New Perspectives on Delocalization Pathways in Aromatic Molecular Chameleons

This study comprehensively analyzes the magnetically induced current density of polycyclic compounds labeled as "aromatic chameleons" since they can arrange their π-electrons to exhibit aromaticity in both the ground and the lowest triplet state. These compounds comprise benzenoid moieties fused to a central skeleton with 4n π-electrons and traditional magnetic descriptors are biased due to the superposition of local magnetic responses. In the S0 state, our analysis reveals that the molecular constituent fragments preserve their (anti)aromatic features in agreement with two types of resonant structures: one associated with aromatic benzenoids and the other with a central antiaromatic ring. Regarding the T1 state, a global and diatropic ring current is revealed. Our aromaticity study is complemented with advanced electronic and geometric descriptors to consider different aspects of aromaticity, particularly important in the evaluation of excited state aromaticity. Remarkably, these descriptors consistently align with the general features on the main delocalization pathways in polycyclic hydrocarbons consisting of fused 4n π-electron rings. Moreover, our study demonstrates an inverse correlation between the singlet-triplet energy difference and the antiaromatic character of the central ring in S0.

Breaking the plane: B5H5 is a three-dimensional structure

In this study, we delved into the structure of B5H5 and questioned some of its accepted assumptions. By exploring the potential energy surface, we found a new three-dimensional structure as the global minimum. This finding is in contrast with the previously hypothesized planar and cage-like models. Our exploration extends to the kinetic stability of various B5H5 isomers, offering insights into the dynamic behavior of these molecules.

Aromaticity and Magnetic Behavior in Benzenoids: Unraveling Ring Current Combinations

Nowadays, an active research topic is the connection between Clar's rule, aromaticity, and magnetic properties of polycyclic benzenoid hydrocarbons. In the present work, we employ a meticulous magnetically induced current density analysis to define the net current flowing through any cyclic circuit, connecting it to aromaticity based on the ring current concept. Our investigation reveals that the analyzed polycyclic systems display a prominent global ring current, contrasting with subdued semi-local and local ring currents. These patterns align with Clar's aromatic π-sextets only in cases where migrating π-sextet structures are invoked. The results of this study will enrich our comprehension of aromaticity and magnetic behavior in such systems, offering significant insights into coexisting ring current circuits in these systems.

Li6 E5 Li6 : Tetrel Sandwich Complexes with 10-π-Electrons

When (4n +2) π-electrons are located in single planar ring, it conventionally qualifies as aromatic. According Hückel's rule, systems possessing ten π-electrons should be aromatic. Herein we report a series of D5h  Li6 E5 Li6 sandwich structures, representing the first global minima featuring ten π-electrons E5 10- ring (E=Si-Pb). However, these π-electrons localize as five π-lone-pairs rather than delocalized orbitals. The high symmetry structure achieved is a direct consequence of σ-aromaticity, particularly favored in elements from Si to Pb, resulting in a pronounced diatropic ring current flow that contributes to the enhanced stability of these systems.

Planar pentacoordinate s-block metals

The presence of a delocalized π-bond is often considered an essential criterion for achieving planar hypercoordination. Herein, we show that σ-delocalization could be sufficient to make the planar configuration the most stable isomer in a series of planar pentacoordinate s-block metals. High-level ab initio computations reveal that the global minimum of a series of interalkali and interalkali-alkaline earth clusters (LiNa5, Li5Mg+, Na5Mg+, K5Ca+, CaRb5+, Rb5Sr+, and SrCs5+) adopts a singlet D5h structure with a planar pentacoordinate lithium or alkaline earth metal (AE = Mg, Ca, Sr). These clusters are unusual combinations to stabilize a planar pentacoordinate atom, as all their constituents are electropositive. Despite the absence of π-electrons, Hückel's rule is fulfilled by the six σ-electrons. Furthermore, the systems exhibit a diatropic ring current in response to an external magnetic field and a strong magnetic shielding, so they might be classified as σ-aromatic. Therefore, multicenter σ-bonds and the resulting σ-delocalization stabilize these clusters, even though they lack π-aromaticity.

Revisiting the potential-energy surface of CnBe3n+2H2n+22+ (n = 2-4) clusters: are planar pentacoordinate carbon structures the global minima?

