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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]

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]

A recently proposed local Fukui function is used to predict the binding site of atomic hydrogen on silicon clusters. To validate the predictions, an extensive search for the more stable SinH (n=3–10) clusters has been done using a modified genetic algorithm. In all cases, the isomer predicted by the Fukui function is found by the search, but it is not always the most stable one. It is discussed that in the cases where the geometrical structure of the bare silicon cluster suffers a considerable change due to the addition of one hydrogen atom, the situation is more complicated and the relaxation effects should be considered. [ABSTRACT FROM AUTHOR]

Photoelectron spectra of anionic clusters of silicon require reliable theoretical calculations for their assignment and interpretation. Electron propagator calculations in the outer valence Green’s-function approximation with two well-characterized, all-electron basis sets on vertical electron detachment energies (VEDEs) of anions are compared to similar calculations that employ Stuttgart pseudopotentials. Tests on Sin- clusters with n=3–7 exhibit an encouraging agreement between the all-electron and pseudopotentials results and between electron propagator predictions and experiments and values obtained from coupled-cluster calculations. To illustrate the capabilities of the new approach based on a Si pseudopotential and electron propagator methods, VEDE calculations on Si10- are presented. [ABSTRACT FROM AUTHOR]

Non-peptidic thrombin inhibitors (TIs; 177 compounds) with diverse groups at motifs P1 (such as oxyguanidine, amidinohydrazone, amidine, amidinopiperidine), P2 (such as cyanofluorophenylacetamide, 2-(2-chloro-6-fluorophenyl)acetamide), and P3 (such as phenylethyl, arylsulfonate groups) were studied using molecular modeling to analyze their interactions with S1, S2, and S3 subsites of the thrombin binding site. Firstly, a protocol combining docking and three dimensional quantitative structure–activity relationship was performed. We described the orientations and preferred active conformations of the studied inhibitors, and derived a predictive CoMSIA model including steric, donor hydrogen bond, and acceptor hydrogen bond fields. Secondly, the dynamic behaviors of some selected TIs (compounds 26, 133, 147, 149, 162, and 177 in this manuscript) that contain different molecular features and different activities were analyzed by creating the solvated models and using molecular dynamics (MD) simulations. We used the conformational structures derived from MD to accomplish binding free energetic calculations using MM-GBSA. With this analysis, we theorized about the effect of van der Waals contacts, electrostatic interactions and solvation in the potency of TIs. In general, the contents reported in this article help to understand the physical and chemical characteristics of thrombin-inhibitor complexes. [ABSTRACT FROM AUTHOR]

Abstract: This Letter deals with matrix extensions of the Fukui and dual-descriptor functions which are represented in a basis set by means of a spin-free treatment. A study of the eigenvalues of these matrices and of the values of the coefficients which express their eigenvectors provides important information concerning molecular reactivity. Numerical determinations performed in selected closed- and open-shell systems at Hartree–Fock and configuration interaction levels of theory show the usefulness of this procedure. A comparison between these results and those arising from other approaches is analyzed in detail. [Copyright &y& Elsevier]

The isomerization energies of 1,2- and 1,3-diazacyclobutadiene, pyrazole and imidazole, and pyridazine and pyrimidine are 10.6, 9.4, and 20.9 kcal/mol, respectively, at the BP86/TZ2P level of theory. These energies are analyzed using a Morokuma-like energy decomposition analysis in conjunction with what we have called turn-upside-down approach. Our results indicate that, in the three cases, the higher stability of the 1,3-isomers is not due to lower Pauli repulsions but because of the more favorable σ-orbital interactions involved in the formation of two C--N bonds in comparison with the generation of C--C and N--N bonds in the 1,2-isomers. [ABSTRACT FROM AUTHOR]

We have explored in detail the potential energy surfaces of the Si5Lin5-6 (n = 5-7) systems. We found that it is feasible to design three-dimensional star-like silicon structures using the appropriate ligands. The global minimum structure for Si5Li7+ has a perfect seven-peak star-like structure. The title compounds comprise, essentially, the Si56- ring interacting with lithium cations. The ionic character of the Si-Li interactions induces the formation of a bridged structure. Concomitantly, our calculations show that the reduction of the Pauli repulsion and the maximization of the orbital contribution are also significant for the star-like structure formation. Additionally, the MO analysis of the systems suggests that the role of the lithium atoms is to provide the precise number of electrons to the central Si5 unit. This is confirmed by the magnetic properties, which show that electron delocalization enhances the stability of the star-like structures proposed here. [ABSTRACT FROM AUTHOR]

