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Open AccessArticle

Fundamental Aspects of Skin Cancer Drugs via Degree-Based Chemical Bonding Topological Descriptors

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Abdul Rauf Khan

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Nadeem ul Hassan Awan

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Molecules 2023, 28(9), 3684; https://doi.org/10.3390/molecules28093684 - 24 Apr 2023

Viewed by 605

Abstract

Due to significant advancements being made in the field of drug design, the use of topological descriptors remains the primary approach. When combined with QSPR models, descriptors illustrate a molecule’s chemical properties numerically. Numbers relating to chemical composition topological indices are structures that [...] Read more.

Due to significant advancements being made in the field of drug design, the use of topological descriptors remains the primary approach. When combined with QSPR models, descriptors illustrate a molecule’s chemical properties numerically. Numbers relating to chemical composition topological indices are structures that link chemical composition to physical characteristics. This research concentrates on the analysis of curvilinear regression models and degree-based topological descriptors for thirteen skin cancer drugs. The physicochemical characteristics of the skin cancer drugs are examined while regression models are built for computed index values. An analysis is performed for several significant results based on the acquired data. Full article

(This article belongs to the Special Issue Fundamental Aspects of Chemical Bonding)

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Open AccessArticle

Substituent Effects in Tetrel Bonds Involving Aromatic Silane Derivatives: An ab initio Study

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Sergi Burguera

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Antonio Frontera

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Antonio Bauzá

Molecules 2023, 28(5), 2385; https://doi.org/10.3390/molecules28052385 - 05 Mar 2023

Viewed by 653

Abstract

In this manuscript substituent effects in several silicon tetrel bonding (TtB) complexes were investigated at the RI-MP2/def2-TZVP level of theory. Particularly, we have analysed how the interaction energy is influenced by the electronic nature of the substituent in both donor and acceptor moieties. [...] Read more.

In this manuscript substituent effects in several silicon tetrel bonding (TtB) complexes were investigated at the RI-MP2/def2-TZVP level of theory. Particularly, we have analysed how the interaction energy is influenced by the electronic nature of the substituent in both donor and acceptor moieties. To achieve that, several tetrafluorophenyl silane derivatives have been substituted at the meta and para positions by several electron donating and electron withdrawing groups (EDG and EWG, respectively), such as –NH₂, –OCH₃, –CH₃, –H, –CF₃ and –CN substituents. As electron donor molecules, we have used a series of hydrogen cyanide derivatives using the same EDGs and EWGs. We have obtained the Hammett’s plots for different combinations of donors and acceptors and in all cases we have obtained good regression plots (interaction energies vs. Hammet’s σ parameter). In addition, we have used the electrostatic potential (ESP) surface analysis as well as the Bader’s theory of atoms in molecules (AIM) and noncovalent interaction plot (NCI plot) techniques to further characterize the TtBs studied herein. Finally, a Cambridge Structural Database (CSD) inspection was carried out, retrieving several structures where halogenated aromatic silanes participate in tetrel bonding interactions, being an additional stabilization force of their supramolecular architectures. Full article

(This article belongs to the Special Issue Fundamental Aspects of Chemical Bonding)

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Open AccessArticle

Unicorns, Rhinoceroses and Chemical Bonds

by

Jordan Gribben

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Timothy R. Wilson

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Mark E. Eberhart

Molecules 2023, 28(4), 1746; https://doi.org/10.3390/molecules28041746 - 12 Feb 2023

Viewed by 699

Abstract

The nascent field of computationally aided molecular design will be built around the ability to make computation useful to synthetic chemists who draw on their empirically based chemical intuition to synthesize new and useful molecules. This fact poses a dilemma, as much of [...] Read more.

