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17 pages, 2819 KiB

Open AccessArticle

An Interacting Quantum Atoms (IQA) and Relative Energy Gradient (REG) Analysis of the Anomeric Effect

by Danish Khan, Leonardo J. Duarte and Paul L. A. Popelier

Molecules 2022, 27(15), 5003; https://doi.org/10.3390/molecules27155003 - 6 Aug 2022

Cited by 2 | Viewed by 1642

Abstract

The explanation of the anomeric effect in terms of underlying quantum properties is still controversial almost 70 years after its introduction. Here, we use a method called Relative Energy Gradient (REG), which is able to compute chemical insight with a view to explaining [...] Read more.

The explanation of the anomeric effect in terms of underlying quantum properties is still controversial almost 70 years after its introduction. Here, we use a method called Relative Energy Gradient (REG), which is able to compute chemical insight with a view to explaining the anomeric effect. REG operates on atomic energy contributions generated by the quantum topological energy decomposition Interacting Quantum Atoms (IQA). Based on the case studies of dimethoxymethane and 2-fluorotetrahydropyran, we show that the anomeric effect is electrostatic in nature rather than governed by hyperconjugation. Full article

(This article belongs to the Special Issue Chemical Bonding: A Commemorative Special Issue Honoring Professor Linus Pauling)

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13 pages, 4136 KiB

Open AccessArticle

Polycation–Polyanion Architecture of the Intermetallic Compound Mg_3−xGa_1+xIr

by Olga Sichevych, Yurii Prots, Walter Schnelle, Frank R. Wagner and Yuri Grin

Molecules 2022, 27(3), 659; https://doi.org/10.3390/molecules27030659 - 20 Jan 2022

Cited by 11 | Viewed by 2404

Abstract

Mg_3−xGa_1+xIr (x = 0.05) was synthesized by direct reaction of the elements in welded tantalum containers at 1200 °C and subsequent annealing at 500 °C for 30 days. Its crystal structure represents a new prototype and [...] Read more.

Mg_3−xGa_1+xIr (x = 0.05) was synthesized by direct reaction of the elements in welded tantalum containers at 1200 °C and subsequent annealing at 500 °C for 30 days. Its crystal structure represents a new prototype and was determined by single-crystal technique as follows: space group P6₃/mcm, Pearson symbol hP90, Z = 18, a = 14.4970(3) Å, c = 8.8638(3) Å. The composition and atomic arrangement in Mg₃GaIr do not follow the 8–N rule due to the lack of valence electrons. Based on chemical bonding analysis in positional space, it was shown that the title compound has a polycationic–polyanionic organization. In comparison with other known intermetallic substances with this kind of bonding pattern, both the polyanion and the polyanion are remarkably complex. Mg_3−xGa_1+xIr is an example of how the general organization of intermetallic substances (e.g., formation of polyanions and polycations) can be understood by extending the principles of 8–N compounds to electron-deficient materials with multi-atomic bonding. Full article

(This article belongs to the Special Issue Chemical Bonding: A Commemorative Special Issue Honoring Professor Linus Pauling)

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15 pages, 2642 KiB

Open AccessArticle

On the Quantum Chemical Nature of Lead(II) “Lone Pair”

by Christophe Gourlaouen and Jean-Philip Piquemal

Molecules 2022, 27(1), 27; https://doi.org/10.3390/molecules27010027 - 22 Dec 2021

Cited by 2 | Viewed by 2379

Abstract

We study the quantum chemical nature of the Lead(II) valence basins, sometimes called the lead “lone pair”. Using various chemical interpretation tools, such as molecular orbital analysis, natural bond orbitals (NBO), natural population analysis (NPA) and electron localization function (ELF) topological analysis, we [...] Read more.

We study the quantum chemical nature of the Lead(II) valence basins, sometimes called the lead “lone pair”. Using various chemical interpretation tools, such as molecular orbital analysis, natural bond orbitals (NBO), natural population analysis (NPA) and electron localization function (ELF) topological analysis, we study a variety of Lead(II) complexes. A careful analysis of the results shows that the optimal structures of the lead complexes are only governed by the 6s and 6p subshells, whereas no involvement of the 5d orbitals is found. Similarly, we do not find any significant contribution of the 6d. Therefore, the Pb(II) complexation with its ligand can be explained through the interaction of the 6s² electrons and the accepting 6p orbitals. We detail the potential structural and dynamical consequences of such electronic structure organization of the Pb (II) valence domain. Full article

(This article belongs to the Special Issue Chemical Bonding: A Commemorative Special Issue Honoring Professor Linus Pauling)

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11 pages, 18966 KiB

Open AccessArticle

Occurrence of Double Bond in π-Aromatic Rings: An Easy Way to Design Doubly Aromatic Carbon-Metal Structures

by Nikolay V. Tkachenko, Alvaro Muñoz-Castro and Alexander I. Boldyrev

Molecules 2021, 26(23), 7232; https://doi.org/10.3390/molecules26237232 - 29 Nov 2021

Cited by 5 | Viewed by 2699

Abstract

A chemical bonding of several metallabenzenes and metallabenzynes was studied via an adaptive natural density partitioning (AdNDP) algorithm and the induced magnetic field analysis. A unique chemical bonding pattern was discovered where the M=C (M: Os, Re) double bond coexists with the delocalized [...] Read more.

A chemical bonding of several metallabenzenes and metallabenzynes was studied via an adaptive natural density partitioning (AdNDP) algorithm and the induced magnetic field analysis. A unique chemical bonding pattern was discovered where the M=C (M: Os, Re) double bond coexists with the delocalized 6c-2e π-bonding elements responsible for aromatic properties of the investigated complexes. In opposition to the previous description where 8 delocalized π-electrons were reported in metallabenzenes and metallabenzynes, we showed that only six delocalized π-electrons are present in those molecules. Thus, there is no deviation from Hückel’s aromaticity rule for metallabenzynes/metallabenzenes complexes. Based on the discovered bonding pattern, we propose two thermodynamically stable novel molecules that possess not only π-delocalization but also retain six σ-delocalized electrons, rendering them as doubly aromatic species. As a result, our investigation gives a new direction for the search for carbon-metal doubly aromatic molecules. Full article

(This article belongs to the Special Issue Chemical Bonding: A Commemorative Special Issue Honoring Professor Linus Pauling)

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10 pages, 1642 KiB

Open AccessArticle

Exploring Orthogonality between Halogen and Hydrogen Bonding Involving Benzene

by Alessandra Forni, Rosario Russo, Giacomo Rapeti, Stefano Pieraccini and Maurizio Sironi

Molecules 2021, 26(23), 7126; https://doi.org/10.3390/molecules26237126 - 25 Nov 2021

Cited by 2 | Viewed by 1856

Abstract

The concept of orthogonality between halogen and hydrogen bonding, brought out by Ho and coworkers some years ago, has become a widely accepted idea within the chemists’ community. While the original work was based on a common carbonyl oxygen as acceptor for both [...] Read more.

The concept of orthogonality between halogen and hydrogen bonding, brought out by Ho and coworkers some years ago, has become a widely accepted idea within the chemists’ community. While the original work was based on a common carbonyl oxygen as acceptor for both interactions, we explore here, by means of M06-2X, M11, ωB97X, and ωB97XD/aug-cc-PVTZ DFT calculations, the interdependence of halogen and hydrogen bonding with a shared π-electron system of benzene. The donor groups (specifically NCBr and H₂O) were placed on either or the same side of the ring, according to a double T-shaped or a perpendicular geometry, respectively. The results demonstrate that the two interactions with benzene are not strictly independent on each other, therefore outlining that the orthogonality between halogen and hydrogen bonding, intended as energetical independence between the two interactions, should be carefully evaluated according to the specific acceptor group. Full article

(This article belongs to the Special Issue Chemical Bonding: A Commemorative Special Issue Honoring Professor Linus Pauling)

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11 pages, 1019 KiB

Open AccessArticle

Electronegativity under Confinement

by Andrés Robles-Navarro, Carlos Cárdenas and Patricio Fuentealba

Molecules 2021, 26(22), 6924; https://doi.org/10.3390/molecules26226924 - 17 Nov 2021

Cited by 2 | Viewed by 2196

Abstract

The electronegativity concept was first formulated by Pauling in the first half of the 20th century to explain quantitatively the properties of chemical bonds between different types of atoms. Today, it is widely known that, in high-pressure regimes, the reactivity properties of atoms [...] Read more.

The electronegativity concept was first formulated by Pauling in the first half of the 20th century to explain quantitatively the properties of chemical bonds between different types of atoms. Today, it is widely known that, in high-pressure regimes, the reactivity properties of atoms can change, and, thus, the bond patterns in molecules and solids are affected. In this work, we studied the effects of high pressure modeled by a confining potential on different definitions of electronegativity and, additionally, tested the accuracy of first-order perturbation theory in the context of density functional theory for confined atoms of the second row at the Hartree–Fock level. As expected, the electronegativity of atoms at high confinement is very different than that of their free counterparts since it depends on the electronic configuration of the atom, and, thus, its periodicity is modified at higher pressures. Full article

(This article belongs to the Special Issue Chemical Bonding: A Commemorative Special Issue Honoring Professor Linus Pauling)

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26 pages, 21033 KiB

Open AccessArticle

A Combined Experimental/Quantum-Chemical Study of Tetrel, Pnictogen, and Chalcogen Bonds of Linear Triatomic Molecules

by Freija De Vleeschouwer, Frank De Proft, Özge Ergün, Wouter Herrebout and Paul Geerlings

Molecules 2021, 26(22), 6767; https://doi.org/10.3390/molecules26226767 - 9 Nov 2021

Cited by 8 | Viewed by 2587

Abstract

Linear triatomic molecules (CO₂, N₂O, and OCS) are scrutinized for their propensity to form perpendicular tetrel (CO₂ and OCS) or pnictogen (N₂O) bonds with Lewis bases (dimethyl ether and trimethyl amine) as compared with their tendency [...] Read more.