Using various exploration strategies, in this study, we investigated the potential energy surfaces (PES) of CBe₅H₅⁺ and C_nBe_3n+2H_2n+2²⁺ (n = 2-4) clusters. Previous studies proposed that the planar pentacoordinate carbons (ppCs) were the global minima of these clusters. However, our study identified new putative global minima and competitive isomers, refuting some previous assignments. We employed several methods, including evolutive-inspired stochastic approaches guided by "chemical criteria", and ab initio molecular dynamics simulations at elevated temperatures. Our results showed that the size of the scanned population significantly affected the evolutive method and that constrained or guided procedures showed an advantage in identifying better minima for larger systems. This study demonstrated that using multiple complementary strategies can result in a wider variety of minima in a given energy range. Our findings provide valuable insights into exploring the potential energy surfaces of clusters, mainly medium-sized clusters, which could be the connections between small clusters and nanomaterials.

B₇Be₆B₇: A Boron-Beryllium Sandwich Complex

Planar boron clusters have often been regarded as "pi-analogous" to aromatic arenes because of their similar delocalized pi-bonding. However, unlike arenes such as C5H5- and C6H6, boron clusters have not previously shown the ability to form sandwich complexes. In this study, we present the first sandwich complex involving beryllium-and boron, B7Be6B7. The global minimum of this combination adopts a unique architecture having a D6h geometry, featuring an unprecedented monocyclic Be6 ring sandwiched between two quasi-planar B7 motifs. The thermochemical and kinetic stability of B7Be6B7 can be attributed to strong electrostatic and covalent interactions between the fragments. Chemical bonding analysis shows that B7Be6B7 can be considered as a [B7]3-[Be6]6+[B7]3- complex. Moreover, there is a significant electron delocalization within this cluster, supported by the local diatropic contributions of the B7 and Be6 rings.

Antioxidant activity and enzymatic of lichen substances: A study based on cyclic voltammetry and theoretical

The antioxidant activity of nine lichen substances, including methylatrarate (1), methyl haematommate (2), lobaric acid (3), fumarprotocetraric acid (4), sphaerophorin (5), subsphaeric acid (6), diffractaic acid (7), barbatolic acid (8) and salazinic acid (9) has been determined through cyclic voltammetry. The compounds 1-4 presented slopes close to the Nernst constant of 0.059 V, indicating a 2H⁺/2e^- relation between protons and electrons, as long as the compounds 5, 6, 7, 8, and 9 present slopes between 0.037 V and 0.032 V, indicating a 1H⁺/2e^- relation between protons and electrons. These results show a high free radical scavenging activity by means of the release of H⁺, suggesting an important antioxidant capacity of these molecules. Theoretical calculations of hydrogen bond dissociation enthalpies (BDE), proton affinities (PA), and Proton Transfer (PT) mechanisms, at M06-2x/6-311+G(d,p) level complement the experimental results. Computations support that the best antioxidant activity is obtained for the molecules (3, 4, 5, 6, 7 and 8), that have a carboxylic acid group close to a phenolic hydroxyl group, through hydrogen atomic transfer (HAT) and sequential proton loss electron transfer (SPLET) mechanisms. Additional computations were performed for modelling binding affinity of the lichen substances with CYPs enzymes, mainly CYP1A2, CYP51, and CYP2C9*2 isoforms, showing strong affinity for all the compounds described in this study.

BH4 Ng+ (Ar-Rn): Viable Compounds with a B-Ng Covalent Bond

In this work, we explore, using high-level calculations, the ability of BH₄ ⁺ to interact with noble gases. The He system is energetically unstable, while the Ne system could only be observed at cryogenic temperatures. In the case of the Ar, Kr and Xe systems, all are energetically stable, even at room temperature. The different chemical bond descriptors reveal a covalent character between B and the noble gas from Ar to Rn. However, this interaction gradually weakens the multicentric bond between the boron atom and the H₂ fragment. Thus, although BH₄ Rn⁺ exhibits a strong covalent bond, it tends to dissociate at room temperature into BH₂ Rn⁺ +H₂ .

Quest for the Most Aromatic Pathway in Charged Expanded Porphyrins

Despite the central role of aromaticity in the chemistry of expanded porphyrins, the evaluation of aromaticity remains difficult for these extended macrocycles. The presence of multiple conjugation pathways and different planar and nonplanar π-conjugation topologies makes the quantification of global and local aromaticity even more challenging. In neutral expanded porphyrins, the predominance of the aromatic conjugation pathway passing through the imine-type nitrogens and circumventing the amino NH groups is established. However, for charged macrocycles, the question about the main conjugation circuit remains open. Accordingly, different conjugation pathways in a set of neutral, anionic, and cationic expanded porphyrins were investigated by means of several aromaticity indices rooted in the structural, magnetic, and electronic criteria. Overall, our results reveal the predominance of the conjugation pathway that passes through all nitrogen atoms to describe the aromaticity of deprotonated expanded porphyrins, while the outer pathway through the perimeter carbon atoms becomes the most aromatic in protonated macrocycles. In nonplanar and charged macrocycles, a discrepancy between electronic and magnetic descriptors is observed. Nevertheless, our work demonstrates AV_min remains the best tool to determine the main conjugation pathway of expanded porphyrins.

