Machine Learning Improves Trace Explosive Selectivity: Application to Nitrate-Based Explosives.

Ion mobility spectrometry (IMS) is the method of choice to detect trace amounts of explosives in most airports and border crossing settings. For most explosives, the IMS detection limits are suitably low enough to meet security requirements. However, for some explosive families, the selectivity is not sufficient. One such family is nitrate-based explosives, where discrimination between various nitrate threats and ambient nitrates is challenging. Using a small database, machine learning methods were utilized to examine the extent of improvement in IMS selectivity for detection of nitrate-based explosives. Five classes were considered in this preliminary study: ammonium nitrate (AN), an ∼95:5 mixture of AN and fuel oil (ANFO), urea nitrate (UN), nitrate due to environmental pollution, and samples that did not contain any explosive (blanks). The preliminary results clearly show that the incorporation of machine learning methods can lead to a significant improvement in IMS selectivity.

Structure, Energies, and Vibrational Frequencies of Solvated Li(+) in Ionic Liquids: Role of Cation Type.

This study examines the structure of five ionic liquids all of them containing bis[(trifluoromethyl)sulfonyl]imide (TFSI) as the anion with five different cations: Dimethylammonium, N-propylammonium, N-methyl-1-propylpiperidinium, N-methyl-3-methylpyridinium, and N-methylpyrrolidinium. This study is based on quantum chemical calculations of structure, energetics, and vibrational spectroscopy associated with solutions of Li(+) in the five ionic liquids examined. We have shown that the Li-TFSI ion-pair stabilization is 2.5-4 fold larger than those of the ion pairs of five cations with TFSI. A large number of different species containing LikTFSInCtm (Ct represent one of five cations studied, k, n, m = 0-2) were examined in detail. The results suggest that Li-(TFSI)2 is a highly stable species and may be responsible for the transport of Li ions in these ionic liquids. The vibrational analysis suggests that the high stability of the Li-TFSI ion pair is mainly due to Coulomb interaction between the Li ion and two oxygen atoms bound to the two sulfur atoms in the TFSI anion. This O-Li-O bond exhibits stretching and bending modes that may allow monitoring of these ion pairs.

Spontaneous penetration of gold nanoparticles through the blood brain barrier (BBB).

BACKGROUND: The blood brain barrier (BBB) controls the brain microenvironment and limits penetration of the central nervous system (CNS) by chemicals, thus creating an obstacle to many medical imaging and treatment procedures. Research efforts to identify viable routes of BBB penetration have focused on structures such as micelles, polymeric nanoparticles and liposomes as drug carriers, however, many of them failed to provide unequivocal proof of BBB penetration. Here we proved that gold nanoparticles (AuNPs) penetrate the BBB in rats to reach brain regions. RESULTS: Injection of AuNPs to the abdominal cavity of rats resulted in levels of gold found in blood, urine, brain regions and body organs. After perfusion the concentration of gold in brain regions diminished dramatically indicating that most of the gold was in venous blood and not in the brain tissues. Injection of Na, K or Ca ion channel blockers reduced BBB penetration by half. A biological half-life of 12.9 ± 4.9 h was found for the gold nanoparticles. Possible mechanisms for the transport of AuNPs through the BBB are discussed. CONCLUSIONS: BBB penetration by AuNPs is spontaneous without the application of an external field. A major amount of gold resides in blood vessels therefore perfusion required. Ion channel blockers can be used to control the transport of AuNPs.

Volatile organic compounds generated by cultures of bacteria and viruses associated with respiratory infections.

Respiratory infections (RI) can be viral or bacterial in origin. In either case, the invasion of the pathogen results in production and release of various volatile organic compounds (VOCs). The present study examines the VOCs released from cultures of five viruses (influenza A, influenza B, adenovirus, respiratory syncitial virus and parainfluenza 1 virus), three bacteria (Moraxella catarrhalis, Haemophilus influenzae and Legionella pneumophila) and Mycoplasma pneumoniae isolated colonies. Our results demonstrate the involvement of inflammation-induced VOCs. Two significant VOCs were identified as associated with infectious bacterial activity, heptane and methylcyclohexane. These two VOCs have been linked in previous studies to oxidative stress effects. In order to distinguish between bacterial and viral positive cultures, we performed principal component analysis including peak identity (retention time) and VOC concentration (i.e. area under the peak) revealing 1-hexanol and 1-heptadecene to be good predictors.