An empirical local hardness index is introduced and tested. The usefulness of this new quantity as an intramolecular selectivity descriptor is illustrated for a set of 49 molecules. The proposed local hardness index appears as a good descriptor of the orientation of the electrophilic aromatic substitution, the selectivity of addition reaction as well as the alkylation and acylation of lithium enolates. The sites for the attack by hard species seem to be correctly predicted by the proposed index. [Copyright &y& Elsevier]

(E)-6-Methoxy-1-methyl-3-(2-(3-methyl-4-nitroisoxazol-5-yl)vinyl)quinolin-2(1H)-one dye (MQI) has been synthesized, and its structural and electronic properties have been characterized by employing UV-vis spectroscopy in combination with computational methods. The MQI dye has been assessed as an activated Michael acceptor-type probe toward bisulfite ions. This reaction was kinetically tested in different mild, cationic (cetyltrimethylammonium bromide, cetyltrimethylammonium chloride, and cetylpyridinium bromide), and zwitterionic (N-decyl-N,N-dimethyl-3-ammonio-1-propanesulfonate, N-tetradecyl-N,N-dimethyl-3-ammonio-1-propanesulfonate, and N-hexacyl-N,N-dimethyl-3-ammonio-1-propanesulfonate) micellar solutions at pH ∼ 5.5. Both micellar media remarkably allow the addition reactions, increasing the reactivity of MQI towards bisulfite ions, the biggest effects were found in the presence of cationic micelles. The binding constants of MQI with the micelles and the rate constants were determined from kinetic data, which were interpreted on the basis of the pseudophase kinetic model. The kinetic study and the product analysis allow us to highlight the relevant role of the association between MQI dye and the micellized surfactant, allowing efficient nucleophilic addition of bisulfite ions. The findings of this work will be valuable for the use of micellar solutions as an alternative medium to replace the use of toxic solvents to carry out organic reactions to perform nucleophilic addition reactions of bisulfite. [ABSTRACT FROM AUTHOR]

This study examines systems containing planar tetracoordinate group 13–15 atoms (E) within pentagonal C4H2E rings bridged by Si or Ge atoms. A detailed chemical bonding analysis of eleven candidates shows that true tetracoordination is achieved only in the C4H2NGe2+ system. [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]

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]

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]

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]

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]

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]

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]

Many protein kinase (PK) inhibitors have been reported in recent years, but only a few have been approved for clinical use. The understanding of the available molecular information using computational tools is an alternative to contribute to this process. With this in mind, we studied the binding modes of 77 maleimide derivates inside the PK glycogen synthase kinase 3 beta (GSK3β) using docking experiments. We found that the orientations that these compounds adopt inside GSK3β binding site prioritize the formation of hydrogen bond (HB) interactions between the maleimide group and the residues at the hinge region (residues Val135 and Asp133), and adopt propeller-like conformations (where the maleimide is the propeller axis and the heterocyclic substituents are two slanted blades). In addition, quantitative structure–activity relationship (QSAR) models using CoMSIA methodology were constructed to explain the trend of the GSK3β inhibitory activities for the studied compounds. We found a model to explain the structure–activity relationship of non-cyclic maleimide (NCM) derivatives (54 compounds). The best CoMSIA model (training set included 44 compounds) included steric, hydrophobic, and HB donor fields and had a good Q2 value of 0.539. It also predicted adequately the most active compounds contained in the test set. Furthermore, the analysis of the plots of the steric CoMSIA field describes the elements involved in the differential potency of the inhibitors that can be considered for the selection of suitable inhibitors. [ABSTRACT FROM AUTHOR]

Highlights: [•] Three heteroarylacrylonitriles-derived fluorescent probes were synthesized. [•] Three heteroarylacrylonitriles-derived fluorescent probes were assessed as Michael acceptors toward cysteine. [•] New compounds for cysteine detection are reported. [•] New probes for cysteine detection localize preferentially at the cytoplasm and endosomes of living cells. [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]

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]

Abstract: 1,3-Dipolar cycloaddition of nitrile imines with α,β-unsaturated five- and six-membered lactones, thiolactones and lactams gave ring-fused pyrazoles. Regioisomeric mixtures have been obtained with the 5-substituted pyrazole as the major cycloadduct. Only with the five-membered lactone the major product was the 4-acyl derivative. Computational studies, the use of the topological analysis of the Fukui functions and the potential energy surfaces (PES) theory allowed a theoretical description of the local reactivity in agreement with the observed high regiochemistry and with the role of the heteroatom adjacent to the carbonyl group. [Copyright &y& Elsevier]

Sigma-1 (σ1) affinities of methyl 2-(aminomethyl)-1-phenylcyclopropane-1-carboxylate (MAPCC) derivatives were modelled by the genetic algorithm with linear assignment of hypermolecular alignment of datasets (GALAHAD) and the comparative molecular field analysis (CoMFA)/comparative molecular similarity indices analysis (CoMSIA) methods. GALAHAD was used for deriving the 3D pharmacophore pattern that encompasses the most potent σ1 ligands within this series. Five MAPCC derivatives with a high σ1 affinity were used for deriving this model. The obtained model included a nitrogen atom, the hydrophobes and the hydrogen bond acceptor features; it was able to identify other potent σ1 ligands. On the other hand, CoMFA and CoMSIA methods were used for deriving quantitative structure–activity relationship (QSAR) models. All QSAR models were trained with 17 compounds, after which they were evaluated for predictive ability with additional five compounds. The best QSAR model was obtained by using CoMSIA, including steric, electrostatic and hydrophobic fields, and had a good predictive quality according to both internal and external validation criteria. In general, the models described herein provide meaningful information relevant for the rational design of new σ1 ligands. [ABSTRACT FROM PUBLISHER]

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]

The minimum energy structures of the Si3C5 and Si4C8 clusters are planar and contain planar tetracoordinate carbons (ptCs). These species have been classified, qualitatively, as global (π) and local (σ) aromatics according to the adaptive natural density partitioning (AdNDP) method, which is an orbital localization method. This work evaluates these species’ aromaticity, focusing on confirming and quantifying their global and local aromatic character. For this purpose, we use an orbital localization method based on the partitioning of the molecular space according to the topology of the electronic localization function (LOC-ELF). In addition, the magnetically induced current density is analyzed. The LOC-ELF-based analysis coincides with the AdNDP study (double aromaticity, global, and local). Moreover, the current density analysis detects global and local ring currents. The strength of the global and local current circuit is significant, involving 4n + 2 π- and σ-electrons, respectively. The latter implicates the Si-ptC-Si fragment, which would be related to the 3c-2e σ-bond detected by the orbital localization methods in this fragment. [ABSTRACT FROM AUTHOR]

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. Our results show that although it is possible to establish the net current flows through C–C bonds, it is impossible to predict all the local and global weak current density flows. Thus, for polycyclic systems, it is essential to analyze magnetically induced current densities in conjunction with NICS measurements, or with induced magnetic fields, to have an adequate representation of the molecules' magnetic behavior and their relationship with the aromaticity phenomenon. [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]

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]

Highly accurate electron affinities and ionization potentials of chemical systems were described by means of the procedure called GHV-EOM (Valdemoro et al, in Int J Quantum Chem 112:2965, 2012), which combines the G-particle-hole hypervirial (GHV) equation method (Alcoba et al, in Int J Quantum Chem 109:3178, 2009) and that of the equations-of-motion (EOM), by Simons and Smith (Simons and Smith, in J Chem Phys 58:4899, 1973). The present work improves that hybrid method by introducing the point group symmetry within its framework, providing a higher computational efficiency. We report results which show the achievements attained by using the symmetry-adapted methodology. The new formulation turns out to be particularly suitable for characterizing solid models, as cyclic one-dimensional chains. [ABSTRACT FROM AUTHOR]

Previous experimental results on the free radical-scavenging properties of boldine, one of the most potent natural antioxidants, suggested that the benzylic hydrogen, neighboring a nitrogen lone electron pair, might be the key to its protective and antioxidant effect, in contrast to the usually assumed labile phenolic hydrogen atoms. Our computations suggest that both boldine and glaucine can undergo two successive hydrogen transfers under attack by an oxidizing radical (from C-6a-H and C-7-H). The hydroxyl groups of boldine could also participate via the HAT mechanism, although to a lesser extent. In the case of quaternary N-methylated derivatives, the sharing of the nitrogen lone pair makes the transfer of the C-6a hydrogen energetically unfeasible, supporting the earlier proposal based on experimental evidence. The hydroxyl groups of boldine and its derivatives could contribute to antioxidant activity via the sequential proton loss electron transfer mechanism, although this would only be relevant at higher pH values. [ABSTRACT FROM AUTHOR]

Herein the performance of a modification within the hybrid algorithm implemented in the AUTOMATON program is introduced and evaluated. For the creation of the initial population, AUTOMATON combines a probabilistic automata procedure with a genetic algorithm used to evolve this population. The proposed modification is addressed to efficiently identify the minimum energy structures of systems composed of more than one type of atom and with a low computational cost. The effectiveness of this approach is evaluated in the determination of the minimum energy structures of Be6B11−. The modification, aimed to explore the potential energy surface, consisted of filling the cells first with Be atoms in the process of creating the initial population. This order obeys the structural pattern established in the Be–B clusters reported to date. The results show that this variation not only identifies a more significant number of viable isomers but also to find a better putative global minimum than those previously reported in the literature. Therefore, it is recommended to be used as a complement to the standard searching process. [ABSTRACT FROM AUTHOR]

