Electron delocalization and aromaticity variations in the stacked nucleic acid base pairs

A newly developed exchange-correlation functional (MPWB1K) in density functional theory has been applied to evaluate the electron delocalization of individual fragments in the stacking interaction between nucleic acid bases (NABs). Electronically and structural-based indices have been employed to investigate the aromaticity variation during stacking interaction. A quantitative study of NABs in their isolated and stacked forms reveals that stacking interaction causes a decrease in bond delocalization. It is shown that the decrease in the aromaticity is accompanied by local decrease in two-center delocalization indices within the pyrimidine rings. We found that the aromaticity exhibits a similar trend for NABs in both their isolated and stacked forms. Moreover, it is indicated that aromatic fluctuation index is more sensible index to delineate the aromaticity variation during stacking interaction.

     

Electron delocalization and aromaticity in low-lying excited states of archetypal organic compounds

Aromaticity is a property usually linked to the ground state of stable molecules. Although it is well-known that certain excited states are unquestionably aromatic, the aromaticity of excited states remains rather unexplored. To move one step forward in the comprehension of aromaticity in excited states, in this work we analyze the electron delocalization and aromaticity of a series of low-lying excited states of cyclobutadiene, benzene, and cyclooctatetraene with different multiplicities at the CASSCF level by means of electron delocalization measures. While our results are in agreement with Baird's rule for the aromaticity of the lowest-lying triplet excited state in annulenes having 4nπ-electrons, they do not support Soncini and Fowler's generalization of Baird's rule pointing out that the lowest-lying quintet state of benzene and septet state of cyclooctatetraene are not aromatic.     

Density functional theoretical investigation of the aromatic nature of BN substituted benzene and four ring polyaromatic hydrocarbons

We have studied the topological and local aromaticity of BN-substituted benzene, pyrene, chrysene, triphenylene and tetracene molecules. The nucleus-independent chemical shielding (NICS), harmonic oscillator model of aromaticity (HOMA), para-delocalization index (PDI) and aromatic fluctuation index (FLU) have been calculated to quantify aromaticity in terms of magnetic and structural criteria. We find that charge separations due to the introduction of heteroatoms largely affect both the local and topological aromaticity of these molecules. Our studies show that the presence of any kind of heteroatom in the ring not only reduces the local delocalization in the six membered ring, but also affects strongly the topological aromaticity. In fact, the relative orders of the topological and local aromaticity depend strongly on the position of the heteroatoms in the structure. In general, more ring shared BN containing molecules are less aromatic than the less ring shared BN molecules. In addition our results provide evidence that the structural stability of the molecule is dominated by the σ bond rather than the π bond.     

An insight into the local aromaticities of polycyclic aromatic hydrocarbons and fullerenes

In this work we quantify the local aromaticity of six-membered rings in a series of planar and bowl-shaped polycyclic aromatic hydrocarbons (PAHs) and fullerenes. The evaluation of local aromaticity has been carried out through the use of structurally (HOMA) and magnetically (NICS) based measures, as well as by the use of a new electronically based indicator of aromaticity, the para delocalization index (PDI), which is defined as the average of all the Bader delocalization indices between para-related carbon atoms in six-membered rings. The series of PAHs selected includes C(10)H(8), C(12)H(8), C(14)H(8), C(20)H(10), C(26)H(12), and C(30)H(12), with benzene and C(60) taken as references. The change in the local aromaticity of the six-membered rings on going from benzene to C(60) is analyzed. Finally, we also compare the aromaticity of C(60) with that of C(70), open [5,6]- and closed [6,6]-C(60)NH systems, and C(60)F(18).     

Chemical graph theory and n-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.     