Decomposition of condensed phase energetic materials: interplay between uni- and bimolecular mechanisms.

Activation energy for the decomposition of explosives is a crucial parameter of performance. The dramatic suppression of activation energy in condensed phase decomposition of nitroaromatic explosives has been an unresolved issue for over a decade. We rationalize the reduction in activation energy as a result of a mechanistic change from unimolecular decomposition in the gas phase to a series of radical bimolecular reactions in the condensed phase. This is in contrast to other classes of explosives, such as nitramines and nitrate esters, whose decomposition proceeds via unimolecular reactions both in the gas and in the condensed phase. The thermal decomposition of a model nitroaromatic explosive, 2,4,6-trinitrotoluene (TNT), is presented as a prime example. Electronic structure and reactive molecular dynamics (ReaxFF-lg) calculations enable to directly probe the condensed phase chemistry under extreme conditions of temperature and pressure, identifying the key bimolecular radical reactions responsible for the low activation route. This study elucidates the origin of the difference between the activation energies in the gas phase (~62 kcal/mol) and the condensed phase (~35 kcal/mol) of TNT and identifies the corresponding universal principle. On the basis of these findings, the different reactivities of nitro-based organic explosives are rationalized as an interplay between uni- and bimolecular processes.

Role of metal ions in the destruction of TATP: theoretical considerations.

The safe decomposition of solid TATP (triacetone triperoxide) explosive is examined theoretically. The route to destruction starts with formation of metal complexes between a metal ion and the TATP molecule. The second step is decomposition of the molecules into stable final products. We examined the structure and stability of both metal ion (including Na(+), Cu(+), Cu(2+), Co(2+), and Zn(2+)) and proton complexes with TATP using quantum chemical calculations at the DFT-PBE0 level of theory. In addition, for each ion complex, we determined the initial steps in the pathway to decomposition together with the associated transition states. We find that the products of decomposition, in particular, acetone, are also stabilized by ion metal complexes. In agreement with experiment, we find the best candidates for metal ion induced decomposition are Cu(2+) and Zn(2+).

Density-dependent liquid nitromethane decomposition: molecular dynamics simulations based on ReaxFF.

The decomposition mechanism of hot liquid nitromethane at various compressions was studied using reactive force field (ReaxFF) molecular dynamics simulations. A competition between two different initial thermal decomposition schemes is observed, depending on compression. At low densities, unimolecular C-N bond cleavage is the dominant route, producing CH(3) and NO(2) fragments. As density and pressure rise approaching the Chapman-Jouget detonation conditions (∼30% compression, >2500 K) the dominant mechanism switches to the formation of the CH(3)NO fragment via H-transfer and/or N-O bond rupture. The change in the decomposition mechanism of hot liquid NM leads to a different kinetic and energetic behavior, as well as products distribution. The calculated density dependence of the enthalpy change correlates with the change in initial decomposition reaction mechanism. It can be used as a convenient and useful global parameter for the detection of reaction dynamics. Atomic averaged local diffusion coefficients are shown to be sensitive to the reactions dynamics, and can be used to distinguish between time periods where chemical reactions occur and diffusion-dominated, nonreactive time periods.

Sublimation rate of TNT microcrystals in air.

Reliable measurements of the sublimation rate of nonuniform layers of trinitrotoluene (TNT) microcrystals were carried out using a quartz crystal microbalance (QCM). The sample layer was prepared by precipitation of TNT from a well-defined volume of its solution in acetonitrile. The TNT solution was placed on the QCM electrode surface to form the precipitated layer of TNT microcrystals. It is shown that the kinetics of small TNT particles sublimation is controlled by the molecular diffusion in air. The sublimation process is well described by simple diffusion expressions that are discussed in the literature for both individual hemispherical-shaped microcrystals and disk-shaped layers. Expressions describing particle size evolution in time were derived based on this diffusion model. It is shown that the expressions developed can be used to simulate particle sublimation in a wide size range, including very small sub-micrometer particles.

