Classical versus Collective Interactions in Asymmetric Trigonal Bipyramidal Alkaline Metal-Boron Halide Complexes.

Collective interactions are a novel type of chemical bond formed between metals and electron-rich substituents around an electron-poor central atom. So far only a limited number of candidates for having collective interactions are reported. In this work, we extend the newly introduced concept of collective bonding to a series of neutral boron complexes with the general formula M2BX3 (M=Li, Na, and K; X=F, Cl, and Br). Our state-of-the-art ab initio computations suggest that these complexes form trigonal bipyramidal structures with a D3h to C3v distortion along the C3 axis of symmetry. The BX3 unit in the complexes distorts from planar to pyramidal akin to a sp3 hybridized atom. Interestingly, the interaction of the metals with the pyramidal side of BX3, where the lone pair in a hypothetical [BX3]2- should be located, is weaker than the interactions of metals with the inverted side, i. e., the middle of three halogen atoms. The origin of this stronger interaction can be explained by the formation of collective interactions between metals and halogen atoms as we explored via energy decomposition within the context of the theory of interacting quantum atoms, IQA.

Tetraquinolines; four linked quinoline units or porphyrinoids.

Tetraquinolines (TEQs) have been recently synthesized and proposed to be a new member of the porphyrinoid family with highly distorted, nonplanar, geometries. In this contribution by studying several molecules, closely related to TEQs, we have suggested that the origin of the nonplanarity of TEQs and their counterparts is a combination of steric strain and the propensity of the molecules to avoid antiaromaticity. The tendency of TEQs to coordinate with doubly charged metal ions can be interpreted in terms of their transition from potential antiaromaticity to nonaromaticity. Even metal-coordinated TEQs do not sustain diatropic ring currents. Although full planarization is not possible because of steric strain, doubly oxidized TEQs and their counterparts sustain moderate global diatropic ring currents and partially planarize. The nature of current density in the molecules is studied in the light of Steiner-Fowler selection rules.

Metallaaromaticity - a protean world.

The nature of magnetically induced current densities (MICD) of metallabenzenes and related compounds has been examined with relativistic DFT calculations to assess the magnetic aromaticity of the molecules. The origin of the total MICD has been analyzed in terms of individual molecular orbital (MO) contributions. Our study reveals that the σ-framework of the molecules always makes a diamagnetic contribution to the MICD. On the other hand, π-MOs and Craig-Möbius type π-MOs, i.e., MOs in which the dxy/dxz orbitals of the metal centers change the phase of the wave function akin to a Möbius twist, may not make a diatropic contribution. We have identified metallabenzenes with multiple magnetic aromaticities. In the case of iridabenzenes, σ-MICD has been found to decrease dramatically from Ir(III) to Ir(V) systems. Furthermore, a brief examination of some recently synthesized metallapolycycles has shown that the metal center in a given ring can strongly modulate the aromaticity of neighboring rings. Finally, the finding that relatively minor perturbations in the ligand environment of the metal can substantially influence the aromaticity of metallabenzenes and related molecules underscores the protean character of metallaaromaticity and the need for even wider-ranging investigations. Considering the conflicts between magnetic response and ground-state aromaticity criteria (energetic, structural, and electronic criteria), we propose that the term aromatic be used for labeling a molecule if and only if all criteria confirm aromaticity. In other words, neither magnetic nor ground-state criteria are necessary and sufficient conditions for labeling a molecule aromatic.

How Does a Container Affect Acidity of its Content: Charge-Depletion Bonding Inside Fullerenes.

