Hypergolic ionic liquids: to be or not to be?

Hypergolic ionic liquids (HIL) - ionic liquids which ignite spontaneously upon contact with an oxidizer - emerged as green space propellants. Exploiting the previously marked hypergolic [EMIM][CBH] - WFNA (1-ethyl-3-methylimidazolium cyanoborohydride - white fuming nitric acid) system as a benchmark, through the utilization of a novel chirped-pulse droplet-merging technique in an ultrasonic levitation environment and electronic structure calculations, this work deeply questions the hypergolicity of the [EMIM][CBH]-WFNA system. Molecular oxygen is critically required for the [EMIM][CBH]-WFNA system to ignite spontaneously. State-of-the-art electronic structure calculations identified the resonantly stabilized N-boryl-N-oxo-formamide [(H3B-N(O)-CHO)-; BOFA] radical anion as the key intermediate in driving the oxidation chemistry upon reaction with molecular oxygen of the ionic liquid. These findings challenge conventional wisdom of 'well-established' test protocols as indicators of the hypergolicity of ionic liquids thus necessitating truly oxygen-free experimental conditions to define the ignition delay upon mixing of the ionic liquid and the oxidizer and hence designating an ionic liquid as truly hypergolic at the molecular level.

Streptomyces rare codon UUA: from features associated with 2 adpA related locations to candidate phage regulatory translational bypassing.

In Streptomyces species, the cell cycle involves a switch from an early and vegetative state to a later phase where secondary products including antibiotics are synthesized, aerial hyphae form and sporulation occurs. AdpA, which has two domains, activates the expression of numerous genes involved in the switch from the vegetative growth phase. The adpA mRNA of many Streptomyces species has a UUA codon in a linker region between 5' sequence encoding one domain and 3' sequence encoding its other and C-terminal domain. UUA codons are exceptionally rare in Streptomyces, and its functional cognate tRNA is not present in a fully modified and acylated form, in the early and vegetative phase of the cell cycle though it is aminoacylated later. Here, we report candidate recoding signals that may influence decoding of the linker region UUA. Additionally, a short ORF 5' of the main ORF has been identified with a GUG at, or near, its 5' end and an in-frame UUA near its 3' end. The latter is commonly 5 nucleotides 5' of the main ORF start. Ribosome profiling data show translation of that 5' region. Ten years ago, UUA-mediated translational bypassing was proposed as a sensor by a Streptomyces phage of its host's cell cycle stage and an effector of its lytic/lysogeny switch. We provide the first experimental evidence supportive of this proposal.

Enhancing reactivity of SiO+ ions by controlled excitation to extreme rotational states.

Optical pumping of molecules provides unique opportunities for control of chemical reactions at a wide range of rotational energies. This work reports a chemical reaction with extreme rotational excitation of a reactant and its kinetic characterization. We investigate the chemical reactivity for the hydrogen abstraction reaction SiO+ + H2 → SiOH+ + H in an ion trap. The SiO+ cations are prepared in a narrow rotational state distribution, including super-rotor states with rotational quantum number (j) as high as 170, using a broad-band optical pumping method. We show that the super-rotor states of SiO+ substantially enhance the reaction rate, a trend reproduced by complementary theoretical studies. We reveal the mechanism for the rotational enhancement of the reactivity to be a strong coupling of the SiO+ rotational mode with the reaction coordinate at the transition state on the dominant dynamical pathway.

Processing of methane and acetylene ices by galactic cosmic rays and implications to the color diversity of Kuiper Belt objects.

