New Mechanistic Insights into the Primary Thermolysis Reactions of 1,3,4,6-Tetranitrooctahydroimidazo-[4,5-d]imidazole (BCHMX) from Predictive Local Coupled Cluster Calculations.

Theoretical studies of the decomposition mechanism of energetic materials quite often scrutinize only the primary thermolysis reactions. However, the secondary reactions are crucial, inter alia, for proper building of the combustion models and understanding the autocatalytic processes. In the present study, we applied predictive DLPNO-CCSD(T) calculations to elucidate the kinetics and decomposition mechanism of a novel promising energetic material, 1,3,4,6-tetranitrooctahydroimidazo [4,5-d] imidazole (BCHMX). We identified eight previously unknown BCHMX conformers, both cis and trans in accordance to the spatial position of the H atoms bonded to a carbon bridge. Among them, the relative enthalpies of cis isomers lie in the narrow range ∼10 kJ mol-1 rendering them thermally accessible in the course of decomposition. The radical N-NO2 bond cleavage via one of the novel conformers is the dominant primary decomposition channel of BCHMX with the kinetic parameters Ea = 168.4 kJ mol-1 and log(A, s-1) = 18.5. We also resolved several contradictory assumptions on the mechanism and key intermediates of BCHMX thermolysis. To get a deeper understanding of the decomposition mechanism, we examined a series of unimolecular and bimolecular secondary channels of BCHMX. Among the former reactions, the C-C bond unzipping followed by another radical elimination of a nitro group is the most energetically favorable pathway with an activation barrier ∼113 kJ mol-1. However, contrary to the literature assumptions, the bimolecular H atom abstraction from a pristine BCHMX molecule by a primary nitramine radical product, not the nitro one, followed by another NO2 radical elimination, is the most important bimolecular secondary thermolysis reaction of BCHMX at lower temperatures. The isokinetic temperature of the bimolecular and unimolecular secondary reactions is ∼620 K. Unimolecular reactions might be important in dilute solutions, where bimolecular reactions are suppressed. The secondary reactions considered in the present work might be pertinent in the case of related energetic nitramines (e.g., RDX, HMX, and CL-20).

Synthesis, Characterization, and Properties of High-Energy Fillers Derived from Nitroisobutylglycerol.

Herein we report a comprehensive laboratory synthesis of a series of energetic azidonitrate derivatives (ANDP, SMX, AMDNNM, NIBTN, NPN, 2-nitro-1,3-dinitro-oxypropane) starting from the readily available nitroisobutylglycerol. This simple protocol allows obtaining the high-energy additives from the available precursor in yields higher than those reported using safe and simple operations not presented in previous works. A detailed characterization of the physical, chemical, and energetic properties including impact sensitivity and thermal behavior of these species was performed for the systematic evaluation and comparison of the corresponding class of energetic compounds.

Thermochemistry, Tautomerism, and Thermal Stability of 5,7-Dinitrobenzotriazoles.

Nitro derivatives of benzotriazoles are safe energetic materials with remarkable thermal stability. In the present study, we report on the kinetics and mechanism of thermal decomposition for 5,7-dinitrobenzotriazole (DBT) and 4-amino-5,7-dinitrobenzotriazole (ADBT). The pressure differential scanning calorimetry was employed to study the decomposition kinetics of DBT experimentally because the measurements under atmospheric pressure are disturbed by competing evaporation. The thermolysis of DBT in the melt is described by a kinetic scheme with two global reactions. The first stage is a strong autocatalytic process that includes the first-order reaction (Ea1I = 173.9 ± 0.9 kJ mol-1, log(A1I/s-1) = 12.82 ± 0.09) and the catalytic reaction of the second order with Ea2I = 136.5 ± 0.8 kJ mol-1, log(A2I/s-1) = 11.04 ± 0.07. The experimental study was complemented by predictive quantum chemical calculations (DLPNO-CCSD(T)). The calculations reveal that the 1H tautomer is the most energetically preferable form for both DBT and ADBT. Theory suggests the same decomposition mechanisms for DBT and ADBT, with the most favorable channels being nitro-nitrite isomerization and C-NO2 bond cleavage. The former channel has lower activation barriers (267 and 276 kJ mol-1 for DBT and ADBT, respectively) and dominates at lower temperatures. At the same time, due to the higher preexponential factor, the radical bond cleavage, with reaction enthalpies of 298 and 320 kJ mol-1, dominates in the experimental temperature range for both DBT and ADBT. In line with the theoretical predictions of C-NO2 bond energies, ADBT is more thermally stable than DBT. We also determined a reliable and mutually consistent set of thermochemical values for DBT and ADBT by combining the theoretically calculated (W1-F12 multilevel procedure) gas-phase enthalpies of formation and experimentally measured sublimation enthalpies.