The nascent field of computationally aided molecular design will be built around the ability to make computation useful to synthetic chemists who draw on their empirically based chemical intuition to synthesize new and useful molecules. This fact poses a dilemma, as much of existing chemical intuition is framed in the language of chemical bonds, which are pictured as possessing physical properties. Unfortunately, it has been posited that calculating these bond properties is impossible because chemical bonds do not exist. For much of the computationalchemistry community, bonds are seen as mythical—the unicorns of the chemical world. Here, we show that this is not the case. Using the same formalism and concepts that illuminated the atoms in molecules, we shine light on the bonds that connect them. The real space analogue of the chemical bond becomes the bond bundle in an extended quantum theory of atoms in molecules (QTAIM). We show that bond bundles possess all the properties typically associated with chemical bonds, including an energy and electron count. In addition, bond bundles are characterized by a number of nontraditional attributes, including, significantly, a boundary. We show, with examples drawn from solid state and molecular chemistry, that the calculated properties of bond bundles are consistent with those that nourish chemical intuition. We go further, however, and show that bond bundles provide new and quantifiable insights into the structure and properties of molecules and materials. Full article

(This article belongs to the Special Issue Fundamental Aspects of Chemical Bonding)

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Open AccessArticle

Trivalent Polyhedra as Duals of Borane Deltahedra: From Molecular Endohedral Germanium Clusters to the Smallest Fullerenes

by

R. Bruce King

Molecules 2023, 28(2), 496; https://doi.org/10.3390/molecules28020496 - 04 Jan 2023

Viewed by 509

Abstract

The duals of the most spherical closo borane deltahedra having from 6 to 16 vertices form a series of homologous spherical trivalent polyhedra with even numbers of vertices from 8 to 28. This series of homologous polyhedra is found in endohedral clusters of [...] Read more.

The duals of the most spherical closo borane deltahedra having from 6 to 16 vertices form a series of homologous spherical trivalent polyhedra with even numbers of vertices from 8 to 28. This series of homologous polyhedra is found in endohedral clusters of the group 14 atoms such as the endohedral germanium cluster anions [[email protected]₁₀]³⁻ (M = Co, Fe) and [[email protected]₁₂]³⁻ The next members of this series have been predicted to be the lowest energy structures of the endohedral silicon clusters [email protected]₁₄ and [email protected]₁₆ (M = Zr, Hf). The largest members of this series correspond to the smallest fullerene polyhedra found in the endohedral fullerenes [email protected]₂₈ (M = Zr, Hf, Th, U). The duals of the oblate (flattened) ellipsoidal deltahedra found in the dirhenaboranes Cp*₂Re₂B_n₋₂H_n₋₂ (Cp* = η⁵-Me₅C₅; 8 ≤ n ≤ 12) are prolate (elongated) trivalent polyhedra as exemplified experimentally by the germanium cluster [Co₂@Ge₁₆]⁴⁻ containing an endohedral Co₂ unit. Full article

(This article belongs to the Special Issue Fundamental Aspects of Chemical Bonding)

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Open AccessArticle

Theoretical Investigation of Geometries and Bonding of Indium Hydrides in the In₂H_x and In₃H_y (x = 0–4,6; y = 0–5) Series

by

Anton S. Pozdeev

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Pavel Rublev

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Steve Scheiner

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Alexander I. Boldyrev

Molecules 2023, 28(1), 183; https://doi.org/10.3390/molecules28010183 - 26 Dec 2022

Cited by 1 | Viewed by 1163

Abstract

Boron hydrides have been an object of intensive theoretical and experimental investigation for many decades due to their unusual and somewhat unique bonding patterns. Despite boron being a neighboring element to carbon, boron hydrides almost always form non-classical structures with multi-center bonds. However, [...] Read more.

Boron hydrides have been an object of intensive theoretical and experimental investigation for many decades due to their unusual and somewhat unique bonding patterns. Despite boron being a neighboring element to carbon, boron hydrides almost always form non-classical structures with multi-center bonds. However, we expect indium to form its interesting molecules with non-classical patterns, though such molecules still need to be extensively studied theoretically. In this work, we investigated indium hydrides of In₂H_x (x = 0–4,6) and In₃H_y (y = 0–5) series via DFT and ab initio quantum chemistry methods, performing a global minimum search, chemical bonding analysis, and studies of their thermodynamical stability. We found that the bonding pattern of indium hydrides differs from the classical structures composed of 1c-2e lone pairs and 2c-2e bonds and the bonding pattern of earlier investigated boron hydrides of the B_nH_n+2 series. The studied stoichiometries are characterized by multi-center bonds, aromaticity, and the tendency for indium to preserve the 1c-2e lone pair. Full article

