On Local Structure Equilibration of Ca2+ in Solution by Ab Initio Molecular Dynamics.

Analyzing the stable isotopic ratio of Ca offers valuable insights into a wide range of applications from climate reconstruction to bone cancer diagnosis and agricultural nutrient improvement. While the first hydration shell of Ca in solution is expected to play a major role in its fractionation properties, the coordination of Ca in water remains a subject of debate. In this work, Ca2+ in water has been modeled by means of ab initio molecular dynamics simulations using various exchange and correlation functionals and at different temperatures. Results show a significant effect of the functional on the average Ca2+ coordination, depending on its tendency to over- or understructure liquid water. The BLYP functional with Grimme-D2 correction was judged as the most accurate among those tested based on its accuracy to reproduce water structural and diffusion properties. Using this functional, the effect of temperature has been systematically investigated, focusing on means to limit the uncertainty in our assessments of the average coordination of Ca2+ ions by (1) estimating the number of water exchanges in the simulations and (2) implementing a statistical approach based on Markov chains. The findings indicate, especially, that our simulations at 300, 350, and 400 K do not yield converged results due to potential equilibration problems. These observations impose substantial constraints on the trustworthiness of numerous estimates in the existing literature that depend on trajectories with insufficient exchanges. We estimate Ca2+ coordination values of 6.8 ± 0.1, 6.8 ± 0.1, 6.7 ± 0.2, and 6.7 ± 0.2 at 600, 550, 500, and 450 K respectively. At lower temperatures (300, 350, and 400 K), while obtaining definitive values for Ca2+ coordination remains challenging, our research does indicate a potential temperature-related influence on coordination with an average Ca2+ coordination at 300 K as low as 6.2.

Exploring the formation of gold/silver nanoalloys with gas-phase synthesis and machine-learning assisted simulations.

While nanoalloys are of paramount scientific and practical interest, the main processes leading to their formation are still poorly understood. Key structural features in the alloy systems, including the crystal phase, chemical ordering, and morphology, are challenging to control at the nanoscale, making it difficult to extend their use to industrial applications. In this contribution, we focus on the gold/silver system that has two of the most prevalent noble metals and combine experiments with simulations to uncover the formation mechanisms at the atomic level. Nanoparticles were produced using a state-of-the-art inert-gas aggregation source and analyzed using transmission electron microscopy and energy-dispersive X-ray spectroscopy. Machine-learning-assisted molecular dynamics simulations were employed to model the crystallization process from liquid droplets to nanocrystals. Our study finds a preponderance of nanoparticles with five-fold symmetric morphology, including icosahedra and decahedra which is consistent with previous results on mono-metallic nanoparticles. However, we observed that gold atoms, rather than silver atoms, segregate at the surface of the obtained nanoparticles for all the considered alloy compositions. These segregation tendencies are in contrast to previous studies and have consequences on the crystallization dynamics and the subsequent crystal ordering. We finally showed that the underpinning of this surprising segregation dynamics is due to charge transfer and electrostatic interactions rather than surface energy considerations.

Silica-induced electron loss of silver nanoparticles.

Despite the frequent use of silver nanoparticles (Ag NPs) embedded in materials for medical or optical applications, the effect of the matrix on the nanoparticle properties remains largely unknown. This study aims to shed light on the effect of an amorphous silica matrix on the structure and charge distribution of 55- and 147-atom silver nanoparticles by means of dispersion-corrected DFT calculations. Particular attention is paid to nanoparticle size and concentration effects and to the impact of the presence of native defects in the matrix. Covalent bonding between the silver nanoparticles and the matrix is found to occur at the interface. Such interface reconstruction involves the breaking of Si-O bonds, which systematically leads to the formation of Ag-Si bonds, and in some cases, to the formation of Ag-O ones. Interestingly, these interface reconstructions are accompanied by electron depletion of the nanoparticles, a substantial number of electrons being transferred from the two outer shells of the Ag NPs to the surrounding silica medium. The electrons lost by the nanoparticles are captured by the Si atoms involved in the interface bonds, but also, unexpectedly, by the undercoordinated silica defects that act as electron pumps and by the atoms of the silica network inside a few angströms spherical shell around the silver nanoparticle. The numbers of interface bonds and electrons transferred to the surrounding silica shell appear to be proportional to the surface area of the Ag NP. The electronic extension within silica goes beyond that attributable to the Ag NP spill-out. The presence of additional electrons in the matrix, especially on defects, is consistent with the experimental literature.

