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.

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.

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.

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.

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.

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.

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.

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.

QM/MM metadynamics study of the direct decarboxylation mechanism for orotidine-5'-monophosphate decarboxylase using two different QM regions: acceleration too small to explain rate of enzyme catalysis.

Despite decades of study, the mechanism by which orotidine-5'-monophosphate decarboxylase (ODCase) catalyzes the decarboxylation of orotidine monophosphate remains unresolved. A computational investigation of the direct decarboxylation mechanism has been performed using mixed quantum mechanical/molecular mechanical (QM/MM) dynamics simulations. The study was performed with the program CP2K that integrates classical dynamics and ab initio dynamics based on the Born-Oppenheimer approach. Two different QM regions were explored. The free energy barriers for direct decarboxylation of orotidine-5'-monophosphate (OMP) in solution and in the enzyme (using the larger QM region) were determined with the metadynamics method to be 40 and 33 kcal/mol, respectively. The calculated change in activation free energy (DeltaDeltaG++) on going from solution to the enzyme is therefore -7 kcal/mol, far less than the experimental change of -23 kcal/ mol (for k(cat.)/k(uncat.): Radzicka, A.; Wolfenden, R., Science 1995, 267, 90-92). These results do not support the direct decarboxylation mechanism that has been proposed for the enzyme. However, in the context of QM/MM calculations, it was found that the size of the QM region has a dramatic effect on the calculated reaction barrier.

Molecular dynamics simulation of liquid water: hybrid density functionals.

The structure, dynamical, and electronic properties of liquid water utilizing different hybrid density functionals were tested within the plane wave framework of first-principles molecular dynamics simulations. The computational approach, which employs modified functionals with short-ranged Hartree-Fock exchange, was first tested in calculations of the structural and bonding properties of the water dimer and cyclic water trimer. Liquid water simulations were performed at the state point of 350 K at the experimental density. Simulations included three different hybrid functionals, a meta-functional, four gradient-corrected functionals, and the local density and Hartree-Fock approximations. It is found that hybrid functionals are superior in reproducing the experimental structure and dynamical properties as measured by the radial distribution function and self-diffusion constant when compared to the pure density functionals. The local density and Hartree-Fock approximations show strongly over- and understructured liquids, respectively. Hydrogen bond analysis shows that the hybrid functionals give slightly smaller average numbers of hydrogen bonds than pure density functionals but similar hydrogen bond populations. The average molecular dipole moments in the liquid from the three hybrid functionals are lower than those of the corresponding pure density functionals.

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.

The Effect of Polarizability for Understanding the Molecular Structure of Aqueous Interfaces.

A review is presented on recent progress of the application of molecular dynamics simulation methods with the inclusion of polarizability for the understanding of aqueous interfaces. Comparisons among a variety of models, including those based on density functional theory of the neat air-water interface, are given. These results are used to describe the effect of polarizability on modeling the microscopic structure of the neat air-water interface, including comparisons with recent spectroscopic studies. Also, the understanding of the contribution of polarization to the electrostatic potential across the air-water interface is elucidated. Finally, the importance of polarizability for understanding anion transfer across an organic-water interface is shown.

Time-Dependent Properties of Liquid Water: A Comparison of Car-Parrinello and Born-Oppenheimer Molecular Dynamics Simulations.

A series of 30 ps first principles molecular dynamics simulations in the microcanonical ensemble were carried out to investigate transport and vibrational properties of liquid water. To allow for sufficient sampling, the thermodynamic constraints were set to an elevated temperature of around 423 K and a density of 0.71 g cm(-)(3) corresponding to the saturated liquid density for the Becke-Lee-Yang-Parr (BLYP) representation of water. Four simulations using the Car-Parrinello molecular dynamics (CPMD) technique with varying values of the fictitious electronic mass (µ) and two simulations using the Born-Oppenheimer molecular dynamics (BOMD) technique are analyzed to yield structural and dynamical information. At the selected state point, the simulations are found to exhibit nonglassy dynamics and yield consistent results for the liquid structure and the self-diffusion coefficient, although the statistical uncertainties in the latter quantity are quite large. Consequently, it can be said that the CPMD and BOMD methods produce equivalent results for these properties on the time scales reported here. However, it was found that the choice of µ affects the frequency spectrum of the intramolecular modes, shifting them slightly to regions of lower frequency. Using a value of µ = 400 au results in a significant drift in the electronic kinetic energy of the system over the course of 30 ps and a downward drift in the ionic temperature. Therefore, for long trajectories at elevated temperatures, lower values of this parameter are recommended for CPMD simulations of water.

Simulating fluid-phase equilibria of water from first principles.

Efficient Monte Carlo algorithms and a mixed-basis set electronic structure program were used to compute from first principles the vapor-liquid coexistence curve of water. A water representation based on the Becke-Lee-Yang-Parr exchange and correlation functionals yields a saturated liquid density of 900 kg/m3 at 323 K and normal boiling and critical temperatures of 350 and 550 K, respectively. An analysis of the structural and electronic properties of the saturated liquid phase shows an increase of the asymmetry of the local hydrogen-bonded structure despite the persistence of a 4-fold coordination and decreases of the molecular dipole moment and of the spread of the lowest unoccupied molecular orbital with increasing temperature.

Bonding in the superionic phase of water.

The predicted superionic phase of water is investigated via ab initio molecular dynamics at densities of 2.0--3.0 g/cc (34-115 GPa) along the 2000 K isotherm. We find that extremely rapid (superionic) diffusion of protons occurs in a fluid phase at pressures between 34 and 58 GPa. A transition to a stable body-centered cubic O lattice with superionic proton conductivity is observed between 70 and 75 GPa, a much higher pressure than suggested in prior work. We find that all molecular species at pressures greater than 75 GPa are too short lived to be classified as bound states. Up to 95 GPa, we find a solid superionic phase characterized by covalent O-H bonding. Above 95 GPa, a transient network phase is found characterized by symmetric O-H hydrogen bonding with nearly 50% covalent character. In addition, we describe a metastable superionic phase with quenched O disorder.

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.