Kuiper Belt objects exhibit a wider color range than any other solar system population. The origin of this color diversity is unknown, but likely the result of the prolonged irradiation of organic materials by galactic cosmic rays (GCRs). Here, we combine ultrahigh-vacuum irradiation experiments with comprehensive spectroscopic analyses to examine the color evolution during GCR processing methane and acetylene under Kuiper Belt conditions. This study replicates the colors of a population of Kuiper Belt objects such as Makemake, Orcus, and Salacia. Aromatic structural units carrying up to three rings as in phenanthrene (C14H10), phenalene (C9H10), and acenaphthylene (C12H8), of which some carry structural motives of DNA and RNA connected via unsaturated linkers, were found to play a key role in producing the reddish colors. These studies demonstrate the level of molecular complexity synthesized of GCR processing hydrocarbon and hint at the role played by irradiated ice in the early production of biological precursor molecules.

Exotic Inverse Kinetic Isotopic Effect in the Thermal Decomposition of Levitated Aluminum Iodate Hexahydrate Particles.

Aluminum iodate hexahydrate ([Al(H2O)6](IO3)3(HIO3)2; AIH) represents a novel, oxidizing material for energetic applications. Recently, AIH was synthesized to replace the aluminum oxide passivation layer of aluminum nanoenergetic materials (ALNEM). The design of reactive coatings for ALNEM-doped hydrocarbon fuels in propulsion systems requires fundamental insights of the elementary steps of the decomposition of AIH. Here, through the levitation of single AIH particles in an ultrasonic field, we reveal a three-stage decomposition mechanism initiated by loss of water (H2O) accompanied by an unconventional inverse isotopic effect and ultimate breakdown of AIH into gaseous elements (iodine and oxygen). Hence, AIH coating on aluminum nanoparticles replacing the oxide layer would provide a critical supply of oxygen in direct contact with the metal surface thus enhancing reactivity and reducing ignition delays, further eliminating decades-old obstacles of passivation layers on nanoenergetic materials. These findings demonstrate the potential of AIH to aid in the development of next-generation propulsion systems.

Unraveling the initial steps of the ignition chemistry of the hypergolic ionic liquid 1-ethyl-3-methylimidazolium cyanoborohydride ([EMIM][CBH]) with nitric acid (HNO3) exploiting chirped pulse triggered droplet merging.

The composition of the products and the mechanistic routes for the reaction of the hypergolic ionic liquid (HIL) 1-ethyl-3-methylimidazolium cyanoborohydride ([EMIM][CBH]) and nitric acid (HNO3) at various concentrations from 10% to 70% were explored using a contactless single droplet merging within an ultrasonic levitation setup in an inert atmosphere of argon to reveal the initial steps that cause hypergolicity. The reactions were initiated through controlled droplet-merging manipulation triggered by a frequency chirp pulse amplitude modulation. Utilizing the high-speed optical and infrared cameras surrounding the levitation process chamber, intriguing visual images were unveiled: (i) extensive gas release and (ii) temperature rises of up to 435 K in the merged droplets. The gas development was validated qualitatively and quantitatively with Fourier Transform Infrared Spectroscopy (FTIR) indicating the major gas-phase products to be hydrogen cyanide (HCN) and nitrous oxide (N2O). The merged droplet was also probed by pulsed Raman spectroscopy which deciphered features for key functional groups of the reaction products and intermediates (-BH, -BH2, -BH3, -NCO); reaction kinetics revealed that the reaction was initiated by the interaction of the [CBH]- anion of the HIL with the oxidizer (HNO3) through proton transfer. Computations indicate the formation of a van-der-Waals complex between the [CBH]- anion and HNO3 initially, followed by proton transfer from the acid to the anion and subsequent extensive isomerization; these rearrangements were found to be essential for the formation of HCN and N2O. The exoergicity observed during the merging process provides a molar enthalpy change up to 10 kJ mol-1 to the system, which could be sufficient for a significant fraction of the reactants of about 11% to overcome the reaction barriers in the individual steps of the computationally determined minimum energy pathways.

Discovery of Discrete Stages in the Oxidation of exo-Tetrahydrodicyclopentadiene (C10H16) Droplets Doped with Titanium-Aluminum-Boron Reactive Mixed-Metal Nanopowder.

