Search

Gold mobilization, transfer, and concentration in the Earth’s crust are controlled by hydrothermal sulfur- and chloride-bearing fluids. Yet the exact chemical identity, structure, and stability of Au-bearing species and, in particular, the respective contributions of the sulfide (HS−) and trisulfur ion (S3⋅−) ligands to Au transport lack direct in situ evidence. Here we employed high energy resolution fluorescence detection X-ray absorption spectroscopy (HERFD-XAS) on aqueous sulfate/sulfide/S3⋅−-bearing solutions at typical hydrothermal temperatures and pressures (T = 350 °C, P = 600 bar) to reveal differences in dissolved Au spectral signatures indicative of contrasting fluid-phase Au speciation as a function of acidity and redox conditions. Combined with in situ Au solubility measurements and quantum-chemical and thermodynamic modeling, our spectroscopic data provide direct evidence for the Au(HS)S3− and Au(HS)2− complexes predominant at acidic-to-neutral and alkaline conditions, respectively. Our findings thus directly confirm a recent speciation scheme for Au in aqueous S-bearing fluids established using less direct methods, and highlight an important role of the trisulfur ion in gold mobilization and concentration in hydrothermal-magmatic deposits associated with subduction zones. More generally, our results show that HERFD-XAS enables the identification of structural and coordination features in metal complexes virtually unresolvable using classical XAS techniques. By avoiding limitations of less direct techniques, our integrated high-resolution spectroscopic approach opens perspectives for studies of the speciation and solubility of gold and other metals in high T-P fluids, and potentially silicate melts, inaccessible to direct observation in nature.

Platinum group elements (PGE) are considered to be very poorly soluble in aqueous fluids in most natural hydrothermal–magmatic contexts and industrial processes. Here, we combined in situ X-ray absorption spectroscopy and solubility experiments with atomistic and thermodynamic simulations to demonstrate that the trisulfur radical ion S(3)(•−) forms very stable and soluble complexes with both Pt(II) and Pt(IV) in sulfur-bearing aqueous solution at elevated temperatures (∼300 °C). These Pt-bearing species enable (re)mobilization, transfer, and focused precipitation of platinum up to 10,000 times more efficiently than any other common inorganic ligand, such as hydroxide, chloride, sulfate, or sulfide. Our results imply a far more important contribution of sulfur-bearing hydrothermal fluids to PGE transfer and accumulation in the Earth’s crust than believed previously. This discovery challenges traditional models of PGE economic concentration from silicate and sulfide melts and provides new possibilities for resource prospecting in hydrothermal shallow crust settings. The exceptionally high capacity of the S(3)(•−) ion to bind platinum may also offer new routes for PGE selective extraction from ore and hydrothermal synthesis of noble metal nanomaterials.

International audience; Platinum group elements (PGE) are considered to be very poorly soluble in aqueous fluids in most natural hydrothermal–magmatic contexts and industrial processes. Here, we combined in situ X-ray absorption spectroscopy and solubility experiments with atomistic and thermodynamic simulations to demonstrate that the trisulfur radical ion S 3 •− forms very stable and soluble complexes with both Pt II and Pt IV in sulfur-bearing aqueous solution at elevated temperatures (∼300 °C). These Pt-bearing species enable (re)mobilization, transfer, and focused precipitation of platinum up to 10,000 times more efficiently than any other common inorganic ligand, such as hydroxide, chloride, sulfate, or sulfide. Our results imply a far more important contribution of sulfur-bearing hydrothermal fluids to PGE transfer and accumulation in the Earth’s crust than believed previously. This discovery challenges traditional models of PGE economic concentration from silicate and sulfide melts and provides new possibilities for resource prospecting in hydrothermal shallow crust settings. The exceptionally high capacity of the S 3 •− ion to bind platinum may also offer new routes for PGE selective extraction from ore and hydrothermal synthesis of noble metal nanomaterials.

We demonstrate the capability of creating robust density functional tight binding (DFTB) models for chemical reactivity in prebiotic mixtures through force matching to short time scale quantum free energy estimates. Molecular dynamics using density functional theory (DFT) is a highly accurate approach to generate free energy surfaces for chemical reactions, but the extreme computational cost often limits the time scales and range of thermodynamic states that can feasibly be studied. In contrast, DFTB is a semiempirical quantum method that affords up to a thousandfold reduction in cost and can recover DFT-level accuracy. Here, we show that a force-matched DFTB model for aqueous glycine condensation reactions yields free energy surfaces that are consistent with experimental observations of reaction energetics. Convergence analysis reveals that multiple nanoseconds of combined trajectory are needed to reach a steady-fluctuating free energy estimate for glycine condensation. Predictive accuracy of force-matched DFTB is demonstrated by direct comparison to DFT, with the two approaches yielding surfaces with large regions that differ by only a few kcal mol

