Water inside carbon nanotubes: structure and dynamics

2016 ◽  
Vol 5 (3) ◽  
Author(s):  
Jamal Hassan ◽  
Georgios Diamantopoulos ◽  
Dirar Homouz ◽  
Georgios Papavassiliou
Keyword(s):  
Carbon Nanotubes ◽  
Molecular Dynamics ◽  
Nuclear Magnetic Resonance ◽  
Md Simulations ◽  
Liquid Transport ◽  
Comprehensive Review ◽  
Structure And Dynamics ◽  
Potential Applications ◽  
Nmr Methods ◽  
Theoretical Results

AbstractStudying the properties of water confined in carbon nanotubes (CNTs) have gained a lot of interest in recent years due to the vast potential applications of systems in nanoscale liquid transport as well as biology functions. This article presents a comprehensive review of recent experimental and theoretical results using nuclear magnetic resonance (NMR) and molecular dynamics (MD) simulations. Different NMR methods including

Molecular Dynamics Simulation of Bi-Carboxyl Sidewall Functionalized Single-Wall Carbon Nanotubes in Water

2015 ◽  
Vol 1131 ◽  
pp. 106-109
Author(s):  
Shongpun Lokavee ◽  
Chatchawal Wongchoosuk ◽  
Teerakiat Kerdcharoen
Keyword(s):  
Carbon Nanotubes ◽  
Molecular Dynamics ◽  
Md Simulations ◽  
Dynamics Simulation ◽  
Single Wall Carbon Nanotubes ◽  
First Principles Calculations ◽  
Carboxylic Groups ◽  
Potential Applications ◽  
Walled Carbon Nanotubes ◽  
Defective Sites

Functionalized single-walled carbon nanotubes (f-SWNTs) have attracted great interest due to their enhancement of SWNT properties leading to an increase in potential applications beyond those of pristine SWNT. In this work, we have investigated the behavior of open-end (9,0) bi-carboxyl sidewall functionalized SWNTs in water using molecular dynamics (MD) technique within GROMACS software package based on the OPLS force fields with modified charges obtained from the first principles calculations. The model tubes including perfect and defective nanotubes covalently functionalized by bi-carboxylic groups on different sidewall surface orientation were fully optimized by B3LYP/6-31G(d,p). The simulations were performed at the constant volume and temperature in a rectangular box with periodic boundary conditions in which each system contains one model tube and ~1680 water molecules. The results form MD simulations showed that functionalization on the central carbon atom in the (C1,C ́1)SW-defective sites strongly affects on the dynamic behavior of CNT in water. Results showed that the hydrophilic behavior of the functionalized SWNT has been improved over the pristine and defective nanotubes.

scholarly journals Sorption, Structure and Dynamics of CO2 and Ethane in Silicalite at High Pressure: A Combined Monte Carlo and Molecular Dynamics Simulation Study

Molecules ◽  
2018 ◽  
Vol 24 (1) ◽  
pp. 99 ◽  
Author(s):  
Siddharth Gautam ◽  
Tingting Liu ◽  
David Cole
Keyword(s):  
Molecular Dynamics ◽  
Monte Carlo ◽  
Time Scales ◽  
Rotational Motion ◽  
High Pressures ◽  
Sorption Isotherms ◽  
Md Simulations ◽  
Dynamics Simulation ◽  
Structure And Dynamics ◽  
Low Pressures

Silicalite is an important nanoporous material that finds applications in several industries, including gas separation and catalysis. While the sorption, structure, and dynamics of several molecules confined in the pores of silicalite have been reported, most of these studies have been restricted to low pressures. Here we report a comparative study of sorption, structure, and dynamics of CO2 and ethane in silicalite at high pressures (up to 100 bar) using a combination of Monte Carlo (MC) and molecular dynamics (MD) simulations. The behavior of the two fluids is studied in terms of the simulated sorption isotherms, the positional and orientational distribution of sorbed molecules in silicalite, and their translational diffusion, vibrational spectra, and rotational motion. Both CO2 and ethane are found to exhibit orientational ordering in silicalite pores; however, at high pressures, while CO2 prefers to reside in the channel intersections, ethane molecules reside mostly in the sinusoidal channels. While CO2 exhibits a higher self-diffusion coefficient than ethane at low pressures, at high pressures, it becomes slower than ethane. Both CO2 and ethane exhibit rotational motion at two time scales. At both time scales, the rotational motion of ethane is faster. The differences observed here in the behavior of CO2 and ethane in silicalite pores can be seen as a consequence of an interplay of the kinetic diameter of the two molecules and the quadrupole moment of CO2.