Autocatalytic decomposition of energetic materials: interplay of theory and thermal analysis in the study of 5-amino-3,4-dinitropyrazole thermolysis.

A reliable kinetic description of the thermal stability of energetic materials (EM) is very important for safety and storage-related problems. Among other pertinent issues, autocatalysis very often complicates the decomposition kinetics of EM. In the present study, the kinetics and decomposition mechanism of a promising energetic compound, 5-amino-3,4-dinitro-1H-pyrazole (5-ADP) were studied using a set of complementary experimental (e.g., differential scanning calorimetry in the solid state, melt, and solution along with advanced thermokinetic models, accelerating rate calorimetry, and evolved gas analysis) and theoretical techniques (CCSD(T)-F12 and DLPNO-CCSD(T) predictive quantum chemical calculations). The experimental study revealed that the strong acceleration of the decomposition rate of 5-ADP is caused by two factors: the progressive liquefaction of the sample directly observed using in situ optical microscopy, and the autocatalysis by reaction products. For the first time, the processing of the non-isothermal data was performed with a formal Manelis-Dubovitsky kinetic model that accounts for both factors. With the aid of quantum chemical calculations, we have rationalized the autocatalysis present in the formal kinetic models at the molecular level. Theory revealed an unusual primary decomposition channel of 5-ADP, viz., the two subsequent sigmatropic H-shifts in the pyrazole ring followed by the C-NO2 bond scission yielding a pyrazolyl and nitrogen dioxide radicals as simple primary products. Moreover, we found the secondary reactions of the latter radical with the 5-ADP to be kinetically unimportant. On the contrary, the substituted pyrazolyl radical turned out to undergo a facile addition to 5-ADP, followed by a fast exothermic elimination of another ˙NO2 species. We believe the latter process to contribute remarkably to the observed autocatalytic behavior of 5-ADP. Most importantly, the calculations provide detailed mechanistic evidence complementing the thermoanalytical experiment and formal kinetic models.

High-pressure crystallography shows noble gas intervention into protein-lipid interaction and suggests a model for anaesthetic action.

In this work we examine how small hydrophobic molecules such as inert gases interact with membrane proteins (MPs) at a molecular level. High pressure atmospheres of argon and krypton were used to produce noble gas derivatives of crystals of three well studied MPs (two different proton pumps and a sodium light-driven ion pump). The structures obtained using X-ray crystallography showed that the vast majority of argon and krypton binding sites were located on the outer hydrophobic surface of the MPs - a surface usually accommodating hydrophobic chains of annular lipids (which are known structural and functional determinants for MPs). In conformity with these results, supplementary in silico molecular dynamics (MD) analysis predicted even greater numbers of argon and krypton binding positions on MP surface within the bilayer. These results indicate a potential importance of such interactions, particularly as related to the phenomenon of noble gas-induced anaesthesia.

Learning to fly: thermochemistry of energetic materials by modified thermogravimetric analysis and highly accurate quantum chemical calculations.