We introduce a novel approach for a fully quantum description of coupled electron-ion systems from first principles. It combines the variational quantum Monte Carlo (QMC) solution of the electronic part with the path integral (PI) formalism for the quantum nuclear dynamics. On the one hand, the PI molecular dynamics includes nuclear quantum effects by adding a set of fictitious classical particles (beads) aimed at reproducing nuclear quantum fluctuations via a harmonic kinetic term. On the other hand, variational QMC can provide Born-Oppenheimer (BO) potential energy surfaces with a precision comparable to the most advanced post Hartree-Fock approaches, and with a favorable scaling with the system size. To deal with the intrinsic QMC noise, we generalize the PI molecular dynamics using a Langevin thermostat correlated according to the covariance matrix of QMC nuclear forces. The variational parameters of the QMC wave function are evolved during the nuclear dynamics, such that the BO potential energy surface is unbiased. Statistical errors on the wave function parameters are reduced by resorting to bead grouping average, which we show to be accurate and well controlled. Our general algorithm relies on a Trotter breakup between the dynamics driven by ionic forces and the one set by the harmonic interbead couplings. The latter is exactly integrated even in presence of the Langevin thermostat, thanks to the mapping onto an Ornstein-Uhlenbeck process. This framework turns out to be very efficient also in the case of deterministic ionic forces. The new implementation is validated on the Zundel ion by direct comparison with standard PI Langevin dynamics calculations made with a coupled cluster potential energy surface. Nuclear quantum effects are confirmed to be dominant over thermal effects well beyond room temperature giving the excess proton an increased mobility by quantum tunneling., Comment: 21 pages, 7 figures

Increasing experimental and theoretical evidence points to formamide as a possible hub in the complex network of prebiotic chemical reactions leading from simple precursors like H2, H2O, N2, NH3, CO, and CO2 to key biological molecules like proteins, nucleic acids, and sugars. We present an in-depth computational study of the formation and decomposition reaction channels of formamide by means of ab initio molecular dynamics. To this aim we introduce a new theoretical method combining the metadynamics sampling scheme with a general purpose topological formulation of collective variables able to track a wide range of different reaction mechanisms. Our approach is flexible enough to discover multiple pathways and intermediates starting from minimal insight on the systems, and it allows passing in a seamless way from reactions in gas phase to reactions in liquid phase, with the solvent active role fully taken into account. We obtain crucial new insight into the interplay of the different formamide reaction channels and into environment effects on pathways and barriers. In particular, our results indicate a similar stability of formamide and hydrogen cyanide in solution as well as their relatively facile interconversion, thus reconciling experiments and theory and, possibly, two different and competing prebiotic scenarios. Moreover, although not explicitly sought, formic acid/ammonium formate is produced as an important formamide decomposition byproduct in solution.

Understanding the mechanism of spontaneous formation of ribonucleotides under realistic prebiotic conditions is a key open issue of origins-of-life research. In cells, de novo and salvage nucleotide enzymatic synthesis combines 5-phospho-α-D-ribose-1-diphosphate (α-PRPP) and nucleobases. Interestingly, these reactants are also known as prebiotically plausible compounds. Combining ab initio simulations with mass spectrometry experiments, we compellingly demonstrate that nucleobases and α-PRPP spontaneously combine, through the same facile mechanism, forming both purine and pyrimidine ribonucleotides, under mild hydrothermal conditions. Surprisingly, this mechanism is very similar to the biological one, and yields ribonucleotides with the same anomeric carbon chirality as in biological systems. These results suggest that natural selection might have optimized – through enzymes – a pre-existing ribonucleotide formation mechanism, carrying it forward to modern life forms.

The Miller–Urey experiments pioneered modern research on the molecular origins of life, but their actual relevance in this field was later questioned because the gas mixture used in their research is considered too reducing with respect to the most accepted hypotheses for the conditions on primordial Earth. In particular, the production of only amino acids has been taken as evidence of the limited relevance of the results. Here, we report an experimental work, combined with state-of-the-art computational methods, in which both electric discharge and laser-driven plasma impact simulations were carried out in a reducing atmosphere containing NH3 + CO. We show that RNA nucleobases are synthesized in these experiments, strongly supporting the possibility of the emergence of biologically relevant molecules in a reducing atmosphere. The reconstructed synthetic pathways indicate that small radicals and formamide play a crucial role, in agreement with a number of recent experimental and theoretical results.

Thermal effects induced on matter by electric fields are well known and largely understood [1].

International audience; We probe the possible inclusion of salt (NaCl) in the ice VII lattice over the pressure range from 2 to 4 gigapascal. We combine data from neutron diffraction experiments under pressure and from computational structure searches based on density functional theory. We observe that the high density amorphous precursor (NaClÁ10.2D 2 O) crystallises during annealing at high pressure in the vicinity of the phase boundary between pure ices VII and VIII. The structure formed is very similar to that of pure ice VII. Our simulations indicate that substituting water molecules in the ice VII lattice with Na + and Cl À ions would lead to a significant expansion of the lattice parameter. Since this expansion was not observed in our experiments, the ice crystallised is likely to be pure D 2 O or contains only a small fraction of the ions from the salt solution.

