Mechanism of Urea Crystal Dissolution in Water from Molecular Dynamics Simulation

Anand, Ankita; Patey, G. N.

doi:10.1021/acs.jpcb.7b07096

Cited by 13 publications

(23 citation statements)

References 49 publications

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“…Studies suggest that the final configuration the crystal has to have at least three layers in order to represent a bulk crystal, 64 and at least 200 urea molecules must be present in the crystal to prevent complete dissolution . 24 There also has to be sufficient separation between crystal faces in adjacent period images and a bulk region for the aqueous solution. To achieve these constraints, we place a 5 × 5 × 6 supercell of urea crystal in the simulation cell and then enclose it in aqueous urea solution with a thickness of ∼1.5 nm.…”

Section: ■ Molecular Dynamics Simulationsmentioning

confidence: 99%

A Transferable Polarizable Force Field for Urea Crystals and Aqueous Solutions

2020

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Urea is an important chemical with many biological and industrial applications. In this work, we develop a first-principles polarizable force field for urea crystals and aqueous solutions within the symmetry-adapted perturbation theory (SAPT) protocol with the SWM4-NDP model for water. We make three adjustments to the SAPT force field protocol: We augment the carbonyl oxygen atom of urea with additional interaction sites in order to address the “chelated” bent double hydrogen bonds in urea, we reduce the polarizability of urea by a factor of 0.70 to reproduce experimental in-crystal dipole moments, and we re-fit atomic pre-exponential parameters to correct the predicted liquid structure. We find that the resulting force field is in good agreement for the static and dynamic properties of aqueous urea solutions when compared to experiment or first-principles molecular dynamics simulations. The polarizable urea model accurately reproduces the crystal-solution phase diagram in the temperature range of 261 to 310 K; for which, it is superior to non-polarizable models. We expect that this force field will be useful in the modeling of complex biomolecular systems and enable studies of polarizability effects of solid–liquid phase behavior of complex fluids.

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Section: ■ Molecular Dynamics Simulationsmentioning

confidence: 99%

A Transferable Polarizable Force Field for Urea Crystals and Aqueous Solutions

2020

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“…In a first approach, some geometric and energetic properties of crystals can be reproduced or predicted by equilibration in Monte Carlo simulations (Gavezzotti, 2013). If, however, the aim is the study of time-or temperature-dependent properties, such as lattice vibration modes (Rothchild et al, 2019), rotational and translational diffusion (Skarmoutsos et al, 2019), disorder (Hsieh & Yip, 1987), phase transitions (van de Streek et al, 2019) or crystal melting (Anand & Patey, 2018), the use of molecular dynamics (MD) is indispensable. MD allows the capture of structural and dynamical features of crystals (van de Streek et al, 2019; Larsen et al, 2017; Chan, 2015) and surfaces (Yu et al, 2019;Gao et al, 2019) far from equilibrium, coping with the very large number of collective variables in large ensembles of interacting molecules, which are not amenable to a full quantum chemical treatment.…”

Section: Introduction and Scopementioning

confidence: 99%

Molecular dynamics simulation of organic crystals: introducing the CLP-dyncry environment

Gavezzotti

Presti

2019

J Appl Cryst

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The CLP‐dyncry molecular dynamics (MD) program suite and force field environment is introduced and validated with its ad hoc features for the treatment of organic crystalline matter. The package, stemming from a preliminary implementation on organic liquids (Gavezzotti & Lo Presti, 2019), includes modules for the preliminary generation of molecular force field files from ab initio derived force constants, and for the preparation of crystalline simulation boxes from general crystallographic information, including Cambridge Structural Database CIFs. The intermolecular potential is the atom–atom Coulomb–London–Pauli force field, well tested as calibrated on sublimation enthalpies of organic crystals. These products are then submitted to a main MD module that drives the time integration and produces dynamic information in the form of coordinate and energy trajectories, which are in turn processed by several kinds of crystal‐oriented analytic modules. The whole setup is tested on a variety of bulk crystals of rigid, non‐rigid and hydrogen‐bonded compounds for the reproduction of radial distribution functions and of crystal‐specific collective orientational variables against X‐ray data. In a series of parallel tests, some advantages of a dedicated program as opposed to software more oriented to biomolecular simulation (Gromacs) are highlighted. The different and improved view of crystal packing that results from joining static structural information from X‐ray analysis with dynamic upgrades is also pointed out. The package is available for free distribution with I/O examples and Fortran source codes.

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“…In this paper, a molecular dynamics simulation method [19,20,21,22,23,24,25,26,27] is used to conduct a comparative analysis of the influence of a thermal field on the thermal stability of crystalline and amorphous regions of meta-aramid fiber from the perspective of an actual thermal field environment inside a transformer. First, we construct a model of meta-aramid with crystalline and amorphous regions using reported experimental data.…”

Section: Introductionmentioning

confidence: 99%

Molecular Simulation on the Thermal Stability of Meta-Aramid Insulation Paper Fiber at Transformer Operating Temperature

Tang

et al. 2018

Polymers

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The influence of the thermal field of a transformer during operation on the thermal stability of meta-aramid insulation paper was studied through molecular dynamics simulations. Models of the crystalline and amorphous regions of meta-aramid fibers were constructed using known parameters. The model of the crystalline area was verified by comparing X-ray diffraction results with experimental data. The reasonableness of the simulation results was judged by the variation of energy, temperature, density, and cell size in relation to the dynamic time. The molecular dynamics simulations revealed that the modulus values in the crystalline regions were two to three times higher than those in the amorphous regions at various temperatures. In addition, the incompressibility, rigidity, deformation resistance, plasticity, and toughness of the crystalline regions were obviously higher than those of amorphous regions, whereas the toughness of the amorphous regions was better than that of the crystalline regions. The mechanical parameters of both the crystalline and amorphous regions of meta-aramid fibers were affected by temperature, although the amorphous regions were more sensitive to temperature than the crystalline regions. The molecular chain motion in the crystalline regions of meta-aramid fibers increased slightly with temperature, whereas that of the amorphous regions was more sensitive to temperature. Analyzing hydrogen bonding revealed that long-term operation at high temperature may destroy the structure of the crystalline regions of meta-aramid fibers, degrading the performance of meta-aramid insulation paper. Therefore, increasing the crystallinity and lowering the transformer operating temperature may improve the thermal stability of meta-aramid insulation paper. However, it should be noted that increasing the crystallinity of insulation paper may lower its toughness. These study results lay a good foundation for further exploration of the ways to improve the performance of meta-aramid insulation paper.

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Mechanism of Urea Crystal Dissolution in Water from Molecular Dynamics Simulation

Cited by 13 publications

References 49 publications

A Transferable Polarizable Force Field for Urea Crystals and Aqueous Solutions

A Transferable Polarizable Force Field for Urea Crystals and Aqueous Solutions

Molecular dynamics simulation of organic crystals: introducing the CLP-dyncry environment

Molecular Simulation on the Thermal Stability of Meta-Aramid Insulation Paper Fiber at Transformer Operating Temperature

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