A recent study (Sci. Adv. 2017, 3, e1602833) has shown that FH⋅⋅⋅OH2 hydrogen bond in a HF⋅H2 O pair substantially shortens, and the H-F bond elongates upon encapsulation of the cluster in C70 fullerene. This has been attributed to compression of the HF⋅H2 O pair inside the cavity of C70 . Herein, we present theoretical evidence that the effect is not caused by a mere compression of the H2 O⋅HF pair, but it is related to a strong lone-pair-π (LP-π) bonding with the fullerene cage. To support this argument, a systematic electronic structure study of selected small molecules (HF, H2 O, and NH3 ) and their pairs enclosed in fullerene cages (C60 , C70 , and C90 ) has been performed. Bonding analysis revealed unique LP-πcage interactions with a charge-depletion character in the bonding region, unlike usual LP-π bonds. The LP-πcage interactions were found to be responsible for elongation of the H-F bond. Thus, the HF appears to be more acidic inside the cage. The shortening of the FH⋅⋅⋅OH2 contact in (HF⋅H2 O)@C70 originates from an increased acidity of the HF inside the fullerenes. Such trends were also observed in other studied systems.

Unification of ground-state aromaticity criteria - structure, electron delocalization, and energy - in light of the quantum chemical topology.

In the present account we investigate a theoretical link between the bond length, electron sharing, and bond energy within the context of quantum chemical topology theories. The aromatic stabilization energy, ASE, was estimated from this theoretical link without using isodesmic reactions for the first time. The ASE values obtained from our method show a meaningful correlation with the number of electrons contributing to the aromaticity. This theoretical link demonstrates that structural, electronic, and energetic criteria of aromaticity - ground-state aromaticity - belong to the same class and guarantees that they assess the same property as aromaticity. Theory suggests that interatomic exchange-correlation potential, obtained from the theory of Interacting Quantum Atoms (IQA), is linearly connected to the delocalization index of Quantum Theory of Atoms in Molecules (QTAIM) and the bond length through a first order approximation. Our study shows that the relationship between energy, structure and electron sharing marginally deviates from the ideal linear form expected from the first order approximation. The observed deviation from linearity was attributed to a different contribution of exchange-correlation to the bond energy for the σ- and π-frameworks. Finally, we proposed two-dimensional energy-structure-based aromaticity indices in analogy to the electron sharing indices of aromaticity.

Multi-center covalency: revisiting the nature of anion-π interactions.

Exploring the nature of anion-π bonding by means of the Quantum Theory of Atoms in Molecules (QTAIM) and an energy decomposition scheme on the basis of Interacting Quantum Atoms (IQA) theory led us to conclude that these non-classical interactions benefit from "multi-center covalency" far more than from the electrostatics. Comparing anion-π systems to closely related covalent anion-σ complexes reveals that the anion-π systems benefit from an extensive degree of electron sharing between the anions and all atoms of the π-rings. Besides, decomposition of the binding energy into classical (electrostatics) and non-classical (exchange-correlation) components demonstrates that in contrast to previous reports, the anion-π complexes are local minima, if and only if the non-classical contribution to binding energy surpasses that of the electrostatics. This suggests that the stable anion-π complexes with the anions atop the π-rings might be prepared with π-systems that benefit more from the exchange-correlation term, such as extended π-systems, but not with strong electrostatic π-receptors. This conclusion is in line with the tendency of strong π-acids to form the σ-complexes with more covalent character instead of the π-complexes.

On the non-classical contribution in lone-pair-π interaction: IQA perspective.

In the present work the nature of lone-pair-π interactions between water molecules and a number of π-rings with different substituents/hetero-atoms in the light of quantum chemical topology approaches is studied. The Quantum Theory of Atoms in Molecules (QTAIM) and Interacting Quantum Atoms (IQA) were employed for distinguishing the role of heteroatoms and electron withdrawing substituents in the complex formation between water and π-rings. Our IQA study identified three classes of water-π complexes on the basis of the relative role of electrostatics (classical) and exchange-correlation (non-classical) factors in the interaction energy between the oxygen of water (the lone-pair donor) and the sp(2) atoms of the π-ring, i.e. the primary lp-π interaction. Considering both the primary and secondary (the rest of interatomic interactions except Owater-π-ring atoms) interactions demonstrates that the exchange-correlation is the dominant contributor to the binding energy. This proves a non-negligible contribution of non-classical factors in the stabilization of the lone-pair-π complexes. However, in spite of a relatively large contribution of the exchange-correlation, this part of the interaction energy is virtually counterbalanced by the deformation energy, i.e. the increase in atomic kinetic energy upon complexation. This finding clarifies why water-π interactions can be modelled by simple electrostatics without the need to invoke quantum effects.