Context. It is well known that hydrogen cyanide and formamide can universally be considered as key molecules in prebiotic synthesis. Despite the fact that formamide has been detected in interplanetary and interstellar environments, other prebiotic species are far more abundant, including, for example, formaldehyde. However, several results indicate that formamide can play the role of important intermediate as well as that of a feedstock molecule in chemical abiogenesis. Diverse recently proposed scenarios of the origins of the first biopolymers show that liquid formamide environments could have been crucial for the formation of nucleobases, nucleosides, and for phosphorylation reactions, which lead to nucleotides. Aims. Here we report on a wide exploration of the formaldehyde reaction network under plasma conditions mimicking an asteroid descent in an Earth-like atmosphere and its impact. Methods. Dielectric breakdown using a high-power kJ-class laser system (PALS – Prague Asterix Laser System) along with quantum mechanical, ab initio molecular dynamics, and enhanced sampling simulations have been employed in order to mimic an asteroid impact plasma. Results. Being more abundant than formamide both in interstellar and interplanetary environments, during the era of early and late heavy bombardment of Earth and other planets, formaldehyde might have been delivered on asteroids to young planets. In the presence of nitrogen-bearing species, this molecule has been reprocessed under plasma conditions mimicking the local environment of an impacting body. We show that plasma reprocessing of formaldehyde leads to the formation of several radical and molecular species along with formamide. Conclusion. All the canonical nucleobases, the simplest amino acid (i.e., glycine), and the sugar ribose, have been detected after treatment of formaldehyde and nitrogen gas with dielectric breakdown. Our results, supported by quantum mechanical and enhanced sampling simulations, show that formaldehyde – by producing inter alia formamide – may have had the role of starting substance in prebiotic synthesis.

The short-range structure of liquid carbon dioxide is investigated at pressures (P) up to 10 GPa and temperatures (T) from 300 to 709 K by means of x-ray diffraction experiments in a diamond anvil cell (DAC) and classical molecular dynamics (MD) simulations. The molecular x-ray structure factor could be measured up to 90 nm(-1) thanks to the use of a multichannel collimator which filters out the large x-ray scattered signal from the diamond anvils. The experimental data show that the short-range structure of fluid CO2 is anisotropic and continuously changes from a low density to a high density form. The MD simulations are used to extract a detailed three-dimensional analysis of the short-range structure over the same P-T range as the experiment. This reveals that upon compression, a fraction of the molecules in the first-neighbor shell change orientation from the (distorted) T shape to the slipped parallel configuration, accounting for the observed structural changes. The local arrangement is found similar to that of the Pa (3) over bar solid at low density and to that of the Cmca crystal at high density. The comparison with other simple quadrupolar liquids, either diatomic (I-2) or triatomic (CS2), suggests that this structural evolution with density is a general one for these systems. Funding Agencies|ESRF [HD-463]; Agence Nationale de la Recherche [ANR 13-BS04-0015]; Grand Equipement National de Calcul Intensif French National Supercomputing Facility [x2013091387]

International audience; It is generally accepted that nuclear quantum effects (NQEs) trigger the transition to the nonmolecular form of ice under increasing pressure. This picture is challenged in salty ice, where Raman scattering measurements up to 130 GPa of molecular ice VII containing NaCl or LiCl impurities show that the transition pressure to the symmetric phase ice X is shifted up by about 30 GPa, even at small salt concentrations. We address the question of how the inclusion of salt induces the drastic reduction of NQEs by selectively including NQEs in ab initio calculations of ice in the presence of distinct ionic impurities. We quantitatively show that this is mainly a consequence of the electric field generated by the ions. We propose a simple model that is able to capture the essence of this phenomenon, generalizing this picture to other charged defects and for any concentration. This result is potentially generalizable to most "dirty" ices in which the electric field due to the doping is much more significant than local lattice distortions.

In this study, we investigated the edge formation energy of hydrogen-terminated graphene nanoribbons as a function of the chemical potential of the environment as well as their electronic and magnetic properties by means of density functional theory. The single-hydrogen-terminated zigzag ribbons, well known for their antiferromagnetic edge states, were found to be stable only under extremely low vacuum pressures. At more standard conditions, the most stable structures are the single- and double-hydrogenated armchair edges and a zigzag edge configuration with one double- and two single-hydrogenated sites. At high hydrogen pressure, the edge formation energy becomes negative, meaning that graphene spontaneously breaks into ribbons. Clar type bond formulas proved to be an excellent tool for the rationale behind the stability, existence of edge states, and appearance of magnetism, and they are in perfect agreement with simulated scanning tunneling microscope (STM) images of the ribbons.

Significance Gold resources on Earth result from an exceptional concentration phenomenon yielding metal contents in ore a thousand to a million times higher than those in common rocks. We show that this process is controlled by sulfur radical ions ( S 3 − ), which strongly bind Au in aqueous solution at elevated temperatures and pressures and allow very efficient extraction, transport, and deposition of gold by geological fluids. Thus, the most inert metal of the periodic table may be very mobile, which explains key features of known gold deposits and offers new possibilities for resource prospecting. Furthermore, the high capacity of the radical ions to solubilize gold may be used for its selective extraction from ores and hydrothermal synthesis of Au-based nanomaterials.

In their letter addressing a recent ab initio density-functional theory-based study of Miller-like experiments (1), Bada and Cleaves (2) downplay the role of formamide, citing its half-life, lower than that of HCN, and the fact that the calculations were performed in aqueous phase rather than in gas phase. Miller’s original experiment had both gas and condensed phases but ab initio modeling of a full biphasic system was beyond the scope of ref. 1. The declared goal of ref. 1, as clearly stated in its abstract and text, was therefore to perform numerical “Miller-like experiments in the condensed phase.” On one hand, it is well known that ab initio calculations are as accurate as they are costly and can only describe few tens … [↵][1]1To whom correspondence should be addressed. Email: marco.saitta{at}impmc.upmc.fr. [1]: #xref-corresp-1-1

