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In this paper, we provide solid evidence to show that among an overwhelming structural diversity, alkaline earth metals (Ca, Sr, Ba) have the ability to form inverted sandwich compounds with C6H6, C7H7+, and C8H82+ of Dnh symmetry and general formula [E–(CnHn)–E]n−6 (n = 6–8) with planar 10-π-electron aromatic cores by virtue of transferring two electrons per metal atom to the ring. However, the origin of the orbital interaction between the metals and the carbon ring is quite different; while [E–(C6H6)–E] complexes are dominated by δ-interactions, both π- and δ-interactions are important in [E–(C7H7)–E]+ and [E–(C8H8)–E]2+ complexes. [ABSTRACT FROM AUTHOR]

The stability of the LinBnH2n (n = 3–6) series was analyzed using quantum chemical calculations, and it was found that cyclic isomers are not energetically favored. This is different to what happens in their organic counterparts (CnH2n), where cyclopentane (C5H10) and cyclohexane (C6H12) are the low-lying isomers. Apparently, aromaticity is a key-stabilizing factor that needs to be considered for designing stable lithium-boron hydride analogues of cyclic organic compounds. This is verified in the Li3B3H3+ system, which has been designed as the smallest aromatic carbocation (C3H3+) analogue. The global minimum structure of Li3B3H3+ contains a triangular B3H32− moiety, which has structural and chemical bonding features similar to its organic counterpart. Besides, this new cluster is classified as aromatic according to both the 4n + 2 Hückel rule and the analysis of the induced magnetic field. This theoretical evidence leads us to propose this cluster as a viable target for experimental detection in the gas phase. [ABSTRACT FROM AUTHOR]

The potential energy surfaces (PESs) of Lin(BH)5n−6 systems (where n = 5, 6, and 7) were explored using the gradient embedded genetic algorithm (GEGA) program, in order to find their global minima conformations. This search predicts that the lowest-energy isomers of Li6(BH)5 and Li7(BH)5+ contain a (BH)56− pentagonal fragment, which is isoelectronic and structurally analogous to the prototypical aromatic hydrocarbon anion C5H5−. Li7(BH)5+, along with Li7C5+, Li7Si5+ and Li7Ge5+, joins a select group of clusters that adopt a seven-peak star-shape geometry, which is favored by aromaticity in the central five-membered ring, and by the preference of Li atoms for bridging positions. The theoretical analysis of chemical bonding, based on magnetic criteria, supports the notion that electronic delocalization is an important stabilization factor in all these star-shaped clusters. [ABSTRACT FROM AUTHOR]

In this investigation, an optimal description of the structure-activity relationship was done for 59 σ1 receptor ligands including arylalkylaminoalcohols, arylalkenylamines, and arylalkylamines (denoted as RC-33 analogs in this manuscript). We used optimal graph-based (GBD) and Simplified Molecular Input Line Entry System (SMILES)-based (SBD) descriptors as molecular characteristics of the structures to explain the differences in σ1 receptor affinity between the ligands. The best graph-based descriptor model (named HFG-EC0 in the manuscript) included hydrogen-filled molecular graphs using the extended connectivity of zero order (EC0). This model has an average correlation coefficient value for external test set of 0.786 with a better statistics when comparing with the best SBD model. The best SBD model (named SSSk in the manuscript) includes only three SMILES elements SSSk and has an average correlation coefficient value for external test set of 0.726. These models identified the molecular features that contribute to a high σ1 receptor ligand affinity. Copyright © 2014 John Wiley & Sons, Ltd. [ABSTRACT FROM AUTHOR]

Starting from a hypothetical but fundamental charge/discharge sequence, the topic of nonlinear optical switching in atomic clusters built from silicon and alkali metals is opened up. The outcomes presented in this work, obtained with ab initio methods of exceptional predictive capabilities, offer strong evidences that sizable hyperpolarizability contrasts between neutral and charged alkali metal doped cluster forms might be simultaneously accomplished. The observed switching procedure involves redox polyatomic clusters formed by Si atoms. These centers function as electron acceptors at the ground state and as electron donors at the excited states facilitating low energy charge transfer transitions upon electronic excitation. © 2014 Wiley Periodicals, Inc. [ABSTRACT FROM AUTHOR]

This work proposes a new molecular orbital localization procedure. The approach is based on the decomposition of the overlap matrix in accordance with the partitioning of the three-dimensional physical space into basins with clear chemical meaning arising from the topological analysis of the electron localization function. The procedure is computationally inexpensive, provides a straightforward interpretation of the resulting orbitals in terms of their localization indices and basin occupancies, and preserves the σ/π-separability in planar N-electron systems. The localization algorithm is tested on selected molecular systems. © 2012 Wiley Periodicals, Inc. [ABSTRACT FROM AUTHOR]