How interface properties control the equilibrium shape of core-shell Fe-Au and Fe-Ag nanoparticles.

While combining two metals in the same nanoparticle can lead to remarkable novel applications, the resulting structure in terms of crystallinity and shape remains difficult to predict. It is thus essential to provide a detailed atomistic picture of the underlying growth processes. In the present work we address the case of core-shell Fe-Au and Fe-Ag nanoparticles. Interface properties between Fe and the noble metals Au and Ag, computed using DFT, were used to parameterize Fe-Au and Fe-Ag pairwise interactions in combination with available many-body potentials for the pure elements. The growth of Au or Ag shells on nanometric Fe cores with prescribed shapes was then modelled by means of Monte Carlo simulations. The shape of the obtained Fe-Au nanoparticles is found to strongly evolve with the amount of metal deposited on the Fe core, a transition from the polyhedral Wulff shape of bare iron to a cubic shape taking place as the amount of deposited gold exceeds two monolayers. In striking contrast, the growth of silver proceeds in a much more anisotropic, Janus-like way and with a lesser dependence on the iron core shape. In both cases, the predicted morphologies are found to be in good agreement with experimental observations in which the nanoparticles are grown by physical deposition methods. Understanding the origin of these differences, which can be traced back to subtle variations in the electronic structure of the Au/Fe and Ag/Fe interfaces, should further contribute to the better design of core-shell bimetallic nanoparticles.

Alloy, Janus and core-shell nanoparticles: numerical modeling of their nucleation and growth in physical synthesis.

While alloy, core-shell and Janus binary nanoclusters are found in more and more technological applications, their formation mechanisms are still poorly understood, especially during synthesis methods involving physical approaches. In this work, we employ a very simple model of such complex systems using Lennard-Jones interactions and inert gas quenching. After demonstrating the ability of the model to well reproduce the formation of alloy, core-shell or Janus nanoparticles, we studied their temporal evolution from the gas via droplets to nanocrystalline particles. In particular, we showed that the growth mechanisms exhibit qualitative differences between these three chemical orderings. Then, we determined how the quenching rate can be used to finely tune structural characteristics of the final nanoparticles, including size, shape and crystallinity.

Quantum Nuclear Dynamics of Protons within Layered Hydroxides at High Pressure.

Studies of the structure of hydroxides under pressure using neutron diffraction reveal that the high concentration of hydrogen is distributed in a disordered network. The disorder in the hydrogen-bond network and possible phase transitions are reported to occur at pressures within the range accessible to experiments for layered calcium hydroxides, which are considered to be exemplary prototype materials. In this study, the static and dynamical properties of these layered hydroxides are investigated using a quantum approach describing nuclear motion, shown herein to be required particularly when studying diffusion processes involving light hydrogen atoms. The effect of high-pressure on the disordered hydrogen-bond network shows that the protons tunnel back and forth across the barriers between three potential minima around the oxygen atoms. At higher pressures the structure has quasi two-dimensional layers of hydrogen atoms, such that at low temperatures this causes the barrier crossing of the hydrogen to be significantly rarefied. Furthermore, for moderate values of both temperature and pressure this process occurs less often than the usual mechanism of proton transport via vacancies, limiting global proton diffusion within layers at high pressure.

Importance of a Fully Anharmonic Treatment of Equilibrium Isotope Fractionation Properties of Dissolved Ionic Species As Evidenced by Li+(aq).

