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11 pages, 1255 KiB

Open AccessArticle

Analysis of the Gas Phase Acidity of Substituted Benzoic Acids Using Density Functional Concepts

by Jorge A. Amador-Balderas, Michael-Adán Martínez-Sánchez, Ramsés E. Ramírez, Francisco Méndez and Francisco J. Meléndez

Molecules 2020, 25(7), 1631; https://doi.org/10.3390/molecules25071631 - 2 Apr 2020

Cited by 4 | Viewed by 2435

Abstract

A theoretical study of the effect of the substituent Z on the gas phase acidity of substituted benzoic acids ZC₆H₄COOH in terms of density functional theory descriptors (chemical potential, softness and Fukui function) is presented. The calculated gas phase [...] Read more.

A theoretical study of the effect of the substituent Z on the gas phase acidity of substituted benzoic acids ZC₆H₄COOH in terms of density functional theory descriptors (chemical potential, softness and Fukui function) is presented. The calculated gas phase Δ_acidG° values obtained were close to the experimental ones reported in the literature. The good relationship between the Δ_acidG° values and the electronegativity of ZC₆H₄COOH and its fragments, suggested a better importance of the inductive than polarizability contributions. The balance of inductive and resonance contributions of the substituent in the acidity of substituted benzoic acids showed that the highest inductive and resonance effects were for the -SO₂CF₃ and -NH₂ substituents in the para- and ortho-position, respectively. The Fukui function confirmed that the electron-releasing substituent attached to the phenyl ring of benzoic acid decreased the acidity in the trend ortho > meta > para, and the electron-withdrawing substituent increased the acidity in the trend ortho < meta < para. Full article

(This article belongs to the Special Issue The Molecular Electron Density Theory in Organic Chemistry)

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16 pages, 4226 KiB

Open AccessArticle

Unveiling the Different Chemical Reactivity of Diphenyl Nitrilimine and Phenyl Nitrile Oxide in [3+2] Cycloaddition Reactions with (R)-Carvone through the Molecular Electron Density Theory

by Mar Ríos-Gutiérrez, Luis R. Domingo, M’hamed Esseffar, Ali Oubella and My Youssef Ait Itto

Molecules 2020, 25(5), 1085; https://doi.org/10.3390/molecules25051085 - 28 Feb 2020

Cited by 29 | Viewed by 2937

Abstract

The [3+2] cycloaddition (32CA) reactions of diphenyl nitrilimine and phenyl nitrile oxide with (R)-carvone have been studied within the Molecular Electron Density Theory (MEDT). Electron localisation function (ELF) analysis of these three-atom-components (TACs) permits its characterisation as carbenoid and zwitterionic TACs, thus having [...] Read more.

The [3+2] cycloaddition (32CA) reactions of diphenyl nitrilimine and phenyl nitrile oxide with (R)-carvone have been studied within the Molecular Electron Density Theory (MEDT). Electron localisation function (ELF) analysis of these three-atom-components (TACs) permits its characterisation as carbenoid and zwitterionic TACs, thus having a different reactivity. The analysis of the conceptual Density Functional Theory (DFT) indices accounts for the very low polar character of these 32CA reactions, while analysis of the DFT energies accounts for the opposite chemoselectivity experimentally observed. Topological analysis of the ELF along the single bond formation makes it possible to characterise the mechanisms of these 32CA reactions as cb- and zw-type. The present MEDT study supports the proposed classification of 32CA reactions into pdr-, pmr-, cb- and zw-type, thus asserting MEDT as the theory able to explain chemical reactivity in Organic Chemistry. Full article

(This article belongs to the Special Issue The Molecular Electron Density Theory in Organic Chemistry)

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18 pages, 3298 KiB

Open AccessArticle

A Molecular Electron Density Theory Study of the Synthesis of Spirobipyrazolines through the Domino Reaction of Nitrilimines with Allenoates

by Luis R. Domingo, Fatemeh Ghodsi and Mar Ríos-Gutiérrez

Molecules 2019, 24(22), 4159; https://doi.org/10.3390/molecules24224159 - 16 Nov 2019

Cited by 11 | Viewed by 2539

Abstract

The reaction of diphenyl nitrilimine (NI) with methyl 1-methyl-allenoate yielding a spirobipyrazoline has been studied within molecular electron density theory (MEDT) at the MPWB1K/6-311G(d) computational level in dichloromethane. This reaction is a domino process that comprises two consecutive 32CA reactions with the formation [...] Read more.