Electronic structures, intramolecular interactions, and aromaticity of substituted 1-(2-iminoethylidene) silan amine: a density functional study

The intramolecular hydrogen bond, molecular structure, π electrons delocalization, and vibrational frequencies in 1-(2-iminoethylidene) silan amine and its derivatives have been investigated by means of density functional method with 6-311++G** basis set, in gas phase, water, and carbon tetrachloride solutions. The obtained results showed that the hydrogen bond strength is mainly governed by resonance variations inside the chelate ring induced by the substituent groups. Furthermore, the topological properties of the electron density distributions for N–H···N intramolecular hydrogen bond were analyzed in terms of the Bader's theory of atoms in molecules. On the other hand, the aromaticity of the ring formed is measured using several well-established indices of aromaticity such as nucleus-independent chemical shift, harmonic oscillator models of the aromaticity, para-delocalization index, average two-center indices, aromatic fluctuation index, and π-fluctuation aromatic index. Natural population analysis data, the electron density and Laplacian properties, as well as γ(NH) and ν(NH) were further used for estimation of the hydrogen bonding interactions and the forces driving their formation.     

Visualizing electron delocalization in contorted polycyclic aromatic hydrocarbons

Electron delocalization in contorted polycyclic aromatic hydrocarbon (PAH) molecules was examined through 3D isotropic magnetic shielding (IMS) contour maps built around the molecules using pseudo-van der Waals surfaces. The resulting maps of electron delocalization provided an intuitive, yet detailed and quantitative evaluation of the aromatic, non aromatic, and antiaromatic character of the local and global conjugated cyclic circuits distributed over the molecules. An attractive pictural feature of the 3D IMS contour maps is that they are reminiscent of the Clar π-sextet model of aromaticity. The difference in delocalization patterns between the two faces of the electron circuits in contorted PAHs was clearly visualized. For π-extended contorted PAHs, some splits of the π system resulted in recognizable patterns typical of smaller PAHs. The differences between the delocalization patterns of diastereomeric chiral PAHs could also be visualized. Mapping IMS on pseudo-van der Waals surfaces around contorted PAHs allowed visualization of their superimposed preferred circuits for electron delocalization and hence their local and global aromaticity patterns.

Electron delocalization in contorted polycyclic aromatic hydrocarbon (PAH) molecules was examined through 3D isotropic magnetic shielding (IMS) contour maps built around the molecules using pseudo-van der Waals surfaces.     

Local aromaticity of [n]acenes, [n]phenacenes, and [n]helicenes (n = 1-9)

The local aromaticity of the six-membered rings in three series of benzenoid compounds, namely, the [n]acenes, [n]phenacenes, and [n]helicenes for n = 1-9, has been assessed by means of three probes of local aromaticity based on structural, magnetic, and electron delocalization properties. For [n]acenes our analysis shows that the more reactive inner rings are more aromatic than the outer rings. For [n]phenacenes, all indicators of aromaticity show that the external rings are the most aromatic. From the external to the central ring, the local aromaticity varies in a damped alternate way. The trends for the [n]helicene series are the same as those found for [n]phenacenes. Despite the departure from planarity in [n]helicenes, only a very slight loss of aromaticity is detected in [n]helicenes as compared to the corresponding [n]phenacenes. Finally, because of magnetic couplings between superimposed six-membered rings in the higher members of the [n]helicenes series, we have demonstrated that the NICS indicator of aromaticity artificially increases the local aromaticity of their most external rings.     

Local aromaticity study of heterocycles using n-center delocalization indices: the role of aromaticity on the relative stability of position isomers

A quantitative study on local aromaticity based on n-center electron delocalization indices, n being the number of atoms in the ring, is performed on a series of heterocycles containing N, O or S. The results indicate that the order of stability within a series of position isomers is not controlled by aromaticity but by other structural factors. Thus, for a certain series of monocycles position isomers (diazoles, triazoles, tetrazoles, diazines, triazines, and tetrazines) the most stable compound is the least aromatic one and vice versa. However, aromaticity controls the stability for series of isomers where these structural factors are similar. For the case of isocompounds, like isobenzopyrrole, isobenzofuran or isobenzothiophene, the large decrease in the aromaticity of the benzene ring with regard to their isomers makes them less stable.     

