Theoretical Investigations of Reaction Mechanisms II

A special issue of Chemistry (ISSN 2624-8549). This special issue belongs to the section "Theoretical and Computational Chemistry".

Deadline for manuscript submissions: closed (30 June 2023) | Viewed by 8582

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Centro de Química Estrutural, Instituto Superior Técnico, Universidade de Lisboa, Avenue Rovisco Pais, 1049-001 Lisbon, Portugal
Interests: computational chemistry; coordination chemistry; molecular catalysis; oxidation of hydrocarbons; activation of small molecules; reaction mechanism; chemical bond nature; cycloaddition; nitriles
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Dear Colleagues,

Molecular design, optimization of reaction conditions, and the planning of a chemical synthesis cannot be achieved without knowledge of reaction mechanisms and driving forces of chemical processes. Computational methods of quantum chemistry represent a powerful tool for the understanding of the reaction mechanisms and key factors governing chemical reactions. Such methods are indispensable for the interpretation and analysis of experimental results and provide invaluable information, complementary to the experimental data, about molecular systems and processes. Computational methods are extremely valuable for mechanistic studies of reactions proceeding via formation of short-lived intermediates that cannot be detected experimentally, being the only possibility to obtain information about intimate details of the chemical processes when experimental methods cannot help in the understanding of the reaction mechanisms. This is a second edition of the Special Issue on this topic. Previously unpublished manuscripts that report mechanistic studies of any organic, inorganic or organometallic reactions with help of computational methods or deal with understanding of the key factors and driving forces governing chemical processes are welcome for this Special Issue.

Dr. Maxim L. Kuznetsov
Guest Editor

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Keywords

  • reaction mechanism
  • computational chemistry
  • density functional theory
  • ab initio
  • quantum chemical calculations
  • reactivity
  • molecular design
  • activation

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Published Papers (5 papers)

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Research

14 pages, 3014 KiB  
Article
Stereoselective Synthesis of a Novel Series of Dispiro-oxindolopyrrolizidines Embodying Thiazolo[3,2-a]benzimidazole Motif: A Molecular Electron Density Theory Study of the Mechanism of the [3 + 2] Cycloaddition Reaction
by Assem Barakat, Saeed Alshahrani, Abdullah Mohammed Al-Majid, Abdullah Saleh Alamary, M. Ali and Mar Ríos-Gutiérrez
Chemistry 2023, 5(4), 2392-2405; https://doi.org/10.3390/chemistry5040158 - 06 Nov 2023
Viewed by 896
Abstract
A one-pot multi-component reaction was employed for the stereoselective synthesis of a novel set of dispiro-oxindolopyrrolizidines analogs incorporating a thiazolo[3,2-a]benzimidazole scaffold based on the [3 + 2] cycloaddition (32CA) reaction approach. The desired novel dispiro-oxindolopyrrolizidines 9ad were achieved using [...] Read more.
A one-pot multi-component reaction was employed for the stereoselective synthesis of a novel set of dispiro-oxindolopyrrolizidines analogs incorporating a thiazolo[3,2-a]benzimidazole scaffold based on the [3 + 2] cycloaddition (32CA) reaction approach. The desired novel dispiro-oxindolopyrrolizidines 9ad were achieved using the 32CA reaction of new ethylene derivatives based on thiazolo[3,2-a]benzimidazole moiety seven with thiazolidine derivatives eight and different substituted isatin compounds 5ad (R = H, Cl, NO2, and Br). The final dispiro-oxindolopyrrolizidines cycloadducts were separated, purified, and fully characterized by means of a set of spectroscopic tools including IR, HNMR, CNMR, and MS. The Molecular Electron Density Theory (MEDT) was applied to explain the mechanism and stereoselectivity in the of the key 32CA reaction step. The reactive pseudo(mono)radical electronic structure of the in situ generated azomethine ylides and the high polar character of the corresponding 32CA reactions account for the low computed activation Gibbs free energies and total endo stereoselectivity of this kinetically controlled exergonic reaction. The computed relative Gibbs free activation energies of competitive reaction paths and regioisomers ratio distribution of 80:20 justify the major formation of 9a via the most favorable ortho/endo reaction path. Full article
(This article belongs to the Special Issue Theoretical Investigations of Reaction Mechanisms II)
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16 pages, 2537 KiB  
Article
Application of DFT/TD-DFT Frameworks in the Drug Delivery Mechanism: Investigation of Chelated Bisphosphonate with Transition Metal Cations in Bone Treatment
by Fatemeh Mollaamin and Majid Monajjemi
Chemistry 2023, 5(1), 365-380; https://doi.org/10.3390/chemistry5010027 - 23 Feb 2023
Cited by 5 | Viewed by 1604
Abstract
Carbon nanotubes (CNTs) are applied in a drug delivery system, which can be reacted with different structures such biomolecules. Bones have vital functions and are the locations of biochemical reactions in cells that might be exposed various diseases. As different metal ions are [...] Read more.
Carbon nanotubes (CNTs) are applied in a drug delivery system, which can be reacted with different structures such biomolecules. Bones have vital functions and are the locations of biochemical reactions in cells that might be exposed various diseases. As different metal ions are integral components of bone tissue with different functions in the physiological cellular medium as well as in bone treatment, they can be used differently as a basis or as a supplement for various materials in the field of bone repair. Therefore, this research aims to represent the recent progress in conjugated bisphosphonate (BP)-divalent transition metal ions of Mn2+, Fe2+, and Co2+ with an emphasis on the properties of interaction with a (6, 6) armchair carbon nanotube as a nanocarrier to exhibit the potential biomedical application of drug delivery. In this article, “CNT” linked to “BP“ of alendronic acid, ibandronic acid, neridronic acid, and pamidronic acid, which are chelated to transition metal cations of Mn2+, Fe2+, and Co2+, was investigated based on DFT insights for obtaining the electron charge density. Transition metals chelating with phosphonate groups, which are large with six O atoms with negative charges, are active in generating chelated complexes with the bisphosphonates [BPs- Mn2+/Fe2+/Co2+] through the status of drug design. In this work, B3LYP/6-311+G(d,p)/lanl2dz we have estimated the susceptibility of CNT for conjugating alendronic acid, ibandronic acid, neridronic acid, and pamidronic acid, which are chelated to transition metal cations of Mn2+, Fe2+, and Co2+ through NMR, NQR, IR, UV-VIS spectroscopy, and HOMO-LUMO analysis. Finally, the obtained results have confirmed that the possibility of applying CNT and BPs of alendronic acid, ibandronic acid, neridronic acid, and pamidronic acid becomes suitable in transition metal chelating for delivery application. The calculated HOMO–LUMO energy gaps for BPs of alendronic acid, ibandronic acid, neridronic acid, and pamidronic acid at the B3LYP/6-311+G (d,p) level have revealed that the energy gap reflects the chemical activity of the molecule. Full article
(This article belongs to the Special Issue Theoretical Investigations of Reaction Mechanisms II)
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13 pages, 1412 KiB  
Article
Conformational Preference of Flavonols and Its Effect on the Chemical Properties Involved in Radical Scavenging Activity
by Hiroko X. Kondo and Yu Takano
Chemistry 2022, 4(4), 1123-1135; https://doi.org/10.3390/chemistry4040076 - 22 Sep 2022
Viewed by 1507
Abstract
Flavonols are compounds with radical-scavenging activities that can prevent the harmful effects of free radicals. Their radical-scavenging activity has attracted significant attention. Recently, quantum chemistry-based methodologies have significantly improved the understanding of the activity due to dramatic increases in computational power and software [...] Read more.
Flavonols are compounds with radical-scavenging activities that can prevent the harmful effects of free radicals. Their radical-scavenging activity has attracted significant attention. Recently, quantum chemistry-based methodologies have significantly improved the understanding of the activity due to dramatic increases in computational power and software improvements. A standardized analysis method for estimating radical scavenging activity, the quantum mechanics-based test for overall free radical scavenging activity (QM-ORSA), has been proposed. An obstacle in applying the QM-ORSA protocol to flavonols is the large number of conformers and hydroxy groups for analysis. In this study, we focused on it and analyzed the conformational dependences of three flavonols (myricetin, quercetin, and kaempferol) on their chemical properties: bond dissociation energy, pKa, and ionization energy. As a result, all chemical properties were insensitive to conformational differences. The conformational search should be performed separately for each in the gas phase and in aqueous solution because of the differences in the major conformer (relative population of each conformer). These results suggest that it is important to perform the conformational search separately in water and in the gas phase and to determine one representative structure for analyzing radical scavenging activity. Full article
(This article belongs to the Special Issue Theoretical Investigations of Reaction Mechanisms II)
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14 pages, 3849 KiB  
Article
Novel Quinazolinone–Isoxazoline Hybrids: Synthesis, Spectroscopic Characterization, and DFT Mechanistic Study
by Yassine Rhazi, Mohammed Chalkha, Asmae Nakkabi, Imad Hammoudan, Mohamed Akhazzane, Mohamed Bakhouch, Samir Chtita and Mohamed El Yazidi
Chemistry 2022, 4(3), 969-982; https://doi.org/10.3390/chemistry4030066 - 30 Aug 2022
Cited by 4 | Viewed by 1966
Abstract
Quinazolinone and isoxazoline systems have attracted much attention due to their interesting pharmacological properties. The association of these two pharmacophores in a single hybrid structure can boost the biological activity or bring a new one. Inspired by this new paradigm, in the present [...] Read more.
Quinazolinone and isoxazoline systems have attracted much attention due to their interesting pharmacological properties. The association of these two pharmacophores in a single hybrid structure can boost the biological activity or bring a new one. Inspired by this new paradigm, in the present work we report the synthesis and spectroscopic characterization of new quinazolinone–isoxazoline hybrids. The target compounds were obtained via 1,3-dipolar cycloaddition reactions of arylnitriloxides and N-allylquinazolinone. The synthesized compounds were characterized using spectroscopic techniques such as IR, 1D NMR (1H and 13C), 2D NMR (COSY and HSQC), and high-resolution mass spectrometry (HRMS). The spectral data show that this reaction leads only to the 3,5-disubstituted isoxazoline regioisomer, and that the observed regiochemistry is not affected by the nature of the substituents in the phenyl ring of the dipole. In addition, a theoretical study was performed using density functional theory (DFT) to support the experimental results in regard to the regiochemistry of the studied reactions. The computational mechanistic study was in good agreement with the experimental data. Full article
(This article belongs to the Special Issue Theoretical Investigations of Reaction Mechanisms II)
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7 pages, 1483 KiB  
Article
Structures and Bonding in Hexacarbonyl Diiron Polyenes: Cycloheptatriene and 1,3,5-Cyclooctatriene
by Min Zhang and Guangchao Liang
Chemistry 2022, 4(2), 447-453; https://doi.org/10.3390/chemistry4020033 - 15 May 2022
Viewed by 1656
Abstract
Structural preferences of (1,3,5-cyclooctatriene) hexacarbonyl diiron [(C8H10)Fe2(CO)6] and cycloheptatriene hexacarbonyl diiron [(C7H8)Fe2(CO)6] were explored using density functional theory (DFT) computations. DFT computations together with experimental results demonstrated [...] Read more.
Structural preferences of (1,3,5-cyclooctatriene) hexacarbonyl diiron [(C8H10)Fe2(CO)6] and cycloheptatriene hexacarbonyl diiron [(C7H8)Fe2(CO)6] were explored using density functional theory (DFT) computations. DFT computations together with experimental results demonstrated that structure with the [η3, (η1, η2)] mode is the preferred structure in (C8H10)Fe2(CO)6, and the [η33] mode is preferred in (C7H8)Fe2(CO)6. For (C8H10)Fe2(CO)6, the conversion between the structures with [η3, (η1, η2)] mode and the [η3, η3] mode is prevented by the relatively high activation barrier. (C8H10)Fe2(CO)6 is indicated as a fluxional molecule with a Gibbs free energy of activation of 8.5 kcal/mol for its ring flicking process, and an excellent linear correlation (R2 = 0.9909) for the DFT simulated 1H-NMR spectra was obtained. Results provided here will develop the understanding on the structures of other polyene analogs. Full article
(This article belongs to the Special Issue Theoretical Investigations of Reaction Mechanisms II)
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