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A: Spectroscopy, Molecular Structure, and Quantum Chemistry
Characterization of Azirine and Its Structural Isomers Claire E Dickerson, Partha P. Bera, and Timothy J Lee J. Phys. Chem. A, Just Accepted Manuscript • DOI: 10.1021/acs.jpca.8b07788 • Publication Date (Web): 23 Oct 2018 Downloaded from http://pubs.acs.org on October 24, 2018
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Characterization of Azirine and its Structural Isomers Claire E. Dickerson1, Partha P Bera2,3*, and Timothy J Lee2* 1 University 2 Space 3 Bay
of Rochester, Rochester, NY 14627
Science and Astrobiology Division, NASA Ames Research Center, Mountain View, CA 94035
Area Environmental Research Institute, Moffett Field, CA 94035
Corresponding author’s e-mail:
[email protected];
[email protected] Abstract 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 2H-azirine (a), 1H2,2H-azirine (b, carbene isomer), and 1H-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 2H-azirine, an imine isomer (a), was found to be the lowest in energy among the cyclic isomers, followed by the carbene isomer (b), and lastly the 1H-azirine, an enamine isomer (c). All three cyclic isomers have a CS symmetry equilibrium structure. Azirines, if identified – three linear C2H3N isomers are already identified in the same source towards the galactic center, Sgr B2 – would be the first nitrogen containing cyclic molecule identified in an astronomical observation.
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I. Introduction Nitrogenous heterocyclic organic molecules are common in most terrestrial biomolecules. Yet, no nitrogen containing cyclic molecules have ever been identified in an extra-terrestrial astrophysical environment in the gas phase thus far, although large organic molecules with nitrogen containing rings have been extracted from meteoritic samples and have been proven to be of extraterrestrial origin.1 Pure carbon containing aliphatic and cyclic organic molecules, as well as nitrogenous organic acyclic molecules are known to be abundant in a variety of astrophysical environments.2 Giant molecular clouds towards the center of the Milky Way galaxy, Sgr A and Sgr B, are reservoirs of molecules with unusual structures.3 A variety of organic molecules are observed in these astrophysical environments; yet many more simple molecules have yet to be identified for many reasons including the lack of appropriate observational data, and lack of high-quality experimental and theoretical data.4
Many
polyatomic molecules and their geometrical isomers were also observed including at least 13 isomer pairs and some isomer triads. The non-cyclic nitrogenous molecules, methyl cyanide, methyl isocyanide, and ketenimine, form a triad that have been previously detected in the molecular clouds, for example, in the giant molecular cloud Sgr B2 towards the center of the galaxy.5-7 Further, methyl isocyanide was shown to have a widespread spatial distribution toward the Sgr B2(N) region. Some observational studies suggest that another isomer of methyl cyanide, keteneimine (H2CCNH), could be present in Sgr B2(N) hot cores.8
“Azirines” are cyclic isomers of methyl cyanide, methyl isocyanide, and keteneimine with the general formula, C2H3N. Azirines are chemically interesting molecules that can act as both nucleophiles as well as electrophiles.9 Because of this versatility they, especially 2H-azirine (a), can be substrates useful in synthesizing larger heterocyclic rings. In the presence of H2O, azirines undergo a ring opening reaction to form alpha-amino ketones. All naturally occurring amino acids contain alpha-amino keto moieties. Azirines (cyclic C2H3N) could, putatively, form via a number of gas phase processes in the molecular clouds including the isomerization of methyl cyanide, methyl isocyanide or any of the linear isomers. Azirines can also be synthesized via the simple association reactions of CH2 with HCN (both of these are known to exist in warmer molecular clouds such as in Sgr B2), or HCCH with NH. Dissociative electron 2 ACS Paragon Plus Environment
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recombination of larger hydrocarbon cations, such as CH3NCH+, are yet another formation mechanism in the gas phase.10-12
Some of the azirines were previously investigated using density functional theory (DFT) (B3LYP/aug-cc-pVTZ), obtaining tautomerism, vibrational frequencies, and molecular parameters.13 A whole host of three-membered cyclic ring compounds were investigated by Lathan et al.14