(This article belongs to the Special Issue Fundamental Aspects of Chemical Bonding)

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Open AccessArticle

Selenoxides as Excellent Chalcogen Bond Donors: Effect of Metal Coordination

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and

Molecules 2022, 27(24), 8837; https://doi.org/10.3390/molecules27248837 - 13 Dec 2022

Cited by 1 | Viewed by 668

Abstract

The chalcogen bond has been recently defined by the IUPAC as the attractive noncovalent interaction between any element of group 16 acting as an electrophile and any atom (or group of atoms) acting as a nucleophile. Commonly used chalcogen bond donor molecules are [...] Read more.

The chalcogen bond has been recently defined by the IUPAC as the attractive noncovalent interaction between any element of group 16 acting as an electrophile and any atom (or group of atoms) acting as a nucleophile. Commonly used chalcogen bond donor molecules are divalent selenium and tellurium derivatives that exhibit two σ-holes. In fact, the presence of two σ-hole confers to the chalcogen bonding additional possibilities with respect to the halogen bond, the most abundant σ-hole interaction. In this manuscript, we demonstrate that selenoxides are good candidates to be used as σ-hole donor molecules. Such molecules have not been analyzed before as chalcogen bond donors, as far as our knowledge extends. The σ-hole opposite to the Se=O bond is adequate for establishing strong and directional ChBs, as demonstrated herein using the Cambridge structural database (CSD) and density functional theory (DFT) calculations. Moreover, the effect of the metal coordination of the selenoxide to transition metals on the strength of the ChB interaction has been analyzed theoretically. The existence of the ChBs has been further supported by the quantum theory of atoms in molecules (QTAIM) and the noncovalent interaction plot (NCIPlot). Full article

(This article belongs to the Special Issue Fundamental Aspects of Chemical Bonding)

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Open AccessArticle

Facile Synthesis of 5-Aryl-N-(pyrazin-2-yl)thiophene-2-carboxamides via Suzuki Cross-Coupling Reactions, Their Electronic and Nonlinear Optical Properties through DFT Calculations

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Muhammad Saeed Akhtar

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Sajjad Haider

Molecules 2021, 26(23), 7309; https://doi.org/10.3390/molecules26237309 - 02 Dec 2021

Cited by 4 | Viewed by 1830

Abstract

Synthesis of 5-aryl-N-(pyrazin-2-yl)thiophene-2-carboxamides (4a–4n) by a Suzuki cross-coupling reaction of 5-bromo-N-(pyrazin-2-yl)thiophene-2-carboxamide (3) with various aryl/heteroaryl boronic acids/pinacol esters was observed in this article. The intermediate compound 3 was prepared by condensation of pyrazin-2-amine [...] Read more.

Synthesis of 5-aryl-N-(pyrazin-2-yl)thiophene-2-carboxamides (4a–4n) by a Suzuki cross-coupling reaction of 5-bromo-N-(pyrazin-2-yl)thiophene-2-carboxamide (3) with various aryl/heteroaryl boronic acids/pinacol esters was observed in this article. The intermediate compound 3 was prepared by condensation of pyrazin-2-amine (1) with 5-bromothiophene-2-carboxylic acid (2) mediated by TiCl₄. The target pyrazine analogs (4a–4n) were confirmed by NMR and mass spectrometry. In DFT calculation of target molecules, several reactivity parameters like FMOs (E_HOMO, E_LUMO), HOMO–LUMO energy gap, electron affinity (A), ionization energy (I), electrophilicity index (ω), chemical softness (σ) and chemical hardness (η) were considered and discussed. Effect of various substituents was observed on values of the HOMO–LUMO energy gap and hyperpolarizability. The p-electronic delocalization extended over pyrazine, benzene and thiophene was examined in studying the NLO behavior. The chemical shifts of ¹H NMR of all the synthesized compounds 4a–4n were calculated and compared with the experimental values. Full article

(This article belongs to the Special Issue Fundamental Aspects of Chemical Bonding)