Molecular dynamics simulations of single-walled carbon nanotubes and polynylon66

2019 ◽  
Vol 33 (23) ◽  
pp. 1950258 ◽  
Author(s):  
Danhui Zhang ◽  
Houbo Yang ◽  
Zhongkui Liu ◽  
Anmin Liu
Keyword(s):  
Carbon Nanotubes ◽  
Molecular Dynamics ◽  
Carbon Nanotube ◽  
High Performance ◽  
Single Walled Carbon Nanotubes ◽  
Md Simulations ◽  
Interfacial Interaction ◽  
Radius Of Gyration ◽  
Single Walled Carbon ◽  
Walled Carbon Nanotubes

Polynylon66, as a kind of important engineering plastics, is widely used in various fields. In this work, we studied the interfacial interactions between polynylon66 and single-walled carbon nanotubes (SWCNTs) using molecular dynamics (MD) simulations. The results showed that the polynylon66 could interact with the SWCNTs and the mechanism of interfacial interaction between polynylon66 and SWCNTs was also discussed. Furthermore, the morphology of polynylon66 adsorbed to the surface of SWCNTs was investigated by the radius of gyration. Influence factors such as the initial angle between polynylon66 chain and nanotube axis, SWCNT radius and length of polynylon66 on interfacial adhesion of single-walled carbon nanotube-polymer and the radius of gyration of the polymers were studied. These results will help to better understand the interfacial interaction between polymer and carbon nanotube (CNT) and also guide the fabrication of high performance polymer/carbon nanotube nanocomposites.

scholarly journals Structure and Dynamics of Glycosphingolipids in Lipid Bilayers: Insights from Molecular Dynamics Simulations

2011 ◽  
Vol 2011 ◽  
pp. 1-9 ◽  
Author(s):  
Ronak Y. Patel ◽  
Petety V. Balaji
Keyword(s):  
Molecular Dynamics ◽  
Lipid Bilayers ◽  
Membrane Structure ◽  
Lipid Membrane ◽  
Biological Membranes ◽  
Md Simulations ◽  
Atomic Level ◽  
Structure And Dynamics ◽  
Hydrogen Bonding Interactions ◽  
Dynamics Simulations

Glycolipids are important constituents of biological membranes, and understanding their structure and dynamics in lipid bilayers provides insights into their physiological and pathological roles. Experimental techniques have provided details into their behavior at model and biological membranes; however, computer simulations are needed to gain atomic level insights. This paper summarizes the insights obtained from MD simulations into the conformational and orientational dynamics of glycosphingolipids and their exposure, hydration, and hydrogen-bonding interactions in membrane environment. The organization of glycosphingolipids in raft-like membranes and their modulation of lipid membrane structure are also reviewed.

Force field development and simulations of senior dialkyl sulfoxides

2016 ◽  
Vol 18 (15) ◽  
pp. 10507-10515 ◽  
Author(s):  
Vitaly V. Chaban
Keyword(s):  
Molecular Dynamics ◽  
Force Field ◽  
Ab Initio ◽  
Md Simulations ◽  
Field Development ◽  
Force Field Development ◽  
Structure And Dynamics ◽  
Ethyl Methyl ◽  
Methyl Sulfoxide ◽  
Diethyl Sulfoxide

Thermodynamics, structure, and dynamics of diethyl sulfoxide (DESO) and ethyl methyl sulfoxide (EMSO) were investigated using ab initio calculations and non-polarizable potential based molecular dynamics (MD) simulations.

scholarly journals Sequence-to-structure dependence of isolated IgG Fc complex biantennary N-glycans: A molecular dynamics study