Linear triatomic molecules (CO₂, N₂O, and OCS) are scrutinized for their propensity to form perpendicular tetrel (CO₂ and OCS) or pnictogen (N₂O) bonds with Lewis bases (dimethyl ether and trimethyl amine) as compared with their tendency to form end-on chalcogen bonds. Comparison of the IR spectra of the complexes with the corresponding monomers in cryogenic solutions in liquid argon enables to determine the stoichiometry and the nature of the complexes. In the present cases, perpendicular tetrel and pnictogen 1:1 complexes are identified mainly on the basis of the lifting of the degenerate ν 2 bending mode with the appearance of both a blue and a red shift. Van ′t Hoff plots of equilibrium constants as a function of temperature lead to complexation enthalpies that, when converted to complexation energies, form the first series of experimental complexation energies on sp¹ tetrel bonds in the literature, directly comparable to quantum-chemically obtained values. Their order of magnitude corresponds with what can be expected on the basis of experimental work on halogen and chalcogen bonds and previous computational work on tetrel bonds. Both the order of magnitude and sequence are in fair agreement with both CCSD(T) and DFA calculations, certainly when taking into account the small differences in complexation energies of the different complexes (often not more than a few kJ mol⁻¹) and the experimental error. It should, however, be noted that the OCS chalcogen complexes are not identified experimentally, most probably owing to entropic effects. For a given Lewis base, the stability sequence of the complexes is first successfully interpreted via a classical electrostatic quadrupole–dipole moment model, highlighting the importance of the magnitude and sign of the quadrupole moment of the Lewis acid. This approach is validated by a subsequent analysis of the molecular electrostatic potential, scrutinizing the σ and π holes, as well as the evolution in preference for chalcogen versus tetrel bonds when passing to “higher” chalcogens in agreement with the evolution of the quadrupole moment. The energy decomposition analysis gives further support to the importance/dominance of electrostatic effects, as it turns out to be the largest attractive term in all cases considered, followed by the orbital interaction and the dispersion term. The natural orbitals for chemical valence highlight the sequence of charge transfer in the orbital interaction term, which is dominated by an electron-donating effect of the N or O lone-pair(s) of the base to the central atom of the triatomics, with its value being lower than in the case of comparable halogen bonding situations. The effect is appreciably larger for TMA, in line with its much higher basicity than DME, explaining the comparable complexation energies for DME and TMA despite the much larger dipole moment for DME. Full article

(This article belongs to the Special Issue Chemical Bonding: A Commemorative Special Issue Honoring Professor Linus Pauling)

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21 pages, 33284 KiB

Open AccessArticle

Alkyne-Functionalized Cyclooctyne on Si(001): Reactivity Studies and Surface Bonding from an Energy Decomposition Analysis Perspective

by Fabian Pieck and Ralf Tonner-Zech

Molecules 2021, 26(21), 6653; https://doi.org/10.3390/molecules26216653 - 2 Nov 2021

Cited by 3 | Viewed by 2450

Abstract

The reactivity and bonding of an ethinyl-functionalized cyclooctyne on Si(001) is studied by means of density functional theory. This system is promising for the organic functionalization of semiconductors. Singly bonded adsorption structures are obtained by [2 + 2] cycloaddition reactions of the cyclooctyne [...] Read more.

The reactivity and bonding of an ethinyl-functionalized cyclooctyne on Si(001) is studied by means of density functional theory. This system is promising for the organic functionalization of semiconductors. Singly bonded adsorption structures are obtained by [2 + 2] cycloaddition reactions of the cyclooctyne or ethinyl group with the Si(001) surface. A thermodynamic preference for adsorption with the cyclooctyne group in the on-top position is found and traced back to minimal structural deformation of the adsorbate and surface with the help of energy decomposition analysis for extended systems (pEDA). Starting from singly bonded structures, a plethora of reaction paths describing conformer changes and consecutive reactions with the surface are discussed. Strongly exothermic and exergonic reactions to doubly bonded structures are presented, while small reaction barriers highlight the high reactivity of the studied organic molecule on the Si(001) surface. Dynamic aspects of the competitive bonding of the functional groups are addressed by ab initio molecular dynamics calculations. Several trajectories for the doubly bonded structures are obtained in agreement with calculations using the nudged elastic band approach. However, our findings disagree with the experimental observations of selective adsorption by the cyclooctyne moiety, which is critically discussed. Full article

(This article belongs to the Special Issue Chemical Bonding: A Commemorative Special Issue Honoring Professor Linus Pauling)

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18 pages, 3345 KiB

Open AccessArticle

Energetic and Geometric Characteristics of the Substituents: Part 2: The Case of NO₂, Cl, and NH₂ Groups in Their Mono-Substituted Derivatives of Simple Nitrogen Heterocycles

by Paweł A. Wieczorkiewicz, Halina Szatylowicz and Tadeusz M. Krygowski

Molecules 2021, 26(21), 6543; https://doi.org/10.3390/molecules26216543 - 29 Oct 2021

Cited by 6 | Viewed by 2755

Abstract

Variously substituted N-heterocyclic compounds are widespread across bio- and medicinal chemistry. The work aims to computationally evaluate the influence of the type of N-heterocyclic compound and the substitution position on the properties of three model substituents: NO₂, Cl, and NH₂ [...] Read more.

Variously substituted N-heterocyclic compounds are widespread across bio- and medicinal chemistry. The work aims to computationally evaluate the influence of the type of N-heterocyclic compound and the substitution position on the properties of three model substituents: NO₂, Cl, and NH₂. For this reason, the energetic descriptor of global substituent effect (E_rel), geometry of substituents, and electronic descriptors (cSAR, pEDA, sEDA) are considered, and interdependences between these characteristics are discussed. Furthermore, the existence of an endocyclic N atom may induce proximity effects specific for a given substituent. Therefore, various quantum chemistry methods are used to assess them: the quantum theory of atoms in molecules (QTAIM), analysis of non-covalent interactions using reduced density gradient (RDG) function, and electrostatic potential maps (ESP). The study shows that the energetic effect associated with the substitution is highly dependent on the number and position of N atoms in the heterocyclic ring. Moreover, this effect due to interaction with more than one endo N atom (e.g., in pyrimidines) can be assessed with reasonable accuracy by adding the effects calculated for interactions with one endo N atom in substituted pyridines. Finally, all possible cases of proximity interactions for the NO₂, Cl, and NH₂ groups are thoroughly discussed. Full article

(This article belongs to the Special Issue Chemical Bonding: A Commemorative Special Issue Honoring Professor Linus Pauling)

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12 pages, 3717 KiB

Open AccessArticle

Charge-Flow Profiles along Curvilinear Paths: A Flexible Scheme for the Analysis of Charge Displacement upon Intermolecular Interactions

by Luca Sagresti and Sergio Rampino

Molecules 2021, 26(21), 6409; https://doi.org/10.3390/molecules26216409 - 23 Oct 2021

Cited by 2 | Viewed by 1935

Abstract

The Charge-Displacement (CD) analysis has proven to be a powerful tool for a quantitative characterization of the electron-density flow occurring upon chemical bonding along a suitably chosen interaction axis. In several classes of interesting intermolecular interactions, however, an interaction axis cannot be straightforwardly [...] Read more.

The Charge-Displacement (CD) analysis has proven to be a powerful tool for a quantitative characterization of the electron-density flow occurring upon chemical bonding along a suitably chosen interaction axis. In several classes of interesting intermolecular interactions, however, an interaction axis cannot be straightforwardly defined, and the CD analysis loses consistency and usefulness. In this article, we propose a general, flexible reformulation of the CD analysis capable of providing a quantitative view of the charge displacement along custom curvilinear paths. The new scheme naturally reduces to ordinary CD analysis if the path is chosen to be a straight line. An implementation based on a discrete sampling of the electron densities and a Voronoi space partitioning is described and shown in action on two test cases of a metal-carbonyl and a pyridine-ammonia complex. Full article

(This article belongs to the Special Issue Chemical Bonding: A Commemorative Special Issue Honoring Professor Linus Pauling)

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8 pages, 1302 KiB

Open AccessArticle

Magic Numbers in Boson ⁴He Clusters: The Auger Evaporation Mechanism

by Elena Spreafico, Giorgio Benedek, Oleg Kornilov and Jan Peter Toennies

Molecules 2021, 26(20), 6244; https://doi.org/10.3390/molecules26206244 - 15 Oct 2021

Cited by 3 | Viewed by 1505

Abstract

The absence of magic numbers in bosonic ⁴He clusters predicted by all theories since 1984 has been challenged by high-resolution matter-wave diffraction experiments. The observed magic numbers were explained in terms of enhanced growth rates of specific cluster sizes for which an [...] Read more.

The absence of magic numbers in bosonic ⁴He clusters predicted by all theories since 1984 has been challenged by high-resolution matter-wave diffraction experiments. The observed magic numbers were explained in terms of enhanced growth rates of specific cluster sizes for which an additional excitation level calculated by diffusion Monte Carlo is stabilized. The present theoretical study provides an alternative explanation based on a simple independent particle model of the He clusters. Collisions between cluster atoms in excited states within the cluster lead to selective evaporation via an Auger process. The calculated magic numbers as well as the shape of the number distributions are in quite reasonable agreement with the experiments. Full article

(This article belongs to the Special Issue Chemical Bonding: A Commemorative Special Issue Honoring Professor Linus Pauling)

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14 pages, 3888 KiB

Open AccessArticle

Polarisation of Electron Density and Electronic Effects: Revisiting the Carbon–Halogen Bonds

by Sébastien Menant, Frédéric Guégan, Vincent Tognetti, Lynda Merzoud, Laurent Joubert, Henry Chermette and Christophe Morell

Molecules 2021, 26(20), 6218; https://doi.org/10.3390/molecules26206218 - 14 Oct 2021

Cited by 4 | Viewed by 2372

Abstract

Electronic effects (inductive and mesomeric) are of fundamental importance to understand the reactivity and selectivity of a molecule. In this article, polarisation temperature is used as a principal index to describe how electronic effects propagate in halogeno-alkanes and halogeno-alkenes. It is found that [...] Read more.

Electronic effects (inductive and mesomeric) are of fundamental importance to understand the reactivity and selectivity of a molecule. In this article, polarisation temperature is used as a principal index to describe how electronic effects propagate in halogeno-alkanes and halogeno-alkenes. It is found that as chain length increases, polarisation temperature decreases. As expected, polarisation is much larger for alkenes than for alkanes. Finally, the polarisation mode of the carbon–fluorine bond is found to be quite different and might explain the unusual reactivity of fluoride compounds. Full article

(This article belongs to the Special Issue Chemical Bonding: A Commemorative Special Issue Honoring Professor Linus Pauling)

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19 pages, 4096 KiB

Open AccessArticle

Principles Determining the Structure of Transition Metals

by Samuel K. Riddle, Timothy R. Wilson, Malavikha Rajivmoorthy and Mark E. Eberhart

Molecules 2021, 26(17), 5396; https://doi.org/10.3390/molecules26175396 - 5 Sep 2021

Cited by 4 | Viewed by 2761

Abstract

For the better part of a century researchers across disciplines have sought to explain the crystallography of the elemental transition metals: hexagonal close packed, body centered cubic, and face centered cubic in a form similar to that used to rationalize the structure of [...] Read more.