International audience; We report a density-functional theory (DFT)-based study of the interface of bulk water with a prototypical oxide surface, MgO(001), and focus our study on the often-overlooked surface electric field. In particular, we observe that the bare MgO(001) surface, although charge-neutral and defectless, has an intense electric field on the Å scale. The MgO(001) surface covered with 1 water monolayer (1 ML) is investigated via a supercell accounting for the experimentally-observed (2 × 3) reconstruction, stable at ambient temperature, and in which two out of six water molecules are dissociated. This 1 ML-hydrated surface is also found to have a high, albeit short-ranged, normal component of the field. Finally, the oxide/water interface is studied via room-temperature ab initio molecular dynamics (AIMD) using 34 H2O molecules between two MgO(001) surfaces. To our best knowledge this is the first AIMD study of the MgO(001)/liquid water interface in which all atoms are treated using DFT and including several layers above the first adsorbed layer. We observe that the surface electric field, averaged over the AIMD trajectories, is still very strong on the fully-wet surface, peaking at about 3 V Å−1. Even in the presence of bulk-like water, the structure of the first layer in contact with the surface remains similar to the (2 × 3)-reconstructed ice ad-layer on MgO(001). Moreover, we observe proton exchange within the first layer, and between the first and second layers – indeed, the O–O distances close to the surface are found to be distributed towards shorter distances, a property which has been shown to directly promote proton transfer.

International audience; The richness of the phase diagram of water reduces drastically atvery high pressures where only two molecular phases, protondisorderedice VII and proton-ordered ice VIII, are known. Bothphases transform to the centered hydrogen bond atomic phase iceX above about 60 GPa, i.e., at pressures experienced in the interiorof large ice bodies in the universe, such as Saturn and Neptune,where nonmolecular ice is thought to be the most abundant phaseof water. In this work, we investigate, by Raman spectroscopy upto megabar pressures and ab initio simulations, how the transformationof ice VII in ice X is affected by the presence of saltinclusions in the ice lattice. Considerable amounts of salt can beincluded in ice VII structure under pressure via rock–ice interactionat depth and processes occurring during planetary accretion. Ourstudy reveals that the presence of salt hinders proton order andhydrogen bond symmetrization, and pushes ice VII to ice X transformationto higher and higher pressures as the concentration ofsalt is increased.

International audience; The structure of amorphous NaCl solutions produced by fast quenching is studied as a function of pressure, up to 4 GPa, by combined neutron diffraction experiments and classical molecular dynamics simulations. Similarly to LiCl solutions the system amorphizes at ambient pressure in a dense phase structurally similar to the e-HDA phase in pure water. The measurement of the static structure factor as a function of pressure allowed us to validate a new polarizable force field developed by Tazi et al., 2012, never tested under non-ambient conditions. We infer from simulations that the hydration shells of Na+ cations form well defined octahedra composed of both H2O molecules and Cl− anions at low pressure. These octahedra are gradually broken by the seventh neighbour moving into the shell of first neighbours yielding an irregular geometry. In contrast to LiCl solutions and pure water, the system does not show a polyamorphic transition under pressure. This confirms that the existence of polyamorphism relies on the tetrahedral structure of water molecules, which is broken here.

International audience; The phase transition from ice VII to ice X under extreme pressures is an example where quantum proton delocalization coexists with classical thermal fluctuations. We investigate this transition, including quantum effects on the nuclear motion through adapted Langevin dynamics. This approach, which allows us to follow the semiclassical trajectories of protons, provides excellent agreement with experimental vibrational spectra indicating a transition pressure of about 65 GPa. Furthermore, we map the full dynamical problem onto a pressure-dependent, one-dimensional mean-field potential for the proton. By solving exactly the corresponding Schr¨odinger equation, we disentangle tunneling and quantum delocalization from classical thermal effects and identify the transition through the topological changes of the proton ground state and its susceptibility. The process is dominated by quantum effects even at ambient temperature and can be considered to be a paradigmatic case of a quantum-driven phase transition.

International audience; The celebrated Miller experiments reported on the spontaneousformation of amino acids from a mixture of simple molecules reactingunder an electric discharge, giving birth to the research field ofprebiotic chemistry. However, the chemical reactions involved inthose experiments have never been studied at the atomic level.Here we report on, to our knowledge, the first ab initio computersimulations of Miller-like experiments in the condensed phase.Our study, based on the recent method of treatment of aqueoussystems under electric fields and on metadynamics analysis ofchemical reactions, shows that glycine spontaneously forms frommixtures of simple molecules once an electric field is switched onand identifies formic acid and formamide as key intermediateproducts of the early steps of the Miller reactions, and the crucibleof formation of complex biological molecules

We report experimental and theoretical evidence that solid molecular ammonia becomes unstable at room temperature and high pressures and transforms into an ionic crystalline form. This material has been characterized in both hydrogenated (NH${}_{3}$) and deuterated (ND${}_{3}$) ammonia samples up to about 180 and 200 GPa, respectively, by infrared absorption, Raman spectroscopy, and x-ray diffraction. The presence of a new strong infrared absorption band centered at 2500 cm${}^{\ensuremath{-}1}$ in NH${}_{3}$ (1900 cm${}^{\ensuremath{-}1}$ in ND${}_{3}$) is in line with previous theoretical predictions regarding the ionization of ammonia molecules into ${{\mathrm{NH}}_{2}}^{\ensuremath{-}}$ and ${{\mathrm{NH}}_{4}}^{+}$ ions. The experimental data suggest the coexistence of two crystalline ionic forms, which our ab initio structure searches predict to be the most stable at the relevant pressures. The ionic crystalline form of ammonia appears stable at low temperatures, which contrasts with the behavior of water in which no equivalent crystalline ionic phase has been found.

