Comparison of real-time and droplet digital PCR to detect and quantify SARS-CoV-2 RNA in plasma.

BACKGROUND: The presence of SARS-CoV-2 RNA in plasma has been linked to disease severity and mortality. We compared RT-qPCR to droplet digital PCR (ddPCR) to detect SARS-CoV-2 RNA in plasma from COVID-19 patients (mild, moderate, and critical disease). METHODS: The presence/concentration of SARS-CoV-2 RNA in plasma was compared in three groups of COVID-19 patients (30 outpatients, 30 ward patients and 30 ICU patients) using both RT-qPCR and ddPCR. Plasma was obtained in the first 24h following admission, and RNA was extracted using eMAG. ddPCR was performed using Bio-Rad SARS-CoV-2 detection kit, and RT-qPCR was performed using GeneFinder™ COVID-19 Plus RealAmp Kit. Statistical analysis was performed using Statistical Package for the Social Science. RESULTS: SARS-CoV-2 RNA was detected, using ddPCR and RT-qPCR, in 91% and 87% of ICU patients, 27% and 23% of ward patients and 3% and 3% of outpatients. The concordance of the results obtained by both methods was excellent (Cohen's kappa index = 0.953). RT-qPCR was able to detect 34/36 (94.4%) patients positive for viral RNA in plasma by ddPCR. Viral RNA load was higher in ICU patients compared with the other groups (P < .001), by both ddPCR and RT-qPCR. AUC analysis revealed Ct values (RT-qPCR) and viral RNA load values (ddPCR) can similarly differentiate between patients admitted to wards and to the ICU (AUC of 0.90 and 0.89, respectively). CONCLUSION: Both methods yielded similar prevalence of RNAemia between groups, with ICU patients showing the highest (>85%). RT-qPCR was as useful as ddPCR to detect and quantify SARS-CoV-2 RNAemia in plasma.

Photoinduced Intermolecular Electron Transfer in Gas Phase Ion Pairs of the 1-Ethyl-3-methylimidazolium Cation and the Bis(trifluoromethylsulfonyl)imide Anion.

In this study, the UV photodissociation of gas phase ion pairs of the ionic liquid 1-ethyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide, [emim]+[tf2n]-, is shown to proceed primarily through radical intermediates. [emim]+[tf2n]- ion pairs have been shown previously to undergo two-photon-dependent dissociation, but the mechanisms of this have not been probed in detail. By employing a two-laser pump probe spectroscopy and time-dependent density functional theory (TD-DFT) calculations, we have illustrated that one of the major UV photodissociation pathways in [emim]+[tf2n]- ion pairs is an intermolecular electron transfer wherein the anion transfers an electron to the cation resulting in two neutral open-shelled products. These products were observable for at least 1.6 µs post photodissociation, the experimental limit, via detection of the [emim]+ cation. This data demonstrates that the likely photoproducts of [emim]+[tf2n]- UV photodissociation are two neutral species that separate spatially, demonstrated through lack of observed relaxation pathways such as electron recombination. TD-DFT and frontier molecular orbital analysis calculations at the MN15/6-311++G(d,p) level are employed to aid in identifying excited state characteristics and support the interpretations of the experimental data. The energetic onset of the intermolecular electron transfer is consistent with previously observed [emim]+[tf2n]- absorption spectra in the bulk and gas phases. The similarities between bulk and gas phase UV spectra imply that this electron-transfer pathway may be a major photodissociation channel in both phases.

Theoretical Investigation of the Reactivity of Sodium Dicyanamide with Nitric Acid.

There is a need to replace current hydrazine fuels with safer propellants, and dicyanamide (DCA-)-based systems have emerged as promising alternatives because they autoignite when mixed with some oxidizers. Previous studies of the hypergolic reaction mechanism have focused on the reaction between DCA- and the oxidizer HNO3; here, we compare the calculated pathway of DCA- + HNO3 with the reaction coordinate of the ion pair sodium dicyanamide with nitric acid, Na[DCA] + HNO3. Enthalpies and free energies are calculated in the gas phase and in solution using a quantum mechanical continuum solvation model, SMD-GIL. The barriers to the Na[DCA] + HNO3 reaction are dramatically lowered relative to those of the reaction with the bare anion, and an exothermic exit channel to produce NaNO3 and the reactive intermediate HDCA appears. These results suggest that Na[DCA] may accelerate the ignition reaction.