Titanium (Ti), aluminum (Al), and boron (B) reactive mixed-metal nanopowders (Ti-Al-B RMNPs) represent attractive additives to hydrocarbon fuels such as exo-tetrahydrodicyclopentadiene (C10H16; JP-10) enhancing the limited volumetric energy densities of traditional hydrocarbons, but fundamental mechanisms and combustion stages in the oxidation have been obscure. This understanding is of vital significance in the development of next-generation propulsion systems and energy-generation technologies. Here, we expose distinct oxidation stages of single droplets of JP-10 doped with Ti-Al-B-RMNP exploiting innovative ultrasonic levitator technology coupled with time-resolved spectroscopic (UV-vis) and imaging diagnostics (optical and infrared). Two spatially and temporally distinct stages of combustion define a glow flame stage in which JP-10 and nanoparticles combust via a homogeneous gas phase (Al) and heterogeneous gas-surface oxidation (Ti, B) and a slower diffusion flame stage associated with the oxidation of JP-10. These findings enable the development of next-generation RMNP fuel additives with superior payload delivery capabilities.

Translational Frameshifting in the chlD Gene Gives a Clue to the Coevolution of the Chlorophyll and Cobalamin Biosyntheses.

Today, hundreds of prokaryotic species are able to synthesize chlorophyll and cobalamin (vitamin B12). An important step in the biosynthesis of these coenzymes is the insertion of a metal ion into a porphyrin ring. Namely, Mg-chelatase ChlIDH and aerobic Co-chelatase CobNST are utilized in the chlorophyll and vitamin B12 pathways, respectively. The corresponding subunits of these enzymes have common evolutionary origin. Recently, we have identified a highly conserved frameshifting signal in the chlD gene. This unusual regulatory mechanism allowed production of both the small and the medium chelatase subunits from the same gene. Moreover, the chlD gene appeared early in the evolution and could be at the starting point in the development of the chlorophyll and B12 pathways. Here, we studied the possible coevolution of these two pathways through the analysis of the chelatase genes. To do that, we developed a specialized Web database with comprehensive information about more than 1200 prokaryotic genomes. Further analysis allowed us to split the coevolution of the chlorophyll and B12 pathway into eight distinct stages.

Dramatic Conformer-Dependent Reactivity of the Acetaldehyde Oxide Criegee Intermediate with Dimethylamine Via a 1,2-Insertion Mechanism.

The reactivity of carbonyl oxides has previously been shown to exhibit strong conformer and substituent dependencies. Through a combination of synchrotron-multiplexed photoionization mass spectrometry experiments (298 K and 4 Torr) and high-level theory [CCSD(T)-F12/cc-pVTZ-F12//B2PLYP-D3/cc-pVTZ with an added CCSDT(Q) correction], we explore the conformer dependence of the reaction of acetaldehyde oxide (CH3CHOO) with dimethylamine (DMA). The experimental data support the theoretically predicted 1,2-insertion mechanism and the formation of an amine-functionalized hydroperoxide reaction product. Tunable-vacuum ultraviolet photoionization probing of anti- or anti- + syn-CH3CHOO reveals a strong conformer dependence of the title reaction. The rate coefficient of DMA with anti-CH3CHOO is predicted to exceed that for the reaction with syn-CH3CHOO by a factor of ∼34,000, which is attributed to submerged barrier (syn) versus barrierless (anti) mechanisms for energetically downhill reactions.

Precisely spun super rotors.

Improved optical control of molecular quantum states promises new applications including chemistry in the quantum regime, precision tests of fundamental physics, and quantum information processing. While much work has sought to prepare ground state molecules, excited states are also of interest. Here, we demonstrate a broadband optical approach to pump trapped SiO+ molecules into pure super rotor ensembles maintained for many minutes. Super rotor ensembles pumped up to rotational state N = 67, corresponding to the peak of a 9400 K distribution, had a narrow N spread comparable to that of a few-kelvin sample, and were used for spectroscopy of the previously unobserved C2Π state. Significant centrifugal distortion of super rotors pumped up to N = 230 allowed probing electronic structure of SiO+ stretched far from its equilibrium bond length.

