Polybenzenoid Hydrocarbons Research Articles

COMPAS-3: a dataset of peri-condensed polybenzenoid hydrocarbons.

We introduce the third installment of the COMPAS Project - a COMputational database of Polycyclic Aromatic Systems, focused on peri-condensed polybenzenoid hydrocarbons. In this installment, we develop two datasets containing the optimized ground-state structures and a selection of molecular properties of ∼39k and ∼9k peri-condensed polybenzenoid hydrocarbons (at the GFN2-xTB and CAM-B3LYP-D3BJ/cc-pvdz//CAM-B3LYP-D3BJ/def2-SVP levels, respectively). The manuscript details the enumeration and data generation processes and describes the information available within the datasets. An in-depth comparison between the two types of computation is performed, and it is found that the geometrical disagreement is maximal for slightly-distorted molecules. In addition, a data-driven analysis of the structure-property trends of peri-condensed PBHs is performed, highlighting the effect of the size of peri-condensed islands and linearly annulated rings on the HOMO-LUMO gap. The insights described herein are important for rational design of novel functional aromatic molecules for use in, e.g., organic electronics. The generated datasets provide a basis for additional data-driven machine- and deep-learning studies in chemistry.

Interpretable Deep-Learning Unveils Structure-Property Relationships in Polybenzenoid Hydrocarbons.

In this work, interpretable deep learning was used to identify structure-property relationships governing the HOMO-LUMO gap and the relative stability of polybenzenoid hydrocarbons (PBHs) using a ring-based graph representation. This representation was combined with a subunit-based perception of PBHs, allowing chemical insights to be presented in terms of intuitive and simple structural motifs. The resulting insights agree with conventional organic chemistry knowledge and electronic structure-based analyses and also reveal new behaviors and identify influential structural motifs. In particular, we evaluated and compared the effects of linear, angular, and branching motifs on these two molecular properties and explored the role of dispersion in mitigating the torsional strain inherent in nonplanar PBHs. Hence, the observed regularities and the proposed analysis contribute to a deeper understanding of the behavior of PBHs and form the foundation for design strategies for new functional PBHs.

Text‐based representations with interpretable machine learning reveal structure–property relationships of polybenzenoid hydrocarbons

AbstractNew tools are developed and applied to enable the use of interpretable machine learning for investigation of structure–property relationships in polybenzenoid hydrocarbons (PBHs). A textual molecular representation, which is based on the annulation sequence of PBHs, is shown to be of utility either in its textual form or as a basis for a curated feature vector. Both forms display interpretability exceeding those achievable by standard SMILES representation; and the former also has increased predictive accuracy. A recently developed model, CUSTODI, was applied for the first time as an interpretable model, identifying important structural features that impact various electronic molecular properties. The resulting insights not only validate several well‐known “rules of thumb” of organic chemistry but also reveal new behaviors and influential structural motifs, thus providing guiding principles for rational design and fine‐tuning of PBHs.

Organic triplets as free radical pairs: Everything old is new again

AbstractMore than a half‐century ago, Michael Dewar devised a theoretical construct whereby the aromatic stabilization of conjugated hydrocarbon rings could be analyzed by imagining them to be formed by combining free radical chains. From the analysis, he also predicted that the rings would reverse their aromaticity in their first excited states. By taking the construct more literally, we were able to calculate the ground state‐to‐triplet energies of twisted conjugated polyenes and to elaborate upon the rules of aromaticity and anti‐aromaticity for hydrocarbon rings. In the present publication, we point out that the spin densities of the triplet states of polybenzenoid hydrocarbons closely mimic those expected for free radicals, and that to some extent, the relative energies of their isomers can be understood in terms of interacting free radical networks.

