Hydrogen Bonding with Hydridic Hydrogen-Experimental Low-Temperature IR and Computational Study: Is a Revised Definition of Hydrogen Bonding Appropriate?

Spectroscopic characteristics of Me3Si-H···Y complexes (Y = ICF3, BrCN, and HCN) containing a hydridic hydrogen were determined experimentally by low-temperature IR experiments based on the direct spectral measurement of supersonically expanded intermediates on a cold substrate or by the technique of argon-matrix isolation as well as computationally at harmonic and one-dimensional anharmonic levels. The computations were based on DFT-D, MP2, MP2-F12, and CCSD(T)-F12 levels using various extended AO basis sets. The formation of all complexes related to the redshift of the Si-H stretching frequency upon complex formation was accompanied by an increase in its intensity. Similar results were obtained for another 10 electron acceptors of different types, positive σ-, π-, and p-holes and cations. The formation of HBe-H···Y complexes, studied only computationally and again containing a hydridic hydrogen, was characterized by the blueshift of the Be-H stretching frequency upon complexation accompanied by an increase in its intensity. The spectral shifts and stabilization energies obtained for all presently studied hydridic H-bonded complexes were comparable to those in protonic H-bonded complexes, which has prompted us to propose a modification of the existing IUPAC definition of H-bonding that covers, besides the classical protonic form, the non-classical hydridic and dihydrogen forms.

Infrared Spectra of Small Radicals for Exoplanetary Spectroscopy: OH, NH, CN and CH: The State of Current Knowledge.

In this study, we present a current state-of-the-art review of middle-to-near IR emission spectra of four simple astrophysically relevant molecular radicals-OH, NH, CN and CH. The spectra of these radicals were measured by means of time-resolved Fourier transform infrared spectroscopy in the 700-7500 cm-1 spectral range and with 0.07-0.02 cm-1 spectral resolution. The radicals were generated in a glow discharge of gaseous mixtures in a specially designed discharge cell. The spectra of short-lived radicals published here are of great importance, especially for the detailed knowledge and study of the composition of exoplanetary atmospheres in selected new planets. Today, with the help of the James Webb telescope and upcoming studies with the help of Plato and Ariel satellites, when the investigated spectral area is extended into the infrared spectral range, it means that detailed knowledge of the infrared spectra of not only stable molecules but also the spectra of short-lived radicals or ions, is indispensable. This paper follows a simple structure. Each radical is described in a separate chapter, starting with historical and actual theoretical background, continued by our experimental results and concluded by spectral line lists with assigned notation.

Prebiotic Route to Thymine from Formamide-A Combined Experimental-Theoretical Study.

Synthesis of RNA nucleobases from formamide is one of the recurring topics of prebiotic chemistry research. Earlier reports suggest that thymine, the substitute for uracil in DNA, may also be synthesized from formamide in the presence of catalysts enabling conversion of formamide to formaldehyde. In the current paper, we show that to a lesser extent conversion of uracil to thymine may occur even in the absence of catalysts. This is enabled by the presence of formic acid in the reaction mixture that forms as the hydrolysis product of formamide. Under the reaction conditions of our study, the disproportionation of formic acid may produce formaldehyde that hydroxymethylates uracil in the first step of the conversion process. The experiments are supplemented by quantum chemical modeling of the reaction pathway, supporting the plausibility of the mechanism suggested by Saladino and coworkers.

Formic Acid, a Ubiquitous but Overlooked Component of the Early Earth Atmosphere.

Terrestrial volcanism has been one of the dominant geological forces shaping our planet since its earliest existence. Its associated phenomena, like atmospheric lightning and hydrothermal activity, provide a rich energy reservoir for chemical syntheses. Based on our laboratory simulations, we propose that on the early Earth volcanic activity inevitably led to a remarkable production of formic acid through various independent reaction channels. Large-scale availability of atmospheric formic acid supports the idea of the high-temperature accumulation of formamide in this primordial environment.

Formation of nucleobases in a Miller-Urey reducing atmosphere.

The Miller-Urey experiments pioneered modern research on the molecular origins of life, but their actual relevance in this field was later questioned because the gas mixture used in their research is considered too reducing with respect to the most accepted hypotheses for the conditions on primordial Earth. In particular, the production of only amino acids has been taken as evidence of the limited relevance of the results. Here, we report an experimental work, combined with state-of-the-art computational methods, in which both electric discharge and laser-driven plasma impact simulations were carried out in a reducing atmosphere containing NH3 + CO. We show that RNA nucleobases are synthesized in these experiments, strongly supporting the possibility of the emergence of biologically relevant molecules in a reducing atmosphere. The reconstructed synthetic pathways indicate that small radicals and formamide play a crucial role, in agreement with a number of recent experimental and theoretical results.