The reaction of diphenyl nitrilimine (NI) with methyl 1-methyl-allenoate yielding a spirobipyrazoline has been studied within molecular electron density theory (MEDT) at the MPWB1K/6-311G(d) computational level in dichloromethane. This reaction is a domino process that comprises two consecutive 32CA reactions with the formation of a pyrazoline intermediate. Analysis of the relative Gibbs free energies indicates that both 32CA reactions are highly regioselective, the first one being also completely chemoselective, in agreement with the experimental outcomes. The geometries of the TSs indicate that they are associated to asynchronous bond formation processes in which the shorter distance involves the C1 carbon of diphenyl NI. Despite the zwitterionic structure of diphenyl NI, the appearance of a pseudoradical structure at the beginning of the reaction path, with a very low energy cost, suggests that the 32CA reaction between diphenyl NI, a strong nucleophile, and the allenoate, a moderate electrophile, should be mechanistically considered on the borderline between pmr-type and cb-type 32CA reactions, somewhat closer to the latter. Full article

(This article belongs to the Special Issue The Molecular Electron Density Theory in Organic Chemistry)

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10 pages, 912 KiB

Open AccessArticle

CDFT-Based Reactivity Descriptors as a Useful MEDT Chemoinformatics Tool for the Study of the Virotoxin Family of Fungal Peptides

by Norma Flores-Holguín, Juan Frau and Daniel Glossman-Mitnik

Molecules 2019, 24(15), 2707; https://doi.org/10.3390/molecules24152707 - 25 Jul 2019

Cited by 5 | Viewed by 2711

Abstract

Virotoxins are monocyclic peptides formed by at least five different compounds: alaviroidin, viroisin, deoxoviroisin, viroidin and deoxovirodin. These are toxic peptides singularly found in Amanita virosa mushrooms. Here we perform computational studies on the structural and electronic conformations of these peptides using the [...] Read more.

Virotoxins are monocyclic peptides formed by at least five different compounds: alaviroidin, viroisin, deoxoviroisin, viroidin and deoxovirodin. These are toxic peptides singularly found in Amanita virosa mushrooms. Here we perform computational studies on the structural and electronic conformations of these peptides using the MN12SX/Def2TZVP/H2O chemistry model to investigate their chemical reactivity. CDFT-based descriptors (for Conceptual Density Functional Theory) (e.g., Parr functions and Nucleophilicity) are also considered. At the same time, other properties (e.g., pKas) will be determined and used to study virotoxins solubility and to inform decisions about repurposing these agents in medicinal chemistry. Full article

(This article belongs to the Special Issue The Molecular Electron Density Theory in Organic Chemistry)

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14 pages, 2493 KiB

Open AccessArticle

A Molecular Electron Density Theory Study of the Chemoselectivity, Regioselectivity, and Diastereofacial Selectivity in the Synthesis of an Anticancer Spiroisoxazoline derived from α-Santonin

by Luis R. Domingo, Mar Ríos-Gutiérrez and Nivedita Acharjee

Molecules 2019, 24(5), 832; https://doi.org/10.3390/molecules24050832 - 26 Feb 2019

Cited by 40 | Viewed by 3194

Abstract

The [3 + 2] cycloaddition (32CA) reaction of an α-santonin derivative, which has an exocyclic C–C double bond, with p-bromophenyl nitrile oxide yielding only one spiroisoxazoline, has been studied within the molecular electron density theory (MEDT) at the MPWB1K/6-311G(d,p) computational level. Analysis [...] Read more.