Planar Elongated B12 Structure in M3B12 Clusters (M = Cu-Au)

Here, it is shown that the M₃B₁₂ (M = Cu-Au) clusters' global minima consist of an elongated planar B₁₂ fragment connected by an in-plane linear M₃ fragment. This result is striking since this B₁₂ planar structure is not favored in the bare cluster, nor when one or two metals are added. The minimum energy structures were revealed by screening the potential energy surface using genetic algorithms and density functional theory calculations. Chemical bonding analysis shows that the strong electrostatic interactions with the metal compensate for the high energy spent in the M₃ and B₁₂ fragment distortion. Furthermore, metals participate in the delocalized π-bonds, which infers an aromatic character to these species.

Hitting the Bull's Eye: Stable HeBeOH+ Complex

It is now known that the heavier noble gases (Ng=Ar-Rn) show some varying degrees of reactivity with a gradual increase in reactivity along Ar-Rn. However, because of their very small size and very high ionization potential, helium and neon are the hardest targets to crack. Although few neon complexes are isolated at very low temperatures, helium needs very extreme situations like very high pressure. Here, we find that protonated BeO, BeOH⁺ can bind helium and neon spontaneously at room temperature. Therefore, extreme conditions like very low temperature and/or high pressure will not be required for their experimental isolation. The Ng-Be bond strength is very high for their heavier homologs and the bond strength shows a gradual increase from He to Rn. Moreover, the Ng-Be attractive energy is almost exclusively originated from the orbital interaction which is composed of one Ng(s/p_σ )→BeOH⁺ σ-donation and two weaker Ng(p_π )→BeOH⁺ π-donations, except for helium. Helium uses its low-lying vacant 2p orbitals to accept π-electron density from BeOH⁺ . Previously, such electron-accepting ability of helium was used to explain a somewhat stronger helium bond than neon for neutral complexes. However, the present results indicate that such π-back donations are too weak in nature to decide any energetic trend between helium and neon.

Designing a Four-Ring Tubular Boron Motif through Metal Doping

Tubular boron clusters represent a class of extremely unusual geometries that can be regarded as a key indicator for the 2D-to-3D boron structural evolution as well as the embryos for boron nanotubes. While a good number of pure boron or metal-doped boron tubular clusters have been reported so far, most of them are two-ring tubular structures, and their higher-ring analogues are very scarce. We report herein the first example of a four-ring tubular boron motif in the cagelike global minimum of Be₂B₂₄⁺. Global-minimum searches of MB₂₄^q and M₂B₂₄^q (M = alkali/alkaline-earth metals; q = 1+, 0, 1-) reveal that the most stable structure of Be₂B₂₄⁺ is a C_2v-symmetric cage having a four-ring tubular boron moiety, whereas it is a high-lying isomer for those having a two/three-ring tubular boron motif for all other systems. The B₂₄ framework in Be₂B₂₄⁺ can be viewed as consisting of two two-ring B₁₂ tubular structures linked together at one side of the B₆ rings along the high-symmetry axis and two offside B₆ rings capped by two Be atoms. The Be₂-B₂₄ bonding is best described as Be₂²⁺ in an excited triplet state, forming two highly polarized covalent bonds with B₂₄^- in a quartet spin state. The unique ability of beryllium to make strong covalent and electrostatic interactions makes the Be₂B₂₄⁺ cluster stable in such an unusual geometry.

Bowl-shaped CuB12- Cluster. A viable Global Minimum with Twofold Aromaticity

A low-lying structure is revealed for the CuB 12 - cluster, which is bowl-shaped. It consists of a triangular CuB 2 base and a B 10 rim. Molecular dynamics simulations evidence its structural robustness; at an elevated temperature (600 K), the base rotates reversibly within the B 10 perimeter. Chemical bonding analysis detects 2σ- and 3π-delocalized bonds, suggesting double aromaticity, which is confirmed by two diatropic and concentric ring currents under an external magnetic field.

Why an integrated approach between search algorithms and chemical intuition is necessary?

