Equilibrium Structures of Three-, Four-, Five-, Six-, and Seven-Membered Unsaturated N-Containing Heterocycles

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.

Photoionization of aziridine: Nonadiabatic dynamics of the first six low-lying electronic states of the aziridine radical cation

In this article, the theoretical photoionization spectroscopy of the aziridine (C2H5N) molecule is investigated. To start with, we have optimized the geometry of this molecule at the neutral electronic ground state at the density functional theory/augmented correlation-consistent polarized valence triple zeta level of theory using the G09 program. The electronic structure calculations were restricted to the first six low-lying electronic states in order to account for the experimental photoelectron spectrum of the C2H5N molecule. The first six low-lying electronic states (X̃2A', Ã2A', B̃2A″, C̃2A″, D̃2A', and Ẽ2A') of the potential energy surfaces (PESs) are calculated by both equation of motion-ionization potential-coupled cluster singles and doubles and multi-configuration quasi-degenerate perturbation theory ab initio quantum chemistry methods along the dimensionless normal displacement coordinates in which multiple conical intersections were established among the considered electronic states. A (6 × 6) model vibronic Hamiltonian is constructed on a diabatic electronic basis, using the symmetry selection rules and Taylor series expansion. The Cs symmetry point group of the aziridine molecule leads to electronic states symmetry of either A' or A″, and these states are close in energy, due to which the same symmetry electronic states avoid each other. To get a smooth diabatic PES, a fourfold diabatization scheme is used, which is implemented in the General Atomic and Molecular Electronic Structure Systems suite of programs. All the parameters used in the diabatic vibronic coupling model Hamiltonian are calculated in terms of the normal modes of vibrational coordinates. Finally, the vibronic model Hamiltonian constructed for the coupled six electronic states is used to solve both time-independent and time-dependent Schrödinger equations using the multi-configuration time-dependent Hartree program module to obtain the dynamical observables. The theoretical vibronic band structure is found to be in good accord with the available experimental results.

5-(Pyridin-3-yl)-3,4-dihydro-2H-furan-1-ium (NNKFI): a computational study of its physico-chemical properties

Recent work on the diazonium ion metabolite of 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone (NNKDI) suggests that 5-(pyridin-3-yl)-3,4-dihydro-2H-furan-1-ium (NNKFI) may form from NNKDI via an intramolecular reaction. NNKDI is an important carcinogen whose role as an alkylating agent has received significant attention. While there is some experimental evidence supporting NNKFI's production in vitro, it has not yet been directly observed. Little is known about NNKFI's structure and reactivity. We report the first in silico examination of this ion. Our study utilized Kohn-Sham density functional theory (B3LYP/6-311G**) and coupled cluster theory (CCSD/6-31G*) to produce energy-optimized structures, vibrational normal modes and molecular orbitals for NNKFI. To gain insight into the chemical properties of this species, we calculated electrostatic potential surfaces, natural population analysis charges and local Fukui indices. We report data and results for NNKFI's cis and trans conformers. Our work confirms C5 as the preferred site for nucleophilic attack in NNKFI. Stretching motions and predicted bond lengths near O1 are consistent with a somewhat weakened carbonyl structure in this ion. Partial charges, electrostatic potential surfaces and local Fukui indices reveal delocalization of cationic charge on the furanium moiety and notable carbocation character at C5.

Triflic Acid-Promoted 1,2-Amino Migration Reactions in α-Arylaminoacrylamides: Access to Substituted β-Aminoamides

A straightforward synthesis of substituted β-aminoamides from α-arylamino-β-hydroxyacrylamides, α-arylamino-β-oxoamides, or their tautomeric mixture has been described. The (E)-enol triflate intermediates are readily generated in situ from these substrates in the presence of triflic anhydride (Tf2O) and triethylamine (Et3N) in a chemoselective manner and undergo triflic acid (TfOH)-promoted cyclization and ring-opening reactions with alcohols to deliver the desired products. The one-pot two-step synthetic protocol features the use of readily available starting materials, mild reaction conditions, high chemoselectivity, operational simplicity, and a wide range of synthetic potential of the products.