A Triply [5]Helicene-Bridged (1,3,5)Cyclophane

A rigid propeller-shaped conjugated triple macrocycle consisting of two nearly perfectly stacked benzene rings and three linking [5]helicene moieties has been synthesized using a glyoxylic Perkin approach. Analysis of the electron delocalization in this atypical aromatic molecule revealed global aromaticity and a 78 π-electron circuit along the edge of its triple loop, to the detriment of the two 6 π-electron circuits in the two stacked benzene rings.     

How electron delocalization influences the electron-withdrawing properties of isomeric benzobischalcogenadiazoles

The fermionic potential and delocalization indices for benzo-bis-1,2,5-chalcogenadiazoles reveal inhomogeneous electron delocalization in their benzene ring, which results in compactly localized lone electron pairs on the chalcogen atoms. These features of (de)localization are rooted in a local increase in the kinetic component of the electron correlation, which expresses the Fermi hole variability and the kinetic potential response to electron density variations in the benzene ring of benzobis-1,2,5-chalcogenadiazoles. This explains their better electron-withdrawing properties compared to benzobis-1,2,3-chalcogenadiazoles     

σ Aromaticity Dominates in the Unsaturated Three‐Membered Ring of Cyclopropametallapentalenes from Groups 7–9: A DFT Study

Aromaticity, an old but still fantastic topic, has long attracted considerable interest of chemists. Generally, π aromaticity is described by π‐electron delocalization in closed circuits of unsaturated compounds whereas σ‐electron delocalization in saturated rings leads to σ aromaticity. Interestingly, our recent study shows that σ aromaticity can be dominating in an unsaturated three‐membered ring (3MR) of cyclopropaosmapentalene. An interesting question is raised: Can the σ aromaticity, which is dominant in the unsaturated 3MR, be extended to other cyclopropametallapentalenes? If so, how could the metal centers, ligands, and substituents affect the σ aromaticity? Here, we report a thorough theoretical study on these issues. The nucleus‐independent chemical shift calculations and the anisotropy of the current‐induced density plots reveal the dominant σ aromaticity in these unsaturated 3MRs. In addition, our calculations show that substituents on the 3MRs have significant effects on the σ aromaticity, whereas the ligand effect is particularly small.     

The role of quantum-mechanical interference and quasi-classical effects in conjugated hydrocarbons

The nature of the chemical bond in conjugated hydrocarbons is analyzed through the generalized product function energy partitioning (GPF-EP) method, which allows the calculation of the quantum-mechanical interference and quasi-classical contributions to the energy. The method is applied to investigate the differences between the chemical bonding in conjugated and non-conjugated hydrocarbon isomers and to evaluate the contribution from the energy components to the stabilization of the molecules. It is shown that in all cases quantum-mechanical interference has the effect of concentrating π electron density between the two carbon atoms directly involved in the (C-C)π bonds. For the conjugated isomers, this effect is accompanied by a substantial reduction of electron density in the π space of the neighbouring (C-C)σ bond. On the other hand, quasi-classical effects are shown to be responsible for the extra stabilization of the conjugated isomers, in which a decrease of the π space kinetic reference energy seems to play an important role. Finally, it is shown that the polarization of p-like orbitals in compounds with alternating single and double bonds ultimately increases electron density in the π space of the neighbouring (C-C)σ bond. Therefore, quasi-classical effects, rather than covalent ones, seem to be responsible for several properties of conjugated molecules, such as thermodynamic stability, planarity and (C-C)σ bond shortening. The shortcomings of the delocalization concept are discussed.     

How Does Aromaticity Rule the Thermodynamic Stability of Hydroporphyrins?

