Hydrogen-bond structure and anharmonicity in croconic acid

2014 ◽  
Vol 16 (47) ◽  
pp. 26234-26239 ◽  
Author(s):  
Sanghamitra Mukhopadhyay ◽  
Matthias Gutmann ◽  
Felix Fernandez-Alonso
Keyword(s):  
Hydrogen Bond ◽  
Layered Structure ◽  
Large Scale ◽  
Md Simulations

Layered structure of croconic acid and radial distributions from large scale MD simulations, highlighting a distinct broadening even at 300 K where the material remains ferroelectric.

A Hydrogen Bond Between Linear Tetrapyrrole and Conserved Aspartate Causes the Far-Red Shifted Absorption of Phytochrome Photoreceptors

2020 ◽  
Author(s):  
Egle Maximowitsch ◽  
Tatiana Domratcheva
Keyword(s):  
Hydrogen Bond ◽  
Light Adaptation ◽  
Positive Charge ◽  
Pyrrole Ring ◽  
Md Simulations ◽  
Spectral Shift ◽  
Specific Domain ◽  
Study Guides ◽  
Rational Engineering ◽  
Tuning Mechanism

Photoswitching of phytochrome photoreceptors between red-absorbing (Pr) and far-red absorbing (Pfr) states triggers light adaptation of plants, bacteria and other organisms. Using quantum chemistry, we elucidate the color-tuning mechanism of phytochromes and identify the origin of the Pfr-state red-shifted spectrum. Spectral variations are explained by resonance interactions of the protonated linear tetrapyrrole chromophore. In particular, hydrogen bonding of pyrrole ring D with the strictly conserved aspartate shifts the positive charge towards ring D thereby inducing the red spectral shift. Our MD simulations demonstrate that formation of the ring D–aspartate hydrogen bond depends on interactions between the chromophore binding domain (CBD) and phytochrome specific domain (PHY). Our study guides rational engineering of fluorescent phytochromes with a far-red shifted spectrum.

Molecular Dynamics Simulation of a Pullout Test on a Carbon Nanotube in a Polymer Matrix

2014 ◽  
Vol 1700 ◽  
pp. 61-66
Author(s):  
Guttormur Arnar Ingvason ◽  
Virginie Rollin
Keyword(s):  
Molecular Dynamics ◽  
Polymer Matrix ◽  
Large Scale ◽  
Md Simulations ◽  
Dynamics Simulation ◽  
Atomistic Simulations ◽  
Polymer Molecules ◽  
Molecular Potential ◽  
Pull Out ◽  
Walled Carbon Nanotubes

ABSTRACTAdding single walled carbon nanotubes (SWCNT) to a polymer matrix can improve the delamination properties of the composite. Due to the complexity of polymer molecules and the curing process, few 3-D Molecular Dynamics (MD) simulations of a polymer-SWCNT composite have been run. Our model runs on the Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS), with a COMPASS (Condensed phase Optimized Molecular Potential for Atomistic Simulations Studies) potential. This potential includes non-bonded interactions, as well as bonds, angles and dihedrals to create a MD model for a SWCNT and EPON 862/DETDA (Diethyltoluenediamine) polymer matrix. Two simulations were performed in order to test the implementation of the COMPASS parameters. The first one was a tensile test on a SWCNT, leading to a Young’s modulus of 1.4 TPa at 300K. The second one was a pull-out test of a SWCNT from an originally uncured EPON 862/DETDA matrix.

scholarly journals Cocrystals of Ethenzamide With 2-Nitrobenzoic Acid - Conformational Analysis, MD Simulations And DFT Investigations

2021 ◽  
Author(s):  
Y. Sheena Mary ◽  
Y. Shyma Mary ◽  
Razieh Razavi
Keyword(s):  
Hydrogen Bond ◽  
Conformational Analysis ◽  
Crystal Engineering ◽  
Energy Charge ◽  
Thermodynamic Characteristics ◽  
Md Simulations ◽  
Pharmaceutical Chemistry ◽  
Nitrobenzoic Acid ◽  
Wide Range ◽  
Stability Energy

Abstract In crystal engineering and pharmaceutical chemistry, cocrystals have a wide range of applications. Ethenzamide (EA) is found to form cocrystal with 2-nitrobenzoic acid (NBA). Geometry properties like stability energy, charge distribution, bond length, electronic properties and thermodynamic characteristics have been analyzed. The C-H…O hydrogen bond involves C-H of EA and oxygen of NBA. Configuration with the angle, N3-C4-C5-C6 gives the lowest energy conformation. Partition coefficient value suggests that EA-NBA has pharmaceutics behavior. RMSD values show the simulation’s relative stability and the complexes, remained stable throughout.

