Molecular dynamics and interactions in liquids, molecular crystals and molecular complexes

AbstractWe have used constant pressure molecular dynamics calculations to explore the behavior at various temperatures of two molecular crystals: benzene and a brominated phenyl compound. We observed a melting transition by heating the crystals from a low temperature. In the case of benzene, we performed one heating run of about 1 ns and obtained agreement with the experimental melting point to within some 8%. We have also simulated the melting of a more complex molecular crystal that contains bromine and phenyl groups. We performed four heating runs, with different rates of heating. For total simulation times of about 100, 220, 770, and 1 I50ps, the heating runs predicted melting temperatures that differed from the experimental melting temperature by 53%, 33%, 25%, and 9% respectively.

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Theoretical Insights into the Electron Capture Behavior of H2SO4···N2O Complex: A DFT and Molecular Dynamics Study

Molecules ◽

10.3390/molecules23092349 ◽

2018 ◽

Vol 23 (9) ◽

pp. 2349 ◽

Cited By ~ 2

Author(s):

Wei-Hua Wang ◽

Wen-Ling Feng ◽

Wen-Liang Wang ◽

Ping Li

Keyword(s):

Molecular Dynamics ◽

Electron Capture ◽

Atmospheric Chemistry ◽

Density Functional ◽

Molecular Complexes ◽

Dft Method ◽

Dynamics Simulation ◽

Oh Radical ◽

Before And After ◽

Reduced Density

Both sulfuric acid (H2SO4) and nitrous oxide (N2O) play a central role in the atmospheric chemistry in regulating the global environment and climate changes. In this study, the interaction behavior between H2SO4 and N2O before and after electron capture has been explored using the density functional theory (DFT) method as well as molecular dynamics simulation. The intermolecular interactions have been characterized by atoms in molecules (AIM), natural bond orbital (NBO), and reduced density gradient (RDG) analyses, respectively. It was found that H2SO4 and N2O can form two transient molecular complexes via intermolecular H-bonds within a certain timescale. However, two molecular complexes can be transformed into OH radical, N2, and HSO4− species upon electron capture, providing an alternative formation source of OH radical in the atmosphere. Expectedly, the present findings not only can provide new insights into the transformation behavior of H2SO4 and N2O, but also can enable us to better understand the potential role of the free electron in driving the proceeding of the relevant reactions in the atmosphere.

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Molecular dynamics simulations of ferroelectricity in di-isopropyl-ammonium halide molecular crystals

Chemical Physics Letters ◽

10.1016/j.cplett.2019.06.019 ◽

2019 ◽

Vol 730 ◽

pp. 367-371

Author(s):

Yundi Huang ◽

Pengfei Hu ◽

Jianing Song ◽

Yongle Li ◽

Alessandro Stroppa

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

Molecular Crystals ◽

Dynamics Simulations

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Insights into mechanochemical reactions at the molecular level: simulated indentations of aspirin and meloxicam crystals

Chemical Science ◽

10.1039/c8sc04971h ◽

2019 ◽

Vol 10 (10) ◽

pp. 2924-2929 ◽

Cited By ~ 8

Author(s):

Michael Ferguson ◽

M. Silvina Moyano ◽

Gareth A. Tribello ◽

Deborah E. Crawford ◽

Eduardo M. Bringa ◽

...

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

Molecular Level ◽

Molecular Crystals ◽

Classical Molecular Dynamics ◽

Dynamics Simulations ◽

Mechanochemical Reactions

Working towards a fundamental description of mechanochemical reactions through the use of classical molecular dynamics simulations. Capturing the transfer of molecules between two non-volatile molecular crystals during mechanochemical events.

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Albumin–Hyaluronan Interactions: Influence of Ionic Composition Probed by Molecular Dynamics

International Journal of Molecular Sciences ◽

10.3390/ijms222212360 ◽

2021 ◽

Vol 22 (22) ◽

pp. 12360

Author(s):

Piotr Bełdowski ◽

Maciej Przybyłek ◽

Przemysław Raczyński ◽

Andra Dedinaite ◽

Krzysztof Górny ◽

...