Direct Interactions with Nascent Transcripts Is Potentially a Common Targeting Mechanism of Long Non-Coding RNAs.

Although thousands of mammalian long non-coding RNAs (lncRNAs) have been reported in the last decade, their functional annotation remains limited. A wet-lab approach to detect functions of a novel lncRNA usually includes its knockdown followed by RNA sequencing and identification of the deferentially expressed genes. However, identification of the molecular mechanism(s) used by the lncRNA to regulate its targets frequently becomes a challenge. Previously, we developed the ASSA algorithm that detects statistically significant inter-molecular RNA-RNA interactions. Here we designed a workflow that uses ASSA predictions to estimate the ability of an lncRNA to function via direct base pairing with the target transcripts (co- or post-transcriptionally). The workflow was applied to 300+ lncRNA knockdown experiments from the FANTOM6 pilot project producing statistically significant predictions for 71 unique lncRNAs (104 knockdowns). Surprisingly, the majority of these lncRNAs were likely to function co-transcriptionally, i.e., hybridize with the nascent transcripts of the target genes. Moreover, a number of the obtained predictions were supported by independent iMARGI experimental data on co-localization of lncRNA and chromatin. We detected an evolutionarily conserved lncRNA CHASERR (AC013394.2 or LINC01578) that could regulate target genes co-transcriptionally via interaction with a nascent transcript by directing CHD2 helicase. The obtained results suggested that this nuclear lncRNA may be able to activate expression of the target genes in trans by base-pairing with the nascent transcripts and directing the CHD2 helicase to the regulated promoters leading to open the chromatin and active transcription. Our study highlights the possible importance of base-pairing between nuclear lncRNAs and nascent transcripts for the regulation of gene expression.

Cooling of a Zero-Nuclear-Spin Molecular Ion to a Selected Rotational State.

We demonstrate rotational cooling of the silicon monoxide cation via optical pumping by a spectrally filtered broadband laser. Compared with diatomic hydrides, SiO^{+} is more challenging to cool because of its smaller rotational interval. However, the rotational level spacing and the large dipole moment of SiO^{+} allows for direct manipulation by microwaves, and the absence of hyperfine structure in its dominant isotopologue greatly reduces demands for pure quantum state preparation. These features make ^{28}Si^{16}O^{+} a good candidate for future applications such as quantum information processing. Cooling to the ground rotational state is achieved on a 100 ms timescale and attains a population of 94(3)%, with an equivalent temperature T=0.53(6) K. We also describe a novel spectral-filtering approach to cool into arbitrary rotational states and use it to demonstrate a narrow rotational population distribution (N±1) around a selected state.

Functional annotation of human long noncoding RNAs via molecular phenotyping.

Long noncoding RNAs (lncRNAs) constitute the majority of transcripts in the mammalian genomes, and yet, their functions remain largely unknown. As part of the FANTOM6 project, we systematically knocked down the expression of 285 lncRNAs in human dermal fibroblasts and quantified cellular growth, morphological changes, and transcriptomic responses using Capped Analysis of Gene Expression (CAGE). Antisense oligonucleotides targeting the same lncRNAs exhibited global concordance, and the molecular phenotype, measured by CAGE, recapitulated the observed cellular phenotypes while providing additional insights on the affected genes and pathways. Here, we disseminate the largest-to-date lncRNA knockdown data set with molecular phenotyping (over 1000 CAGE deep-sequencing libraries) for further exploration and highlight functional roles for ZNF213-AS1 and lnc-KHDC3L-2.

Two Cobalt Chelatase Subunits Can Be Generated from a Single chlD Gene via Programed Frameshifting.