Though search algorithms are appropriate tools for identifying low-energy isomers, fixing several constraints seems to be a fundamental prerequisite to successfully running any structural search program. This causes some potential setbacks as far as identifying all possible isomers, close to the lowest-energy isomer, for any elemental composition. The number of explored candidates, the choice of method, basis set, and availability of CPU time needed to analyze the various initial test structures become necessary restrictions in resolving the issues of structural isomerism reasonably. While one could arrive at new structures through chemical intuition, reproducing or achieving those exact same structures requires increasing the number of variables in any given program, which causes further constraints in exploring the potential energy surface in a reasonable amount of time. Thus, it is emphasized here that an integrated approach between search algorithms and chemical intuition is necessary by taking the C₁₂O₂Mg₂ system as an example. Our initial search through the AUTOMATON program yielded 1450 different geometries. However, through chemical intuition, we found eighteen new geometries within 40.0 kcal mol^-1 at the PBE0-D3/def2-TZVP level. These results indirectly emphasize that an integrated approach between search algorithms and chemical intuition is necessary to further our knowledge in chemical space for any given elemental composition.

E6C15 (E = Si-Pb): Polycyclic Aromatic Compounds with Three planar Tetracoordinate Carbons

A systematic exploration of the potential energy surface reveals two global minima with three planar tetra coordinate carbons (ptCs) and two global minima with three quasi-ptCs for E6C15 (E =...

Cluster Assembled Silicon-Lithium Nanostructures: A Nanowire Confined Inside a Carbon Nanotube

We computationally explore an alternative to stabilize one-dimensional (1D) silicon-lithium nanowires (NWs). The Li₁₂Si₉ Zintl phase exhibits the NW [Li6Si5]∞1, combined with Y-shaped Si₄ structures. Interestingly, this NW could be assembled from the stacking of the Li₆Si₅ aromatic cluster. The [Li6Si5]∞1@CNT nanocomposite has been investigated with density functional theory (DFT), including molecular dynamics simulations and electronic structure calculations. We found that van der Waals interaction between Li’s and CNT’s walls is relevant for stabilizing this hybrid nanocomposite. This work suggests that nanostructured confinement (within CNTs) may be an alternative to stabilize this free NW, cleaning its properties regarding Li₁₂Si₉ solid phase, i.e., metallic character, concerning the perturbation provided by their environment in the Li₁₂Si₇ compound.

Planar Hypercoordinate Carbons in Alkali Metal Decorated CE3 2- and CE2 2- Dianions

After exploring the potential energy surfaces of M_m CE₂ ^p (E=S-Te, M=Li-Cs, m=2, 3 and p=m-2) and M_n CE₃ ^q (E=S-Te, M=Li-Cs, n=1, 2, q=n-2) combinations, we introduce 38 new global minima containing a planar hypercoordinate carbon atom (24 with a planar tetracoordinate carbon and 14 with a planar pentacoordinate carbon). These exotic clusters result from the decoration of V-shaped CE₂ ^2- and Y-shaped CE₃ ^2- dianions, respectively, with alkali counterions. All these 38 systems fulfill the geometrical and electronic criteria to be considered as true planar hypercoordinate carbon systems. Chemical bonding analyses indicate that carbon is covalently bonded to chalcogens and ionically connected to alkali metals.

Kick-Fukui: A Fukui Function-Guided Method for Molecular Structure Prediction

Here, we introduce a hybrid method, named Kick-Fukui, to explore the potential energy surface (PES) of clusters and molecules using the Coulombic integral between the Fukui functions in the first screening of the best individuals. In the process, small stable molecules or clusters whose combination has the stoichiometry of the explored species are used as assembly units. First, a small set of candidates has been selected from a large and stochastically generated (Kick) population according to the maximum value of the Coulombic integral between the Fukui functions of both fragments. Subsequently, these few candidates are optimized using a gradient method and density functional theory (DFT) calculations. The performance of the program has been evaluated to explore the PES of various systems, including atomic and molecular clusters. In most cases studied, the global minimum (GM) has been identified with a low computational cost. The strategy does not allow to identify the GM of some silicon clusters; however, it predicts local minima very close in energy to the GM that could be used as the initial population of evolutionary algorithms.

Theobroma cacao L. compounds: Theoretical study and molecular modeling as inhibitors of main SARS-CoV-2 protease

Cocoa beans contain antioxidant molecules with the potential to inhibit type 2 coronavirus (SARS-CoV-2), which causes a severe acute respiratory syndrome (COVID-19). In particular, protease. Therefore, using in silico tests, 30 molecules obtained from cocoa were evaluated. Using molecular docking and quantum mechanics calculations, the chemical properties and binding efficiency of each ligand was evaluated, which allowed the selection of 5 compounds of this series. The ability of amentoflavone, isorhoifolin, nicotiflorin, naringin and rutin to bind to the main viral protease was studied by means of free energy calculations and structural analysis performed from molecular dynamics simulations of the enzyme/inhibitor complex. Isorhoifolin and rutin stand out, presenting a more negative binding ΔG than the reference inhibitor N-[(5-methylisoxazol-3-yl)carbonyl]alanyl-l-valyl-N~1~-((1R,2Z)−4-(benzyloxy)−4-oxo-1-{[(3R)−2-oxopyrrolidin-3-yl]methyl}but-2-enyl)-L-leucinamide (N3). These results are consistent with high affinities of these molecules for the major SARS-CoV-2. The results presented in this paper are a solid starting point for future in vitro and in vivo experiments aiming to validate these molecules and /or test similar substances as inhibitors of SARS-CoV-2 protease.

