Ab initio molecular dynamics with variable cell shape: Application to MgSiO3

Effect of conjugation on the vibrational modes of a carbon nanotube dimer

First Principles simulation studies using the density functional theory have been performed to investigate the effect of conjugation on vibrational modes when two CNTs of different chiralities are held together to constitute an inhomogeneous dimer. Raman Spectra of a (5, 0) CNT; a (6,0) CNT and a (5,0)- (6,0) CNT dimer comprising of parallel standing (5,0) and (6,0) CNTs held by weak Van der Waals were simulated. Various vibrational modes in different frequency regions have been discussed in detail. A red shift is observed overall that clearly affirms the stability and existence of the structure formed by conjugation of CNTs. In the RBM (Radial Breathing Mode) region, additional peaks can be seen arising out of the coupled vibrations. D-band peaks of the dimer cover the D-band peaks of both the CNTs as disorder in the constituents reflects in its constitution. In the G-band region of the dimer spectrum, a low wavelength component with Lorentzian shape and a weak high wavelength component with a Breit Wigner Fano (BWF) kind of line-shape suggest metallic nature of the inhomogeneous CNT dimer.

Effects of Induced Stress on Seismic Waves: Validation Based on Ab Initio Calculations

When a continuum is subjected to an induced stress, the equations that govern seismic wave propagation are modified in two ways. First, the equation of conservation of linear momentum gains terms related to the induced deviatoric stress, and, second, the elastic constitutive relationship acquires terms linear in the induced stress. This continuum mechanics theory makes testable predictions with regard to stress-induced changes in the elastic tensor. Specifically, it predicts that induced compression linearly affects the prestressed moduli with a slope determined by their local adiabatic pressure derivatives and that induced deviatoric stress produces anisotropic compressional and shear wave speeds. In this article we successfully compare such predictions against ab initio mineral physics calculations for NaCl and MgO.

Nature of the Volume Isotope Effect in Ice

The substitution of hydrogen (H) by deuterium (D) in ice Ih and in its H-ordered version, ice XI, produces an anomalous form of volume isotope effect (VIE), i.e., volume expansion. This VIE contrasts with the normal VIE (volume contraction) predicted in ice-VIII and in its H-disordered form, ice VII. Here we investigate the VIE in ice XI and in ice VIII using first principles quasiharmonic calculations. We conclude that normal and anomalous VIEs can be produced in ice VIII and ice XI in sequence by application of pressure (ice XI starting at negative pressures) followed by a third type-anomalous VIE with zero-point volume contraction. The latter should also contribute to the isotope effect in the ice VII → ice X transition. The predicted change between normal and anomalous VIE in ice VIII at 14.3 GPa and 300 K is well reproduced experimentally in ice VII using x-ray diffraction measurements. The present discussion of the VIE is general, and conclusions should be applicable to other solid phases of H(2)O, possibly to liquid water under pressure, and to other H-bonded materials.

Searching for high magnetization density in bulk Fe: the new metastable Fe₆ phase

We report the discovery of a new allotrope of iron by first principles calculations. This phase has Pmn2(1) symmetry, a six-atom unit cell (hence the name Fe6), and the highest magnetization density (Ms) among all the known crystalline phases of iron. Obtained from the structural optimizations of the Fe3C-cementite crystal upon carbon removal, Pmn2(1) Fe6 is shown to result from the stabilization of a ferromagnetic FCC phase, further strained along the Bain path. Although metastable from 0 to 50 GPa, the new phase is more stable at low pressures than the other well-known HCP and FCC allotropes and smoothly transforms into the FCC phase under compression. If stabilized to room temperature, for example, by interstitial impurities, Fe6 could become the basis material for high Ms rare-earth-free permament magnets and high-impact applications such as light-weight electric engine rotors or high-density recording media. The new phase could also be key to explaining the enigmatic high Ms of Fe16N2, which is currently attracting intense research activity.

First principles investigation of NO2 and SO2 adsorption on γ-Al2O3 supported mono- and diatomic metal clusters

Atomistic simulations of NO₂ and SO₂ adsorption on γ-Al₂O₃ supported mono and diatomic clusters of Pt and Rh show that enhanced sulfur tolerance with respect to pristine metallic surfaces or extended nanoparticles, can be achieved.

