Aromaticity in heterocycles: new HOMA index parametrization

Photochemical Synthesis of 7,12-Dioxa[8]helicene and Density Functional Theory Studies: Unravelling the One-Way Valve System Involving Steric Crowding and Aromatic Stability

C2 symmetric chiral 7,12-dioxa[8]helicenes were synthesized through a series of photochemical E-Z isomerization, electrocyclic reaction, and oxidation steps in a stepwise sequential manner at both the ends of 2,9-di((E)-styryl)naphtho[2,1-b:7,8-b']difuran. The chemical transformations complemented with density functional theory (DFT) studies delineate some fundamental concepts, exhibiting counter current effects, namely, destabilization caused by increasing steric crowding and stabilization caused by aromatic units on the overall transformation. The calculated energy profile diagram unravels the formation of photoinduced intermediate species with increasing free energies for the E-Z isomerization and the electrocyclic reactions; the reverse processes for the said steps are prevented by a specific barrier-less oxidation step forming aromatic rings, presenting a one-way valve situation. The steric crowding-related increase in free energy and its counterbalancing by aromaticity have been illustrated for the helicene system using DFT studies. HOMA analysis shows that each individual ring in 7,12-dioxa[8]helicene exhibits a strong aromatic character, supporting the Fries model empirically. Interestingly, despite the nonplanar and sterically crowded geometry, 7,12-dioxa[8]helicene displayed a large HOMO-LUMO gap, typical of aromatic compounds.

Pd(II) and Cu(III) Complexes of Multiply Fused Pentaphyrin Isomers with Tunable Structures and NIR Absorption

Fused porphyrinoids have received increasing interest in light of their extended conjugation and unique coordination behavior. On the basis of our previously reported multiply fused pentaphyrin isomers 1 and 2, a novel isomer 3 has been synthesized in this work. 3 possesses a hexacyclic fused moiety with a nearly coplanar CCNN cavity involving an inverted pyrrole, which is slightly different from the CNNN ones of 1 and 2 involving an N-confused pyrrole. 1-3 possess cavities with three depronatable protons and thus they all can generate Cu(III) complexes. However, only 3Cu is stable under ambient conditions. On the other hand, 3 remains intact upon treatment with Pd(II) ions, while 1 and 2 could undergo structural rearrangement to accommodate Pd(II), affording 1Pd and 2Pd accompanied by the formation of a lactone ring and the addition of a methoxy group, respectively. Compared with the free bases, the complexes show distinct aromaticity and more intense near-infrared (NIR) absorption up to ca. 1600, 1170, and 1500 nm, respectively. The results indicate that the subtle modification of the linking modes between the pyrrolic units in the fused pentaphyrinoids is effective in modulating the coordination behavior for synthesizing complexes with tunable aromaticity and NIR absorption.

The σ+π dual aromaticity of typical bi-tetrazole ring molecule TKX-50

Two complexes of dihydroxylammonium 5,5'-bistetrazole-1,1'-diolate (TKX-50) were employed to evaluate the aromaticity of their tetrazole rings via deep analysis such as the electronic structure, the ZZ component of the natural chemical shielding tensor (NICSZZ) and component orbitals, localized orbital locator purely contributed by σ-orbitals (LOL-σ) and localized orbital locator purely contributed by π-orbitals (LOL-π), the anisotropy of the induced current density (AICD) and the ZZ component of iso-chemical shielding surface (ICSSZZ) of these tetrazole rings thereof. The conclusion shows: that all tetrazole rings and bi-tetrazole rings in complexes have strong σ and a comparable strength π double aromaticity; all these magnetic shields almost symmetrically increase from the central axis to the tetrazole ring atoms; tetrazole rings in complex II show a little stronger dual aromaticity than that in complex I mainly due to the different orientation of the fragment 2 encompassing two hydroxylamine groups resulting in different effects on the contributions of σ orbitals and π orbitals to total aromaticity of tetrazole rings thereof; the difference in aromaticity is fundamentally caused by the atoms O with stronger electron-withdrawing than atom N in fragment 2 interact with bi-tetrazole ring through O in complex I but through N in complex II.