In 2015 Liu et al. explored the mechanistic aspects of decomposition of 2H-
azirine (a) –see Fig. 1– using molecular dynamics simulations.7
In another investigation
conducted in 2014 Csaszar et al. explored the equilibrium structures of three, four, and fivemembered unsaturated N-containing heterocycles using the CCSD(T) method along with a weighted correlation consistent polarized weighted core-valence triple zeta (cc-pwCVTZ) basis set.15 In that study Csaszar et al. investigated the structures of 2H-azirine (a), and 1H-azirine (c), but did not investigate the carbene isomer (b). Other past studies of azirines have included characterization of linear isomers, as well as cationic and anionic derivatives.16 Formation of pure and nitrogenated hydrocarbons in the environments such as carbonaceous clouds of star forming regions have been studied in the recent past.17, 18
In this study, we have investigated the heterocycles 2H-azirine (a), carbene isomer(b) and 1H-azirine (c) for their structures, harmonic vibrational frequencies, IR intensities, rotational spectroscopic constants, dipole moments, components of the dipole moments, and transition states for rearrangement by employing state-of-the-art quantum chemistry methods. Since the acyclic isomers have been identified in the interstellar medium, and some cyclic isomers are relatively lower in energy compared to the acyclic isomers, it is possible that these cyclic isomers could also exist in similar environments. The aim of this study is to characterize the three azirine cyclic isomers using high level ab initio quantum chemical coupled cluster methods, and to further our understanding of their spectra in order for their future theoretical refinement, and astronomical detection.
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II. Methods The molecular geometries were optimized using coupled cluster singles and doubles with perturbative triples (CCSD(T)),19 and density functional theory with a range-separated ωB97-X functional20 that has been shown to perform extraordinarily well across the board,21 along with Dunning’s correlation consistent basis sets cc-pVTZ.22
The CCSD(T) calculations were
performed at using Dunning’s cc-pVQZ, aug-cc-pVQZ, and cc-pV5Z basis sets. Harmonic vibrational frequencies were computed at the above-mentioned levels of theory, and the double harmonic intensities were computed using the ωB97-X method. As reported earlier, using the CCSD(T) method the basis set limit in bond distances within a few thousandths of an Angstroms is achieved with the cc-pVQZ basis.23, 24 The harmonic vibrational frequencies are off by just a few cm-1 using the same level of theory.25-28 Dipole moments were computed at the CCSD(T)/ccpVQZ equilibrium geometry numerically, after applying finite electric fields of 0.005 au along the x, y, and z axes. The components of the dipole moment along the x, y, and z coordinates are provided in the supporting information in electronic form. All ωB97-X calculations were performed using the Q-Chem 4 quantum chemistry package.29 The MOLPRO 2015.1 quantum chemistry package was used to run all coupled cluster calculations.30
III. Results and Discussions 2H-Azirine (a, Figure 1a) is the lowest energy cyclic isomer, followed by the carbene isomer (b, Figure 1b), which is 29.8 kcal mol-1 higher in energy, and followed by the 1H-azirine isomer (c, Figure 1c) which is 33.5 kcal mol-1 above 2H-azirine. The relative energies of these isomers can be seen in Table 1 at the ωB97-X and CCSD(T) levels of theory. Previous studies of azirines have yielded a similar energy ordering.13, 15 At each level of theory that has been used, the energy ordering of the azirine isomers is consistently: (a) < (b) < (c). In the following sections we discuss the structural and spectroscopic characteristics of the isomers in the order of their relative energies.
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2H-Azirine (a).
The lowest energy cyclic isomer, 2H-azirine (a, Fig. 1a) is a 3-
membered cyclic ring, composed of two carbons and one nitrogen. Three hydrogen atoms are attached, two on one carbon, and the third on the second carbon. Molecules with carbon nitrogen double bonds are called imines, which occur often in biomolecules; azirine is a cyclic imine. For all methods and basis sets used, the lowest energy cyclic minimum, a, has CS point group symmetry, and possesses a 1A electronic ground state.15 At our best CCSD(T)/cc-pV5Z level of theory, the bond angles and bond lengths are:
