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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]

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]

Planar boron clusters have often been regarded as "π‐analogous" to aromatic arenes because of their similar delocalized π‐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 fragments. [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]

After exploring the potential energy surfaces of MmCE2p (E=S−Te, M=Li−Cs, m=2, 3 and p=m‐2) and MnCE3q (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 CE22− and Y‐shaped CE32− 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. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

Herein, the first global minima containing a planar hexacoordinate carbon (phC) atom are reported. The fifteen structures belong to the CE3M3+ (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 D3h CO3Li3+ 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. [ABSTRACT FROM AUTHOR]

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. Interpreting aromaticity: Here, we introduced the bifurcation analysis of the induced magnetic field to interpret the aromatic or antiaromatic character of a representative set of 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, providing a useful tool to assess aromaticity according to the magnetic criteria. [ABSTRACT FROM AUTHOR]

Extensive explorations of their potential energy surfaces, combined with high‐level quantum chemical computations, strikingly show that the lowest energy structures of the (Li6Si5)2–5 systems consist of 2–5 Si56− aromatic units, surrounded by Li+ counterions, respectively. These viable gas‐phase compounds are the pioneering reported cases of oligomers made by planar aromatic silicon rings. Based on the key evidence that these oligomers are energetically favored, and that their silicon rings aromaticity is thoroughly preserved, the Li6Si5 cluster is proposed as a potential assembly unit to build silicon‐lithium nanostructures, thus opening new paths to design Zintl compounds at the nanoscale level. Aromatic building blocks: After a systematic exploration of the potential energy surface of the (Li6Si5)2–5 clusters, it was found that the lowest energy structures in all cases are formed by multiple aromatic Si56− pentagonal units interacting electrostatically with lithium cations. These units maintain their geometric and electronic properties as revealed by chemical bonding and magnetic response analyses. [ABSTRACT FROM AUTHOR]

We present new evidence that supports the aromatic character of the clusters of formula: [M3(µ‐X)3X6]0/2– (M = Re and Tc, X = Cl, Br, I). Our computations clearly show that these clusters present a special response to an applied external magnetic field, which is characteristic of aromatic systems. Both analyzed response properties, the magnetically induced current density and the induced magnetic field, agree that the magnetic perturbation induces two concentric diatropic ring currents: the inner one inside the M3 core and the outer one around the M3(µ‐X)3 triangle. The flow strength of these two ring currents is significant, confirming the high diatropicity of these clusters. In the dianionic species, aromaticity is increased, mainly by an increment of the diatropicity of the inner ring current. These findings support a chemical bonding pattern with delocalized M–M bonds in these species. [ABSTRACT FROM AUTHOR]

Abstract: This work describes a procedure for localizing orbitals based on the topological analysis of the electron localization function at correlated level. The decomposition of the overlap matrix according to the partitioning of the three dimensional physical space into basins provided by that function allows us to define a localization index to be maximized using isopycnic orbital transformations. The localization algorithm has been computationally implemented and its efficiency tested on selected molecular systems at equilibrium, stretched, and twisted geometries. We report results which allow to analyze the influence of the correlated and uncorrelated treatments on the orbital localization. [ABSTRACT FROM AUTHOR]

Abstract: Herein we report the systematic exploration of the potential energy surfaces of a series of clusters with formula E5M7+ (E=C‐Pb and M=Li‐Cs). Fifteen of these combinations adopt a D5h three‐dimensional seven‐pointed star‐like structure in a singlet state, where M atoms interact electrostatically with the E5 ring. The determining factors in the relative preference of having the D5h structure over the most competitive isomer or vice‐versa are analyzed. These star‐shaped systems satisfy the 4n+2 Hückel's rule and exhibit a strong diatropic (σ and π) response to an external magnetic field. [ABSTRACT FROM AUTHOR]

Protein kinases (PKs) discriminate between closely related sequences that contain serine, threonine, and/or tyrosine residues. Such specificity is defined by the amino acid sequence surrounding the phosphorylatable residue, so that it is possible to identify an optimal recognition motif (ORM) for each PK. The ORM for the protein kinase A (PKA), a well‐known member of the PK family, is the sequence RRX(S/T)X, where arginines at the −3 and −2 positions play a key role with respect to the primed phosphorylation site. In this work, differential affinities of PKA for the peptide substrate Kemptide (LRRASLG) and mutants that substitute the arginine residues by the unnatural peptide homoarginine were evaluated through molecular dynamics (MD) and free energy perturbation (FEP) calculations. The FEP study for the homoarginine mutants required previous elaboration of a CHARMM “arginine to homoarginine” (R2B) hybrid topology file which is available in this manuscript as Supporting Information. Mutants substituting the arginine residues by alanine, lysine, and histidine were also considered in the comparison by using the same protocol. FEP calculations allowed estimating the free energy changes from the free PKA to PKA‐substrate complex (ΔΔGE→ES) when Kemptide structure was mutated. Both ΔΔGS→ES values for homoarginine mutants were predicted with a difference below 1 kcal/mol. In addition, FEP correctly predicted that all the studied mutations decrease the catalytic efficiency of Kemptide for PKA. © 2018 Wiley Periodicals, Inc. [ABSTRACT FROM AUTHOR]

