Cavity Ring-Down Spectroscopy of Anthracene, 9-Methylanthracene, and 2-Methylanthracene in Supersonic Expansion.

The S0-S1 absorption spectra of anthracene (C14H10), 9-methylanthracene (C15H12), and 2-methylanthracene (C15H12) are measured in the ultraviolet region between 330 and 375 nm (26,666 to 30,303 cm-1) with cavity ring-down spectroscopy in supersonic free-jet expansions of argon. The associated vibronic band systems and their spectroscopic assignments are discussed and compared to previous studies performed using fluorescence excitation and dispersed fluorescence techniques. Density functional theory (DFT) calculations were carried out to study the structures and evaluate the vibrational transitions of the ground and excited states. Time-dependent DFT calculations of the first electronic excited states and Franck-Condon factor calculations were carried out to assist in the assignment of the experimentally measured vibronic bands. The vibronic spectra obtained in absorption agree well with fluorescence excitation spectra in terms of peak positions but exhibit different relative band intensities. We find a very good match between experimentally obtained vibronic line positions and the peak positions of the quantum chemically calculated Franck-Condon excitation lines.

Energy Landscape and Structural and Spectroscopic Characterization of Diazirine and Its Cyclic Isomers.

Identifying new nitrogenated hydrocarbon molecules in the interstellar medium (ISM) is challenging because of the lack of comprehensive spectroscopic data from experiments. In this computational work, we focus on investigating the structures, relative energies, spectroscopic constants, and energy landscape of the cyclic isomers of diazirine (c-CH2N2) using ab initio quantum chemical methods. Density functional theory (DFT) methods and coupled cluster theory with singles and doubles including perturbative triples [CCSD(T)] and CCSD(T) with the explicitly correlated F12b correction [CCSD(T)-F12b] were employed for this purpose along with large correlation consistent cc-pVTZ, cc-pVQZ, and cc-pV5Z basis sets. Harmonic vibrational frequencies, infrared vibrational intensities, rotational constants, and dipole moments are reported. Anharmonic vibrational fundamentals along with centrifugal distortion constants, and vibration-rotation interaction constants are also reported for all the cyclic isomers. The energies computed with the CCSD(T) and CCSD(T)-F12b methods were extrapolated to the one-particle complete basis set (CBS) limit following a three-point formula. At the CCSD(T)-F12b/CBS level of theory, the 3,3H-diazirine (c-CH2N2) is the lowest energy cyclic isomer followed by 1,3H-diazirine, (E)-1,2H-diazirine, and (Z)-1,2H-diazirine, which are 20.1, 47.8, and 51.3 kcal mol-1 above the 3,3H-diazirine, respectively. Accurate structures and spectroscopic constants that are reported here could be useful for future identification of these cyclic nitrogenated organic molecules in the interstellar medium or circumstellar disks.

Molecular growth upon ionization of van der Waals clusters containing HCCH and HCN is a pathway to prebiotic molecules.

The growth mechanisms of organic molecules in an ionizing environment such as the interstellar medium are not completely understood. Here we examine by means of ab initio molecular dynamics (AIMD) simulations and density functional theory (DFT) computations the possibility of bond formation and molecular growth upon ionization of van der Waals clusters of pure HCN clusters, and mixed clusters of HCN and HCCH, both of which are widespread in the interstellar medium. Ionization of van der Waals clusters can potentially lead to growth in low temperature and low-density environments. Our results show, that upon ionization of the pure HCN clusters, strongly bound stable structures are formed that contain NH bonds, and growth beyond pairwise HCN molecules is seen only in a small percentage of cases. In contrast, mixed clusters, where HCCH is preferentially ionized over HCN, can grow up to 3 or 4 units long with new carbon-carbon and carbon-nitrogen covalent bonds. Moreover, cyclic molecules formed, such as the radical cation of pyridine, which is a prebiotic molecule. The results presented here are significant as they provide a feasible pathway for molecular growth of small organic molecules containing both carbon and nitrogen in cold and relatively denser environments such as in dense molecular clouds but closer to the photo-dissociation regions, and protoplanetary disks. In the mechanism we propose, first, a neutral van der Waals cluster is formed. Once the cluster is formed it can undergo photoionization which leads to chemical reactivity without any reaction barrier.

Pyruvate Aldol Condensation Product: A Metabolite That Escaped Synthetic Preparation for Over a Century.