We report an extensive theoretical study of the protonated water dimer (Zundel ion) by means of the highly correlated variational Monte Carlo and lattice regularized Monte Carlo approaches. This system represents the simplest model for proton transfer (PT) and a correct description of its properties is essential in order to understand the PT mechanism in more complex acqueous systems. Our Jastrow correlated AGP wave function ensures an accurate treatment of electron correlations. Exploiting the advantages of contracting the primitive basis set over atomic hybrid orbitals, we are able to limit dramatically the number of variational parameters with a systematic control on the numerical precision, crucial in order to simulate larger systems. We investigate energetics and geometrical properties of the Zundel ion as a function of the oxygen-oxygen distance, taken as reaction coordinate. In both cases, our QMC results are found in excellent agreement with coupled cluster CCSD(T) technique, the quantum chemistry "gold standard". Calculations on proton transfer static barriers and dissociation energies display the same agreement. A comparison with density functional theory (DFT) results in the PBE approximation points out the crucial role of electron correlations for a correct description of the PT in the dimer. Our method is able to resolve the tiny energy differences (~ 0.1 Kcal/mol) and the corresponding structural variations at which the proton transfer takes place; it combines these features with a N^3-N^4 scaling with number of particles (favorable with respect to other post-DFT methods), as proven by a benchmark calculation on a larger protonated water cluster. The QMC approach used here represents a promising candidate to provide the first high-level ab initio description of PT in water., 16 pages, 6 figures

The cubic-to-orthorhombic structural transition occurring in CsH at a pressure of about 17 GPa is studied by ab initio calculations. The relative stability of the competing structures and the transition pressure are correctly predicted. We show that this pressure-induced first-order transition is intimately related to a displacive second-order transition which would occur upon application of a shear strain to the (110) planes. The resulting instability is rationalized in terms of the pressure-induced modifications of the electronic structure., 5 pages, latex file, 5 figures

International audience; First measurements of the self-dynamics of liquid water in the GPa range are reported. The GPa range has here become accessible through a new setup for the Paris-Edinburgh press specially conceived for quasielastic neutron scattering studies. A direct measurement of both the translational and rotational diffusion coefficients of water along the 400 K isotherm up to 3 GPa, corresponding to the melting point of ice VII, is provided and compared with molecular dynamics simulations. The translational diffusion is observed to strongly decrease with pressure, though its variation slows down for pressures higher than 1 GPa and decouples from that of the shear viscosity. The rotational diffusion turns out to be insensitive to pressure. Through comparison with structural data and molecular dynamics simulations, we show that this is a consequence of the rigidity of the first neighbors shell and of the invariance of the number of hydrogen bonds of a water molecule under high pressure. These results show the inadequacy of the Stokes-Einstein- Debye equations to predict the self-diffusive behavior of water at high temperature and high pressure, and challenge the usual description of hot dense water behaving as a simple liquid.

International audience; We report the experimental discovery of a new phase of ammonia ice, stable at pressures above 57 GPa and temperatures above 700 K. The combination of our experimental results and ab initio molecular dynamics simulations reveal that this new phase is a superionic conductor, characterized by a large proton diffusion coefficient (1:0 Â 10 À4 cm 2 =s at 70 GPa, 850 K). Proton diffusion occurs via a Grotthuss-like mechanism, at a surprisingly lower temperature than in water ice. This may have implications for the onset of superionicity in the molecular ice mixtures present in Jovian planets. Our simulations further suggest that the anisotropic proton hopping along different H bonds in the molecular solid may explain the formation of the recently predicted ionic phase at low temperatures.

From simultaneous X-ray diffraction and EXAFS experiments, structural properties in the Wurtzite phase of ZnO have been measured up to the transition pressure (9 GPa). These results are compared with first-principles calculations and discussed in terms of wurtzite mechanical stability at high pressure.

We present Kelvin probe force microscopy measurements of single-and few-layer graphene resting on SiO2 substrates. We compare the layer thickness dependency of the measured surface potential with ab initio density functional theory calculations of the work function for substrate-doped graphene. The ab initio calculations show that the work function of single-and bilayer graphene is mainly given by a variation of the Fermi energy with respect to the Dirac point energy as a function of doping, and that electrostatic interlayer screening only becomes relevant for thicker multilayer graphene. From the Raman G-line shift and the comparison of the Kelvin probe data with the ab initio calculations, we independently find an interlayer screening length in the order of four to five layers. Furthermore, we describe in-plane variations of the work function, which can be attributed to partial screening of charge impurities in the substrate, and result in a nonuniform charge density in single-layer graphene.

International audience; We investigated the metastable phase diagram of an ionic salt aqueous solution, LiCl:6D2O, at high pressure and low temperature by neutron diffraction measurements and computer simulations. We show that the presence of salt triggers a stepwise transformation, under annealing at high pressure, to a new very high-density amorphous form. The transition occurs abruptly at 120 K and 2 GPa, is reversible, and is characterized by a sizeable enthalpy release. Simulations suggest that the polyamorphic transition is linked to a local structural reorganization of water molecules around the Li ions.