The most stable forms of E5Li7+ (E=Ge, Sn, and Pb) have been explored by means of a stochastic search of their potential-energy surfaces by using the gradient embedded genetic algorithm (GEGA). The preferred isomer of the Ge5Li7+ ion is a slightly distorted analogue of the D5 h three-dimensional seven-pointed starlike structure adopted by the lighter C5Li7+ and Si5Li7+ clusters. In contrast, the preferred structures for Sn5Li7+ and Pb5Li7+ are quite different. By starting from the starlike arrangement, corresponding lowest-energy structures are generated by migration of one of the E atoms out of the plane with the a corresponding rearrangement of the Li atoms. To understand these structural preferences, we propose a new energy decomposition analysis based on isomerizations (isomerization energy decomposition analysis (IEDA)), which enable us to extract energetic information from isomerization between structures, mainly from highly charged fragments. [ABSTRACT FROM AUTHOR]

We performed global minimum searches for the B nH n+2 ( n=2-5) series and found that classical structures composed of 2c-2e BH and BB bonds become progressively less stable along the series. Relative energies increase from 2.9 kcal mol−1 in B2H4 to 62.3 kcal mol−1 in B5H7. We believe this occurs because boron atoms in the studied molecules are trying to avoid sp2 hybridization and trigonal structure at the boron atoms, as in that case one 2p-AO is empty, which is highly unfavorable. This affinity of boron to have some electron density on all 2p-AOs and avoiding having one 2p-AO empty is a main reason why classical structures are not the most stable configurations and why multicenter bonding is so important for the studied boron-hydride clusters as well as for pure boron clusters and boron compounds in general. [ABSTRACT FROM AUTHOR]

The B19- anion and other boron species have been dubbed 'Wankel motors' for the almost barrierless rotation of inner and outer concentric rings relative to each other in these compounds. A single substitution in B19- is shown to shut down the well-established fluxionality in the anion. A carbon atom substituted in the structure to give a neutral CB18 species is shown computationally to enforce bond localization. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

In 1977 Weiss and Grimes, by means of mass spectrometry and 1H and 11B NMR spectroscopy, proposed two structures (I and II) for the ferraborane (η5‐C5H5)Fe(B5H10), isoelectronic with ferrocene. In this work, by means of high‐level quantum‐chemical computations, we confirm the experimental structures of the two isomers with their corresponding energies, and assign the reported 1H and 11B NMR chemical shifts. A striking result from this study is the planarization (3D→2D) of the B5H10− ligand – an unknown isolated anion, isoelectronic with aromatic cyclopentadienyl anion C5H5− – when attached to the (η5‐C5H5)Fe+ moiety, thus resulting in a more stable ferraborane isomer II. [ABSTRACT FROM AUTHOR]

In this study, we report about the relativistic effects on the aromaticity of borazine, B3N3H6, and their halogenated derivatives (B3N3F6, B3N3Cl6, B3N3Br6, B3N3I6, and B3N3At6), via the magnetically‐induced current density method. All‐electron density functional theory calculations were carried out using the four‐component Dirac‐Coulomb hamiltonian, including scalar and spin‐orbit relativistic effects. Ring current strengths were obtained by numerical integration over the current flow. These values were compared to the spin‐free (scalar relativistic) and nonrelativistic values, to assess the corresponding contributions to aromaticity. It was found that in B3N3I6 and B3N3At6 there exists a significant spin‐orbit influence, in line with the expected relativistic effects associated to the heavy elements, iodine, and astatine. Borazine, B3N3H6, is known to be slightly aromatic, but much less aromatic than benzene. The application of an external magnetic field induces a current density, that accounts for the delocalization and mobility of electrons in a molecule. Using this theoretical method, the aromaticity of the derivatives B3N3X6(X = H, F, Cl, Br, I, At) was investigated. The inclusion of heavy elements requires a relativistic treatment where the spin‐orbit coupling must be included. The figure shows the three‐dimensional pathways of the current density flow in B3N3At6. The any particle molecular orbital (APMO) approach extends regular electronic structure methods to study atomic and molecular systems in which electrons and other particles are treated simultaneously as quantum waves. A number of electronic structure methodologies have been extended under the APMO framework and applied to investigate nuclear quantum effects, proton binding energies and affinities, and physical and chemical properties of atomic and molecular systems containing exotic subatomic particles. [ABSTRACT FROM AUTHOR]

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 Li6E5Li6 sandwich structures, representing the first global minima featuring ten π‐electrons E510− 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. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

