Urea homogeneous nucleation mechanism is solvent dependent

2015 ◽  
Vol 179 ◽  
pp. 291-307 ◽  
Author(s):  
Matteo Salvalaglio ◽  
Marco Mazzotti ◽  
Michele Parrinello
Keyword(s):  
Finite Size ◽  
Single Step ◽  
Crystal Nucleation ◽  
Primary Role ◽  
Nucleation Process ◽  
Polymorphic Transitions ◽  
Dynamics Simulations ◽  
A Minor ◽  
Energy Surfaces ◽  
The Impact

The composition of the mother phase plays a primary role in crystallization processes, affecting both crystal nucleation and growth. In this work, the influence of solvents on urea nucleation has been investigated by means of enhanced sampling molecular dynamics simulations. We find that, depending on the solvent, the nucleation process can either follow a single-step or a two-step mechanism. While in methanol and ethanol a single-step nucleation process is favored, in acetonitrile a two-step process emerges as the most likely nucleation pathway. We also find that solvents have a minor impact on polymorphic transitions in the early stages of urea nucleation. The impact of finite size effects on the free energy surfaces is systematically considered and discussed in relation to the simulation setup.

scholarly journals Silver Hardening via Hypersonic Impacts

MRS Advances ◽  
2018 ◽  
Vol 3 (8-9) ◽  
pp. 493-498 ◽  
Author(s):  
Eliezer Fernando Oliveira ◽  
Pedro Alves da Silva Autreto ◽  
Douglas Soares Galvão
Keyword(s):  
Rigid Wall ◽  
Strengthening Mechanism ◽  
Research Area ◽  
Single Step ◽  
High Impact ◽  
Step Method ◽  
Silver Nanocubes ◽  
Active Research ◽  
Dynamics Simulations ◽  
The Impact

ABSTRACTThe search for new ultra strong materials has been a very active research area. With relation to metals, a successful way to improve their strength is by the creation of a gradient of nanograins (GNG) inside the material. Recently, R. Thevamaran et al. [Science v354, 312-316 (2016)] propose a single step method based on high velocity impact of silver nanocubes to produce high-quality GNG. This method consists of producing high impact collisions of silver cubes at hypersonic velocity (∼400 m/s) against a rigid wall. Although they observed an improvement in the mechanical properties of the silver after the impact, the GNG creation and the strengthening mechanism at nanoscale remain unclear. In order to gain further insights about these mechanisms, we carried out fully atomistic molecular dynamics simulations (MD) to investigate the atomic conformations/rearrangements during and after high impact collisions of silver nanocubes at ultrasonic velocity. Our results indicate the co-existence of polycrystalline arrangements after the impact formed by core HCP domains surrounded by FCC ones, which could also contribute to explain the structural hardening.

Active Learning Accelerates Ab Initio Molecular Dynamics on Pericyclic Reactive Energy Surfaces

2020 ◽  
Author(s):  
Shi Jun Ang ◽  
Wujie Wang ◽  
Daniel Schwalbe-Koda ◽  
Simon Axelrod ◽  
Rafael Gomez-Bombarelli
Keyword(s):  
Molecular Dynamics ◽  
Potential Energy ◽  
Transition State ◽  
Potential Energy Surface ◽  
Ab Initio ◽  
Energy Surface ◽  
Computational Cost ◽  
Reactive Trajectories ◽  
Dynamics Simulations ◽  
Energy Surfaces

<div>Modeling dynamical effects in chemical reactions, such as post-transition state bifurcation, requires <i>ab initio</i> molecular dynamics simulations due to the breakdown of simpler static models like transition state theory. However, these simulations tend to be restricted to lower-accuracy electronic structure methods and scarce sampling because of their high computational cost. Here, we report the use of statistical learning to accelerate reactive molecular dynamics simulations by combining high-throughput ab initio calculations, graph-convolution interatomic potentials and active learning. This pipeline was demonstrated on an ambimodal trispericyclic reaction involving 8,8-dicyanoheptafulvene and 6,6-dimethylfulvene. With a dataset size of approximately</div><div>31,000 M062X/def2-SVP quantum mechanical calculations, the computational cost of exploring the reactive potential energy surface was reduced by an order of magnitude. Thousands of virtually costless picosecond-long reactive trajectories suggest that post-transition state bifurcation plays a minor role for the reaction in vacuum. Furthermore, a transfer-learning strategy effectively upgraded the potential energy surface to higher</div><div>levels of theory ((SMD-)M06-2X/def2-TZVPD in vacuum and three other solvents, as well as the more accurate DLPNO-DSD-PBEP86 D3BJ/def2-TZVPD) using about 10% additional calculations for each surface. Since the larger basis set and the dynamic correlation capture intramolecular non-covalent interactions more accurately, they uncover longer lifetimes for the charge-separated intermediate on the more accurate potential energy surfaces. The character of the intermediate switches from entropic to thermodynamic upon including implicit solvation effects, with lifetimes increasing with solvent polarity. Analysis of 2,000 reactive trajectories on the chloroform PES shows a qualitative agreement with the experimentally-reported periselectivity for this reaction. This overall approach is broadly applicable and opens a door to the study of dynamical effects in larger, previously-intractable reactive systems.</div>

scholarly journals The Impact of Metabolic Scion–Rootstock Interactions in Different Grapevine Tissues and Phloem Exudates

