Molecular Dynamics Study of Collective Behavior of Carbon Nanotori in Columnar Phase

Supramolecular interaction of carbon nanotori in a columnar phase is described using the methods of classical molecular dynamics. The collective behavior and dynamic properties of toroidal molecules arising under the action of the van der Waals forces are studied. The conditions under which columnar structures based on molecular tori become unstable and rearrange into another structure are investigated. The reasons for the appearance of two types of directed rotational motion from the chaotic motion of molecules are discussed.

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Charge Transfer and Polarisability in Ionic Liquids

Physical Chemistry Chemical Physics ◽

10.1039/d1cp04592j ◽

2021 ◽

Author(s):

Frederik Philippi ◽

Kateryna Goloviznina ◽

Zheng Gong ◽

Sascha Gehrke ◽

Barbara Kirchner ◽

...

Keyword(s):

Molecular Dynamics ◽

Ionic Liquids ◽

Charge Transfer ◽

Dynamic Properties ◽

Md Simulations ◽

Classical Molecular Dynamics

The practical use of ionic liquids (ILs) is benefiting from a growing understanding of the underpinning structural and dynamic properties, facilitated through classical molecular dynamics (MD) simulations. The predictive and...

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Phase Transition of Argon in a Nanocavity

Heat Transfer: Volume 1 ◽

10.1115/ht2005-72390 ◽

2005 ◽

Author(s):

Philipp A. E. Schoen ◽

Dimos Poulikakos

Keyword(s):

Phase Transition ◽

Molecular Dynamics ◽

Phase Diagram ◽

Molecular Dynamics Simulations ◽

Van Der Waals ◽

Van Der Waals Forces ◽

Constant Volume ◽

Substrate Interface ◽

Dynamics Simulations

We performed molecular dynamics simulations of argon liquid enclosed in an infinitely extended channel made out of platinum atoms. It was found that for small temperatures the van der Waals forces at the liquid-substrate interface are increased. Using this fact and the nature of argon, that this liquid thermally contracts if cooled, phase transition of liquid to vapor could also be achieved in this nanocavity of constant volume. However, the phase diagram is altered significantly compared to bulk argon.

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van der Waals potential barrier for cobaltocene encapsulation into single-walled carbon nanotubes: classical molecular dynamics andab initiostudy

Molecular Simulation ◽

10.1080/08927022.2010.537093 ◽

2011 ◽

Vol 37 (9) ◽

pp. 746-751 ◽

Cited By ~ 1

Author(s):

David L. Azevedo ◽

Fernando Sato ◽

Antonio Gomes de Sousa Filho ◽

Douglas S. Galvão

Keyword(s):

Carbon Nanotubes ◽

Molecular Dynamics ◽

Potential Barrier ◽

Van Der Waals ◽

Single Walled Carbon Nanotubes ◽

Single Walled Carbon ◽

Classical Molecular Dynamics ◽

Walled Carbon Nanotubes

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Collective behavior in the single-electron charging regime through classical molecular dynamics

Physical Review B ◽

10.1103/physrevb.53.10154 ◽

1996 ◽

Vol 53 (15) ◽

pp. 10154-10159

Author(s):

C. M. Carbonaro ◽

R. Bertoncini ◽

F. Meloni ◽

M. Rovere

Keyword(s):

Molecular Dynamics ◽

Collective Behavior ◽

Single Electron ◽

Classical Molecular Dynamics

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Assessment of dynamic properties of water around a monovalent ion: A classical molecular dynamics simulation study

Computational and Theoretical Chemistry ◽

10.1016/j.comptc.2011.02.004 ◽

2011 ◽

Vol 966 (1-3) ◽

pp. 26-30 ◽

Cited By ~ 10

Author(s):

Ikuo Kurisaki ◽

Takuya Takahashi

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulation ◽

Simulation Study ◽

Dynamic Properties ◽

Dynamics Simulation ◽

Classical Molecular Dynamics ◽

Monovalent Ion

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Self-Assembly of a Chiral Cubic Three-Connected Net from the High Symmetry Molecules C60 and SnI4

10.26434/chemrxiv.12196788 ◽

2020 ◽

Author(s):

Daniel B. Straus ◽

Robert J. Cava

Keyword(s):

Organic Synthesis ◽

Self Assembly ◽

Van Der Waals ◽

Van Der Waals Forces ◽

High Symmetry ◽

Molecular Chirality ◽

Chiral Materials ◽

Self Assembled ◽

Chiral Centers

The design of new chiral materials usually requires stereoselective organic synthesis to create molecules with chiral centers. Less commonly, achiral molecules can self-assemble into chiral materials, despite the absence of intrinsic molecular chirality. Here, we demonstrate the assembly of high-symmetry molecules into a chiral van der Waals structure by synthesizing crystals of C60(SnI4)2 from icosahedral buckminsterfullerene (C60) and tetrahedral SnI4 molecules through spontaneous self-assembly. The SnI4 tetrahedra template the Sn atoms into a chiral cubic three-connected net of the SrSi2 type that is held together by van der Waals forces. Our results represent the remarkable emergence of a self-assembled chiral material from two of the most highly symmetric molecules, demonstrating that almost any molecular, nanocrystalline, or engineered precursor can be considered when designing chiral assemblies.

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A Conserved Asparagine in a Ubiquitin Conjugating Enzyme Positions the Substrate for Nucleophilic Attack

10.26434/chemrxiv.7019579.v1 ◽

2018 ◽

Cited By ~ 1

Author(s):

Walker M. Jones ◽

Aaron G. Davis ◽

R. Hunter Wilson ◽

Katherine L. Elliott ◽

Isaiah Sumner

Keyword(s):

Molecular Dynamics ◽

Quantum Mechanics ◽

Molecular Mechanics ◽

Reaction Rates ◽

Nucleophilic Attack ◽

Classical Molecular Dynamics ◽

Ubiquitin Conjugating Enzyme ◽

Conjugating Enzyme

We present classical molecular dynamics (MD), Born-Oppenheimer molecular dynamics (BOMD), and hybrid quantum mechanics/molecular mechanics (QM/MM) data. MD was performed using the GPU accelerated pmemd module of the AMBER14MD package. BOMD was performed using CP2K version 2.6. The reaction rates in BOMD were accelerated using the Metadynamics method. QM/MM was performed using ONIOM in the Gaussian09 suite of programs. Relevant input files for BOMD and QM/MM are available.

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