The standard state enthalpy of formation and the enthalpy of sublimation are essential thermochemical parameters determining the performance and application prospects of energetic materials (EM). Direct experimental measurements of these properties are complicated by low volatility and high heat release in bomb calorimetry experiments. As a result, the uncertainties in the reported enthalpies of formation for a number of even well-known CHNO-containing compounds might amount up to tens kJ mol-1, while for some novel high-nitrogen molecules they reach even hundreds of kJ mol-1. The present study reports a facile approach to determining the solid-state formation enthalpies comprised of complementary high-level quantum chemical calculations of the gas-phase thermochemistry and advanced thermal analysis techniques yielding sublimation enthalpies. The thermogravimetric procedure for the measurement of sublimation enthalpy was modified by using low external pressures (down to 0.2 Pa). This allows for observing sublimation/vaporization instead of thermal decomposition of the compounds studied. Extensive benchmarking on nonenergetic and energetic compounds reveals the average and maximal absolute errors of the sublimation enthalpies of 3.3 and 11.0 kJ mol-1, respectively. The comparison of the results with those obtained from the widely used Trouton-Williams empirical equation shows that the latter underestimates the sublimation enthalpy up to 140 kJ mol-1. Therefore, we performed a reparametrization of the latter equation with simple chemical descriptors that reduces the mean error down to 30 kJ mol-1. Highly accurate multi-level procedures W2-F12 and/or W1-F12 in conjunction with the atomization energy approach were used to calculate theoretically the gas-phase formation enthalpies. In several cases, the DLPNO-CCSD(T) enthalpies of isodesmic reactions were also employed to obtain the gas-phase thermochemistry for medium-sized important EMs. Combining the obtained thermochemical properties, we determined the solid-state enthalpies of formation for nearly 60 species containing various important explosophoric groups, from common nitroaromatics, nitroethers, and nitramines to novel nitrogen-rich heterocyclic species (e.g., the derivatives of pyrazole, tetrazole, furoxan, etc.). The large-scale benchmarking against the available experimental solid-state enthalpies of formation yielded the maximal inaccuracy of the proposed method of 25 kJ mol-1.

Molecular model of a sensor of two-component signaling system.

Two-component systems (TCS) are widespread signaling systems present in all domains of life. TCS typically consist of a signal receptor/transducer and a response regulator. The receptors (histidine kinases, chemoreceptors and photoreceptors) are often embedded in the membrane and have a similar modular structure. Chemoreceptors were shown to function in highly ordered arrays, with trimers of dimers being the smallest functional unit. However, much less is known about photoreceptors. Here, we use small-angle scattering (SAS) to show that detergent-solubilized sensory rhodopsin II in complex with its cognate transducer forms dimers at low salt concentration, which associate into trimers of dimers at higher buffer molarities. We then fit an atomistic model of the whole complex into the SAS data. The obtained results suggest that the trimer of dimers is "tripod"-shaped and that the contacts between the dimers occur only through their cytoplasmic regions, whereas the transmembrane regions remain unconnected.

Nitro-, Cyano-, and Methylfuroxans, and Their Bis-Derivatives: From Green Primary to Melt-Cast Explosives.

In the present work, we studied in detail the thermochemistry, thermal stability, mechanical sensitivity, and detonation performance for 20 nitro-, cyano-, and methyl derivatives of 1,2,5-oxadiazole-2-oxide (furoxan), along with their bis-derivatives. For all species studied, we also determined the reliable values of the gas-phase formation enthalpies using highly accurate multilevel procedures W2-F12 and/or W1-F12 in conjunction with the atomization energy approach and isodesmic reactions with the domain-based local pair natural orbital (DLPNO) modifications of the coupled-cluster techniques. Apart from this, we proposed reliable benchmark values of the formation enthalpies of furoxan and a number of its (azo)bis-derivatives. Additionally, we reported the previously unknown crystal structure of 3-cyano-4-nitrofuroxan. Among the monocyclic compounds, 3-nitro-4-cyclopropyl and dicyano derivatives of furoxan outperformed trinitrotoluene, a benchmark melt-cast explosive, exhibited decent thermal stability (decomposition temperature >200 °C) and insensitivity to mechanical stimuli while having notable volatility and low melting points. In turn, 4,4'-azobis-dicarbamoyl furoxan is proposed as a substitute of pentaerythritol tetranitrate, a benchmark brisant high explosive. Finally, the application prospects of 3,3'-azobis-dinitro furoxan, one of the most powerful energetic materials synthesized up to date, are limited due to the tremendously high mechanical sensitivity of this compound. Overall, the investigated derivatives of furoxan comprise multipurpose green energetic materials, including primary, secondary, melt-cast, low-sensitive explosives, and an energetic liquid.