Equilibrium fractionation of stable isotopes is critically important in fields ranging from chemistry, including medicinal chemistry, electrochemistry, geochemistry, and nuclear chemistry, to environmental science. The dearth of reliable estimates of equilibrium fractionation factors, from experiment or from natural observations, has created a need for accurate computational approaches. Because isotope fractionation is a purely quantum mechanical phenomenon, exact calculation of fractionation factors is nontrivial. Consequently, a severe approximation is often made, in which it is assumed that the system can be decomposed into a set of independent harmonic oscillators. Reliance on this often crude approximation is one of the primary reasons that theoretical prediction of isotope fractionation has lagged behind experiment. A class of problems for which one might expect the harmonic approximation to perform most poorly is the isotopic fractionation between solid and solution phases. In order to illustrate the errors associated with the harmonic approximation, we have considered the fractionation of Li isotopes between aqueous solution and phyllosilicate minerals, where we find that the harmonic approximation overestimates isotope fractionation factors by as much as 30% at 25 °C. Lithium is a particularly interesting species to examine, as natural lithium isotope signatures provide information about hydrothermal processes, carbon cycle, and regulation of the Earth's climate by continental alteration. Further, separation of lithium isotopes is of growing interest in the nuclear industry due to a need for pure 6Li and 7Li isotopes. Moving beyond the harmonic approximation entails performing exact quantum calculations, which can be achieved using the Feynman path integral formulation of quantum statistical mechanics. In the path integral approach, a system of quantum particles is represented as a set of classical-like ring-polymer chains, whose interparticle interactions are determined by the rules of quantum mechanics. Because a classical isomorphism exists between the true quantum system and the system of ring-polymers, classical-like methods can be applied. Recent developments of efficient path integral approaches for the exact calculation of isotope fractionation now allow the case of the aforementioned dissolved Li fractionation properties to be studied in detail. Applying this technique, we find that the calculations yield results that are in good agreement with both experimental data and natural observations. Importantly, path integral methods, being fully atomistic, allow us to identify the origins of anharmonic effects and to make reliable predictions at temperatures that are experimentally inaccessible yet are, nevertheless, relevant for natural phenomena.

Prediction of Co nanoparticle morphologies stabilized by ligands: towards a kinetic model.

Cobalt nanoparticles (NPs) synthesized in liquid environments present anisotropic shaped nanocrystals such as disks, plates, rods, wires or cubes. Though the synthesis parameters (precursor, reducing agent, stabilizing ligands, concentration, temperature or rate of precursor injection) controlling the final morphologies are experimentally well controlled, little is known concerning the growth mechanisms at the atomic scale. In this work, we intend to predict the morphology variation of hcp cobalt NPs as a function of the ligand concentration. To this aim, we consider two well-established thermodynamic models and develop a new kinetic one. These models require the knowledge of the adsorption behaviors of stabilizing molecules as a function of surface coverage on preferential facets of NPs. To this end, density functional theory (DFT) calculations were performed on the adsorption of a model carboxylate ligand CH3COO on different Co crystalline surfaces. The shapes of the Co NPs obtained by these models are compared to experimental morphologies and other theoretical results from the literature. While thermodynamic models are in poor agreement with experimental observations, the variety of shapes predicted by the kinetic model is much more promising. Our study confirms that the morphological control of NPs is mostly driven by kinetic effects.

Theoretical study of the atrazine pesticide interaction with pyrophyllite and Ca(2+) -montmorillonite clay surfaces.