Theoretical studies are essential for the structural characterization of clusters, when it comes to rationalize their unique size-dependent properties and composition. However, the rapid growth of local minima on the potential energy surface (PES), with respect to cluster size, makes the candidate identification a challenging undertaking. In this article, we introduce a hybrid strategy to explore the PES of clusters. This proposal involves the use of a biased initial population of a genetic algorithm procedure. Each individual in this population is built by assembling small fragments, according to the best matching of the Fukui function. The performance of a genetic algorithm procedure. The performance of the method is assessed on the PES exploration of medium-sized Si n clusters ( n = 12-20). The most relevant results are: (a) the method converges at almost half of the time used by the canonical version of the GA and, (b) in all the studied cases, with the exception of Si13 and Si16, the method allowed to identify the global minimum (GM) and other important low-lying structures. Additionally, the apparent deficiency of the proposal to identify the GM was corrected when a Si atom, or other low-lying isomers, were considered to build the clusters. © 2017 Wiley Periodicals, Inc. [ABSTRACT FROM AUTHOR]

The prediction of reactivity is one of the long-standing objectives of chemistry, contributing to enforce the link between theory and experiment. In particular, the regioselectivity of aromatic molecules has motivated the proposal of different reactivity descriptors based on foundational theories, like Frontier Molecular Orbital (FMO) theory and density functional theory, to predict and rationalize such regioselectivity. This article examines cases where reactivity descriptors, based on FMO theories, are known to have failed, specifically on electrophilic aromatic substitution reactions, through a simple but effective new reactivity model: the Orbital-weighted Fukui function ( [ABSTRACT FROM AUTHOR]

Keywords: annulene model; aromaticity; charged macrocycles; porphyrinoids; ring currents EN annulene model aromaticity charged macrocycles porphyrinoids ring currents 1 1 1 02/01/23 20230127 NES 230127 B The aromaticity b of charged expanded porphyrins turns out to be much more complex to study than that of their planar neutral analogues. We have demonstrated that the largest charged porphyrins do not present a clear main conjugation pathway. [Extracted from the article]

The electron delocalization of benzene (C6H6) and hexafluorobenzene (C6F6) was analyzed in terms of the induced magnetic field, nucleus-independent chemical shift (NICS), and ring current strength (RCS). The computed out-of-plane component of the induced magnetic field at a distance ( r) greater than or equal to 1.0 Å above the ring center correlates well ( R2>0.99) with the RCS value. According to these criteria, fluorination has two effects on the C6 skeleton; concomitantly, the resonant effects diminish the π electron delocalization and the inductive effects decrease the charge density at the ring center and therefore reduce the magnitude of the paratropic current generated in this region. The equilibrium between both effects decreases aromaticity in the fluorinated benzene derivatives. These results can be extrapolated to determine the aromaticity of any derivative within the series of fluorinated benzene derivatives (C6H(6− n)F n, where n=1-5). [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]

The reaction of 3,6-dichloro-1,2,4,5-tetrazine (DCT) with a series of biothiols RSH: (cysteine, homocysteine, cysteinyl-glycine, N-acetylcysteine, and glutathione) is subjected to a kinetic investigation. The reactions are studied by following spectrophotometrically the disappearance of DCT at 370 nm. In the case of an excess of N-acetylcysteine and glutathione, clean pseudo first-order rate constants ( kobs1) are found. However, for cysteine, homocysteine and cysteinyl-glycine, two consecutive reactions are observed. The first one is the of the chlorine by the sulfhydryl group of these biothiols (RSH) and the second one is the and of their alkylthio with the amine group of RSH to give the di-substituted compound. Therefore, in these cases, two pseudo first-order rate constants ( kobs1 and kobs2, respectively) are found under biothiol excess. Plots of kobs1 versus free thiol concentration at constant pH are linear, with the slope ( kN) independent of pH (from 6.8 to 7.4). The kinetic data analysis (Brønsted-type plot and activation parameters) is consistent with an mechanism with the attack as the rate-determining step. 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]

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]

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]

Docking of 3-amino-1H-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 (IC(50) ) of the studied compounds were obtained by 3D-QSAR methods CoMFA and CoMSIA. Ligand-based and receptor-guided alignment methods were utilized. Adequate R(2) and Q(2) 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., (© 2011 John Wiley & Sons A/S.)