scholarly journals Exploring New Crystal Structures of Glycine via Electric Field-Induced Structural Transformations with Molecular Dynamics Simulations

Processes ◽  
2019 ◽  
Vol 7 (5) ◽  
pp. 268 ◽  
Author(s):  
Pelin Su Bulutoglu ◽  
Conor Parks ◽  
Nandkishor K. Nere ◽  
Shailendra Bordawekar ◽  
Doraiswami Ramkrishna
Keyword(s):  
Crystal Structure ◽  
Molecular Dynamics ◽  
Solid State ◽  
Electric Field ◽  
Physical Properties ◽  
Molecular Dynamics Simulations ◽  
Crystal Structures ◽  
Electric Fields ◽  
High Intensity ◽  
Dynamics Simulations

Being able to control polymorphism of a crystal is of great importance to many industries, including the pharmaceutical industry, since the crystal’s structure determines significant physical properties of a material. While there are many conventional methods used to control the final crystal structure that comes out of a crystallization unit, these methods fail to go beyond a few known structures that are kinetically accessible. Recent studies have shown that externally applied fields have the potential to effectively control polymorphism and to extend the set of observable polymorphs that are not accessible through conventional methods. This computational study focuses on the application of high-intensity dc electric fields (e-fields) to induce solid-state transformation of glycine crystals to obtain new polymorphs that have not been observed via experiments. Through molecular dynamics simulations of solid-state α -, β -, and γ -glycine crystals, it has been shown that the new polymorphs sustain their structures within 125 ns after the electric field has been turned off. It was also demonstrated that strength and direction of the electric field and the initial structure of the crystal are parameters that affect the resulting polymorph. Our results showed that application of high-intensity dc electric fields on solid-state crystals can be an effective crystal structure control method for the exploration of new crystal structures of known materials and to extend the range of physical properties a material can have.

scholarly journals Molecular Dynamics Simulations of Liquid-Liquid Interfaces in an Electric Field: the Water-1,2-Dichloroethane Interface

2020 ◽  
Author(s):  
Paolo Raiteri ◽  
Peter Kraus ◽  
Julian Gale
Keyword(s):  
Molecular Dynamics ◽  
Electric Field ◽  
Molecular Dynamics Simulations ◽  
External Electric Field ◽  
Electric Fields ◽  
Liquid Interfaces ◽  
Ewald Summation ◽  
External Electric Fields ◽  
Simulation Cell ◽  
Dynamics Simulations

Molecular dynamics simulations of the liquid-liquid interface between water and 1,2-Dichloroethane in the presence of weak external electric fields.<div>The effect of the use of 3D periodic Ewald summation and the effect of the simulation setup are discussed.</div><div>A new simple geometric method for designing the simulation cell is proposed. This method was thoroughly tested shown that it mitigates any artefacts to the use of 3D Ewald summation with external electric field.</div>

scholarly journals Analysis of an all-solid state nanobattery using molecular dynamics simulations under an external electric field

2021 ◽  
Vol 23 (1) ◽  
pp. 597-606
Author(s):  
Victor Ponce ◽  
Diego E. Galvez-Aranda ◽  
Jorge M. Seminario
Keyword(s):  
Molecular Dynamics ◽  
Solid State ◽  
Electric Field ◽  
Molecular Dynamics Simulations ◽  
External Electric Field ◽  
Dynamics Simulations

Speciation at the SEI and SSE of a solid-state nanobattery.

scholarly journals Reducing Crystal Structure Overprediction of Ibuprofen with Large Scale Molecular Dynamics Simulations

2021 ◽  
Author(s):  
Nicholas Francia ◽  
Louise Price ◽  
Matteo Salvalaglio
Keyword(s):  
Crystal Structure ◽  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Crystal Structures ◽  
Finite Temperature ◽  
Structure Prediction ◽  
Large Scale ◽  
Lattice Energy ◽  
Racemic Mixture ◽  
Dynamics Simulations

