Non-aromatic Ring Research Articles

Selectively Extending the Curved Side of N-Doped Hexa-peri- hexabenzocoronene.

A curved nanographene, conceptually by insertion of nitrogen into a trapezoidal planar nanographene at the edge was synthesized by π-extension of the nitrogen-doped hexa-peri-hexabenzocoronene. This N-doped nanographene exhibited a π-electronic concave face containing a nonaromatic azepine ring in the middle with a size of 14.0 Å length and 4.0 Å depth, which represents an unprecedented half-side concave geometry of curved nanographene. The bent π-extension exhibited a low degree of conjugation suggested by calculation results. Due to the unique 3D structure and electron-rich property, this nanographene showed pronounced intermolecular charge transfer with C60.

Pillarurilarenes: Glycoluril-Expanded Pillararenes.

Glycoluril-expanded pillararenes composed of glycoluril and dialkoxybenzene units, namely, pillarurilarenes (PURA), were synthesized through a fragment coupling macrocyclization strategy. Partial replacement of dialkoxybenzene with glycoluril endows PURA with polarized equatorial methine protons for derivatization or CH-anion binding. Crystal structures of pillar[2]uril[4]arene and pillar[1]uril[4]arene containing two glycoluril units and one glycoluril unit, respectively, indicated the inward orientation of the glycoluril unit, as also suggested by 1H nuclear magnetic resonance and density functional theory calculation. This work lays a good foundation for expanding pillararenes using non-aromatic rings.

Expected values of sum-based topological indices of random cyclodecane chains

Cyclodecanes, belonging to the class of aliphatic cycloalkanes, comprise non-aromatic carbon-atom rings. Within the 10-membered ring, cyclodecanes exhibit various isomers, characterized by different spatial arrangements of carbon atoms. Serving as model compounds in organic studies, cyclodecanes offer insights into the properties and reactivity of cyclic hydrocarbons. The chemistry of cyclodecane serves as a valuable foundation for understanding the behavior of more complex hydrocarbons. In this paper, we explore the potential probabilities of random cyclodecane chains Dtρ of length t ≥ 3. We derive exact expressions for the expected values of the modified second Zagreb index, inverse index, and second NDe index. A theoretical comparative analysis of these descriptors is provided, accompanied by graphical and numerical representations of the obtained results.

The effect of functional groups on the glass transition temperature of atmospheric organic compounds: a molecular dynamics study.

Organic compounds constitute a substantial part of atmospheric particulate matter not only in terms of mass concentration but also in terms of distinct functional groups. The glass transition temperature provides an indirect way to investigate the phase state of the organic compounds, playing a crucial role in understanding their behavior and influence on aerosol processes. Molecular dynamics (MD) simulations were implemented here to predict the glass transition temperature (Tg) of atmospherically relevant organic compounds as well as the influence of their functional groups and length of their carbon chain. The cooling step used in the simulations was chosen to be neither too low (to supress crystallization) nor too high (to avoid Tg overprediction). According to the MD simulations, the predicted Tg is sensitive to the functional groups as follows: carboxylic acid (-COOH) > hydroxyl (-OH) and (-COOH) > carbonyls (-CO). Increasing the number of carbon atoms leads to higher Tg for the linearly structured compounds. Linear compounds with lower molecular weight were found to exhibit a lower Tg. No clear correlation between O : C and Tg was observed. The architecture of the carbon chain (linear, or branched, or ring) was also found to impact the glass transition temperature. Compounds containing a non-aromatic carbon ring are characterized by a higher Tg compared to linear and branched ones with the same number of carbon atoms.

The influence of heteroatoms on the circularly polarized luminescence performance of [7]helicene derivatives: aromatic vs. non-aromatic five-membered rings.

