scholarly journals Surface Stability and Morphology of Calcium Phosphate Tuned by pH Values and Lactic Acid Additives: Theoretical and Experimental Study

2021 ◽  
Author(s):  
Hongwei Chen ◽  
Changchang Lv ◽  
Lin Guo ◽  
Ming Ma ◽  
Xiangfeng Li ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Lactic Acid ◽  
Calcium Phosphate ◽  
Coordination Number ◽  
Density Functional ◽  
Md Simulations ◽  
Ab Initio Molecular Dynamics ◽  
Surface Stability ◽  
Ph Values ◽  
Phosphate Species

The ubiquitous mineralization of calcium phosphate (CaP) facilitates biological organisms to produce hierarchically structured minerals. The coordination number and strength of Ca2+ ions with phosphate species, oxygen-containing additives, and solvent molecules played a crucial role in tuning nucleation processes and surface stability of CaP under the simulated body fluid (SBF) or aqueous solutions upon the addition of oligomeric lactic acid (LACn, n=1, 8) and changing pH values. As revealed by ab initio molecular dynamics (AIMD), density functional theory (DFT), and molecular dynamics (MD) simulations as well as high-throughput experimentation (HTE), the binding of LAC molecules with Ca2+ ions and phosphate species could stabilize both pre-nucleation clusters and brushite (DCPD, CaHPO4·2H2O) surface through intermolecular electrostatic and hydrogen bonding interactions. When the concentration of Ca2+ ions ([Ca2+]) is very low, the amount of the formed precipitation decreased with the addition of LAC based on UV-Vis spectroscopic analysis due to the reduced chance for the LAC capped Ca2+ ions to coordinate with phosphates and the increased solubility in acid solution. With the increasing [Ca2+] concentration, the kinetically stable DCPD precipitation was obtained with high Ca2+ coordination number and low surface energy. Morphologies of DCPD precipitation are in plate, needle, or rod, depending on the initial pH values that tuned by adding NH3·H2O, HCl, or CH3COOH. The prepared samples at pH ≈ 7.4 with different Ca/P ratios exhibited negative zeta potential values, which were correlated with the surface electrostatic potential distributions and potential biological applications.

Energetics and diffusion of liquid water and hydrated ions through nanopores in graphene: ab initio molecular dynamics simulation

2017 ◽  
Vol 19 (31) ◽  
pp. 20551-20558 ◽  
Author(s):  
Raúl Guerrero-Avilés ◽  
Walter Orellana
Keyword(s):  
Molecular Dynamics ◽  
Ab Initio ◽  
Density Functional ◽  
Density Functional Theory Calculations ◽  
Md Simulations ◽  
Dynamics Simulation ◽  
Ab Initio Molecular Dynamics ◽  
Functional Theory ◽  
Hydrated Ions ◽  
And Diffusion

The energetics and diffusion of water molecules and hydrated ions (Na+, Cl−) passing through nanopores in graphene are addressed by dispersion-corrected density functional theory calculations and ab initio molecular dynamics (MD) simulations.

scholarly journals Ab Initio Molecular Dynamics Simulations to Interpret the Molecular Fragmentation Induced in Deoxyribose by Synchrotron Soft X-Rays

2019 ◽  
Vol 3 (4) ◽  
pp. 24
Author(s):  
Marie-Anne Hervé du Penhoat ◽  
Anis Hamila ◽  
Marie-Pierre Gaigeot ◽  
Rodolphe Vuilleumier ◽  
Kentaro Fujii ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Ab Initio ◽  
Density Functional ◽  
Md Simulations ◽  
Ab Initio Molecular Dynamics ◽  
X Rays ◽  
Auger Decay ◽  
Hydration Layer ◽  
The Core ◽  
Dynamics Simulations

It has been suggested that core ionization in DNA atoms could induce complex, irreparable damage. Synchrotron soft X-rays have been used to probe the damage induced by such events in thin films of DNA components. In a complementary approach, we investigate the fragmentation dynamics following a carbon or oxygen K-shell ionization in 2-deoxy-D-ribose (DR), a major component in the DNA chain. Core ionization of the sugars hydration layer is also studied. To that aim, we use state-of-the-art ab initio Density Functional Theory-based Molecular Dynamics (MD) simulations. The ultrafast dissociation dynamics of the core ionized molecule, prior Auger decay, is modeled for about 10 fs. We show that the core-ionization of oxygen atoms within DR or its hydration layer may induce proton transfers towards nearby molecules, before Auger decay. In a second step, we model an Auger effect occurring either at the beginning or at the end of the core–hole dynamics. Two electrons are removed from the deepest valence molecular orbitals localized on the initially core-ionized oxygen atom (O*), and this electronic state is propagated by means of Ehrenfest MD. We show an ultrafast dissociation of the DR2+ molecule C-O* bonds, which, in most cases, seems independent of the time at which Auger decay occurs.

