Breaking the plane: B5H5 is a three-dimensional structure.

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

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

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

Unveiling the electronic and structural consequences of removing two electrons from B12H122.

The notion that a regular icosahedron is unattainable in neutral B12H12 has persisted for nearly 70 years. This is because 24 valence electrons are used for B-H bonds, while another 24 electrons are necessary to maintain the deltahedron, unlike the 26 used in the dianion. According to Wade-Mingos rules, the neutral system should be a deltahedron with a capped face. Nevertheless, our exploration of the potential energy surface of B12H12 reveals that the global minimum is a closed-shell form with an H2 unit attached to a boron vertex of B12H10, preserving the deltahedral boron skeleton.

Strong carbon - noble gas covalent bond and fluxionality in hypercoordinate compounds.

Thermodynamic, kinetic, and chemical bonding analysis at the coupled cluster level has been carried out for a series of hypercoordinated carbon compounds with formula CH4Ng2+ (Ng = He-Rn). Results show that these compounds could be stable at room temperature and Born-Oppenheimer molecular dynamics simulations (BOMD) in conjunction with activation energies indicate high kinetic stability. In addition, all chemical bonding descriptors agree with a strong C-Ng covalent bond and a bonding pattern similar to that of CH5+. Finally, BOMD simulations showed that these compounds are fluxional, with a continuous formation/breaking of H-H and C-H bonds. To the best of the authors' knowledge, these results represent the first series of fluxional compounds possessing a covalent bond between a main group element and a noble gas atom.

Exploration of the potential energy surface in mixed Zintl clusters applying an automatic Johnson polyhedra generator: the case of arachno E6M24- (E = Si, Ge, Sn; M = Sb, Bi).

A new algorithm called Automatic Johnson Cluster Generator (AJCG) is presented, which, as its name indicates, allows the definition of the desired Johnson polyhedron to subsequently carry out all the possible permutations between the atoms that form this polyhedron. This new algorithm allows the exhaustive study of the structures' potential energy surface (PES). In addition, the AJCG algorithm is helpful for the study of three-dimensional compounds such as boranes or Zintl clusters and their structural derivatives with two or more different atoms. The automatic filling of vertices is particularly useful in mixed compounds because of the possibility of taking into account all possible configurations in the structure. As a test system, we investigated the arachno-type E6M24- (E = Si, Ge, Sn; M = Sb, Bi) structure which has eight vertices and complies with Wade-Mingos rules. Initially, we defined a bipyramidal structure (10 vertices), and filled the vertices with the atoms in all possible configurations. Since the selected system has eight atoms, the two remaining vertices were filled with pseudo atoms to complete the structure. After re-optimizing the initial population generated with AJCG, a large number of isomers with energy below 10 kcal mol-1 are identified. These results show that the most stable isomers possess homonuclear M-M bonds, except Sn6Bi24-. Although the overall putative minima differ at the PBE0-D3 and DLPNO-CCSD(T) levels, they are always competitive minima. In addition to using high-precision methodologies to correctly study relative energies, applying solvent effects in highly charged systems becomes mandatory. The aromatic character of these studied systems was demonstrated qualitatively with two- and three-dimensional mapping and quantitatively by calculating the value of the z-component of the induced magnetic field at the cage center, including scalar and spin-orbit correction for relativistic effects. The compounds studied have a high degree of aromaticity, which allows us to establish that despite structural modifications (i.e., from closo to arachno), the aromaticity is preserved.

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

Using various exploration strategies, in this study, we investigated the potential energy surfaces (PES) of CBe5H5+ and 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.

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

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

E6C15 (E = Si-Pb): polycyclic aromatic compounds with three planar tetracoordinate carbons.

A systematic exploration of the potential energy surface reveals two global minima with three planar tetra coordinate carbons (ptCs) and two global minima with three quasi-ptCs for E6C15 (E = Si-Pb) combinations. These consist of aromatic polycyclic templates suitable for further design of different materials without hindering the ptC texture.

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

A low-lying structure is revealed for the CuB12 - cluster, which is bowl-shaped. It consists of a triangular CuB2 base and a B10 rim. Molecular dynamics simulations indicates its structural robustness; at an elevated temperature (600 K), the base rotates reversibly within the B10 perimeter. Chemical bonding analysis detects 2σ- and 3π-delocalized bonds, suggesting double aromaticity. This is also confirmed by two diatropic and concentric ring currents under an external magnetic field.

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

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

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

We computationally explore an alternative to stabilize one-dimensional (1D) silicon-lithium nanowires (NWs). The Li12Si9 Zintl phase exhibits the NW [ Li 6 Si 5 ] ∞ 1 , combined with Y-shaped Si4 structures. Interestingly, this NW could be assembled from the stacking of the Li6Si5 aromatic cluster. The [ Li 6 Si 5 ] ∞ 1 @CNT nanocomposite has been investigated with density functional theory (DFT), including molecular dynamics simulations and electronic structure calculations. We found that van der Waals interaction between Li's and CNT's walls is relevant for stabilizing this hybrid nanocomposite. This work suggests that nanostructured confinement (within CNTs) may be an alternative to stabilize this free NW, cleaning its properties regarding Li12Si9 solid phase, i.e., metallic character, concerning the perturbation provided by their environment in the Li12Si7 compound.

