Ab initio structural dynamics of pure and nitrogen-containing amorphous carbon.

Amorphous carbon (a-C) has attracted considerable interest due to its desirable properties, which are strongly dependent on its structure, density and impurities. Using ab initio molecular dynamics simulations we show that the sp2/sp3 content and underlying structural order of a-C produced via liquid quenching evolve at high temperatures and pressures on sub-nanosecond timescales. Graphite-like densities ([Formula: see text] 2.7 g/cc) favor the formation of layered arrangements characterized by sp2 disordered bonding resembling recently synthesized monolayer amorphous carbon (MAC), while at diamond-like densities ([Formula: see text] 3.3 g/cc) the resulting structures are dominated by disordered tetrahedral sp3 hybridization typical of diamond-like amorphous carbon (DLC). At intermediate densities the system is a highly compressible mixture of coexisting sp2 and sp3 regions that continue to segregate over 10's of picoseconds. The addition of nitrogen (20.3%) (a-CN) generates major system features similar with those of a-C, but has the unexpected effect of reinforcing the thermodynamically disfavored carbon structural motifs at low and high densities, while inhibiting phase separation in the intermediate region. At the same time, no nitrogen elimination from the carbon framework is observed above [Formula: see text] 2.8 g/cc, suggesting that nitrogen impurities are likely to remain embedded in the carbon structures during fast temperature quenches at high pressures.

Single-Step Mechanism for Regioselective Nitration of 9,10-BN-Napthalene with Acetyl Nitrate in the Gas Phase.

The energetics of the regioselective mononitration of 9,10-BN-naphthalene with acetyl nitrate (H3C2NO4) were modeled with ab initio simulations in the gas phase and an acetonitrile solvent. The single-electron-transfer (SET) nitration mechanism leading to a σ-complex and a single-step nitration mechanism were modeled. The energy barrier for the single-step mechanism was lower than that for the SET mechanism in the gas phase. However, the two are much more energetically competitive in the solvent. The σ-complex was found to be unstable in the gas phase owing to the interaction with the counterion. Using the single-step mechanism, the carbon site 1 nearest boron had the lowest activation energy for nitration of 22.6 kcal/mol, while site 3 had the second lowest barrier of 24.6 kcal/mol. Details on the molecular structures at intermediate and transition states as well as charges in different configurations are discussed.

Mono- and Dinitro-BN-Naphthalenes: Formation and Characterization.

Mono- and dinitro-BN-naphthalenes, i.e., 1-nitro-, 3-nitro-, 1,6-dinitro-, 3,6-dinitro-, and 1,8-dinitro-BNN, were generated in the nitration of 9,10-BN-naphthalene (BNN), a boron-nitrogen (BN) bond-embedded naphthalene, with AcONO2 and NO2BF4 in acetonitrile. The nitrated products were isolated and characterized by NMR, GC-MS, IR, and X-ray single crystallography. The effects of the nitration on the electron density and aromaticity of BNN were evaluated by B-11 NMR analysis and HOMA calculations.

Predicted Reaction Mechanisms, Product Speciation, Kinetics, and Detonation Properties of the Insensitive Explosive 2,6-Diamino-3,5-dinitropyrazine-1-oxide (LLM-105).

2,6-Diamino-3,5-dinitropyrazine-1-oxide (LLM-105) is a relatively new and promising insensitive high-explosive (IHE) material that remains only partially characterized. IHEs are of interest for a range of applications and from a fundamental science standpoint, as the root causes behind insensitivity are poorly understood. We adopt a multitheory approach based on reactive molecular dynamic simulations performed with density functional theory, density functional tight-binding, and reactive force fields to characterize the reaction pathways, product speciation, reaction kinetics, and detonation performance of LLM-105. We compare and contrast these predictions to 1,3,5-triamino-2,4,6-trinitrobenzene (TATB), a prototypical IHE, and 1,3,5,7-tetranitro-1,3,5,7-tetrazoctane (HMX), a more sensitive and higher performance material. The combination of different predictive models allows access to processes operative on progressively longer timescales while providing benchmarks for assessing uncertainties in the predictions. We find that the early reaction pathways of LLM-105 decomposition are extremely similar to TATB; they involve intra- and intermolecular hydrogen transfer. Additionally, the detonation performance of LLM-105 falls between that of TATB and HMX. We find agreement between predictive models for first-step reaction pathways but significant differences in final product formations. Predictions of detonation performance result in a wide range of values, and one-step kinetic parameters show the similar reaction rates at high temperatures for three out of four models considered.