The [3 + 2] cycloaddition (32CA) reaction of an α-santonin derivative, which has an exocyclic C–C double bond, with p-bromophenyl nitrile oxide yielding only one spiroisoxazoline, has been studied within the molecular electron density theory (MEDT) at the MPWB1K/6-311G(d,p) computational level. Analysis of the conceptual density functional theory (CDFT) reactivity indices and the global electron density transfer (GEDT) account for the non-polar character of this zwitterionic-type 32CA reaction, which presents an activation enthalpy of 13.3 kcal·mol⁻¹. This 32CA reaction takes place with total ortho regioselectivity and syn diastereofacial selectivity involving the exocyclic C–C double bond, which is in complete agreement with the experimental outcomes. While the C–C bond formation involving the β-conjugated carbon of α-santonin derivative is more favorable than the C–O one, which is responsible for the ortho regioselectivity, the favorable electronic interactions taking place between the oxygen of the nitrile oxide and two axial hydrogen atoms of the α-santonin derivative are responsible for the syn diastereofacial selectivity. Full article

(This article belongs to the Special Issue The Molecular Electron Density Theory in Organic Chemistry)

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28 pages, 9767 KiB

Open AccessArticle

Li and Na Adsorption on Graphene and Graphene Oxide Examined by Density Functional Theory, Quantum Theory of Atoms in Molecules, and Electron Localization Function

by Nicholas Dimakis, Isaiah Salas, Luis Gonzalez, Om Vadodaria, Korinna Ruiz and Muhammad I. Bhatti

Molecules 2019, 24(4), 754; https://doi.org/10.3390/molecules24040754 - 19 Feb 2019

Cited by 41 | Viewed by 5726

Abstract

Adsorption of Li and Na on pristine and defective graphene and graphene oxide (GO) is studied using density functional theory (DFT) structural and electronic calculations, quantum theory of atoms in molecules (QTAIM), and electron localization function (ELF) analyses. DFT calculations show that Li [...] Read more.

Adsorption of Li and Na on pristine and defective graphene and graphene oxide (GO) is studied using density functional theory (DFT) structural and electronic calculations, quantum theory of atoms in molecules (QTAIM), and electron localization function (ELF) analyses. DFT calculations show that Li and Na adsorptions on pristine graphene are not stable at all metal coverages examined here. However, the presence of defects on graphene support stabilizes both Li and Na adsorptions. Increased Li and Na coverages cause metal nucleation and weaken adsorption. Defective graphene is associated with the presence of band gaps and, thus, Li and Na adsorptions can be used to tune these gaps. Electronic calculations show that Li– and Na–graphene interactions are Coulombic: as Li and Na coverages increase, the metal valences partially hybridize with the graphene bands and weaken metal–graphene support interactions. However, for Li adsorption on single vacancy graphene, QTAIM, ELF, and overlap populations calculations show that the Li-C bond has some covalent character. The Li and Na adsorptions on GO are significantly stronger than on graphene and strengthen upon increased coverages. This is due to Li and Na forming bonds with both carbon and oxygen GO atoms. QTAIM and ELF are used to analyze the metal–C and metal–metal bonds (when metal nucleation is present). The Li and Na clusters may contain both covalent and metallic intra metal–metal bonds: This effect is related to the adsorption support selection. ELF bifurcation diagrams show individual metal–C and metal–metal interactions, as Li and Na are adsorbed on graphene and GO, at the metal coverages examined here. Full article

(This article belongs to the Special Issue The Molecular Electron Density Theory in Organic Chemistry)

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12 pages, 2341 KiB

Open AccessArticle

Understanding the Molecular Mechanism of the Rearrangement of Internal Nitronic Ester into Nitronorbornene in Light of the MEDT Study

by Agnieszka Kącka-Zych

Molecules 2019, 24(3), 462; https://doi.org/10.3390/molecules24030462 - 28 Jan 2019

Cited by 17 | Viewed by 2693

Abstract

The characterization of the structure of nitronic esters and their rearrangement into nitronorbornene reactions has been analyzed within the Molecular Electron Density Theory (MEDT) using Density Functional Theory (DFT) calculations at the B3LYP/6-31G(d) computational level. Quantum-chemical calculations indicate that this rearrangement takes place [...] Read more.

