Potential energy function for apatites

Hauptmann, Sven; Dufner, Hagen; Brickmann, Jürgen; Kast, Stefan M.; Berry, R. Stephen

doi:10.1039/b208209h

Cited by 122 publications

(138 citation statements)

References 40 publications

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“…The bond, angle and dihedral parameters were derived from both quantum-mechanics calculations and experimental data. The force field has been validated in earlier works (Bhowmik et al, 2007;Dubey and Tomar, 2009;Hauptmann et al, 2003;Qin et al, 2012;Shen et al, 2008).…”

Section: Force Fieldmentioning

confidence: 99%

“…Qin et al included parameters derived from quantum mechanics calculations (Park et al, 2005) for hydroxyproline (HYP), a nonessential amino acid typical of collagen but not present in other proteins, and added nonbonded parameters, calculated by using a Born-Mayer-Huggins model (Bhowmik et al, 2007;Hauptmann et al, 2003). The bond, angle and dihedral parameters were derived from both quantum-mechanics calculations and experimental data.…”

Section: Force Fieldmentioning

confidence: 99%

See 1 more Smart Citation

Mechanics of collagen–hydroxyapatite model nanocomposites

Libonati

Nair

Vergani

et al. 2014

Mechanics Research Communications

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a b s t r a c tBone is a hierarchical biological composite made of a mineral component (hydroxyapatite crystals) and an organic part (collagen molecules). Small-scale deformation phenomena that occur in bone are thought to have a significant influence on the large scale behavior of this material. However, the nanoscale behavior of collagen-hydroxyapatite composites is still relatively poorly understood. Here we present a molecular dynamics study of a bone model nanocomposite that consist of a simple sandwich structure of collagen and hydroxyapatite, exposed to shear-dominated loading. We assess how the geometry of the composite enhances the strength, stiffness and capacity to dissipate mechanical energy. We find that Hbonds between collagen and hydroxyapatite play an important role in increasing the resistance against catastrophic failure by increasing the fracture energy through a stick-slip mechanism.

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Section: Force Fieldmentioning

confidence: 99%

Section: Force Fieldmentioning

confidence: 99%

Mechanics of collagen–hydroxyapatite model nanocomposites

Libonati

Nair

Vergani

et al. 2014

Mechanics Research Communications

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“…oxygen, the FF for bonded terms are different in minerals and biomolecules. Specifically, minerals are ionic systems and are best represented by ionic bonds based on Coulomb electrostatics and Pauli repulsion terms (Hauptmann et al 2003). In contrast, biomolecules are covalently bonded.…”

Section: Mineral Surfacesmentioning

confidence: 99%

“…A FF for HAP has been developed with a Born-Mayer-Huggins potential with an exponential repulsion term similar to that of Buckingham potential instead of the standard Lennard-Jones plus Coulomb expression for the non-bonded interactions. The FF parameters were derived by fitting the QM electrostatic field in a 3D crystal environment and experimental crystal parameters (Hauptmann et al 2003). This FF was subsequently re-parameterized for monoclinic hydroxyapatite using an energy function consistent with common biomolecular FFs (Bhowmik et al 2007).…”

Section: Mineral Surfacesmentioning

confidence: 99%

Modeling and simulation of protein–surface interactions: achievements and challenges

Ozboyaci

Kokh

Corni

et al. 2016

Quart. Rev. Biophys.

197

199

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Abstract. Understanding protein-inorganic surface interactions is central to the rational design of new tools in biomaterial sciences, nanobiotechnology and nanomedicine. Although a significant amount of experimental research on protein adsorption onto solid substrates has been reported, many aspects of the recognition and interaction mechanisms of biomolecules and inorganic surfaces are still unclear. Theoretical modeling and simulations provide complementary approaches for experimental studies, and they have been applied for exploring protein-surface binding mechanisms, the determinants of binding specificity towards different surfaces, as well as the thermodynamics and kinetics of adsorption. Although the general computational approaches employed to study the dynamics of proteins and materials are similar, the models and force-fields (FFs) used for describing the physical properties and interactions of material surfaces and biological molecules differ. In particular, FF and water models designed for use in biomolecular simulations are often not directly transferable to surface simulations and vice versa. The adsorption events span a wide range of time-and length-scales that vary from nanoseconds to days, and from nanometers to micrometers, respectively, rendering the use of multi-scale approaches unavoidable. Further, changes in the atomic structure of material surfaces that can lead to surface reconstruction, and in the structure of proteins that can result in complete denaturation of the adsorbed molecules, can create many intermediate structural and energetic states that complicate sampling. In this review, we address the challenges posed to theoretical and computational methods in achieving accurate descriptions of the physical, chemical and mechanical properties of protein-surface systems. In this context, we discuss the applicability of different modeling and simulation techniques ranging from quantum mechanics through all-atom molecular mechanics to coarse-grained approaches. We examine uses of different sampling methods, as well as free energy calculations. Furthermore, we review computational studies of protein-surface interactions and discuss the successes and limitations of current approaches.

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“…Jiang et al [20] studied the adsorption of aspartic acid on brushite and as a part of their study attempted to reproduce the SXRD spectrum from Arsic et al [16]. The force field employed was based upon existing interatomic potentials (OPLS-AA [21], TIP3P water model [22]) with modifications for brushite based on Hauptmann's model [23] with partial charges from density functional theory (DFT). There was no specific parameterisation of the force field for aqueous-mineral interfaces and the thermodynamic accuracy of the model was not validated.…”

Section: Introductionmentioning

confidence: 99%

Water Structure, Dynamics and Ion Adsorption at the Aqueous {010} Brushite Surface

Garcia

Raiteri

Vlieg³

et al. 2018

Minerals

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Abstract:Understanding the growth processes of calcium phosphate minerals in aqueous environments has implications for both health and geology. Brushite, in particular, is a component of certain kidney stones and is used as a bone implant coating. Understanding the water-brushite interface at the molecular scale will help inform the control of its growth. Liquid-ordering and the rates of water exchange at the brushite-solution interface have been examined through the use of molecular dynamics simulation and the results compared to surface X-ray diffraction data. This comparison highlights discrepancies between the two sets of results, regardless of whether force field or first principles methods are used in the simulations, or the extent of water coverage. In order to probe other possible reasons for this difference, the free energies for the adsorption of several ions on brushite were computed. Given the exothermic nature found in some cases, it is possible that the discrepancy in the surface electron density may be caused by adsorption of excess ions.

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Potential energy function for apatites

Cited by 122 publications

References 40 publications

Mechanics of collagen–hydroxyapatite model nanocomposites

Mechanics of collagen–hydroxyapatite model nanocomposites

Modeling and simulation of protein–surface interactions: achievements and challenges

Water Structure, Dynamics and Ion Adsorption at the Aqueous {010} Brushite Surface

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