Low-temperature elastic anomalies in CaTiO3: dynamical characterization

Pulse-echo ultrasonic measurements of elastic coefficients of CaTiO(3) show anomalous behavior around 200 K, with a notable rise in the attenuation coefficient. Molecular dynamics simulation is used to simulate the elastic response of a mono-domain (MDm) and a poly-domain (PDm) configuration of CaTiO(3) using the Vashishta-Raman interatomic potential. The PDm is obtained by cooling the melt from 3600 to 300 K at a rate of 0.5 K ps(-1), so that it recrystallizes to the PDm orthorhombic configuration. The elastic behavior is simulated in the temperature range from 300 to 20 K. In the MDm, it is observed that the bulk modulus varies linearly with temperature, while in the PDm an anomalous hardening is seen around 210 K. The bulk modulus of the PDm fluctuates strongly and is lower than that of the MDm. Neither the pair correlation function nor the Ti-Ti-O bonding angle indicate a true structural phase transition in this range of temperatures. Given the absence of any apparent change in the structure, a possible explanation for this phenomenon is the emergence of a certain class of dynamical instability associated with domain wall motion. Curiously, the pressure fluctuations in both the MDm and PDm configurations follow a power law distribution f ~ P(-α), with the exponent independent of applied strain and temperature. Time series for pressure are used to analyze the dynamics by time-delay reconstruction techniques. The calculus of embedding and correlation dimension indicates that in the polycrystalline configuration, low-dimension dynamics (<26) appears, which tend to disappear at higher temperatures.

Spin-state crossover and hyperfine interactions of ferric iron in MgSiO(3) perovskite

Using density functional theory plus Hubbard U calculations, we show that the ground state of (Mg,Fe)(Si,Fe)O(3) perovskite, the major mineral phase in Earth's lower mantle, has high-spin ferric iron (S=5/2) at both dodecahedral (A) and octahedral (B) sites. With increasing pressure, the B-site iron undergoes a spin-state crossover to the low-spin state (S=1/2) between 40 and 70 GPa, while the A-site iron remains in the high-spin state. This B-site spin-state crossover is accompanied by a noticeable volume reduction and an increase in quadrupole splitting, consistent with recent x-ray diffraction and Mössbauer spectroscopy measurements. The anomalous volume reduction leads to a significant softening in bulk modulus during the crossover, suggesting a possible source of seismic-velocity anomalies in the lower mantle.

The chemistry of acetone at extreme conditions by density functional molecular dynamics simulations

Density functional molecular dynamics simulations have been performed in the NVT ensemble (moles (N), volume (V) and temperature (T)) on a system formed by ten acetone molecules at a temperature of 2000 K and density ρ = 1.322 g cm(-3). These conditions resemble closely those realized at the interface of an acetone vapor bubble in the early stages of supercompression experiments and result in an average pressure of 5 GPa. Two relevant reactive events occur during the simulation: the condensation of two acetone molecules to give hexane-2,5-dione and dihydrogen and the isomerization to the enolic propen-2-ol form. The mechanisms of these events are discussed in detail.

First-principles study on thermodynamic properties and phase transitions in TiS(2)

Structural and vibrational properties of TiS(2) with the CdI(2) structure have been studied to high pressures from density functional calculations with the local density approximation (LDA). The calculated axial compressibility of the CdI(2)-type phase agrees well with experimental data and is typical of layered transition-metal dichalcogenides. The obtained phonon dispersions show a good correspondence with available experiments. A phonon anomaly is revealed at 0 GPa, but is much reduced at 20 GPa. The thermodynamic properties of this phase were also calculated at high pressures and high temperatures using the quasi-harmonic approximation. Our LDA study on the pressure-induced phase transition sequence predicts that the CdI(2)-type TiS(2), the phase stable at ambient conditions, should transform to the cotunnite phase at 15.1 GPa, then to a tetragonal phase (I4/mmm) at 45.0 GPa. The tetragonal phase remains stable to at least 500 GPa. The existence of the tetragonal phase at high pressures is consistent with our previous findings in NiS(2) (Yu and Ross 2010 J. Phys.: Condens. Matter 22 235401). The cotunnite phase, although only stable in a narrow pressure range between 15.1 and 45.0 GPa, displays the formation of a compact S network between 100 and 200 GPa, which is evidenced by a kink in the variation of unit cell lengths with pressure. The electron density analysis in cotunnite shows that valence electrons are delocalized from Ti atoms and concentrated near the S network.