scholarly journals FrustratometeR: an R-package to compute Local frustration in protein structures, point mutants and MD simulations

2020 ◽  
Author(s):  
Atilio O. Rausch ◽  
Maria I. Freiberger ◽  
Cesar O. Leonetti ◽  
Diego M. Luna ◽  
Leandro G. Radusky ◽  
...  
Keyword(s):  
Protein Interactions ◽  
Large Scale ◽  
Protein Structures ◽  
Md Simulations ◽  
R Package ◽  
Protein Protein Interactions ◽  
Large Scale Analysis ◽  
Functional Aspects ◽  
Catalytic Sites ◽  
Polypeptide Chains

Once folded natural protein molecules have few energetic conflicts within their polypeptide chains. Many protein structures do however contain regions where energetic conflicts remain after folding, i.e. they have highly frustrated regions. These regions, kept in place over evolutionary and physiological timescales, are related to several functional aspects of natural proteins such as protein-protein interactions, small ligand recognition, catalytic sites and allostery. Here we present FrustratometeR, an R package that easily computes local energetic frustration on a personal computer or a cluster. This package facilitates large scale analysis of local frustration, point mutants and MD trajectories, allowing straightforward integration of local frustration analysis in to pipelines for protein structural analysis.Availability and implementation: https://github.com/proteinphysiologylab/frustratometeR

scholarly journals Antimicrobial action of the cationic peptide, chrysophsin-3: a coarse-grained molecular dynamics study

Soft Matter ◽  
2018 ◽  
Vol 14 (15) ◽  
pp. 2796-2807 ◽  
Author(s):  
Andrea Catte ◽  
Mark R. Wilson ◽  
Martin Walker ◽  
Vasily S. Oganesyan
Keyword(s):  
Molecular Dynamics ◽  
Large Scale ◽  
Md Simulations ◽  
Antimicrobial Action ◽  
Coarse Grained ◽  
Cationic Peptide ◽  
Coarse Grained Molecular Dynamics

Antimicrobial action of a cationic peptide is modelled by large scale MD simulations.

Multiscale Simulations of Domains in Ferroelectrics

Domain Walls ◽  
2020 ◽  
pp. 311-339
Author(s):  
S. Liu ◽  
I. Grinberg ◽  
A. M. Rappe
Keyword(s):  
Density Functional ◽  
Large Scale ◽  
Mean Field Theory ◽  
Mean Field ◽  
Md Simulations ◽  
Relaxor Ferroelectrics ◽  
Ferroelectric Materials ◽  
Multiscale Simulations ◽  
Challenges And Opportunities ◽  
Physically Based

This chapter focuses on recent studies of ferroelectrics, where large-scale molecular dynamics (MD) simulations using first-principles-based force fields played a central role in revealing important physics inaccessible to direct density functional theory (DFT) calculations but critical for developing physically-based free energy functional for coarse-grained phase-field-type simulations. After reviewing typical atomistic potentials of ferroelectrics for MD simulations, the chapter describes a progressive theoretical framework that combines DFT, MD, and a mean-field theory. It then focuses on relaxor ferroelectrics. By examining the spatial and temporal polarization correlations in prototypical relaxor ferroelectrics with million-atom MD simulations and novel analysis techniques, this chapter shows that the widely accepted model of polar nanoregions embedded in a non-polar matrix is incorrect for Pb-based relaxors. Rather, the unusual properties of theses relaxor ferroelectrics stem from the presence of a multi-domain state with extremely small domain sizes (2–10 nanometers), giving rise to a greater flexibility for polarization rotations and the ultrahigh dielectric and piezoelectric responses. Finally, this chapter discusses the challenges and opportunities for multiscale simulations of ferroelectric materials.

scholarly journals Terbium-Tetracarboxylate Framework as a Luminescent Probe for the Selective Detection of Nitrofurazone

Crystals ◽  
2020 ◽  
Vol 10 (3) ◽  
pp. 222
Author(s):  
Qipeng Li ◽  
Yanqiong Shen ◽  
Junsong Zhao ◽  
Zejun Zhang ◽  
Jinjie Qian
Keyword(s):  
Hydrogen Bond ◽  
Layered Structure ◽  
Sensitive Detection ◽  
Fluorescence Properties ◽  
Selective Detection ◽  
Supramolecular Framework ◽  
Luminescent Probe ◽  
Hydrogen Bond Interactions ◽  
Secondary Building Units