Switchable Design of Redox-Enhanced Nonaromatic Quinones Enabled by Conjugation Recovery

An innovative switchable design strategy for modulating the electronic structures of quinones is proposed herein, leading to remarkably enhanced intrinsic redox potentials by restoring conjugated but nonaromatic backbone architectures. Computational validation of two fundamental hypotheses confirms the recovery of backbone conjugation and optimal utilization of the inductive effect in switched quinones, which affords significantly improved redox chemistry and overall performance compared to reference quinones. Geometric and electronic analyses provide strong evidence for the restored backbone conjugation and nonaromaticity in the switched quinones, while highlighting the reinforcement of the inductive effect and suppression of the resonance effect. This strategic approach facilitates the development of an exceptional quinone, viz. 2,6-naphthoquinone, with outstanding performance parameters (338.9 mAh g-1 and 912.9 mWh g-1). Furthermore, 2,6-anthraquinone with superior cyclic stability, demonstrates comparable performance (257.4 mAh g-1 and 702.8 mWh g-1). These findings offer valuable insights into the design of organic cathode materials with favorable redox chemistry in secondary batteries.

Synthesis of mesoionic triazolones via a formal [3+2] cycloaddition between 4-phenyl-1,2,4-triazoline-3,5-dione and alkynes

1,2,4-Triazoline-3,5-diones (TADs) are versatile reagents and have found widespread adoption in chemical science. Despite their remarkable reactivity toward a wide array of unsaturated hydrocarbons, the chemical reaction between TADs and alkynes has remained largely unexplored. Herein, we demonstrate that 1,1,1,3,3,3-hexafluoro-2-propanol facilitates the unusual [3+2] cycloaddition between 4-phenyl-1,2,4-triazoline-3,5-dione and alkynes, resulting in the formation of unprecedented mesoionic triazolones. Moreover, the structural properties of the resulting triazolone have been investigated by employing X-ray diffraction analysis and Density Functional Theory (DFT) calculations.

HOMA Index Establishes Similarity to a Reference Molecule

The article shows that the definition of the HOMA index of geometrical aromaticity satisfies the axioms of a similarity function between the examined and benzene ring. Consequently, for purely mathematical reasons, the index works exceptionally well as an index of aromaticity: it expresses a geometric similarity to the archetypal aromatic benzene. Thus, if the molecule is geometrically similar to benzene, then it is also chemically similar, and therefore, it is aromatic. However, the similarity property legitimizes using the HOMA-like indices to express similarity to molecules other than benzene, whether cyclic or linear and existing or hypothetical. The paper demonstrates an example of HOMA-similarity to cyclohexane, which expresses a (relaxed)-saturicity property not accompanied by strong structural strains or steric hindrances. Further, it is also shown that the HOMA index can evaluate the properties of whole molecules, such as 25 unbranched catacondensed isomers of hexacene. The index exhibits a significant quadratic correlation with the total energy differences of planar isomers from which the nonplanar ones deviate. Moreover, the HOMA index of hexacene isomers significantly correlates with the Kekulé count connected to the resonance energy in the Hückel approximation. As a result, the study shows that the HOMA index can be used not only for aromaticity analyses but also as a general chemical descriptor applicable to rings, chains, composed molecular moieties, or even whole molecules.

The role of aromaticity in the cyclization and polymerization of alkyne-substituted porphyrins on Au(111)

Aromaticity is an established and widely used concept for the prediction of the reactivity of organic molecules. However, its role remains largely unexplored in on-surface chemistry, where the interaction with the substrate can alter the electronic and geometric structure of the adsorbates. Here we investigate how aromaticity affects the reactivity of alkyne-substituted porphyrin molecules in cyclization and coupling reactions on a Au(111) surface. We examine and quantify the regioselectivity in the reactions by scanning tunnelling microscopy and bond-resolved atomic force microscopy at the single-molecule level. Our experiments show a substantially lower reactivity of carbon atoms that are stabilized by the aromatic diaza[18]annulene pathway of free-base porphyrins. The results are corroborated by density functional theory calculations, which show a direct correlation between aromaticity and thermodynamic stability of the reaction products. These insights are helpful to understand, and in turn design, reactions with aromatic species in on-surface chemistry and heterogeneous catalysis.

Gad S, M. El-Mehasseb I, E. El-Kelany K. Isosterism in pyrrole via azaboroles substitution, a theoretical investigation for electronic structural, stability and aromaticity

This work uses ab-initio CBS-QB3 and density functional theory (B3LYP) to analyze the structure, stability, and aromaticity of all isosteric nitrogen-boron pyrroles. The mono-NB unit substituted group of the isosteric NB pyrrole has four isosteres, whereas the multi-NB unit substituted group has two isosteres. These two groups make up all isosteric NB pyrrole. For structural, energetic, magnetic, and electron delocalization criteria, the results highlight the predominance of the PN3B2 isostere and its greater stability over other conformers. In addition, the global reactivity indices, ESP, HOMO-LUMO, and NBO charges have all been estimated to forecast the active side's electron donation and acceptance. These isosteres are categorized as weak electrophiles and marginal nucleophiles. NB-isosteres have poorer stability, HOMO-LUMO gap, and aromaticity than the parent (pyrrole). In general, NB compounds with more ring sharing are less aromatic than NB molecules with less ring sharing. The current study is anticipated to help in understanding of the chemistry of NB substituted molecules and their experimental identification and characterization.

