Theoretical analysis of the OH-initiated atmospheric oxidation reactions of imidazole.

Imidazoles are present in Earth's atmosphere in both the gas-phase and in aerosol particles, and have been implicated in the formation of brown carbon aerosols. The gas-phase oxidation of imidazole (C3N2H4) by hydroxyl radicals has been shown to be preferentially initiated via OH-addition to position C5, producing the 5-hydroxyimidazolyl radical adduct. However, the fate of this adduct upon reaction with O2 in the atmospheric gas-phase is currently unknown. We employed an automated approach to investigate the reaction mechanism and kinetics of imidazole's OH-initiated gas-phase oxidation, in the presence of O2 and NOx. The explored mechanism included reactions available to first-generation RO2 radicals, as well as alkoxyl radicals produced from RO2 + NO reactions. Product distributions were obtained by assembling and solving a master equation, under conditions relevant to the Earth's atmosphere. Our calculations show a complex, branched reaction mechanism, which nevertheless converges to yield two major closed-shell products: 4H-imidazol-4-ol (4H-4ol) and N,N'-diformylformamidine (FMF). At 298 K and 1 atm, we estimate the yields of 4H-4ol and FMF from imidazole oxidation initiated via OH-addition to position C5 to be 34 : 66, 12 : 85 and 2 : 95 under 10 ppt, 100 ppt and 1 ppb of NO respectively. This work also revealed O2-migration pathways between the α-N-imino peroxyl radical isomers. This reaction channel is fast for the first-generation RO2 radicals, and may be important during the atmospheric oxidation of other unsaturated organic nitrogen compounds as well.

Rotational spectroscopy of methyl tert-butyl ether with a new Ka band chirped-pulse Fourier transform microwave spectrometer.

Chirped-pulse Fourier transform microwave (CP-FTMW) spectroscopy is a powerful tool for performing broadband gas-phase rotational spectroscopy, and its applications include discovery of new molecules, complex mixture analysis, and exploration of fundamental molecular physics. Here we report the development of a new Ka band (26.5-40 GHz) CP-FTMW spectrometer that is equipped with a pulsed supersonic expansion source and a heated reservoir for low-volatility samples. The spectrometer is built around a 150 W traveling wave tube amplifier and has an instantaneous bandwidth that covers the entire Ka band spectral range. To test the performance of the spectrometer, the rotational spectrum of methyl tert-butyl ether (MTBE), a former gasoline additive and environmental pollutant, has been measured for the first time in this spectral range. Over 1000 spectroscopic transitions have been measured and assigned to the vibrational ground state and a newly-identified torsionally excited state; all transitions were fit using the XIAM program to a root-mean-square deviation of 22 kHz. The spectrum displays internal rotation splitting, nominally forbidden transitions, and an intriguing axis-switching effect between the ground and torsionally excited state that is a consequence of MTBE's extreme near-prolate nature. Finally, the sensitivity of the spectrometer enabled detection of all singly-substituted 13C and 18O isotopologues in natural abundance. This set of isotopic spectra allowed for a partial r0 structure involving the heavy atoms to be derived, resolving a structural discrepancy in the literature between previous microwave and electron diffraction measurements.

Automated Reaction Kinetics of Gas-Phase Organic Species over Multiwell Potential Energy Surfaces.

Automation of rate-coefficient calculations for gas-phase organic species became possible in recent years and has transformed how we explore these complicated systems computationally. Kinetics workflow tools bring rigor and speed and eliminate a large fraction of manual labor and related error sources. In this paper we give an overview of this quickly evolving field and illustrate, through five detailed examples, the capabilities of our own automated tool, KinBot. We bring examples from combustion and atmospheric chemistry of C-, H-, O-, and N-atom-containing species that are relevant to molecular weight growth and autoxidation processes. The examples shed light on the capabilities of automation and also highlight particular challenges associated with the various chemical systems that need to be addressed in future work.

Rotational and Vibrational Spectra of the Pyridyl Radicals: A Coupled-Cluster Study.

Pyridyl is a prototypical nitrogen-containing aromatic radical that may be a key intermediate in the formation of nitrogen-containing aromatic molecules under astrophysical conditions. On meteorites, a variety of complex molecules with nitrogen-containing rings have been detected with nonterrestrial isotopic abundances, and larger nitrogen-containing polycyclic aromatic hydrocarbons (PANHs) have been proposed to be responsible for certain unidentified infrared emission bands in the interstellar medium. In this work, the three isomers of pyridyl (2-, 3-, and 4-pyridyl) have been investigated with coupled cluster methods. For each species, structures were optimized at the CCSD(T)/cc-pwCVTZ level of theory and force fields were calculated at the CCSD(T)/ANO0 level of theory. Second-order vibrational perturbation theory (VPT2) was used to derive anharmonic vibrational frequencies and vibrationally corrected rotational constants, and resonances among vibrational states below 3500 cm-1 were treated variationally with the VPT2+K method. The results yield a complete set of spectroscopic parameters needed to simulate the pure rotational spectrum of each isomer, including electron-spin, spin-spin, and nuclear hyperfine interactions, and the calculated hyperfine parameters agree well with the limited available data from electron paramagnetic resonance spectroscopy. For the handful of experimentally measured vibrational frequencies determined from photoelectron spectroscopy and matrix isolation spectroscopy, the typical agreement is comparable to experimental uncertainty. The predicted parameters for rotational spectroscopy reported here can guide new experimental investigations into the yet-unobserved rotational spectra of these radicals.