Revisiting the superaromatic stabilization energy as a local aromaticity index for excited states

AbstractThe graph theory of aromaticity is a useful framework for analyzing the aromatic properties of polycyclic aromatic hydrocarbons. We present here the magnetically based superaromatic stabilization energy (m‐SSE) as a local aromaticity index and validate it against its topologically based counterpart t‐SSE. By comparing to DFT‐computed aromaticity indices of triplet state excited polybenzenoid hydrocarbons, we find that semi‐quantitative agreement can be reached by using the variable method to account for bond‐length alternation. The m‐SSE can further be separated into orbital and circuit contributions to gain insight into the basis of the aromatic properties of individual rings. Fully automated algorithms for calculating both m‐SSE and t‐SSE are now available in the COULSON package. We envision that these graph theoretical aromaticity indices will be of great use to the community to analyze the local aromaticity of excited states.

Prediction of Spin Density, Baird-Antiaromaticity, and Singlet-Triplet Energy Gap in Triplet-State Polybenzenoid Systems from Simple Structural Motifs.

Triplet-state aromaticity has been recently proposed as a strategy for designing functional organic electronic compounds, many of which are polycyclic aromatic systems. However, in many cases, the aromatic nature of the triplet state cannot be easily predicted. Moreover, it is often unclear how specific structural manipulations affect the electronic properties of the excited-state compounds. Herein, the relationship between the structure of polybenzenoid hydrocarbons (PBHs) and their spin-density distribution and aromatic character in the first triplet excited state is studied. Although a direct link is not immediately visible, classifying the PBHs according to their annulation sequence reveals regularities. Based on these, a set of guidelines is defined to qualitatively predict the location of spin and paratropicity and the singlet-triplet energy gap in larger PBHs, using only their smaller tri- and tetracyclic components, and subsequently tested on larger systems.

Cover Feature: Prediction of Spin Density, Baird‐Antiaromaticity, and Singlet–Triplet Energy Gap in Triplet‐State Polybenzenoid Systems from Simple Structural Motifs (Chem. Eur. J. 23/2021)

Structure, sequence, spin: The structures of polybenzenoid hydrocarbons are analyzed in terms of the sequence of tricyclic annulations, revealing regularities in the location of spin density and Baird-antiaromaticity. The two properties localize onto specific tri- and tetracyclic substructures according to a hierarchy: linear, zig-zag, curved. The same preferences are reflected in the relative energy of the T1 systems and in the singlet-triplet energy gaps. More information can be found in the Full Paper by R. Gershoni-Poranne et al. on page 6923.

Predicting bond-currents in polybenzenoid hydrocarbons with an additivity scheme.

We report on the construction and application of a new bond-current additivity scheme for polybenzenoid hydrocarbons. The method is based on identification of the smaller substructures contained in the system, up to tricyclic subunits. Thus, it enables the prediction of any cata-condensed unbranched polybenzenoid hydrocarbon, using a library consisting of only four building blocks. The predicted bond-currents can then be used to generate Nucleus Independent Chemical Shift (NICS) values, the results of which validate previous observations of additivity with NICS-XY-Scans. The limitations of the method are probed, leading to clearly delineated and apparently constant error boundaries, which are independent of the molecular size. It is shown that there is a relationship between the accuracy of the predictions and the molecular structure and specific motifs that are especially challenging are identified. The results of the additivity method, combined with the transparent description of its strengths and weaknesses, ensure that this method can be used with well-defined reliability for characterization of polybenzenoid hydrocarbons. The resource-efficient and rapid nature of the method makes it a promising tool for screening and molecular design.

The Clar Structure in Inorganic BN Analogues of Polybenzenoid Hydrocarbons: Does it Exist or Not?

The Clar structure of polybenzenoid hydrocarbons (PBHs) have attracted considerable interest of both theoretical and experimental chemists since it was proposed in the 1950s. However, it remains unclear whether the Clar structure could exist in inorganic PBHs, the boron nitride (BN) analogues where the alternate boron and nitrogen atoms are used to replace the carbon atoms of PBHs. Here, we carry out thorough density functional theory (DFT) calculations to probe the possibility of Clar structures in BN analogues of PBHs. A strong correlation (r(2) =0.975) between the ring number (n=3-10) of BN analogues of [n]acenes and energy differences between the most and least stable isomers is identified, suggesting the existence of Clar structures in inorganic PBHs. In addition, the slightly weaker correlations in comparison to that (r(2) =0.989) of the organic PBHs is rationalized by the reduced aromaticity, which is revealed by two aromatic indices: ELFπ and SCI.