Magnesium chelatase chlIDH and cobalt chelatase cobNST enzymes are required for biosynthesis of (bacterio)chlorophyll and cobalamin (vitamin B12), respectively. Each enzyme consists of large, medium, and small subunits. Structural and primary sequence similarities indicate common evolutionary origin of the corresponding subunits. It has been reported earlier that some of vitamin B12 synthesizing organisms utilized unusual cobalt chelatase enzyme consisting of a large cobalt chelatase subunit (cobN) along with a medium (chlD) and a small (chlI) subunits of magnesium chelatase. In attempt to understand the nature of this phenomenon, we analyzed >1,200 diverse genomes of cobalamin and/or chlorophyll producing prokaryotes. We found that, surprisingly, genomes of many cobalamin producers contained cobN and chlD genes only; a small subunit gene was absent. Further on, we have discovered a diverse group of chlD genes with functional programed ribosomal frameshifting signals. Given a high similarity between the small subunit and the N-terminal part of the medium subunit, we proposed that programed translational frameshifting may allow chlD mRNA to produce both subunits. Indeed, in genomes where genes for small subunits were absent, we observed statistically significant enrichment of programed frameshifting signals in chlD genes. Interestingly, the details of the frameshifting mechanisms producing small and medium subunits from a single chlD gene could be prokaryotic taxa specific. All over, this programed frameshifting phenomenon was observed to be highly conserved and present in both bacteria and archaea.

Practical Guidance in Genome-Wide RNA:DNA Triple Helix Prediction.

Long noncoding RNAs (lncRNAs) play a key role in many cellular processes including chromatin regulation. To modify chromatin, lncRNAs often interact with DNA in a sequence-specific manner forming RNA:DNA triple helices. Computational tools for triple helix search do not always provide genome-wide predictions of sufficient quality. Here, we used four human lncRNAs (MEG3, DACOR1, TERC and HOTAIR) and their experimentally determined binding regions for evaluating triplex parameters that provide the highest prediction accuracy. Additionally, we combined triplex prediction with the lncRNA secondary structure and demonstrated that considering only single-stranded fragments of lncRNA can further improve DNA-RNA triplexes prediction.

Sensitive Mass Spectrometer for Time-Resolved Gas-Phase Chemistry Studies at High Pressures.

We report a new experimental apparatus for direct time-resolved probing of high-pressure gas-phase chemical reactions by photoionization mass spectrometry. The apparatus uses a laser photolysis flow reactor, capable of operating at P = 0.3-100 bar and T = 300-1000 K. We initiate reactions in homogeneous gas mixtures by the photolysis of an appropriate radical precursor using laser pulses at repetition rates of 1-10 Hz. The reacting mixture is continuously sampled into a vacuum chamber, ionized by vacuum-ultraviolet (VUV) photons from laboratory-based discharge lamps or from a synchrotron beamline, and analyzed by a custom mass spectrometer. Soft near-threshold ionization by tunable synchrotron radiation enables spectroscopic quantification of many key intermediates and products of chemical reactions. A novel ionization scheme in the high-density region of the sample jet expansion increases the experimental sensitivity 100-fold, compared with the existing instruments, without compromising mass resolution. A 40 kHz pulsed reflectron time-of-flight mass spectrometer achieves simultaneous detection of all ionized species with 25 µs time resolution. We demonstrate the capability of this apparatus by probing the ethyl radical oxidation reaction using very dilute (<1012 molecules·cm-3) ethyl concentrations at pressures up to 25 bar.

To Boldly Look Where No One Has Looked Before: Identifying the Primary Photoproducts of Acetylacetone.