Coupled Cluster Characterization of 1-, 2-, and 3-Pyrrolyl: Parameters for Vibrational and Rotational Spectroscopy.

Pyrrolyl (C4H4N) is a nitrogen-containing aromatic radical that is a derivative of pyrrole (C4H5N) and is an important intermediate in the combustion of biomass. It is also relevant for chemistry in Titan's atmosphere and may be present in the interstellar medium. The lowest-energy isomer, 1-pyrrolyl, has been involved in many experimental and theoretical studies of the N-H photodissociation of pyrrole, yet it has only been directly spectroscopically detected via electron paramagnetic resonance and through the photoelectron spectrum of the pyrrolide anion, yielding three vibrational frequencies. No direct measurements of 2- or 3-pyrrolyl have been made, and little information is known from theoretical calculations beyond their relative energies. Here, we present an ab initio quantum chemical characterization of the three pyrrolyl isomers at the CCSD(T) level of theory in their ground electronic states, with an emphasis on spectroscopic parameters relevant for vibrational and rotational spectroscopy. Equilibrium geometries were optimized at the CCSD(T)/cc-pwCVTZ level of theory, and the quadratic, cubic, and partial quartic force constants were evaluated at CCSD(T)/ANO0 for analysis using second-order vibrational perturbation theory to obtain harmonic and anharmonic vibrational frequencies. In addition, zero-point-corrected rotational constants, electronic spin-rotation tensors, and nuclear hyperfine tensors are calculated for rotational spectroscopy. Our computed structures and energies agree well with earlier density functional theory calculations, and spectroscopic parameters for 1-pyrrolyl are compared with the limited existing experimental data. Finally, we discuss strategies for detecting these radicals using rotational and vibrational spectroscopy on the basis of the calculated spectroscopic constants.

Rotational Spectrum of the ß-Cyanovinyl Radical: A Possible Astrophysical N-Heterocycle Precursor.

A fundamental question in the field of astrochemistry is whether the molecules essential to life originated in the interstellar medium (ISM), and, if so, how they were formed. Nitrogen-containing heterocycles are of particular interest because of their role in biology; however, to date, no N-heterocycle has been detected in the ISM, and it is unclear how and where such species might form. Recently, the ß-cyanovinyl radical (HCCHCN) was implicated in the low-temperature gas-phase formation of pyridine. While neutral vinyl cyanide (H2CCHCN) has been rotationally characterized and detected in the ISM, HCCHCN has not. Here, we present the first theoretical study of all three cyanovinyl isomers at the CCSD(T)/ANO1 level of theory and the experimental rotational spectra of cis- and trans-HCCHCN, as well as those of their 15N isotopologues, from 5 to 75 GHz. The observed spectra are in good agreement with calculations and provide a basis for further laboratory and astronomical investigations of these radicals.

Reactant Discovery with an Ab Initio Nanoreactor: Exploration of Astrophysical N-Heterocycle Precursors and Formation Pathways.

The incorporation of nitrogen atoms into cyclic compounds is essential for terrestrial life; nitrogen-containing (N-)heterocycles make up DNA and RNA nucleobases, several amino acids, B vitamins, porphyrins, and other components of biomolecules. The discovery of these molecules on meteorites with non-terrestrial isotopic abundances supports the hypothesis of exogenous delivery of prebiotic material to early Earth; however, there has been no detection of these species in interstellar environments, indicating that there is a need for greater knowledge of their astrochemical formation and destruction pathways. Here, we present results of simulations of gas-phase pyrrole and pyridine formation from an ab initio nanoreactor, a first-principles molecular dynamics simulation method that accelerates reaction discovery by applying non-equilibrium forces that are agnostic to individual reaction coordinates. Using the nanoreactor in a retrosynthetic mode, starting with the N-heterocycle of interest and a radical leaving group, then considering the discovered reaction pathways in reverse, a rich landscape of N-heterocycle-forming reactivity can be found. Several of these reaction pathways, when mapped to their corresponding minimum energy paths, correspond to novel barrierless formation pathways for pyridine and pyrrole, starting from both detected and hypothesized astrochemical precursors. This study demonstrates how first-principles reaction discovery can build mechanistic knowledge in astrochemical environments as well as in early Earth models such as Titan's atmosphere where N-heterocycles have been tentatively detected.

The affinity of MhuD for heme is consistent with a heme degrading function in vivo.

MhuD is a protein found in mycobacteria that can bind up to two heme molecules per protein monomer and catalyze the degradation of heme to mycobilin in vitro. Here the Kd1 for heme dissociation from heme-bound MhuD was determined to be 7.6 ± 0.8 nM and the Kd2 for heme dissocation from diheme-bound MhuD was determined to be 3.3 ± 1.1 µM. These data strongly suggest that MhuD is a competent heme oxygenase in vivo.