For the better part of a century researchers across disciplines have sought to explain the crystallography of the elemental transition metals: hexagonal close packed, body centered cubic, and face centered cubic in a form similar to that used to rationalize the structure of organic molecules and inorganic complexes. Pauling himself tried with limited success to address the origins of transition metal stability. These early investigators were handicapped, however, by incomplete knowledge regarding the structure of metallic electron density. Here, we exploit modern approaches to electron density analysis to first comprehensively describe transition metal electron density. Then, we use topological partitioning and quantum mechanically rigorous treatments of kinetic energy to account for the structure of the density as arising from the interactions between metallic polyhedra. We argue that the crystallography of the early transition metals results from charge transfer from the so called “octahedral” to “tetrahedral cages” while the face centered cubic structure of the late transition metals is a consequence of anti-bonding interactions that increase octahedral hole kinetic energy. Full article

(This article belongs to the Special Issue Chemical Bonding: A Commemorative Special Issue Honoring Professor Linus Pauling)

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18 pages, 3110 KiB

Open AccessEditor’s ChoiceArticle

Nucleus-Independent Chemical Shift (NICS) as a Criterion for the Design of New Antifungal Benzofuranones

by María de los Ángeles Zermeño-Macías, Marco Martín González-Chávez, Francisco Méndez, Arlette Richaud, Rodolfo González-Chávez, Luis Enrique Ojeda-Fuentes, Perla del Carmen Niño-Moreno and Roberto Martínez

Molecules 2021, 26(16), 5078; https://doi.org/10.3390/molecules26165078 - 21 Aug 2021

Cited by 4 | Viewed by 3421

Abstract

The assertion made by Wu et al. that aromaticity may have considerable implications for molecular design motivated us to use nucleus-independent chemical shifts (NICS) as an aromaticity criterion to evaluate the antifungal activity of two series of indol-4-ones. A linear regression analysis of [...] Read more.

The assertion made by Wu et al. that aromaticity may have considerable implications for molecular design motivated us to use nucleus-independent chemical shifts (NICS) as an aromaticity criterion to evaluate the antifungal activity of two series of indol-4-ones. A linear regression analysis of NICS and antifungal activity showed that both tested variables were significantly related (p < 0.05); when aromaticity increased, the antifungal activity decreased for series I and increased for series II. To verify the validity of the obtained equations, a new set of 44 benzofuran-4-ones was designed by replacing the nitrogen atom of the five-membered ring with oxygen in indol-4-ones. The NICS(0) and NICS(1) of benzofuran-4-ones were calculated and used to predict their biological activities using the previous equations. A set of 10 benzofuran-4-ones was synthesized and tested in eight human pathogenic fungi, showing the validity of the equations. The minimum inhibitory concentration (MIC) in yeasts was 31.25 µg·mL^–1 for Candida glabrata, Candida krusei and Candida guilliermondii with compounds 15-32, 15-15 and 15-1. The MIC for filamentous fungi was 1.95 µg·mL^–1 for Aspergillus niger for compounds 15-1, 15-33 and 15-34. The results obtained support the use of NICS in the molecular design of compounds with antifungal activity. Full article

(This article belongs to the Special Issue Chemical Bonding: A Commemorative Special Issue Honoring Professor Linus Pauling)

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17 pages, 5033 KiB

Open AccessFeature PaperArticle

The Effects of Chemical Bonding at Subatomic Resolution: A Case Study on α-Boron

by Andreas Fischer, Georg Eickerling and Wolfgang Scherer

Molecules 2021, 26(14), 4270; https://doi.org/10.3390/molecules26144270 - 14 Jul 2021

Cited by 2 | Viewed by 2467

Abstract

Similar to classical asphericity shifts, aspherical deformations of the electron density in the atomic core region can result in core asphericity shifts in refinements using a Hansen-Coppens multipolar model (HCM), especially when highly precise experimental datasets with resolutions far beyond sin(θ)/λ ≤ [...] Read more.

Similar to classical asphericity shifts, aspherical deformations of the electron density in the atomic core region can result in core asphericity shifts in refinements using a Hansen-Coppens multipolar model (HCM), especially when highly precise experimental datasets with resolutions far beyond sin(θ)/λ ≤ 1.0 Å⁻¹ are employed. These shifts are about two orders of magnitude smaller than their counterparts caused by valence shell deformations, and their underlying deformations are mainly of dipolar character for 1st row atoms. Here, we analyze the resolution dependence of core asphericity shifts in α-boron. Based on theoretical structure factors, an appropriate Extended HCM (EHCM) is developed, which is tested against experimental high-resolution (sin(θ)/λ ≤ 1.6 Å⁻¹) single-crystal diffraction data. Bond length deviations due to core asphericity shifts of α-boron in the order of 4–6·10⁻⁴ Å are small but significant at this resolution and can be effectively compensated by an EHCM, although the correlation of the additional model parameters with positional parameters prevented a free refinement of all core model parameters. For high quality, high resolution data, a proper treatment with an EHCM or other equivalent methods is therefore highly recommended. Full article

(This article belongs to the Special Issue Chemical Bonding: A Commemorative Special Issue Honoring Professor Linus Pauling)

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17 pages, 23168 KiB

Open AccessArticle

Topology of the Electron Density and of Its Laplacian from Periodic LCAO Calculations on f-Electron Materials: The Case of Cesium Uranyl Chloride

by Alessandro Cossard, Silvia Casassa, Carlo Gatti, Jacques K. Desmarais and Alessandro Erba

Molecules 2021, 26(14), 4227; https://doi.org/10.3390/molecules26144227 - 12 Jul 2021

Cited by 10 | Viewed by 3750

Abstract

The chemistry of f-electrons in lanthanide and actinide materials is yet to be fully rationalized. Quantum-mechanical simulations can provide useful complementary insight to that obtained from experiments. The quantum theory of atoms in molecules and crystals (QTAIMAC), through thorough topological analysis of [...] Read more.

The chemistry of f-electrons in lanthanide and actinide materials is yet to be fully rationalized. Quantum-mechanical simulations can provide useful complementary insight to that obtained from experiments. The quantum theory of atoms in molecules and crystals (QTAIMAC), through thorough topological analysis of the electron density (often complemented by that of its Laplacian) constitutes a general and robust theoretical framework to analyze chemical bonding features from a computed wave function. Here, we present the extension of the Topond module (previously limited to work in terms of s-, p- and d-type basis functions only) of the Crystal program to f- and g-type basis functions within the linear combination of atomic orbitals (LCAO) approach. This allows for an effective QTAIMAC analysis of chemical bonding of lanthanide and actinide materials. The new implemented algorithms are applied to the analysis of the spatial distribution of the electron density and its Laplacian of the cesium uranyl chloride, Cs

_{2}

UO

_{2}

Cl

_{4}

, crystal. Discrepancies between the present theoretical description of chemical bonding and that obtained from a previously reconstructed electron density by experimental X-ray diffraction are illustrated and discussed. Full article

(This article belongs to the Special Issue Chemical Bonding: A Commemorative Special Issue Honoring Professor Linus Pauling)

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25 pages, 12740 KiB

Open AccessArticle

Electronic Currents Induced by Optical Fields and Rotatory Power Density in Chiral Molecules

by Francesco Ferdinando Summa, Guglielmo Monaco, Riccardo Zanasi, Stefano Pelloni and Paolo Lazzeretti

Molecules 2021, 26(14), 4195; https://doi.org/10.3390/molecules26144195 - 10 Jul 2021

Cited by 9 | Viewed by 2070

Abstract

The electric dipole–magnetic dipole polarizability tensor

κ^{'}

, introduced to interpret the optical activity of chiral molecules, has been expressed in terms of a series of density functions

k_{α β}^{'}

, which can be integrated all over the three-dimensional space [...] Read more.

The electric dipole–magnetic dipole polarizability tensor

κ^{'}

, introduced to interpret the optical activity of chiral molecules, has been expressed in terms of a series of density functions

k_{α β}^{'}

, which can be integrated all over the three-dimensional space to evaluate components

κ_{α β}^{'}

and trace

κ_{α α}^{'}

. A computational approach to

k_{α β}^{'}

, based on frequency-dependent electronic current densities induced by monochromatic light shining on a probe molecule, has been developed. The dependence of

k_{α β}^{'}

on the origin of the coordinate system has been investigated in connection with the corresponding change of

κ_{α β}^{'}

. It is shown that only the trace

k_{α α}^{'}

of the density function defined via dynamic current density evaluated using the continuous translation of the origin of the coordinate system is invariant of the origin. Accordingly, this function is recommended as a tool that is quite useful for determining the molecular domains that determine optical activity to a major extent. A series of computations on the hydrogen peroxide molecule, for a number of different HO–OH dihedral angles, is shown to provide a pictorial documentation of the proposed method. Full article

(This article belongs to the Special Issue Chemical Bonding: A Commemorative Special Issue Honoring Professor Linus Pauling)

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15 pages, 9971 KiB

Open AccessArticle

Ni Oxidation State and Ligand Saturation Impact on the Capability of Octaazamacrocyclic Complexes to Bind and Reduce CO₂

by Barbora Vénosová, Ingrid Jelemenská, Jozef Kožíšek, Peter Rapta, Michal Zalibera, Michal Novotný, Vladimir B. Arion and Lukáš Bučinský

Molecules 2021, 26(14), 4139; https://doi.org/10.3390/molecules26144139 - 7 Jul 2021

Cited by 1 | Viewed by 2741

Abstract

Two 15-membered octaazamacrocyclic nickel(II) complexes are investigated by theoretical methods to shed light on their affinity forwards binding and reducing CO₂. In the first complex ¹[Ni^IIL]⁰, the octaazamacrocyclic ligand is grossly unsaturated (π-conjugated), while [...] Read more.