Li8 Si8 , Li10 Si9 , and Li12 Si10 : Assemblies of Lithium-Silicon Aromatic Units

We report the global minima structures of Li₈ Si₈ , Li₁₀ Si₉ , and Li₁₂ Si₁₀ systems, in which silicon moieties maintain structural and chemical bonding characteristics similar to those of their building blocks: the aromatic clusters T_d -Li₄ Si₄ and C_2v -Li₆ Si₅ . Electron counting rules, chemical bonding analysis, and magnetic response properties verify the silicon unit's aromaticity persistence. This study demonstrates the feasibility of assembling silicon-based nanostructures from aromatics clusters as building blocks.

Neither too Classic nor too Exotic: One-Electron Na⋅B Bond in NaBH3 - Cluster

It is here reported that the NaBH₃ ^- cluster exhibits a Na⋅B one-electron bond, a well-established type of electron-deficient bonding in the literature. The topological analysis of the electron localization function, at the correlated level, reveals that Na^- , when approaching the bonding distance, fairly distributes its valence electron pair between two lobes. One of these electrons is used to bond with BH₃ , which participates through its boron empty p-orbital. Furthermore, the bonding situation of LiBH₃ ^- , KBH₃ ^- , MgBH₃ , and CaBH₃ global minima structures are similar to that of NaBH₃ ^- , extending the family of these new one-electron bond systems with biradicaloid character.

Planar Tetracoordinate Carbons in Allene-Type Structures

The exhaustive exploration of the potential energy surfaces of CE₂M₂ (E = Si-Pb; M = Li and Na) revealed seven global minima containing a planar tetracoordinate carbon (ptC). The design, based on a π-localization strategy, resulted in a ptC with two double bonds forming a linear or a bent allene-type E═C═E motif. The magnetic response of the bent E═C═E fragments support a σ-aromaticity. The bonding analysis indicated that the ptCs form C-E covalent bonds and C-M electrostatic interactions.

Planar Hexacoordinate Carbons: Half Covalent, Half Ionic

Herein, the first global minima containing a planar hexacoordinate carbon (phC) atom are reported. The fifteen structures belong to the CE₃ M₃ ⁺ (E=S-Te and M=Li-Cs) series and satisfy both geometric and electronic criteria to be considered as a true phC. The design strategy consisted of replacing oxygen in the D_3h  CO₃ Li₃ ⁺ structure with heavy and less electronegative chalcogens, inducing a negative charge on the C atom and an attractive electrostatic interaction between C and the alkali-metal cations. The chemical bonding analyses indicate that carbon is covalently bonded to three chalcogens and ionically connected to the three alkali metals.

In Silico Study of Coumarins and Quinolines Derivatives as Potent Inhibitors of SARS-CoV-2 Main Protease

The pandemic that started in Wuhan (China) in 2019 has caused a large number of deaths, and infected people around the world due to the absence of effective therapy against coronavirus 2 of the severe acute respiratory syndrome (SARS-CoV-2). Viral maturation requires the activity of the main viral protease (Mpro), so its inhibition stops the progress of the disease. To evaluate possible inhibitors, a computational model of the SARS-CoV-2 enzyme Mpro was constructed in complex with 26 synthetic ligands derived from coumarins and quinolines. Analysis of simulations of molecular dynamics and molecular docking of the models show a high affinity for the enzyme (∆E binding between -5.1 and 7.1 kcal mol-1). The six compounds with the highest affinity show K d between 6.26 × 10-6 and 17.2 × 10-6, with binding affinity between -20 and -25 kcal mol-1, with ligand efficiency less than 0.3 associated with possible inhibitory candidates. In addition to the high affinity of these compounds for SARS-CoV-2 Mpro, low toxicity is expected considering the Lipinski, Veber and Pfizer rules. Therefore, this novel study provides candidate inhibitors that would allow experimental studies which can lead to the development of new treatments for SARS-CoV-2.

Structure–antioxidant activity relationships in boldine and glaucine: a DFT study

DFT calculations indicate that boldine and glaucine exhibit direct antioxidant activity through the HAT and SPLET (at high pH values) mechanisms.

On the NICS limitations to predict local and global current pathways in polycyclic systems

Here, we analyze the possibility of predicting local and global current densities in a series of bicyclic hydrocarbons with 4n and 4n + 2 π-electrons from the nucleus-independent chemical shifts (NICS) computations.