Helicenes are promising candidates for circularly polarized luminescence (CPL) materials, although the performance is poor due to the unsatisfactory dissymmetric factor (glum) and fluorescence quantum efficiency (ΦF). Herein, the influence of heteroatoms (C, Si, Ge, O, S and Se) on the electronic structures and chiroptical properties of [7]helicene derivatives is systematically investigated using density functional theory (DFT) and time-dependent DFT calculations combined with the thermal vibration correlation function theory. The results reveal that the non-radiative energy consumption processes for helicene systems are closely related to the variation of bond length upon electronic excitation. Moreover, by introducing five-membered rings and heteroatoms, the dipole-forbidden S1 → S0 emission of [7]helicene changes to dipole-allowed transition due to the rearrangement of occupied orbitals and lifting of the nearly degenerate orbitals, resulting in an enhancement of ΦF. As the heteroatomic radius increases, ΦF decreases while the glum increases. Compared with the derivatives containing aromatic five-membered rings ([7]H-O, [7]H-S, and [7]H-Se), the non-aromatic counterparts ([7]H-C, [7]H-Si, and [7]H-Ge) exhibit a balance in ΦF and glum values. The present study helps to clarify the relationship between structures and chiroptical properties and offers a feasible strategy for the future design of helicene-based CPL materials.

Crystal Structure of Zwitterionic (E)-9-(((3-hydroxyphenyl)iminio)methyl)-1,2,3,5,6,7- Hexahydropyrido[3,2,1-ij]Quinolin-8-Olate

The title compound (1), C19H20N2O2, crystallized with single molecule in the asymmetric unit and is present in the zwitterionic form. The compound was synthesized from the condensation reaction of 8-hydroxyjulolidine-9-carbaldehyde and 3-aminophenol. In solid state compound adopts the keto–amine tautomeric form, with the H atom attached to the N atom, which participates in an intramolecular N—H···O hydrogen bond with an S(6) ring motif. The conformation about the C=N bond is E. The aromatic ring of the julolidine moiety is inclined to the phenol ring by 13.00 (10)°. The fused non-aromatic rings of the julolidine moiety adopts a screw-boat conformations. In the crystal, the molecules are connected by N—H···O and O—H···O hydrogen bonds, with adjacent molecules related by a 21 screw axis, generating– A–B–A–B–zigzag chains extending along [010]. Furthermore, adjacent molecules are linked by pairs of C—H···O interactions, forming a ladder-like structure propagating along the a-axis direction. Density functional theory (DFT) optimized structures at the B3LYP/6–311 G(d,p) level is compared with the experimentally determined molecular structure in the solid state.

Efficient separation of indole from fossil fuel pyrolysis products by carboxylic acid non-aromatic ring ionic liquids: Experiment and mechanism exploration

Indole is a nitrogen-containing compound that is obtained from fossil fuel pyrolysis products. Its usage is not only related to the production of fine chemicals and medicines, but it also has the potential to benefit environmental protection. To separate indole through liquid–liquid extraction with ionic liquids, two types of carboxylic acid non-aromatic ring ionic liquids (CNILs) were successfully synthesized and characterized in this work. The effects of stirring time, mCNILs: mmixtures, and extraction temperature were extensively investigated in this work. The results indicate that the adopted CNIL, [N-tmg][Bpc], which processes multifunctional sites, exhibited better extraction performance for indole. Under the optimized conditions (mCNILs: mmixtures = 1:5, temperature, 25 °C, stirring time, 30 min) and initial indole content, mindole: moil = 5:100, the extraction efficiency of indole was found to be 97.08% using the CNIL [N-tmg][Bpc]. Additionally, the molecular polarity, bond length, interaction energy, and non-covalent interaction were evaluated via quantum chemistry calculation, and found that the non-covalent interaction between the CNIL anions and indole was the primary driver of extraction, and the multifunctional sites in CNIL anions improved the ability of CNILs to extract indole. Finally, the reusability of CNIL, [N-tmg][Bpc], was tested through repeated extraction experiments, and the recovered [N-tmg][Bpc] was found to efficiently extract indole. The successful synthesis of CNILs with high extraction performance for indole provides a novel route to develop new ionic liquid separation agents. The finding in this work contributes to the chemical industry's efforts to develop appropriate and sustainable technologies for indole separation.

