Ab initio simulation of the equation of state and kinetics of shocked water

First principles reaction discovery: from the Schrodinger equation to experimental prediction for methane pyrolysis

Our recent success in exploiting graphical processing units (GPUs) to accelerate quantum chemistry computations led to the development of the ab initio nanoreactor, a computational framework for automatic reaction discovery and kinetic model construction. In this work, we apply the ab initio nanoreactor to methane pyrolysis, from automatic reaction discovery to path refinement and kinetic modeling. Elementary reactions occurring during methane pyrolysis are revealed using GPU-accelerated ab initio molecular dynamics simulations. Subsequently, these reaction paths are refined at a higher level of theory with optimized reactant, product, and transition state geometries. Reaction rate coefficients are calculated by transition state theory based on the optimized reaction paths. The discovered reactions lead to a kinetic model with 53 species and 134 reactions, which is validated against experimental data and simulations using literature kinetic models. We highlight the advantage of leveraging local brute force and Monte Carlo sensitivity analysis approaches for efficient identification of important reactions. Both sensitivity approaches can further improve the accuracy of the methane pyrolysis kinetic model. The results in this work demonstrate the power of the ab initio nanoreactor framework for computationally affordable systematic reaction discovery and accurate kinetic modeling.

Laser pulses into bullets: tabletop shock experiments

This article discusses tabletop high-throughput laser experiments on shock waves in solids and liquids, where the more usual laser pump pulse is replaced by a 0.5 mm diameter laser-launched bullet, a thin metal disk called a flyer plate. The hypervelocity flyer (up to 6 km s^-1 or Mach 18) can have kinetic energy (∼1 J) to briefly produce extreme conditions of temperature and pressure, thousands of K and tens of GPa (1 GPa = 10 000 bar) in a small volume with a rise time <2 ns. The experiments are performed using a "shock compression microscope", a microscope fitted with the laser flyer launcher plus an optical velocimeter, a high-speed laser interferometer that measures the motion of the flyer plate or the sample material after impact. This makes it possible to generate extreme conditions at the push of a button in an intrinsically safe environment, and probe with any of the diagnostics used in microscope experiments, such as high-speed video, optical emission, nonlinear coherent spectroscopies and so on. The barrier to entering this field is relatively low since many laser laboratories already possess much of the needed instrumentation. A brief introduction to shock waves and instrumentation is presented. Then several examples of recent applications are described, including shocked water, the photophysics of fluorescent molecules under extreme conditions, shocked protein solutions, shocked metal-organic frameworks (MOFs), shocked explosives, chemical catalysis in a shocked liquid, and molecules at shocked interfaces. Since one can shoot a bullet at practically anything, there are many emerging opportunities in chemistry, biophysics, materials science, physics and hypervelocity aerodynamics.

Investigating 3,4-bis(3-nitrofurazan-4-yl)furoxan detonation with a rapidly tuned density functional tight binding model

We describe a machine learning approach to rapidly tune density functional tight binding models for the description of detonation chemistry in organic molecular materials. Resulting models enable simulations on the several 10s of ps scales characteristic to these processes, with "quantum-accuracy." We use this approach to investigate early shock chemistry in 3,4-bis(3-nitrofurazan-4-yl)furoxan, a hydrogen-free energetic material known to form onion-like nanocarbon particulates following detonation. We find that the ensuing chemistry is significantly characterized by the formation of large C_xN_yO_z species, which are likely precursors to the experimentally observed carbon condensates. Beyond utility as a means of investigating detonation chemistry, the present approach can be used to generate quantum-based reference data for the development of full machine-learned interatomic potentials capable of simulation on even greater time and length scales, i.e., for applications where characteristic time scales exceed the reach of methods including Kohn-Sham density functional theory, which are commonly used for reference data generation.