A density functional theory study of the molecular structure, reactivity, and spectroscopic properties of 2-(2-mercaptophenyl)-1-azaazulene tautomers and rotamers

Five stable tautomer and rotamers of the 2-(2-Mercaptophenyl)-1-azaazulene (thiol, thione, R1, R2, and R3) molecules were studied using density functional theory (DFT). The geometries of the studied tautomer and rotamers were fully optimized at the B3LYP/6-31G(d,p) level. Thermodynamic calculations were performed at M06-2X/6-311G++(2d,2p) and ωB97XD/6-311G++(2d,2p) in the gas phase and ethanol solution conditions modeled by the solvation model based on density (SMD). The kinetic constant of tautomer and rotamers conversion was calculated in the temperature range 270-320 K using variational transition state theory (VTST) accompanied by one-dimensional wigner tunneling correction. Energy refinement at CCSD(T)/6-311++G(2d,2p) in the gas phase has been calculated. All the studied DFT methods qualitatively give similar tautomer stability orders in the gas phase. The ethanol solvent causes some reordering of the relative stability of 2-(2-Mercaptophenyl)-1-azaazulene conformers. The transition states for the 2-(2-Mercaptophenyl)-1-azaazulene tautomerization and rotamerization processes were also determined. The reactivity, electric dipole moment, and spectroscopic properties of the studied tautomer and rotamers were computed. The hyper-Rayleigh scattering (βHRS), and depolarization ratio (DR) exhibited promising optical properties when nonlinear optical properties were calculated.

A novel coumarin-triazole-thiophene hybrid: synthesis, characterization, ADMET prediction, molecular docking and molecular dynamics studies with a series of SARS-CoV-2 proteins

Synthesis, characterization and theoretical studies of a novel coumarin-triazole-thiophene hybrid 4-(((4-ethyl-5-(thiophen-2-yl)-4H-1,2,4-triazol-3-yl)thio)methyl)-6,7-dimethyl-2H-chromen-2-one (1), which was fabricated from 4-ethyl-5-(thiophen-2-yl)-4H-1,2,4-triazole-3-thiol and 4-(chloromethyl)-6,7-dimethyl-2H-chromen-2-one, are reported. The resulting compound was characterized by microanalysis, IR, 1H, and 13C APT NMR spectroscopy. The DFT calculations examined the structure and electronic properties of 1 in gas phase. Its reactivity descriptors and molecular electrostatic potential revealed the reactivity and the reactive centers of 1. ADMET properties of 1 were evaluated using the respective online tools. It was established that 1 exhibit positive gastrointestinal absorption properties and negative human blood-brain barrier penetration. The Toxicity Model Report revealed that 1 belongs to toxicity class 4. Molecular docking was additionally applied to study the interaction of 1 with some SARS-CoV-2 proteins. It was established that the title compound is active against all the applied proteins with the most efficient interaction with Papain-like protease (PLpro). The interaction of 1 with the applied proteins was also studied using molecular dynamics simulations.

Graphical abstract

A novel coumarin-triazole-thiophene hybrid 4-(((4-ethyl-5-(thiophen-2-yl)-4H-1,2,4-triazol-3-yl)thio)methyl)-6,7-dimethyl-2H-chromen-2-one (1) is reported. The structure and electronic properties of 1 were examined by the DFT calculations. ADMET properties of 1 were also evaluated. Molecular docking and molecular dynamics simulations were applied to study interactions of 1 with a series of the SARS-CoV-2 proteins.

Supplementary Information

The online version contains supplementary material available at 10.1007/s12039-022-02127-0.