Anelastic loss behaviour of mobile microstructures in SrZr(1-x)Ti(x)O3 perovskites

Anelastic loss mechanisms associated with phase transitions in SrZr(1-x)Ti(x)O(3) perovskites (x = 0.375, 0.450, 0.550, 0.775) have been investigated by dynamic mechanical analysis between 128 and 723 K at frequencies of 0.1-50 Hz. Distinctive patterns of changes in the elastic moduli due to octahedral tilting transitions correlate closely with data for the shear modulus obtained previously by resonant ultrasound spectroscopy at high frequencies (∼0.5 MHz). The I4/mcm <--> Imma transition is first order and has a characteristic minimum in the shear modulus and Young's modulus. For x = 0.450 and 0.550, a dissipation peak occurs at the transition temperature, the maximum of which varies with frequency according to a power law relationship of the form tanδ = Af(n), with n≈ - 0.3. Debye-like dissipation peaks in the stability field of the Imma structure at x = 0.375 have a frequency and temperature dependence consistent with twin wall pinning by defects with an activation energy ∼ 184 kJ mol(-1). These results indicate that there is diversity of pinning and relaxation processes for transformation twin walls and interfaces in different perovskites with I4/mcm, Imma and Pnma structures.

Prediction of high-pressure polymorphism in NiS2 at megabar pressures

A sequence of pressure-induced phase transitions of vaesite, NiS(2), with pyrite structure, has been established from static LDA calculations. A dozen AX(2) candidate structures have been studied at high pressures including cotunnite (α-PbCl(2)), which is commonly observed in other AX(2) compounds at high pressures. At 150 GPa, vaesite transforms to a tetragonal phase (P4(2)/n) rather than cotunnite. This tetragonal structure is characterized by layers of Ni atoms in eight-fold coordination with S atoms rather than the nine-fold coordination observed in cotunnite. With further compression to about 7.5 Mbar, the tetragonal phase transforms into a hexagonal AlB(2)-type structure (P6/mmm) which is characterized by planar hexagonal layers of S intercalated by Ni atoms where each Ni atom is 12-fold coordinated by S atoms. Calculated band structures and valence electron density maps show S-S and Ni-S bonded interactions for NiS(2) under these extremely compressed conditions. The tetragonal phase may have geophysical implications if present in the Earth's core.

Hole-mediated hydrogen spillover mechanism in metal-organic frameworks

Hydrogen spillover on carbon-based systems has been proposed as a viable alternative for room-temperature storage. Given the strength of the C-H bonds, however, it is unclear if spillover indeed takes place in such materials. We performed a first-principles study of H spillover on IRMOF-1. Spillover becomes thermodynamically stable only at high H coverage with a calculated Gibbs free energy of -14  kJ/mol at ambient condition. In general, however, spillover may not proceed due to high-energy states at lower H coverage. We propose that hole doping can substantially lower the energies as well as barriers to enable spillover at ambient conditions.

Body-centered tetragonal C4: a viable sp3 carbon allotrope

We have investigated by first principles the electronic, vibrational, and structural properties of bct C4, a new form of crystalline sp{3} carbon recently found in molecular dynamics simulations of carbon nanotubes under pressure. This phase is transparent, dynamically stable at zero pressure, and more stable than graphite beyond 18.6 GPa. Coexistence of bct C4 with M carbon can explain better the x-ray diffraction pattern of a transparent and hard phase of carbon produced by the cold compression of graphite. Its structure appears to be intermediate between that of graphite and hexagonal diamond. These facts suggest that bct C4 is an accessible form of sp{3} carbon along the graphite-to-hexagonal diamond transformation path.

Density functional theory for transition metals and transition metal chemistry

We introduce density functional theory and review recent progress in its application to transition metal chemistry. Topics covered include local, meta, hybrid, hybrid meta, and range-separated functionals, band theory, software, validation tests, and applications to spin states, magnetic exchange coupling, spectra, structure, reactivity, and catalysis, including molecules, clusters, nanoparticles, surfaces, and solids.