High-Pressure Equation of State of 1,3,5-triamino-2,4,6-trinitrobenzene: Insights into the Monoclinic Phase Transition, Hydrogen Bonding, and Anharmonicity.

The high-pressure equation of state (EOS) of energetic materials (EMs) is important for continuum and mesoscale models of detonation performance and initiation safety. Obtaining a high-fidelity EOS of the insensitive EM 1,3,5-triamino-2,4,6-trinitrobenzene (TATB) has proven to be difficult because of challenges in experimental characterization at high pressures (HPs). In this work, powder X-ray diffraction patterns were fitted using the recently discovered monoclinic I2/a phase above 4 GPa, which shows that TATB is less compressible than when indexed with the triclinic P1̅ phase. First-principles calculations were performed with Perdew-Burke-Ernzerhof (PBE) and PBE0 functionals including thermal effects using the P1̅ phase. PBE0 improves the description of hydrogen bonding and thus predicts accurate planar a and b lattice parameters under ambient conditions. However, discrepancies in the predicted lattice parameters above 4-10 GPa compared with experimental measurements indexed with P1̅ are further evidence of a structural modification at high pressure. Layer sliding defects are formed during molecular dynamics simulations, which induces an anharmonic effect on the thermal expansion of the c lattice parameter. In short, the results provide several insights into determining high-fidelity EOS parameters for TATB and other molecular crystals.

Mechanochemical synthesis of glycine oligomers in a virtual rotational diamond anvil cell.

Mechanochemistry of glycine under compression and shear at room temperature is predicted using quantum-based molecular dynamics (QMD) and a simulation design based on rotational diamond anvil cell (RDAC) experiments. Ensembles of high throughput semiempirical density functional tight binding (DFTB) simulations are used to identify chemical trends and bounds for glycine chemistry during rapid shear under compressive loads of up to 15.6 GPa. Significant chemistry is found to occur during compressive shear above 10 GPa. Recovered products consist of small molecules such as water, structural analogs to glycine, heterocyclic molecules, large oligomers, and polypeptides including the simplest polypeptide glycylglycine at up to 4% mass fraction. The population and size of oligomers generally increases with pressure. A number of oligomeric polypeptide precursors and intermediates are also identified that consist of two or three glycine monomers linked together through C-C, C-N, and/or C-O bridges. Even larger oligomers also form that contain peptide C-N bonds and exhibit branched structures. Many of the product molecules exhibit one or more chiral centers. Our simulations demonstrate that athermal mechanical compressive shearing of glycine is a plausible prebiotic route to forming polypeptides.

An Isosymmetric High-Pressure Phase Transition in α-Glycylglycine: A Combined Experimental and Theoretical Study.

We investigated the effects of hydrostatic pressure on α-glycylglycine (α-digly) using a combined experimental and theoretical approach. The results of powder X-ray diffraction show a change in compressibility of the axes above 6.7 GPa, but also indicate that the structure remains in the same monoclinic space group, suggesting an isosymmetric phase transition. A noticeable change in the Raman spectra between 6 and 7.5 GPa further supports the observed phase transition. First-principles-based calculations combined with the crystal structure prediction code USPEX predict a number of possible polymorphs at high pressure. An orthorhombic structure with a bent peptide backbone is the lowest enthalpy polymorph above 6.4 GPa; however, it is not consistent with experimental observations. A second monoclinic structure isosymmetric to α-digly, α'-digly, is predicted to become more stable above 11.4 GPa. The partial atomic charges in α'-digly differ from α-digly, and the molecule is bent, possibly indicating different reactivity of α'-digly. The similarity in the lattice parameters predicted from calculations and the axial changes observed experimentally support that the α'-digly phase is likely observed at high pressure. A possible explanation for the isosymmetric phase transition is discussed in terms of relaxing strained hydrogen bonding interactions. Such combined experimental and modeling efforts provide atomic-level insight into how pressure-driven conformational changes alter hydrogen-bonding networks in complicated molecular crystals.