Experimental and theoretical characterization of chelidonic acid structure

Chelidonic acid (4-oxo-4H-pyran-2,6-dicarboxylic acid) is present in plants of Papaveraceae family, especially in Chelidonium majus. Due to its anticancer, antibacterial, hepatoprotective, and antioxidant properties, it has been used in medical treatments. In this work, the X-ray structure of methanol solvate of chelidonic acid was determined. Layers of chelidonic acid are held by hydrogen bonds via COOH and C = O fragments and additionally bridged by methanol. The formed H-bond network between two acid units is different from typical –COOH dimers observed, e.g., in crystals of isophtalic acid. The molecular structure of 2,6-dimethyl-γ-pyrone (2Me4PN) and chelidonic acid, a 2,6-dicarboxylic derivate of γ-pyrone (4PN), was verified in silico using density functional theory (DFT-B3LYP) combined with large correlation-consistent basis sets. The impact of –CH3 and –COOH substituents on 4PN ring structure, dipole moments, geometric/magnetic indexes of aromaticity, and NBO charges was assessed following unconstrained geometry optimization in the gas phase, chloroform, methanol, DMSO, and water with solvent effect introduced using the polarized continuous model (PCM). H-bond network formed in chelidonic acid–methanol complex was analyzed and their interaction energy estimated. Theoretical modeling enabled prediction of accurate structural parameters, dipole moments, and geometric/magnetic indexes of aromaticity of the studied 4PN, 2Me4PN, and chelidonic acid molecules.

Aromaticity Concepts Derived from Experiments

Aromaticity, a very important term in organic chemistry, has never been defined unambiguously. Various ways to describe it come from different phenomena that have been experimentally observed. The most important examples related to some theoretical concepts are presented here.

Structures, Energetics, and Spectra of (NH) and (OH) Tautomers of 2-(2-Hydroxyphenyl)-1-azaazulene: A Density Functional Theory/Time-Dependent Density Functional Theory Study

Tautomerization of 2-(2-hydroxyphenyl)-1-azaazulene (2OHPhAZ) in the gas phase and ethanol has been studied using B3LYP, M06-2X, and ωB97XD density functional theory (DFT) with different basis sets. For more accurate data, energies were refined at CCSD(T)/6-311++G(2d,2p) in the gas phase. Nuclear magnetic resonance (NMR), aromaticity, Fukui functions, acidity, and basicity were also calculated and compared with experimental data. Time-dependent density functional theory (TDDFT)-solvation model based on density (TDDFT-SMD) calculations in acetonitrile have been utilized for the simulation of UV-vis electronic spectra. In addition, electronic structures of the investigated system have been discussed. The results reveal that the enol form (2OHPhAZ) is thermodynamically and kinetically stable relative to the keto tautomer (2OPhAZ) and different rotamers (2OHPhAZ-R1:R3) in the gas phase and ethanol. A comparison with the experiment illustrates a good agreement and supports the computational findings.

Self-Assembled Lanthanide Antenna Glutathione Sensor for the Study of Immune Cells

The small molecule 8-methoxy-2-oxo-1,2,4,5-tetrahydrocyclopenta[de]quinoline-3-carboxylic acid (2b) behaves as a reactive non-fluorescent Michael acceptor, which after reaction with thiols becomes fluorescent, and an efficient Eu³⁺ antenna, after self-assembling with this cation in water. This behavior makes 2b a highly selective GSH biosensor, which has demonstrated high potential for studies in murine and human cells of the immune system (CD4⁺ T, CD8⁺ T, and B cells) using flow cytometry. GSH can be monitored by the fluorescence of the product of addition to 2b (445 nm) or by the luminescence of Eu³⁺ (592 nm). 2b was able to capture baseline differences in GSH intracellular levels among murine and human CD4⁺ T, CD8⁺ T, and B cells. We also successfully used 2b to monitor intracellular changes in GSH associated with the metabolic variations governing the induction of CD4⁺ naïve T cells into regulatory T cells (T_REG).

Superlow Friction of a-C:H Coatings in Vacuum: Passivation Regimes and Structural Characterization of the Sliding Interfaces

A combination of atomistic simulations and vacuum tribometry allows atomic-scale insights into the chemical structure of superlubricious hydrogenated diamond-like carbon (a-C:H) interfaces in vacuum. Quantum molecular dynamics shearing simulations provide a structure-property map of the friction regimes that characterize the dry sliding of a-C:H. Shear stresses and structural properties at the sliding interfaces are crucially determined by the hydrogen content CH in the shear zone of the a-C:H coating. Extremely small CH (below 3 at.%) cause cold welding, mechanical mixing and high friction. At intermediate CH (ranging approximately from 3 to 20 at.%), cold welding in combination with mechanical mixing remains the dominant sliding mode, but some a-C:H samples undergo aromatization, resulting in a superlubricious sliding interface. A further increase in CH (above 20 at.%) prevents cold welding completely and changes the superlubricity mechanism from aromatic to hydrogen passivation. The hydrogen-passivated surfaces are composed of short hydrocarbon chains hinting at a tribo-induced oligomerization reaction. In the absence of cold welding, friction strongly correlates with nanoscale roughness, measured by the overlap of colliding protrusions at the sliding interface. Finally, the atomistic friction map is related to reciprocating friction experiments in ultrahigh vacuum. Accompanying X-ray photoelectron and Auger electron spectroscopy (XPS, XAES) analyses elucidate structural changes during vacuum sliding of a hydrogen-rich a-C:H with 36 at.% hydrogen. Initially, the a-C:H is covered by a nanometer-thick hydrogen-depleted surface layer. After a short running-in phase that results in hydrogen accumulation, superlubricity is established. XPS and XAES indicate a non-aromatic 1–2-nm-thick surface layer with polyethylene-like composition in agreement with our simulations.