This study delves into the potential of MB 36 clusters (where M = Fe, Co, Ni) supported on graphene as effective single-atom catalysts (SACs). Our research is methodically segmented into several stages, each designed to validate the feasibility of the proposed material. We begin by investigating the potential energy surface of MB 36 clusters. Our findings reveal a preference for metallic atoms to position themselves above the central hexagonal vacancy of the B 36 cluster. This factor significantly contributes to the stabilization of the resultant MB 36 system. Subsequently, we employ ab-initio molecular dynamic simulations to affirm the stability of the graphene-supported MB 36 clusters. In the final stage, we evaluate the system's catalytic capability for the oxygen reduction reaction (ORR) by calculating the dissociation energy of O 2 and OOH post their adsorption on the M atom of the graphene-supported MB 36 cluster. These simulations suggest that FeB 36 could maintain stability at room temperature, exhibiting activation energies for O 2 and OOH dissociation lower than those previously reported on Fe/N/C-type SACs, approaching those found on the Pt(111) surface, the most efficient ORR electrocatalyst. This computational study suggests that graphene-supported FeB 36 clusters could emerge as a promising candidate for SACs. [Display omitted] [ABSTRACT FROM AUTHOR]

Autistic Spectrum Disorder (ASD) is characterized by the impairment of socio-communicative skills and the presence of restricted and stereotyped behavior patterns. Recent researches have revealed the influence of mitochondrial physiology on the development of ASD. Several research groups have identified defects in respiratory complexes, coenzyme-Q10 deficiency, increased oxidative damage, decreased of superoxide dismutase (SOD2). A study on the influence of mitochondrial physiology on the development of ASD can provide new alternatives and challenges. That is why we set ourselves the general objective to initiate studies of mitochondrial physiology in Chilean children with ASD. A sample of oral mucosa was collected in a group of 12 children diagnosed with ASD and 12 children without ASD. In children with ASD, we found a significant increase in mitochondrial DNA levels. Likewise, in these children, an increase in the protein oxidation was observed. Finally, a downward trend in the expression of the HIGD2A and SOD2 genes was observed, while DRP1, FIS1, MFN1, MFN2, and OPA1 gene expression show an upward trend. The increment of mitochondrial DNA, high oxidative stress, and high expression of the MFN2 gene could help as a scanner of the mitochondrial function in children with ASD. [ABSTRACT FROM AUTHOR]

A simple and chemically intuitive approach is used to design ptC-containing E–C clusters (E = Si–Pb). This approach consists in replacing three or two consecutive protons from an aromatic hydrocarbon by one E24+ or one E2+ fragment, respectively. In the model, electrons from E are removed from the pz orbitals, emptying them. Si–Pb favors the formation of a 3c-2e (E–C–E) σ-bond, which involves the ptC. Additionally, the π-electronic cloud is delocalized through the E-pz orbitals allowing the E atoms to effectively take part in the electronic delocalization, preserving the 4n + 2 Hückel's rule from the parent hydrocarbon. Two aromatic monocycles and one aromatic bicycle – benzene (C6H6), cyclopentadienyl anion (C5H5−) and pentalene dianion (C8H62−) – have been transformed into C–E systems. After an extensive exploration of their potential energy surfaces, four new global minima with ptC are identified, resulting from the substitution of the protons by Si and Ge cations in C5H5− and C8H62− (E3C5 and E4C8). The analysis of both the chemical bonding and the magnetic response to an external magnetic field confirms the aromatic character of these species. [ABSTRACT FROM AUTHOR]

Isomers of (NaCl)n(H2O)2n clusters, with n = 1, 2 and 4, were investigated using an implementation of the simulated annealing method that imposes a virtual confinement on each isomer to stay within a sphere with an arbitrary radius. By using several confinement radii, we reported 2, 56 and 38 isomers for n = 1, 2 and 4, respectively. For n = 1, the CCSD(T)/aug-cc-pVTZ method was used as a reference by optimizing the corresponding isomers. These results were contrasted with those obtained by the MP2 method and eight exchange–correlation functionals: PBE, PBE0, B3LYP, PBE-D3, PBE0-D3, B3LYP-D3, LC-̉PBE and M06-2X. From this analysis we conclude that the M06-2X method gives reliable results and then, isomers with n = 2 and 4 were analyzed with this exchange–correlation functional. From the analysis of these two systems, the resulting isomers with the lowest energy showed cuboid structures and no breaking bond was present for NaCl molecules. Thus, in the nucleation process of the NaCl dihydrate our results suggest that the Na–Cl bond is present. Besides, bond length and electron density evaluated at bond critical points for the biggest system delivered values close to those found in the crystal structure. [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]