Atrazine, a pesticide belonging to the s-triazine family, is one of the most employed pesticides. Due to its negative impact on the environment, it has been forbidden within the European Union since 2004 but remains abundant in soils. For these reasons, its behavior in soils and water at the atomic scale is of great interest. In this article, we have investigated, using DFT, the adsorption of atrazine onto two different clay surfaces: a pyrophyllite clay and an Mg-substituted clay named montmorillonite, with Ca2+ compensating cations on its surface. The calculations show that the atrazine molecule is physisorbed on the pyrophyllite surface, evidencing the necessity to use dispersion-corrected computational methods. The adsorption energies of atrazine on montmorillonite are two to three times larger than on pyrophyllite, depending on the adsorption pattern. The computed adsorption energy is of about -30 kcal mol-1 for the two most stable montmorillonite-atrazine studied isomers. For these complexes, the large adsorption energy is related to the strong interaction between the chlorine atom of the atrazine molecule and one of the Ca2+ compensating cations of the clay surface. The structural modifications induced by the adsorption are localized: for the surface, close to substitutions and particularly below the Ca2+ cations; in the molecule, around the chlorine atom when Ca2+ interacts strongly with this basic site in a monodentate mode. This study shows the important role of the alkaline earth cations on the adsorption of atrazine on clays, suggesting that the atrazine pesticide retention will be significant in Ca2+ -montmorillonite clays. © 2016 Wiley Periodicals, Inc.

Adsorption energy of small molecules on core-shell Fe@Au nanoparticles: tuning by shell thickness.

The adsorption of several small molecules on different gold surfaces, Au(001), strained Au(001) and Au(001) epitaxied on Fe(001), has been characterized using density functional theory. The surface strain leads to a less energetically favourable adsorption for all studied molecules. Moreover, the presence of the iron substrate induces an additional decrease of the binding energy, for 1 and 2 Au monolayers. For carbon monoxide (CO), the structural and energetic variations with the number of Au monolayers deposited on Fe have been analyzed and correlated with the distance between the carbon atom and the gold surface. The effect of the subsurface layer has been evidenced for 1 and 2 monolayers. The other molecules show different quantitative behavior depending on the type of their interaction with the gold surface. However, the iron substrate weakens the interaction, either for the chemisorbed species or for the physisorbed species. 2 Au monolayers seem to be the best compromise to decrease the reactivity of the gold surface towards adsorption while preventing the Fe oxidation.

Efficient Calculation of Free Energy Differences Associated with Isotopic Substitution Using Path-Integral Molecular Dynamics.

The problem of computing free energy differences due to isotopic substitution in chemical systems is discussed. The shift in the equilibrium properties of a system upon isotopic substitution is a purely quantum mechanical effect that can be quantified using the Feynman path integral approach. In this paper, we explore two developments that lead to a highly efficient path integral scheme. First, we employ a mass switching function inspired by the work of Ceriotti and Markland [ J. Chem. Phys. 2013, 138, 014112] that is based on the inverse square root of the mass and which leads to a perfectly constant free energy derivative with respect to the switching parameter in the harmonic limit. We show that even for anharmonic systems, this scheme allows a single-point thermodynamic integration approach to be used in the construction of free energy differences. In order to improve the efficiency of the calculations even further, however, we derive a set of free energy derivative estimators based on the fourth-order scheme of Takahashi and Imada [ J. Phys. Soc. Jpn. 1984, 53, 3765]. The Takahashi-Imada procedure generates a primitive fourth-order estimator that allows the number of imaginary time slices in the path-integral approach to be reduced substantially. However, as with all primitive estimators, its convergence is plagued by numerical noise. In order to alleviate this problem, we derive a fourth-order virial estimator based on a transferring of the difference between second- and fourth-order primitive estimators, which remains relatively constant as a function of the number of configuration samples, to the second-order virial estimator. We show that this new estimator converges as smoothly as the second-order virial estimator but requires significantly fewer imaginary time points.

First-principles calculation of the 17O NMR parameters of a calcium aluminosilicate glass.