scholarly journals The Effect of Hydrogen on the Stress-Strain Response in Fe3Al: An ab initio Molecular-Dynamics Study

Materials ◽  
2021 ◽  
Vol 14 (15) ◽  
pp. 4155
Author(s):  
Petr Šesták ◽  
Martin Friák ◽  
Mojmír Šob
Keyword(s):  
Molecular Dynamics ◽  
Ab Initio ◽  
Density Functional ◽  
Intrinsic Property ◽  
Md Simulations ◽  
Ab Initio Molecular Dynamics ◽  
Uniaxial Deformation ◽  
Ambient Conditions ◽  
Hydrogen Atoms ◽  
Octahedral Sites

We performed a quantum-mechanical molecular-dynamics (MD) study of Fe3Al with and without hydrogen atoms under conditions of uniaxial deformation up to the point of fracture. Addressing a long-lasting problem of hydrogen-induced brittleness of iron-aluminides under ambient conditions, we performed our density-functional-theory (DFT) MD simulations for T = 300 K (room temperature). Our MD calculations include a series of H concentrations ranging from 0.23 to 4 at. % of H and show a clear preference of H atoms for tetrahedral-like interstitial positions within the D03 lattice of Fe3Al. In order to shed more light on these findings, we performed a series of static lattice-simulations with the H atoms located in different interstitial sites. The H atoms in two different types of octahedral sites (coordinated by either one Al and five Fe atoms or two Al and four Fe atoms) represent energy maxima.Our structural relaxation of the H atoms in the octahedral sites lead to minimization of the energy when the H atom moved away from this interstitial site into a tetrahedral-like position with four nearest neighbors representing an energy minimum. Our ab initio MD simulations of uniaxial deformation along the ⟨001⟩ crystallographic direction up to the point of fracture reveal that the hydrogen atoms are located at the newly-formed surfaces of fracture planes even for the lowest computed H concentrations. The maximum strain associated with the fracture is then lower than that of H-free Fe3Al. We thus show that the hydrogen-related fracture initiation in Fe3Al in the case of an elastic type of deformation as an intrinsic property which is active even if all other plasticity mechanism are absent. The newly created fracture surfaces are partly non-planar (not atomically flat) due to thermal motion and, in particular, the H atoms creating locally different environments.

scholarly journals Ab initio molecular dynamics of hydrogen on tungsten surfaces

2021 ◽  
Author(s):  
Alberto Rodríguez-Fernández ◽  
Laurent Bonnet ◽  
Pascal Larrégaray ◽  
Ricardo Díez Muiño
Keyword(s):  
Molecular Dynamics ◽  
Density Functional Theory ◽  
Ab Initio ◽  
Density Functional ◽  
Ab Initio Molecular Dynamics ◽  
Dissociation Process ◽  
Functional Theory ◽  
Classical Molecular Dynamics ◽  
Hydrogen Molecules

The dissociation process of hydrogen molecules on W(110) was studied using density functional theory and classical molecular dynamics.

scholarly journals Computational Methods for Ab Initio Molecular Dynamics

2018 ◽  
Vol 2018 ◽  
pp. 1-14 ◽  
Author(s):  
Eric Paquet ◽  
Herna L. Viktor
Keyword(s):  
Molecular Dynamics ◽  
Quantum Mechanics ◽  
Ab Initio ◽  
First Principles ◽  
Density Functional ◽  
Path Integrals ◽  
Ab Initio Molecular Dynamics ◽  
Molecular Systems ◽  
Hartree Fock ◽  
Computational Perspective

Ab initio molecular dynamics is an irreplaceable technique for the realistic simulation of complex molecular systems and processes from first principles. This paper proposes a comprehensive and self-contained review of ab initio molecular dynamics from a computational perspective and from first principles. Quantum mechanics is presented from a molecular dynamics perspective. Various approximations and formulations are proposed, including the Ehrenfest, Born–Oppenheimer, and Hartree–Fock molecular dynamics. Subsequently, the Kohn–Sham formulation of molecular dynamics is introduced as well as the afferent concept of density functional. As a result, Car–Parrinello molecular dynamics is discussed, together with its extension to isothermal and isobaric processes. Car–Parrinello molecular dynamics is then reformulated in terms of path integrals. Finally, some implementation issues are analysed, namely, the pseudopotential, the orbital functional basis, and hybrid molecular dynamics.

scholarly journals Solvent Effect on the Structure and Properties of RGD Peptide (1FUV) at Body Temperature (310 K) Using Ab Initio Molecular Dynamics