Detection and characterisation of oxocyclohexan[b]indoles by combined application of vibrational spectroscopy and mass spectrometry

The vibrational and mass spectra of a representative set of nine oxocyclohexan[b]indoles (tricyclic indoles with a 6,5,6 ring pattern) with a carbonyl group in each of the four positions of the third non-aromatic ring and up to two methyl substituent(s) attached to the carbon atoms in the other positions of this ring are reported and discussed. Particular attention is focused on the use of infrared spectroscopy to determine whether these compounds may best be described as ketoindoles or hydroxyindolenines. Most of these spectra indicate that the tricyclic heterocycles exist preferentially at ketoindoles, but the solid state infrared spectra of oxocyclohexan[b]indoles with the oxygen function in the 4-position are highly unusual, giving the initial impression that these compounds are hydroxyindolenines. Computational modelling supports the interpretation that the 4-ketoindole tautomer has a lower energy than either of its most stable isomeric indolenines conformers. Mass spectrometry is shown to provide valuable confirmatory evidence to differentiate the isomeric ionised oxocyclohexan[b]indoles, which dissociate via distinctive and informative fragmentation routes, in which the stability of intermediate distonic ions appears to be profoundly influenced by participation of the lone pair of electrons on the nitrogen atom. Many of these fragmentations are better described by stepwise mechanisms, rather than as concerted cycloreversions.

Screening of Ionic Liquid-Based Electrolytes for Al Dual-Ion Batteries: Thermodynamic Cycle and Combined MD-DFT Approaches

The electrochemical window (ECW) of the ionic liquid (IL) is the fundamental parameter to understand the stability of the electrolyte for a given electrode material. Here, we have considered room-temperature and molten salt-based 16 IL-based electrolytes, consisting of imidazolium-, pyrrolidinium-, urea-, and acetamide-based cations coupled with AlCl4 and OTf (trifluoromethanesulfonate) anions. Three different high-throughput computational screening techniques have been implemented to calculate the ECW of these electrolytes for dual-ion batteries (DIBs). The thermodynamic cycle method has been employed to calculate the oxidation and reduction potentials with respect to the Al3+/Al reference electrode for the individual ions of the IL. Classical molecular dynamics followed by DFT methods (MD + DFT) have been considered to calculate anodic and cathodic limiting potentials. From the MD + DFT, we have classified two methods, AIMD-min and AIMD-sp. The calculated ECWs for all considered ILs using the AIMD-min method are found to be close to experimental outcomes compared to other two methods. We show that the alkyl group of the imidazolium ring has a very limited effect on the ECW values. On the other hand, aromatic imidazolium rings are more prone to reduction compared to the nonaromatic pyrrolidinium ring. Moreover, we have investigated the contribution of cations and anions in cathodic and anodic potentials, from the study of density of states. Along with that, we have tested the robustness capability of the AIMD-min method and established a superior technique for other liquid systems to calculate the ECW. This work facilitates a step forward in selecting nonaqueous electrolytes for rechargeable DIBs.

Overlooked Contribution of the Indole Moiety to the Formation of Haloacetonitrile Disinfection Byproducts

Haloacetonitriles (HANs) are a group of disinfection byproducts with high toxicity and frequent occurrence. Past studies have focused on the free amine groups, especially those in amino acids, as HAN precursors. This study reports, for the first time, that the indole moiety such as that in the tryptophan side chain is also a potent precursor for the most common HANs dichloroacetonitrile, bromochloroacetonitrile, and dibromoacetonitrile. 3-Indolepropionic acid, differing from tryptophan only in the absence of the free amine group, formed HANs at levels 57-76% of those by tryptophan at a halogen/nitrogen molar ratio of 10. Experiments with tryptophan-(amino-15N) showed that the indole contributed to 28-51% of the HANs formed by tryptophan. At low oxidant excess (e.g., halogen/precursor = 5), 3-indolepropionic acid even formed more HANs than Trp by 3.5-, 2.5-, and 1.8-fold during free chlorination, free bromination, and chlorination in the presence of bromide (0.6 mg/L), respectively. Indole's HAN formation pathway was investigated by exploring the chlorination/bromination products of 3-indolepropionic acid using liquid chromatography-orbitrap high-resolution mass spectrometry. A total of 22 intermediates were detected, including pyrrole ring-opening products with an N-formyl group, 2-substituted anilines with different hydroxyl/halogen substitutions, and an intermediate with a postulated non-aromatic ring structure.

