Ab Initio Molecular Dynamics Reveals New Metal-Binding Sites in Atomically Dispersed Pt1/TiO2 Catalysts

2020 ◽  
Vol 124 (44) ◽  
pp. 24187-24195
Author(s):  
Nicholas Humphrey ◽  
Selin Bac ◽  
Shaama Mallikarjun Sharada
Keyword(s):  
Molecular Dynamics ◽  
Ab Initio ◽  
Metal Binding ◽  
Binding Sites ◽  
Ab Initio Molecular Dynamics ◽  
Metal Binding Sites

scholarly journals Molecular dynamics simulations of zfP2X4 receptors

2021 ◽  
Author(s):  
kalyan immadisetty ◽  
Peter Kekenes-Huskey
Keyword(s):  
Molecular Dynamics ◽  
Crystal Structures ◽  
Metal Binding ◽  
Binding Sites ◽  
Molecular Mechanisms ◽  
Pain Perception ◽  
Gulf Coast ◽  
Md Simulations ◽  
P2x Receptor ◽  
Metal Binding Sites

The ATP activated P2X4 receptor plays a prominent role in pain perception and modulation and thus may constitute an alternative therapeutic target for controlling pain. Given the biomedical relevance of P2X4 receptors, and poor understanding of molecular mechanisms that describe its gating by ATP, a fundamental understanding of the functional mechanism of these channels is warranted. Through classical all-atom molecular dynamics (MD) simulations we investigated the number of ATP molecules required to open (activate) the receptor for it to conduct ions. Since crystal structures of human P2X4 are not yet available, the crystal structures of highly-homologous zebrafish P2X4 (zfP2X4) structures were utilized for this study. It has been identified that at least two ATP molecules are required to prevent the open state receptor from collapsing back to a closed state. Additionally, we have discovered two metal binding sites, one at the intersection of the three monomers in the ectodomain (MBS1) and the second one near the ATP binding site (MBS2), both of which are occupied by the potassium ions. This observation draws its comparison to the gulf coast P2X receptor that it possesses the same two metal binding sites, however, MBS1 and MBS2 in this receptor are occupied by zinc and magnesium, respectively.

Combustion Driven by Fragment-based Ab Initio Molecular Dynamics Simulation

2019 ◽  
Author(s):  
Liqun Cao ◽  
Jinzhe Zeng ◽  
Mingyuan Xu ◽  
Chih-Hao Chin ◽  
Tong Zhu ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Ab Initio ◽  
Large Scale ◽  
Methane Combustion ◽  
Combustion Method ◽  
Dynamics Simulation ◽  
Ab Initio Molecular Dynamics ◽  
Computational Time ◽  
Combustion Mechanism ◽  
Daily Lives

Combustion is a kind of important reaction that affects people's daily lives and the development of aerospace. Exploring the reaction mechanism contributes to the understanding of combustion and the more efficient use of fuels. Ab initio quantum mechanical (QM) calculation is precise but limited by its computational time for large-scale systems. In order to carry out reactive molecular dynamics (MD) simulation for combustion accurately and quickly, we develop the MFCC-combustion method in this study, which calculates the interaction between atoms using QM method at the level of MN15/6-31G(d). Each molecule in systems is treated as a fragment, and when the distance between any two atoms in different molecules is greater than 3.5 Å, a new fragment involved two molecules is produced in order to consider the two-body interaction. The deviations of MFCC-combustion from full system calculations are within a few kcal/mol, and the result clearly shows that the calculated energies of the different systems using MFCC-combustion are close to converging after the distance thresholds are larger than 3.5 Å for the two-body QM interactions. The methane combustion was studied with the MFCC-combustion method to explore the combustion mechanism of the methane-oxygen system.

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