We have computed the (17)O NMR parameters of an amorphous calcium aluminosilicate (CAS) from first-principles. The atomic coordinates of a CAS glass of composition (CaO)(0.21)(Al(2)O (3))(0.12)(SiO (2))(0.67) were obtained by quenching a liquid to room temperature by the means of ab initio molecular-dynamics simulations of the Car-Parrinello type. The structure of the glass is found to be overall in good agreement with diffraction experiments. Some excess nonbridging O (NBO) atoms are found and are compensated by tricluster O atoms, i.e., by 3-fold coordinated O atoms to 4-fold coordinated Al or Si atoms. The glass coordinates were used to compute the (17)O NMR parameters using GGA-DFT and a correction of the Ca 3d orbital energy. The chemical shifts and the electric field gradients were obtained with the gauge including projector augmented-wave (GIPAW) and the projector augmented-wave (PAW) methods, respectively. The simulated 2D-3QMAS NMR spectrum of the CAS glass is in very good agreement with the available experimental data, notably because it takes into account the disorder present in the glass. This agreement further validates our CAS glass model. We show that the oxygen triclusters are not visible in a 2D-3QMAS NMR (17)O spectrum since their NMR parameters overlap with those of the Al-O-Si, Si-O-Si, or Al-O-Al sites. Finally, correlations between the structural characteristics and the values of the NMR parameters are extracted from the calculation with the aim of helping the interpretation of NMR spectra of glasses of similar compositions.

First-principles calculation of the 17O NMR parameters in Ca oxide and Ca aluminosilicates: the partially covalent nature of the Ca-O bond, a challenge for density functional theory.

We apply density functional theory (DFT) to the calculation of the (17)O NMR parameters in Ca and Mg oxides and aluminosilicates. We study the accuracy of the Perdew, Burke, and Ernzerhof (PBE) generalized-gradient approximation to DFT in the description of these systems and the origin of the experimentally observed large dependence of the (17)O chemical shift on the alkaline earth ion. We find that (i) the partially covalent nature of the Ca-O bond has a huge impact on the O chemical shifts. The Ca-O covalence alone explains why in Ca oxides and aluminosilicates the (17)O chemical shifts are much more deshielded than those of the corresponding Mg compounds. (ii) The Ca-O covalence is overestimated by the PBE functional. Thus PBE-DFT is not able to reproduce the measured (17)O NMR parameters in Ca oxide and Ca aluminosilicates. (iii) It is possible to correct for the PBE-DFT deficiency in a simple and transferable way and to predict very accurate (17)O NMR parameters. Such accuracy allows us to assign the (17)O NMR spectra of two important model systems: the grossite aluminate (CaAl(4)O(7)) and the wollastonite (CaSiO(3)) silicate.

Structural properties of a calcium aluminosilicate glass from molecular-dynamics simulations: a finite size effects study.

We study a calcium aluminosilicate glass of composition (SiO(2))(0.67)-(Al(2)O(3))(0.12)-(CaO)(0.21) by means of molecular-dynamics simulations, using a potential made of two-body and three-body interactions. In order to prepare small samples that can subsequently be studied by first principles, the finite size effects on the liquid dynamics and on the glass structural properties are investigated. We find that finite size effects affect the Si-O-Si and Si-O-Al angular distributions, the first peaks of the Si-O, Al-O, and Ca-O pair correlation functions, the Ca coordination, and the oxygen atoms' environment in the smallest system (100 atoms). We give evidence that these finite size effects can be directly attributed to the use of three-body interactions.

Reassigning hydrogen-bond centering in dense ice.

Hydrogen bonds in H2O ice change dramatically upon compression. Thereby a hydrogen-bonded molecular crystal, ice VII, is transformed to an atomic crystal, ice X. Car-Parrinello simulations reproduce the features of the x-ray diffraction spectra up to about 170 GPa but allow for analysis in real space. Starting from molecular ice VII with static orientational disorder, dynamical translational disordering occurs first via creation of ionic defects, which results in a systematic violation of the ice rules. As a second step, the transformation to an atomic solid and thus hydrogen-bond centering occurs around 110 GPa at 300 K and no novel phase is found up to at least 170 GPa.