Solvation of simple ions in water at extreme conditions

The interaction of ions and water at high pressure and temperature plays a critical role in Earth and planetary science yet remains poorly understood. Aqueous fluids affect geochemical properties ranging from water phase stability to mineral solubility and reactivity. Here, we report first-principles molecular dynamics simulations of mono-valent ions (Li⁺, K⁺, Cl^-) as well as NaCl in liquid water at temperatures and pressures relevant to the Earth's upper mantle (11 GPa, 1000 K) and concentrations in the dilute limit (0.44-0.88 m), in the regime of ocean salinity. We find that, at extreme conditions, the average structural and vibrational properties of water are weakly affected by the presence of ions, beyond the first solvation shell, similar to what was observed at ambient conditions. We also find that the ionic conductivity of the liquid increases in the presence of ions by less than an order of magnitude and that the dielectric constant is moderately reduced by at most ∼10% at these conditions. Our findings may aid in the parameterization of deep earth water models developed to describe water-rock reactions.

Carbon dioxide, bicarbonate and carbonate ions in aqueous solutions under deep Earth conditions

We investigate the effect of pressure, temperature and acidity on the composition of water-rich carbon-bearing fluids under thermodynamic conditions that correspond to the Earth's deep crust and upper mantle. Our first-principles molecular dynamics simulations provide mechanistic insight into the hydration shell of carbon dioxide, bicarbonate and carbonate ions, and into the pathways of the acid/base reactions that convert these carbon species into one another in aqueous solutions. At temperatures of 1000 K and higher, our simulations can sample the chemical equilibrium of these acid/base reactions, thus allowing us to estimate the chemical composition of diluted carbon dioxide and (bi)carbonate ions as a function of acidity and thermodynamic conditions. We find that, especially at the highest temperature, the acidity of the solution is essential to determine the stability domain of CO₂vs. HCO₃^-vs. CO₃^2-.

Synthesis of functionalized nitrogen-containing polycyclic aromatic hydrocarbons and other prebiotic compounds in impacting glycine solutions

Proteinogenic amino acids can be produced on or delivered to a planet via impacting abiotic sources and consequently were likely present before the emergence of life on Earth. However, the role that these materials played in prebiotic scenarios remains an open question, in part because little is known about the survivability and reactivity of astrophysical organic compounds upon impact with a planetary surface. To this end, we use a force-matched semi-empirical quantum simulation method to study impacts of aqueous proteinogenic amino acids at conditions reaching 48 GPa and 3000 K. Here, we probe a relatively unstudied mechanism for prebiotic synthesis where sudden heating and pressurization causes condensation of complex carbon-rich structures from mixtures of glycine, the simplest protein-forming amino acid. These carbon-containing clusters are stable on short timescales and undergo a fundamental structural transition upon expansion and cooling from predominantly sp3-bonded tetrahedral-like moieties to those that are more sp2-bonded and planar. The recovered sp2-bonded structures include large nitrogen containing polycyclic aromatic hydrocarbons (NPAHs) with a number of different functional groups and embedded bonded regions akin to oligo-peptides. A number of small organic molecules with prebiotic relevance are also predicted to form. This work presents an alternate route to gas-phase synthesis for the formation of NPAHs of high complexity and highlights the significance of both the thermodynamic path and local chemical self-assembly in forming prebiotic species during shock synthesis. Our results help determine the role of comets and other celestial bodies in both the delivery and synthesis of potentially significant life building compounds on early Earth.

First principles simulation of damage to solvated nucleotides due to shock waves

We present a first-principles molecular dynamics study of the effect of shock waves (SWs) propagating in a model biological medium. We find that the SW can cause chemical modifications through varied and complex mechanisms, in particular, phosphate-sugar and sugar-base bond breaks. In addition, the SW promotes the dissociation of water molecules, thus enhancing the ionic strength of the medium. Freed protons can hydrolyze base and sugar rings previously opened by the shock. However, many of these events are only temporary, and bonds reform rapidly. Irreversible damage is observed for pressures above 15-20 GPa. These results are important to gain a better understanding of the microscopic damage mechanisms underlying cosmic-ray irradiation in space and ion-beam cancer therapy.