Two 15-membered octaazamacrocyclic nickel(II) complexes are investigated by theoretical methods to shed light on their affinity forwards binding and reducing CO₂. In the first complex ¹[Ni^IIL]⁰, the octaazamacrocyclic ligand is grossly unsaturated (π-conjugated), while in the second ¹[Ni^IILH]²⁺ one, the macrocycle is saturated with hydrogens. One and two-electron reductions are described using Mulliken population analysis, quantum theory of atoms in molecules, localized orbitals, and domain averaged fermi holes, including the characterization of the Ni-C_CO2 bond and the oxidation state of the central Ni atom. It was found that in the [NiLH] complex, the central atom is reduced to Ni⁰ and/or Ni^I and is thus able to bind CO₂ via a single σ bond. In addition, the two-electron reduced ³[NiL]²⁻ species also shows an affinity forwards CO₂. Full article

(This article belongs to the Special Issue Chemical Bonding: A Commemorative Special Issue Honoring Professor Linus Pauling)

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15 pages, 6282 KiB

Open AccessArticle

Pauling’s Conceptions of Hybridization and Resonance in Modern Quantum Chemistry

by Eric D. Glendening and Frank Weinhold

Molecules 2021, 26(14), 4110; https://doi.org/10.3390/molecules26144110 - 6 Jul 2021

Cited by 17 | Viewed by 4469

Abstract

We employ the tools of natural bond orbital (NBO) and natural resonance theory (NRT) analysis to demonstrate the robustness, consistency, and accuracy with which Linus Pauling’s qualitative conceptions of directional hybridization and resonance delocalization are manifested in all known variants of modern computational [...] Read more.

We employ the tools of natural bond orbital (NBO) and natural resonance theory (NRT) analysis to demonstrate the robustness, consistency, and accuracy with which Linus Pauling’s qualitative conceptions of directional hybridization and resonance delocalization are manifested in all known variants of modern computational quantum chemistry methodology. Full article

(This article belongs to the Special Issue Chemical Bonding: A Commemorative Special Issue Honoring Professor Linus Pauling)

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28 pages, 25197 KiB

Open AccessFeature PaperArticle

Probing the Nature of Chemical Bonds by Atomic Force Microscopy

by Franz J. Giessibl

Molecules 2021, 26(13), 4068; https://doi.org/10.3390/molecules26134068 - 3 Jul 2021

Cited by 11 | Viewed by 6418

Abstract

The nature of the chemical bond is important in all natural sciences, ranging from biology to chemistry, physics and materials science. The atomic force microscope (AFM) allows to put a single chemical bond on the test bench, probing its strength and angular dependence. [...] Read more.

The nature of the chemical bond is important in all natural sciences, ranging from biology to chemistry, physics and materials science. The atomic force microscope (AFM) allows to put a single chemical bond on the test bench, probing its strength and angular dependence. We review experimental AFM data, covering precise studies of van-der-Waals-, covalent-, ionic-, metallic- and hydrogen bonds as well as bonds between artificial and natural atoms. Further, we discuss some of the density functional theory calculations that are related to the experimental studies of the chemical bonds. A description of frequency modulation AFM, the most precise AFM method, discusses some of the experimental challenges in measuring bonding forces. In frequency modulation AFM, forces between the tip of an oscillating cantilever change its frequency. Initially, cantilevers were made mainly from silicon. Most of the high precision measurements of bonding strengths by AFM became possible with a technology transfer from the quartz watch technology to AFM by using quartz-based cantilevers (“qPlus force sensors”), briefly described here. Full article

(This article belongs to the Special Issue Chemical Bonding: A Commemorative Special Issue Honoring Professor Linus Pauling)

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18 pages, 820 KiB

Open AccessArticle

Measuring Shared Electrons in Extended Molecular Systems: Covalent Bonds from Plane-Wave Representation of Wave Function

by Giovanni La Penna, Davide Tiana and Paolo Giannozzi

Molecules 2021, 26(13), 4044; https://doi.org/10.3390/molecules26134044 - 1 Jul 2021

Cited by 1 | Viewed by 2594

Abstract

In the study of materials and macromolecules by first-principle methods, the bond order is a useful tool to represent molecules, bulk materials and interfaces in terms of simple chemical concepts. Despite the availability of several methods to compute the bond order, most applications [...] Read more.

In the study of materials and macromolecules by first-principle methods, the bond order is a useful tool to represent molecules, bulk materials and interfaces in terms of simple chemical concepts. Despite the availability of several methods to compute the bond order, most applications have been limited to small systems because a high spatial resolution of the wave function and an all-electron representation of the electron density are typically required. Both limitations are critical for large-scale atomistic calculations, even within approximate density-functional theory (DFT) approaches. In this work, we describe our methodology to quickly compute delocalization indices for all atomic pairs, while keeping the same representation of the wave function used in most compute-intensive DFT calculations on high-performance computing equipment. We describe our implementation into a post-processing tool, designed to work with Quantum ESPRESSO, a popular open-source DFT package. In this way, we recover a description in terms of covalent bonds from a representation of wave function containing no explicit information about atomic types and positions. Full article

(This article belongs to the Special Issue Chemical Bonding: A Commemorative Special Issue Honoring Professor Linus Pauling)

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12 pages, 5952 KiB

Open AccessArticle

Hydrogen-Bonded and Halogen-Bonded: Orthogonal Interactions for the Chloride Anion of a Pyrazolium Salt

by Steven van Terwingen, Daniel Brüx, Ruimin Wang and Ulli Englert

Molecules 2021, 26(13), 3982; https://doi.org/10.3390/molecules26133982 - 29 Jun 2021

Cited by 9 | Viewed by 2847

Abstract

In the hydrochloride of a pyrazolyl-substituted acetylacetone, the chloride anion is hydrogen-bonded to the protonated pyrazolyl moiety. Equimolar co-crystallization with tetrafluorodiiodobenzene (TFDIB) leads to a supramolecular aggregate in which TFDIB is situated on a crystallographic center of inversion. The iodine atom in the [...] Read more.

In the hydrochloride of a pyrazolyl-substituted acetylacetone, the chloride anion is hydrogen-bonded to the protonated pyrazolyl moiety. Equimolar co-crystallization with tetrafluorodiiodobenzene (TFDIB) leads to a supramolecular aggregate in which TFDIB is situated on a crystallographic center of inversion. The iodine atom in the asymmetric unit acts as halogen bond donor, and the chloride acceptor approaches the

σ

-hole of this TFDIB iodine subtending an almost linear halogen bond, with Cl···I =

3.1653 (11)

Å and Cl···I–C = 179.32(6)°. This contact is roughly orthogonal to the N–H···Cl hydrogen bond. An analysis of the electron density according to Bader’s Quantum Theory of Atoms in Molecules confirms bond critical points (bcps) for both short contacts, with

ρ_{bcp}

= 0.129 for the halogen and

0.321

e

Å^{- 3}

for the hydrogen bond. Our halogen-bonded adduct represents the prototype for a future class of co-crystals with tunable electron density distribution about the

σ

-hole contact. Full article

(This article belongs to the Special Issue Chemical Bonding: A Commemorative Special Issue Honoring Professor Linus Pauling)

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13 pages, 3027 KiB

Open AccessArticle

Combining Molecular Dynamic Information and an Aspherical-Atom Data Bank in the Evaluation of the Electrostatic Interaction Energy in Multimeric Protein-Ligand Complex: A Case Study for HIV-1 Protease

by Prashant Kumar and Paulina Maria Dominiak

Molecules 2021, 26(13), 3872; https://doi.org/10.3390/molecules26133872 - 24 Jun 2021

Cited by 6 | Viewed by 2560

Abstract

Computational analysis of protein–ligand interactions is of crucial importance for drug discovery. Assessment of ligand binding energy allows us to have a glimpse of the potential of a small organic molecule to be a ligand to the binding site of a protein target. [...] Read more.

Computational analysis of protein–ligand interactions is of crucial importance for drug discovery. Assessment of ligand binding energy allows us to have a glimpse of the potential of a small organic molecule to be a ligand to the binding site of a protein target. Available scoring functions, such as in docking programs, all rely on equations that sum each type of protein–ligand interactions in order to predict the binding affinity. Most of the scoring functions consider electrostatic interactions involving the protein and the ligand. Electrostatic interactions constitute one of the most important part of total interactions between macromolecules. Unlike dispersion forces, they are highly directional and therefore dominate the nature of molecular packing in crystals and in biological complexes and contribute significantly to differences in inhibition strength among related enzyme inhibitors. In this study, complexes of HIV-1 protease with inhibitor molecules (JE-2147 and darunavir) were analyzed by using charge densities from the transferable aspherical-atom University at Buffalo Databank (UBDB). Moreover, we analyzed the electrostatic interaction energy for an ensemble of structures, using molecular dynamic simulations to highlight the main features of electrostatic interactions important for binding affinity. Full article

(This article belongs to the Special Issue Chemical Bonding: A Commemorative Special Issue Honoring Professor Linus Pauling)

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17 pages, 1391 KiB

Open AccessArticle

The Different Story of π Bonds

by Marco Cappelletti, Mirko Leccese, Matteo Cococcioni, Davide M. Proserpio and Rocco Martinazzo

Molecules 2021, 26(13), 3805; https://doi.org/10.3390/molecules26133805 - 22 Jun 2021

Cited by 2 | Viewed by 3367

Abstract

We revisit “classical” issues in multiply bonded systems between main groups elements, namely the structural distortions that may occur at the multiple bonds and that lead, e.g., to trans-bent and bond-length alternated structures. The focus is on the role that orbital hybridization and [...] Read more.

We revisit “classical” issues in multiply bonded systems between main groups elements, namely the structural distortions that may occur at the multiple bonds and that lead, e.g., to trans-bent and bond-length alternated structures. The focus is on the role that orbital hybridization and electron correlation play in this context, here analyzed with the help of simple models for

σ

- and

π

-bonds, numerically exact solutions of Hubbard Hamiltonians and first principles (density functional theory) investigations of an extended set of systems. Full article

(This article belongs to the Special Issue Chemical Bonding: A Commemorative Special Issue Honoring Professor Linus Pauling)

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19 pages, 2533 KiB

Open AccessArticle

Further Validation of Quantum Crystallography Approaches

by Monika Wanat, Maura Malinska, Anna A. Hoser and Krzysztof Woźniak

Molecules 2021, 26(12), 3730; https://doi.org/10.3390/molecules26123730 - 18 Jun 2021

Cited by 10 | Viewed by 3223

Abstract

Quantum crystallography is a fast-developing multidisciplinary area of crystallography. In this work, we analyse the influence of different charge density models (i.e., the multipole model (MM), Hirshfeld atom refinement (HAR), and the transferable aspherical atom model (TAAM)), modelling of the thermal motion of [...] Read more.