International audience; It is widely accepted that ice, no matter what phase, is unable to incorporate large amounts of salt into its structure. This conclusion is based on the observation that on freezing of salt water, ice expels the salt almost entirely as brine. Here, we show that this behaviour is not an intrinsic physico-chemical property of ice phases. We demonstrate by neutron diffraction that substantial amounts of dissolved LiCl can be built homogeneously into the ice VII structure if it is produced by recrystallization of its glassy (amorphous) state under pressure. Such 'alloyed' ice VII has significantly different structural properties compared with pure ice VII, such as an 8% larger unit cell volume, 5 times larger displacement factors, an absence of a transition to an ordered ice VIII structure and plasticity. Our study suggests that there could be a whole new class of 'salty' high-pressure ice forms.

The electronic properties and optical gap of (Zn,Mg)(S,Se) wide-gap solid solutions are studied using ab initio techniques and starting from the previously determined atomistic structure of the alloy. Compositional disorder is shown to close the gap substantially with respect to the predictions of the virtual-crystal approximation. The bowing of the fundamental gap versus composition predicted by our calculations is in very good agreement with experiments available for the Zn(S,Se) pseudobinary alloy. At temperatures typical of molecular-beam epitaxy growth, the quaternary alloy displays a rather large amount of short-range order whose effect is to slightly but unmistakably open the gap. Our results agree well with recent experimental data for the quaternary alloy.

International audience; X-ray and neutron-diffraction investigations of rubidium-intercalated single-walled carbon nanotubes are reported. Ab initio calculations conducted in combination with our experiments show that for a single Rb ion the most energetically favorable intercalation site is the interstitial channel between three tubes in a bundle. At higher doping levels, as the Rb content increases, this site becomes however unfavored with respect to the interior of the tubes or the external surface of the bundle. Model simulations of the diffraction patterns, capable of well reproducing both the x-ray and neutron-diffraction patterns, indicate that only the latter insertion sites are compatible with the experimental data. Finally we show that the bundle surface site is the most probable one in the case of saturation at an estimated stoichiometry close to RbC8.

The high-density (HDA) and the very high-density (VHDA) amorphous forms of ice are studied through computer simulations. The structural transformations involve, at different stages of compression, two different subgroups of second-shell neighbors. The interplay between these subgroups is found to be crucial in the mechanism of high-pressure differentiation between HDA and VHDA: in HDA they are more separated and the first subgroup is locked in the anti-tetrahedral, ice-VII-like positions all along the downstroke to ambient pressure. In VHDA the annealing under pressure triggers instead the merging of the two subgroups through a counter-intuitive outward displacement of one subgroup of neighbors, resulting then in a local decrease of the coordination number, a more random-close-packed arrangement and a different equation of state.

We present a neutron diffraction study of liquid water to 6.5 GPa and 670 K. From the measured structure factors we determine radial and angular distributions. It is shown that with increasing density water approaches a local structure common to a simple liquid while distorting only a little the tetrahedral first-neighbor coordination imposed by hydrogen bonds that remain intact.

We present an extensive analysis of the Raman spectrum of ammonia IV, for both ${\mathrm{NH}}_{3}$ and ${\mathrm{ND}}_{3}$, between 6 and $11\phantom{\rule{0.3em}{0ex}}\mathrm{GPa}$. Polarized Raman scattering experiments were performed at low temperature $(20--80\phantom{\rule{0.3em}{0ex}}\mathrm{K})$ on single-crystalline samples grown in a diamond anvil cell. This method enabled us to discern very weak features of the Raman spectrum, including previously unobserved bending modes ${\ensuremath{\nu}}_{2}--{\ensuremath{\nu}}_{4}$. In parallel, we used first-principles methods, based on density functional theory, to compute the theoretical Raman spectra at the conditions of our experiments. An overall good agreement is found between experiment and theory. The results of the measurements with different polarizations and a comparison with our calculations allowed an unambiguous determination of the Raman modes. The assignment was further confirmed by examination of the isotopic ratios and Gr\"uneisen parameters. This study thus provides a much more complete picture of the Raman spectrum of phase IV than available before and constitutes a solid basis for the investigation of ammonia at higher pressures.

The high-pressure phases of solid ammonia have been investigated by x-ray diffraction in a diamond anvil cell at room temperature. Despite the first-order solid phase transition at 4 GPa, quasi-single crystals of NH3 and ND3 could be obtained and compressed to 123 and 62 GPa, respectively. The observed reflections above 4 GPa are compatible with the structure determined by neutron diffraction on ND3. We found strong evidence for an isosymmetric transition at 12 GPa in NH3 and 18 GPa in ND3. This transition is more likely due to rearrangements of the hydrogen atoms, whereas the N atoms remain on their quasi-hcp sites. The experimental equation of state (EOS) is compared to the one derived from first-principles calculations. A stiffening of the EOS above 55 GPa could indicate the onset of a quantum-disordered regime for some of the H bonds.