On the aromaticity of actinide compounds.

The chemistry of actinides has flourished since the late 2010s with the synthesis of new actinide complexes and clusters. On the theoretical side, a range of tools is available for the characterization of these heavy element-containing compounds, but discrepancies in the assessment of aromaticity using different tools have led to controversies. In this Perspective, we examine the origin of controversies relating to the aromaticity of metallic compounds, with a focus on actinides. The aromaticity of actinides is important, not because these molecules are numerous or have a special role in catalysis or reactivity, but because this topic pushes theories of aromaticity to their limits. Owing to its reference independence, the magnetic criterion of aromaticity has been the most popular choice for the characterization of the aromaticity of metallic compounds, including actinide compounds. Through examination of several case studies, we show why this criterion might be misleading for metallic species and explain how findings relating to actinide compounds could reshape theories of aromaticity, not just for actinides but perhaps also for well-known hydrocarbons.

Comparison the salivary streptococcus mutans levels between caries-active and caries-free children from Birjand, Iran: A case-control study.

Objective: Dental plaque bacteria, including Streptococcus mutans (SM), play a role in the pathogenesis of the dental caries. There are conflicting results regarding the association of salivary SM level and dental caries susceptibility. Our aim was to compare salivary SM levels in colony-forming units (CFU) between children with active caries and caries-free children in Birjand, Iran. Methods: This case-control study included 61 six-year-old children referred to health centers in Birjand city, Iran, in 2022. The children were divided into two groups: case (dmft/DMFT>0 with active caries) (including 31 children) and control (dmft/DMFT = 0 [caries-free]) (including 30 children). Demographic information and dental history were recorded. Oral examinations were also performed by the dentist. Unstimulated saliva samples were collected from children. The number of salivary SM colonies was determined using the microbial culture and confirmed using the polymerase chain reaction (PCR). The data were analyzed using Chi-square and T-tests at a significance level of p < 0.05. Results: The mean number of SM colonies was 126.24 ± 92.78 CFU/ml and 92.38 ± 75.34 CFU/ml in case and control groups, respectively. No significant difference was found in salivary SM levels between case and control groups (P = 0.125). No significant association was observed between caries experience with gender (P = 0.363), type of school (public/private) (P = 0.296), receiving oral health education (P = 0.072) and frequency of tooth brushing (P = 0.935). The mean gingival index (P = 0.001) and plaque index (P = 0.025) in case group were significantly higher than control group. Conclusion: There is no significant difference in salivary SM levels between caries-active and caries-free children in Birjandi children.

Method/basis set dependence of NICS values among metallic nano-clusters and hydrocarbons.

The influence of various all-electron basis sets and effective core potentials employed along with several DFT functionals (B3LYP, B3PW91, BLYP, BP86 and M06) on the magnitude of nucleus independent chemical shift (NICS) values in different metallic nano-clusters and hydrocarbons is studied. In general, it is demonstrated that the NICS values are very sensitive to the applied method/basis set; however, the method/basis set dependence is more prominent for computed NICS values in transition metal clusters. In hydrocarbons, medium-size basis sets perform roughly similar to large basis sets in most cases. It is also found that NICS(0) values are more sensitive to the method/basis set variation compared to the NICS values computed at 1 or 2 Å above the ring plane. However, in many cases, no broad-spectrum regulation is found for the effect of basis set/method on the magnitude of NICS values. A detailed study showed that bond length alternation in a molecule has an insignificant effect on the magnitude of NICS values so the influence of method/basis sets on the magnitude of NICS values mostly arises from the different predicted ring current intensities at various computational levels.

