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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]

This study explored the inhibitory potential of gallium maltolate against severe acute respiratory syndrome coronavirus 2 and main and papain-like proteases. Computational methods, including density functional theory and molecular docking, were used to assess gallium maltolate reactivity and binding interactions. Density functional theory calculations revealed gallium maltolate's high electron-capturing capacity, particularly around the gallium metal atom, which may contribute to their activity. Molecular docking demonstrated that gallium maltolate can form strong hydrogen bonds with key amino acid residues like glutamate-166 and cysteine-145, tightly binding to main and papain-like proteases. The binding energy and interactions of gallium maltolate were comparable to known SARS-CoV-2 inhibitors like N-[(5-methyl-1,2-oxazol-3-yl)carbonyl]-L-alanyl-L-valyl-N-{(2S,3E)-5-(benzyloxy)-5-oxo-1-[(3S)-2-oxopyrrolidin-3-yl]pent-3-en-2-yl}-L-leucinamide, indicating its potential as an antiviral agent. However, further experimental validation is required to confirm its effectiveness in inhibiting SARS-CoV-2 replication and treating COVID-19. [ABSTRACT FROM AUTHOR]

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

Using various exploration strategies, in this study, we investigated the potential energy surfaces (PES) of CBe5H5+ and CnBe3n+2H2n+22+ (n = 2–4) clusters. Previous studies proposed that the planar pentacoordinate carbons (ppCs) were the global minima of these clusters. However, our study identified new putative global minima and competitive isomers, refuting some previous assignments. We employed several methods, including evolutive-inspired stochastic approaches guided by "chemical criteria", and ab initio molecular dynamics simulations at elevated temperatures. Our results showed that the size of the scanned population significantly affected the evolutive method and that constrained or guided procedures showed an advantage in identifying better minima for larger systems. This study demonstrated that using multiple complementary strategies can result in a wider variety of minima in a given energy range. Our findings provide valuable insights into exploring the potential energy surfaces of clusters, mainly medium-sized clusters, which could be the connections between small clusters and nanomaterials. [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]

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]

Here, we present evidence that the D2h M2C50/2+ (M = Li-K, Be-Ca, Al-In, and Zn) species comprises planar hexacoordinate carbon (phC) structures that exhibit four covalent and two electrostatic interactions. These findings have been made possible using evolutionary methods for exploring the potential energy surface (AUTOMATON program) and the Interacting Quantum Atoms (IQA) methodology, which support the observed bonding interactions. It is worth noting, however, that these structures are not the global minimum. Nonetheless, incorporating two cyclopentadienyl anion ligands (Cp) into the CaC52+ system has enhanced the relative stability of the phC isomer. Moreover, cycloparaphenylene ([8]CPP) provides system protection and kinetic stability. These results indicate that using appropriate ligands presents a promising approach for expanding the chemistry of phC species. [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]

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

Recently, we reported a series of global minima whose structures consist of carbon rings decorated with heavier group 14 elements. Interestingly, these structures feature planar tetracoordinate carbons (ptCs) and result from the replacement of five or six protons (H+) from the cyclopentadienyl anion (C5H5−) or the pentalene dianion (C8H62−) by three or four E2+ dications (E = Si–Pb), respectively. The silicon derivatives of these series are the Si3C5 and Si4C8 clusters. Here we show that ptC persists in some clusters with an equivalent number of C and Si atoms, i.e., Si5C5, Si8C8, and Si9C9. In all these species, the ptC is embedded in a pentagonal C5 ring and participates in a three-center, two-electron (3c-2e) Si-ptC-Si σ-bond. Furthermore, these clusters are π-aromatic species according to chemical bonding analysis and magnetic criteria. [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]

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]

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]

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]

The relativistic effects on the aromaticity of a set of benzene analogues, E3M3H3 (E = C–Pb; M = N–Bi) heterocycles, using magnetically induced current density (MICD) and the NICSzz component of the conventional nucleus independent chemical shift (NICS), is hereby examined. The relativistic effects were evaluated by means of four-component relativistic MICD, and two-component NMR relativistic shielding tensor methods. MICD and NICS were also computed in a non-relativistic fashion, to assess the influence of scalar-relativistic and spin–orbit effects. Most of the studied compounds exhibit a net diatropic ring current (aromatic), excluding the nitrogen-containing compounds which are non-aromatic (except for C3N3H3), in agreement with their higher E–N electronegativity difference. Only in the case of bismuth compounds, E3Bi3H3, aromaticity is substantially decreased when relativistic effects are included (mainly due to the spin–orbit contribution). The larger the mass of the system, the larger the magnitude of this change, in line with the expected relativistic effects for heavier elements. The analysis based on the NICSzz computations agrees with that of the MICD, thus supporting both the magnetic behavior and the aromatic character of these compounds. [ABSTRACT FROM AUTHOR]

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

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

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]