Favipiravir: insight into the crystal structure, Hirshfeld surface analysis and computational study

In this work we report structural and computational studies of favipiravir, which is now used as a drug for COVID-19 treatment. The molecule is completely flat and stabilized by an intramolecular O–H···O hydrogen bond, yielding a six-membered pseudo-aromatic ring. The aromaticity index of this pseudo-aromatic ring was found to be 0.748, while the same indix for the pyrazine ring in favipiravir was found to be 0.954. The crystal packing of favipiravir is mainly constructed through intermolecular N–H···O, N–H···N and C–H···O hydrogen bonds, yielding a 3D supramolecular framework with a zst topology defined by the point symbol of (6⁵·8). The crystal structure of favipiravir is further stabilized by weak C–F···F–C intermolecular type II dihalogen interactions, yielding a 1D supramolecular polymeric chain. More than 80% of the total Hirshfeld surface area for favipiravir is occupied by H···H/C/N/O/F and C···N/O contacts. Energy frameworks have been calculated to additionally analyze the overall crystal packing. It was established that the structure of favipiravir is mainly characterized by the dispersion energy framework followed by the less significant electrostatic energy framework contribution. Finally, by using density functional theory (DFT) calculations and the quantum theory of atoms in molecules, we have assigned the interaction energy of each hydrogen bond, which can be helpful to develop scoring functions to be used in force fields/docking calculations.

Theoretical modeling of optical spectra of N(1) and N(10) substituted lumichrome derivatives

A systematic study of (7,8-dimethylated) alloxazine, isoalloxazine, and their derivatives with substituted N(1) and N(10) positions was conducted using the density functional theory. The main aim of this work was the direct investigation of substituent effect on the molecular structure. Furthermore, HOMED aromaticity indices were calculated to describe the scope of the geometry changes. Frontier molecular orbitals of reference alloxazine, isoalloxazine and lumichrome derivatives were discussed by means of changes in their shape and energy levels. Photophysical properties were analyzed by determination of optical transition energies using the TD-DFT method. Obtained results were compared with previously published experimental data.

Triplet State Baird Aromaticity in Macrocycles: Scope, Limitations, and Complications

The aromaticity of cyclic 4nπ-electron molecules in their first ππ* triplet state (T1), labeled Baird aromaticity, has gained growing attention in the past decade. Here we explore computationally the limitations of T1 state Baird aromaticity in macrocyclic compounds, [n]CM's, which are cyclic oligomers of four different monocycles (M = p-phenylene (PP), 2,5-linked furan (FU), 1,4-linked cyclohexa-1,3-diene (CHD), and 1,4-linked cyclopentadiene (CPD)). We strive for conclusions that are general for various DFT functionals, although for macrocycles with up to 20 π-electrons in their main conjugation paths we find that for their T1 states single-point energies at both canonical UCCSD(T) and approximative DLPNO-UCCSD(T) levels are lowest when based on UB3LYP over UM06-2X and UCAM-B3LYP geometries. This finding is in contrast to what has earlier been observed for the electronic ground state of expanded porphyrins. Yet, irrespective of functional, macrocycles with 2,5-linked furans ([n]CFU's) retain Baird aromaticity until larger n than those composed of the other three monocycles. Also, when based on geometric, electronic and energetic aspects of aromaticity, a 3[n]CFU with a specific n is more strongly Baird-aromatic than the analogous 3[n]CPP while the magnetic indices tell the opposite. To construct large T1 state Baird-aromatic [n]CM's, the design should be such that the T1 state Baird aromaticity of the macrocyclic perimeter dominates over a situation with local closed-shell Hückel aromaticity of one or a few monocycles and semilocalized triplet diradical character. Monomers with lower Hückel aromaticity in S0 than benzene (e.g., furan) that do not impose steric congestion are preferred. Structural confinement imposed by, e.g., methylene bridges is also an approach to larger Baird-aromatic macrocycles. Finally, by using the Zilberg-Haas description of T1 state aromaticity, we reveal the analogy to the Hückel aromaticity of the corresponding closed-shell dications yet observe stronger Hückel aromaticity in the macrocyclic dications than Baird aromaticity in the T1 states of the neutral macrocycles.