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

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

Effects of Temperature on Enantiomerization Energy and Distribution of Isomers in the Chiral Cu13 Cluster.

In this study, we report the lowest energy structure of bare Cu13 nanoclusters as a pair of enantiomers at room temperature. Moreover, we compute the enantiomerization energy for the interconversion from minus to plus structures in the chiral putative global minimum for temperatures ranging from 20 to 1300 K. Additionally, employing nanothermodynamics, we compute the probabilities of occurrence for each particular isomer as a function of temperature. To achieve that, we explore the free energy surface of the Cu13 cluster, employing a genetic algorithm coupled with density functional theory. Moreover, we discuss the energetic ordering of isomers computed with various density functionals. Based on the computed thermal population, our results show that the chiral putative global minimum strongly dominates at room temperature.

Theoretical Prediction of Structures, Vibrational Circular Dichroism, and Infrared Spectra of Chiral Be4B8 Cluster at Different Temperatures.

Lowest-energy structures, the distribution of isomers, and their molecular properties depend significantly on geometry and temperature. Total energy computations using DFT methodology are typically carried out at a temperature of zero K; thereby, entropic contributions to the total energy are neglected, even though functional materials work at finite temperatures. In the present study, the probability of the occurrence of one particular Be4B8 isomer at temperature T is estimated by employing Gibbs free energy computed within the framework of quantum statistical mechanics and nanothermodynamics. To identify a list of all possible low-energy chiral and achiral structures, an exhaustive and efficient exploration of the potential/free energy surfaces is carried out using a multi-level multistep global genetic algorithm search coupled with DFT. In addition, we discuss the energetic ordering of structures computed at the DFT level against single-point energy calculations at the CCSD(T) level of theory. The total VCD/IR spectra as a function of temperature are computed using each isomer's probability of occurrence in a Boltzmann-weighted superposition of each isomer's spectrum. Additionally, we present chemical bonding analysis using the adaptive natural density partitioning method in the chiral putative global minimum. The transition state structures and the enantiomer-enantiomer and enantiomer-achiral activation energies as a function of temperature evidence that a change from an endergonic to an exergonic type of reaction occurs at a temperature of 739 K.

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

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

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

We report the global minima structures of Li8 Si8 , Li10 Si9 , and Li12 Si10 systems, in which silicon moieties maintain structural and chemical bonding characteristics similar to those of their building blocks: the aromatic clusters Td -Li4 Si4 and C2v -Li6 Si5 . Electron counting rules, chemical bonding analysis, and magnetic response properties verify the silicon unit's aromaticity persistence. This study demonstrates the feasibility of assembling silicon-based nanostructures from aromatics clusters as building blocks.

Planar Hexacoordinate Carbons: Half Covalent, Half Ionic.

Herein, the first global minima containing a planar hexacoordinate carbon (phC) atom are reported. The fifteen structures belong to the CE3 M3 + (E=S-Te and M=Li-Cs) series and satisfy both geometric and electronic criteria to be considered as a true phC. The design strategy consisted of replacing oxygen in the D3h  CO3 Li3 + structure with heavy and less electronegative chalcogens, inducing a negative charge on the C atom and an attractive electrostatic interaction between C and the alkali-metal cations. The chemical bonding analyses indicate that carbon is covalently bonded to three chalcogens and ionically connected to the three alkali metals.

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

The relativistic effects on the aromaticity of a set of benzene analogues, E3M3H3 (E = C-Pb; M = N-Bi) heterocycles, using magnetically induced current density (MICD) and the 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.

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

Inspired by the double-aromatic (σ and π) C6H3 +, C6I6 2+, and C6(SePh)6 2+ ring-shaped compounds, herein we theoretically study their borazine derivative analogues. The systems studied are the cation and dications with formulas B3N3H3 +, B3N3Br6 2+, B3N3I6 2+, B3N3(SeH)6 2+, and B3N3(TeH)6 2+. Our DFT calculations indicate that the ring-shaped planar structures of B3N3H3 +, B3N3I6 2+, and B3N3(TeH)6 2+ are more stable in the singlet state, while those of B3N3Br6 2+ and B3N3(SeH)6 2+ prefer the triplet state. Besides, exploration of the potential energy surface shows that the ring-shaped structure is the putative global minimum only for B3N3I6 2+. According to chemical bonding analysis, B3N3H3 +, B3N3I6 2+, and B3N3(TeH)6 2+ have σ and π delocalized bonds. The number of delocalized σ/π electrons is 2/6 for the first, and 10/6 for the second and third, similar to what their carbon analogs exhibit. Finally, the analysis of the magnetically induced current density allows B3N3H3 +, B3N3I6 2+, and B3N3(TeH)6 2+ to be classified as strongly σ aromatic, and poorly π aromatic compounds.

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

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