The homoaldol condensation product of pyruvate, 2-methyl-4-oxopent-2-enedioic acid (OMPD), has been recently implicated as a catabolic intermediate in the bacterial degradation of lignin and previously identified from other biological sources in reports ranging over 60 years. Yet, while a preparation of the pyruvate homoaldol product precursor, 4-hydroxy-4-methyl-2-oxoglutaric acid (HMOG/Parapyruvate), was first reported in 1901, there has not been a complete published synthesis of OMPD. Analyses of reaction mixtures have helped identify zymonic acid, the lactone of HMOG, as the direct precursor to OMPD. The reaction appears to proceed through an acid- or base-mediated ring opening that does not involve formal lactone hydrolysis. In addition to a preparative protocol, we provide a proposed mechanism for the formation of methylsuccinic acid that arises from the nonoxidative decarboxylation of OMPD. Finally, we calculated the relative stability of the isomers of OMPD and found Z-OMPD to be the lowest in energy. These computations also support our observations that Z-OMPD is the most abundant isomer across a range of pH values.

Climate Metrics for C1-C4 Hydrofluorocarbons (HFCs).

Hydrofluorocarbons (HFCs) are potent greenhouse gases that are potential substitutes for ozone depleting substances. The Kigali amendment lists 17 HFCs that are currently in commercial use to be regulated under the Montreal Protocol. Future commercial applications may explore the use of other HFCs, most of which currently lack an evaluation of their climate metrics. In this work, atmospheric lifetimes, radiative efficiencies (REs), global warming potentials (GWPs), and global temperature change potentials (GTPs) for all saturated HFCs with fewer than 5 carbon atoms are estimated to help guide future usage and policy decisions. Atmospheric lifetimes were estimated using a structure activity relationship (SAR) for OH radical reactivity and estimated O(1D) reactivity. Radiative metrics were obtained using theoretically calculated infrared absorption spectra that were presented in a previous work. Calculations for some additional HFCs not included in the previous work were performed in this work. The HFCs display unique infrared spectra with strong absorption in the Earth's atmospheric infrared window region, primarily due to the C-F stretching vibration. Results from this study show that the HFC global atmospheric lifetimes and REs are dependent upon their H atom content and molecular structure. Therefore, the HFC radiative metric evaluation requires a case-by-case evaluation. A thorough experimental evaluation of a targeted HFC's atmospheric lifetime and climate metrics is always highly recommended. However, in cases where it is experimentally difficult to separate isomers, the new results from this study should help guide the experiments, as well as provide relevant climate metrics with uncertainties and policy relevant data.

Prebiotic Astrochemistry and the Formation of Molecules of Astrobiological Interest in Interstellar Clouds and Protostellar Disks.

Despite the generally hostile nature of the environments involved, chemistry does occur in space. Molecules are seen in environments that span a wide range of physical and chemical conditions and that clearly were created by a multitude of chemical processes, many of which differ substantially from those associated with traditional equilibrium chemistry. The wide range of environmental conditions and processes involved with chemistry in space yields complex populations of materials, and because the elements H, C, O, and N are among the most abundant in the universe, many of these are organic in nature, including some of direct astrobiological interest. Much of this chemistry occurs in "dense" interstellar clouds and protostellar disks surrounding forming stars because these environments have higher relative densities and more benign radiation fields than in stellar ejectae or the diffuse interstellar medium. Because these are the environments in which new planetary systems form, some of the chemical species made in these environments are expected to be delivered to the surfaces of planets where they can potentially play key roles in the origin of life. Because these chemical processes are universal and should occur in these environments wherever they are found, this implies that some of the starting materials for life are likely to be widely distributed throughout the universe.

The Production and Potential Detection of Hexamethylenetetramine-Methanol in Space.

Numerous laboratory studies of astrophysical ice analogues have shown that their exposure to ionizing radiation leads to the production of large numbers of new, more complex compounds, many of which are of astrobiological interest. We show here that the irradiation of astrophysical ice analogues containing H2O, CH3OH, CO, and NH3 yields quantities of hexamethylenetetramine-methanol (hereafter HMT-methanol; C7N4H14O) that are easily detectible in the resulting organic residues. This molecule differs from simple HMT, which is known to be abundant in similar ice photolysis residues, by the replacement of a peripheral H atom with a CH2OH group. As with HMT, HMT-methanol is likely to be an amino acid precursor. HMT has tetrahedral (Td) symmetry, whereas HMT-methanol has C1 symmetry. We report the computed expected infrared spectra for HMT and HMT-methanol obtained using ab initio quantum chemistry methods and show that there is a good match between the observed and computed spectra for regular HMT. Since HMT-methanol lacks the high symmetry of HMT, it produces rotational transitions that could be observed at longer wavelengths, although establishing the exact positions of these transitions may be challenging. It is likely that HMT-methanol represents an abundant member of a larger family of functionalized HMT molecules that may be present in cold astrophysical environments.

