Testing the effectiveness of the isoelectronic substitution principle through the transformation of aromatic osmathiophene derivatives into their inorganic analogues

The objective of the current work is to evaluate the effectiveness of the isoelectronic substitution (IS) principle on a series of complexes with the general formula OsCl2(SX3H3)(PH3)(2), where X-3 represents the moieties CCC, CCB, CCN, CBN, CNB or NCB, formed by substitution of the carbon atoms in CCC by either the isoelectronic B- or N+ separately, or by both. The SX3H3 moiety forms, together with Os, an aromatic five-membered ring (5-MR) called osmathiophene. The preservation of stability and aromaticity in the resulting systems is used to indicate the effectiveness of the IS principle. The aromaticity of the proposed molecules is analyzed according to the magnetic (induced magnetic field (B-ind)) and electronic (through the multicenter index (MCI)) criteria. In addition a chemical bonding analysis on selected species is performed by the adaptive natural density partitioning (AdNDP) method

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

Indexación: ScopusCocoa 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. © 2021 The Author

Testing the effectiveness of the isoelectronic substitution principle through the transformation of aromatic osmathiophene derivatives into their inorganic analogues

The objective of the current work is to evaluate the effectiveness of the isoelectronic substitution (IS) principle on a series of complexes with the general formula OsCl2(SX3H3)(PH3)(2), where X-3 represents the moieties CCC, CCB, CCN, CBN, CNB or NCB, formed by substitution of the carbon atoms in CCC by either the isoelectronic B- or N+ separately, or by both. The SX3H3 moiety forms, together with Os, an aromatic five-membered ring (5-MR) called osmathiophene. The preservation of stability and aromaticity in the resulting systems is used to indicate the effectiveness of the IS principle. The aromaticity of the proposed molecules is analyzed according to the magnetic (induced magnetic field (B-ind)) and electronic (through the multicenter index (MCI)) criteria. In addition a chemical bonding analysis on selected species is performed by the adaptive natural density partitioning (AdNDP) method

Boron avoids cycloalkane-like structures in the LinBnH2n series

Artículo de publicación ISIThe stability of the LinBnH2n (n = 3-6) series was analyzed using quantum chemical calculations, and it was found that cyclic isomers are not energetically favored. This is different to what happens in their organic counterparts (CnH2n), where cyclopentane (C5H10) and cyclohexane (C6H12) are the low-lying isomers. Apparently, aromaticity is a key-stabilizing factor that needs to be considered for designing stable lithium-boron hydride analogues of cyclic organic compounds. This is verified in the Li3B3H3+ system, which has been designed as the smallest aromatic carbocation (C3H3+) analogue. The global minimum structure of Li3B3H3+ contains a triangular B3H32- moiety, which has structural and chemical bonding features similar to its organic counterpart. Besides, this new cluster is classified as aromatic according to both the 4n + 2 Huckel rule and the analysis of the induced magnetic field. This theoretical evidence leads us to propose this cluster as a viable target for experimental detection in the gas phase.Fondecyt 1140358 1130202 3140439 1140306 Universidad Andres Bello DI-619-14/I DI-540-14/R CONCYTEC 011-2014-FONDECYT CONICYT: CONICYT-PCHA/Doctorado-Nacional 2013-6313004

Planar Hexacoordinate Carbons: Half Covalent Half Ionic

The global minima of thirteen combinations of atoms with formula CE3M3+ (E=S-Te and M=Li-Cs) adopt a planar structure with carbon covalently bonded to three chalcogens and ionically bonded to the three alkali-metals to stabilize the first global minima structures containing planar hexacoordinate carbon atoms.</div

Chemical bonding analysis in boron clusters by means of localized orbitals according to the electron localization function topology

A series of small planar boron clusters has extensively been studied in the past using different theoretical approximations, and their chemical bonding has been rationalized in terms of aromaticity, antiaromaticity and conflicting aromaticity. Here, we study these systems by means of our recently proposed orbital localization procedure based on the partitioning of the space according to the electron localization function (ELF) topology. The results are compared with those obtained from the adaptive natural density partitioning (AdNDP) method, which is a most extensively tested orbital localization procedure. Minor discrepancies have been found, especially in large clusters. In those cases, an alternative set of localized AdNDP orbitals recovered the representation obtained by ELF localization procedure. These results support the need for multicenter bonding incorporation into the localization models for rationalizing chemical bonding in atomic clusters. Additionally, the aromatic character of the clusters, when it is present, is adequately supported by the more classical treatment based on the ELF topological analysis.Facultad de Ciencias ExactasInstituto de Investigaciones Fisicoquímicas Teóricas y Aplicada

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

Here, it is shown that the M3B12 (M = Cu-Au) clusters&rsquo; 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 &pi;-bonds, which infers an aromatic character to these species

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

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