Local and macrocyclic (anti)aromaticity of porphyrinoids revealed by the topology of the induced magnetic field

The aromaticity in porphyrinoids results from the π conjugation through two different annular perimeters: the macrocyclic ring and the local heterocyclic rings appended to it. Analyses, based on aromatic stabilization energies (ASE), indicate that the local circuits (6π) are responsible for the significant aromatic stabilization of these systems. This local aromaticity can be coupled with the one from 4n + 2π macrocyclic circuit. It can either compensate for the destabilization due to a 4n π macrocyclic circuit, or be the only source of aromatic stabilization in porphyrinoids with macrocycles without π-conjugated bonds. This "multifaceted" aromatic character of porphyrinoids makes it challenging to analyze their aromaticity using magnetic descriptors because of the intricate interaction of local versus macro-cyclic circulation. In this contribution, we show that the analysis of the bifurcation of the induced magnetic field, Bind, allows clear identification and quantification of both local, and macrocyclic aromaticity, in a representative group of porphyrinioids. In porphyrin, bifurcation values accurately predict the local and macrocyclic contribution rate to overall aromatic stabilization determined by ASE.

Biosystem Analysis of the Hypoxia Inducible Domain Family Member 2A: Implications in Cancer Biology

The expression of HIGD2A is dependent on oxygen levels, glucose concentration, and cell cycle progression. This gene encodes for protein HIG2A, found in mitochondria and the nucleus, promoting cell survival in hypoxic conditions. The genomic location of HIGD2A is in chromosome 5q35.2, where several chromosomal abnormalities are related to numerous cancers. The analysis of high definition expression profiles of HIGD2A suggests a role for HIG2A in cancer biology. Accordingly, the research objective was to perform a molecular biosystem analysis of HIGD2A aiming to discover HIG2A implications in cancer biology. For this purpose, public databases such as SWISS-MODEL protein structure homology-modelling server, Catalogue of Somatic Mutations in Cancer (COSMIC), Gene Expression Omnibus (GEO), MethHC: a database of DNA methylation and gene expression in human cancer, and microRNA-target interactions database (miRTarBase) were accessed. We also evaluated, by using Real-Time Quantitative Reverse Transcription Polymerase Chain Reaction (qRT-PCR), the expression of Higd2a gene in healthy bone marrow-liver-spleen tissues of mice after quercetin (50 mg/kg) treatment. Thus, among the structural features of HIG2A protein that may participate in HIG2A translocation to the nucleus are an importin α-dependent nuclear localization signal (NLS), a motif of DNA binding residues and a probable SUMOylating residue. HIGD2A gene is not implicated in cancer via mutation. In addition, DNA methylation and mRNA expression of HIGD2A gene present significant alterations in several cancers; HIGD2A gene showed significant higher expression in Diffuse Large B-cell Lymphoma (DLBCL). Hypoxic tissues characterize the “bone marrow-liver-spleen” DLBCL type. The relative quantification, by using qRT-PCR, showed that Higd2a expression is higher in bone marrow than in the liver or spleen. In addition, it was observed that quercetin modulated the expression of Higd2a gene in mice. As an assembly factor of mitochondrial respirasomes, HIG2A might be unexpectedly involved in the change of cellular energetics happening in cancer. As a result, it is worth continuing to explore the role of HIGD2A in cancer biology.

Aromatic ouroboroi: heterocycles involving a σ-donor-acceptor bond and 4n + 2 π-electrons

The aromaticity and dynamics of a set of recently proposed neutral 5- and 6-membered heterocycles that are closed by dative (donor-acceptor) or multi-center σ bonds, and have resonance forms with a Hückel number of π-electrons, are examined. The donors and acceptors in the rings include N, O, and F, and B, Be, and Mg, respectively. The planar geometry of the rings, coupled with evidence from different measures of aromaticity, namely the NICSzz, and NICSπzz components of the conventional nucleus independent chemical shifts (NICS), and ring current strengths (RCS), indicate non-trivial degrees of aromaticity in certain cases, including the cyclic C3B2OH6 and C3BOH5 isomers, both with three bonds to the O site in the ring. The former is lower in energy by at least 17.6 kcal mol-1 relative to linear alternatives obtained from molecular dynamics simulations in this work. Some of the other systems examined are best described as non-aromatic. Ring opening, closing, and isomerization are observed in molecular dynamics simulations for some of the systems studied. In a few cases, the ring indeed persists.

