Rigid Body Molecular Dynamics within the Domain Decomposition Framework of DL_POLY_4

Todorov, Ilian T.; Ellison, Laurence; Smith, William R.

doi:10.1007/978-3-642-39958-9_40

Cited by 9 publications

(16 citation statements)

References 6 publications

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“…The molecular dynamic simulations were carried out with the DL_POLY_4 , code, version 4.03.4, using an integration time step of 1.0 fs and a distance cutoff of 12.0 Å for the 12/6 Lennard-Jones potential and the shifted Coulomb potential. Temperature adjustment is controlled by the Langevin thermostat with a relaxation constant of 0.25 ps –1 , to allow for melting/annealing runs at a range of heating/cooling rates as described in the following.…”

Section: Methodsmentioning

confidence: 99%

Size-Dependent Local Ordering in Melanin Aggregates and Its Implication on Optical Properties

et al. 2019

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We present atomic scale models of differently sized eumelanin nanoaggregates from molecular dynamics simulations combined with a simulated annealing procedure. The analysis reveals the formation of secondary structures due to π-stacking on one hand, but on the other hand a broad distribution of stack geometries in terms of stack size, horizontal displacement angles, and relative torsion angles. The displacement angle distribution, which is a measure of the occurrence of zigzag and linear stacking motives, respectively, strongly depends on the aggregate sizeand is hence controlled by the interplay of surface and bulk energy terms. Semiempirical spectra calculations of small stacks (up to five protomolecules) reveal a strong dependence on the precise stack structure and allow for a direct structure–property correlation. The observed spectral shifts result in an overall spectral broadening and, hence, further support the geometric disorder model, which complements the chemical disorder model in the interpretation of eumelanin’s monotonically increasing broad-band absorption.

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Section: Methodsmentioning

confidence: 99%

Size-Dependent Local Ordering in Melanin Aggregates and Its Implication on Optical Properties

et al. 2019

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“…Parameters in Table correspond to the following analytical expression for the potential ( U ) where r is the interatomic distance.…”

Section: Computational Detailsmentioning

confidence: 99%

“…Bending of all intramolecular angles of the O–C 5 H 11 groups was modeled and parametrized using the harmonic cosine potential where k 3 = 112.499693 kcal/mol is the force constant, and θ 0 = 109.471° is the equilibrium bond angle …”

Section: Computational Detailsmentioning

confidence: 99%

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Wettability of Fully Hydroxylated and Alkylated (001) α-Quartz Surface in Carbon Dioxide Atmosphere

2019

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Wettability of alkylated quartz surfaces is of primary importance in several technological applications, including the development of oil and gas reservoirs and carbon geo-sequestration. It is intuitively understood and experimentally confirmed that hydroxylated quartz surfaces are hydrophilic. By gradually saturating a hydroxylated (001) α-quartz surface with pentyl groups, we show using molecular dynamics simulations that the surface can also exhibit extreme hydrophobicity. Within a range of surface pentyl group density from 0.29 to 3.18/nm2, the contact angle of a water droplet under 10 MPa pressure of carbon dioxide at 300 K changes from 10–20 to 180°. This study has shown that a complete description of wettability of alkylated quartz surfaces requires three contact anglesone at the tip level of pentyl groups and two at the level of the quartz surface. The latter two are the contact angle of the spherical droplet and the hidden contact angle of a water “skirt” formed between the tip level of pentyl groups and the quartz surface. Analysis of the hidden contact angle unveils a binary wettability, where the surface relatively abruptly transforms from hydrophilic (the contact angle is less than 90°) to hydrophobic (the contact angle is 180°) with an increase in surface pentyl group concentration.

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“…Although ab initio MD simulation avoids the use of interatomic potentials, large simulations of trace Ca 2+ in concentrated LiCl brine, with thousands of atoms requiring nanoseconds, are too lengthy for the ab initio MD method. Classical MD simulation, which generally deals interatomic interactions with classical two- or three-body interatomic potentials, has been proven to be an efficient tool and is used extensively to investigate various properties of larger systems. − Therefore, classical MD simulation was used to investigate the presence and structural characteristics of high-order Ca–Cl complexes in concentrated LiCl brine, and all MD simulations were performed using the DL_POLY_4.03 software package. , In this study, the interatomic interactions between water and ions were defined by pairwise potentials, where van der Waals interactions were modeled through the Lennard-Jones (LJ) potential, whereas the electrostatic interactions resulted from the partial charges on each atomic center. The LJ potential was used in previous MD study on alkaline earth metal–chloride complexation in aqueous solution. ,,, There are several successful applications of the extended simple point charge (SPC/E) water model for brine systems, , so the SPC/E model was also used in this work.…”

Section: Methodsmentioning

confidence: 99%

High-Order Ca(II)–Chloro Complexes in Mixed CaCl₂–LiCl Aqueous Solution: Insights from Density Functional Theory and Molecular Dynamics Simulations

Wang

2016

J. Phys. Chem. A

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In this study, the structural characteristics of high-coordinated Ca-Cl complexes present in mixed CaCl2-LiCl aqueous solution were investigated using density functional theory (DFT) and molecular dynamics (MD) simulations. The DFT results show that [CaClx](2-x) (x = 4-6) clusters are quite unstable in the gas phase, but these clusters become metastable when hydration is considered. The MD simulations show that high-coordinated Ca-chloro complexes are possible transient species that exist for up to nanoseconds in concentrated (11.10 mol·kg(-1)) Cl(-) solution at 273 and 298 K. As the temperature increases to 423 K, these high-coordinated structures tend to disassociate and convert into smaller clusters and single free ions. The presence of high-order Ca-Cl species in concentrated LiCl solution can be attributed to their enhanced hydration shell and the inadequate hydration of ions. The probability of the [CaClx](2-x)aq (x = 4-6) species being present in concentrated LiCl solution decreases greatly with increasing temperature, which also indicates that the formation of the high-coordinated Ca-Cl structure is related to its hydration characteristics.

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Rigid Body Molecular Dynamics within the Domain Decomposition Framework of DL_POLY_4

Cited by 9 publications

References 6 publications

Size-Dependent Local Ordering in Melanin Aggregates and Its Implication on Optical Properties

Size-Dependent Local Ordering in Melanin Aggregates and Its Implication on Optical Properties

Wettability of Fully Hydroxylated and Alkylated (001) α-Quartz Surface in Carbon Dioxide Atmosphere

High-Order Ca(II)–Chloro Complexes in Mixed CaCl₂–LiCl Aqueous Solution: Insights from Density Functional Theory and Molecular Dynamics Simulations

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Rigid Body Molecular Dynamics within the Domain Decomposition Framework of DL_POLY_4

Cited by 9 publications

References 6 publications

Size-Dependent Local Ordering in Melanin Aggregates and Its Implication on Optical Properties

Size-Dependent Local Ordering in Melanin Aggregates and Its Implication on Optical Properties

Wettability of Fully Hydroxylated and Alkylated (001) α-Quartz Surface in Carbon Dioxide Atmosphere

High-Order Ca(II)–Chloro Complexes in Mixed CaCl2–LiCl Aqueous Solution: Insights from Density Functional Theory and Molecular Dynamics Simulations

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About

High-Order Ca(II)–Chloro Complexes in Mixed CaCl₂–LiCl Aqueous Solution: Insights from Density Functional Theory and Molecular Dynamics Simulations