Polymers ◽  
2021 ◽  
Vol 13 (19) ◽  
pp. 3434
Author(s):  
Khagendra Baral ◽  
Puja Adhikari ◽  
Bahaa Jawad ◽  
Rudolf Podgornik ◽  
Wai-Yim Ching
Keyword(s):  
Molecular Dynamics ◽  
Body Temperature ◽  
Ab Initio ◽  
Density Functional ◽  
Density Functional Theory Calculations ◽  
Rgd Peptide ◽  
Ab Initio Molecular Dynamics ◽  
Quantum Mechanical ◽  
Aqueous Environment ◽  
Structure And Properties

The structure and properties of the arginine-glycine-aspartate (RGD) sequence of the 1FUV peptide at 0 K and body temperature (310 K) are systematically investigated in a dry and aqueous environment using more accurate ab initio molecular dynamics and density functional theory calculations. The fundamental properties, such as electronic structure, interatomic bonding, partial charge distribution, and dielectric response function at 0 and 310 K are analyzed, comparing them in dry and solvated models. These accurate microscopic parameters determined from highly reliable quantum mechanical calculations are useful to define the range and strength of complex molecular interactions occurring between the RGD peptide and the integrin receptor. The in-depth bonding picture analyzed using a novel quantum mechanical metric, the total bond order (TBO), quantifies the role played by hydrogen bonds in the internal cohesion of the simulated structures. The TBO at 310 K decreases in the dry model but increases in the solvated model. These differences are small but extremely important in the context of conditions prevalent in the human body and relevant for health issues. Our results provide a new level of understanding of the structure and properties of the 1FUV peptide and help in advancing the study of RGD containing other peptides.

scholarly journals Unexpectedly Large Couplings Between Orthogonal Units in Anthraquinone Polymers

2019 ◽  
Author(s):  
Rocco Peter Fornari ◽  
Piotr de Silva
Keyword(s):  
Molecular Dynamics ◽  
Density Functional Theory ◽  
Ab Initio ◽  
Density Functional ◽  
Lone Pair ◽  
Localized States ◽  
Ab Initio Molecular Dynamics ◽  
Coupling Mechanism ◽  
Functional Theory ◽  
Pi Interactions

Directly linked polyanthraquinones have relatively large electronic couplings between charge-localized states despite near-orthogonality of the monomer units. By using density functional theory (DFT) and ab initio molecular dynamics (AIMD) simulations, we investigate this unusual coupling mechanism and show that this is due to strong lone pair-pi interactions, which are maximized around orthogonal conformations. We find that such materials are largely resilient to dynamic disorder and are promising for organic electronics applications.

Molecular Dynamic Structure Investigations of the Surface Stability and Adsorption of H, H2, CH3, C2H2: (100) Diamond

1992 ◽  
Vol 270 ◽  
Author(s):  
Th. Frauenheim ◽  
P. Blaudeck ◽  
D. Porezag
Keyword(s):  
Density Functional ◽  
Dynamic Structure ◽  
Md Simulations ◽  
Diamond Surface ◽  
Diamond Growth ◽  
Minimal Basis ◽  
Surface Stability ◽  
Hydrogen Supply ◽  
Reaction Processes ◽  
Structure Investigations

ABSTRACTSurface properties - stability and reconstruction - of clean and hydrogenated diamond (100) have been studied by real temperature molecular dynarnic (MD) simulations using an approximate density functional (DF) theory expanding the total electronic wave function in a minimal basis of localized atomic valence electron orbitals (LCAO - ansatz). The clean surface is highly unstable against a spontaneous dimerization resulting in a 2×1 reconstruction. Atomic hydrogen in the gas phase above the top surface at all temperatures and H2 molecules approaching the center of the dimer bond at room temperature are reactive in breaking the dimer π-bonds forming a monohydrogenated surface which maintains a stable 2×1 structure but with elongated surface C-C dimer bonds remaining stable against continuing hydrogen supply. The dihydrogenated surface taking a 1×1 structure, because of steric overcrowding dynamically becomes unstable against forming a 1×1 (alternating) di-, monohydrogenated surface. As first elementary reaction processes which may be discussed in relation to diamond growth we studied the thermal adsorption of CH3 and C2H2 onto a clean 2×l reconstructed (100) diamond surface.

Geometry of OH⋯O interactions in the liquid state of linear alcohols from ab initio molecular dynamics simulations

2020 ◽  
Vol 22 (12) ◽  
pp. 6690-6697 ◽  
Author(s):  
Aman Jindal ◽  
Sukumaran Vasudevan
Keyword(s):  
Molecular Dynamics ◽  
Hydrogen Bonding ◽  
Ab Initio ◽  
Molecular Dynamics Simulations ◽  
Liquid State ◽  
Crystalline State ◽  
Md Simulations ◽  
Ab Initio Molecular Dynamics ◽  
Linear Alcohols ◽  
Dynamics Simulations

Hydrogen bonding OH···O geometries in the liquid state of linear alcohols, derived from ab initio MD simulations, show no change from methanol to pentanol, in contrast to that observed in their crystalline state.

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