Cation, Anion, and Radical Isomers of C4H4N: Computational Characterization and Implications for Astrophysical and Planetary Environments.

Nitrogen-containing ions and molecules in the gas phase have been detected in non-Earth environments such as dark molecular clouds and more recently in the atmosphere of Saturn's moon Titan. These molecules may serve as precursors to larger heterocyclic structures that provide the foundation of complex biological molecules. On Titan, molecules of m/z 66 have been detected by the Cassini mission, and species of the empirical formula C4H4N may contribute to this signature. We have characterized seven isomers of C4H4N in anionic, neutral radical, and cationic states using density functional theory. Structures were optimized using the range-separated hybrid ωB97X-V with the cc-pVTZ and aug-cc-pVTZ basis sets. Anionic and radical C4H4N favor cyclic structures with aromatic and quasi-aromatic electron arrangements, respectively. Interestingly, ionization from the radical surface to the cation induces significant changes in structural stability, and the global minimum for positively charged isomers is CH2CCHCNH+, a pseudo-linear species reminiscent of cyanoallene. Select formation pathways to these structures from Titan's existing or postulated gas-phase species, reactions that are also relevant for other astrophysical environments, are discussed. By characterizing C4H4N isomers, we have identified energetically stable anionic, radical, and cationic structures that may be present in Titan's atmosphere and dark molecular clouds.

Highly Accurate Quartic Force Field and Rovibrational Spectroscopic Constants for the Azirinyl Cation (c-C2NH2+) and Its Isomers.

The azirinyl cation is an aromatic cyclic molecule that is isoelectronic with cyclopropenylidene, c-C3H2, and c-C3H3+. Cyclopropenylidene has been shown to be ubiquitous, existing in many different astrophysical environments. Given the similar chemistry between C and N, and the relative abundances between C and N in astrophysical environments, it is expected that there should be aromatic ringed molecules that incorporate N in the ring, but as yet, no such molecule has been identified. To address this issue, the present study uses high levels of electronic structure theory to compute a highly accurate quartic force field (QFF) for the azirinyl cation and its two lowest lying isomers, the cyanomethyl and isocyanomethyl cations. The theoretical approach uses the singles and doubles coupled-cluster method that includes a perturbative correction for connected triple excitations, CCSD(T), together with extrapolation to the one-particle basis set limit and corrections for scalar relativity and core-correlation. The QFF is then used in a second-order vibrational perturbation theory analysis (VPT2) to compute the fundamental vibrational frequencies and rovibrational spectroscopic constants for all three C2NH2+ isomers. The reliability of the VPT2 vibrational frequencies is tested by comparison to vibrational configuration interaction (VCI) calculations, and excellent agreement is found between the two approaches. Fundamental vibrational frequencies and rovibrational spectroscopic constants for all singly substituted 13C, 15N, and D isotopologues are also reported. It is expected that the highly accurate spectroscopic data reported herein will be useful in the identification of these cations in high-resolution experimental or astronomical observations.

Characterization of Azirine and Its Structural Isomers.

The structures and spectroscopic properties of azirine (C2H3N), a nitrogen-containing three-membered cyclic molecule, and its isomers were studied with state-of-the-art ab initio quantum chemical methods. Azirine is isomeric with methyl cyanide (CH3CN) and methyl isocyanide (CH3NC)-both observed in the star-forming regions of Sgr B2. In this study, we characterize the stationary points on the potential energy surface, relative energies, dipole moments, rotational constants, and harmonic vibrational frequencies of the 2 H-azirine ( a), 1 H-2,2 H-azirine ( b, carbene isomer), and 1 H-azirine ( c) cyclic isomers. The CCSD(T) method and density functional theory (DFT), using the ωB97-X functional, along with Dunning's cc-pVXZ (X = T and Q) basis sets were used to optimize molecular geometries and calculate vibrational frequencies. The 2 H-azirine, an imine isomer ( a), was found to be the lowest in energy among the cyclic isomers, followed by the carbene isomer ( b), and last the 1 H-azirine, an enamine isomer ( c). All three cyclic isomers have a C s symmetry equilibrium structure. Azirines, if identified (three linear C2H3N isomers are already identified in the same source toward the galactic center, Sgr B2), would be the first nitrogen-containing cyclic molecules identified in an astronomical observation.