First-Principles Molecular Dynamics Study of a Deep Eutectic Solvent: Choline Chloride/Urea and Its Mixture with Water.

First-principles molecular dynamics simulations in the canonical ensemble at temperatures of 333 and 363 K and at the corresponding experimental densities are carried out to investigate the behavior of the 1:2 choline chloride/urea (reline) deep eutectic solvent and its equimolar mixture with water. Analysis of atom-atom radial and spatial distribution functions and of the H-bond network reveals the microheterogeneous structure of these complex liquid mixtures. In neat reline, the structure is governed by strong H-bonds of the trans- and cis-H atoms of urea to the chloride ion. In hydrous reline, water competes for the anions, and the H atoms of urea have similar propensities to bond to the chloride ions and the O atoms of urea and water. The vibrational spectra exhibit relatively broad peaks reflecting the heterogeneity of the environment. Although the 100 ps trajectories allow only for a qualitative assessment of transport properties, the simulations indicate that water is more mobile than the other species and its addition also fosters faster motion of urea.

First-Principles Monte Carlo Simulations of Reaction Equilibria in Compressed Vapors.

Predictive modeling of reaction equilibria presents one of the grand challenges in the field of molecular simulation. Difficulties in the study of such systems arise from the need (i) to accurately model both strong, short-ranged interactions leading to the formation of chemical bonds and weak interactions arising from the environment, and (ii) to sample the range of time scales involving frequent molecular collisions, slow diffusion, and infrequent reactive events. Here we present a novel reactive first-principles Monte Carlo (RxFPMC) approach that allows for investigation of reaction equilibria without the need to prespecify a set of chemical reactions and their ideal-gas equilibrium constants. We apply RxFPMC to investigate a nitrogen/oxygen mixture at T = 3000 K and p = 30 GPa, i.e., conditions that are present in atmospheric lightning strikes and explosions. The RxFPMC simulations show that the solvation environment leads to a significantly enhanced NO concentration that reaches a maximum when oxygen is present in slight excess. In addition, the RxFPMC simulations indicate the formation of NO2 and N2O in mole fractions approaching 1%, whereas N3 and O3 are not observed. The equilibrium distributions obtained from the RxFPMC simulations agree well with those from a thermochemical computer code parametrized to experimental data.

The high pressure structure and equation of state of 2,6-diamino-3,5-dinitropyrazine-1-oxide (LLM-105) up to 20 GPa: X-ray diffraction measurements and first principles molecular dynamics simulations.

Recent theoretical studies of 2,6-diamino-3,5-dinitropyrazine-1-oxide (C4H4N6O5 Lawrence Livermore Molecule No. 105, LLM-105) report unreacted high pressure equations of state that include several structural phase transitions, between 8 and 50 GPa, while one published experimental study reports equation of state (EOS) data up to a pressure of 6 GPa with no observed transition. Here we report the results of a synchrotron-based X-ray diffraction study and also ambient temperature isobaric-isothermal atomistic molecular dynamics simulations of LLM-105 up to 20 GPa. We find that the ambient pressure phase remains stable up to 20 GPa; there is no indication of a pressure induced phase transition. We do find a prominent decrease in b-axis compressibility starting at approximately 13 GPa and attribute the stiffening to a critical length where inter-sheet distance becomes similar to the intermolecular distance within individual sheets. The ambient temperature isothermal equation of state was determined through refinements of measured X-ray diffraction patterns. The pressure-volume data were fit using various EOS models to yield bulk moduli with corresponding pressure derivatives. We find very good agreement between the experimental and theoretically derived EOS.

First-principles high-pressure unreacted equation of state and heat of formation of crystal 2,6-diamino-3, 5-dinitropyrazine-1-oxide (LLM-105).