Aromaticity of Closed-Shell Charged Polybenzenoid Hydrocarbons

The aromatic stabilization of closed-shell charged polybenzenoid hydrocarbons (PBHs) has been scrutinized by means of energetic and magnetic aromaticity criteria and by direct measures of electron delocalization. Thus, topological resonance energies and their circuit contributions, ring current maps, and multicenter delocalization indices have been calculated for a series of 18 polybenzenoid cations containing from 3 to 10 benzene rings. All calculations indicate that the closed-shell cations have a similar degree of aromaticity compared to that of the corresponding closed-shell neutral PBHs. All cations investigated display a large degree of electronic delocalization in the ring, accompanied by significant aromatic stabilization and a strong diatropic peripheral electron current. Graph theoretical models describe perfectly the aromatic features of these hydrocarbon fragments, showing how they can be understood as a superposition of specific neutral PBHs. The large aromatic character of these systems suggests they may be relatively stable upon formation at combustion conditions, like those given in the interstellar medium. It has been postulated that closed-shell fragments of PBHs may play an important role in the photoluminescent phenomenon known as extended red emission.

On the Importance of Clar Structures of Polybenzenoid Hydrocarbons as Revealed by the π-Contribution to the Electron Localization Function

The degree of p-electron (de)localization and aromaticity of a series of polybenzenoid hydrocarbons (PBHs) has been analyzed through the π-contribution to the electron localization function (ELFπ), calculated at the B3LYP/6-311G(d,p) hybrid density functional theory level. The extent of p-electron delocalization in the various hexagons of a PBH was determined through analysis of the bifurcation values of the ELFp basins (BV(ELFp)), the spans in the bifurcation values in each hexagon (ΔBV(ELFπ)), and the ring-closure bifurcation values of the ELFπ (RCBV(ELFπ)). These computed results were compared to the qualitative description of local aromaticities of the different hexagons in terms of Clar structures with p-sextets. Benzene, [18]annulene, and thirty two PBHs were analyzed at their equilibrium geometries, and benzene and triphenylene were also analyzed at bond length distorted structures. In general, the description of PBHs in terms of Clar valence structures is supported by the ELFp properties, although there are exceptions. For PBHs at their equilibrium geometries there is a clear sigmoidal relationship between the CC bond lengths and the amount of p-electron (de)localization at these bonds, however, this relationship is lost for bond distorted geometries. In the latter cases, we specifically examined benzene in D3h symmetric “1,3,5-cyclohexatriene” structures and triphenylene in eight different structures. From the distorted benzenes and triphenylenes it becomes clear that there is a distinct tendency for the p-electron network to retain delocalization (aromaticity). The ELFp analysis thus reveals an antidistortive rather than a distortive behavior of the p-electrons in these investigated compounds.

Electrophile Affinity: Quantifying Reactivity for the Bromination of Arenes

Electrophile affinity (Ealpha), a recently proposed theoretical construct based on computed energies of arenium ion formation, rationalizes the substrate reactivity and regioselectivity of S(E)Ar bromination of three sets of available experimental arene data where closely related conditions had been employed uniformly. The Ealpha parameters (computed at B3LYP/6-311+G(2d,2p)) correlated very well (r = 0.987) with the partial rate factors (log f) for 18 regiospecific brominations of benzene and various methyl benzenes. Analysis of the bromination reactivities of 32 mono- and polysubstituted benzenes including various polar groups gave similar results (r = 0.982). The electrophile affinity treatment also accounted satisfactorily (r = 0.957) for bromination reactivities of polybenzenoid hydrocarbons. Conversely, comparisons with NBO-based charges and the electrostatic potential at nuclei (EPN) were not generally successful. The uniform effectiveness of Ealpha treatments for the cases analyzed with regard both to relative substrate reactivity (e.g., benzene vs toluene) and to regiospecificity (e.g., the positional reactivity of toluene) supports the "limiting case" conventional interpretation of the electrophilic aromatic substitution mechanism as being governed by the energy of sigma-complex formation. Although other mechanisms are possible under different conditions, the computed energies of arene-dibromine pi-complex formation for the polysubstituted benzene set examined correlated poorly with experimental reactivity data (r = 0.714) and only varied from 1.8 (for benzene) to 3.5 kcal/mol, in contrast to the 10(12) range in reactivity measured experimentally.