On the aromaticity of uracil and its 5-halogeno derivatives as revealed by theoretically derived geometric and magnetic indexes

The problem of aromaticity in heterocyclic rings of uracil and its 5-halogenoderivatives (5XU) was analyzed theoretically by calculating modified harmonic oscillator model of aromaticity (HOMA) for Heterocycle Electron Delocalization (HOMHED), nucleus-independent chemical shift parameters (NICS) and the so-called scan experiments, using helium-3 atom as a magnetic probe. The impact of halogen electronegativity on C5 atom’s NBO charges was also investigated. Water, as a polar environment, has a negligible impact on 5XU aromaticity. The most stable diketo tautomer shows a very low aromaticity while the “rare” dihydroxy form (tautomer No 6) is aromatic and resembles benzene. This is in agreement with traditional drawing of chemical formula of uracil’s six-membered ring, directly showing three alternating single and double bonds in its tautomer No 6. No good correlation between magnetic and geometric indexes of aromaticity for the studied 5XU tautomers was found. Linear correlation between the magnitude of NICS minimum, as well as the distance of the minimum above uracil ring plane center from 3He NMR chemical shift scan plot with respect to halogen electronegativity were observed. A strong linear dependence of magnetic index of aromaticity and the electronegativity of 5X substituent was observed.

Machine Learning Predicts Degree of Aromaticity from Structural Fingerprints

Prediction of whether a compound is "aromatic" is at first glance a relatively simple task-does it obey Hückel's rule (planar cyclic π-system with 4n + 2 electrons) or not? However, aromaticity is far from a binary property, and there are distinct variations in the chemical and biological behavior of different systems which obey Hückel's rule and are thus classified as aromatic. To that end, the aromaticity of each molecule in a large public dataset was quantified by an extension of the work of Raczyńska et al. Building on this data, a method is proposed for machine learning the degree of aromaticity of each aromatic ring in a molecule. Categories are derived from the numeric results, allowing the differentiation of structural patterns between them and thus a better representation of the underlying chemical and biological behavior in expert and (Q)SAR systems.

Expanded N-Confused Phlorin: A Platform for a Multiply Fused Polycyclic Ring System via Oxidation within the Macrocycle

Novel interrupted π-conjugated macrocycles derived from expanded porphyrinoids were synthesized, and their unique reactivity was investigated in this work. The specific porphyrin analogs, so-called phlorins and isoporphyrins, possess a meso-sp³ methylene moiety, showing inner 3NH and 1NH pyrrolic cores, respectively, and extended near-infrared (NIR) absorption. Expanded N-confused pentapyrrolic phlorin analog 1 bears an interrupted cyclic π-conjugated system that is featured by a distinct higher HOMO and a lower LUMO. Oxidation of 1 allowed structural transformations through the expanded isoporphyrin-like species 2. One of the representative products is a spiro-carbon-bridged multiply N-fused product 3 comprising a fused [5.6.5.7.6.5]-hexacyclic ring obtained by oxidation with 2,3-dichloro-5,6-dicyano-p-benzoquinone. When magic blue was used as the oxidant, an aromatic N-confused pentaphyrin 4 was obtained via migration of one of the meso-phenyl groups to the β-position of the neighboring pyrrolic ring. By employing the flexible cavity of 1 for metal coordination, Pd(II) complexation occurred with a specific meso oxygenation to give a bimetallic complex 5. In contrast to the rich oxidation reactions, reduction of 1 with NaBH₄ resulted in the regioselective nucleophilic hydrogen substitution reaction at the para position of one of the meso-C₆F₅ groups. These results provide a practical approach for synthesizing novel interrupted or aromatic π-conjugated frameworks showing NIR absorptions.