Quantum crystallography is a fast-developing multidisciplinary area of crystallography. In this work, we analyse the influence of different charge density models (i.e., the multipole model (MM), Hirshfeld atom refinement (HAR), and the transferable aspherical atom model (TAAM)), modelling of the thermal motion of hydrogen atoms (anisotropic, isotropic, and with the aid of SHADE or NoMoRe), and the type of radiation used (Mo Kα and Cu Kα) on the final results. To achieve this aim, we performed a series of refinements against X-ray diffraction data for three model compounds and compared their final structures, geometries, shapes of ADPs, and charge density distributions. Our results were also supported by theoretical calculations that enabled comparisons of the lattice energies of these structures. It appears that geometrical parameters are better described (closer to the neutron values) when HAR is used; however, bonds to H atoms more closely match neutron values after MM or TAAM refinement. Our analysis shows the superiority of the NoMoRe method in the description of H-atom ADPs. Moreover, the shapes of the ADPs of H atoms, as well as their electron density distributions, were better described with low-resolution Cu Kα data in comparison to low-resolution Mo Kα data. Full article

(This article belongs to the Special Issue Chemical Bonding: A Commemorative Special Issue Honoring Professor Linus Pauling)

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25 pages, 3530 KiB

Open AccessArticle

From Electronegativity towards Reactivity—Searching for a Measure of Atomic Reactivity

by Sture Nordholm

Molecules 2021, 26(12), 3680; https://doi.org/10.3390/molecules26123680 - 16 Jun 2021

Cited by 5 | Viewed by 2952

Abstract

Pauling introduced the concept of electronegativity of an atom which has played an important role in understanding the polarity and ionic character of bonds between atoms. We set out to define a related concept of atomic reactivity in such a way that it [...] Read more.

Pauling introduced the concept of electronegativity of an atom which has played an important role in understanding the polarity and ionic character of bonds between atoms. We set out to define a related concept of atomic reactivity in such a way that it can be quantified and used to predict the stability of covalent bonds in molecules. Guided by the early definition of electronegativity by Mulliken in terms of first ionization energies and Pauling in terms of bond energies, we propose corresponding definitions of atomic reactivity. The main goal of clearly distinguishing the inert gas atoms as nonreactive is fulfilled by three different proposed measures of atomic reactivity. The measure likely to be found most useful is based on the bond energies in atomic hydrides, which are related to atomic reactivities by a geometric average. The origin of the atomic reactivity is found in the symmetry of the atomic environment and related conservation laws which are also the origin of the shell structure of atoms and the periodic table. The reactive atoms are characterized by degenerate or nearly degenerate (several states of the same or nearly the same energy) ground states, while the inert atoms have nondegenerate ground states and no near-degeneracies. We show how to extend the use of the Aufbau model of atomic structure to qualitatively describe atomic reactivity in terms of ground state degeneracy. The symmetry and related conservation laws of atomic electron structures produce a strain (energy increase) in the structure, which we estimate by use of the Thomas-Fermi form of DFT implemented approximately with and without the symmetry and conservation constraints. This simplified and approximate analysis indicates that the total strain energy of an atom correlates strongly with the corresponding atomic reactivity measures but antibonding mechanisms prevent full conversion of strain relaxation to bonding. Full article

(This article belongs to the Special Issue Chemical Bonding: A Commemorative Special Issue Honoring Professor Linus Pauling)

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14 pages, 3596 KiB

Open AccessFeature PaperArticle

Large Stabilization Effects by Intramolecular Beryllium Bonds in Ortho-Benzene Derivatives

by Tsai I-Ting, M. Merced Montero-Campillo, Ibon Alkorta, José Elguero and Manuel Yáñez

Molecules 2021, 26(11), 3401; https://doi.org/10.3390/molecules26113401 - 4 Jun 2021

Cited by 2 | Viewed by 2337

Abstract

Intramolecular interactions are shown to be key for favoring a given structure in systems with a variety of conformers. In ortho-substituted benzene derivatives including a beryllium moiety, beryllium bonds provide very large stabilizations with respect to non-bound conformers and enthalpy differences above [...] Read more.

Intramolecular interactions are shown to be key for favoring a given structure in systems with a variety of conformers. In ortho-substituted benzene derivatives including a beryllium moiety, beryllium bonds provide very large stabilizations with respect to non-bound conformers and enthalpy differences above one hundred kJ·mol⁻¹ are found in the most favorable cases, especially if the newly formed rings are five or six-membered heterocycles. These values are in general significantly larger than hydrogen bonds in 1,2-dihidroxybenzene. Conformers stabilized by a beryllium bond exhibit the typical features of this non-covalent interaction, such as the presence of a bond critical point according to the topology of the electron density, positive Laplacian values, significant geometrical distortions and strong interaction energies between the donor and acceptor quantified by using the Natural Bond Orbital approach. An isodesmic reaction scheme is used as a tool to measure the strength of the beryllium bond in these systems in terms of isodesmic energies (analogous to binding energies), interaction energies and deformation energies. This approach shows that a huge amount of energy is spent on deforming the donor–acceptor pairs to form the new rings. Full article

(This article belongs to the Special Issue Chemical Bonding: A Commemorative Special Issue Honoring Professor Linus Pauling)

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7 pages, 1468 KiB

Open AccessArticle

The Topological Analysis of the ELF_x Localization Function: Quantitative Prediction of Hydrogen Bonds in the Guanine–Cytosine Pair

by Johanna Klein, Paul Fleurat-Lessard and Julien Pilmé

Molecules 2021, 26(11), 3336; https://doi.org/10.3390/molecules26113336 - 1 Jun 2021

Cited by 4 | Viewed by 2855

Abstract

In this contribution, we recall and test a new methodology designed to identify the favorable reaction pathway between two reactants. Applied to the formation of the DNA guanine (G) –cytosine (C) pair, we successfully predict the best orientation between the base pairs held [...] Read more.

In this contribution, we recall and test a new methodology designed to identify the favorable reaction pathway between two reactants. Applied to the formation of the DNA guanine (G) –cytosine (C) pair, we successfully predict the best orientation between the base pairs held together by hydrogen bonds and leading to the formation of the typical Watson Crick structure of the GC pair. Beyond the global minimum, some local stationary points of the targeted pair are also clearly identified. Full article

(This article belongs to the Special Issue Chemical Bonding: A Commemorative Special Issue Honoring Professor Linus Pauling)

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11 pages, 2950 KiB

Open AccessArticle

Fragment-Based Ab Initio Molecular Dynamics Simulation for Combustion

by Liqun Cao, Jinzhe Zeng, Mingyuan Xu, Chih-Hao Chin, Tong Zhu and John Z. H. Zhang

Molecules 2021, 26(11), 3120; https://doi.org/10.3390/molecules26113120 - 23 May 2021

Cited by 1 | Viewed by 3904

Abstract

We develop a fragment-based ab initio molecular dynamics (FB-AIMD) method for efficient dynamics simulation of the combustion process. In this method, the intermolecular interactions are treated by a fragment-based many-body expansion in which three- or higher body interactions are neglected, while two-body interactions [...] Read more.

We develop a fragment-based ab initio molecular dynamics (FB-AIMD) method for efficient dynamics simulation of the combustion process. In this method, the intermolecular interactions are treated by a fragment-based many-body expansion in which three- or higher body interactions are neglected, while two-body interactions are computed if the distance between the two fragments is smaller than a cutoff value. The accuracy of the method was verified by comparing FB-AIMD calculated energies and atomic forces of several different systems with those obtained by standard full system quantum calculations. The computational cost of the FB-AIMD method scales linearly with the size of the system, and the calculation is easily parallelizable. The method is applied to methane combustion as a benchmark. Detailed reaction network of methane reaction is analyzed, and important reaction species are tracked in real time. The current result of methane simulation is in excellent agreement with known experimental findings and with prior theoretical studies. Full article

(This article belongs to the Special Issue Chemical Bonding: A Commemorative Special Issue Honoring Professor Linus Pauling)

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19 pages, 4749 KiB

Open AccessArticle

Anharmonic Thermal Motion Modelling in the Experimental XRD Charge Density Determination of 1-Methyluracil at T = 23 K

by Riccardo Destro, Pietro Roversi, Mario Barzaghi and Leonardo Lo Presti

Molecules 2021, 26(11), 3075; https://doi.org/10.3390/molecules26113075 - 21 May 2021

Cited by 5 | Viewed by 2894

Abstract

The experimental electron density distribution (EDD) of 1-methyluracil (1-MUR) was obtained by single crystal X-ray diffraction (XRD) experiments at 23 K. Four different structural models fitting an extensive set of XRD data to a resolution of (sinθ/λ)_max = 1.143 Å⁻¹ are [...] Read more.

The experimental electron density distribution (EDD) of 1-methyluracil (1-MUR) was obtained by single crystal X-ray diffraction (XRD) experiments at 23 K. Four different structural models fitting an extensive set of XRD data to a resolution of (sinθ/λ)_max = 1.143 Å⁻¹ are compared. Two of the models include anharmonic temperature factors, whose inclusion is supported by the Hamilton test at a 99.95% level of confidence. Positive Fourier residuals up to 0.5 eÅ^–3 in magnitude were found close to the methyl group and in the region of hydrogen bonds. Residual density analysis (RDA) and molecular dynamics simulations in the solid-state demonstrate that these residuals can be likely attributed to unresolved disorder, possibly dynamical and long–range in nature. Atomic volumes and charges, molecular moments up to hexadecapoles, as well as maps of the molecular electrostatic potential were obtained from distributed multipole analysis of the EDD. The derived electrostatic properties neither depend on the details of the multipole model, nor are significantly affected by the explicit inclusion of anharmonicity in the least–squares model. The distribution of atomic charges in 1-MUR is not affected by the crystal environment in a significant way. The quality of experimental findings is discussed in light of in-crystal and gas-phase quantum simulations. Full article

(This article belongs to the Special Issue Chemical Bonding: A Commemorative Special Issue Honoring Professor Linus Pauling)

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22 pages, 3099 KiB

Open AccessArticle

Modeling Adsorption and Optical Properties for the Design of CO₂ Photocatalytic Metal-Organic Frameworks

by Priscila Chacón, Joseelyne G. Hernández-Lima, Adán Bazán-Jiménez and Marco A. García-Revilla

Molecules 2021, 26(10), 3060; https://doi.org/10.3390/molecules26103060 - 20 May 2021

Cited by 5 | Viewed by 3198

Abstract

Four Metal-Organic Frameworks (MOFs) were modeled (IRMOF-C-BF₂, IRMOF-C-(2)-BF₂, IRMOF-C’-BF₂, and IRMOF-C-CH₂BF₂) based on IRMOF-1. A series of linkers, based on Frustrated Lewis Pairs and coumarin moieties, were attached to IRMOF-1 to obtain MOFs [...] Read more.

