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The Molecular Electron Density Theory: A Modern View of Molecular Reactivity in Organic Chemistry

A special issue of Molecules (ISSN 1420-3049). This special issue belongs to the section "Computational and Theoretical Chemistry".

Deadline for manuscript submissions: closed (30 December 2017) | Viewed by 40185

Special Issue Editors

Prof. Dr. Luis R. Domingo

E-Mail Website
Guest Editor
Department of Organic Chemistry, University of Valencia, Dr. Moliner 50, Burjassot, 46100 Valencia, Spain
Interests: molecular electron density theory (MEDT); theoretical organic chemistry; chemical concepts; structure and reactivity; molecular mechanisms and selectivities; quantum-chemical topology
Special Issues, Collections and Topics in MDPI journals
Prof. Dr. Miquel Solà

E-Mail Website
Guest Editor
Institut de Química Computacional i Catàlisi (IQCC) and Departament de Química, Universitat de Girona, c/ Maria Aurèlia Capmany 6, 17003 Girona, Catalonia, Spain
Interests: computational and theoretical chemistry; density functional theory; conceptual DFT reactivity indices; electron delocalisation; conjugation; aromaticity; molecular clusters; molecular mechanisms; reactivity

Special Issue Information

Dear Colleagues,

Recently, the Molecular Electron Density Theory (MEDT), in which changes in electron density along an organic reaction, and not molecular orbital (MO) interactions, are responsible for the molecular organic reactivity, has been proposed (Molecules 2016, 21, 1319).

Since 1965, the Frontier Molecular Orbital (FMO) theory has been widely used in Organic Chemistry as a theoretical model to study chemical reactivity. However, such as with Schrödinger’s wavefunction, MOs have no physical significance; only the square of the wavefunction is related to the electron density, which is the only physically-observable factor.

Parallel to the establishment of the FMO theory, the Conceptual Density Functional Theory (CDFT), a DFT-subfield that allows the study the molecular reactivity at the ground state, was developed. Later, the Quantum Theory of Atoms in Molecules (QTAIM) and the Electron Localisation Function (ELF), which permit the topological analysis of the molecular electron density, were developed. Finally, Non-Covalent Interaction (NCIs) analyses have been recently proposed for the study of weak interactions.

All these quantum chemical tools, which allow the analysis of the molecular electron density, let know the electronic structure of the species involved in an organic reaction, and thus, to study chemical organic reactivity from a modern point of view based on electron density being the only physical observable.

The present Special Issue will collect theoretical studies based on the MEDT, with the aim of establishing and spreading a new perspective of the chemical organic reactivity based only on the analysis of the molecular electron density.

Keywords

  • Molecular Electron Density Theory
  • Electron Density
  • Chemical Organic Reactivity
  • Reaction Mechanisms
  • Conceptual Density Functional Theory Indices
  • Electron Localisation Function
  • Quantum Theory of Atoms in Molecules
  • Bonding Evolution Theory
  • Non Covalent interactions

Prof. Dr. Luis R. Domingo
Prof. Dr. Miquel Solà
Guest Editors

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Published Papers (7 papers)