Ab initio spectroscopy and ionic conductivity of water under Earth mantle conditions

The phase diagram of water at extreme conditions plays a critical role in Earth and planetary science, yet remains poorly understood. Here we report a first-principles investigation of the liquid at high temperature, between 11 GPa and 20 GPa-a region where numerous controversial results have been reported over the past three decades. Our results are consistent with the recent estimates of the water melting line below 1,000 K and show that on the 1,000-K isotherm the liquid is rapidly dissociating and recombining through a bimolecular mechanism. We found that short-lived ionic species act as charge carriers, giving rise to an ionic conductivity that at 11 GPa and 20 GPa is six and seven orders of magnitude larger, respectively, than at ambient conditions. Conductivity calculations were performed entirely from first principles, with no a priori assumptions on the nature of charge carriers. Despite frequent dissociative events, we observed that hydrogen bonding persists at high pressure, up to at least 20 GPa. Our computed Raman spectra, which are in excellent agreement with experiment, show no distinctive signatures of the hydronium and hydroxide ions present in our simulations. Instead, we found that infrared spectra are sensitive probes of molecular dissociation, exhibiting a broad band below the OH stretching mode ascribable to vibrations of complex ions.

Shock response of condensed-phase RDX: molecular dynamics simulations in conjunction with the MSST method

We have performed molecular dynamics simulations in conjunction with the multiscale shock technique (MSST) to study the initial chemical processes of condensed-phase RDX under various shock velocities (8 km s⁻¹, 10 km s⁻¹ and 11 km s⁻¹).

A metastable phase of shocked bulk single crystal copper: an atomistic simulation study

Structural phase transformation in bulk single crystal Cu in different orientation under shock loading of different intensities has been investigated in this article. Atomistic simulations, such as, classical molecular dynamics using embedded atom method (EAM) interatomic potential and ab-initio based molecular dynamics simulations, have been carried out to demonstrate FCC-to-BCT phase transformation under shock loading of 〈100〉 oriented bulk single crystal copper. Simulated x-ray diffraction patterns have been utilized to confirm the structural phase transformation before shock-induced melting in Cu(100).

High pressure chemistry of thioaldehydes: A first-principles molecular dynamics study

First-principles molecular dynamics simulations are used to investigate the chemical behavior of bulk thioacetaldehyde (MeC(H)S) in response to changes in pressure, P. The simulations show that these molecules oligomerize in response to applied P. Oligomerization is initiated through C-S bond formation, with constrained dynamics simulations showing that the barrier to this reaction step is lowered significantly by applied P. Subsequent reactions involving the formation of additional C-S bonds or radical processes that lead to S-S and C-C bonds lengthen the oligomers. Oligomerization is terminated through proton transfer or the formation of rings. The mechanistic details of all reactions are examined. The results indicate that the P-induced reactivity of the MeC(H)S-based system differs significantly from that of analogous MeC(H)O-based systems, which have been reported previously. Comparison with the MeC(H)O study shows that replacing oxygen with sulfur significantly lowers the P required to initiate oligomerization (from 26 GPa to 5 GPa), increases the types of reactions in which systems of this type can take part, and increases the variety of products formed through these reactions. These differences can be explained in terms of the electronic structures of these systems, which may be useful for certain high P applications.

Laser vaporization of cirrus-like ice particles with secondary ice multiplication

We investigate the interaction of ultrashort laser filaments with individual 90-μm ice particles, representative of cirrus particles. The ice particles fragment under laser illumination. By monitoring the evolution of the corresponding ice/vapor system at up to 140,000 frames per second over 30 ms, we conclude that a shockwave vaporization supersaturates the neighboring region relative to ice, allowing the nucleation and growth of new ice particles, supported by laser-induced plasma photochemistry. This process constitutes the first direct observation of filament-induced secondary ice multiplication, a process that strongly modifies the particle size distribution and, thus, the albedo of typical cirrus clouds.