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Open AccessArticle

Comparative Study of Phosgene Gas Sensing Using Carbon and Boron Nitride Nanomaterials—A DFT Approach

by

Emmanuel Obroni Kweitsu

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Stephen Kanga Armoo

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Kwabena Kan-Dapaah

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Eric Kwabena Kyeh Abavare

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David Dodoo-Arhin

and

Abu Yaya

Molecules 2021, 26(1), 120; https://doi.org/10.3390/molecules26010120 - 29 Dec 2020

Cited by 8 | Viewed by 2514

Abstract

Phosgene (COCl₂), a valuable industrial compound, maybe a public safety and health risk due to potential abuse and possible accidental spillage. Conventional techniques suffer from issues related to procedural complexity and sensitivity. Therefore, there is a need for the development of [...] Read more.

Phosgene (COCl₂), a valuable industrial compound, maybe a public safety and health risk due to potential abuse and possible accidental spillage. Conventional techniques suffer from issues related to procedural complexity and sensitivity. Therefore, there is a need for the development of simple and highly sensitive techniques that overcome these challenges. Recent advances in nanomaterials science offer the opportunity for the development of such techniques by exploiting the unique properties of these nanostructures. In this study, we investigated the potential of six types of nanomaterials: three carbon-based ([5,0] CNT, C60, C70) and three boron nitride-based (BNNT, BN60, BN70) for the detection of COCl₂. The local density approximation (LDA) approach of the density functional theory (DFT) was used to estimate the adsorption characteristics and conductivities of these materials. The results show that the COCl₂ molecule adsorbed spontaneously on the Fullerene or nanocages and endothermically on the pristine zigzag nanotubes. Using the magnitude of the bandgap modulation, the order of suitability of the different nanomaterials was established as follows: PBN60 (0.19%) < PC70 (1.39%) < PC60 (1.77%) < PBNNT (27.64%) < PCNT (65.29%) < PBN70 (134.12%). Since the desired criterion for the design of an electronic device is increased conductivity after adsorption due to the resulting low power consumption, PC60 was found to be most suitable because of its power consumption as it had the largest decrease of 1.77% of the bandgap. Full article

(This article belongs to the Special Issue Fundamental Aspects of Chemical Bonding)

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Review

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On the Nature of the Partial Covalent Bond between Noble Gas Elements and Noble Metal Atoms

by

Ranita Pal

and

Pratim Kumar Chattaraj

Molecules 2023, 28(7), 3253; https://doi.org/10.3390/molecules28073253 - 05 Apr 2023

Viewed by 976

Abstract

This article provides a discussion on the nature of bonding between noble gases (Ng) and noble metals (M) from a quantum chemical perspective by investigating compounds such as NgMY (Y=CN, O, NO₃, SO₄, CO₃), [NgM−(bipy)]+, NgMCCH, and [...] Read more.

This article provides a discussion on the nature of bonding between noble gases (Ng) and noble metals (M) from a quantum chemical perspective by investigating compounds such as NgMY (Y=CN, O, NO₃, SO₄, CO₃), [NgM−(bipy)]+, NgMCCH, and MCCNgH complexes, where M=Cu, Ag, Au and Ng=Kr−Rn, with some complexes containing the lighter noble gas atoms as well. Despite having very low chemical reactivity, noble gases have been observed to form weak bonds with noble metals such as copper, gold, and silver. In this study, we explore the factors that contribute to this unusual bonding behavior, including the electronic structure of the atoms involved and the geometric configuration of the concerned fragments. We also investigate the metastable nature of the resulting complexes by studying the energetics of their possible dissociation and internal isomerization channels. The noble gas-binding ability of the bare metal cyanides are higher than most of their bromide counterparts, with CuCN and AgCN showing higher affinity than their chloride analogues as well. In contrast, the oxides seem to have lower binding power than their corresponding halides. In the oxide and the bipyridyl complexes, the Ng-binding ability follows the order Au > Cu > Ag. The dissociation energies calculated, considering the zero-point energy correction for possible dissociation channels, increase as we move down the noble gas group. The bond between the noble gases and the noble metals in the complexes are found to have comparable weightage of orbital and electrostatic interactions, suggestive of a partial covalent nature. The same is validated from the topological analysis of electron density. Full article

(This article belongs to the Special Issue Fundamental Aspects of Chemical Bonding)

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