We investigate the gas-phase photochemistry of the enolone tautomer of acetylacetone (pentane-2,4-dione) following S2(ππ*) ← S0 excitation at λ = 266 and 248 nm, using three complementary time-resolved spectroscopic methods. Contrary to earlier reports, which claimed to study one-photon excitation of acetylacetone and found OH and CH3 as the only important gas-phase products, we detect 15 unique primary photoproducts and demonstrate that five of them, including OH and CH3, arise solely by multiphoton excitation. We assign the one-photon products to six photochemical channels and show that the most significant pathway is phototautomerization to the diketone form, which is likely an intermediate in several of the other product channels. Furthermore, we measure the equilibrium constant of the tautomerization of the enolone to diketone on S0 from 320 to 600 K and extract Δ H = 4.1 ± 0.3 kcal·mol-1 and Δ S = 6.8 ± 0.5 cal·mol-1·K-1 using a van't Hoff analysis. We correct the C-OH bond dissociation energy in acetylacetone, previously determined as 90 kcal·mol-1 by theory and experiment, to a new value of 121.7 kcal·mol-1. Our experiments and electronic structure calculations provide evidence that some of the product channels, including phototautomerization, occur on S0, while others likely occur on excited triplet surfaces. Although the large oscillator strength of the S2 ← S0 transition results from the (ππ*) excitation of the C═C-C═O backbone, similar to conjugated polyenes, the participation of triplets in the dissociation pathways of acetylacetone appears to have more in common with ketone photochemistry.

Influence of the Ether Functional Group on Ketohydroperoxide Formation in Cyclic Hydrocarbons: Tetrahydropyran and Cyclohexane.

Photolytically initiated oxidation experiments were conducted on cyclohexane and tetrahydropyran using multiplexed photoionization mass spectrometry to assess the impact of the ether functional group in the latter species on reaction mechanisms relevant to autoignition. Pseudo-first-order conditions, with [O2]0:[R•]0 > 2000, were used to ensure that R• + O2 → products were the dominant reactions. Quasi-continuous, tunable vacuum ultraviolet light from a synchrotron was employed over the range 8.0-11.0 eV to measure photoionization spectra of the products at two pressures (10 and 1520 Torr) and three temperatures (500, 600, and 700 K). Photoionization spectra of ketohydroperoxides were measured in both species and were qualitatively identical, within the limit of experimental noise, to those of analogous species formed in n-butane oxidation. However, differences were noted in the temperature dependence of ketohydroperoxide formation between the two species. Whereas the yield from cyclohexane is evident up to 700 K, ketohydroperoxides in tetrahydropyran were not detected above 650 K. The difference indicates that reaction mechanisms change due to the ether group, likely affecting the requisite •QOOH + O2 addition step. Branching fractions of nine species from tetrahydropyran were quantified with the objective of determining the role of ring-opening reactions in diminishing ketohydroperoxide. The results indicate that products formed from unimolecular decomposition of R• and •QOOH radicals via concerted C-C and C-O ß-scission are pronounced in tetrahydropyran and are insignificant in cyclohexane oxidation. The main conclusion drawn is that, under the conditions herein, ring-opening pathways reduce the already low steady-state concentration of •QOOH, which in the case of tetrahydropyran prevents •QOOH + O2 reactions necessary for ketohydroperoxide formation. Carbon balance calculations reveal that products from ring opening of both R• and •QOOH, at 700 K, account for >70% at 10 Torr and >55% at 1520 Torr. Three pathways are confirmed to contribute to the depletion of •QOOH in tetrahydropyran including (i) γ-•QOOH → pentanedial + •OH, (ii) γ-•QOOH → vinyl formate + ethene + •OH, and (iii) γ-•QOOH → 3-butenal + formaldehyde + •OH. Analogous mechanisms in cyclohexane oxidation leading to similar intermediates are compared and, on the basis of mass spectral results, confirm that no such ring-opening reactions occur. The implication from the comparison to cyclohexane is that the ether group in tetrahydropyran increases the propensity for ring-opening reactions and inhibits the formation of ketohydroperoxide isomers that precede chain-branching. On the contrary, the absence of such reactions in cyclohexane enables ketohydroperoxide formation up to 700 K and perhaps higher temperature.

Experimental and computational studies of Criegee intermediate reactions with NH3 and CH3NH2.

