Molecular dynamics simulations of molten calcium hydroxyapatite

Cruz, Fernando J. A. L.; Lopes, José N. Canongia; Calado, Jorge C. G.

doi:10.1016/j.fluid.2005.12.021

Cited by 14 publications

(5 citation statements)

References 26 publications

(33 reference statements)

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“…The isothermal bulk modulus ( k T ) is a uniform resistance against compressibility that can be directly measured from knowledge of the isothermal compressibility factor. Accordingly, it can be computed as …”

Section: Resultsmentioning

confidence: 99%

Biodegradable Ionic Liquids: Effects of Temperature, Alkyl Side-Chain Length, and Anion on the Thermodynamic Properties and Interaction Energies As Determined by Molecular Dynamics Simulations Coupled with ab Initio Calculations

Fakhraee

Gholami

2015

Ind. Eng. Chem. Res.

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The effects of incorporating the ester functional group (COO) into the side chain of the 1-alkyl-3methylimidazolium cation ([C 1 COOC n C 1 im] + , n = 1, 2, 4) paired with [Br] − , [NO 3 ] − , [BF 4 ] − , [PF 6 ] − , [TfO] − , and [Tf 2 N] − anions on the various thermodynamic properties and interaction energies of these biodegradable ionic liquids (ILs) were investigated by means of molecular dynamics (MD) simulations combined with ab initio calculations in the temperature range of 298−550 K. Excluding the simulated density, the highest values of the volumetric properties such as molar volume, isobaric expansion coefficient, and isothermal compressibility coefficient can be attributed to the largest cation incorporated with the weakest coordinating anion, [Tf 2 N] − , and the minimum of the corresponding properties correspond to the smallest cation, especially when combined with the smaller anions, including [NO 3 ] − and [Br] − . In addition, ion-pair, cationic, and anionic volumes were computed using MD simulations as well as ab initio calculations. The results revelaed an increasing trend in the molar enthalpy of vaporization. The reverse trends of the volumetric properties were observed for the cohesive energy density, Hildebrand solubility parameter, surface tension, surface excess enthalpy, lattice energy, thermal pressure, internal pressure, binding energy, and interaction energy. On the basis of the optimized structures, we believed that a reduction in the strength of the hydrogen bonds due to the larger charge distribution and steric hindrance of bulkier ions is responsible for the observed trends. These results were also confirmed by calculating the critical and boiling temperatures (by two different empirical equation), surface excess enthalpies, parachors, and standard molar entropies. The other derivatives of the thermodynamic properties such as the isobaric and isochoric heat capacities, isothermal bulk moduli, and speeds of sound in the ILs were computed as functions of temperature. Interestingly, a direct relationship was found between the simulated results for the surface tension and the computed values of the bulk modulus. Furthermore, it was found that sound waves are transmitted faster in a compact IL than in a compressible IL. In addition, for each IL, the molar refraction, refractive index, dielectric constant, and mean static polarizability were approximated at room temperature. The smallest values of these properties were observed for ILs composed of the spherically symmetric anions [PF 6 ] − and [BF 4 ] − . In addition, the formation of multiple intramolecular hydrogen bonds between the O atoms of the ester functional group and the hydrogen atoms of the cation was also observed for all optimized conformations. Finally, the obtained results demonstrate that the introduction of an ester group significantly increases the interionic interactions and, subsequently, the packing efficiency of these ILs in comparison with those of conventional imidazolium-based ILs.

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Section: Resultsmentioning

confidence: 99%

Biodegradable Ionic Liquids: Effects of Temperature, Alkyl Side-Chain Length, and Anion on the Thermodynamic Properties and Interaction Energies As Determined by Molecular Dynamics Simulations Coupled with ab Initio Calculations

Fakhraee

Gholami

2015

Ind. Eng. Chem. Res.

