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Reactivity and Properties of Radicals and Radical Ions

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

Deadline for manuscript submissions: closed (30 September 2021) | Viewed by 18248

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Prof. Dr. Vincenzo Barone

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Scuola Normale Superiore di Pisa, Piazza dei Cavalieri, I-56126 Pisa, Italy
Interests: theoretical and computational chemistry; astrochemistry; reactivity and kinetics; solvent effects; density functional theory; computational spectroscopy
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Special Issue Information

Dear Colleagues,

Free radicals and free radical ions play an increasing role in several physical-chemical processes of interest in several fields like, e.g., astrochemistry, atmospheric chemistry, and biochemistry. However, the structural characterization of these highly reactive species faces against a number of difficulties and strongly benefits from integrated theoretical-experimental strategies. From the experimental point of view, high-resolution spectroscopic studies in the gas-phase or in inert matrices are providing a large amount of data, which calls for unambiguous assignment and interpretation. From the theoretical point of view, electronic structure computations for open-shell species are inherently more complicated than for the corresponding closed-shell systems. In the same vein, the kinetics of radical-neutral and radical-radical reactions often involves barrierless processes, which are more difficult to describe than activated processes in the framework of conventional approaches like the transition state theory. On these grounds, the aim of this special issue is to highlight the significant developments in all these areas, which are being achieved in recent years and to point out new perspectives and yet unsolved problems. Experimental, theoretical and joint contributions are welcome both from the point of view of methodological or instrumental developments and of significant new applications to systems of scientific or technological interest.

Prof. Dr. Vincenzo Barone
Guest Editor

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Keywords

open-shell systems
structure
reactivity
astrochemistry
atmospheric chemistry
biochemistry
spectroscopy
quantum chemistry

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Published Papers (6 papers)

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Research

14 pages, 667 KiB

Open AccessArticle

Ab Initio Study of Fine and Hyperfine Interactions in Triplet POH

by Luca Bizzocchi, Silvia Alessandrini, Mattia Melosso, Víctor M. Rivilla and Cristina Puzzarini

Molecules 2022, 27(1), 302; https://doi.org/10.3390/molecules27010302 - 4 Jan 2022

Cited by 1 | Viewed by 2270

Abstract

Phosphorous-containing molecules have a great relevance in prebiotic chemistry in view of the fact that phosphorous is a fundamental constituent of biomolecules, such as RNA, DNA, and ATP. Its biogenic importance has led astrochemists to investigate the possibility that P-bearing species could have formed in the interstellar medium (ISM) and subsequently been delivered to early Earth by rocky bodies. However, only two P-bearing molecules have been detected so far in the ISM, with the chemistry of interstellar phosphorous remaining poorly understood. Here, in order to shed further light on P-carriers in space, we report a theoretical spectroscopic characterisation of the rotational spectrum of POH in its

^{3}

^{″}

ground electronic state. State-of-the-art coupled-cluster schemes have been employed to derive rotational constants, centrifugal distortion terms, and most of the fine and hyperfine interaction parameters, while the electron spin–spin dipolar coupling has been investigated using the multi-configuration self-consistent-field method. The computed spectroscopic parameters have been used to simulate the appearance of triplet POH rotational and ro-vibrational spectra in different conditions, from cold to warm environments, either in gas-phase experiments or in molecular clouds. Finally, we point out that the predicted hyperfine structures represent a key pattern for the recognition of POH in laboratory and interstellar spectra. Full article

(This article belongs to the Special Issue Reactivity and Properties of Radicals and Radical Ions)

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12 pages, 415 KiB

Open AccessArticle

A Computational Journey across Nitroxide Radicals: From Structure to Spectroscopic Properties and Beyond

by Vincenzo Barone, Marco Fusè, Sandra Mónica Vieira Pinto and Nicola Tasinato

Molecules 2021, 26(23), 7404; https://doi.org/10.3390/molecules26237404 - 6 Dec 2021

Cited by 6 | Viewed by 2718

Abstract

Nitroxide radicals are characterized by a long-lived open-shell electronic ground state and are strongly sensitive to the chemical environment, thus representing ideal spin probes and spin labels for paramagnetic biomolecules and materials. However, the interpretation of spectroscopic parameters in structural and dynamic terms requires the aid of accurate quantum chemical computations. In this paper we validate a computational model rooted into double-hybrid functionals and second order vibrational perturbation theory. Then, we provide reference quantum chemical results for the structures, vibrational frequencies and other spectroscopic features of a large panel of nitroxides of current biological and/or technological interest. Full article

(This article belongs to the Special Issue Reactivity and Properties of Radicals and Radical Ions)

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20 pages, 3253 KiB

Open AccessArticle

A Path Integral Molecular Dynamics Simulation of a Harpoon-Type Redox Reaction in a Helium Nanodroplet

by Alvaro Castillo-García, Andreas W. Hauser, María Pilar de Lara-Castells and Pablo Villarreal

Molecules 2021, 26(19), 5783; https://doi.org/10.3390/molecules26195783 - 24 Sep 2021

Cited by 11 | Viewed by 4498

Abstract

We present path integral molecular dynamics (PIMD) calculations of an electron transfer from a heliophobic Cs

_{2}

dimer in its (

^{3} Σ_{u}

) state, located on the surface of a He droplet, to a heliophilic, fully immersed C

_{60}

molecule. Supported [...] Read more.