Ammonia and amines are emitted into the troposphere by various natural and anthropogenic sources, where they have a significant role in aerosol formation. Here, we explore the significance of their removal by reaction with Criegee intermediates, which are produced in the troposphere by ozonolysis of alkenes. Rate coefficients for the reactions of two representative Criegee intermediates, formaldehyde oxide (CH2OO) and acetone oxide ((CH3)2COO) with NH3 and CH3NH2 were measured using cavity ring-down spectroscopy. Temperature-dependent rate coefficients, k(CH2OO + NH3) = (3.1 ± 0.5) × 10-20T2 exp(1011 ± 48/T) cm3 s-1 and k(CH2OO + CH3NH2) = (5 ± 2) × 10-19T2 exp(1384 ± 96/T) cm3 s-1 were obtained in the 240 to 320 K range. Both the reactions of CH2OO were found to be independent of pressure in the 10 to 100 Torr (N2) range, and average rate coefficients k(CH2OO + NH3) = (8.4 ± 1.2) × 10-14 cm3 s-1 and k(CH2OO + CH3NH2) = (5.6 ± 0.4) × 10-12 cm3 s-1 were deduced at 293 K. An upper limit of ≤2.7 × 10-15 cm3 s-1 was estimated for the rate coefficient of the (CH3)2COO + NH3 reaction. Complementary measurements were performed with mass spectrometry using synchrotron radiation photoionization giving k(CH2OO + CH3NH2) = (4.3 ± 0.5) × 10-12 cm3 s-1 at 298 K and 4 Torr (He). Photoionization mass spectra indicated production of NH2CH2OOH and CH3N(H)CH2OOH functionalized organic hydroperoxide adducts from CH2OO + NH3 and CH2OO + CH3NH2 reactions, respectively. Ab initio calculations performed at the CCSD(T)(F12*)/cc-pVQZ-F12//CCSD(T)(F12*)/cc-pVDZ-F12 level of theory predicted pre-reactive complex formation, consistent with previous studies. Master equation simulations of the experimental data using the ab initio computed structures identified submerged barrier heights of -2.1 ± 0.1 kJ mol-1 and -22.4 ± 0.2 kJ mol-1 for the CH2OO + NH3 and CH2OO + CH3NH2 reactions, respectively. The reactions of NH3 and CH3NH2 with CH2OO are not expected to compete with its removal by reaction with (H2O)2 in the troposphere. Similarly, losses of NH3 and CH3NH2 by reaction with Criegee intermediates will be insignificant compared with reactions with OH radicals.

Prediction of lncRNAs and their interactions with nucleic acids: benchmarking bioinformatics tools.

The genomes of mammalian species are pervasively transcribed producing as many noncoding as protein-coding RNAs. There is a growing body of evidence supporting their functional role. Long noncoding RNA (lncRNA) can bind both nucleic acids and proteins through several mechanisms. A reliable computational prediction of the most probable mechanism of lncRNA interaction can facilitate experimental validation of its function. In this study, we benchmarked computational tools capable to discriminate lncRNA from mRNA and predict lncRNA interactions with other nucleic acids. We assessed the performance of 9 tools for distinguishing protein-coding from noncoding RNAs, as well as 19 tools for prediction of RNA-RNA and RNA-DNA interactions. Our conclusions about the considered tools were based on their performances on the entire genome/transcriptome level, as it is the most common task nowadays. We found that FEELnc and CPAT distinguish between coding and noncoding mammalian transcripts in the most accurate manner. ASSA, RIBlast and LASTAL, as well as Triplexator, turned out to be the best predictors of RNA-RNA and RNA-DNA interactions, respectively. We showed that the normalization of the predicted interaction strength to the transcript length and GC content may improve the accuracy of inferring RNA interactions. Yet, all the current tools have difficulties to make accurate predictions of short-trans RNA-RNA interactions-stretches of sparse contacts. All over, there is still room for improvement in each category, especially for predictions of RNA interactions.