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Research

28 pages, 7018 KiB  
Article
Aromaticity as a Guiding Concept for Spectroscopic Features and Nonlinear Optical Properties of Porphyrinoids
by Tatiana Woller, Paul Geerlings, Frank De Proft, Benoît Champagne and Mercedes Alonso
Molecules 2018, 23(6), 1333; https://doi.org/10.3390/molecules23061333 - 1 Jun 2018
Cited by 42 | Viewed by 6665
Abstract
With their versatile molecular topology and aromaticity, porphyrinoid systems combine remarkable chemistry with interesting photophysical properties and nonlinear optical properties. Hence, the field of application of porphyrinoids is very broad ranging from near-infrared dyes to opto-electronic materials. From previous experimental studies, aromaticity emerges [...] Read more.
With their versatile molecular topology and aromaticity, porphyrinoid systems combine remarkable chemistry with interesting photophysical properties and nonlinear optical properties. Hence, the field of application of porphyrinoids is very broad ranging from near-infrared dyes to opto-electronic materials. From previous experimental studies, aromaticity emerges as an important concept in determining the photophysical properties and two-photon absorption cross sections of porphyrinoids. Despite a considerable number of studies on porphyrinoids, few investigate the relationship between aromaticity, UV/vis absorption spectra and nonlinear properties. To assess such structure-property relationships, we performed a computational study focusing on a series of Hückel porphyrinoids to: (i) assess their (anti)aromatic character; (ii) determine the fingerprints of aromaticity on the UV/vis spectra; (iii) evaluate the role of aromaticity on the NLO properties. Using an extensive set of aromaticity descriptors based on energetic, magnetic, structural, reactivity and electronic criteria, the aromaticity of [4n+2] π-electron porphyrinoids was evidenced as was the antiaromaticity for [4n] π-electron systems. In agreement with previous studies, the absorption spectra of aromatic systems display more intense B and Q bands in comparison to their antiaromatic homologues. The nature of these absorption bands was analyzed in detail in terms of polarization, intensity, splitting and composition. Finally, quantities such as the average polarizability and its anisotropy were found to be larger in aromatic systems, whereas first and second hyperpolarizability are influenced by the interplay between aromaticity, planarity and molecular symmetry. To conclude, aromaticity dictates the photophysical properties in porphyrinoids, whereas it is not the only factor determining the magnitude of NLO properties. Full article
(This article belongs to the Special Issue The Molecular Electron Density Theory: A Modern View of Molecular Reactivity in Organic Chemistry)
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15 pages, 397 KiB  
Article
Molecular Reactivity and Absorption Properties of Melanoidin Blue-G1 through Conceptual DFT
by Juan Frau and Daniel Glossman-Mitnik
Molecules 2018, 23(3), 559; https://doi.org/10.3390/molecules23030559 - 2 Mar 2018
Cited by 36 | Viewed by 4858
Abstract
This computational study presents the assessment of eleven density functionals that include CAM-B3LYP, LC-wPBE, M11, M11L, MN12L, MN12SX, N12, N12SX, wB97, wB97X and wB97XD related to the Def2TZVP basis sets together with the Solvation Model Density (SMD) solvation model in calculating the molecular [...] Read more.
This computational study presents the assessment of eleven density functionals that include CAM-B3LYP, LC-wPBE, M11, M11L, MN12L, MN12SX, N12, N12SX, wB97, wB97X and wB97XD related to the Def2TZVP basis sets together with the Solvation Model Density (SMD) solvation model in calculating the molecular properties and structure of the Blue-G1 intermediate melanoidin pigment. The chemical reactivity descriptors for the system are calculated via the conceptual Density Functional Theory (DFT). The choice of the active sites related to the nucleophilic, electrophilic, as well as radical attacks is made by linking them with the Fukui function indices, the electrophilic Parr functions and the condensed dual descriptor Δ f ( r ) . The prediction of the maximum absorption wavelength tends to be considerably accurate relative to its experimental value. The study found the MN12SX and N12SX density functionals to be the most appropriate density functionals in predicting the chemical reactivity of the studied molecule. Full article
(This article belongs to the Special Issue The Molecular Electron Density Theory: A Modern View of Molecular Reactivity in Organic Chemistry)
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10 pages, 1917 KiB  
Article
On the Reaction Mechanism of the 3,4-Dimethoxybenzaldehyde Formation from 1-(3′,4′-Dimethoxyphenyl)Propene
by Sebastián Cuesta, Josefa Arias, Felipe Gallegos, Jans Alzate-Morales and Lorena Meneses
Molecules 2018, 23(2), 412; https://doi.org/10.3390/molecules23020412 - 14 Feb 2018
Cited by 1 | Viewed by 5138
Abstract
Lignin peroxidase (LiP) is an important enzyme for degrading aromatic hydrocarbons not only in nature but also in industry. In the presence of H2O2, this enzyme can easily decompose lignin and analogue compounds under mild conditions. In this reaction [...] Read more.
Lignin peroxidase (LiP) is an important enzyme for degrading aromatic hydrocarbons not only in nature but also in industry. In the presence of H2O2, this enzyme can easily decompose lignin and analogue compounds under mild conditions. In this reaction mechanism, LiP catalyzes the C–C cleavage of a propenyl side chain, being able to produce veratraldehyde (VAD) from 1-(3′,4′-dimethoxyphenyl) propene (DMPP). One of the few and complete proposed mechanisms includes several non-enzymatic reactions. In this study, we performed a computational study to gain insight about the non-enzymatic steps involved in the reaction mechanism of VAD formation from DMPP using LiP as a catalyst. A kinetic characterization of the reaction using the reaction force and the reaction force constant concepts within the density functional theory (DFT) framework is proposed. All theoretical calculations for the reaction pathway were performed using the Minnesota Global Hybrid functional M06-2X and a 6-31++G(d,p) basis set. The complete reaction comprises seven steps (five steps not including LiP as a catalyst), which include radical species formation, bond transformation, water and oxygen addition, atom reordering, and deacetylation. The overall mechanism is an endothermic process with mixed activation energies depending on the four transition states. These results are the first attempt to fully understand the catalytic role of LiP in the degradation of lignin and its aromatic derivative compounds in terms of the electronic structure methods and future hybrid calculation approaches that we have recently been performing. Full article
(This article belongs to the Special Issue The Molecular Electron Density Theory: A Modern View of Molecular Reactivity in Organic Chemistry)
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4250 KiB  
Article
Mechanistic Study of Copper-Catalyzed C-H Hydroxylation/C-S Coupling by ESI-HR MS and DFT Calculations
by Runsheng Xu, Rongrong Cai, Sixian Zhou, Zhuoda Zhou, Beibei Li and Dihui Xu
Molecules 2017, 22(11), 1912; https://doi.org/10.3390/molecules22111912 - 6 Nov 2017
Viewed by 4941
Abstract
The reaction mechanism of Cu-catalyzed C-H hydroxylation/C-S coupling was studied using electrospray ionization high resolution mass spectrometry (ESI-HR MS) and density functional theory calculations (DFT). Notably, a series of CuI and CuIII complexes were observed as key intermediates and identified using [...] Read more.
The reaction mechanism of Cu-catalyzed C-H hydroxylation/C-S coupling was studied using electrospray ionization high resolution mass spectrometry (ESI-HR MS) and density functional theory calculations (DFT). Notably, a series of CuI and CuIII complexes were observed as key intermediates and identified using ESI-HR MS. Furthermore, a catalyst cycle involving proton abstraction/oxidative addition/reductive elimination was proposed. This study is important and valuable with respect to C-H functionalization. Full article
(This article belongs to the Special Issue The Molecular Electron Density Theory: A Modern View of Molecular Reactivity in Organic Chemistry)
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3480 KiB  
Article
BET & ELF Quantum Topological Analysis of Neutral 2-Aza-Cope Rearrangement of γ-Alkenyl Nitrones
by Pedro Merino, Maria A. Chiacchio, Laura Legnani and Tomás Tejero
Molecules 2017, 22(8), 1371; https://doi.org/10.3390/molecules22081371 - 19 Aug 2017
Cited by 5 | Viewed by 5712
Abstract
The 2-Aza-Cope rearrangement of γ-alkenyl nitrones is a rare example of the neutral thermal 2-aza-Cope process that usually takes place with cationic species. During the rearrangement, a redistribution of bonds and electronic density occurs in one kinetic step. However, the introduction of substituents [...] Read more.
The 2-Aza-Cope rearrangement of γ-alkenyl nitrones is a rare example of the neutral thermal 2-aza-Cope process that usually takes place with cationic species. During the rearrangement, a redistribution of bonds and electronic density occurs in one kinetic step. However, the introduction of substituents with different steric requirements and electronic features might alter the activation energies and the synchronicity of the reaction. The electron localization function (ELF) analysis and its application to Bonding Evolution Theory (BET) analysis within the context of Molecular Electron Density Theory (MEDT) is an excellent tool to monitor the electron density along the reaction coordinate and thus investigate in detail bond breaking and formation and the corresponding energy barriers. By analyzing topological ELF calculations of seventeen 2-aza-Cope nitrone rearrangements with selected substituents, the main factors influencing the synchronicity of the process were investigated. This MEDT study results revealed that the rearrangement is a non-polar process mostly influenced by steric factors rather than by electronic ones, and confirms the pseudoradical character of the process rather than any pericyclic electron-reorganization. Full article
(This article belongs to the Special Issue The Molecular Electron Density Theory: A Modern View of Molecular Reactivity in Organic Chemistry)
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5112 KiB  
Article
A Molecular Electron Density Theory Study of the Reactivity of Azomethine Imine in [3+2] Cycloaddition Reactions
by Luis R. Domingo and Mar Ríos-Gutiérrez
Molecules 2017, 22(5), 750; https://doi.org/10.3390/molecules22050750 - 6 May 2017
Cited by 91 | Viewed by 7337
Abstract
The electronic structure and the participation of the simplest azomethine imine (AI) in [3+2] cycloaddition (32CA) reactions have been analysed within the Molecular Electron Density Theory (MEDT) using Density Functional Theory (DFT) calculations at the MPWB1K/6-311G(d) level. Topological analysis of the electron localisation [...] Read more.
The electronic structure and the participation of the simplest azomethine imine (AI) in [3+2] cycloaddition (32CA) reactions have been analysed within the Molecular Electron Density Theory (MEDT) using Density Functional Theory (DFT) calculations at the MPWB1K/6-311G(d) level. Topological analysis of the electron localisation function reveals that AI has a pseudoradical structure, while the conceptual DFT reactivity indices characterises this three-atom-component (TAC) as a moderate electrophile and a good nucleophile. The non-polar 32CA reaction of AI with ethylene takes place through a one-step mechanism with moderate activation energy, 8.7 kcal·mol−1. A bonding evolution theory study indicates that this reaction takes place through a non-concerted [2n + 2τ] mechanism in which the C–C bond formation is clearly anticipated prior to the C–N one. On the other hand, the polar 32CA reaction of AI with dicyanoethylene takes place through a two-stage one-step mechanism. Now, the activation energy is only 0.4 kcal·mol−1, in complete agreement with the high polar character of the more favourable regioisomeric transition state structure. The current MEDT study makes it possible to extend Domingo’s classification of 32CA reactions to a new pseudo(mono)radical type (pmr-type) of reactivity. Full article
(This article belongs to the Special Issue The Molecular Electron Density Theory: A Modern View of Molecular Reactivity in Organic Chemistry)
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303 KiB  
Article
Computational Prediction of the Protonation Sites of Ac-Lys-(Ala)n-Lys-NH2 Peptides through Conceptual DFT Descriptors
by Sebastián Sastre, Juan Frau and Daniel Glossman-Mitnik
Molecules 2017, 22(3), 458; https://doi.org/10.3390/molecules22030458 - 13 Mar 2017
Cited by 8 | Viewed by 4104
Abstract
Six density functionals (M11, M11L, MN12L, MN12SX, N12, and N12SX) in connection with the Def2TZVP basis set and the SMD solvation model (water as a solvent) have been assessed for the calculation of the molecular structure and properties of several peptides with the [...] Read more.
Six density functionals (M11, M11L, MN12L, MN12SX, N12, and N12SX) in connection with the Def2TZVP basis set and the SMD solvation model (water as a solvent) have been assessed for the calculation of the molecular structure and properties of several peptides with the general formulaAc-Lys-(Ala)n-Lys-NH2,withn=0to5  [...] Full article
(This article belongs to the Special Issue The Molecular Electron Density Theory: A Modern View of Molecular Reactivity in Organic Chemistry)
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