Hydroxyl Radical Fluorescence and Quantum Yield Following Lyman-α Photoexcitation of Water Vapor in a Room Temperature Cell and Cooled in a Supersonic Expansion.

Photoexcitation of water by Lyman-α (121.6 nm) induces a dissociation reaction that produces OH(A2Σ+) + H. Despite this reaction being part of numerous studies, a combined understanding of the product and fluorescence yields is still lacking. Here, the rotational and vibrational distributions of OH(A) are determined from dispersed fluorescence following photoexcitation of both room-temperature and jet-cooled water vapor, for the first time in the same experiment. This work compares new data of state-resolved fluorescence with literature molecular branching ratios and brings previous studies into agreement through careful consideration of OH(A) fluorescent and predissociation lifetimes and confirms a fluorescent quantum yield of 8%. Comparison of the room-temperature and jet-cooled OH(A) populations indicate the temperature of H2O prior to excitation has subtle effects on the OH(A) population distribution, such as altering the rotational distribution in the ν' = 0 population and affecting the population in the ν' = 1 state. These results indicate jet-cooled water vapor may have a 1% higher fluorescence quantum yield compared to room-temperature water vapor.

Identification of multiple conformers of the ionic liquid [emim][tf2n] in the gas phase using IR/UV action spectroscopy.

In this study we investigate the effect of deuteration and molecular beam temperature on the hydrogen bond in the ionic liquid [emim][tf2n]. Using IR/UV double resonance spectroscopy, we probe the microscopic structure of the [emim][tf2n] ion pair and its mono-deuterated, [emim-d1][tf2n], analog. Comparisons of the infrared absorption frequencies between these two species show that there are multiple conformers of the ion pair present in the gas phase and trapped through the molecular beam cooling process. Furthermore, each conformer has a characteristic red shift in the frequency of its C2-H group that reveals the variation in strength of a hydrogen bond between the cation and anion.

Further studies into the photodissociation pathways of 2-bromo-2-nitropropane and the dissociation channels of the 2-nitro-2-propyl radical intermediate.

These experiments investigate the decomposition mechanisms of geminal dinitro energetic materials by photolytically generating two key intermediates: 2-nitropropene and 2-nitro-2-propyl radicals. To characterize the unimolecular dissociation of each intermediate, we form them under collision-free conditions using the photodissociation of 2-bromo-2-nitropropane; the intermediates are formed at high internal energies and undergo a multitude of subsequent unimolecular dissociation events investigated herein. Complementing our prior work on this system, the new data obtained with a crossed-laser molecular beam scattering apparatus with VUV photoionization detection at Taiwan's National Synchrotron Radiation Research Center (NSRRC) and new velocity map imaging data better characterize two of the four primary 193 nm photodissociation channels. The C-Br photofission channel forming the 2-nitro-2-propyl radicals has a trimodal recoil kinetic energy distribution, P(ET), suggesting that the 2-nitro-2-propyl radicals are formed both in the ground electronic state and in two low-lying excited electronic states. The new data also revise the HBr photoelimination P(ET) forming the 2-nitropropene intermediate. We then resolved the multiple competing unimolecular dissociation channels of each photoproduct, confirming many of the channels detected in the prior study, but not all. The new data detected HONO product at m/e = 47 using 11.3 eV photoionization from both intermediates; analysis of the momentum-matched products allows us to establish that both 2-nitro-2-propyl → HONO + CH3CCH2 and 2-nitropropene → HONO + C3H4 occur. Photoionization at 9.5 eV allowed us to detect the mass 71 coproduct formed in OH loss from 2-nitro-2-propyl; a channel missed in our prior study. The dynamics of the highly exothermic 2-nitro-2-propyl → NO + acetone dissociation is also better characterized; it evidences a sideways scattered angular distribution. The detection of some stable 2-nitropropene photoproducts allows us to fit signal previously assigned to H loss from 2-nitro-2-propyl radicals. Overall, the data provide a comprehensive study of the unimolecular dissociation channels of these important nitro-containing intermediates.