In this paper we investigate the vibrational properties of $\mathrm{Cu}\mathrm{Ga}{\mathrm{O}}_{2}$ delafossite by means of Raman experiments and ab initio calculations. Both investigations have been performed at ambient pressure and also at high pressure. The two Raman-active modes have frequencies ${w}_{{E}_{g}}=368\ifmmode\pm\else\textpm\fi{}1\phantom{\rule{0.3em}{0ex}}{\mathrm{cm}}^{\ensuremath{-}1}$ and ${w}_{{A}_{1g}}=729\ifmmode\pm\else\textpm\fi{}1\phantom{\rule{0.3em}{0ex}}{\mathrm{cm}}^{\ensuremath{-}1}$, and pressure coefficients $2.78\ifmmode\pm\else\textpm\fi{}0.03\phantom{\rule{0.3em}{0ex}}{\mathrm{cm}}^{\ensuremath{-}1}∕\mathrm{GPa}$ $({E}_{g})$ and $4.64\ifmmode\pm\else\textpm\fi{}0.09\phantom{\rule{0.3em}{0ex}}{\mathrm{cm}}^{\ensuremath{-}1}∕\mathrm{GPa}$ $({A}_{1g})$. Raman experiments indicate the existence of a phase transition beginning at $26\ifmmode\pm\else\textpm\fi{}1\phantom{\rule{0.3em}{0ex}}\mathrm{GPa}$. At about the same pressure, ab initio calculations show the presence of a dynamical instability, possibly related to the phase transition. The phonon dispersion curves are also discussed.

We present a neutron diffraction study of the transition between low-density and high-density amorphous ice (LDA and HDA, respectively) under pressure at $\ensuremath{\sim}0.3\text{ }\text{ }\mathrm{G}\mathrm{P}\mathrm{a}$, at 130 K. All the intermediate diffraction patterns can be accurately decomposed into a linear combination of the patterns of pure LDA and HDA. This progressive transformation of one distinct phase to another, with phase coexistence at constant pressure and temperature, gives direct evidence of a classical first-order transition. In situ Raman measurements and visual observation of the reverse transition strongly support these conclusions, which have implications for models of water and the proposed second critical point in the undercooled region of liquid water.

We review recent in situ neutron diffraction studies on the structural pressure dependence and the recrystallization of dense amorphous ices up to 2 GPa. Progress in high pressure techniques and data analysis methods allows the reliable determination of all three partial structure factors of amorphous ice under pressure. The strong pressure dependence of the gOO(r) correlation function shows that the isothermal compression of high density amorphous ice (HDA) at 100 K is achieved by a contraction ({\sim }20\%) of the second-neighbour coordination shell leading to a strong increase in coordination. The gDD(r) and gOD(r) structure factors are, in contrast, only weakly sensitive to pressure. These data allow a comparison with structural features of the recently reported 'very high density amorphous ice' (VHDA) which indicates that VHDA at ambient pressure is very similar to compressed HDA, at least up to the second-neighbour shell. The recrystallization of HDA has been investigated in the range 0.3–2 GPa. It is shown that hydrogen-disordered phases are produced which normally grow only from the liquid, such as ice XII, and in particular ice IV. These findings are in good agreement with results on quench-recovered samples.

We report measurements of the phonon dispersion of ice Ih under hydrostatic pressure up to 0.5 GPa, at 140 K, using inelastic neutron scattering. They reveal a pronounced softening of various low-energy modes, in particular, those of the transverse acoustic phonon branch in the [100] direction and polarization in the hexagonal plane. We demonstrate with the aid of a lattice dynamical model that these anomalous features in the phonon dispersion are at the origin of the negative thermal expansion (NTE) coefficient in ice below 60 K. Moreover, extrapolation to higher pressures shows that the mode frequencies responsible for the NTE approach zero at approximately 2.5 GPa, which explains the known pressure-induced amorphization (PIA) in ice. These results give the first clear experimental evidence that PIA in ice is due to a lattice instability, i.e., mechanical melting.

The high-pressure local structure of zinc oxide has been studied at room temperature using combined energy-dispersive x-ray-diffraction and x-ray-absorption spectroscopy experiments. The structural parameter u and the lattice-parameter ratio $c/a$ of the wurtzite phase is given as a function of pressure and compared with results from ab initio calculations based on a plane-wave pseudopotential method within the density-functional theory. It is shown that an accurate study of ZnO requires the explicit treatment of the d electrons of Zn as valence electrons. In good agreement with present calculations, our experimental data do not show any variation of $u(P)$ in the low-pressure wurtzite phase between 0 and 9 GPa, pressure at which the phase transition to the rocksalt phase occurs. Moreover, no dramatic modification of the r-phase K-edge position up to $\ensuremath{\sim}20\mathrm{GPa}$ is observed, indicating the absence of metallization. In view of all these results, theoretical models identifying the wurtzite-to-rocksalt transition as an homogeneous path are discussed.

International audience; We present a joint experimental and theoretical study of the superconductivity in doped silicon clathrates. The critical temperature in Ba8@Si–46 is shown to strongly decrease with applied pressure. These results are corroborated by ab initio calculations using MacMillan's formulation of the BCS theory with the electron-phonon coupling constant lambda calculated from perturbative density functional theory. Further, the study of I8@Si–46 and of gedanken pure silicon diamond and clathrate phases doped within a rigid-band approach show that the superconductivity is an intrinsic property of the sp3 silicon network. As a consequence, carbon clathrates are predicted to yield large critical temperatures with an effective electron-phonon interaction much larger than in C60.

The structural properties of the (Zn, Mg) (S, Se) solid solutions are determined by a combination of the computational alchemy and the cluster expansion methods with Monte Carlo simulations. We determine the phase diagram of the alloy and show that the homogeneous phase is characterized by a large amount of short-range order occurring among first-nearest neighbors. Electronic-structure calculations performed using the special quasirandom structure approach indicate that the energy gap of the alloy is rather sensitive to this short-range order.