The characterization of the structure of nitronic esters and their rearrangement into nitronorbornene reactions has been analyzed within the Molecular Electron Density Theory (MEDT) using Density Functional Theory (DFT) calculations at the B3LYP/6-31G(d) computational level. Quantum-chemical calculations indicate that this rearrangement takes place according to a one-step mechanism. The sequential bonding changes received from the Bonding Evolution Theory (BET) analysis of the rearrangement of internal nitronic ester to nitronorbornene allowed us to distinguish seven different phases. This fact clearly contradicts the formerly-proposed concerted pericyclic mechanism. Full article

(This article belongs to the Special Issue The Molecular Electron Density Theory in Organic Chemistry)

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Review

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23 pages, 3835 KiB

Open AccessEditor’s ChoiceReview

How Far Can One Push the Noble Gases Towards Bonding?: A Personal Account

by Ranajit Saha, Gourhari Jana, Sudip Pan, Gabriel Merino and Pratim Kumar Chattaraj

Molecules 2019, 24(16), 2933; https://doi.org/10.3390/molecules24162933 - 13 Aug 2019

Cited by 33 | Viewed by 6756

Abstract

Noble gases (Ngs) are the least reactive elements in the periodic table towards chemical bond formation when compared with other elements because of their completely filled valence electronic configuration. Very often, extreme conditions like low temperatures, high pressures and very reactive reagents are [...] Read more.

Noble gases (Ngs) are the least reactive elements in the periodic table towards chemical bond formation when compared with other elements because of their completely filled valence electronic configuration. Very often, extreme conditions like low temperatures, high pressures and very reactive reagents are required for them to form meaningful chemical bonds with other elements. In this personal account, we summarize our works to date on Ng complexes where we attempted to theoretically predict viable Ng complexes having strong bonding to synthesize them under close to ambient conditions. Our works cover three different types of Ng complexes, viz., non-insertion of NgXY type, insertion of XNgY type and Ng encapsulated cage complexes where X and Y can represent any atom or group of atoms. While the first category of Ng complexes can be thermochemically stable at a certain temperature depending on the strength of the Ng-X bond, the latter two categories are kinetically stable, and therefore, their viability and the corresponding conditions depend on the size of the activation barrier associated with the release of Ng atom(s). Our major focus was devoted to understand the bonding situation in these complexes by employing the available state-of-the-art theoretic tools like natural bond orbital, electron density, and energy decomposition analyses in combination with the natural orbital for chemical valence theory. Intriguingly, these three types of complexes represent three different types of bonding scenarios. In NgXY, the strength of the donor-acceptor Ng→XY interaction depends on the polarizing power of binding the X center to draw the rather rigid electron density of Ng towards itself, and sometimes involvement of such orbitals becomes large enough, particularly for heavier Ng elements, to consider them as covalent bonds. On the other hand, in most of the XNgY cases, Ng forms an electron-shared covalent bond with X while interacting electrostatically with Y representing itself as [XNg]⁺Y⁻. Nevertheless, in some of the rare cases like NCNgNSi, both the C-Ng and Ng-N bonds can be represented as electron-shared covalent bonds. On the other hand, a cage host is an excellent moiety to examine the limits that can be pushed to attain bonding between two Ng atoms (even for He) at high pressure. The confinement effect by a small cage-like B₁₂N₁₂ can even induce some covalent interaction within two He atoms in the He₂@B₁₂N₁₂ complex. Full article

(This article belongs to the Special Issue The Molecular Electron Density Theory in Organic Chemistry)

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