Ab initio theory of planetary materials

Ab initio simulations play an increasingly important role in the studies of deep planetary interiors. Here we review the current state of this field, concentrating on studies of the materials of the Earth’s deep interior (MgO—SiO2—FeO—Al2O3, Fe—Si—S—O) and of the interiors of giant planets (H—He system, H2O—CH4—NH3 system). In particular, novel phases and phase diagrams, insights into structural and electronic phase transitions, melting curves, thermoelasticity and the effects of impurities on physical properties of planet-forming materials are discussed.

Elastic anomalies associated with transformation sequences in perovskites: I. Strontium zirconate, SrZrO(3)

Elastic behaviour associated with the hierarchy of tilting transitions in SrZrO(3) has been examined using resonant ultrasound spectroscopy on a ceramic sample at temperatures between 153 and 1531 K. Changes in slope of the evolution of resonance frequencies with temperature indicate that phase transitions occur at 1038 K ([Formula: see text]), 1122 K ([Formula: see text]), and 1367 K ([Formula: see text]). Strain analysis of previously recorded neutron diffraction data shows that the [Formula: see text] and [Formula: see text] transitions are close to tricritical in character, and that [Formula: see text] is first order. Deviations from the form of the elastic behaviour predicted by Landau theory are found. In particular, elastic softening in the vicinity of the [Formula: see text] transition suggests that local dynamical fluctuations between individual tilt systems occur, rather than a discontinuous switch from one phase to another. Determinations of the mechanical quality factor, Q, show that SrZrO(3) in the [Formula: see text] phase is a classically high-Q (i.e. non-dissipating) cubic material. I4/mcm and Imma phases both have much greater dissipation (low Q), which is tentatively attributed to the mobility of twin walls. The room temperature Pnma phase is unexpectedly much stiffer than both I4/mcm and Imma phases and has high Q. It appears that when two separate tilt systems operate, as in Pnma, they can interact to reduce strain/order parameter relaxations.

Prediction of an U2S3-type polymorph of Al2O3 at 3.7 Mbar

We predict by first principles a phase transition in alumina at approximately 3.7 Mbar and room temperature from the CaIrO(3)-type polymorph to another with the U(2)S(3)-type structure. Because alumina is used as window material in shock-wave experiments, this transformation should be important for the analysis of shock data in this pressure range. Comparison of our results on all high-pressure phases of alumina with shock data suggests the presence of two phase transitions in shock experiments: the corundum to Rh(2)O(3)(II)-type structure and the Rh(2)O(3)(II)-type to CaIrO(3)-type structure. The transformation to the U(2)S(3)-type polymorph is in the pressure range reached in the mantle of recently discovered terrestrial exoplanets and suggests that the multi-megabar crystal chemistry of planet-forming minerals might be related to that of the rare-earth sulfides.

Zigzag graphene nanoribbons with saturated edges

Zigzag graphene nanoribbons with saturated edges are investigated by first principles calculations. In these structures edge carbons have either two H or two F atoms, and are of sp(3) type. Compared to the previously studied ribbons with all carbons of sp(2) type, several similarities and differences are found. Specifically, in narrower ribbons the closed shell electronic state is the most stable one. In wider ribbons a state with antiferromagnetically spin-polarized edges is the lowest in energy, similarly to the ribbons with all sp(2) type carbons. A notable feature of narrower ribbons is significant single-double carbon bond alternation across the ribbon. Calculated Raman spectra contain a distinct blue shift signature of such alternation, which perhaps can be used for the experimental identification of ribbons of this type.

Raman spectra of graphite oxide and functionalized graphene sheets

We investigate Raman spectra of graphite oxide and functionalized graphene sheets with epoxy and hydroxyl groups and Stone-Wales and 5-8-5 defects by first-principles calculations to interpret our experimental results. Only the alternating pattern of single-double carbon bonds within the sp2 carbon ribbons provides a satisfactory explanation for the experimentally observed blue shift of the G band of the Raman spectra relative to graphite. To obtain these single-double bonds, it is necessary to have sp3 carbons on the edges of a zigzag carbon ribbon.