A novel terbium-tetracarboxylate framework with the 5,5’-(diazene-1,2-iyl)diisophthalic acid (H4abtc) ligand, formulated as [Tb(Habtc)(DMSO)(H2O)2]n (ZTU-5), has been synthesized and structurally characterized. ZTU-5 features a 2D-layered structure constructed by the binuclear terbium secondary building units (SBUs) and abtc4– ligand, which can be further expanded into a 3D-supramolecular framework by the hydrogen bond interactions. In addition, the magnetic and fluorescence properties of ZTU-5 are investigated and ZTU-5 exhibits highly selective and sensitive detection of nitrofurazone (NZF).

scholarly journals Molecular dynamics simulations for genetic interpretation in protein coding regions: where we are, where to go and when

2019 ◽  
Author(s):  
Juan J Galano-Frutos ◽  
Helena García-Cebollada ◽  
Javier Sancho
Keyword(s):  
Molecular Dynamics ◽  
Amino Acid ◽  
Large Scale ◽  
Binary Classification ◽  
Chemical Properties ◽  
Md Simulations ◽  
Single Amino Acid ◽  
Medical Decision ◽  
Evolutionary Information ◽  
Protein Variants

Abstract The increasing ease with which massive genetic information can be obtained from patients or healthy individuals has stimulated the development of interpretive bioinformatics tools as aids in clinical practice. Most such tools analyze evolutionary information and simple physical–chemical properties to predict whether replacement of one amino acid residue with another will be tolerated or cause disease. Those approaches achieve up to 80–85% accuracy as binary classifiers (neutral/pathogenic). As such accuracy is insufficient for medical decision to be based on, and it does not appear to be increasing, more precise methods, such as full-atom molecular dynamics (MD) simulations in explicit solvent, are also discussed. Then, to describe the goal of interpreting human genetic variations at large scale through MD simulations, we restrictively refer to all possible protein variants carrying single-amino-acid substitutions arising from single-nucleotide variations as the human variome. We calculate its size and develop a simple model that allows calculating the simulation time needed to have a 0.99 probability of observing unfolding events of any unstable variant. The knowledge of that time enables performing a binary classification of the variants (stable-potentially neutral/unstable-pathogenic). Our model indicates that the human variome cannot be simulated with present computing capabilities. However, if they continue to increase as per Moore’s law, it could be simulated (at 65°C) spending only 3 years in the task if we started in 2031. The simulation of individual protein variomes is achievable in short times starting at present. International coordination seems appropriate to embark upon massive MD simulations of protein variants.

scholarly journals Hydrogenation Dynamics of Biphenylene Carbon (Graphenylene) Membranes

MRS Advances ◽  
2017 ◽  
Vol 2 (29) ◽  
pp. 1571-1576
Author(s):  
Vinicius Splugues ◽  
Pedro Alves da Silva Autreto ◽  
Douglas S. Galvao
Keyword(s):  
Molecular Dynamics ◽  
Large Scale ◽  
Materials Science ◽  
Md Simulations ◽  
Structural Transformations ◽  
Extensive Study ◽  
Massively Parallel ◽  
Porous Membranes ◽  
Two Dimensional ◽  
Reactive Force

ABSTRACTThe advent of graphene created a revolution in materials science. Because of this there is a renewed interest in other carbon-based structures. Graphene is the ultimate (just one atom thick) membrane. It has been proposed that graphene can work as impermeable membrane to standard gases, such argon and helium. Graphene-like porous membranes, but presenting larger porosity and potential selectivity would have many technological applications. Biphenylene carbon (BPC), sometimes called graphenylene, is one of these structures. BPC is a porous two-dimensional (planar) allotrope carbon, with its pores resembling typical sieve cavities and/or some kind of zeolites. In this work, we have investigated the hydrogenation dynamics of BPC membranes under different conditions (hydrogenation plasma density, temperature, etc.). We have carried out an extensive study through fully atomistic molecular dynamics (MD) simulations using the reactive force field ReaxFF, as implemented in the well-known Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS) code. Our results show that the BPC hydrogenation processes exhibit very complex patterns and the formation of correlated domains (hydrogenated islands) observed in the case of graphene hydrogenation was also observed here. MD results also show that under hydrogenation BPC structure undergoes a change in its topology, the pores undergoing structural transformations and extensive hydrogenation can produce significant structural damages, with the formation of large defective areas and large structural holes, leading to structural collapse.

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