Resonance Assisted Hydrogen Bonding Phenomenon Unveiled through Both Experiments and Theory: A New Family of Ethyl N-Salicylideneglycinate Dyes

Extensive experimental and theoretical investigations are reported on the nature of resonance-assisted hydrogen bonding phenomenon (RAHB) and its influence on photophysical properties of the newly designed dyes differing in donor-acceptor properties, namely ethyl N-salicylideneglycinate (1), ethyl N-(5-methoxysalicylidene)glycinate (2), ethyl N-(5-bromosalicylidene)glycinate (3) and ethyl N-(5-nitrosalicylidene)glycinate (4). All compounds are thermochromic in the solid state and they contain a typical intramolecular O-H⋅⋅⋅N hydrogen bond formed between the hydroxyl hydrogen atom and the imine nitrogen atom, yielding the enol form in the solid state. It is unveiled, that the magnitude of RAHB effect fine tunes the strength of the O-H⋅⋅⋅N bonding and accordingly the relative populations of the enol, cis-keto and trans-keto forms leading to variation of the photophysical properties of 1-4. It is determined, that the electron-withdrawing NO₂ in 4 amplifies the most RAHB effect causing the breaking of the O-H⋅⋅⋅N hydrogen bond and accordingly formation of the dominant cis-keto isomer in both the solid state and EtOH. To this end, the UV/Vis spectra of 1-3 in EtOH revealed the exclusive presence of the enol form, while the prevalent contribution of the cis-keto form was found for 4. Furthermore, only compound 4 is emissive in the solid state in ambient condition due to dual emission arising from the cis-keto* and trans-keto* forms, while 2 was found to be highly emissive in EtOH. It is revealed qualitatively and quantitatively, based on the ETS-NOCV charge and energy decomposition scheme and the EDDB population-based method, that RAHB is strongly a non-local phenomenon based on electrons pumping or sucking through both the π- and σ-channels, which accordingly exerts chemical bonding changes at both the phenyl ring and predominantly a distant O-H⋅⋅⋅N area.

Factors Governing the Chemical Stability and NMR Parameters of Uracil Tautomers and Its 5-Halogen Derivatives

We report on the density functional theory (DFT) modelling of structural, energetic and NMR parameters of uracil and its derivatives (5-halogenouracil (5XU), X = F, Cl, Br and I) in vacuum and in water using the polarizable continuum model (PCM) and the solvent model density (SMD) approach. On the basis of the obtained results, we conclude that the intramolecular electrostatic interactions are the main factors governing the stability of the six tautomeric forms of uracil and 5XU. Two indices of aromaticity, the harmonic oscillator model of aromaticity (HOMA), satisfying the geometric criterion, and the nuclear independent chemical shift (NICS), were applied to evaluate the aromaticity of uracil and its derivatives in the gas phase and water. The values of these parameters showed that the most stable tautomer is the least aromatic. A good performance of newly designed xOPBE density functional in combination with both large aug-cc-pVQZ and small STO(1M)-3G basis sets for predicting chemical shifts of uracil and 5-fluorouracil in vacuum and water was observed. As a practical alternative for calculating the chemical shifts of challenging heterocyclic compounds, we also propose B3LYP calculations with small STO(1M)-3G basis set. The indirect spin-spin coupling constants predicted by B3LYP/aug-cc-pVQZ(mixed) method reproduce the experimental data for uracil and 5-fluorouracil well.

DFT studies on vibrational and electronic spectra, HOMO-LUMO, MEP, HOMA, NBO and molecular docking analysis of benzyl-3-N-(2,4,5-trimethoxyphenylmethylene)hydrazinecarbodithioate

Benzyl-3-N-(2,4,5-trimethoxyphenylmethylene)hydrazinecarbodithioate (compound 1) is a bidentate and nitrogen-sulfur containing Schiff base, which has been synthesized by the condensation reaction of S-benzylndithiocarbazate and 2,4,5-trimethoxybenzaldehyde. The theoretical calculations of the mentioned compound have been carried out using the more popular density functional theory method, Becke-3-Parameter-Lee-Yang-Parr (B3LYP) in 6-31G+(d,p) basis set. The computational results of the compound were compared with the obtained experimental value. Moreover, the highest occupied molecular orbital, the lowest unoccupied molecular orbital, molecular electrostatic potential, chemical reactivity parameters and natural bond orbital of the optimized structure have been evaluated at the same level of theory. Furthermore, the UV–Vis spectrum of the compound has been carried out for the better understanding of electronic absorption spectra with the help of the time-dependent density functional theory at room temperature. Besides, the molecular docking simulation of the mentioned molecule with target protein was also investigated. In addition, in silico studies were performed to predict absorption, distribution, metabolism, excretion and toxicity profiles of the designed compound. The results indicated that the theoretical data have well correlated with the observed values. The narrow frontier orbital gap indicated that the eventual charge transfer interaction occurs within the studied molecule and showed high chemical reactivity. The global reactivity values showed that the compound is soft molecule, electrophilic species and has strong binding ability with biomolecules. The molecular electrostatic potential structure indicated that the negative and positive potential sites are around electronegative atoms and hydrogen atoms of studied compound, respectively. The natural bond orbital data revealed that the compound contains 97.42% Lewis and 2.58% non-Lewis structure. The intra and inter-molecular charge transfers process occur within the studied compound. The studied compound showed more binding energy (−6.0 kcal/mol) with target protein than hydroxychloroquine (−5.6 kcal/mol). The absorption, distribution, metabolism, excretion and toxicity investigation predicted that the compound has good drug like character.