First-principles study of the elastic and thermodynamic properties of CaSiO(3) perovskite

The thermodynamic and elastic properties of CaSiO(3) perovskite are investigated at high pressures and temperatures using the plane wave pseudopotential method within the local density approximation. The athermal elastic moduli of CaSiO(3) perovskite are calculated as a function of pressure up to 200 GPa. The calculated results are in excellent agreement with available experimental data at high pressure, and compare favourably with other pseudopotential predictions over the pressure regime studied. It is also found that the elastic anisotropy drops rapidly with the increase of pressure initially, and then decreases more slowly at higher pressures. The thermodynamic properties of CaSiO(3) perovskite are predicted using the quasi-harmonic Debye model for the first time; the heat capacity and the thermal expansion coefficient agree with the observed values at ambient conditions and the other calculations at high pressures and temperatures.

Orientational Melting and Reorientational Motion in a Cubane Molecular Crystal: A Molecular Simulation Study

Detailed molecular simulations are carried out to investigate the effect of temperature on orientational order in cubane molecular crystal. We report a transition from an orientationally ordered to an orientationally disordered plastic crystalline phase in the temperature range 425-450 K. This is similar to the experimentally reported transition at 395 K. The nature of this transition is first order and is associated with a 4.8% increase in unit cell volume that is comparable to the experimentally reported unit cell volume change of 5.4% (Phys. Rev. Lett. 1997, 78, 4938). An orientational order parameter, eta(T), has been defined in terms of average angle of libration of a molecular 3-fold axis and the orientational melting has been characterized by using eta(T). The orientational melting is associated with an anomaly in specific heat at constant pressure (C(P)) and compressibility (kappa). The enthalpy of transition and entropy of transition associated with this orientational melting are 20.8 J mol(-1) and 0.046 J mol(-1) K(-1), respectively. The structure of crystalline as well as plastic crystalline phases is characterized by using various radial distribution functions and orientational distribution functions. The coefficient of thermal expansion of the plastic crystalline phase is more than twice that of the crystalline phase.

Isobaric-Isothermal Monte Carlo Simulations from First Principles: Application to Liquid Water at Ambient Conditions

A series of first-principles Monte Carlo simulations in the isobaric-isothermal ensemble were carried out for liquid water at ambient conditions (T=298 K and p=1 atm). The Becke-Lee-Yang-Parr (BLYP) exchange and correlation energy functionals and norm-conserving Goedecker-Teter-Hutter (GTH) pseudopotentials were employed with the CP2 K simulation package to examine systems consisting of 64 water molecules. The fluctuations in the system volume encountered in simulations in the isobaric-isothermal ensemble require a reconsideration of the suitability of the typical charge-density cutoff and the regular grid-generation method previously used for the computation of the electrostatic energy in first-principles simulations in the microcanonical or canonical ensembles. In particular, it is noted that a much higher cutoff is needed and that the most computationally efficient method of creating grids can result in poor simulations. Analysis of the simulation trajectories using a very large charge-density cutoff at 1200 Ry and four different grid-generation methods point to a significantly underestimated liquid density of about 0.8 g cm-3 resulting in a somewhat understructured liquid (with a value of about 2.7 for the height of the first peak in the oxygen-oxygen radial distribution function) for BLYP-GTH water at ambient conditions. In addition, a simulation using a charge-density cutoff at 280 Ry yields a higher density of 0.9 g cm-3, showing the sensitivity of the simulation outcome to this parameter.

High-pressure melting of MgSiO3

The melting curve of MgSiO(3) perovskite has been determined by means of ab initio molecular dynamics complemented by effective pair potentials, and a new phenomenological model of melting. Using first principles ground state calculations, we find that the MgSiO(3) perovskite phase transforms into post perovskite at pressures above 100 GPa, in agreement with recent theoretical and experimental studies. We find that the melting curve of MgSiO(3), being very steep at pressures below 60 GPa, rapidly flattens on increasing pressure. The experimental controversy on the melting of the MgSiO(3) perovskite at high pressures is resolved, confirming the data by Zerr and Boehler.