2018 ◽  
Author(s):  
Aoife M Harbison ◽  
Lorna P Brosnan ◽  
Keith Fenlon ◽  
Elisa Fadda
Keyword(s):  
Molecular Dynamics ◽  
Structural Integrity ◽  
Md Simulations ◽  
Structure And Dynamics ◽  
Differential Recognition ◽  
Dependent Cell ◽  
Function Relationship ◽  
Simulation Time ◽  
Core Fucosylation

AbstractFc glycosylation of human immunoglobulins G (IgGs) is essential for their structural integrity and activity. Interestingly, the specific nature of the Fc glycoforms is known to modulate the IgG effector function. Indeed, while core-fucosylation of IgG Fc-glycans greatly affects the antibody-dependent cell-mediated cytotoxicity (ADCC) function, with obvious repercussions in the design of therapeutic antibodies, sialylation can reverse the antibody inflammatory response, and galactosylation levels have been linked to aging, to the onset of inflammation, and to the predisposition to rheumatoid arthritis. Within the framework of a structure-to-function relationship, we have studied the role of the N-glycan sequence on its intrinsic conformational propensity. Here we report the results of a systematic study, based on extensive molecular dynamics (MD) simulations in excess of 62 µs of cumulative simulation time, on the effect of sequence on the structure and dynamics of increasingly larger, complex biantennary N-glycoforms, i.e. from chitobiose to the larger N-glycan species commonly found in the Fc region of human IgGs. Our results show that while core fucosylation and sialylation do not affect the intrinsic dynamics of the isolated (unbound) N-glycans, galactosylation of the α(1-6) arm shifts dramatically its conformational equilibrium from an outstretched to a folded conformation. These findings are in agreement with and can help rationalize recent experimental evidence showing a differential recognition of positional isomers in glycan array data and also the preference of sialyltransferase for the more reachable, outstretched α(1-3) arm in both isolated and Fc-bound N-glycans.

Molecular dynamics simulations of simple aromatic compounds adsorption on single-walled carbon nanotubes

RSC Advances ◽  
2016 ◽  
Vol 6 (84) ◽  
pp. 80972-80980 ◽  
Author(s):  
Han Ding ◽  
Xin Shen ◽  
Chao Chen ◽  
Xiaojian Zhang
Keyword(s):  
Carbon Nanotubes ◽  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Aromatic Compounds ◽  
Single Walled Carbon Nanotubes ◽  
Md Simulations ◽  
Single Walled Carbon ◽  
Dynamics Simulations ◽  
Walled Carbon Nanotubes

We have conducted MD simulations and RDG calculations to reveal the mechanisms of simple aromatic compounds adsorption on SWCNTs.

The Anisotropy of the Molecular Reorientational Motions in Liquid Methanol

1995 ◽  
Vol 50 (2-3) ◽  
pp. 211-216 ◽  
Author(s):  
R. Ludwig ◽  
Ph. A. Bopp ◽  
M. D. Zeidler
Keyword(s):  
Molecular Dynamics ◽  
Nuclear Magnetic Resonance ◽  
Low Temperatures ◽  
Nmr Relaxation ◽  
Md Simulations ◽  
Pure Liquid ◽  
Correlation Times ◽  
Detailed Understanding ◽  
Nmr Relaxation Time ◽  
Reorientational Dynamics

Abstract Nuclear magnetic resonance (NMR) relaxation time measurements on isotopically substituted samples yield a detailed understanding of the molecular reorientational dynamics in liquids. Reorientational correlation times obtained from such experiments are reported for two molecule-fixed vectors in pure liquid methanol. While the reorientational motions of single molecules are nearly isotropic at temperatures below 250 K, at 308 K the reorientational correlation time of the O-H vector becomes 2.3 times larger than that of the O-C vector. Molecular dynamics (MD) simulations give access to the complete correlation functions of the reorientational motions. Correlation times extracted from these functions fit well to the experiment in case of the O-C vector. At low temperatures, however, these times lie markedly above those obtained in the experiment for the O-H vector. Thus, the simulation yields reorientation times for the O-H vector that are, independent of the temperature, twice as large as those of the O-C vector.

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