist boundary below 1000K, whereas it starts diffusing along the grain boundary above 1000K. For long-time processes in nanostructure formation, we apply the stochastic-difference-equation method to accelerate the simulations for microstructure evolution. The method bridges the states separated by high-energy barriers in a configuration space by optimizing an action, defined as an error accumulation along a reaction pathway. As an example, a SDE simulation is performed for Cu thin-film formation via nanocluster deposition. We show that the method can be applied effectively to search for the long-time process which involves a rare event due to a large potential barrier between two atomic configurations.

scholarly journals Temporary Intermediates of L-Trp Along the Reaction Pathway of Human Indoleamine 2,3-Dioxygenase 1 and Identification of an Exo Site

2021 ◽  
Vol 14 ◽  
pp. 117864692110529
Author(s):  
Manon Mirgaux ◽  
Laurence Leherte ◽  
Johan Wouters
Keyword(s):  
Molecular Dynamics ◽  
Reaction Mechanism ◽  
Crystal Structures ◽  
Protein Dynamics ◽  
Active Site ◽  
Reaction Pathway ◽  
Small Unit ◽  
Indoleamine 2,3 Dioxygenase ◽  
Dynamics Simulations

Protein dynamics governs most of the fundamental processes in the human body. Particularly, the dynamics of loops located near an active site can be involved in the positioning of the substrate and the reaction mechanism. The understanding of the functioning of dynamic loops is therefore a challenge, and often requires the use of a multi-disciplinary approach mixing, for example, crystallographic experiments and molecular dynamics simulations. In the present work, the dynamic behavior of the JK-loop of the human indoleamine 2,3-dioxygenase 1 hemoprotein, a target for immunotherapy, is investigated. To overcome the lack of knowledge on this dynamism, the study reported here is based on 3 crystal structures presenting different conformations of the loop, completed with molecular dynamics trajectories and MM-GBSA analyses, in order to trace the reaction pathway of the enzyme. In addition, the crystal structures identify an exo site in the small unit of the enzyme, that is populated redundantly by the substrate or the product of the reaction. The role of this newer reported exo site still needs to be investigated.

An Efficient Reaction Pathway Search Method Applied to the Decomposition of Glycerol on Platinum

2011 ◽  
Vol 115 (38) ◽  
pp. 18707-18720 ◽  
Author(s):  
Y. Chen ◽  
M. Salciccioli ◽  
D. G. Vlachos
Keyword(s):  
Reaction Pathway ◽  
Search Method ◽  
Pathway Search
Sign in / Sign up

Export Citation Format

Share Document