The Laplacian of electron density versus NICSzz scan: measuring magnetic aromaticity among molecules with different atom types.

The electron density versus NICS(zz) (the out-of-plane component of nucleus-independent chemical shifts (NICS)) scan for assessing magnetic aromaticity among similar molecules with different ring sizes is improved by scanning the Laplacian of electron density versus NICS(zz) to include molecules containing different types of atoms. It is demonstrated that the new approach not only reproduces the results of the previous method but also surpasses that in the case of species with different atom types. The relative positions of curves in the plots of the Laplacian of electron density versus NICS(zz) correlate well with the ring current intensities of these molecules both near and far from the ring planes of the considered molecules. Accordingly, relative magnetic aromaticity of a number of planar hydrocarbons and a group of double aromatic metallic/semimetallic species are studied and discussed.

Composite 5-methylations of cytosines modulate i-motif stability in a sequence-specific manner: Implications for DNA nanotechnology and epigenetic regulation of plant telomeric DNA.

BACKGROUND: The i-motif is a tetrameric DNA structure based on the formation of hemiprotonated cytosine-cytosine (C+.C) base pairs. i-motifs are widely used in nanotechnology. In biological systems, i-motifs are involved in gene regulation and in control of genome integrity. In vivo, the i-motif forming sequences are subjects of epigenetic modifications, particularly 5-cytosine methylation. In plants, natively occurring methylation patterns lead to a complex network of C+.C, 5mC+.C and 5mC+.5mC base-pairs in the i-motif stem. The impact of complex methylation patterns (CMPs) on i-motif formation propensity is currently unknown. METHODS: We employed CD and UV-absorption spectroscopies, native PAGE, thermal denaturation and quantum-chemical calculations to analyse the effects of native, native-like, and non-native CMPs in the i-motif stem on the i-motif stability and pKa. RESULTS: CMPs have strong influence on i-motif stability and pKa and influence these parameters in sequence-specific manner. In contrast to a general belief, i) CMPs do not invariably stabilize the i-motif, and ii) when the CMPs do stabilize the i-motif, the extent of the stabilization depends (in a complex manner) on the number and pattern of symmetric 5mC+.5mC or asymmetric 5mC+.C base pairs in the i-motif stem. CONCLUSIONS: CMPs can be effectively used to fine-tune i-motif properties. Our data support the notion of epigenetic modifications as a plausible control mechanism of i-motif formation in vivo. GENERAL SIGNIFICANCE: Our results have implications in epigenetic regulation of telomeric DNA in plants and highlight the potential and limitations of engineered patterning of cytosine methylations on the i-motif scaffold in nanotechnological applications.

All-Metal Aromaticity: Revisiting the Ring Current Model among Transition Metal Clusters.

We present new insight into the nature of aromaticity in metal clusters. We give computational arguments in favor of using the ring-current model over local indices, such as nucleus independent chemical shifts, for the determination of the magnetic aromaticity. Two approaches for estimating magnetically induced ring currents are employed for this purpose, one based on the quantum theory of atoms in molecules (QTAIM) and the other where magnetically induced current densities (MICD) are explicitly calculated. We show that the two-zone aromaticity/antiaromaticity of a number of 3d metallic clusters (Sc3(-), Cu3(+), and Cu4(2-)) can be explained using the QTAIM-based magnetizabilities. The reliability of the calculated atomic and bond magnetizabilities of the metallic clusters are verified by comparison with MICD computed at the multiconfiguration self-consistent field (MCSCF) and density functional levels of theory. Integrated MCSCF current strength susceptibilities as well as a visual analysis of the calculated current densities confirm the interpretations based on the QTAIM magnetizabilities. In view of the new findings, we suggest a simple explanation based on classical electromagnetic theory to explain the anomalous magnetic shielding in different transition metal clusters. Our results suggest that the nature of magnetic aromaticity/antiaromaticity in transition-metal clusters should be assessed more carefully based on global indices.