We report dispersion-corrected density functional theoretical calculations of the unreacted equation of state (EOS) of crystal 2,6-diamino-3, 5-dinitropyrazine-1-oxide (LLM-105) under hydrostatic compression of up to 45 GPa. Convergence tests for k-points sampling in the Brillouin zone show that a 3 × 1 × 2 mesh is required to reproduce the X-ray crystal structure at ambient conditions, and we confirm our finding with a separate supercell calculation. Our high-pressure EOS yields a bulk modulus of 19.2 GPa, and indicates a tendency towards anisotropic compression along the b lattice vector due to molecular orientations within the lattice. We find that the electronic energy band gap decreases from a semiconductor type of 1.3 eV at 0 GPa to quasi-metallic type of 0.6 eV at 45 GPa. The extensive intermolecular hydrogen bonds involving the oxide (-NO) and dioxide (-NO2) interactions with the amine (-NH2) group showed enhanced interactions with increasing pressure that should be discernible in the mid IR spectral region. We do not find evidence for structural phase transitions or chemically induced transformations within the pressure range of our study. The gas phase heat of formation is calculated at the G4 level of theory to be 22.48 kcal/mol, while we obtain 25.92 kcal/mol using the ccCA-PS3 method. Density functional theory calculations of the crystal and the gas phases provided an estimate for the heat of sublimation of 32.4 kcal/mol. We thus determine the room-temperature solid heat of formation of LLM-105 to be -9.9 or -6.5 kcal/mol based on the G4 or ccCA-PS3 methods, respectively.

Toward a unified picture of the water self-ions at the air-water interface: a density functional theory perspective.

The propensities of the water self-ions, H3O(+) and OH(-), for the air-water interface have implications for interfacial acid-base chemistry. Despite numerous experimental and computational studies, no consensus has been reached on the question of whether or not H3O(+) and/or OH(-) prefer to be at the water surface or in the bulk. Here we report a molecular dynamics simulation study of the bulk vs interfacial behavior of H3O(+) and OH(-) that employs forces derived from density functional theory with a generalized gradient approximation exchange-correlation functional (specifically, BLYP) and empirical dispersion corrections. We computed the potential of mean force (PMF) for H3O(+) as a function of the position of the ion in the vicinity of an air-water interface. The PMF suggests that H3O(+) has equal propensity for the interface and the bulk. We compare the PMF for H3O(+) to our previously computed PMF for OH(-) adsorption, which contains a shallow minimum at the interface, and we explore how differences in solvation of each ion at the interface vs in the bulk are connected with interfacial propensity. We find that the solvation shell of H3O(+) is only slightly dependent on its position in the water slab, while OH(-) partially desolvates as it approaches the interface, and we examine how this difference in solvation behavior is manifested in the electronic structure and chemistry of the two ions.

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.

First-principles molecular dynamics simulations of condensed-phase V-type nerve agent reaction pathways and energy barriers.

Computational studies of condensed-phase chemical reactions are challenging in part because of complexities in understanding the effects of the solvent environment on the reacting chemical species. Such studies are further complicated due to the demanding computational resources required to implement high-level ab initio quantum chemical methods when considering the solvent explicitly. Here, we use first-principles molecular dynamics simulations to examine condensed-phase decontamination reactions of V-type nerve agents in an explicit aqueous solvent. Our results include a detailed study of hydrolysis, base-hydrolysis, and nucleophilic oxidation of both VX and R-VX, as well as their protonated counterparts (i.e., VXH(+) and R-VXH(+)). The decontamination mechanisms and chemical reaction energy barriers, as determined from our simulations, are found to be in good agreement with experiment. The results demonstrate the applicability of using such simulations to assist in understanding new decontamination technologies or other applications that require computational screening of condensed-phase chemical reaction mechanisms.

Liquid structures of water, methanol, and hydrogen fluoride at ambient conditions from first principles molecular dynamics simulations with a dispersion corrected density functional.

Using first principles molecular dynamics simulations in the isobaric-isothermal ensemble (T = 300 K, p = 1 atm) with the Becke-Lee-Yang-Parr exchange/correlation functional and a dispersion correction due to Grimme, the hydrogen bonding networks of pure liquid water, methanol, and hydrogen fluoride are probed. Although an accurate density is found for water with this level of electronic structure theory, the average liquid densities for both hydrogen fluoride and methanol are overpredicted by 50 and 25%, respectively. The radial distribution functions indicate somewhat overstructured liquid phases for all three compounds. The number of hydrogen bonds per molecule in water is about twice as high as for methanol and hydrogen fluoride, though the ratio of cohesive energy over number of hydrogen bonds is lower for water. An analysis of the hydrogen-bonded aggregates revealed the presence of mostly linear chains in both hydrogen fluoride and methanol, with a few stable rings and chains spanning the simulation box in the case of hydrogen fluoride. Only an extremely small fraction of smaller clusters was found for water, indicating that its hydrogen bond network is significantly more extensive. A special form of water with on average about two hydrogen bonds per molecule yields a hydrogen-bonding environment significantly different from the other two compounds.