Sensor Histidine Kinase NarQ Activates via Helical Rotation, Diagonal Scissoring, and Eventually Piston-Like Shifts.

Membrane-embedded sensor histidine kinases (HKs) and chemoreceptors are used ubiquitously by bacteria and archaea to percept the environment, and are often crucial for their survival and pathogenicity. The proteins can transmit the signal from the sensor domain to the catalytic kinase domain reliably over the span of several hundreds of angstroms, and regulate the activity of the cognate response regulator proteins, with which they form two-component signaling systems (TCSs). Several mechanisms of transmembrane signal transduction in TCS receptors have been proposed, dubbed (swinging) piston, helical rotation, and diagonal scissoring. Yet, despite decades of studies, there is no consensus on whether these mechanisms are common for all TCS receptors. Here, we extend our previous work on Escherichia coli nitrate/nitrite sensor kinase NarQ. We determined a crystallographic structure of the sensor-TM-HAMP fragment of the R50S mutant, which, unexpectedly, was found in a ligand-bound-like conformation, despite an inability to bind nitrate. Subsequently, we reanalyzed the structures of the ligand-free and ligand-bound NarQ and NarX sensor domains, and conducted extensive molecular dynamics simulations of ligand-free and ligand-bound wild type and mutated NarQ. Based on the data, we show that binding of nitrate to NarQ causes, first and foremost, helical rotation and diagonal scissoring of the α-helices at the core of the sensor domain. These conformational changes are accompanied by a subtle piston-like motion, which is amplified by a switch in the secondary structure of the linker between the sensor and TM domains. We conclude that helical rotation, diagonal scissoring, and piston are simply different degrees of freedom in coiled-coil proteins and are not mutually exclusive in NarQ, and likely in other nitrate sensors and TCS proteins as well.

Pelagic occurrences of the ice amphipod Apherusa glacialis throughout the Arctic.

Apherusa glacialis is a common, sea ice-associated amphipod found throughout the Arctic Ocean and has long been considered permanently associated with the sea ice habitat. However, pelagic occurrences of A. glacialis have also been reported. It was recently suggested that A. glacialis overwinters at depth within the Atlantic-water inflow near Svalbard, to avoid being exported out of the Arctic Ocean through the Fram Strait. This study collated pelagic occurrence records over a 71-year period and found that A. glacialis was consistently found away from its presumed sea ice habitat on a pan-Arctic scale, in different depths and water masses. In the Svalbard region, A. glacialis was found in Atlantic Water both in winter and summer. Additionally, we analyzed A. glacialis size distributions throughout the year, collected mostly from sea ice, in order to elucidate potential life cycle strategies. The majority of young-of-the-year A. glacialis was found in the sea ice habitat during spring, supporting previous findings. Data on size distributions and sex ratios suggest a semelparous lifestyle. A synchronous seasonal vertical migration was not evident, but our data imply a more complex life history than previously assumed. We provide evidence that A. glacialis can no longer be regarded as an autochthonous sympagic species.

The complex analysis of X-ray mesh scans for macromolecular crystallography.

In macromolecular crystallography, mesh (raster) scans are carried out either as part of X-ray-based crystal-centring routines or to identify positions on the sample holder from which diffraction images can be collected. Here, the methods used in MeshBest, software which automatically analyses diffraction images collected during a mesh scan and produces a two-dimensional crystal map showing estimates of the dimensions, centre positions and diffraction qualities of each crystal contained in the mesh area, are presented. Sample regions producing diffraction images resulting from the superposition of more than one crystal are also distinguished from regions with single-crystal diffraction. The applicability of the method is demonstrated using several cases.

Sea ice meiofauna distribution on local to pan-Arctic scales.