Two asymmetric small molecule acceptors with aromatic and non-aromatic ring side chains were developed for organic solar cells

Asymmetric side-chain engineering has been demonstrated to be an effective approach for modifying the solubility and morphology of non-fullerene small molecule acceptors (NF-SMAs). However, prior research has mostly concentrated on optimizing the length and branching locations of alkyl chains. Phenyl and cyclohexyl groups suspended on the side chains have been shown to be effective for tuning the crystallinity and self-assembly of symmetric organic molecules for efficient organic solar cells. To investigate the impact of the aromatic and non-aromatic ring side chains on the performance of asymmetric NF-SMAs, two asymmetric acceptors, Y-Ph4F and Y–CH4F, are designed with phenyl and cyclohexyl as two distinct side chains, respectively, in this work. Due to their common backbone, the two NF-SMAs exhibit similar absorption spectra and energy levels as determined by UV–vis absorption, cyclic voltammetry, and density functional theory calculations. Differential scanning calorimetry (DSC) and powder X-ray diffraction (XRD) demonstrate that Y–CH4F with 4-cyclohexylbutyl side chains has stronger molecular packing and crystallinity in the solid state compared to Y-Ph4F with 4-phenylbutyl side chains. By pairing these NFAs with a well-known polymer donor PM6, both PM6:Y-Ph4F and PM6:Y-Ph4F-based organic solar cells (OSCs) achieve power conversion efficiencies (PCEs) of more than 15%. When fabricated with a 1 cm2 active area, the Y-Ph4F and Y–CH4F-based devices can also obtain exceptional PCEs of 15.05% and 14.10%, respectively. These findings suggest that the aromatic and non-aromatic ring side chains can effectively tune the molecular packing and crystallinity for efficient OSCs.

Determination of Barbiturates by Femtosecond Ionization Mass Spectrometry.

Barbiturates are highly susceptible to dissociation in mass spectrometry (MS) because of their long side chains combined with a nonaromatic ring consisting of several carbonyl and amine groups. As a result, they exhibit extensive α-cleavage and subsequent rearrangement, making the identification of these compounds difficult. Although a library of electron ionization MS (EIMS) is available, most barbiturates have very similar fragment patterns. Accordingly, it would be desirable to develop a technique for soft ionization, providing a molecular ion and large fragment ions as well. In this study, a molecular ion was clearly observed, in addition to large fragment ions, for a variety of barbiturates based on multiphoton ionization MS (MPIMS) using a tunable ultraviolet femtosecond laser as the ionization source (fs-LIMS). This favorable result was achieved when the optimal laser wavelength for minimizing the excess energy remaining in the ionic state was used. An examination of the photofragmentation pathways suggested that an H atom in the side chain was abstracted by an oxygen atom in the carbonyl group in the ring structure thus initiating fragmentation and subsequent rearrangement. Barbiturates that are substituted with alkyl groups (amobarbital and pentobarbital) had narrower spectral regions for optimal ionization than the other barbiturates with alkyl and alkenyl groups (butalbital and secobarbital) and more with alkyl and phenyl groups (phenobarbital). All of the barbiturates studied provided unique mass spectral patterns in fs-LIMS, which was useful for the reliable identification of these compounds in practical trace analysis.