Thermal decomposition pathways for 1,1-diamino-2,2-dinitroethene (FOX-7).

In this study, we computationally investigate the initial and subsequent steps in the chemical mechanism for the gas-phase thermal decomposition of 1,1-diamino-2,2-dinitroethene (FOX-7). We determine the key exothermic step in the gas-phase thermal decomposition of FOX-7 and explore the similarities and differences between FOX-7 and other geminal dinitro energetic materials. The calculations reveal a mechanism for NO loss involving a 3-member cyclic intermediate, rather than a nitro-nitrite isomerization, that occurs in the radical intermediates formed throughout the decomposition mechanism.

Elucidating the decomposition mechanism of energetic materials with geminal dinitro groups using 2-bromo-2-nitropropane photodissociation.

These experiments photolytically generate two key intermediates in the decomposition mechanisms of energetic materials with nitro substituents, 2-nitropropene, and 2-nitro-2-propyl radicals. These intermediates are produced at high internal energies and access a number of competing unimolecular dissociation channels investigated herein. We use a combination of crossed laser-molecular beam scattering and velocity map imaging to study the photodissociation of 2-bromo-2-nitropropane at 193 nm and the subsequent unimolecular dissociation of the intermediates above. Our results demonstrate that 2-bromo-2-nitropropane has four primary photodissociation pathways: C-Br bond fission yielding the 2-nitro-2-propyl radical, HBr elimination yielding 2-nitropropene, C-N bond fission yielding the 2-bromo-2-propyl radical, and HONO elimination yielding 2-bromopropene. The photofragments are formed with significant internal energy and undergo many secondary dissociation events, including the exothermic dissociation of 2-nitro-2-propyl radicals to NO + acetone. Calculations at the G4//B3LYP/6-311++g(3df,2p) level show that the presence of a radical at a nitroalkyl center changes the mechanism for and substantially lowers the barrier to NO loss. This mechanism involves an intermediate with a three-center ring rather than the intermediate formed during the traditional nitro-nitrite isomerization. The observed dissociation pathways of the 2-nitro-2-propyl radical and 2-nitropropene help elucidate the decomposition mechanism of larger energetic materials with geminal dinitro groups.

Ten-nanometer dense hole arrays generated by nanoparticle lithography.

Large area dense hole arrays with a feature size of ~10 nm were generated using self-assembled monolayers of nanoparticles as etch masks. To fabricate the hole arrays, monolayers of nanoparticles were irradiated by electron beam to turn surfactants into amorphous carbon, treated by acid to remove the nanoparticle cores, and then etched by CF(4) to deepen the holes. Evaporated gold films preferentially diffuse into the holes to generate gold nanoparticle arrays. However no obvious diffusion into holes was observed for a sputtered iron platinum film.

Characterizing the rovibrational distribution of CD2CD2OH radicals produced via the photodissociation of 2-bromoethanol-d4.

This work characterizes the internal energy distribution of the CD(2)CD(2)OH radical formed via photodissociation of 2-bromoethanol-d(4). The CD(2)CD(2)OH radical is the first radical adduct in the addition of the hydroxyl radical to C(2)D(4) and the product branching of the OH + C(2)D(4) reaction is dependent on the total internal energy of this adduct and how that energy is partitioned between rotation and vibration. Using a combination of a velocity map imaging apparatus and a crossed laser-molecular beam scattering apparatus, we photodissociate the BrCD(2)CD(2)OH precursor at 193 nm and measure the velocity distributions of the Br atoms, resolving the Br((2)P(1/2)) and Br((2)P(3/2)) states with [2 + 1] resonance enhanced multiphoton ionization (REMPI) on the imaging apparatus. We also detect the velocity distribution of the subset of the nascent momentum-matched CD(2)CD(2)OH cofragments that are formed stable to subsequent dissociation. Invoking conservation of momentum and conservation of energy and a recently developed impulsive model, we determine the vibrational energy distribution of the nascent CD(2)CD(2)OH radicals from the measured velocity distributions.