<p>The control of the crystal form is a central issue in the pharmaceutical industry. The identification of putative polymorphs through Crystal Structure Prediction (CSP) methods is based on lattice energy calculations, which are known to significantly over-predict the number of plausible crystal structures. A valuable tool to reduce overprediction is to employ physics-based, dynamic simulations to coalesce lattice energy minima separated by small barriers into a smaller number of more stable geometries once thermal effects are introduced. Molecular dynamics simulations and enhanced sampling methods can be employed in this context to simulate crystal structures at finite temperature and pressure. </p><p>Here we demonstrate the applicability of approaches based on molecular dynamics to systematically process realistic CSP datasets containing several hundreds of crystal structures. The system investigated is ibuprofen, a conformationally flexible active pharmaceutical ingredient that crystallises both in enantiopure forms and as a racemic mixture. By introducing a hierarchical approach in the analysis of finite-temperature supercell configurations, we can post-process a dataset of 555 crystal structures, identifying 65% of the initial structures as labile, while maintaining all the experimentally known crystal structures in the final, reduced set. Moreover, the extensive nature of the initial dataset allows one to gain quantitative insight into the persistence and the propensity to transform of crystal structures containing common hydrogen-bonded intermolecular interaction motifs.</p>

scholarly journals Molecular Dynamics Simulations of Liquid-Liquid Interfaces in an Electric Field: the Water-1,2-Dichloroethane Interface

2020 ◽  
Author(s):  
Paolo Raiteri ◽  
Peter Kraus ◽  
Julian Gale
Keyword(s):  
Molecular Dynamics ◽  
Electric Field ◽  
Molecular Dynamics Simulations ◽  
External Electric Field ◽  
Electric Fields ◽  
Liquid Interfaces ◽  
Ewald Summation ◽  
External Electric Fields ◽  
Simulation Cell ◽  
Dynamics Simulations

Molecular dynamics simulations of the liquid-liquid interface between water and 1,2-Dichloroethane in the presence of weak external electric fields.<div>The effect of the use of 3D periodic Ewald summation and the effect of the simulation setup are discussed.</div><div>A new simple geometric method for designing the simulation cell is proposed. This method was thoroughly tested shown that it mitigates any artefacts to the use of 3D Ewald summation with external electric field.</div>

scholarly journals Tubulin as a sensitive target of nanosecond-scale intense electric field: quantitative insights from molecular dynamics simulations

2019 ◽  
Author(s):  
Paolo Marracino ◽  
Daniel Havelka ◽  
Jiří Průša ◽  
Micaela Liberti ◽  
Jack A. Tuszynski ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Cell Division ◽  
Electric Field ◽  
Molecular Dynamics Simulations ◽  
Electric Fields ◽  
Binding Sites ◽  
Fine Tuning ◽  
Electric Pulses ◽  
Dynamics Simulations ◽  
Tubulin Protein

AbstractIntense pulsed electric fields are known to act at the cell membrane level and are already being exploited in biomedical and biotechnological applications. However, it is not clear if intra-cellular components such as cytoskeletal proteins could be directly influenced by electric pulses within biomedically-attainable parameters. If so, a molecular mechanism of action could be uncovered for therapeutic applications of such electric fields. To help clarify this question, we first identified that a tubulin heterodimer is a natural biological target for intense electric fields due to its exceptional electric properties and crucial roles played in cell division. Using molecular dynamics simulations, we then demonstrated that an intense - yet experimentally attainable - electric field of nanosecond duration can affect the β-tubulin’s C-terminus conformations and also influence local electrostatic properties at the GTPase as well as the binding sites of major tubulin drugs site. Our results suggest that intense nanosecond electric pulses could be used for physical modulation of microtubule dynamics. Since a nanosecond pulsed electric field can penetrate the tissues and cellular membranes due to its broadband spectrum, our results are also potentially significant for the development of novel therapeutic protocols.Author summaryα/β-tubulin heterodimers are the basic building blocks of microtubules, that form diverse cellular structures responsible for essential cell functions such as cell division and intracellular transport. The ability of tubulin protein to adopt distinct conformations contributes to control the architecture of microtubule networks, microtubule-associated proteins, and motor proteins; moreover, it regulates microtubule growth, shrinkage, and the transitions between these states. Previous recent molecular dynamics simulations demonstrated that the interaction of the tubulin protein macrodipole with external electric field modifies orientation and conformations of key loops involved in lateral contacts: as a result, the stability of microtubules can be modulated by such fields. In this study, we seek to exploit these findings by investigating the possibility of fine-tuning the dipolar properties of binding sites of major drugs, by means of the action of electric fields. This may open the way to control tubulin-drug interactions using electric fields, thus modulating and altering the biological functions relative to the molecular vectors of microtubule assembly or disassembly. The major finding of our study reveals that intense (> 20 MV/m) ultra-short (30 ns) electric fields induce changes in the major residues of selected binding sites in a field strength-dependent manner.

