Molecular Dynamics Investigation on Thermal Stability and Shape Evolution of Pd-Au Heterostructured Nanorods: Implications for Catalysis

2021 ◽  
Author(s):  
Tao Zhao ◽  
Lei Li ◽  
Rao Huang ◽  
Yu-Hua Wen
Keyword(s):  
Molecular Dynamics ◽  
Thermal Stability ◽  
Shape Evolution

Simulation of Thermal Stability and Friction: A Lubricant Confined Between Monolayers of Wear Inhibitors on Iron Oxide

1998 ◽  
Vol 543 ◽  
Author(s):  
T. Çağin ◽  
Y. Zhou ◽  
E. S. Yamaguchi ◽  
R. Frazier ◽  
A. Ho ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Thermal Stability ◽  
Quantum Chemical ◽  
Md Simulations ◽  
Atomic Level ◽  
The Self ◽  
Self Assembled Monolayer ◽  
Thermal Stabilities ◽  
Frictional Forces ◽  
Thermal Stability Of

AbstractTo understand antiwear phenomena in motor engines at the atomic level and provide evidence inselecting future ashless wear inhibitors, we studied the thermal stability of the self-assembled monolayer(SAM) model for dithiophosphate (DTP) and dithiocarbamate (DTC) molecules on the iron oxidesurface using molecular dynamics. The interactions for DTP, DTC and Fe2O3 are evaluated based on aforce field derived from fitting to ab initio quantum chemical calculations of dimethyl DTP (and DTC)and Fe(OH)2(H2O)2-DTP (DTC) clusters. MD simulations at constant-NPT are conducted to assesrelative thermal stabilities of the DTP and DTC with different pendant groups (n-propyl, i-propyl, npentyl.and i-pentyl). To investigate frictional process, we employ a steady state MD method, in whichone of the Fe2O3 slabs maintained at a constant linear velocity. We obtain the time averaged normaland frictional forces from the interatomic forces. Then, we calculated the friction coefficient at theinterface between SAMs of DTP and the confined lubricant, hexadecane, to assess the shear stability ofDTPs with different pendant groups.

scholarly journals A Possible Mechanism of Graphene Oxide to Enhance Thermostability of D-Psicose 3-Epimerase Revealed by Molecular Dynamics Simulations

2021 ◽  
Vol 22 (19) ◽  
pp. 10813
Author(s):  
Congcong Li ◽  
Zhongkui Lu ◽  
Min Wang ◽  
Siao Chen ◽  
Lu Han ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Thermal Stability ◽  
Graphene Oxide ◽  
Md Simulations ◽  
Strong Interactions ◽  
Limiting Factor ◽  
Active Site Residues ◽  
Detailed Mechanism ◽  
Dynamics Simulations ◽  
Thermal Stability Of

Thermal stability is a limiting factor for effective application of D-psicose 3-epimerase (DPEase) enzyme. Recently, it was reported that the thermal stability of DPEase was improved by immobilizing enzymes on graphene oxide (GO) nanoparticles. However, the detailed mechanism is not known. In this study, we investigated interaction details between GO and DPEase by performing molecular dynamics (MD) simulations. The results indicated that the domain (K248 to D268) of DPEase was an important anchor for immobilizing DPEase on GO surface. Moreover, the strong interactions between DPEase and GO can prevent loop α1′-α1 and β4-α4 of DPEase from the drastic fluctuation. Since these two loops contained active site residues, the geometry of the active pocket of the enzyme remained stable at high temperature after the DPEase was immobilized by GO, which facilitated efficient catalytic activity of the enzyme. Our research provided a detailed mechanism for the interaction between GO and DPEase at the nano–biology interface.

scholarly journals Synthesis, Structural and Thermal Studies of 3-(1-Benzyl-1,2,3,6-tetrahydropyridin-4-yl)-5-ethoxy-1H-indole (D2AAK1_3) as Dopamine D2 Receptor Ligand

Molecules ◽  
2018 ◽  
Vol 23 (9) ◽  
pp. 2249 ◽  
Author(s):  
Magda Kondej ◽  
Agata Bartyzel ◽  
Monika Pitucha ◽  
Tomasz Wróbel ◽  
Andrea Silva ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Thermal Stability ◽  
Dopamine D2 Receptor ◽  
Thermal Studies ◽  
D2 Receptor ◽  
Thermal Characterization ◽  
X Ray ◽  
Good Thermal Stability ◽  
Dopamine D2

Compound D2AAK1_3 was designed as a modification of the lead structure D2AAK1 (an in vivo active multi-target compound with nanomolar affinity to a number of aminergic GPCRs) and synthesized in the reaction of 5-ethoxyindole and 1-benzyl-4-piperidone. This compound has an affinity to the human dopamine D2 receptor with Ki of 151 nM. The aim of these studies was the structural and thermal characterization of the compound D2AAK1_3. In particular; X-ray studies; molecular docking and molecular dynamics as well as thermal analysis were performed. The studied compound crystallizes in orthorhombic system; in chiral space group P212121. The compound has a non-planar conformation. The studied compound was docked to the novel X-ray structure of the human dopamine D2 receptor in the inactive state (PDB ID: 6CM4) and established the main contact between its protonatable nitrogen atom and Asp (3.32) of the receptor. The obtained binding pose was stable in molecular dynamics simulations. Thermal stability of the compound was investigated using the TG-DSC technique in the air atmosphere, while TG-FTIR analyses in air and nitrogen atmospheres were also performed. The studied compound is characterized by good thermal stability. The main volatile products of combustion are the following gases: CO2; H2O toluene and CO while in the case of pyrolysis process in the FTIR spectra; the characteristic bands of NH3; piperidine and indole are additionally observed.

Thermal stability of zirconia-doped ceria surfaces: A first-principles molecular dynamics study

2020 ◽  
Vol 507 ◽  
pp. 144942
Author(s):  
Gege Zhou ◽  
Wen-Tong Geng ◽  
Wei Xiao ◽  
Lu Sun ◽  
Jianwei Wang ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Thermal Stability ◽  
First Principles ◽  
Doped Ceria ◽  
Thermal Stability Of ◽  
First Principles Molecular Dynamics

scholarly journals Experimental evaluation of single‐domain antibodies predicted by molecular dynamics simulations to have elevated thermal stability

2019 ◽  
Vol 28 (10) ◽  
pp. 1909-1912 ◽  
Author(s):  
Dan Zabetakis ◽  
Lisa C. Shriver‐Lake ◽  
Mark A. Olson ◽  
Ellen R. Goldman ◽  
George P. Anderson
Keyword(s):  
Molecular Dynamics ◽  
Thermal Stability ◽  
Molecular Dynamics Simulations ◽  
Experimental Evaluation ◽  
Single Domain ◽  
Single Domain Antibodies ◽  
Dynamics Simulations
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