Four Metal-Organic Frameworks (MOFs) were modeled (IRMOF-C-BF₂, IRMOF-C-(2)-BF₂, IRMOF-C’-BF₂, and IRMOF-C-CH₂BF₂) based on IRMOF-1. A series of linkers, based on Frustrated Lewis Pairs and coumarin moieties, were attached to IRMOF-1 to obtain MOFs with photocatalytic properties. Four different linkers were used: (a) a BF₂ attached to a coumarin moiety at position 3, (b) two BF₂ attached to a coumarin moiety in positions 3 and 7, (c) a BF₂ attached in the coumarin moiety at position 7, and (d) a CH₂BF₂ attached at position 3. An analysis of the adsorption properties of H₂, CO₂, H₂O and possible CO₂ photocatalytic capabilities was performed by means of computational modeling using Density Functional Theory (DFT), Time-Dependent Density Functional (TD-DFT) methods, and periodic quantum chemical wave function approach. The results show that the proposed linkers are good enough to improve the CO₂ adsorption, to hold better bulk properties, and obtain satisfactory optical properties in comparison with IRMOF-1 by itself. Full article

(This article belongs to the Special Issue Chemical Bonding: A Commemorative Special Issue Honoring Professor Linus Pauling)

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10 pages, 1298 KiB

Open AccessArticle

The Neglected Nuclei

by Peter Politzer and Jane S. Murray

Molecules 2021, 26(10), 2982; https://doi.org/10.3390/molecules26102982 - 18 May 2021

Cited by 18 | Viewed by 2454

Abstract

Since the nuclei in a molecule are treated as stationary, it is perhaps natural that interpretations of molecular properties and reactivity have focused primarily upon the electronic density distribution. The role of the nuclei has generally received little explicit consideration. Our objective has [...] Read more.

Since the nuclei in a molecule are treated as stationary, it is perhaps natural that interpretations of molecular properties and reactivity have focused primarily upon the electronic density distribution. The role of the nuclei has generally received little explicit consideration. Our objective has been to at least partially redress this imbalance in emphasis. We discuss a number of examples in which the nuclei play the determining role with respect to molecular properties and reactive behavior. It follows that conventional interpretations based solely upon electronic densities and donating or withdrawing tendencies should be made with caution. Full article

(This article belongs to the Special Issue Chemical Bonding: A Commemorative Special Issue Honoring Professor Linus Pauling)

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12 pages, 854 KiB

Open AccessFeature PaperArticle

Understanding Topological Insulators in Real Space

by Angel Martín Pendás, Francisco Muñoz, Carlos Cardenas and Julia Contreras-García

Molecules 2021, 26(10), 2965; https://doi.org/10.3390/molecules26102965 - 17 May 2021

Cited by 1 | Viewed by 2879

Abstract

A real space understanding of the Su–Schrieffer–Heeger model of polyacetylene is introduced thanks to delocalization indices defined within the quantum theory of atoms in molecules. This approach enables to go beyond the analysis of electron localization usually enabled by topological insulator indices—such as [...] Read more.

A real space understanding of the Su–Schrieffer–Heeger model of polyacetylene is introduced thanks to delocalization indices defined within the quantum theory of atoms in molecules. This approach enables to go beyond the analysis of electron localization usually enabled by topological insulator indices—such as IPR—enabling to differentiate between trivial and topological insulator phases. The approach is based on analyzing the electron delocalization between second neighbors, thus highlighting the relevance of the sublattices induced by chiral symmetry. Moreover, the second neighbor delocalization index,

δ_{i, i + 2}

, also enables to identify the presence of chirality and when it is broken by doping or by eliminating atom pairs (as in the case of odd number of atoms chains). Hints to identify bulk behavior thanks to

δ_{1, 3}

are also provided. Overall, we present a very simple, orbital invariant visualization tool that should help the analysis of chirality (independently of the crystallinity of the system) as well as spreading the concepts of topological behavior thanks to its relationship with well-known chemical concepts. Full article

(This article belongs to the Special Issue Chemical Bonding: A Commemorative Special Issue Honoring Professor Linus Pauling)

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15 pages, 1206 KiB

Open AccessArticle

Multiconfiguration Pair-Density Functional Theory for Transition Metal Silicide Bond Dissociation Energies, Bond Lengths, and State Orderings

by Meagan S. Oakley, Laura Gagliardi and Donald G. Truhlar

Molecules 2021, 26(10), 2881; https://doi.org/10.3390/molecules26102881 - 13 May 2021

Cited by 8 | Viewed by 2652

Abstract

Transition metal silicides are promising materials for improved electronic devices, and this motivates achieving a better understanding of transition metal bonds to silicon. Here we model the ground and excited state bond dissociations of VSi, NbSi, and TaSi using a complete active space [...] Read more.

Transition metal silicides are promising materials for improved electronic devices, and this motivates achieving a better understanding of transition metal bonds to silicon. Here we model the ground and excited state bond dissociations of VSi, NbSi, and TaSi using a complete active space (CAS) wave function and a separated-pair (SP) wave function combined with two post-self-consistent field techniques: complete active space with perturbation theory at second order and multiconfiguration pair-density functional theory. The SP approximation is a multiconfiguration self-consistent field method with a selection of configurations based on generalized valence bond theory without the perfect pairing approximation. For both CAS and SP, the active-space composition corresponds to the nominal correlated-participating-orbital scheme. The ground state and low-lying excited states are explored to predict the state ordering for each molecule, and potential energy curves are calculated for the ground state to compare to experiment. The experimental bond dissociation energies of the three diatomic molecules are predicted with eight on-top pair-density functionals with a typical error of 0.2 eV for a CAS wave function and a typical error of 0.3 eV for the SP approximation. We also provide a survey of the accuracy achieved by the SP and extended separated-pair approximations for a broader set of 25 transition metal–ligand bond dissociation energies. Full article

(This article belongs to the Special Issue Chemical Bonding: A Commemorative Special Issue Honoring Professor Linus Pauling)

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17 pages, 5785 KiB

Open AccessEditor’s ChoiceArticle

Predicting Accurate Lead Structures for Screening Molecular Libraries: A Quantum Crystallographic Approach

by Suman Kumar Mandal and Parthapratim Munshi

Molecules 2021, 26(9), 2605; https://doi.org/10.3390/molecules26092605 - 29 Apr 2021

Cited by 1 | Viewed by 3047

Abstract

Optimization of lead structures is crucial for drug discovery. However, the accuracy of such a prediction using the traditional molecular docking approach remains a major concern. Our study demonstrates that the employment of quantum crystallographic approach-counterpoise corrected kernel energy method (KEM-CP) can improve [...] Read more.

Optimization of lead structures is crucial for drug discovery. However, the accuracy of such a prediction using the traditional molecular docking approach remains a major concern. Our study demonstrates that the employment of quantum crystallographic approach-counterpoise corrected kernel energy method (KEM-CP) can improve the accuracy by and large. We select human aldose reductase at 0.66 Å, cyclin dependent kinase 2 at 2.0 Å and estrogen receptor β at 2.7 Å resolutions with active site environment ranging from highly hydrophilic to moderate to highly hydrophobic and several of their known ligands. Overall, the use of KEM-CP alongside the GoldScore resulted superior prediction than the GoldScore alone. Unlike GoldScore, the KEM-CP approach is neither environment-specific nor structural resolution dependent, which highlights its versatility. Further, the ranking of the ligands based on the KEM-CP results correlated well with that of the experimental IC₅₀ values. This computationally inexpensive yet simple approach is expected to ease the process of virtual screening of potent ligands, and it would advance the drug discovery research. Full article

(This article belongs to the Special Issue Chemical Bonding: A Commemorative Special Issue Honoring Professor Linus Pauling)

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31 pages, 4332 KiB

Open AccessArticle

Study of Beryllium, Magnesium, and Spodium Bonds to Carbenes and Carbodiphosphoranes

by Mirosław Jabłoński

Molecules 2021, 26(8), 2275; https://doi.org/10.3390/molecules26082275 - 14 Apr 2021

Cited by 21 | Viewed by 3336

Abstract

The aim of this article is to present results of theoretical study on the properties of C⋯M bonds, where C is either a carbene or carbodiphosphorane carbon atom and M is an acidic center of MX

_{2}

(M = Be, Mg, Zn). Due [...] Read more.

The aim of this article is to present results of theoretical study on the properties of C⋯M bonds, where C is either a carbene or carbodiphosphorane carbon atom and M is an acidic center of MX

_{2}

(M = Be, Mg, Zn). Due to the rarity of theoretical data regarding the C⋯Zn bond (i.e., the zinc bond), the main focus is placed on comparing the characteristics of this interaction with C⋯Be (beryllium bond) and C⋯Mg (magnesium bond). For this purpose, theoretical studies (

ω

B97X-D/6-311++G(2df,2p)) have been performed for a large group of dimers formed by MX

_{2}

(X = H, F, Cl, Br, Me) and either a carbene ((NH

_{2}

)

_{2}

C, imidazol-2-ylidene, imidazolidin-2-ylidene, tetrahydropyrymid-2-ylidene, cyclopropenylidene) or carbodiphosphorane ((PH

_{3}

)

_{2}

C, (NH

_{3}

)

_{2}

C) molecule. The investigated dimers are characterized by a very strong charge transfer effect from either the carbene or carbodiphosphorane molecule to the MX

_{2}

one. This may even be over six times as strong as in the water dimer. According to the QTAIM and NCI method, the zinc bond is not very different than the beryllium bond, with both featuring a significant covalent contribution. However, the zinc bond should be definitely stronger if delocalization index is considered. Full article

(This article belongs to the Special Issue Chemical Bonding: A Commemorative Special Issue Honoring Professor Linus Pauling)

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22 pages, 8402 KiB

Open AccessArticle

Hydrogen Bonding in Natural and Unnatural Base Pairs—A Local Vibrational Mode Study

by Nassim Beiranvand, Marek Freindorf and Elfi Kraka

Molecules 2021, 26(8), 2268; https://doi.org/10.3390/molecules26082268 - 14 Apr 2021

Cited by 33 | Viewed by 3789

Abstract

In this work hydrogen bonding in a diverse set of 36 unnatural and the three natural Watson Crick base pairs adenine (A)–thymine (T), adenine (A)–uracil (U) and guanine (G)–cytosine (C) was assessed utilizing local vibrational force constants derived from the local mode analysis, [...] Read more.

