scholarly journals Molecular Dynamics Simulation Studies of p-Xylene in OH-free Si-MCM-41

2005 ◽  
Vol 60 (11-12) ◽  
pp. 805-813 ◽  
Author(s):  
Tanin Nanok ◽  
Philippe A. Bopp ◽  
Jumras Limtrakul
Keyword(s):  
Molecular Dynamics ◽  
Electrostatic Interactions ◽  
Zeolite Catalysts ◽  
Van Der Waals Interactions ◽  
Dynamics Simulation ◽  
Guest Molecules ◽  
Self Diffusion ◽  
Order Of Magnitude ◽  
Average Potential Energy ◽  
Mcm 41

We report on modeling efforts and molecular dynamics computer simulations of the structure and self-diffusion of p-xylene in OH-free Si-MCM-41 as a function of loading. Both the guest molecules and Si-MCM-41 are modeled as flexible entities. With this newly developped intermolecular force field the average potential energy of p-xylene in the pore increases with increasing loading. The adsorption of p-xylene in MCM-41 is primarily associated with the van der Waals interactions of the model, whereas the contribution from electrostatic interactions is relatively small (about 2 kcal/mol), in accordance with other aromatic hydrocarbons adsorbed in zeolite catalysts. The calculated selfdiffusion coefficients of p-xylene in Si-MCM-41 are well comparable with diffusion coefficients of pyridine in MCM-41 and of the same order of magnitude as in liquid p-xylene. Increasing the loading results in non-negligible mutual p-xylene interaction, thus leading to a decrease of the self-diffusion coefficient.

scholarly journals Effect of Lysyllysine on non-covalent hybridization of single walled carbon nanotube by single-stranded DNA homodimer: in silico approach

2019 ◽  
Vol 9 (4) ◽  
pp. 315-321
Author(s):  
Fateme Bagherolhashemi ◽  
Mohammad Reza Bozorgmehr ◽  
Mohammad Momen-Heravi
Keyword(s):  
Molecular Dynamics ◽  
Carbon Nanotube ◽  
Electrostatic Interactions ◽  
Membered Ring ◽  
Binding Energies ◽  
Van Der Waals Interactions ◽  
Dynamics Simulation ◽  
Quantum Calculations ◽  
Single Walled Carbon Nanotube ◽  
Sensor Properties

Abstract In this work, the interactions between adenine–adenine di-nucleotide (DA2N) and carbon nanotube (CNT) in the presence of Lysyllysine (LL) was studied by the molecular dynamics simulation. Different carbon nanotubes including (5.5), (6.6) and (7.7) were used to investigate the effect of CNT type. The binding energies were calculated using the molecular mechanics-Poisson Bolzmann surface area method. The results showed that the contribution of the van der Waals interactions between DA2N and CNT was greater than that of the electrostatic interactions. The LL significantly enhanced the electrostatic interactions between the DA2N and CNT (6.6). The quantum calculations revealed that the sensor properties of the DA2N were not significantly affected by the CNT and LL. However, the five-membered ring of adenine played a more important role in the sensing properties of the DA2N. The obtained results are consistent with the previous experimental observations that can help to understand the molecular mechanism of the interaction of DA2N with CNT. Graphic abstract

A STUDY ON SELF-INSERTION OF PEPTIDES INTO SINGLE-WALLED CARBON NANOTUBES BASED ON MOLECULAR DYNAMICS SIMULATION

2005 ◽  
Vol 16 (08) ◽  
pp. 1239-1250 ◽  
Author(s):  
G. R. LIU ◽  
Y. CHENG ◽  
DONG MI ◽  
Z. R. LI
Keyword(s):  
Carbon Nanotubes ◽  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Electrostatic Interactions ◽  
Water Environment ◽  
Single Walled Carbon Nanotubes ◽  
Van Der Waals Interactions ◽  
Dynamics Simulation ◽  
Single Walled Carbon ◽  
Walled Carbon Nanotubes

Molecular dynamics simulation is performed to investigate self-insertion behaviors of peptides into single-walled carbon nanotubes (SWCNTs) in water environment. Peptides of different hydrophobicities and varied lengths are tested to show that the propensities of peptides to self-insert into SWCNTs differ drastically. Our results indicate that there exists a potential well for the system of SWCNT and peptide that is able to self-insert into the nanotube. Further investigations of energy components demonstrate that electrostatic interactions, combined with van der Waals interactions, play dominant roles in the self-insertion of peptides into nanotubes. In addition, we also observe a significant correlation between the propensity of a peptide to insert into nanotube and its hydrophobicity. Such results provide valuable information on the potential applications of carbon nanotubes in the fields of drug delivery, drug design and protein control, etc.