Post-Perovskite Phase Transition in MgSiO 3

In situ x-ray diffraction measurements of MgSiO 3 were performed at high pressure and temperature similar to the conditions at Earth's core-mantle boundary. Results demonstrate that MgSiO 3 perovskite transforms to a new high-pressure form with stacked SiO 6 -octahedral sheet structure above 125 gigapascals and 2500 kelvin (2700-kilometer depth near the base of the mantle) with an increase in density of 1.0 to 1.2%. The origin of the D″ seismic discontinuity may be attributed to this post-perovskite phase transition. The new phase may have large elastic anisotropy and develop preferred orientation with platy crystal shape in the shear flow that can cause strong seismic anisotropy below the D″ discontinuity.

Post-Perovskite Phase Transition in MgSiO3

In situ x-ray diffraction measurements of MgSiO3 were performed at high pressure and temperature similar to the conditions at Earth's core-mantle boundary. Results demonstrate that MgSiO3 perovskite transforms to a new high-pressure form with stacked SiO6-octahedral sheet structure above 125 gigapascals and 2500 kelvin (2700-kilometer depth near the base of the mantle) with an increase in density of 1.0 to 1.2%. The origin of the D" seismic discontinuity may be attributed to this post-perovskite phase transition. The new phase may have large elastic anisotropy and develop preferred orientation with platy crystal shape in the shear flow that can cause strong seismic anisotropy below the D" discontinuity.

Anomalous pressure-induced transition(s) in ice XI

The effects of pressure on the structure of ice XI-an ordered form of the phase of ice Ih, which is known to amorphize under pressure-are investigated theoretically using density-functional theory. We find that pressure induces a mechanical instability, which is initiated by the softening of an acoustic phonon occurring at an incommensurate wavelength, followed by the collapse of the entire acoustic band and by the violation of the Born stability criteria. It is argued that phonon collapse may be a quite general feature of pressure-induced amorphization. The implications of our findings for the amorphization of ice Ih are also discussed.

Thermoelastic properties of MgSiO(3)-perovskite: insights on the nature of the Earth's lower mantle

We have determined by means of first principles quasiharmonic calculations the elastic constants and acoustic velocities of MgSiO3 perovskite, the most abundant mineral of the Earth's lower mantle (LM), at pertinent pressures and temperatures. Using these results, along with the effects of low concentration iron alloying and the thermoelasticity of the most important secondary LM phase, MgO, we predict the isotropic elastic moduli of likely LM aggregates. Comparison with seismic values extracted from the preliminary reference Earth model indicates that the top of the LM behaves as a typical aggregate of pyrolitic composition, likewise the upper mantle. But systematic deviations that cannot be accounted for by alterations in the geotherm alone develop toward the deep LM. This result could be viewed as evidence in support of radially inhomogeneous LM models.

First-principles determination of elastic anisotropy and wave velocities of MgO at lower mantle conditions

The individual elastic constants of magnesium oxide (MgO) have been determined throughout Earth's lower mantle (LM) pressure-temperature regime with density functional perturbation theory. It is shown that temperature effects on seismic observables (density, velocities, and anisotropy) are monotonically suppressed with increasing pressure. Therefore, at realistic LM conditions, the isotropic wave velocities of MgO remain comparable to seismic velocities, as previously noticed in athermal high-pressure calculations. Also, the predicted strong pressure-induced anisotropy is preserved toward the bottom of the LM, so lattice-preferred orientations in MgO may contribute substantially to the observed seismic anisotropy in the D" layer.

Polymorphs of Alumina Predicted by First Principles: Putting Pressure on the Ruby Pressure Scale

Fully optimized quantum mechanical calculations indicate that Al2O3 transforms from the corundum structure to the as yet unobserved Rh2O3 (II) structure at about 78 gigapascals, and it further transforms to Pbnm-perovskite structure at 223 gigapascals. The predicted x-ray spectrum of the Rh2O3 (II) structure is similar to that of the corundum structure, suggesting that the Rh2O3 (II) structure could go undetected in high-pressure x-ray measurements. It is therefore possible that the ruby (Cr3+-doped corundum) fluorescence pressure scale is sensitive to the thermal history of the ruby chips in a given experiment.