In this work hydrogen bonding in a diverse set of 36 unnatural and the three natural Watson Crick base pairs adenine (A)–thymine (T), adenine (A)–uracil (U) and guanine (G)–cytosine (C) was assessed utilizing local vibrational force constants derived from the local mode analysis, originally introduced by Konkoli and Cremer as a unique bond strength measure based on vibrational spectroscopy. The local mode analysis was complemented by the topological analysis of the electronic density and the natural bond orbital analysis. The most interesting findings of our study are that (i) hydrogen bonding in Watson Crick base pairs is not exceptionally strong and (ii) the N–H⋯N is the most favorable hydrogen bond in both unnatural and natural base pairs while O–H⋯N/O bonds are the less favorable in unnatural base pairs and not found at all in natural base pairs. In addition, the important role of non-classical C–H⋯N/O bonds for the stabilization of base pairs was revealed, especially the role of C–H⋯O bonds in Watson Crick base pairs. Hydrogen bonding in Watson Crick base pairs modeled in the DNA via a QM/MM approach showed that the DNA environment increases the strength of the central N–H⋯N bond and the C–H⋯O bonds, and at the same time decreases the strength of the N–H⋯O bond. However, the general trends observed in the gas phase calculations remain unchanged. The new methodology presented and tested in this work provides the bioengineering community with an efficient design tool to assess and predict the type and strength of hydrogen bonding in artificial base pairs. Full article

(This article belongs to the Special Issue Chemical Bonding: A Commemorative Special Issue Honoring Professor Linus Pauling)

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5 pages, 371 KiB

Open AccessArticle

Was Pauling Mistaken about Metals?

by Andreas Savin

Molecules 2021, 26(7), 1930; https://doi.org/10.3390/molecules26071930 - 30 Mar 2021

Cited by 3 | Viewed by 1995

Abstract

Pauling described metallic bonds using resonance. The maximum probability domains in the Kronig–Penney model can show a picture of it. When the walls are opaque (and the band gap is large) the maximum probability domain for an electron pair essentially corresponds to the [...] Read more.

Pauling described metallic bonds using resonance. The maximum probability domains in the Kronig–Penney model can show a picture of it. When the walls are opaque (and the band gap is large) the maximum probability domain for an electron pair essentially corresponds to the region between the walls: the electron pairs are localized within two consecutive walls. However, when the walls become transparent (and the band gaps closes), the maximum probability domain can be moved through the system without a significant loss in probability. Full article

(This article belongs to the Special Issue Chemical Bonding: A Commemorative Special Issue Honoring Professor Linus Pauling)

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10 pages, 3006 KiB

Open AccessArticle

Nature of the Hydrogen Bond Enhanced Halogen Bond

by Susana Portela and Israel Fernández

Molecules 2021, 26(7), 1885; https://doi.org/10.3390/molecules26071885 - 26 Mar 2021

Cited by 9 | Viewed by 3098

Abstract

The factors responsible for the enhancement of the halogen bond by an adjacent hydrogen bond have been quantitatively explored by means of state-of-the-art computational methods. It is found that the strength of a halogen bond is enhanced by ca. 3 kcal/mol when the [...] Read more.

The factors responsible for the enhancement of the halogen bond by an adjacent hydrogen bond have been quantitatively explored by means of state-of-the-art computational methods. It is found that the strength of a halogen bond is enhanced by ca. 3 kcal/mol when the halogen donor simultaneously operates as a halogen bond donor and a hydrogen bond acceptor. This enhancement is the result of both stronger electrostatic and orbital interactions between the XB donor and the XB acceptor, which indicates a significant degree of covalency in these halogen bonds. In addition, the halogen bond strength can be easily tuned by modifying the electron density of the aryl group of the XB donor as well as the acidity of the hydrogen atoms responsible for the hydrogen bond. Full article

(This article belongs to the Special Issue Chemical Bonding: A Commemorative Special Issue Honoring Professor Linus Pauling)

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13 pages, 15707 KiB

Open AccessArticle

Deformation Potentials: Towards a Systematic Way beyond the Atomic Fragment Approach in Orbital-Free Density Functional Theory

by Kati Finzel

Molecules 2021, 26(6), 1539; https://doi.org/10.3390/molecules26061539 - 11 Mar 2021

Cited by 5 | Viewed by 2296

Abstract

This work presents a method to move beyond the recently introduced atomic fragment approximation. Like the bare atomic fragment approach, the new method is an ab initio, parameter-free, orbital-free implementation of density functional theory based on the bifunctional formalism that treats the potential [...] Read more.

This work presents a method to move beyond the recently introduced atomic fragment approximation. Like the bare atomic fragment approach, the new method is an ab initio, parameter-free, orbital-free implementation of density functional theory based on the bifunctional formalism that treats the potential and the electron density as two separate variables, and provides access to the Kohn–Sham Pauli kinetic energy for an appropriately chosen Pauli potential. In the present ansatz, the molecular Pauli potential is approximated by the sum of the bare atomic fragment approach, and a so-called deformation potential that takes the interaction between the atoms into account. It is shown that this model can reproduce the bond-length contraction due to multiple bonding within the list of second-row homonuclear dimers. The present model only relies on the electron densities of the participating atoms, which themselves are represented by a simple monopole expansion. Thus, the bond-length contraction can be rationalized without referring to the angular quantum numbers of the participating atoms. Full article

(This article belongs to the Special Issue Chemical Bonding: A Commemorative Special Issue Honoring Professor Linus Pauling)

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13 pages, 2722 KiB

Open AccessArticle

A Valence-Bond-Based Multiconfigurational Density Functional Theory: The λ-DFVB Method Revisited

by Peikun Zheng, Chenru Ji, Fuming Ying, Peifeng Su and Wei Wu

Molecules 2021, 26(3), 521; https://doi.org/10.3390/molecules26030521 - 20 Jan 2021

Cited by 5 | Viewed by 5393

Abstract

A recently developed valence-bond-based multireference density functional theory, named λ-DFVB, is revisited in this paper. λ-DFVB remedies the double-counting error of electron correlation by decomposing the electron–electron interactions into the wave function term and density functional term with a variable parameter λ. The [...] Read more.

A recently developed valence-bond-based multireference density functional theory, named λ-DFVB, is revisited in this paper. λ-DFVB remedies the double-counting error of electron correlation by decomposing the electron–electron interactions into the wave function term and density functional term with a variable parameter λ. The λ value is defined as a function of the free valence index in our previous scheme, denoted as λ-DFVB(K) in this paper. Here we revisit the λ-DFVB method and present a new scheme based on natural orbital occupation numbers (NOONs) for parameter λ, named λ-DFVB(IS), to simplify the process of λ-DFVB calculation. In λ-DFVB(IS), the parameter λ is defined as a function of NOONs, which are straightforwardly determined from the many-electron wave function of the molecule. Furthermore, λ-DFVB(IS) does not involve further self-consistent field calculation after performing the valence bond self-consistent field (VBSCF) calculation, and thus, the computational effort in λ-DFVB(IS) is approximately the same as the VBSCF method, greatly reduced from λ-DFVB(K). The performance of λ-DFVB(IS) was investigated on a broader range of molecular properties, including equilibrium bond lengths and dissociation energies, atomization energies, atomic excitation energies, and chemical reaction barriers. The computational results show that λ-DFVB(IS) is more robust without losing accuracy and comparable in accuracy to high-level multireference wave function methods, such as CASPT2. Full article

(This article belongs to the Special Issue Chemical Bonding: A Commemorative Special Issue Honoring Professor Linus Pauling)

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19 pages, 3654 KiB

Open AccessArticle

Comparison of Bifurcated Halogen with Hydrogen Bonds

by Steve Scheiner

Molecules 2021, 26(2), 350; https://doi.org/10.3390/molecules26020350 - 12 Jan 2021

Cited by 13 | Viewed by 3216

Abstract

Bifurcated halogen bonds are constructed with FBr and FI as Lewis acids, paired with NH₃ and NCH bases. The first type considered places two bases together with a single acid, while the reverse case of two acids sharing a single base constitutes [...] Read more.

Bifurcated halogen bonds are constructed with FBr and FI as Lewis acids, paired with NH₃ and NCH bases. The first type considered places two bases together with a single acid, while the reverse case of two acids sharing a single base constitutes the second type. These bifurcated systems are compared with the analogous H-bonds wherein FH serves as the acid. In most cases, a bifurcated system is energetically inferior to a single linear bond. There is a larger energetic cost to forcing the single σ-hole of an acid to interact with a pair of bases, than the other way around where two acids engage with the lone pair of a single base. In comparison to FBr and FI, the H-bonding FH acid is better able to participate in a bifurcated sharing with two bases. This behavior is traced to the properties of the monomers, in particular the specific shape of the molecular electrostatic potential, the anisotropy of the orbitals of the acid and base that interact directly with one another, and the angular extent of the total electron density of the two molecules. Full article

(This article belongs to the Special Issue Chemical Bonding: A Commemorative Special Issue Honoring Professor Linus Pauling)

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13 pages, 2324 KiB

Open AccessArticle

Metal–Metal Bond in the Light of Pauling’s Rules

by Elena Levi, Doron Aurbach and Carlo Gatti

Molecules 2021, 26(2), 304; https://doi.org/10.3390/molecules26020304 - 8 Jan 2021

Cited by 8 | Viewed by 3079

Abstract

About 70 years ago, in the framework of his theory of chemical bonding, Pauling proposed an empirical correlation between the bond valences (or effective bond orders (BOs)) and the bond lengths. Till now, this simple correlation, basic in the bond valence model (BVM), [...] Read more.