scholarly journals Molecular Dynamics Simulation on the Interaction between Palygorskite Coating and Linear Chain Alkane Base Lubricant

Coatings ◽  
2021 ◽  
Vol 11 (3) ◽  
pp. 286
Author(s):  
Jin Zhang ◽  
Lv Yang ◽  
Yue Wang ◽  
Huaichao Wu ◽  
Jiabin Cai ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Structural Changes ◽  
Molecular Diffusion ◽  
Linear Chain ◽  
Interfacial Interaction ◽  
Dynamics Simulation ◽  
Electrostatic Energy ◽  
Experimental Development ◽  
Practical Applications ◽  
Self Diffusion

Molecular dynamics (MD) simulations were conducted to investigate the interactions between a palygorskite coating and linear chain alkanes (dodecane C12, tetradecane C14, hexadecane C16, and octadecane C18), representing base oils in this study. The simulation models were built by placing the alkane molecules on the surface of the palygorskite coating. These systems were annealed and geometrically optimized to obtain the corresponding stable configurations, followed by the analysis of the structural changes occurring during the MD process. The interfacial interaction energies, mean square displacements, and self-diffusion coefficients of the systems were evaluated to characterize the interactions between base lubricant molecules and palygorskite coating. It was found that the alkanes exhibited self-arrangement ability after equilibrium. The interfacial interaction was attractive, and the electrostatic energy was the main component of the binding energy. The chain length of the linear alkanes had a significant impact on the intensity of the interfacial interactions and the molecular diffusion behavior. Moreover, the C12 molecule exhibited higher self-diffusion coefficient values than C14, C16 and C18. Therefore, it could be the best candidate to form an orderliness and stable lubricant film on the surface of the palygorskite coating. The present work provides new insight into the optimization of the structure and composition of coatings and lubricants, which will guide the experimental development of these systems for practical applications.

scholarly journals Hydrogen Inter-Cage Hopping and Cage Occupancies inside Hydrogen Hydrate: Molecular-Dynamics Analysis

2020 ◽  
Vol 11 (1) ◽  
pp. 282
Author(s):  
Yogeshwaran Krishnan ◽  
Mohammad Reza Ghaani ◽  
Arnaud Desmedt ◽  
Niall J. English
Keyword(s):  
Molecular Dynamics ◽  
Energy Barrier ◽  
Guest Molecule ◽  
Arrhenius Equation ◽  
Dynamics Simulation ◽  
Type Ii ◽  
Large Cage ◽  
Guest Molecules ◽  
Simulation Time ◽  
Average Occupancy

The inter-cage hopping in a type II clathrate hydrate with different numbers of H2 and D2 molecules, from 1 to 4 molecules per large cage, was studied using a classical molecular dynamics simulation at temperatures of 80 to 240 K. We present the results for the diffusion of these guest molecules (H2 or D2) at all of the different occupations and temperatures, and we also calculated the activation energy as the energy barrier for the diffusion using the Arrhenius equation. The average occupancy number over the simulation time showed that the structures with double and triple large-cage H2 occupancy appeared to be the most stable, while the small cages remained with only one guest molecule. A Markov model was also calculated based on the number of transitions between the different cage types.

scholarly journals Self-diffusion of Fe and Pt in L1-Ordered FePt: Molecular Dynamics simulation

2021 ◽  
Vol 192 ◽  
pp. 110337
Author(s):  
S.I. Konorev ◽  
R. Kozubski ◽  
M. Albrecht ◽  
I.A. Vladymyrskyi
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Dynamics Simulation ◽  
Self Diffusion

Self-diffusion of lignite/water under different temperatures and pressure: A molecular dynamics study

2016 ◽  
Vol 30 (01) ◽  
pp. 1550253 ◽  
Author(s):  
Xinjian Liu ◽  
Yu Jin ◽  
Congliang Huang ◽  
Jingfeng He ◽  
Zhonghao Rao ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Water System ◽  
Simulation Method ◽  
The Self ◽  
Dynamics Simulation ◽  
Low Rank ◽  
Self Diffusion ◽  
Change Mechanism ◽  
Different Temperatures ◽  
Temperature And Pressure