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“…Recently, a developed ab initio method has been applied successfully to simulate the adsorption of Gly at the pyrite−water interface; however, tremendous computing resources are required for the large system (>8000 atoms) and the relatively long simulation time (>2 ns) by the ab initio method. Previously, empirical force fields have been established for the simulation of apatite crystals. ,,− The simulation results can be in good agreement with the real crystal structure, ,− IR spectra, and molar enthalpy, etc. ,, The interfacial structures of the apatite−water interface , also have been studied by using this method. MD simulations may provide another view of how amino acids adsorb and interact on/with the HAP faces at the atomic level, which would explain their effect on crystal habits.…”

Section: Introductionmentioning

confidence: 89%

“…23,25,[27][28][29] The simulation results can be in good agreement with the real crystal structure, 23,[27][28][29][30] IR spectra, 27 enthalpy, etc. 29,31,32 The interfacial structures of the apatitewater interface 33,34 also have been studied by using this method. MD simulations may provide another view of how amino acids adsorb and interact on/with the HAP faces at the atomic level, which would explain their effect on crystal habits.…”

Section: Introductionmentioning

confidence: 99%

Adsorption Processes of Gly and Glu Amino Acids on Hydroxyapatite Surfaces at the Atomic Level

et al. 2007

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The regulation mechanism of organic additives on the crystallization of inorganic crystal is fundamentally important in biomineralization. Experimentally, it was found that the amino acids glycine (Gly) and glutamic acid (Glu) could lead to the formation of rod- and plate-like hydroxyapatite (HAP) crystallites, respectively. The detailed adsorption behavior of Gly and Glu on HAP crystal faces was studied by molecular dynamics (MD) simulation. The specific adsorption sites and patterns of Gly and Glu on the (100) and (001) faces of HAP crystals were revealed at the atomic level. The amino acids adsorbed on the HAP (001) and (100) faces with their positive amino groups occupied vacant calcium sites, and their negative carboxylate groups occupied vacant P or OH sites precisely and formed an ordered adsorption layer. The atomic force microscopy pulling simulation and free energy calculation showed that Glu was much more difficult to depart from the HAP (001) face than that from the (100) face. This result indicated that Glu preferred to adsorb strongly onto the HAP (001) face, which resulted in the formation of plate-like HAP. However, Gly did not show any significantly preferential adsorption between these two HAP faces. Thus, the habits of HAP, rod-like crystallites, were not altered during the HAP crystallization in the presence of Gly. Combined with experimental results, our study demonstrated that the MD simulation of interfacial structures could improve our understanding of biological regulation in mineralization processes at the atomic level.

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“…Note that eq leads to the correct asymptotic limit, predicting V = 0 at infinite pressure. The PM-EoS robustness has been put to the test using compressed ionic solids − and molten salts at temperatures up to 3000 K and pressures p < 75 × 10 3 bar, always achieving precisions better than 0.07–1%, however, its accuracy has not been addressed for temperatures below the water freezing point. The PM-EoS is employed herein to correlate p – V data obtained in the calculations, and the corresponding isotherms are plotted in Figure a.…”

Section: Resultsmentioning

confidence: 99%

Low-Temperature Thermodynamic Study of the Metastable Empty Clathrate Hydrates Using Molecular Simulations

Cruz

Alavi

Mota

2019

ACS Earth Space Chem.

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The thermodynamics of metastable empty sI-clathrate hydrates are probed over broad temperature and pressure ranges, 100 ≤ T (K) ≤ 220 and 1 ≤ p (bar) ≤ 5000, respectively, by large-scale simulations and compared with experimental data at 1 bar. The whole p–V–T surface obtained is fitted by the universal form of the Parsafar and Mason equation of state with an accuracy of 99.7–99.9%. Framework deformation brought about by the applied temperature follows a parabolic law, and there is a critical temperature above which the isobaric thermal expansion becomes negative, ranging from 194.7 K at 1 bar to 166.2 K at 5000 bar. That response to the applied (p, T) field is analyzed in terms of angle and distance descriptors of a classical tetrahedral structure and observed to occur essentially by means of angular alteration for (p, T) > (2000 bar, 200 K). The length of the hydrogen bonds responsible for framework integrity is insensitive to the thermodynamic conditions and its average value is nm.

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Molecular dynamics simulations of molten calcium hydroxyapatite

Cited by 14 publications

References 26 publications

Biodegradable Ionic Liquids: Effects of Temperature, Alkyl Side-Chain Length, and Anion on the Thermodynamic Properties and Interaction Energies As Determined by Molecular Dynamics Simulations Coupled with ab Initio Calculations

Biodegradable Ionic Liquids: Effects of Temperature, Alkyl Side-Chain Length, and Anion on the Thermodynamic Properties and Interaction Energies As Determined by Molecular Dynamics Simulations Coupled with ab Initio Calculations

Adsorption Processes of Gly and Glu Amino Acids on Hydroxyapatite Surfaces at the Atomic Level

Low-Temperature Thermodynamic Study of the Metastable Empty Clathrate Hydrates Using Molecular Simulations

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