Perception of Mg adsorption on the BC2N nanotube as a anode for rechargeable Mg ion batteries

Owing to their cost-effectiveness and the natural abundance of magnesium, magnesium-ion batteries (MIBs) were introduced as encouraging alternatives to Lithium-ion batteries. Following the successful synthesis of carbon nano-tube, its B and N doped derivatives which were doped with B and N enjoyed the attention of researchers as novel anode materials (AM) for MIBs. Here, we investigated a BC2N nano-tube (BC2NNT) as an encouraging AM for MIBs. To have a deeper understanding of the electrochemical properties, cycling stability, specific capacity (SC) and the adsorption behavior of this nano-tube, first-principles density functional theory computations were performed. By performing NMR calculations, we identified two types of non-aromatic hexagonal rings, namely B2C2N2 (I) and BC4N (II). Magnesium was adsorbed onto I with the adsorption energy of −40.38 kcal/mol and on II with the adsorption energy −20.15 kcal/mol. The SCs were as high as 783 mAh/g. The predicted average open-circuit voltage for BC2NNT was 1.94 V, which was greater than that of other 2D materials. The findings demonstrated the possibility of utilizing the BC2NNT as an AM for MIBs. The results can provide useful insights into the design of boron-carbon-nitrogen-based AMs for MIBs.

Complete Set of Diketopyrrolopyrrole Centrosymmetrical Cofacial Stacked Pairs.

Stacked centrosymmetrical dimers and simultaneously H-bonded and stacked hexamers of thiophene-substituted diketopyrrolopyrrole (ThDPP) were studied using DFT as models for crystals with slipped-stacked molecules in 1D columns. Eight stacked dimer arrangements were found, six of which are driven by the minimisation of electron repulsion and realised by placing the partially negatively charged atoms of the diketopyrrolopyrrole rings below the centre of an adjacent thiophene ring. Four of these stacks are related to N,N'-dialkylated derivatives of ThDPP found in the literature, while a further one is related to an N,N'-diacylated derivative. An analogous set of eight stacks was discovered computationally for phenyl-substituted DPP (PhDPP), four of which are known among H-bonded DPP pigments, and one more among N,N'-dialkylated PhDPP derivatives. The results shed more light on the mechanisms that drive the formation of stacks between nonaromatic (DPP) and aromatic (Th, Ph) rings. The excitation energies of the lowest four singlet states computed by TD DFT enabled excitonic coupling and energy separation between Frenkel-resonance-type and charge-transfer states to be established, depending on the equilibrium stack geometry.

Automation of AMOEBA polarizable force field for small molecules: Poltype 2.

A next-generation protocol (Poltype 2) has been developed which automatically generates AMOEBA polarizable force field parameters for small molecules. Both features and computational efficiency have been drastically improved. Notable advances include improved database transferability using SMILES, robust torsion fitting, non-aromatic ring torsion parameterization, coupled torsion-torsion parameterization, Van der Waals parameter refinement using ab initio dimer data and an intelligent fragmentation scheme that produces parameters with dramatically reduced ab initio computational cost. Additional improvements include better local frame assignment for atomic multipoles, automated formal charge assignment, Zwitterion detection, smart memory resource defaults, parallelized fragment job submission, incorporation of Psi4 quantum package, ab initio error handling, ionization state enumeration, hydration free energy prediction and binding free energy prediction. For validation, we have applied Poltype 2 to ~1000 FDA approved drug molecules from DrugBank. The ab initio molecular dipole moments and electrostatic potential values were compared with Poltype 2 derived AMOEBA counterparts. Parameters were further substantiated by calculating hydration free energy (HFE) on 40 small organic molecules and were compared with experimental data, resulting in an RMSE error of 0.59 kcal/mol. The torsion database has expanded to include 3543 fragments derived from FDA approved drugs. Poltype 2 provides a convenient utility for applications including binding free energy prediction for computational drug discovery. Further improvement will focus on automated parameter refinement by experimental liquid properties, expansion of the Van der Waals parameter database and automated parametrization of modified bio-fragments such as amino and nucleic acids.

(E)-5-(4-Methyl-benzyl-idene)-1-phenyl-4,5,6,7-tetra-hydro-1H-indazol-4-one.