scholarly journals Water structure in solution and crystal molecular dynamics simulations compared to protein crystal structures

RSC Advances ◽  
2020 ◽  
Vol 10 (14) ◽  
pp. 8435-8443
Author(s):  
Octav Caldararu ◽  
Majda Misini Ignjatović ◽  
Esko Oksanen ◽  
Ulf Ryde
Keyword(s):  
Crystal Structure ◽  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Crystal Structures ◽  
Water Structure ◽  
Protein Crystal ◽  
Local Clustering ◽  
Dynamics Simulations ◽  
Structure In Solution

Molecular dynamics simulations can reproduce the water structure around proteins in crystal structure only if a local clustering is performed.

Solid state to solution: crystal structure and molecular dynamics simulations of a polyammonium nitrate host

1999 ◽  
Vol 23 (10) ◽  
pp. 1007-1013 ◽  
Author(s):  
Joanna Wiórkiewicz-Kuczera ◽  
Krzysztof Kuczera ◽  
Carla Bazzicalupi ◽  
Andrea Bencini ◽  
Barbara Valtancoli ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Molecular Dynamics ◽  
Solid State ◽  
Molecular Dynamics Simulations ◽  
Dynamics Simulations

scholarly journals Fast water channeling across carbon nanotubes in far infrared terahertz electric fields

Nanoscale ◽  
2016 ◽  
Vol 8 (4) ◽  
pp. 1886-1891 ◽  
Author(s):  
Qi-Lin Zhang ◽  
Rong-Yao Yang ◽  
Wei-Zhou Jiang ◽  
Zi-Qian Huang
Keyword(s):  
Carbon Nanotubes ◽  
Molecular Dynamics ◽  
Electric Field ◽  
Molecular Dynamics Simulations ◽  
Electric Fields ◽  
Far Infrared ◽  
Single Walled Carbon Nanotubes ◽  
Frequency Range ◽  
Dynamics Simulations ◽  
Walled Carbon Nanotubes

Using molecular dynamics simulations, we demonstrate that the water channeling across single-walled carbon nanotubes can greatly be affected by the terahertz electric field through the resonant mechanisms induced by various vortical modes in a broad frequency range.

Conformational transitions and helical structures of a dipolar chain in external electric fields

Soft Matter ◽  
2021 ◽  
Author(s):  
Yulia D. Gordievskaya ◽  
Elena Yu. Kramarenko
Keyword(s):  
Molecular Dynamics ◽  
Electric Field ◽  
Molecular Dynamics Simulations ◽  
Electric Fields ◽  
Conformational Transitions ◽  
Uniform Electric Field ◽  
Conformational Behavior ◽  
Helical Structures ◽  
External Electric Fields ◽  
Dynamics Simulations

The conformational behavior of a single dipolar chain in a uniform electric field is investigated by molecular dynamics simulations.

Molecular dynamics simulations of electric field induced water flow inside a carbon nanotorus: a molecular cyclotron

2017 ◽  
Vol 19 (19) ◽  
pp. 12384-12393 ◽  
Author(s):  
Hassan Sabzyan ◽  
Maryam Kowsar
Keyword(s):  
Molecular Dynamics ◽  
Electric Field ◽  
Molecular Dynamics Simulations ◽  
Water Flow ◽  
Electric Fields ◽  
Water Molecules ◽  
Dynamics Simulations

A nano-flow is induced by applying gigahertz rotating electric fields (EFs) of different strengths and frequencies on a carbon nanotorus filled with water molecules, using molecular dynamics simulations.

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