Quantum tunneling of hydrogen atom in dissociation of photoexcited methylamine.

The probability of hydrogen atom release, following photoexcitation of methylamine, CH(3)NH(2), is found to increase extensively as higher vibrational states on the first excited electronic state are accessed. This behavior is consistent with theoretical calculations, based on the probability of H atom tunneling through an energy barrier on the excited potential energy surface, implying that N-H bond breaking is dominated by quantum tunneling.

Time-dependent quantum wave-packet description of H and D atom tunneling in N-H and N-D photodissociation of methylamine and methylamine-d2.

The degree to which tunneling through a barrier in the N-H and N-D photodissociation channels of methylamine (CH3NH2) and its deuterated variant (CH3ND2), respectively, plays a role was investigated by time-dependent quantum wave-packet dynamics calculations. Two dimensional potential energy surfaces (PESs) of methylamine, presenting the N-H stretch and the HNC bend, were constructed employing multireference ab initio electronic-structure methods, allowing full description of the H motion on the HC-NH2 plane. The time-dependent Schrödinger equation was solved employing the Fourier method for calculating the Hamiltonian operation together with the Chebychev polynomial expansion of the evolution operator. The results show that tunneling and decay to vibrational resonant states on the first excited electronic PES are faster for the H atom than for the D. The decay into two of the resonant states found on the first PES strongly depends on the initially excited vibrational state on the ground electronic PES.

Raman and infrared fingerprint spectroscopy of peroxide-based explosives.

A comparative study of the vibrational spectroscopy of peroxide-based explosives is presented. Triacetone triperoxide (TATP) and hexamethyl-enetriperoxide-diamine (HMTD), now commonly used by terrorists, are examined as well as other peroxide-ring structures: DADP (diacetone diperoxide); TPTP [3,3,6,6,9,9-Hexaethyl-1,2,4,5,7,8-hexaoxo-nonane (tripentanone triperoxide)]; DCypDp {6,7,13,14-Tetraoxadispiro [4.2.4.2]tetradecane (dicyclopentanone diperoxide)}; TCypDp {6,7,15,16,22,23-Hexaoxatrispiro[4.2.4.2.4.2] henicosane (tricyclopentanone triperoxide)}; DCyhDp {7,8,15,16-tetraoxadispiro [5.2.5.2] hexadecane (dicyclohexanone diperoxide)}; and TCyhTp {7,8,14,15,21,22-hexaoxatrispiro [5.2.5.2.5.2] tetracosane (tricyclohexanone triperoxide)}. Both Raman and infrared (IR) spectra were measured and compared to theoretical calculations. The calculated spectra were obtained by calculation of the harmonic frequencies of the studied compounds, at the density functional theory (DFT) B3LYP/cc-pVDZ level of theory, and by the use of scaling factors. It is found that the vibrational features related to the peroxide bonds are strongly mixed. As a result, the spectrum is congested and highly sensitive to minor changes in the molecule.

Vibrational spectroscopy of triacetone triperoxide (TATP): anharmonic fundamentals, overtones and combination bands.

The vibrational spectrum of triacetone triperoxide (TATP) is studied by the correlation-corrected vibrational self-consistent field (CC-VSCF) method which incorporates anharmonic effects. Fundamental, overtone, and combination band frequencies are obtained by using a potential based on the PM3 method and yielding the same harmonic frequencies as DFT/cc-pVDZ calculations. Fundamentals and overtones are also studied with anharmonic single-mode (without coupling) DFT/cc-pVDZ calculations. Average deviations from experiment are similar for all methods: 2.1-2.5%. Groups of degenerate vibrations form regions of numerous combination bands with low intensity: the 5600-5800 cm(-1) region contains ca. 70 overtones and combinations of CH stretches. Anharmonic interactions are analyzed.

Enhanced Particle Swarm Optimization Algorithm: Efficient Training of ReaxFF Reactive Force Fields.