3-Fluoro-2H-azirine: Generation, Characterization, and Photochemistry

The elusive 3-fluoro-2H-azirine, cyclic NCH2CF, has been generated through the stepwise decomposition of the acryloyl azide CH2CFC(O)N3 in an N2-matrix at 10 K. The characterization of cyclic NCH2CF with matrix-isolation IR spectroscopy is supported by 15N isotope labeling and the calculations with density functional theory (DFT) at the B3LYP/6-311++G(3df,3pd) level of theory. Upon irradiation at 193 nm, cyclic NCH2CF undergoes ring opening by forming the more stable nitrile isomer CH2FCN. In contrast to the photodecomposition reactions, the high-vacuum flash pyrolysis of CH2CFC(O)N3 in the gas phase at 500 °C yields the Curtius rearrangement product CH2CFNCO along with secondary fragmentation to the atmospherically relevant fluorocarbonyl radical (FCO) and cyanomethyl radical (CH2CN). Calculations on the potential energy profile for the decomposition reactions of CH2CFC(O)N3 demonstrate that the excessive energy, arising from the highly exothermic Curtius rearrangement of the azide, plays a key role in driving further dissociation reactions of CH2CFNCO by overcoming the formidable barriers (>50 kcal mol-1) under the pyrolysis conditions.

Precise equilibrium structures of 1H- and 2H-1,2,3-triazoles (C2H3N3) by millimeter-wave spectroscopy

The 1H- and 2H-1,2,3-triazoles are isomeric five-membered ring, aromatic heterocycles that may undergo chemical equilibration by virtue of intramolecular hydrogen migration (tautomerization). Using millimeter-wave spectroscopy in the 130-375 GHz frequency range, we measured the spectroscopic constants for thirteen 1H-1,2,3-triazole and sixteen 2H-1,2,3-triazole isotopologues. Herein, we provide highly accurate and highly precise semi-experimental equilibrium (re SE) structures for the two tautomers based on the spectroscopic constants of each set of isotopologues, together with vibration-rotation interaction and electron-mass distribution corrections calculated using coupled-cluster singles, doubles, and perturbative triples calculations [CCSD(T)/cc-pCVTZ]. The resultant structures are compared with a "best theoretical estimate" (BTE), which has recently been shown to be in exceptional agreement with the semi-experimental equilibrium structures of other aromatic molecules. Bond distances of the 1H tautomer are determined to <0.0008 Å and bond angles to <0.2°. For the 2H tautomer, bond angles are also determined to <0.2°, but bond distances are less precise (2σ ≤ 0.0015). Agreement between BTE and re SE values is discussed.

Accurate Ring Strain Energies of Unsaturated Three-Membered Heterocycles with One Group 13-16 Element

High-quality ring strain energy (RSE) data for 1H-unsaturated (CH)₂X parent rings, where X is a group 13–16 element, are reported in addition to the 2H-isomers of the pnictogenirene rings. RSE data are obtained from appropriate homosdesmotic reactions and calculated at the DLPNO-CCSD(T)/def2-TZVPP//B3LYP-D3/def2-TZVP(ecp) level. 1H-Tallirene and 1H-plumbirene have unique donor–acceptor structures between an acetylene π(CC) orbital and an empty p orbital of a metallylene subunit (a Dewar–Chatt–Duncanson description) and therefore cannot be described as proper rings but as pseudocyclic structures. Also, 1H-indirene and 1H-oxirene lack ring critical points and constitute borderline cases of pseudorings. 1H-Unsaturated rings exhibit enhanced RSE compared to their saturated homologues. The mechanism of ring strain relaxation by increasing the s character in the lone pair (LP) of group 15–16 elements is remarkable and increases on descending the groups. Furthermore, RSE is affected by the aromatic character of group 13 rings and certain aromatic or antiaromatic character in group 14 or 15–16 rings, respectively, which tend to vanish on descending the group as shown by NICS(1) values. 2H-Unsaturated rings were found only for group 15 elements (although only 2H-azirine shows a proper cyclic structure) and displayed lower RSE (higher stability) than the corresponding 1H-isomers.