Identifying Molecular Structural Aromaticity for Hydrocarbon Classification.

Determination of aromaticity in hydrocarbons may be as simple as determining the average bond length for the molecule of interest. This would greatly assist in classifying the nature of hydrocarbon chemistry, especially for large molecules such as polycyclic aromatic hydrocarbons (PAHs) where today's aromatic classification methods are prohibitively expensive. The average C-C bond lengths for a test set of known aromatic, antiaromatic, and aliphatic cyclic hydrocarbons are computed here, and they show strong delineating patterns for the structural discernment of these aromaticity classifications. Aromatic molecules have average C-C bond lengths of 1.41 Å or less with the largest molecules, PAHs, having the longest average C-C bond lengths; aliphatic species have such lengths of 1.50 Å or more; and antiaromatic species fall between the two. Consequently, a first-order guess as to the aromaticity of a system may simply arise from its geometry. Although this prediction will likely have exceptions, such simple screening can easily classify most cases, and more advanced techniques can be brought to bear on the cases that lie in the boundaries. Benchmarks for hydrocarbons are provided here, but other classes of molecular structural aromaticity likely will have to be defined on an ad hoc basis.

Mechanisms of the Formation of Adenine, Guanine, and Their Analogues in UV-Irradiated Mixed NH3:H2O Molecular Ices Containing Purine.

We investigated the formation mechanisms of the nucleobases adenine and guanine and the nucleobase analogues hypoxanthine, xanthine, isoguanine, and 2,6-diaminopurine in a UV-irradiated mixed 10:1 H2O:NH3 ice seeded with precursor purine by using ab initio and density functional theory computations. Our quantum chemical investigations suggest that a multistep reaction mechanism involving purine cation, hydroxyl and amino radicals, together with water and ammonia, explains the experimentally obtained products in an independent study. The relative abundances of these products appear to largely follow from relative thermodynamic stabilities. The key role of the purine cation is likely to be the reason why purine is not functionalized in pure ammonia ice, where cations are promptly neutralized by free electrons from NH3 ionization. Amine group addition to purine is slightly favored over hydroxyl group attachment based on energetics, but hydroxyl is much more abundant due to higher abundance of H2O. The amino group is preferentially attached to the 6 position, giving 6-aminopurine, that is, adenine, while the hydroxyl group is preferentially attached to the 2 position, leading to 2-hydroxypurine. A second substitution by hydroxyl or amino group occurs at either the 6 or the 2 position depending on the first substitution. Given that H2O is far more abundant than NH3 in the experimentally studied ices (as well as based on interstellar abundances), xanthine and isoguanine are expected to be the most abundant bi-substituted photoproducts. Key Words: Astrophysical ice-Abiotic organic synthesis-Nucleic acids-Origin of life-RNA world. Astrobiology 17, 771-785.

Mechanisms for the formation of thymine under astrophysical conditions and implications for the origin of life.

Nucleobases are the carriers of the genetic information in ribonucleic acid and deoxyribonucleic acid (DNA) for all life on Earth. Their presence in meteorites clearly indicates that compounds of biological importance can form via non-biological processes in extraterrestrial environments. Recent experimental studies have shown that the pyrimidine-based nucleobases uracil and cytosine can be easily formed from the ultraviolet irradiation of pyrimidine in H2O-rich ice mixtures that simulate astrophysical processes. In contrast, thymine, which is found only in DNA, is more difficult to form under the same experimental conditions, as its formation usually requires a higher photon dose. Earlier quantum chemical studies confirmed that the reaction pathways were favorable provided that several H2O molecules surrounded the reactants. However, the present quantum chemical study shows that the formation of thymine is limited because of the inefficiency of the methylation of pyrimidine and its oxidized derivatives in an H2O ice, as supported by the laboratory studies. Our results constrain the formation of thymine in astrophysical environments and thus the inventory of organic molecules delivered to the early Earth and have implications for the role of thymine and DNA in the origin of life.

Characterization of the Azirinyl Cation and Its Isomers.

The azirinyl cation (C2H2N(+)) and its geometrical isomers could be present in the interstellar medium. The C2H2N(+) isomers are, however, difficult to identify in interstellar chemistry because of the lack of high-resolution spectroscopic data from laboratory experiments. Ab initio quantum chemical methods were used to characterize the structures, relative energies, and spectroscopic and physical properties of the low energy isomers of the azirinyl cation. We have employed second-order Møller-Plesset perturbation theory (MP2), second-order Z-averaged perturbation theory (ZAPT2), and coupled cluster theory with singles and doubles with perturbative triples CCSD(T) methods along with large correlation consistent basis sets such as cc-pVTZ, cc-pCVTZ, cc-pVQZ, cc-pCVQZ, and cc-pV5Z. Harmonic vibrational frequencies, dipole moments, rotational constants, and proton affinities for the lowest energy isomers were calculated using the CCSD(T) method. Azirinyl cation, a cyclic isomer, is lowest in energy at all levels of theory employed. Azirinyl cation is followed by the cyanomethyl cation (H2CCN)(+), isocyanomethyl cation (H2CNC)(+), and a quasilinear HCCNH(+) cation, which are 13.8, 17.3, and 21.5 kcal mol(-1) above the cyclic isomer, respectively, at the CCSD(T)/cc-pV5Z level of theory. The lowest three isomers all have C2v symmetry and (1)A1 ground electronic states. The quasilinear HCCNH(+) cation has a Cs symmetry planar structure, and a (3)A″ electronic ground state, unlike what some previous work suggested.

Hydrocarbon growth via ion-molecule reactions: computational studies of the isomers of C4H22⁺, C6H2⁺ and C6H4⁺ and their formation paths from acetylene and its fragments.

We seek insight into the origin of observations made in plasma experiments mimicking interstellar and circumstellar conditions. To this end theory is applied to the low-energy isomers of C4H2(+), C6H2(+) and C6H4(+) and their formation paths from acetylene and its fragments. Ab initio molecular dynamics trajectories are performed to explore which isomers are readily accessible from acetylene and its ion fragments. Structural information at a high level of electronic structure theory [CCSD(T)/cc-pVTZ], as well as information on the vibrational [UMP2] and electronic spectra [ωB97X] of the low-energy isomers is reported.

Photosynthesis and photo-stability of nucleic acids in prebiotic extraterrestrial environments.

Laboratory experiments have shown that the UV photo-irradiation of low-temperature ices of astrophysical interest leads to the formation of organic molecules, including molecules important for biology such as amino acids, quinones, and amphiphiles. When pyrimidine is introduced into these ices, the products of irradiation include the nucleobases uracil, cytosine, and thymine, the informational sub-units of DNA and RNA, as well as some of their isomers. The formation of these compounds, which has been studied both experimentally and theoretically, requires a succession of additions of OH, NH2, and CH3groups to pyrimidine. Results show that H2O ice plays key roles in the formation of the nucleobases, as an oxidant, as a matrix in which reactions can take place, and as a catalyst that assists proton abstraction from intermediate compounds. As H2O is also the most abundant icy component in most cold astrophysical environments, it probably plays the same roles in space in the formation of biologically relevant compounds. Results also show that although the formation of uracil and cytosine from pyrimidine in ices is fairly straightforward, the formation of thymine is not. This is mostly due to the fact that methylation is a limiting step for its formation, particularly in H2O-rich ices, where methylation must compete with oxidation. The relative inefficiency of the abiotic formation of thymine to that of uracil and cytosine, together with the fact that thymine has not been detected in meteorites, are not inconsistent with the RNA world hypothesis. Indeed, a lack of abiotically produced thymine delivered to the early Earth may have forced the choice for an RNA world, in which only uracil and cytosine are needed, but not thymine.

Formation and stability of C6H3⁺ isomers.

The stability of the five main isomers of C6H3(+) was investigated using quantum chemical calculations. The cyclic isomers are stabilized by two complementary aromatic effects, first 6-electron π aromaticity, and second a more unusual three-center two-electron σ aromaticity. Two cyclic isomers sit at the bottom of the potential energy surface with energies very close to each other, with a third cyclic isomer slightly higher. The reaction barriers for the interconversion of these isomers, as well as to convert to low-energy linear isomers, are found to be very high with transition states that break both the π and the σ aromaticities. Finally, possibilities for forming the cyclic isomers via association reactions are discussed.

Evidence for the Formation of Pyrimidine Cations from the Sequential Reactions of Hydrogen Cyanide with the Acetylene Radical Cation.

Herein, we report the first direct evidence for the formation of pyrimidine ion isomers by sequential reactions of HCN with the acetylene radical cation in the gas phase at ambient temperature using the mass-selected variable temperature and pressure ion mobility technique. The formation and structures of the pyrimidine ion isomers are theoretically predicted via coupled cluster and density functional theory calculations. This ion-molecule synthesis may indicate that pyrimidine is produced in the gas phase in space environments before being incorporated into condensed-phase ices and transformed into nucleic acid bases such as uracil.