The Michaelis–Menten mechanism, which describes the binding of a substrate to an enzyme, is a simplification of the process on a molecular scale. A more detailed model should include the binding of the substrate to precatalytic binding sites (PCBSs) prior to the transition to the catalytic site. Our work shows that the incorporation of PCBSs, in steady-state conditions, generates a Michaelis–Menten-type expression, in which the kinetic parameters KM and Vmax adopt more complex expressions than in the model without PCBSs. The equations governing reaction kinetics can be seen as generalized symmetries, relative to time translation actions over the state space of the underlying chemical system. The study of their structure and defining parameters can be interpreted as looking for invariants associated with these time evolution actions. The expression of K M decreases as the number of PCBSs increases, while V m a x reaches a minimum when the first PCBSs are incorporated into the model. To evaluate the trend of the dynamic behavior of the system, numerical simulations were performed based on schemes with different numbers of PCBSs and six conditions of kinetic constants. From these simulations, with equal kinetic constants for the formation of the Substrate/PCBS complex, it is observed that K M and V m a x are lower than those obtained with the Michaelis–Menten model. For the model with PCBSs, the V m a x reaches a minimum at one PCBS and that value is maintained for all of the systems evaluated. Since K M decreases with the number of PCBSs, the catalytic efficiency increases for enzymes fitting this model. All of these observations are consistent with the general equation obtained. This study allows us to explain, on the basis of the PCBS to K M and V m a x ratios, the effect on enzyme parameters due to mutations far from the catalytic site, at sites involved in the first enzyme/substrate interaction. In addition, it incorporates a new mechanism of enzyme activity regulation that could be fundamental to search for new activity-modulating sites or for the design of mutants with modified enzyme parameters. [ABSTRACT FROM AUTHOR]

This study scrutinizes the complexities of designing and exploring the potential energy surfaces of systems containing more than twenty atoms with planar tetracoordinate carbons (ptCs). To tackle this issue, we utilized an established design rule to design a Naphtho [1,2-b:3,4-b′:5,6-b″:7,8-b′′′]tetrathiophene derivative computationally. This process began with substituting S atoms with CH− units, then replacing three sequential protons with two Si2+ units in the resultant polycyclic aromatic hydrocarbon polyanion. Despite not representing the global minimum, the newly designed Si8C22 system with four ptCs provided valuable insights into strategic design and potential energy surface exploration. Our results underscore the importance of employing adequate methodologies to confirm the stability of newly designed molecular structures containing planar hypercoordinate carbons. [ABSTRACT FROM AUTHOR]

Docking of 3-amino-1 H-indazoles complexed with glycogen synthase kinase 3 beta (GSK3β) was performed to gain insight into the structural requirements and preferred conformations of these inhibitors. The study was conducted on a selected set of 57 compounds with variation in structure and activity. We found that the most active compounds established three hydrogen bonds with the residues of the hinge region of GSK3β, but some of the less active compounds have other binding modes. In addition, models able to predict GSK3β inhibitory activities (IC50) of the studied compounds were obtained by 3D-QSAR methods CoMFA and CoMSIA. Ligand-based and receptor-guided alignment methods were utilized. Adequate R2 and Q2 values were obtained by each method, although some striking differences existed between the obtained contour maps. Each of the predictive models exhibited a similar ability to predict the activity of a test set. The application of docking and quantitative structure-activity relationship together allowed conclusions to be drawn for the choice of suitable GSK3β inhibitors. [ABSTRACT FROM AUTHOR]

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 AVmin remains the best tool to determine the main conjugation pathway of expanded porphyrins. [ABSTRACT FROM AUTHOR]

Here we show that substituting the ten protons in the dianion of a bispentalene derivative (C18H102−) by six Si2+ dications produces a minimum energy structure with two planar tetracoordinate carbons (ptC). In Si6C18, the ptCs are embedded in the terminal C5 pentagonal rings and participate in a three‐center, two‐electron (3c‐2e) Si‐ptC‐Si σ‐bond. Our exploration of the potential energy surface identifies a triphenylene derivative as the putative global minimum. Nevertheless, robustness to Born–Oppenheimer molecular dynamics (BOMD) simulations at 900 and 1500 K supports bispentalene derivative kinetic stability. Chemical bonding analysis reveals ten delocalized π‐bonds, which, according to Hückel's 4n + 2 π‐electron rule, would classify it as an aromatic system. Magnetically induced current density analysis reveals the presence of intense local paratropic currents and a weakly global diatropic current, the latter agreeing with the possible global aromatic character of this specie. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

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 = Si–Pb) combinations. These consist of aromatic polycyclic templates suitable for further design of different materials without hindering the ptC texture. [ABSTRACT FROM AUTHOR]