Embedding a Planar Hypercoordinate Carbon Atom into a [4n+2] π-System

Through delicate tuning of the electronic structure, we report herein a rational design of seventeen new putative global minimum energy structures containing a planar tetra- or pentacoordinate carbon atom embedded in an aromatic hydrocarbon. These structures are the result of replacing three consecutive hydrogen atoms of an aromatic hydrocarbon by less electronegative groups, forming a multicenter σ-bond with the planar hypercoordinate carbon atom and participating in the π-electron delocalization. This strategy that maximizes both mechanical and electronic effects through aromatic architectures can be extended to several molecular combinations to achieve new and diverse compounds containing planar hypercoordinate carbon centers.

Relativistic effects on the aromaticity of E3M3H3 (E = C–Pb; M = N–Bi) benzene analogues

The relativistic effects on the aromaticity of a set of benzene analogues, E₃M₃H₃ (E = C–Pb; M = N–Bi) heterocycles, using magnetically induced current density (MICD) and the NICS_zz component of the conventional nucleus independent chemical shift (NICS), is hereby examined.

Searching for double σ- and π-aromaticity in borazine derivatives

Inspired by the double-aromatic (σ and π) C₆H₃⁺, C₆I₆²⁺, and C₆(SePh)₆²⁺ ring-shaped compounds, herein we theoretically study their borazine derivative analogues. The systems studied are the cation and dications with formulas B₃N₃H₃⁺, B₃N₃Br₆²⁺, B₃N₃I₆²⁺, B₃N₃(SeH)₆²⁺, and B₃N₃(TeH)₆²⁺. Our DFT calculations indicate that the ring-shaped planar structures of B₃N₃H₃⁺, B₃N₃I₆²⁺, and B₃N₃(TeH)₆²⁺ are more stable in the singlet state, while those of B₃N₃Br₆²⁺ and B₃N₃(SeH)₆²⁺ prefer the triplet state. Besides, exploration of the potential energy surface shows that the ring-shaped structure is the putative global minimum only for B₃N₃I₆²⁺. According to chemical bonding analysis, B₃N₃H₃⁺, B₃N₃I₆²⁺, and B₃N₃(TeH)₆²⁺ have σ and π delocalized bonds. The number of delocalized σ/π electrons is 2/6 for the first, and 10/6 for the second and third, similar to what their carbon analogs exhibit. Finally, the analysis of the magnetically induced current density allows B₃N₃H₃⁺, B₃N₃I₆²⁺, and B₃N₃(TeH)₆²⁺ to be classified as strongly σ aromatic, and poorly π aromatic compounds.

Evolutionary algorithms, Born–Oppenheimer molecular dynamics and the magnetic criteria of aromaticity have been used to evaluate the stability and σ–π aromaticity of borazine derivatives in order to expand the family of double aromatics systems.

Theoretical Study of the Antioxidant Activity of Quercetin Oxidation Products

It was recently shown that, when tested in cellular systems, quercetin oxidized products (Qox) have significantly better antioxidant activity than quercetin (Q) itself. The main Qox identified in the experiments are either 2,5,7,3',4'-pentahydroxy-3,4-flavandione (Fl) or its tautomer, 2-(3,4-dihydroxybenzoyl)-2,4,6-trihydroxy-3(2H)-benzofuranone (Bf). We have now performed a theoretical evaluation of different physicochemical properties using density functional theory (DFT) calculations on Q and its main Qox species. The most stable structures (for Q and Qox) were identified after a structural search on their potential energy surface. Since proton affinities (PAs) are much lower than the bond dissociation enthalpies (BDEs) of phenolic hydrogens, we consider that direct antioxidant activity in these species is mainly due to the sequential proton loss electron transfer (SPLET) mechanism. Moreover, our kinetic studies, according to transition state theory, show that Q is more favored by this mechanism. However, Qox have lower PAs than Q, suggesting that antioxidant activity by the SPLET mechanism should be a result of a balance between proclivity to transfer protons (which favors Qox) and the reaction kinetics of the conjugated base in the sequential electron transfer mechanism (which favors Q). Therefore, our results support the idea that Q is a better direct antioxidant than its oxidized derivatives due to its kinetically favored SPLET reactions. Moreover, our molecular docking calculations indicate a stabilizing interaction between either Q or Qox and the kelch-like ECH-associated protein-1 (Keap1), in the nuclear factor erythroid 2-related factor 2 (Nrf2)-binding site. This should favor the release of the Nrf2 factor, the master regulator of anti-oxidative responses, promoting the expression of the antioxidant responsive element (ARE)-dependent genes. Interestingly, the computed Keap1-metabolite interaction energy is most favored for the Bf compound, which in turn is the most stable oxidized tautomer, according to their computed energies. These results provide further support for the hypothesis that Qox species may be better indirect antioxidants than Q, reducing reactive oxygen species in animal cells by activating endogenous antioxidants.