About 70 years ago, in the framework of his theory of chemical bonding, Pauling proposed an empirical correlation between the bond valences (or effective bond orders (BOs)) and the bond lengths. Till now, this simple correlation, basic in the bond valence model (BVM), is widely used in crystal chemistry, but it was considered irrelevant for metal–metal bonds. An extensive analysis of the quantum chemistry data computed in the last years confirms very well the validity of Pauling’s correlation for both localized and delocalized interactions. This paper briefly summarizes advances in the application of the BVM for compounds with TM–TM bonds (TM = transition metal) and provides further convincing examples. In particular, the BVM model allows for very simple but precise calculations of the effective BOs of the TM–TM interactions. Based on the comparison between formal and effective BOs, we can easily describe steric and electrostatic effects. A possible influence of these effects on materials stability is discussed. Full article

(This article belongs to the Special Issue Chemical Bonding: A Commemorative Special Issue Honoring Professor Linus Pauling)

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Review

Jump to: Research, Other

31 pages, 13862 KiB

Open AccessReview

The Relevance of Experimental Charge Density Analysis in Unraveling Noncovalent Interactions in Molecular Crystals

by Sajesh P. Thomas, Amol G. Dikundwar, Sounak Sarkar, Mysore S. Pavan, Rumpa Pal, Venkatesha R. Hathwar and Tayur N. Guru Row

Molecules 2022, 27(12), 3690; https://doi.org/10.3390/molecules27123690 - 8 Jun 2022

Cited by 18 | Viewed by 3087

Abstract

The work carried out by our research group over the last couple of decades in the context of quantitative crystal engineering involves the analysis of intermolecular interactions such as carbon (tetrel) bonding, pnicogen bonding, chalcogen bonding, and halogen bonding using experimental charge density [...] Read more.

The work carried out by our research group over the last couple of decades in the context of quantitative crystal engineering involves the analysis of intermolecular interactions such as carbon (tetrel) bonding, pnicogen bonding, chalcogen bonding, and halogen bonding using experimental charge density methodology is reviewed. The focus is to extract electron density distribution in the intermolecular space and to obtain guidelines to evaluate the strength and directionality of such interactions towards the design of molecular crystals with desired properties. Following the early studies on halogen bonding interactions, several “sigma-hole” interaction types with similar electrostatic origins have been explored in recent times for their strength, origin, and structural consequences. These include interactions such as carbon (tetrel) bonding, pnicogen bonding, chalcogen bonding, and halogen bonding. Experimental X-ray charge density analysis has proved to be a powerful tool in unraveling the strength and electronic origin of such interactions, providing insights beyond the theoretical estimates from gas-phase molecular dimer calculations. In this mini-review, we outline some selected contributions from the X-ray charge density studies to the field of non-covalent interactions (NCIs) involving elements of the groups 14–17 of the periodic table. Quantitative insights into the nature of these interactions obtained from the experimental electron density distribution and subsequent topological analysis by the quantum theory of atoms in molecules (QTAIM) have been discussed. A few notable examples of weak interactions have been presented in terms of their experimental charge density features. These examples reveal not only the strength and beauty of X-ray charge density multipole modeling as an advanced structural chemistry tool but also its utility in providing experimental benchmarks for the theoretical studies of weak interactions in crystals. Full article

(This article belongs to the Special Issue Chemical Bonding: A Commemorative Special Issue Honoring Professor Linus Pauling)

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24 pages, 5505 KiB

Open AccessReview

Density-Based Descriptors of Redox Reactions Involving Transition Metal Compounds as a Reality-Anchored Framework: A Perspective

by Daniel Koch, Mohamed Chaker, Manabu Ihara and Sergei Manzhos

Molecules 2021, 26(18), 5541; https://doi.org/10.3390/molecules26185541 - 13 Sep 2021

Cited by 5 | Viewed by 2868

Abstract

Description of redox reactions is critically important for understanding and rational design of materials for electrochemical technologies, including metal-ion batteries, catalytic surfaces, or redox-flow cells. Most of these technologies utilize redox-active transition metal compounds due to their rich chemistry and their beneficial physical [...] Read more.

Description of redox reactions is critically important for understanding and rational design of materials for electrochemical technologies, including metal-ion batteries, catalytic surfaces, or redox-flow cells. Most of these technologies utilize redox-active transition metal compounds due to their rich chemistry and their beneficial physical and chemical properties for these types of applications. A century since its introduction, the concept of formal oxidation states (FOS) is still widely used for rationalization of the mechanisms of redox reactions, but there exists a well-documented discrepancy between FOS and the electron density-derived charge states of transition metal ions in their bulk and molecular compounds. We summarize our findings and those of others which suggest that density-driven descriptors are, in certain cases, better suited to characterize the mechanism of redox reactions, especially when anion redox is involved, which is the blind spot of the FOS ansatz. Full article

(This article belongs to the Special Issue Chemical Bonding: A Commemorative Special Issue Honoring Professor Linus Pauling)

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13 pages, 1157 KiB

Open AccessReview

The Valence-Bond (VB) Model and Its Intimate Relationship to the Symmetric or Permutation Group

by Marco Antonio Chaer Nascimento

Molecules 2021, 26(15), 4524; https://doi.org/10.3390/molecules26154524 - 27 Jul 2021

Cited by 3 | Viewed by 2528

Abstract

VB and molecular orbital (MO) models are normally distinguished by the fact the first looks at molecules as a collection of atoms held together by chemical bonds while the latter adopts the view that each molecule should be regarded as an independent entity [...] Read more.

VB and molecular orbital (MO) models are normally distinguished by the fact the first looks at molecules as a collection of atoms held together by chemical bonds while the latter adopts the view that each molecule should be regarded as an independent entity built up of electrons and nuclei and characterized by its molecular structure. Nevertheless, there is a much more fundamental difference between these two models which is only revealed when the symmetries of the many-electron Hamiltonian are fully taken into account: while the VB and MO wave functions exhibit the point-group symmetry, whenever present in the many-electron Hamiltonian, only VB wave functions exhibit the permutation symmetry, which is always present in the many-electron Hamiltonian. Practically all the conflicts among the practitioners of the two models can be traced down to the lack of permutation symmetry in the MO wave functions. Moreover, when examined from the permutation group perspective, it becomes clear that the concepts introduced by Pauling to deal with molecules can be equally applied to the study of the atomic structure. In other words, as strange as it may sound, VB can be extended to the study of atoms and, therefore, is a much more general model than MO. Full article

(This article belongs to the Special Issue Chemical Bonding: A Commemorative Special Issue Honoring Professor Linus Pauling)

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25 pages, 1826 KiB

Open AccessReview

Electrostatic Potential Topology for Probing Molecular Structure, Bonding and Reactivity

by Shridhar R. Gadre, Cherumuttathu H. Suresh and Neetha Mohan

Molecules 2021, 26(11), 3289; https://doi.org/10.3390/molecules26113289 - 29 May 2021

Cited by 122 | Viewed by 5759

Abstract

Following the pioneering investigations of Bader on the topology of molecular electron density, the topology analysis of its sister field viz. molecular electrostatic potential (MESP) was taken up by the authors’ groups. Through these studies, MESP topology emerged as a powerful tool for [...] Read more.

Following the pioneering investigations of Bader on the topology of molecular electron density, the topology analysis of its sister field viz. molecular electrostatic potential (MESP) was taken up by the authors’ groups. Through these studies, MESP topology emerged as a powerful tool for exploring molecular bonding and reactivity patterns. The MESP topology features are mapped in terms of its critical points (CPs), such as bond critical points (BCPs), while the minima identify electron-rich locations, such as lone pairs and π-bonds. The gradient paths of MESP vividly bring out the atoms-in-molecule picture of neutral molecules and anions. The MESP-based characterization of a molecule in terms of electron-rich and -deficient regions provides a robust prediction about its interaction with other molecules. This leads to a clear picture of molecular aggregation, hydrogen bonding, lone pair–π interactions, π-conjugation, aromaticity and reaction mechanisms. This review summarizes the contributions of the authors’ groups over the last three decades and those of the other active groups towards understanding chemical bonding, molecular recognition, and reactivity through topology analysis of MESP. Full article

(This article belongs to the Special Issue Chemical Bonding: A Commemorative Special Issue Honoring Professor Linus Pauling)

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24 pages, 3625 KiB

Open AccessFeature PaperReview

Valence Bond Theory—Its Birth, Struggles with Molecular Orbital Theory, Its Present State and Future Prospects

by Sason Shaik, David Danovich and Philippe C. Hiberty

Molecules 2021, 26(6), 1624; https://doi.org/10.3390/molecules26061624 - 15 Mar 2021

Cited by 32 | Viewed by 11988

Abstract

This essay describes the successive births of valence bond (VB) theory during 1916–1931. The alternative molecular orbital (MO) theory was born in the late 1920s. The presence of two seemingly different descriptions of molecules by the two theories led to struggles between the [...] Read more.

This essay describes the successive births of valence bond (VB) theory during 1916–1931. The alternative molecular orbital (MO) theory was born in the late 1920s. The presence of two seemingly different descriptions of molecules by the two theories led to struggles between the main proponents, Linus Pauling and Robert Mulliken, and their supporters. Until the 1950s, VB theory was dominant, and then it was eclipsed by MO theory. The struggles will be discussed, as well as the new dawn of VB theory, and its future. Full article

(This article belongs to the Special Issue Chemical Bonding: A Commemorative Special Issue Honoring Professor Linus Pauling)

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Other

Jump to: Research, Review

14 pages, 1220 KiB

Open AccessEssay

A Critical Look at Linus Pauling’s Influence on the Understanding of Chemical Bonding

by Sudip Pan and Gernot Frenking

Molecules 2021, 26(15), 4695; https://doi.org/10.3390/molecules26154695 - 3 Aug 2021

Cited by 11 | Viewed by 5148

Abstract

The influence of Linus Pauling on the understanding of chemical bonding is critically examined. Pauling deserves credit for presenting a connection between the quantum theoretical description of chemical bonding and Gilbert Lewis’s classical bonding model of localized electron pair bonds for a wide [...] Read more.

The influence of Linus Pauling on the understanding of chemical bonding is critically examined. Pauling deserves credit for presenting a connection between the quantum theoretical description of chemical bonding and Gilbert Lewis’s classical bonding model of localized electron pair bonds for a wide range of chemistry. Using the concept of resonance that he introduced, he was able to present a consistent description of chemical bonding for molecules, metals, and ionic crystals which was used by many chemists and subsequently found its way into chemistry textbooks. However, his one-sided restriction to the valence bond method and his rejection of the molecular orbital approach hindered further development of chemical bonding theory for a while and his close association of the heuristic Lewis binding model with the quantum chemical VB approach led to misleading ideas until today. Full article

(This article belongs to the Special Issue Chemical Bonding: A Commemorative Special Issue Honoring Professor Linus Pauling)

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