Air-Stable Oxyallyl Patterns and a Switchable N-Heterocyclic Carbene

Oxyallyl derivatives are typically elusive compounds. Even recently reported "stabilized" 1,3-diaminooxyallyl species are still highly reactive and have short lifetimes at room temperature. Herein, we report the synthesis and preliminary study of mesoionic pyrimidine derivatives that feature 1,3-bis(dimethylamino)oxyallyl patterns with an unprecedented level of stabilization. The latter are not only insensitive towards air and moisture, but they are also compatible with the formation of an ancillary stable N-heterocyclic carbene moiety. As the oxyallyl pattern is proton-responsive, it allows the reversible switching of the electronic properties of the carbene, as a ligand.

Electronic effects in tautomeric equilibria: the case of chiral imines from d-glucamine and 2-hydroxyacetophenones

A one-pot procedure for preparing a series of chiral imines by direct condensation of d-glucamine with 2-hydroxyacetophenones is described. Under conventional acetylation an unexpected mixture of two different peracetylated molecules is obtained, one with an open enamine structure, and the other incorporating an N-acetyl-1,3-oxazolidine into the acyclic skeleton. Surprisingly, both molecules coexist within the crystal's unit cell, as inferred from single-crystal X-ray analysis of a 5-bromo-substituted aryl derivative. Moreover, the 1,3-oxazolidine ring exists as rotational conformers (E,Z) owing to the restricted rotation around the N-acetyl bond. The equilibrium involving imine and enamine structures has been assessed in detail, providing in addition linear free-energy relationships between the tautomerization constants (K_T) and the electronic effect of the substituents.

Three Queries about the HOMA Index

HOMA (Harmonic Oscillator Model of Aromaticity) is a simple, successful, and widely used geometrical aromaticity index. However, HOMA can also be used as a general molecular descriptor appropriate for any type of molecule. It reaches the global maximum for benzene, whereas the potent magnetic aromaticity NICS index has no lower or upper limits. Hence, questions arise and go beyond mere differences between the geometric and magnetic aspects of aromaticity: (1) Does a molecule of aromaticity greater than that of benzene, but undisclosed by the HOMA definition, exist? (2) Can the Kekuléne cyclohexatriene moiety with HOMA = 0 exist as a part of a larger system? (3) Can the geometrical aromaticity index be defined better? Our answer to the first query is "It is not likely enough", to the second, "Why not define HOMA using a less mysterious molecule than cyclohexatriene?", and to the third, "It is possible to construct another fair geometrical index, but is it better for evaluating aromaticity?" To find these answers, we have studied: (1) the HOMA and NICS indices of over 50 hexahomosubstituted benzenes, (2) the HOMA, as well as EN and GEO, indices of over 100 triply fused hexasubstituted benzenes, and (3) the HOMA and new Geometrical Auxiliary Index (GAI) , of different unsaturated and saturated, aromatic and aliphatic hydrocarbons including all alkane constitutional isomers composed of up to nine carbon atoms.

Captodative Substitution Enhances the Diradical Character of Compounds, Reduces Aromaticity, and Controls Single-Molecule Conductivity Patterns: A Valence Bond Study

The present contribution uses a valence bond (VB) perspective to consider the captodative substitution strategy, a method to enhance the diradical character of (potentially aromatic) compounds. We confirm the qualitative reasoning that has generally been used to rationalize the diradical-character-enhancing effect of captodative substitution: this type of substitution scheme disproportionally stabilizes specific Dewar/diradical(oid) VB structures, thus increasing their weight in the full ground-state wave function. Furthermore, we assess the effect of captodative substitution on the aromaticity of the considered compound. We observe a clear trade-off between diradical character and aromaticity for our model systems: as one of these properties increases, the other decreases. This finding is especially significant within the field of single-molecule electronics because it enables unification of the previously observed inverse proportionality between the aromaticity of a compound and the magnitude of conductance through that molecule, with the observed proportionality between diradical character and the magnitude of conductance associated with a compound. To some extent, both properties, i.e., aromaticity and diradical character, appear to be the flip-sides of the same coin.