Understanding the surface potential of water.

We have resolved the inconsistency in quantifying the surface potential at the liquid-vapor interface when using explicit ab initio electronic charge density and effective atomic partial charge models of liquid water. This is related, in part, to the fact that the resulting electric potentials from partial-charge models and ab initio charge distributions are quite different except for those regions of space between the molecules. We show that the electrostatic surface potential from a quantum mechanical charge distribution compares well to high-energy electron diffraction and electron holography measurements, as opposed to the comparison with electrochemical measurements. We suggest that certain regions of space be excluded when comparing computed surface potentials with electrochemical measurements. This work describes a novel interpretation of ab initio computed surface potentials through high-energy electron holography measurements as useful benchmarks toward a better understanding of electrochemistry.

The mechanical properties of PCNA: implications for the loading and function of a DNA sliding clamp.

Sliding clamps are toroidal proteins that encircle DNA and act as mobile platforms for DNA replication and repair machinery. To be loaded onto DNA, the eukaryotic sliding clamp Proliferating Cell Nuclear Antigen (PCNA) must be splayed open at one of the subunit-subunit interfaces by the ATP-dependent clamp loader, Replication Factor C, whose clamp-interacting sites form a right-handed spiral. Earlier molecular dynamics (MD) studies suggested that when PCNA opens, it preferentially adopts a right-handed spiral to match the spiral of the clamp loader. Here, analysis of considerably longer MD simulations shows that although the opened form of PCNA can achieve conformations matching the helical pitch of Replication Factor C, it is not biased toward a right-handed spiral structure. A coarse-grained elastic model was also built; its strong correspondence to the all-atom MD simulations of PCNA suggests that the behavior of the open clamp is primarily due to elastic deformation governed by the topology of the clamp domains. The elastic model was further used to construct the energy landscape of the opened PCNA clamp, including conformations that would allow binding to the clamp loader and loading onto double-stranded DNA. A picture of PCNA emerges of a rather flexible protein that, once opened, is mechanically compliant in the clamp opening process.

Interfacial behavior of perchlorate versus chloride ions in aqueous solutions.

In recent years, theoretical as well as experimental studies have presented a novel view of the aqueous interface, wherein hard and/or multiply charged ions are excluded from the interface but large polarizable anions show interfacial enhancement relative to the bulk. The observed trend in the propensity of anions to adsorb at the air/water interface appears to follow an inverse order of the Hofmeister series for anions. This study focuses on experimental and theoretical examination of the partitioning behavior of perchlorate (ClO(4)(-)) and chloride (Cl(-)) ions at the air/water interface. We have used ambient pressure X-ray photoelectron spectroscopy to directly probe the interfacial concentrations of ClO(4)(-) and Cl(-) ions in sodium perchlorate and sodium chloride solutions, respectively. In the case of ClO(4)(-) ion, experimental observations are compared with molecular dynamics simulations utilizing both first principles based interaction potentials as well as polarizable classical force fields. Both the experimental and the theoretical results show enhancement of ClO(4)(-) ion at the interface, compared with the absence of such enhancement in the case of the Cl(-) ion. Our observations are in agreement with the expected trend in the interfacial propensity of anions based on the Hofmeister series.

Electronic effects on the surface potential at the vapor-liquid interface of water.

The surface potential of the vapor-liquid interface of pure water is relevant to electrochemistry, solvation thermodynamics of ions, and interfacial reactivity. The chemistry of an ion near the vapor-liquid interface is influenced by the surface potential. Indirect determinations of the surface potential have been experimentally attempted many times, yet there has been little agreement as to its magnitude and sign (-1.1 to +0.5 V). We present the first computation of the surface potential of water using ab initio molecular dynamics and find a surface potential of -18 mV with a maximum interfacial electric field of +8.9 x 10(7) V/m, which are consistent with structural data from experiment. A comparison is made between our results and those from experiments and previous molecular simulations. The associated electric field can alter interfacial reactivity and transport, while the surface potential can be used to determine the "chemical" contribution to the real and electrochemical potentials for ion transport through the vapor-liquid interface.