Accurate ring strain energies (RSE) are calculated for three-membered 1H-unsaturated rings containing a 13−16 group element and group 15 2H-isomers. The presence or absence of lone pairs at the heteroatom and the existence of intrinsic or residual (anti)aromaticity were shown to affect the RSE.

A Photoionization Reflectron Time-of-Flight Mass Spectrometric Study on the Detection of Ethynamine (HCCNH2 ) and 2H-Azirine (c-H2 CCHN)

Ices of acetylene (C₂ H₂ ) and ammonia (NH₃ ) were irradiated with energetic electrons to simulate interstellar ices processed by galactic cosmic rays in order to investigate the formation of C₂ H₃ N isomers. Supported by quantum chemical calculations, experiments detected product molecules as they sublime from the ices using photoionization reflectron time-of-flight mass spectrometry (PI-ReTOF-MS). Isotopically-labeled ices confirmed the C₂ H₃ N assignments while photon energies of 8.81 eV, 9.80 eV, and 10.49 eV were utilized to discriminate isomers based on their known ionization energies. Results indicate the formation of ethynamine (HCCNH₂ ) and 2H-azirine (c-H₂ CCHN) in the irradiated C₂ H₂ :NH₃ ices, and the energetics of their formation mechanisms are discussed. These findings suggest that these two isomers can form in interstellar ices and, upon sublimation during the hot core phase, could be detected using radio astronomy.

Dipole moments of conjugated donor-acceptor substituted systems: calculations vs. experiments

We find that quantum mechanical calculations using B3LYP/aug-cc-pVTZ model chemistry involving anharmonic correction on simple conjugated organic compounds without rotating moieties provide the dipole moment values and molecular geometries with high accuracy. In the presence of one or two conjugated electron donating or accepting substituents capable of hindered rotation, the calculated dipole moments reproduce the experimental results equally well only in the cases when the experiments were done at the temperatures at which rotation of substituents remains hindered. In order to reproduce the experimental dipole moments determined at higher temperatures, a model assuming free (unhindered) rotation should be applied. In these cases, the contribution of each rotamer is equal and using anharmonic correction is not necessary. The APFD functional produces similar results and the M062X functional yields larger deviations from the experimental data. The other methods, like HF and MP2, are the least accurate with the basis sets usually employed for interpreting the experimental data.

B3LYP functional can reproduce the experimental dipole moments of conjugated organic molecules with high accuracy.

Predicted Reversal in N-Methylazepine/N-Methyl-7-azanorcaradiene Equilibrium Upon Formation of Their N-Oxides

Density functional calculations and up to five different basis sets have been applied to the exploration of the structural, enthalpy and free energy changes upon conversion of the azepine to the corresponding N-oxide. Although it is well known that azepines are typically much more stable than their 7-azanorcaradiene valence isomers, the stabilities are reversed for the corresponding N-oxides. Structural, thermochemical as well as nucleus-independent chemical shift (NICS) criteria are employed to probe the potential aromaticity, antiaromaticity and nonaromaticity of N-methylazepine, its 7-azanorcaradiene valence isomer. For the sake of comparison, analogous studies are performed on N-methylpyrrole and its N-oxide.

Four undescribed sulfur-containing indole alkaloids with nitric oxide inhibitory activities from Isatis tinctoria L. roots

Four undescribed sulfur-containing indole alkaloids, isatisindigoticanines H, I and isatindigosides F, G along with three known analogues were obtained from Isatis tinctoria L. roots. Isatisindigoticanines H and I contained an unusual 1-(thiazol-4-yl)butane-1,2,3,4-tetraol moiety while isatindigosides F and G possessed a new 3-[3-(1H-indole-2-yl)azet-2-yl]-1H-indole skeleton. The putative biosynthetic pathways of isatisindigoticanines H, I and isatindigosides F, G are proposed. The isolated compounds showed nitric oxide inhibitory effects with IC₅₀ values ranging from 4.3 to 70.3 μM.