Several measures of aromaticity including energetic, magnetic, and electron density criteria are employed to show how aromatic stabilization can explain the stability sequence of hydroporphyrins, ranging from porphin to octahydroporphin, and their preferred hydrogenation paths. The methods employed involve topological resonance energies and their circuit energy effects, bond resonance energies, multicenter delocalization indices, ring current maps, magnetic susceptibilities, and nuclear-independent chemical shifts. To compare the information obtained by the different methods, the results have been put in the same scale by using recently proposed approaches. It is found that all of them provide essentially the same information and lead to similar conclusions. Also, hydrogenation energies along different hydrogenation paths connecting porphin with octahydroporphin have been calculated with density functional theory. It is shown by using the methods mentioned above that the relative stability of different hydroporphyrin isomers and the observed inaccessibility of octahydroporphin both synthetically and in nature can be perfectly rationalized in terms of aromaticity.     

Aromaticity and Stability of Azaborines

The influence of the relative boron and nitrogen positions on aromaticity of the three isomeric 1,2‐, 1,3‐, and 1,4‐azaborines has been investigated by computing the extra cyclic resonance energy, NICS(0)_πzz index and by visualizing the π‐electron (de)shielding pattern as a response of the π system to a perpendicular magnetic field. The origin of the known stability trend, in which the 1,2‐/1,3‐isomer is the most/least stable, was examined by using an isomerization energy decomposition analysis. The 1,3‐arrangement of B and N atoms creates a charge separation in the π‐electron system, which was found to be responsible for the lowest stability of 1,3‐azaborine. This charge separation can, in turn, be considered as a driving force for the strongest cyclic π‐electron delocalization, making this same isomer the most aromatic. Despite the well‐known fact that the B?N bond attenuates electron delocalization due to large electronegativity difference between the atoms, the 1,4‐B,N relationship reduces aromaticity to a greater extent by making the π‐electron delocalization more one‐directional (from N to B) than cyclic. Thus, 1,4‐azaborine was found to be the least aromatic. Its lower stability with respect to the 1,2‐isomer was explained by the larger exchange repulsion.     

Multidimensionality of delocalization indices and nucleus independent chemical shifts in polycyclic aromatic hydrocarbons

The aromaticity and local-aromaticity of a large set of polycyclic aromatic hydrocarbons (PAHs) is studied using multicenter delocalization indices from generalized population analysis and the popular nucleus independent chemical shift (NICS) index. A method for the fast computation of the NICS values is introduced, using the so-called pseudo-pi-method. A detailed examination is made of the multidimensional nature of aromaticity. The lack of a good correlation between the NICS and the multicenter delocalization indices is reported and the grounds discussed. It is shown through a thorough statistical analysis that the NICS values arise not only from local aromaticity of the benzenoid rings, but also from other circuits. It is shown that the NICS indices do not reveal the individual aromatic nature of a specific ring, contrary to the delocalization indices.     

Tuning the Structure and Properties of N-doped Positively Charged Polycyclic Aromatic Hydrocarbons

A detailed study of the geometry, aromatic character, electronic and magnetic properties for a series of positively charged N-doped polycyclic aromatic hydrocarbons (PAHs) was performed. Magnetic properties of the examined molecules were analyzed by means of the magnetically induced current density calculated using the diamagnetic-zero version of the continuous transformation of origin of current density (CTOCD-DZ) method. The comparative study of the local aromaticity of the studied molecules was performed using several different indices: energy effect (ef), harmonic oscillator model of aromaticity (HOMA) index, six centre delocalization index (SCI) and nucleus independent chemical shifts (NICS). The presence of N-atoms in the inner rings was found to cause a planarity distortion in the studied N-doped systems. The geometric changes and charged nature of the studied N-doped systems do not significantly influence the current density and the local aromaticity distribution in comparison with the corresponding parent benzenoid hydrocarbons. The present study demonstrates how quantum chemical calculations can be used for rational design of novel PAHs and for fine tuning of their properties.