Particle swarm optimization (PSO) is a powerful metaheuristic population-based global optimization algorithm. However, when it is applied to nonseparable objective functions, its performance on multimodal landscapes is significantly degraded. Here we show that a significant improvement in the search quality and efficiency on multimodal functions can be achieved by enhancing the basic rotation-invariant PSO algorithm with isotropic Gaussian mutation operators. The new algorithm demonstrates superior performance across several nonlinear, multimodal benchmark functions compared with the rotation-invariant PSO algorithm and the well-established simulated annealing and sequential one-parameter parabolic interpolation methods. A search for the optimal set of parameters for the dispersion interaction model in the ReaxFF- lg reactive force field was carried out with respect to accurate DFT-TS calculations. The resulting optimized force field accurately describes the equations of state of several high-energy molecular crystals where such interactions are of crucial importance. The improved algorithm also presents better performance compared to a genetic algorithm optimization method in the optimization of the parameters of a ReaxFF- lg correction model. The computational framework is implemented in a stand-alone C++ code that allows the straightforward development of ReaxFF reactive force fields.

Early non-invasive detection of breast cancer using exhaled breath and urine analysis.

The main focus of this pilot study is to develop a statistical approach that is suitable to model data obtained by different detection methods. The methods used in this study examine the possibility to detect early breast cancer (BC) by exhaled breath and urine samples analysis. Exhaled breath samples were collected from 48 breast cancer patients and 45 healthy women that served as a control group. Urine samples were collected from 37 patients who were diagnosed with breast cancer based on physical or mammography tests prior to any surgery, and from 36 healthy women. Two commercial electronic noses (ENs) were used for the exhaled breath analysis. Urine samples were analyzed using Gas-Chromatography Mass-Spectrometry (GC-MS). Statistical analysis of results is based on an artificial neural network (ANN) obtained following feature extraction and feature selection processes. The model obtained allows classification of breast cancer patients with an accuracy of 95.2% ±â€¯7.7% using data of one EN, and an accuracy of 85% for the other EN and for urine samples. The developed statistical analysis method enables accurate classification of patients as healthy or with BC based on simple non-invasive exhaled breath and a urine sample analysis. This study demonstrates that available commercial ENs can be used, provided that the data analysis is carried out using an appropriate scheme.

Cavitation-Induced Synthesis of Biogenic Molecules on Primordial Earth.

Despite decades of research, how life began on Earth remains one of the most challenging scientific conundrums facing modern science. It is agreed that the first step was synthesis of organic compounds essential to obtain amino acids and their polymers. Several possible scenarios that could accomplish this step, using simple inorganic molecules, have been suggested and studied over the years. The present study examines, using atomistic reactive molecular dynamics simulations, the long-standing suggestion that natural cavitation in primordial oceans was a dominant mechanism of organic molecule synthesis. The simulations allow, for the first time, direct observation of the rich and complex sonochemistry occurring inside a collapsing bubble filled with water and dissolved gases of the early atmosphere. The simulation results suggest that dissolved CH4 is the most efficient carbon source to produce amino acids, while CO and CO2 lead to amino acid synthesis with lower yields. The efficiency of amino acid synthesis also depends on the nitrogen source used (i.e., N2, NH3) and on the presence of HCN. Moreover, cavitation may have contributed to the increase in concentration of NH3 in primordial oceans and to the production and liberation of molecular O2 into the early atmosphere. Overall, the picture that emerges from the simulations indicates that collapsing bubbles may have served as natural bioreactors in primordial oceans, producing the basic chemical ingredients required for the beginning of life.

Correction: Distinctive hippocampal zinc distribution patterns following stress exposure in an animal model of PTSD.

Correction for 'Distinctive hippocampal zinc distribution patterns following stress exposure in an animal model of PTSD' by Hagit Sela et al., Metallomics, 2017, 9, 323-333.

Distinctive hippocampal zinc distribution patterns following stress exposure in an animal model of PTSD.