Temperature and pressure have direct and remarkable implications for drying and dewatering effect of low rank coals such as lignite. To understand the microenergy change mechanism of lignite, the molecular dynamics simulation method was performed to study the self-diffusion of lignite/water under different temperatures and pressure. The results showed that high temperature and high pressure can promote the diffusion of lignite/water system, which facilitates the drying and dewatering of lignite. The volume and density of lignite/water system will increase and decrease with temperature increasing, respectively. Though the pressure within simulation range can make lignite density increase, the increasing pressure showed a weak impact on variation of density.

scholarly journals Investigation of Microscopic Structure and Ion Dynamics in Liquid Li(Na, K)EutecticCl Systems by Molecular Dynamics Simulation

2018 ◽  
Vol 8 (10) ◽  
pp. 1874 ◽  
Author(s):  
Jie Wu ◽  
Jia Wang ◽  
Haiou Ni ◽  
Guimin Lu ◽  
Jianguo Yu
Keyword(s):  
Molecular Dynamics ◽  
Ionic Conductivity ◽  
Shear Viscosity ◽  
Ion Pairs ◽  
Liquid Structure ◽  
Distribution Functions ◽  
Dynamics Simulation ◽  
Molten Chloride ◽  
Ion Clusters ◽  
Self Diffusion

Molten chloride salts are the main components in liquid metal batteries, high-temperature heat storage materials, heat transfer mediums, and metal electrolytes. In this paper, interest is centered on the influence of the LiCl component and temperature on the local structure and transport properties of the molten LiCl-NaCl-KCl system over the temperature range of 900 K to 1200 K. The liquid structure and properties have been studied across the full composition range by molecular dynamics (MD) simulation of a sufficient length to collect reliable values, such as the partial radial distribution function, angular distribution functions, coordination numbers distribution, density, self-diffusion coefficient, ionic conductivity, and shear viscosity. Densities obtained from simulations were underestimated by an average 5.7% of the experimental values. Shear viscosities and ionic conductivity were in good agreement with the experimental data. The association of all ion pairs (except for Li-Li and Cl-Cl) was weakened by an increasing LiCl concentration. Ion clusters were formed in liquids with increasing temperatures. The self-diffusion coefficients and ionic conductivity showed positive dependences on both LiCl concentration and temperature, however, the shear viscosity was the opposite. By analyzing the hydrodynamic radii of each ion and the coordination stability of cation-anion pairs, it was speculated that ion clusters could be the cation-anion coordinated structure and affected the macro properties.

scholarly journals Prediction of GluN2B-CT1290-1310/DAPK1 Interaction by Protein–Peptide Docking and Molecular Dynamics Simulation

Molecules ◽  
2018 ◽  
Vol 23 (11) ◽  
pp. 3018 ◽  
Author(s):  
Gao Tu ◽  
Tingting Fu ◽  
Fengyuan Yang ◽  
Lixia Yao ◽  
Weiwei Xue ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Free Energy ◽  
Electrostatic Interactions ◽  
Binding Free Energy ◽  
Computational Simulation ◽  
Critical Role ◽  
Dynamics Simulation ◽  
Peptide Docking ◽  
C Terminus ◽  
Free Energy Decomposition

The interaction of death-associated protein kinase 1 (DAPK1) with the 2B subunit (GluN2B) C-terminus of N-methyl-D-aspartate receptor (NMDAR) plays a critical role in the pathophysiology of depression and is considered a potential target for the structure-based discovery of new antidepressants. However, the 3D structures of C-terminus residues 1290–1310 of GluN2B (GluN2B-CT1290-1310) remain elusive and the interaction between GluN2B-CT1290-1310 and DAPK1 is unknown. In this study, the mechanism of interaction between DAPK1 and GluN2B-CT1290-1310 was predicted by computational simulation methods including protein–peptide docking and molecular dynamics (MD) simulation. Based on the equilibrated MD trajectory, the total binding free energy between GluN2B-CT1290-1310 and DAPK1 was computed by the mechanics generalized born surface area (MM/GBSA) approach. The simulation results showed that hydrophobic, van der Waals, and electrostatic interactions are responsible for the binding of GluN2B-CT1290–1310/DAPK1. Moreover, through per-residue free energy decomposition and in silico alanine scanning analysis, hotspot residues between GluN2B-CT1290-1310 and DAPK1 interface were identified. In conclusion, this work predicted the binding mode and quantitatively characterized the protein–peptide interface, which will aid in the discovery of novel drugs targeting the GluN2B-CT1290-1310 and DAPK1 interface.

Sign in / Sign up

Export Citation Format

Share Document