Metabolites ◽  
2021 ◽  
Vol 11 (6) ◽  
pp. 349
Author(s):  
Sara Tedesco ◽  
Alexander Erban ◽  
Saurabh Gupta ◽  
Joachim Kopka ◽  
Pedro Fevereiro ◽  
...  
Keyword(s):  
Agronomic Traits ◽  
Phloem Exudate ◽  
Graft Union ◽  
Reciprocal Effect ◽  
Metabolic Markers ◽  
Interaction Studies ◽  
Metabolic Interactions ◽  
A Minor ◽  
The Impact ◽  
Related Compounds

In viticulture, grafting is used to propagate Phylloxera-susceptible European grapevines, thereby using resistant American rootstocks. Although scion–rootstock reciprocal signaling is essential for the formation of a proper vascular union and for coordinated growth, our knowledge of graft partner interactions is very limited. In order to elucidate the scale and the content of scion–rootstock metabolic interactions, we profiled the metabolome of eleven graft combination in leaves, stems, and phloem exudate from both above and below the graft union 5–6 months after grafting. We compared the metabolome of scions vs. rootstocks of homografts vs. heterografts and investigated the reciprocal effect of the rootstock on the scion metabolome. This approach revealed that (1) grafting has a minor impact on the metabolome of grafted grapevines when tissues and genotypes were compared, (2) heterografting affects rootstocks more than scions, (3) the presence of a heterologous grafting partner increases defense-related compounds in both scion and rootstocks in shorter and longer distances from the graft, and (4) leaves were revealed as the best tissue to search for grafting-related metabolic markers. These results will provide a valuable metabolomics resource for scion–rootstock interaction studies and will facilitate future efforts on the identification of metabolic markers for important agronomic traits in grafted grapevines.

scholarly journals The Impact of Microclimate on the Reproductive Phenology of Female Populus tomentosa in a Micro-Scale Urban Green Space in Beijing

2021 ◽  
Vol 13 (6) ◽  
pp. 3518
Author(s):  
Xiaoyi Xing ◽  
Li Dong ◽  
Cecil Konijnendijk ◽  
Peiyao Hao ◽  
Shuxin Fan ◽  
...  
Keyword(s):  
Seed Dispersal ◽  
Spatial Variation ◽  
Air Temperature ◽  
Green Space ◽  
Populus Tomentosa ◽  
Early Spring ◽  
Reproductive Phenology ◽  
Primary Role ◽  
Micro Scale ◽  
The Impact

The spatial variation of poplars’ reproductive phenology in Beijing’s urban area has aggravated the threat of poplar fluff (cotton-like flying seeds) to public health. This research explored the impact of microclimate conditions on the reproductive phenology of female Populus tomentosa in Taoranting Park, a micro-scale green space in Beijing (range <1 km). The observed phenophases covered flowering, fruiting, and seed dispersal, and ENVI-MET was applied to simulate the effect of the microclimate on SGS (start day of the growing season). The results showed that a significant spatial variation in poplar reproductive phenology existed at the research site. The variation was significantly affected by the microclimate factors DMT (daily mean temperature) and DMH (daily mean heat transfer coefficient), with air temperature playing a primary role. Specifically, the phenology of flowering and fruiting phenophases (BBB, BF, FF, FS) was negatively correlated with DMT (−0.983 ≤ r ≤ −0.908, p <0.01) and positively correlated with DMH (0.769 ≤ r ≤ 0.864, p < 0.05). In contrast, DSD (duration of seed dispersal) showed a positive correlation with DMT (r = 0.946, p < 0.01) and a negative correlation with DMH (r = −0.922, p < 0.01). Based on the findings, the increase in air convection with lower air temperature and decrease in microclimate variation in green space can be an effective way to shorten the seed-flying duration to tackle poplar fluff pollution in Beijing’s early spring.

scholarly journals Sweet taste of heavy water

2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Natalie Ben Abu ◽  
Philip E. Mason ◽  
Hadar Klein ◽  
Nitzan Dubovski ◽  
Yaron Ben Shoshan-Galeczki ◽  
...  
Keyword(s):  
Heavy Water ◽  
Calcium Release ◽  
Homology Modelling ◽  
Taste Receptor ◽  
Chemical Properties ◽  
Sweet Taste ◽  
Minor Effect ◽  
Dynamics Simulations ◽  
A Minor ◽  
Physical And Chemical