In the title compound, C21H18N2O, the non-aromatic six-membered ring adopts a distorted envelope conformation with one of the methyl-ene-C atoms being the flap atom. The dihedral angle between the phenyl and 4-tolyl rings is 75.3 (1)°. The 1,2-diazole ring forms dihedral angles of 41.9 (1) and 65.5 (1)° with the phenyl and 4-tolyl rings, respectively. In the crystal, stabilizing C-H⋯O, C-H⋯π and π-π inter-actions are evident. The calculated Hirshfeld surfaces highlight the prominent role of C-H⋯O inter-actions (8.6%), along with H⋯H (51.7%) and C⋯H/H⋯C (29.2%) surface contacts.

A conjugated diosma-octacyclic complex and its mixed-valence singly reduced state

A conjugated diosma-octacyclic complex, with aromatic osmapentalene termini and the rigid naphthalene bridge linked by non-aromatic osmafuran rings, forms a singly reduced valence-trapped species characterised at low temperature.

Optical Characteristics and Applications of AIE Racemic C6-Unsubstituted Tetrahydropyrimidines.

Racemic C6-unsubstituted tetrahydropyrimidines (THPs) are the products of an efficient five-component reaction that we developed. THPs show strong AIE characteristics, that is, completely no fluorescence in different solvents but strong emission with fluorescence quantum yields (Φ F) up to 100% upon aggregation. However, the Φ F values of their pure enantiomers are lower than 46%. Unlike common AIE compounds with crowded aryl rotors on a π-bond or on an aryl ring, THPs have three completely non-crowded aryl rotors on a non-aromatic chiral central ring (tetrahydropyrimidine). In this mini review, we first discuss the AIE characteristics of THPs and the influences of molecular structures on their molecular packing modes and optical properties, and then present their applications and forecast the development of other racemic AIE compounds.

(E)-5-(4-Chloro-benzyl-idene)-1-phenyl-4,5,6,7-tetra-hydro-1H-indazol-4-one: crystal structure and Hirshfeld surface analysis.

In the title compound, C20H15ClN2O, the non-aromatic six-membered ring adopts a distorted envelope conformation with methyl-ene-C atom nearest to the five-membered ring being the flap atom. The dihedral angle between the phenyl and chloro-benzene rings is 74.5 (1)°. The heterocyclic ring forms dihedral angles of 37.9 (1) and 64.3 (1)° with the phenyl and chloro-benzene rings, respectively. In the crystal, weak C-H⋯O inter-actions feature predominantly within the three-dimensional architecture. The inter-molecular inter-actions are further analysed with the calculation of the Hirshfeld surfaces highlighting the prominent role of C-H⋯O inter-actions, along with H⋯H (36.8%) and C⋯H/H⋯C (26.5%) contacts.

Large-Scale Analysis of Bioactive Ligand Conformational Strain Energy by Ab Initio Calculation.

Ligand conformational strain energy (LCSE) plays an important role in virtual screening and lead optimization. While various studies have provided insights into LCSE for small-molecule ligands in the Protein Data Bank (PDB), conclusions are inconsistent mainly due to small datasets, poor quality control of crystal structures, and molecular mechanics (MM) or low-level quantum mechanics (QM) calculations. Here, we built a high-quality dataset (LigBoundConf) of 8145 ligand-bound conformations from PDB crystal structures and calculated LCSE at the M062X-D3/ma-TZVPP (SMD)//M062X-D3/def2-SVP(SMD) level for each case in the dataset. The mean/median LCSE is 4.6/3.7 kcal/mol for 6672 successfully calculated cases, which is significantly lower than the estimates based on molecular mechanics in many previous analyses. Especially, when removing ligands with nonaromatic ring(s) that are prone to have large LCSEs due to electron density overfitting, the mean/median LCSE was reduced to 3.3/2.5 kcal/mol. We further reveal that LCSE is correlated with several ligand properties, including formal atomic charge, molecular weight, number of rotatable bonds, and number of hydrogen-bond donors and acceptors. In addition, our results show that although summation of torsion strains is a good approximation of LCSE for most cases, for a small fraction (about 6%) of our dataset, it underestimates LCSEs if ligands could form nonlocal intramolecular interactions in the unbound state. Taken together, our work provides a comprehensive profile of LCSE for ligands in PDB, which could help ligand conformation generation, ligand docking pose evaluation, and lead optimization.