Keyword(s):

Molecular Dynamics ◽

Synovial Fluid ◽

Divalent Cations ◽

Ionic Composition ◽

Inorganic Ions ◽

Molecular Complexes ◽

Charge Compensation ◽

Ionic Species ◽

Intermolecular Forces ◽

Lubrication Performance

The lubrication mechanism in synovial fluid and joints is not yet fully understood. Nevertheless, intermolecular interactions between various neutral and ionic species including large macromolecular systems and simple inorganic ions are the key to understanding the excellent lubrication performance. An important tool for characterizing the intermolecular forces and their structural consequences is molecular dynamics. Albumin is one of the major components in synovial fluid. Its electrostatic properties, including the ability to form molecular complexes, are closely related to pH, solvation, and the presence of ions. In the context of synovial fluid, it is relevant to describe the possible interactions between albumin and hyaluronate, taking into account solution composition effects. In this study, the influence of Na+, Mg2+, and Ca2+ ions on human serum albumin–hyaluronan interactions were examined using molecular dynamics tools. It was established that the presence of divalent cations, and especially Ca2+, contributes mostly to the increase of the affinity between hyaluronan and albumin, which is associated with charge compensation in negatively charged hyaluronan and albumin. Furthermore, the most probable binding sites were structurally and energetically characterized. The indicated moieties exhibit a locally positive charge which enables hyaluronate binding (direct and water mediated).

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The effect of alkyl chain length on the structure and thermodynamics of protic–aprotic ionic liquid mixtures: a molecular dynamics study

Physical Chemistry Chemical Physics ◽

10.1039/c8cp00575c ◽

2018 ◽

Vol 20 (15) ◽

pp. 9938-9949 ◽

Cited By ~ 8

Author(s):

Borja Docampo-Álvarez ◽

Víctor Gómez-González ◽

Trinidad Méndez-Morales ◽

Julio R. Rodríguez ◽

Oscar Cabeza ◽

...

Keyword(s):

Molecular Dynamics ◽

Ionic Liquid ◽

Ionic Liquids ◽

Chain Length ◽

Alkyl Chain ◽

Molecular Complexes ◽

Liquid Mixtures ◽

Alkyl Chain Length ◽

Ideal Behavior

Mixtures of protic and aprotic ionic liquids exhibit non-ideal behavior with increasing alkyl chain length, caused by the formation of molecular complexes.

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ProLIF: a library to encode molecular interactions as fingerprints

Journal of Cheminformatics ◽

10.1186/s13321-021-00548-6 ◽

2021 ◽

Vol 13 (1) ◽

Author(s):

Cédric Bouysset ◽

Sébastien Fiorucci

Keyword(s):

Machine Learning ◽

Molecular Dynamics ◽

Data Analysis ◽

Three Dimensional ◽

Molecular Complexes ◽

Use Case ◽

Docking Simulations ◽

Rna Molecules ◽

Vector Representations ◽

Interaction Fingerprints

AbstractInteraction fingerprints are vector representations that summarize the three-dimensional nature of interactions in molecular complexes, typically formed between a protein and a ligand. This kind of encoding has found many applications in drug-discovery projects, from structure-based virtual-screening to machine-learning. Here, we present ProLIF, a Python library designed to generate interaction fingerprints for molecular complexes extracted from molecular dynamics trajectories, experimental structures, and docking simulations. It can handle complexes formed of any combination of ligand, protein, DNA, or RNA molecules. The available interaction types can be fully reparametrized or extended by user-defined ones. Several tutorials that cover typical use-case scenarios are available, and the documentation is accompanied with code snippets showcasing the integration with other data-analysis libraries for a more seamless user-experience. The library can be freely installed from our GitHub repository (https://github.com/chemosim-lab/ProLIF).

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