Chemical graph theory andn‐center electron delocalization indices: A study on polycyclic aromatic hydrocarbons

Relations between aromaticity indices derived from chemical graph theory and those based on 6-center electron delocalization are investigated for a series of polybenzenoid hydrocarbons. Aromatic stabilization obtained by means of the effective scaled electron delocalization is highly correlated to the resonance energy, RE, obtained both from SCF MO calculations and conjugated ring circuits model. Local aromaticity of benzene rings is discussed using two different criteria, in one of them aromaticity is just given by the cyclic pi-electron conjugation of the ring, whereas terms involving more than one ring are also considered in the other one. Indices derived from chemical graph theory and those obtained from the 6-center electron delocalization give rise to the same local aromaticity. Moreover, 6-center electron delocalization provides more quantitative information.

Towards graphite: magnetic properties of large polybenzenoid hydrocarbons.

The geometries of four different series of D(6h)-symmetric polybenzenoid hydrocarbons (PBH) up to and including C(222)H(42) have been optimized at the B3LYP/6-31G(d) level of theory. Excluding C(48)H(24) and C(138)H(42), which have D(3d) minima due to 1,5 H...H repulsions between adjacent perimeter rings, optimized geometries are planar D(6h) minima. Nucleus Independent Chemical Shifts (NICS), at the same level, indicate the presence of individual aromatic rings, which correspond to Clar's qualitative sextets rule (Clar, E. TheAromatic Sextet; Wiley: London, 1972). NICS and the Clar valence electron topologies agree perfectly in the molecule plane; however, the NICS values computed in parallel planes further away from the molecular surface converge, indicating the presence of a uniform magnetic shielding field. For each series, PBH total NICS values (i.e., the sum of NICS values for all rings in the PBH) correlate linearly with the number of carbon atoms, indicating constant magnetic field development within a series. The C-C lengths depend on their proximity to the more olefinic rich molecular perimeters. However, the large PBH (> or =C(48)H(24)) internal C-C distances converge to approximately 1.426 A. In agreement with Clar's rule, HF/6-31G(d)//B3LYP/6-31G(d) vertical ionization potentials and B3LYP/6-31G(d) HOMO-LUMO gaps are largest within the "fully benzenoid" series, where all carbon atoms are members of a single sextet. The largest members of the four series studied are predicted to exhibit semiconducting properties.

Is 2D graphite an ultimate large hydrocarbon?: III. Structure and energy spectra of large polybenzenoid hydrocarbons with different edge structures

The structure and energy spectra of very large polybenzenoid alternant hydrocarbons (with up to N∼10 3 C-atoms) with different edge structures and defects were investigated theoretically. In all the cases, the calculated values of the energy gap width tend monotonically to a value different from zero when the electron correlation is taken into account. Typical surface (Tamm) states, namely non-bonding MOs, appear in the cases of non-Kekulé, open-shell hydrocarbons featuring point defects with a definite topology. The electrons occupying the non-bonding MOs are ferromagnetically coupled. These hydrocarbons are in fact polyradicals with a substantial value of the specific π-electron energy, which determines their relative stability.