Arctic sea ice provides microhabitats for biota that inhabit the liquid-filled network of brine channels and the ice-water interface. We used meta-analysis of 23 published and unpublished datasets comprising 721 ice cores to synthesize the variability in composition and abundance of sea ice meiofauna at spatial scales ranging from within a single ice core to pan-Arctic and seasonal scales. Two-thirds of meiofauna individuals occurred in the bottom 10 cm of the ice. Locally, replicate cores taken within meters of each other were broadly similar in meiofauna composition and abundance, while those a few km apart varied more; 75% of variation was explained by station. At the regional scale (Bering Sea first-year ice), meiofauna abundance varied over two orders of magnitude. At the pan-Arctic scale, the same phyla were found across the region, with taxa that have resting stages or tolerance to extreme conditions (e.g., nematodes and rotifers) dominating abundances. Meroplankton, however, was restricted to nearshore locations and landfast sea ice. Light availability, ice thickness, and distance from land were significant predictor variables for community composition on different scales. On a seasonal scale, abundances varied broadly for all taxa and in relation to the annual ice algal bloom cycle in both landfast and pack ice. Documentation of ice biota composition, abundance, and natural variability is critical for evaluating responses to decline in Arctic sea ice. Consistent methodology and protocols must be established for comparability of meiofauna monitoring across the Arctic. We recommend to (1) increase taxonomic resolution of sea ice meiofauna, (2) focus sampling on times of peak abundance when seasonal sampling is impossible, (3) include the bottom 30 cm of ice cores rather than only bottom 10 cm, (4) preserve specimens for molecular analysis to improve taxonomic resolution, and (5) formulate a trait-based framework that relates to ecosystem functioning.

Inward H+ pump xenorhodopsin: Mechanism and alternative optogenetic approach.

Generation of an electrochemical proton gradient is the first step of cell bioenergetics. In prokaryotes, the gradient is created by outward membrane protein proton pumps. Inward plasma membrane native proton pumps are yet unknown. We describe comprehensive functional studies of the representatives of the yet noncharacterized xenorhodopsins from Nanohaloarchaea family of microbial rhodopsins. They are inward proton pumps as we demonstrate in model membrane systems, Escherichia coli cells, human embryonic kidney cells, neuroblastoma cells, and rat hippocampal neuronal cells. We also solved the structure of a xenorhodopsin from the nanohalosarchaeon Nanosalina (NsXeR) and suggest a mechanism of inward proton pumping. We demonstrate that the NsXeR is a powerful pump, which is able to elicit action potentials in rat hippocampal neuronal cells up to their maximal intrinsic firing frequency. Hence, inwardly directed proton pumps are suitable for light-induced remote control of neurons, and they are an alternative to the well-known cation-selective channelrhodopsins.

Fast iodide-SAD phasing for high-throughput membrane protein structure determination.

We describe a fast, easy, and potentially universal method for the de novo solution of the crystal structures of membrane proteins via iodide-single-wavelength anomalous diffraction (I-SAD). The potential universality of the method is based on a common feature of membrane proteins-the availability at the hydrophobic-hydrophilic interface of positively charged amino acid residues with which iodide strongly interacts. We demonstrate the solution using I-SAD of four crystal structures representing different classes of membrane proteins, including a human G protein-coupled receptor (GPCR), and we show that I-SAD can be applied using data collection strategies based on either standard or serial x-ray crystallography techniques.

Mechanism of transmembrane signaling by sensor histidine kinases.

One of the major and essential classes of transmembrane (TM) receptors, present in all domains of life, is sensor histidine kinases, parts of two-component signaling systems (TCSs). The structural mechanisms of TM signaling by these sensors are poorly understood. We present crystal structures of the periplasmic sensor domain, the TM domain, and the cytoplasmic HAMP domain of the Escherichia coli nitrate/nitrite sensor histidine kinase NarQ in the ligand-bound and mutated ligand-free states. The structures reveal that the ligand binding induces rearrangements and pistonlike shifts of TM helices. The HAMP domain protomers undergo leverlike motions and convert these pistonlike motions into helical rotations. Our findings provide the structural framework for complete understanding of TM TCS signaling and for development of antimicrobial treatments targeting TCSs.