Shock melting method to determine melting curve by molecular dynamics: Cu, Pd, and Al

A melting simulation method, the shock melting (SM) method, is proposed and proved to be able to determine the melting curves of materials accurately and efficiently. The SM method, which is based on the multi-scale shock technique, determines melting curves by preheating and/or prepressurizing materials before shock. This strategy was extensively verified using both classical and ab initio molecular dynamics (MD). First, the SM method yielded the same satisfactory melting curve of Cu with only 360 atoms using classical MD, compared to the results from the Z-method and the two-phase coexistence method. Then, it also produced a satisfactory melting curve of Pd with only 756 atoms. Finally, the SM method combined with ab initio MD cheaply achieved a good melting curve of Al with only 180 atoms, which agrees well with the experimental data and the calculated results from other methods. It turned out that the SM method is an alternative efficient method for calculating the melting curves of materials.

Discovering chemistry with an ab initio nanoreactor

Chemical understanding is driven by the experimental discovery of new compounds and reactivity, and is supported by theory and computation that provides detailed physical insight. While theoretical and computational studies have generally focused on specific processes or mechanistic hypotheses, recent methodological and computational advances harken the advent of their principal role in discovery. Here we report the development and application of the ab initio nanoreactor – a highly accelerated, first-principles molecular dynamics simulation of chemical reactions that discovers new molecules and mechanisms without preordained reaction coordinates or elementary steps. Using the nanoreactor we show new pathways for glycine synthesis from primitive compounds proposed to exist on the early Earth, providing new insight into the classic Urey-Miller experiment. These results highlight the emergence of theoretical and computational chemistry as a tool for discovery in addition to its traditional role of interpreting experimental findings.

A density functional tight binding model with an extended basis set and three-body repulsion for hydrogen under extreme thermodynamic conditions

We present a new DFTB-p3b density functional tight binding model for hydrogen at extremely high pressures and temperatures, which includes a polarizable basis set (p) and a three-body environmentally dependent repulsive potential (3b). We find that use of an extended basis set is necessary under dissociated liquid conditions to account for the substantial p-orbital character of the electronic states around the Fermi energy. The repulsive energy is determined through comparison to cold curve pressures computed from density functional theory (DFT) for the hexagonal close-packed solid, as well as pressures from thermally equilibrated DFT-MD simulations of the liquid phase. In particular, we observe improved agreement in our DFTB-p3b model with previous theoretical and experimental results for the shock Hugoniot of hydrogen up to 100 GPa and 25000 K, compared to a standard DFTB model using pairwise interactions and an s-orbital basis set, only. The DFTB-p3b approach discussed here provides a general method to extend the DFTB method for a wide variety of materials over a significantly larger range of thermodynamic conditions than previously possible.

Pressure-induced metallization of condensed phase β-HMX under shock loadings via molecular dynamics simulations in conjunction with multi-scale shock technique

The electronic structure and initial decomposition in high explosive HMX under conditions of shock loading are examined. The simulation is performed using quantum molecular dynamics in conjunction with multi-scale shock technique (MSST). A self-consistent charge density-functional tight-binding (SCC-DFTB) method is adapted. The results show that the N-N-C angle has a drastic change under shock wave compression along lattice vector b at shock velocity 11 km/s, which is the main reason that leads to an insulator-to-metal transition for the HMX system. The metallization pressure (about 130 GPa) of condensed-phase HMX is predicted firstly. We also detect the formation of several key products of condensed-phase HMX decomposition, such as NO2, NO, N2, N2O, H2O, CO, and CO2, and all of them have been observed in previous experimental studies. Moreover, the initial decomposition products include H2 due to the C-H bond breaking as a primary reaction pathway at extreme condition, which presents a new insight into the initial decomposition mechanism of HMX under shock loading at the atomistic level.

Ultrafast shock initiation of exothermic chemistry in hydrogen peroxide

We report observations of shock compressed, unreacted hydrogen peroxide at pressures up to the von Neumann pressure for a steady detonation wave, using ultrafast laser-driven shock wave methods. At higher laser drive energy we find evidence of exothermic chemical reactivity occurring in less than 100 ps after the arrival of the shock wave in the sample. The results are consistent with our MD simulations and analysis and suggest that reactivity in hydrogen peroxide is initiated on a sub-100 ps time scale under conditions found just subsequent to the lead shock in a steady detonation wave.