AbstractHydrogen to deuterium isotopic substitution has only a minor effect on physical and chemical properties of water and, as such, is not supposed to influence its neutral taste. Here we conclusively demonstrate that humans are, nevertheless, able to distinguish D2O from H2O by taste. Indeed, highly purified heavy water has a distinctly sweeter taste than same-purity normal water and can add to perceived sweetness of sweeteners. In contrast, mice do not prefer D2O over H2O, indicating that they are not likely to perceive heavy water as sweet. HEK 293T cells transfected with the TAS1R2/TAS1R3 heterodimer and chimeric G-proteins are activated by D2O but not by H2O. Lactisole, which is a known sweetness inhibitor acting via the TAS1R3 monomer of the TAS1R2/TAS1R3, suppresses the sweetness of D2O in human sensory tests, as well as the calcium release elicited by D2O in sweet taste receptor-expressing cells. The present multifaceted experimental study, complemented by homology modelling and molecular dynamics simulations, resolves a long-standing controversy about the taste of heavy water, shows that its sweet taste is mediated by the human TAS1R2/TAS1R3 taste receptor, and opens way to future studies of the detailed mechanism of action.

scholarly journals Nonlocal and Size-Dependent Dielectric Function for Plasmonic Nanoparticles

2019 ◽  
Vol 9 (15) ◽  
pp. 3083
Author(s):  
Kai-Jian Huang ◽  
Shui-Jie Qin ◽  
Zheng-Ping Zhang ◽  
Zhao Ding ◽  
Zhong-Chen Bai
Keyword(s):  
Metallic Nanoparticles ◽  
High Efficiency ◽  
Finite Size ◽  
Plasmonic Nanostructures ◽  
Accurate Analysis ◽  
Finite Size Effects ◽  
Size Dependent ◽  
Quantum Size ◽  
The Impact ◽  
Electron Energy Loss

We develop a theoretical approach to investigate the impact that nonlocal and finite-size effects have on the dielectric response of plasmonic nanostructures. Through simulations, comprehensive comparisons of the electron energy loss spectroscopy (EELS) and the optical performance are discussed for a gold spherical dimer system in terms of different dielectric models. Our study offers a paradigm of high efficiency compatible dielectric theoretical framework for accounting the metallic nanoparticles behavior combining local, nonlocal and size-dependent effects in broader energy and size ranges. The results of accurate analysis and simulation for these effects unveil the weight and the evolution of both surface and bulk plasmons vibrational mechanisms, which are important for further understanding the electrodynamics properties of structures at the nanoscale. Particularly, our method can be extended to other plasmonic nanostructures where quantum-size or strongly interacting effects are likely to play an important role.

scholarly journals Molecular Dynamics Simulations of Crystal Nucleation near Interfaces in Incompatible Polymer Blends

Polymers ◽  
2021 ◽  
Vol 13 (3) ◽  
pp. 347
Author(s):  
Wenlin Zhang ◽  
Lingyi Zou
Keyword(s):  
Molecular Dynamics ◽  
Polymer Blends ◽  
Md Simulations ◽  
Nucleation And Growth ◽  
Crystal Nucleation ◽  
Crystalline Order ◽  
Mobile Species ◽  
Deep Supercooling ◽  
Crystallizable Polymer ◽  
Dynamics Simulations

We apply molecular dynamics (MD) simulations to investigate crystal nucleation in incompatible polymer blends under deep supercooling conditions. Simulations of isothermal nucleation are performed for phase-separated blends with different degrees of incompatibility. In weakly segregated blends, slow and incompatible chains in crystallizable polymer domains can significantly hinder the crystal nucleation and growth. When a crystallizable polymer is blended with a more mobile species in interfacial regions, enhanced molecular mobility leads to the fast growth of crystalline order. However, the incubation time remains the same as that in pure samples. By inducing anisotropic alignment near the interfaces of strongly segregated blends, phase separation also promotes crystalline order to grow near interfaces between different polymer domains.

Molecular Dynamics Study of Ion Impact Phenomena and Compressive Stress in Thin Films

1993 ◽  
Vol 317 ◽  
Author(s):  
N.A. Marks ◽  
P. Guan ◽  
D.R. Mckenzie ◽  
B.A. PailThorpe
Keyword(s):  
Molecular Dynamics ◽  
Three Dimensional ◽  
Carbon Films ◽  
Loss Mechanism ◽  
Ion Energy ◽  
Lennard Jones ◽  
Impact Phenomena ◽  
Ion Impact ◽  
Dynamics Simulations ◽  
The Impact

ABSTRACTMolecular dynamics simulations of nickel and carbon have been used to study the phenomena due to ion impact. The nickel and carbon interactions were described using the Lennard-Jones and Stillinger-Weber potentials respectively. The phenomena occurring after the impact of 100 e V to 1 keV ions were studied in the nickel simulations, which were both two and three-dimensional. Supersonic focussed collision sequences (or focusons) were observed, and associated with these focusons were unexpected sonic bow waves, which were a major energy loss mechanism for the focuson. A number of 2D carbon films were grown and the stress in the films as a function of incident ion energy was Measured. With increasing energy the stress changed from tensile to compressive and reached a maximum around 50 eV, in agreement with experiment.

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