During this thesis two major problems were studied : the liquid-liquid transition and the homogeneous nucleation of ice in water. To achieve this, we used state-of-the-art enhanced sampling methods, coupled with a new collective variable which store the relevant topological information of a system, the PIV. By rigorous calculation of free energy profile for various conditions of pressure and temperature, we have been able to show the lack of free energy barrier and thereof a second critical point for the liquid-liquid transition, with the TIP4P/2005 model of water. By sampling the transition path ensemble with a new TPS algorithm, we have been able to precisely study the homogeneous nucleation of ice in water with the TIP4P/Ice model, showing that critical nuclei arrange themselves optimaly in stacking disorder ice, with purely hexagonal or cubic nuclei spontaneously evolving toward this structure. The insight we obtained includes a two-step mechanism for the aggregation of new hexagonal ice molecules to the critical nucleus, compared to a one-step process for the addition of cubic ice molecules. Finally we performed a quantitative assessment of the quality of the PIV topological metric as reaction coordinate for nucleation : analysis by means of a rigorous likelihood optimization technique based on committor information, indicates that this coordinate outperforms a large set of previously considered coordinates.; Au cours de cette thèse deux problèmes majeurs pour l’eau ont été étudiés : la transition liquide-liquide et la nucléation homogène de la glace. Pour cela nous avons utilisé l'état de l'art des méthodes d’échantillonnage amélioré, couplé avec une nouvelle variable qui contient les informations topologiques pertinentes des systèmes étudiés, le PIV. En calculant des profils d'énergie libre pour différentes conditions de pression et de température, nous avons pu montrer rigoureusement l’absence de barrière d’énergie libre et de second point critique pour la transition liquide-liquide avec le modèle TIP4P/2005. En échantillonnant l'ensemble des chemins de transition grâce à un nouvel algorithme TPS, nous avons aussi pu étudier précisément le mécanisme de nucléation homogène de l’eau avec le modèle TIP4P/Ice, montrant que la structure optimale des noyaux critiques est un empilement désordonné, les noyaux critiques purement cubique ou hexagonaux évoluant spontanément vers cette structure. De plus, nous avons pu montrer que la glace hexagonale s’agrégeait majoritairement en deux étapes, là où la glace cubique s’agrégeait en une étape. Finalement nous avons quantifié rigoureusement la qualité de notre métrique topologique PIV comme coordonnée de réaction pour étudier la nucléation : une analyse réalisée avec la méthode d'optimisation de la vraisemblance maximale basée sur la fonction de réalisation, indique que cette coordonnée surpasse un large éventail de coordonnées utilisées précédemment pour étudier ce problème.

Although carbon dioxide is well known for its impact on the atmosphere, it is also an important constituent of the mantle of earth. As such, it is implicated in a number of geological events, notably in earthquakes and volcanism. In this thesis we aim at understanding the behavior of carbon dioxide in the lower mantle, where it is likely formed through reactions between carbonates and silicon dioxide. Indeed, the properties of carbon dioxide, and most notably its polymerization mechanisms may impact the reactivity of the mantle and therefore impact the chemical properties occurring within it. In this work we use state of the art topological descriptors and ab initio simulation methods to study the polymerization mechanisms that occurs under the extreme conditions corresponding to the lower mantle of Earth. We notably show the existence of four distinctive fluids that coexist at those conditions, including: a reactive molecular fluid with the regular formation of dimers allowing the exchange of oxygen between carbon dioxide molecules; a very reactive polymeric fluid which forms a complex network in perpetual evolution; and a very sluggish liquid, very similar to an amorphous solid ; and the standard molecular liquid with long range interactions between carbon dioxide molecules. All of those different fluids occur within the experimental conditions of the lower mantle and therefore may have potential implications for its reactivity and transport properties. The reactive molecular liquid, for example, implies that carbon dioxide will take an important part in the chemical reactions of the mantle.; Le dioxyde de carbone est un constituant important du manteau de la Terre et intervient dans de nombreux processus géologiques, notamment sismiques et volcaniques. Dans cette thèse, nous étudions les transformations du dioxyde de carbone dans les conditions extrêmes du manteau inférieur de la Terre. En effet, la compréhension du comportement du dioxyde de carbone et notamment de ses mécanismes de polymérisation dans ces conditions pourrait apporter un éclairage supplémentaire sur les propriétés du manteau inférieur. Nous utilisons ici des outils topologiques avancées et des méthodes de simulation aux premiers principes (ab initio) afin d’étudier ces mécanismes de polymérisation du dioxyde de carbone dans des conditions de températures et de pressions extrêmes du manteau. Ce faisant nous mettons en évidence quatre comportements fluides différents dans ces conditions géothermiques: le liquide moléculaire classique, avec des interactions faibles entre molécules de dioxyde de carbone ; un liquide moléculaire réactif dans lequel ces molécules réagissent fréquemment et forment d’éphèmes dimères permettant l’échange d’oxygène entre elles ; un liquide polymérique hautement réactif formant un réseau complexe de chaînes moléculaires en perpétuelles évolutions ; une forme liquide avec très peu de diffusion, semblable à un amorphe. Tous ces fluides peuvent apparaître dans les conditions expérimentales du manteau inférieur; leur propriétés peuvent donc impacter la réactivité et les propriétés de transport de ce dernier. Par exemple, le liquide moléculaire réactif semble indiquer une participation accrue du dioxyde de carbone dans les réactions du manteau.