Orbital-Weighted Dual Descriptor for the Study of Local Reactivity of Systems with (Quasi-) Degenerate States

An alternative response function, based on the dual descriptor in terms of Koopmans' approximation, is hereby proposed for the description of chemical reactivity in systems with (quasi-) degenerate frontier molecular orbitals. This descriptor is constructed from Fukui functions that include contributions from different orbitals, i.e., orbital-weighted Fukui functions. The methodology is applied to three case studies: the first case consists of a series of benchmark organic and inorganic molecules from which the dual descriptor, based only on frontier orbitals, is not appropriate to describe their reactivity. The second case deals with the proper description of chemical reactivity in Diels-Alder reactions between fullerene C₆₀ and cyclopentadiene (CP), revealing the importance of considering secondary orbital interactions for an adequate regioselectivity description. The third, and last case, consists of a series of polycyclic aromatic hydrocarbons (PAHs) possessing molecular orbital degeneracy. By means of analyzing of this descriptor, an alternative approach to the description of aromaticity is proposed. In all cases, the proposed index called "orbital-weighted dual descriptor" has proven to accurately describe the chemical reactivity and aromaticity of the studied systems.

Exploring the Potential Energy Surface of Trimetallic Deltahedral Zintl Ions: Lowest-Energy [Sn6Ge2Bi]3- and [(Sn6Ge2Bi)2]4- Structures

The synthesis and structural characterization of the dimer [(Sn₆Ge₂Bi)₂]^4- raise the possibility of obtaining a broad variety of analogous compounds with different Sn/Ge/Bi proportions. Several combinations of nine atoms have been detected by electrospray mass spectrometry as potential assembly units. However, [(Sn₆Ge₂Bi)₂]^4- remains as the unique experimentally characterized species in this series. This fact has motivated us to explore its potential energy surface, as well as its monomers' [Sn₆Ge₂Bi]^3-/2-, in an effort to gain insight into the factors that might be privileging the experimental viability of this species. Our results show that the lowest-energy [Sn₆Ge₂Bi]^3- structure remains in its oxidized product [Sn₆Ge₂Bi]^2-, which corresponds to that identified in the dimer [(Sn₆Ge₂Bi)₂]^4-. Additionally, local minima, very close in energy to the lowest-energy monomer, are chiral mixtures that dimerize into diverse structures with a probable energetic cost, making them noncompetitive isomers. Finally, the global minimum of the dimer [(Sn₆Ge₂Bi)₂]^4- presents the most stable monomers as assembly units. These results show the importance of considering the simultaneity of all of these conditions for the viability of these types of compounds.

Interpreting Aromaticity and Antiaromaticity through Bifurcation Analysis of the Induced Magnetic Field

In all molecules, a current density is induced when the molecule is subjected to an external magnetic field. In turn, this current density creates a particular magnetic field. In this work, the bifurcation value of the induced magnetic field is analyzed in a representative set of aromatic, non-aromatic and antiaromatic monocycles, as well as a set of polycyclic hydrocarbons. The results show that the bifurcation value of the ring-shaped domain adequately classifies the studied molecules according to their aromatic character. For aromatic and nonaromatic molecules, it is possible to analyze two ring-shaped domains, one diatropic (inside the molecular ring) and one paratropic (outside the molecular ring). Meanwhile, for antiaromatic rings, only a diatropic ring-shaped domain (outside the molecular ring) is possible to analyze, since the paratropic domain (inside the molecular ring) is irreducible with the maximum value (attractor) at the center of the molecular ring. In some of the studied cases, i. e., in heteroatomic species, bifurcation values do not follow aromaticity trends and present some inconsistencies in comparison to ring currents strengths, showing that this approximation provides only a qualitative estimation about (anti)aromaticity.

Reply to the ‘Comment on “Exploiting electronic strategies to stabilize a planar tetracoordinate carbon in cyclic aromatic hydrocarbons”’ by V. S. Thimmakondu, Chem. Commun., 2019, DOI: 10.1039/c9cc04639a

The authors respond to the Comment by Thimmakondu, showing that the effectiveness of their approach to stabilize a planar tetracoordinate (ptC) carbon in cyclic aromatic hydrocarbons is unquestionable, since their results are reproducible and reliable.

Carbon rings decorated with group 14 elements: new aromatic clusters containing planar tetracoordinate carbon

A simple and chemically intuitive approach is used to design ptC-containing E–C clusters (E = Si–Pb).

Formation of small clusters of NaCl dihydrate in the gas phase

Sodium chloride dihydrates form cuboid structures in initial stages of nucleation, preserving the NaCl interaction.