Prebiotic chemistry within a simple impacting icy mixture

We present results of prebiotic organic synthesis in shock compressed mixtures of simple ices from quantum molecular dynamics (MD) simulations extended to close to equilibrium time scales. Given the likelihood of an inhospitable prebiotic atmosphere on early Earth, it is possible that impact processes of comets or other icy bodies were a source of prebiotic chemical compounds on the primitive planet. We observe that moderate shock pressures and temperatures within a CO2-rich icy mixture (36 GPa and 2800 K) produce a number of nitrogen containing heterocycles, which dissociate to form functionalized aromatic hydrocarbons upon expansion and cooling to ambient conditions. In contrast, higher shock conditions (48-60 GPa, 3700-4800 K) resulted in the synthesis of long carbon-chain molecules, CH4, and formaldehyde. All shock compression simulations at these conditions have produced significant quantities of simple C-N bonded compounds such as HCN, HNC, and HNCO upon expansion and cooling to ambient conditions. Our results elucidate a mechanism for impact synthesis of prebiotic molecules at realistic impact conditions that is independent of external constraints such as the presence of a catalyst, illuminating UV radiation, or pre-existing conditions on a planet.

Dynamical screening and ionic conductivity in water from ab initio simulations

We present a method to calculate ionic conductivities of complex fluids from ab initio simulations. This is achieved by combining density functional theory molecular dynamics simulations with polarization theory. Conductivities are then obtained via a Green-Kubo formula using time-dependent effective charges of electronically screened ions. The method is applied to two different phases of warm dense water. We observe large fluctuations in the effective charges; protons can transport effective charges greater than +e for ultrashort time scales. Furthermore, we compare our results with a simpler model of ionic conductivity in water that is based on diffusion coefficients. Our approach can be directly applied to study ionic conductivities of electronically insulating materials of arbitrary composition, e.g., complex molecular mixtures under such extreme conditions that occur deep inside giant planets.

New Developments in the Physical Chemistry of Shock Compression

This review discusses new developments in shock compression science with a focus on molecular media. Some basic features of shock and detonation waves, nonlinear excitations that can produce extreme states of high temperature and high pressure, are described. Methods of generating and detecting shock waves are reviewed, especially those using tabletop lasers that can be interfaced with advanced molecular diagnostics. Newer compression methods such as shockless compression and precompression shock that generate states of cold dense molecular matter are discussed. Shock compression creates a metallic form of hydrogen, melts diamond, and makes water a superionic liquid with unique catalytic properties. Our understanding of detonations at the molecular level has improved a great deal as a result of advanced nonequilibrium molecular simulations. Experimental measurements of detailed molecular behavior behind a detonation front might be available soon using femtosecond lasers to produce nanoscale simulated detonation fronts.

Anomalous sound propagation and slow kinetics in dynamically compressed amorphous carbon

We have performed molecular-dynamics simulations of dynamic compression waves propagating through amorphous carbon using the Tersoff potential and find that a variety of dynamic compression features appear for two different initial densities. These features include steady elastic shocks, steady chemically reactive shocks, unsteady elastic waves, and unsteady chemically reactive waves. We show how these features can be distinguished by analyzing time-dependent propagation speeds, time-dependent sound speeds, and comparison to multiscale shock technique (MSST) simulations. Understanding such features is a key challenge in quasi-isentropic experiments involving phase transformations. In addition to direct simulations of dynamic compression, we employ the MSST and find agreement with the direct method for this system for the shocks observed. We show how the MSST can be extended to include explicit material viscosity and demonstrate on an amorphous Lennard-Jones system.

Estimating the quantum effects from molecular vibrations of water under high pressures and temperatures

We present a simple model which estimates the influence of quantum effects from molecular vibrations on the equation of state of water under high pressures and temperatures. This model is combined with an ab initio equation of state of water generated by quantum molecular dynamics (QMD) simulations employing density functional theory for the electrons and a classical algorithm for the ions. We calculate the specific heat capacity as well as the principal Hugoniot curve, especially the Hugoniot temperature, in accordance with experiments.