A quantum-based molecular dynamics study of the ICM-102/HNO3 host–guest reaction at high temperatures

2020 ◽  
Vol 22 (46) ◽  
pp. 27002-27012
Author(s):  
Yiwen Xiao ◽  
Lang Chen ◽  
Deshen Geng ◽  
Kun Yang ◽  
Jianying Lu ◽  
...  

The quantum-based MD method is used to investigate the reaction mechanism of a host–guest explosive system for the first time.

Author(s):  
Toshihiro Kaneko ◽  
Kenji Yasuoka ◽  
Ayori Mitsutake ◽  
Xiao Cheng Zeng

Multicanonical molecular dynamics simulations are applied, for the first time, to study the liquid-solid and solid-solid transitions in Lennard-Jones (LJ) clusters. The transition temperatures are estimated based on the peak position in the heat capacity versus temperature curve. For LJ31, LJ58 and LJ98, our results on the solid-solid transition temperature are in good agreement with previous ones. For LJ309, the predicted liquid-solid transition temperature is also in agreement with previous result.


Biomolecules ◽  
2020 ◽  
Vol 11 (1) ◽  
pp. 27
Author(s):  
Iwona Sadura ◽  
Dariusz Latowski ◽  
Jana Oklestkova ◽  
Damian Gruszka ◽  
Marek Chyc ◽  
...  

Plants have developed various acclimation strategies in order to counteract the negative effects of abiotic stresses (including temperature stress), and biological membranes are important elements in these strategies. Brassinosteroids (BR) are plant steroid hormones that regulate plant growth and development and modulate their reaction against many environmental stresses including temperature stress, but their role in modifying the properties of the biological membrane is poorly known. In this paper, we characterise the molecular dynamics of chloroplast membranes that had been isolated from wild-type and a BR-deficient barley mutant that had been acclimated to low and high temperatures in order to enrich the knowledge about the role of BR as regulators of the dynamics of the photosynthetic membranes. The molecular dynamics of the membranes was investigated using electron paramagnetic resonance (EPR) spectroscopy in both a hydrophilic and hydrophobic area of the membranes. The content of BR was determined, and other important membrane components that affect their molecular dynamics such as chlorophylls, carotenoids and fatty acids in these membranes were also determined. The chloroplast membranes of the BR-mutant had a higher degree of rigidification than the membranes of the wild type. In the hydrophilic area, the most visible differences were observed in plants that had been grown at 20 °C, whereas in the hydrophobic core, they were visible at both 20 and 5 °C. There were no differences in the molecular dynamics of the studied membranes in the chloroplast membranes that had been isolated from plants that had been grown at 27 °C. The role of BR in regulating the molecular dynamics of the photosynthetic membranes will be discussed against the background of an analysis of the photosynthetic pigments and fatty acid composition in the chloroplasts.


2021 ◽  
Vol 22 (3) ◽  
pp. 1400
Author(s):  
Ciresthel Bello-Rios ◽  
Sarita Montaño ◽  
Olga Lilia Garibay-Cerdenares ◽  
Lilian Esmeralda Araujo-Arcos ◽  
Marco Antonio Leyva-Vázquez ◽  
...  

The oncogenic potential of high-risk human papillomavirus (HPV) is predicated on the production of the E6 and E7 oncoproteins, which are responsible for disrupting the control of the cell cycle. Epidemiological studies have proposed that the presence of the N29S and H51N variants of the HPV16 E7 protein is significantly associated with cervical cancer. It has been suggested that changes in the amino acid sequence of E7 variants may affect the oncoprotein 3D structure; however, this remains uncertain. An analysis of the structural differences of the HPV16 E7 protein and its variants (N29S and H51N) was performed through homology modeling and structural refinement by molecular dynamics simulation. We propose, for the first time, a 3D structure of the E7 reference protein and two of Its variants (N29S and H51N), and conclude that the mutations induced by the variants in N29S and H51N have a significant influence on the 3D structure of the E7 protein of HPV16, which could be related to the oncogenic capacity of this protein.


ACS Catalysis ◽  
2021 ◽  
pp. 11626-11638
Author(s):  
Carola Jerves ◽  
Rui P. P. Neves ◽  
Maria J. Ramos ◽  
Saulo da Silva ◽  
Pedro A. Fernandes

RSC Advances ◽  
2016 ◽  
Vol 6 (88) ◽  
pp. 85603-85611 ◽  
Author(s):  
Jinyang Wang ◽  
Wei Gao ◽  
Haimin Zhong ◽  
Canjian Liang ◽  
Xiaojuan Chen ◽  
...  

Intradiffusion coefficients ofN,N-dimethylformamide (DDMF) and water (DW) in their mixtures were measured as a function of temperature, pressure and composition for the first time using the PGSE-NMR technique.


Author(s):  
Francesca Ferrari ◽  
Maicol Bissaro ◽  
Simone Fabbian ◽  
Jessica de Almeida Roger ◽  
Stefano Mammi ◽  
...  

<p>In this manuscript, for the first time, we presented a fragment library and we validated its performance by comparison with a well-established technique for fragment screening as solution NMR. We were able to screen 400 different fragments producing a total of 1200 independent fragment-protein recognition pathways. As far as we know, this represents the largest screening based on Molecular dynamics ever reported. Our simulations successfully detected the true binders in the library in a prospective study, showing a notable agreement with a state-of-art screening we performed by NMR on the same dataset.</p>


2020 ◽  
Author(s):  
Jin Soo Lim ◽  
Jonathan Vandermause ◽  
Matthijs A. van Spronsen ◽  
Albert Musaelian ◽  
Yu Xie ◽  
...  

Restructuring of interfaces plays a crucial role in materials science and heterogeneous catalysis. Bimetallic systems, in particular, often adopt very different composition and morphology at surfaces compared to the bulk. For the first time, we reveal a detailed atomistic picture of long-timescale restructuring of Pd deposited on Ag, using microscopy, spectroscopy, and novel simulation methods. By developing and performing accelerated machine-learning molecular dynamics followed by an automated analysis method, we discover and characterize previously unidentified surface restructuring mechanisms in an unbiased fashion, including Pd-Ag place exchange and Ag pop-out, as well as step ascent and descent. Remarkably, layer-by-layer dissolution of Pd into Ag is always preceded by an encapsulation of Pd islands by Ag, resulting in a significant migration of Ag out of the surface and a formation of extensive vacancy pits within a period of microseconds. These metastable structures are of vital catalytic importance, as Ag-encapsulated Pd remains much more accessible to reactants than bulk-dissolved Pd. Our approach is broadly applicable to complex multimetallic systems and enables the previously intractable mechanistic investigation of restructuring dynamics at atomic resolution.


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