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.

Experiment and theory at the convergence limit: accurate equilibrium structure of picolinic acid by gas-phase electron diffraction and coupled-cluster computations

The accurate molecular structure of picolinic acid has been determined from experimental data and computed at the coupled cluster level of theory. Only one conformer with the O[double bond, length as m-dash]C-C-N and H-O-C[double bond, length as m-dash]O fragments in antiperiplanar (ap) positions, ap-ap, has been detected under conditions of the gas-phase electron diffraction (GED) experiment (Tnozzle = 375(3) K). The semiexperimental equilibrium structure, rsee, of this conformer has been derived from the GED data taking into account the anharmonic vibrational effects estimated from the ab initio force field. The equilibrium structures of the two lowest-energy conformers, ap-ap and ap-sp (with the synperiplanar H-O-C[double bond, length as m-dash]O fragment), have been fully optimized at the CCSD(T)_ae level of theory in conjunction with the triple-ζ basis set (cc-pwCVTZ). The quality of the optimized structures has been improved due to extrapolation to the quadruple-ζ basis set. The high accuracy of both GED determination and CCSD(T) computations has been disclosed by a correct comparison of structures having the same physical meaning. The ap-ap conformer has been found to be stabilized by the relatively strong NH-O hydrogen bond of 1.973(27) Å (GED) and predicted to be lower in energy by 16 kJ mol-1 with respect to the ap-sp conformer without a hydrogen bond. The influence of this bond on the structure of picolinic acid has been analyzed within the Natural Bond Orbital model. The possibility of the decarboxylation of picolinic acid has been considered in the GED analysis, but no significant amounts of pyridine and carbon dioxide could be detected. To reveal the structural changes reflecting the mesomeric and inductive effects due to the carboxylic substituent, the accurate structure of pyridine has been also computed at the CCSD(T)_ae level with basis sets from triple- to 5-ζ quality. The comprehensive structure computations for pyridine as well as for carbon dioxide have been used to examine the convergence with respect to the basis set size.

Reaction of 2H-Azirine-Phosphine Oxides and -Phosphonates with Enolates Derived from β-Keto Esters

Cyclopenta[b]-pyrrole-2-phosphine oxides 4a and -phosphonates 4b,c are generated by the addition of cyclic enolates derived from ethyl 2-oxo-cyclopentanecarboxylate 2 to phosphorated 2H-azirines 1. However, the addition of enolate derived from acyclic 2-oxo-butanoate 10 to 2H-azirine phosphine oxide 1 led to vinylogous N-acyl-α-aminoalkyl phosphine oxides 12, involving the carbonyl group and the Cα of the keto ester 10. Ring closure of vinylogous derivative 12 in the presence of base afforded pyrrole-2-phosphine oxide 11. The addition of enolates derived from indenone-carboxylate 15 to 2H-azirines 1 led to the formation of functionalized N-substituted 1H-benzo[d]azepine derivatives 17.

Semiexperimental equilibrium structures for building blocks of organic and biological molecules: the B2PLYP route

The B2PLYP double hybrid functional, coupled with the correlation-consistent triple-ζ cc-pVTZ (VTZ) basis set, has been validated in the framework of the semiexperimental (SE) approach for deriving accurate equilibrium structures of molecules containing up to 15 atoms. A systematic comparison between new B2PLYP/VTZ results and several equilibrium SE structures previously determined at other levels, in particular B3LYP/SNSD and CCSD(T) with various basis sets, has put in evidence the accuracy and the remarkable stability of such model chemistry for both equilibrium structures and vibrational corrections. New SE equilibrium structures for phenylacetylene, pyruvic acid, peroxyformic acid, and phenyl radical are discussed and compared with literature data. Particular attention has been devoted to the discussion of systems for which lack of sufficient experimental data prevents a complete SE determination. In order to obtain an accurate equilibrium SE structure for these situations, the so-called templating molecule approach is discussed and generalized with respect to our previous work. Important applications are those involving biological building blocks, like uracil and thiouracil. In addition, for more general situations the linear regression approach has been proposed and validated.