High-energy chemistry of formamide: a unified mechanism of nucleobase formation.

The coincidence of the Late Heavy Bombardment (LHB) period and the emergence of terrestrial life about 4 billion years ago suggest that extraterrestrial impacts could contribute to the synthesis of the building blocks of the first life-giving molecules. We simulated the high-energy synthesis of nucleobases from formamide during the impact of an extraterrestrial body. A high-power laser has been used to induce the dielectric breakdown of the plasma produced by the impact. The results demonstrate that the initial dissociation of the formamide molecule could produce a large amount of highly reactive CN and NH radicals, which could further react with formamide to produce adenine, guanine, cytosine, and uracil. Based on GC-MS, high-resolution FTIR spectroscopic results, as well as theoretical calculations, we present a comprehensive mechanistic model, which accounts for all steps taking place in the studied impact chemistry. Our findings thus demonstrate that extraterrestrial impacts, which were one order of magnitude more abundant during the LHB period than before and after, could not only destroy the existing ancient life forms, but could also contribute to the creation of biogenic molecules.

Spectroscopic investigations of high-energy-density plasma transformations in a simulated early reducing atmosphere containing methane, nitrogen and water.

Large-scale plasma was created in gas mixtures containing methane using high-power laser-induced dielectric breakdown (LIDB). The composition of the mixtures corresponded to a cometary and/or meteoritic impact into the early atmosphere of either Titan or Earth. A multiple-centimeter-sized fireball was created by focusing a single 100 J, 450 ps near-infrared laser pulse into the center of a 15 L gas cell. The excited reaction intermediates formed during the various stages of the LIDB plasma chemical evolution were investigated using optical emission spectroscopy (OES) with temporal resolution. The chemical consequences of laser-produced plasma generation in a CH4-N2-H2O mixture were investigated using high resolution Fourier-transform infrared absorption spectroscopy (FTIR) and gas selected ion flow tube spectrometry (SIFT). Several simple inorganic and organic compounds were identified in the reaction mixture exposed to ten laser sparks. Deuterated water (D2O) in a gas mixture was used to separate several of the produced isotopomers of acetylene, which were then quantified using the FTIR technique.

Prebiotic synthesis of nucleic acids and their building blocks at the atomic level - merging models and mechanisms from advanced computations and experiments.

The origin of life on Earth is one of the most fascinating questions of contemporary science. Extensive research in the past decades furnished diverse experimental proposals for the emergence of first informational polymers that could form the basis of the early terrestrial life. Side by side with the experiments, the fast development of modern computational chemistry methods during the last 20 years facilitated the use of in silico modelling tools to complement the experiments. Modern computations can provide unique atomic-level insights into the structural and electronic aspects as well as the energetics of key prebiotic chemical reactions. Many of these insights are not directly obtainable from the experimental techniques and the computations are thus becoming indispensable for proper interpretation of many experiments and for qualified predictions. This review illustrates the synergy between experiment and theory in the origin of life research focusing on the prebiotic synthesis of various nucleic acid building blocks and on the self-assembly of nucleotides leading to the first functional oligonucleotides.

High-energy chemistry of formamide: a simpler way for nucleobase formation.

The formation of nucleobases from formamide during a high-energy density event, i.e., the impact of an extraterrestrial body into the planetary atmosphere, was studied by irradiation of formamide ice and liquid samples with a high-power laser in the presence of potential catalysts. FTIR spectroscopy, time-resolved emission spectroscopy, and GC-MS were subsequently used to monitor the dissociation of this molecule into stable molecular fragments (HCN, H2O, HNCO, H2, CO, and NH3) and unstable species (HNC, •CN, and •NH). The kinetic and thermodynamic models of the high-energy density event molecular dynamics have been suggested together with the reaction routes leading from the dissociation products to the nucleobases. In addition, using theoretical calculations, we propose a simple new reaction pathway for the formation of both pyrimidine and purine nucleobases involving •CN radical chemistry.

A Novel Abiotic Pathway for Phosphine Synthesis over Acidic Dust in Venus' Atmosphere.

Recent ground-based observations of Venus have detected a single spectral feature consistent with phosphine (PH3) in the middle atmosphere, a gas which has been suggested as a biosignature on rocky planets. The presence of PH3 in the oxidized atmosphere of Venus has not yet been explained by any abiotic process. However, state-of-the-art experimental and theoretical research published in previous works demonstrated a photochemical origin of another potential biosignature-the hydride methane-from carbon dioxide over acidic mineral surfaces on Mars. The production of methane includes formation of the HC · O radical. Our density functional theory (DFT) calculations predict an energetically plausible reaction network leading to PH3, involving either HC · O or H· radicals. We suggest that, similarly to the photochemical formation of methane over acidic minerals already discussed for Mars, the origin of PH3 in Venus' atmosphere could be explained by radical chemistry starting with the reaction of ·PO with HC·O, the latter being produced by reduction of CO2 over acidic dust in upper atmospheric layers of Venus by ultraviolet radiation. HPO, H2P·O, and H3P·OH have been identified as key intermediate species in our model pathway for phosphine synthesis.

Optical fiber interferometer array for scanless Fourier-transform spectroscopy.

We report a spatial heterodyne Fourier-transform spectrometer implemented with an array of optical fiber interferometers. This configuration generates a wavelength-dependent stationary interferogram from which the input spectrum is retrieved in a single shot without scanning elements. Furthermore, fabrication and experimental deviations from the ideal behavior of the device are corrected by spectral inversion algorithms. The spectral resolution of our system can be readily scaled up by incorporating longer optical fiber delays, providing a pathway toward surpassing current spectroscopy resolution limits.

Excitation of helium Rydberg states and doubly excited resonances in strong extreme ultraviolet fields: full-dimensional quantum dynamics using exponentially tempered Gaussian basis sets.

Recently optimized exponentially tempered Gaussian basis sets [P. R. Kapralova-Zdanska and J. Smydke, J. Chem. Phys. 138, 024105 (2013)] are employed in quantitative simulations of helium absorption cross-sections and two-photon excitation yields of doubly excited resonances. Linearly polarized half-infinite and Gaussian laser pulses at wavelengths 38-58 nm and large intensities up to 100 TW/cm(2) are considered. The emphasis is laid on convergence of the results with respect to the quality of the Gaussian basis sets (typically limited by a number of partial waves, density, and spatial extent of the basis functions) as well as to the quality of the basis set of field-free states (typically limited by the maximum rotational quantum number and maximum excitation of the lower electron). Particular attention is paid to stability of the results with respect to varying complex scaling parameter. Moreover, the study of the dynamics is preceded by a thorough check of helium energies and oscillator strengths as they are obtained with the exponentially tempered Gaussian basis sets, being also compared with yet unpublished emission wavelengths measured in electric discharge experiments.

On the road from formamide ices to nucleobases: IR-spectroscopic observation of a direct reaction between cyano radicals and formamide in a high-energy impact event.

The formamide-based synthesis of nucleic acids is considered as a nonaqueous scenario for the emergence of biomolecules from inorganic matter. In the current study, we scrutinized the chemical composition of formamide ices mixed with an FeNi meteorite material treated with laser-induced dielectric breakdown plasma created in nitrogen buffer gas. These experiments aimed to capture the first steps of those chemical transformations that may lead to the formation of nucleobases during the impact of an extraterrestrial icy body containing formamide on an early Earth atmosphere. High-resolution FT-IR spectroscopy combined with quantum chemical calculations was used to analyze the volatile fraction of the products formed during such an event. We have found that the spectrum of the evaporated formamide ices is dominated by the spectral signatures of the dimeric form of formamide. Upon exposure to laser sparks, new well-defined bands appear in the spectrum centered at ~820, ~995, and ~1650 cm(-1). On the basis of quantum chemical calculations, these bands can be assigned to the absorptions of 2-amino-2-hydroxy-acetonitrile and to 2-amino-2-hydroxy-malononitrile, which are formed in a direct reaction between formamide and CN(•) radicals upon the high-energy impact event. We also show that there is an exergonic reaction route via these intermediates leading to diaminomaleonitrile, which is generally considered to play a key role in the synthesis of nucleobases.

Combining Fourier transform nuclear quadrupole resonance (FT-NQR) spectroscopy and mass spectrometry (MS) to study the electronic structure of titanocene dichlorides.

A combination of nuclear quadrupole resonance spectroscopy (NQR) and mass spectrometry (MS) has been used to observe trends in electronic structure in three titanocenes: bis(cyclopentadienyl) titanium dichloride (η(5)-C(5)H(5))(2)TiCl(2), bis(pentamethylcyclopentadienyl) titanium dichloride (η(5)-C(5)(CH(3))(5))(2)TiCl(2) and dimethylsilylene-bridged ansa bis(cyclopentadienyl) titanium dichloride Si(CH(3))(2)(η(5)-C(5)H(5))(2)TiCl(2). Using MS, electron ionisation mass spectra of these compounds are presented within the context of the entire homologous series with one to five methyl groups on each cyclopentadienyl ligand. A dedicated NQR spectrometer was constructed for this study with a sensitivity sufficient to precisely determine the NQR resonant frequency of (35)Cl atoms using 3 g samples of these titanocenes. The observed frequencies are thus 11.784, 11.930 and 10.863 MHz at 298 K. The results demonstrate that NQR using a relatively simple apparatus can be used as a sensitive and cost effective probe into the molecular structure of organometallic chlorides, which complements the information inferred from the mass spectra.

Time-resolved Fourier transform emission spectroscopy of He/CH4 in a positive column discharge.

Time-resolved Fourier transform infrared emission spectroscopy was applied to the study of a pulsed discharge in a He/CH(4) mixture. The dynamics of the formation and decay of acetylene ν(3) (3289 cm(-1)), methane ν(3) (3019 cm(-1)) and ν(1) (2917 cm(-1)), the CH radical electronic ground state X(2)Π(r) (2309-2953 cm(-1)), C(2) Bernath electronic transition B(1)Δ(g)-A(1)Π(u) (3337-3606 cm(-1)), molecular hydrogen emission transitions 5g-4f and 2p-2s, atomic hydrogen, and atomic helium were monitored in the 1800-4000 cm(-1) region. The time profile of the rotational and vibrational temperature of the CH radical was obtained for a 30 µs time interval during and after the discharge pulse. A kinetic model was used for the study of the chemical dynamics of the formation and decay of the individual fragments. The results from the model were compared to the experimental emission spectra.

New physical insights: Formamide discharge decomposition and the role of fragments in the formation of large biomolecules.

In this work we present a time-resolved FTIR spectroscopic study on kinetics of atomic and molecular species, specifically CO, CN radical, N2, HCN and CO2 generated in a glow discharge of formamide-nitrogen-water mixture in a helium buffer gas. Radicals such as NH, CH and OH have been proven to be fundamental stones of subsequent chemical reactions having a crucial role in a prebiotic synthesis of large organic molecules. This work contains three main goals. Firstly, we present our time-resolved spectra of formamide decomposition products and discuss the mechanism of collisional excitations between specific species. Secondly, according to our time resolution, we demonstrate and explain the band shape of CO's first overtone and the energy transfer between excited nitrogen and CO, present in our spectra. Lastly, we present theoretical results for the non-LTE modelling of the spectra using bi-temperature approach and a 1D harmonic Franck-Condon approach for the multi-molecule spectra of the formamide decomposition process in the 1800-5600 cm-1 spectral range.

Laser ablation of FOX-7: proposed mechanism of decomposition.

A novel high-energy explosive material, FOX-7 (1,1-diamino-2,2-dinitroethylene), was studied using a combination of laser-induced breakdown spectroscopy (LIBS) and selected ion flow tube mass spectrometry (SIFT-MS). The LIBS technique uses short laser pulses (an ArF excimer laser) as the energy source to convert small quantities of a sample into plasma and to induce the emission of its molecular fragments or atoms. SIFT-MS is a novel method for absolute quantification based on chemical ionization using three reagent ions, with the ability to determine concentrations of trace gases and vapors of volatile organic compounds in real time. SIFT-MS was used to study the release of NO, NO(2), HCN, HONO, HCHO, CH(3)CH(2)OH, and C(2)H(2) after laser ablation of the explosive compound FOX-7 in solid crystalline form. The radiation emitted after excitation was analyzed using a time-resolved UV-vis spectrometer with an ICCD detector. The electronic bands of CN (388 nm), OH (308.4 nm), and NO (237.1 nm) radicals and the atomic lines of C, N, and H were identified.

Oxygen-isotope labeled titania: Ti(18)O2.

(18)O-isotope labelled titania (anatase, rutile) was synthesized. The products were characterized by Raman spectra together with their quantum chemical modelling. The interaction with carbon dioxide was investigated using high-resolution FTIR spectroscopy, and the oxygen isotope exchange at the Ti(18)O(2)/C(16)O(2) interface was elucidated.

HNC/HCN ratio in acetonitrile, formamide, and BrCN discharge.

Time-resolved Fourier transform (FT) spectrometry was used to study the dynamics of radical reactions forming the HCN and HNC isomers in pulsed glow discharges through vapors of BrCN, acetonitrile (CH(3)CN), and formamide (HCONH(2)). Stable gaseous products of discharge chemistry were analyzed by selected ion flow tube mass spectrometry (SIFT-MS). Ratios of concentrations of the HNC/HCN isomers obtained using known transition dipole moments of rovibrational cold bands v(1) were found to be in the range 2.2-3%. A kinetic model was used to assess the roles the radical chemistry and ion chemistry play in the formation of these two isomers. Exclusion of the radical reactions from the model resulted in a value of the HNC/HCN ratio 2 orders of magnitude lower than the experimental results, thus confirming their dominant role. The major process responsible for the formation of the HNC isomer is the reaction of the HCN isomer with the H atoms. The rate constant determined using the kinetic model from the present data for this reaction is 1.13 (±0.2) × 10(-13) cm(3) s(-1).