Is 2-D Graphite an Ultimate Large Hydrocarbon? II. Structure and Energy Spectra of Polycyclic Aromatic Hydrocarbons with Defects

The structure and energy spectra of four classes of polybenzenoid hydrocarbons with different edge structures, a large number N (N ∼ 104) of carbon atoms, and different types of defect states (Tamm, Schottky and chemisorption states) have been studied theoretically. Several types of (probably) stable monoradicals and triplet biradicals with singly occupied MOs in the energy gap (molecular analogues of semiconductors with defect states) are characterized which could be used in the molecular electronics. A new concept for viewing high-spin π systems with ferromagnetically coupled electrons within the half-filled band of NBMOs in term of point defects (vacancies) was developed. The NBMOs can be considered as surface states (Tamm or Schottky).

Is 2-D Graphite an Ultimate Large Hydrocarbon? 1. Energy Spectra of Giant Polycyclic Aromatic Hydrocarbons

The energy spectra of three classes of polybenzenoid hydrocarbons with a large number N (N ≈ 103) of carbon atoms have been studied theoretically. It is shown that in the asymptotic case N → ∞ the energy gap (EG) ΔE(N→∞) is different from zero if the electron correlation is taken into account; that is, the π systems calculated should possess semiconductor properties. The results for the ΔE(N→∞) ≠ 0 of the hydrocarbons are in qualitative agreement with the results calculated for the EG of three classes of 1-D ladder polymers, which can be considered as models of quasi-1-D graphite. With increasing width (L) of the polymers, the band gap ΔE(L→∞) approaches a value different from zero. The problem of the existence of defect states of hydrocarbons with vacancies is briefly discussed.

Polyphenylene Dendrimers: From Three‐Dimensional to Two‐Dimensional Structures

An elegant route to aromatic hydrocarbon dendrimers, such as 1 with pentaphenylbenzene units, and to extremely large polybenzenoid hydrocarbons is based on Diels–Alder cycloadditions of 3,4-bis-[4-(triisopropylsilylethynyl)phenyl]-2, 5-diphenylcyclopenta-2,4-dienone and aromatic oligoethynyl compounds such as 3,3′,5,5′-tetraethynylbiphenyl. The type of linkage and the high packing density of the benzene rings facilitate the cyclodehydrogenation of appropriate dendrimeric subunits to yield planar disks.

Role of lysosomes in adrenal necrosis caused by dimethylbenzanthracene.

IT has long been recognized that carcinogenic chemicals, including polybenzenoid hydrocarbons, have injurious effects on cells1,2. Evidence has been presented that polybenzenoid hydrocarbons are concentrated in the lysosomes of living cells and the suggestion was made that release of lysosomal enzymes may play an important part in their cytotoxic action3. The necrosis of rat adrenal cortical cells produced by 7,12-dimethylbenz(a)anthracene (DMBA)4 provided an opportunity to test this hypothesis in more detail, because it is specific in two ways. First, the degeneration is organ specific, adrenal cortical cells of the rat being much more sensitive than the cells of other organs. Secondly, it appears to be specifically produced by one compound, 7-hydroxymethyl-12-methylbenz(a)anthracene (7-OHM-12-MBA), which is a metabolite of DMBA: an isomeric metabolite, 12-hydroxymethyl-7-methylbenz(a)anthracene (12-OHM-7-MBA), does not produce adrenal damage5. Rats can be protected against adrenal damage after administration of DMBA by previous treatment with a number of aromatic hydrocarbons and amines, which diminish the formation of 7-OHM-12-MBA from DMBA5. Hence it seems that the metabolite is more active than the parent compound in producing adrenal necrosis.

INTERMOLECULAR FORCES IN ASSOCIATION OF PURINES WITH POLYBENZENOID HYDROCARBONS.

The interactions in solution between purine or pyrimidine bases and polybenzenoid aromatic hydrocarbons probably consist in a vertical, stacking-type physical association. By molecular orbital calculations the role of the Van der Waals-London intermolecular forces in these interactions is determined. The electrostatic dipole-dipole forces are negligible, the polarization (or induction) dipole-induced dipole forces are contributory, but most important are the dispersion (or fluctuation) forces. This loose, physical type of interaction should not show any specificity with respect to the carcinogenic activity of the hydrocarbons.