Emerging evidence suggests that zinc (Zn) deficiency is associated with depression and anxiety in both human and animal studies. The present study sought to assess whether there is an association between the magnitude of behavioral responses to stress and patterns of Zn distribution. The work has focused on one case study, the association between an animal model of posttraumatic stress disorder (PTSD) and the Zn distribution in the rat hippocampus. Behaviors were assessed with the elevated plus-maze and acoustic startle response tests 7 days later. Preset cut-off criteria classified exposed animals according to their individual behavioral responses. To further characterize the distribution of Zn that occurs in the hippocampus 8 days after the exposure, laser ablation-inductively coupled plasma-mass spectrometry (LA-ICP-MS) imaging was used. It has been found that Zn distribution in the dentate gyrus (DG) sub-region in the hippocampus is clearly more widely spread for rats that belong to the extreme behavioral response (EBR) group as compared to the control group. Comparison of the Zn concentration changes in the cornu ammonis 1 (CA1) and the DG sub-regions of the hippocampus shows that the concentration changes are statistically significantly higher in the EBR rats compared to the rats in the control and minimal behavioral response (MBR) groups. In order to understand the mechanism of stress-induced hippocampal Zn dyshomeostasis, relative quantitative analyses of metallothionein (MT), B-cell lymphoma 2 (Bcl-2) and caspase 3 immunoreactivity were performed. Significant differences in the number of caspase-ir and Bcl-2 cells were found in the hippocampal DG sub-region between the EBR group and the control and MBR groups. The results of this study demonstrate a statistically significant association between the degree of behavioral disruption resulting from stress exposure and the patterns of Zn distribution and concentration changes in the various hippocampal regions. Taken together, these findings indicate that Zn distribution patterns play an active role in the neurobiological response to predator scent stress.

Bomb swab: Can trace explosive particle sampling and detection be improved?

The marked increase in international terror in recent years requires the development of highly efficient methods to detect trace amounts of explosives at airports, border crossings and check points. The preferred analytical method worldwide is the ion mobility spectrometry (IMS) that is capable of detecting most explosives at the nano-gram level. Sample collection for the IMS analysis is based on swabbing of a passenger's belongings to collect possible explosive residues. The present study examines a wide range of issues related to swab-based particle collection and analysis, in the hope of gaining deeper understanding into this technique that will serve to improve the detection process. The adhesion of explosive particles to three typical materials, plastic, metal and glass, were measured using atomic force microscopy (AFM). We found that a strong contribution of capillary forces to adhesion on glass and metal surfaces renders these substrates more promising materials upon which to find and collect explosive residues. The adhesion of explosives to different swipe materials was also examined. Here we found that Muslin, Nomex® and polyamide membrane surfaces are the most promising materials for use as swipes. Subsequently, the efficiency of multiple swipe use - for collecting explosive residues from a glass surface using Muslin, Nomex® and Teflon™ swipes - was examined. The study suggests that swipes used in about 5-10 "sampling and analysis cycles" have higher efficiency as compared to new unused swipes. The reason for this behavior was found to be related to the increased roughness of the swipe surface following a few swab measurements. Lastly, GC-MS analysis was employed to examine the nature of contaminants collected by the three types of swipe. The relative amounts of different contaminants are reported. The existence and interference of these contaminants have to be considered in relation to the detection efficiency of the various explosives by the IMS.

Oxidation mechanism of porous Zr2Fe used as a hydrogen getter.

We determined the oxidation mechanism of porous ST-198, which mainly comprises Zr2Fe. Oxidation kinetics depended on temperature, oxygen partial pressure, and oxidation extent. The passivation role of oxidation in hydrogen scavenging is probably due to the development of a surface oxide, independent of oxygen concentration. Zr2Fe would be a superior hydrogen getter in oxygen-contaminated environments at high temperatures, as most oxygen will be consumed at the outer shell by mass transfer limitations, protecting the bulk of the getter for hydrogen scavenging.

Role of vibrationally excited NO in promoting electron emission when colliding with a metal surface: a nonadiabatic dynamic model.

A nonadiabatic quantum dynamic model has been developed to study the process of electron emission from a low-work-function metal surface. The process is initiated by scattering a highly vibrationally excited NO molecule from a surface composed of a Cs layer covering a Ru crystal. The model addresses the increasing quantum yield of the electron emission as a function of the molecular vibrational excitation and incident kinetic energy. The reaction mechanism is identified as a long-range harpooning electron transfer to a molecular ion which is then accelerated toward the surface. Upon impact, the molecular ion emits its excess electron.