We present path integral molecular dynamics (PIMD) calculations of an electron transfer from a heliophobic Cs

_{2}

dimer in its (

^{3} Σ_{u}

) state, located on the surface of a He droplet, to a heliophilic, fully immersed C

_{60}

molecule. Supported by electron ionization mass spectroscopy measurements (Renzler et al., J. Chem. Phys.2016, 145, 181101), this spatially quenched reaction was characterized as a harpoon-type or long-range electron transfer in a previous high-level ab initio study (de Lara-Castells et al., J. Phys. Chem. Lett.2017, 8, 4284). To go beyond the static approach, classical and quantum PIMD simulations are performed at 2 K, slightly below the critical temperature for helium superfluidity (2.172 K). Calculations are executed in the NVT ensemble as well as the NVE ensemble to provide insights into real-time dynamics. A droplet size of 2090 atoms is assumed to study the impact of spatial hindrance on reactivity. By changing the number of beads in the PIMD simulations, the impact of quantization can be studied in greater detail and without an implicit assumption of superfluidity. We find that the reaction probability increases with higher levels of quantization. Our findings confirm earlier, static predictions of a rotational motion of the Cs

_{2}

dimer upon reacting with the fullerene, involving a substantial displacement of helium. However, it also raises the new question of whether the interacting species are driven out-of-equilibrium after impurity uptake, since reactivity is strongly quenched if a full thermal equilibration is assumed. More generally, our work points towards a novel mechanism for long-range electron transfer through an interplay between nuclear quantum delocalization within the confining medium and delocalized electronic dispersion forces acting on the two reactants. Full article

(This article belongs to the Special Issue Reactivity and Properties of Radicals and Radical Ions)

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11 pages, 1315 KiB

Open AccessArticle

Evaluation of the Free Radical Scavenging Activities of Ellagic Acid and Ellagic Acid Peracetate by EPR Spectrometry

by Ajit Kumar, Preeti Kaushik, Sandra Incerpi, Jens Z. Pedersen, Sanjay Goel, Ashok K. Prasad, Vishwajeet Rohil, Virinder S. Parmar, Luciano Saso and Christophe Len

Molecules 2021, 26(16), 4800; https://doi.org/10.3390/molecules26164800 - 8 Aug 2021

Cited by 18 | Viewed by 2894

Abstract

The purpose of this study was to examine the free radical scavenging and antioxidant activities of ellagic acid (EA) and ellagic acid peracetate (EAPA) by measuring their reactions with the radicals, 2,2-diphenyl-1-picrylhydrazyl and galvinoxyl using EPR spectroscopy. We have also evaluated the influence of EA and EAPA on the ROS production in L-6 myoblasts and rat liver microsomal lipid peroxidation catalyzed by NADPH. The results obtained clearly indicated that EA has tremendous ability to scavenge free radicals, even at concentration of 1 µM. Interestingly even in the absence of esterase, EAPA, the acetylated product of EA, was also found to be a good scavenger but at a relatively slower rate. Kinetic studies revealed that both EA and EAPA have ability to scavenge free radicals at the concentrations of 1 µM over extended periods of time. In cellular systems, EA and EAPA were found to have similar potentials for the inhibition of ROS production in L-6 myoblasts and NADPH-dependent catalyzed microsomal lipid peroxidation. Full article

(This article belongs to the Special Issue Reactivity and Properties of Radicals and Radical Ions)

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15 pages, 6752 KiB

Open AccessArticle

Free Radical Isomerizations in Acetylene Bromoboration Reaction

by Hugo Semrád, Ctibor Mazal and Markéta Munzarová

Molecules 2021, 26(9), 2501; https://doi.org/10.3390/molecules26092501 - 25 Apr 2021

Cited by 1 | Viewed by 2726

Abstract

The experimentally motivated question of the acetylene bromoboration mechanism was addressed in order to suggest possible radical isomerization pathways for the syn-adduct. Addition–elimination mechanisms starting with a bromine radical attack at the “bromine end” or the “boron end” of the C=C bond were considered. Dispersion-corrected DFT and MP2 methods with the SMD solvation model were employed using three all-electron bases as well as the ECP28MWB ansatz. The rate-determining, elimination step had a higher activation energy (12 kcal mol⁻¹) in case of the “bromine end” attack due to intermediate stabilization at both the MP2 and DFT levels. In case of the “boron end” attack, two modes of C–C bond rotation were followed and striking differences in MP2 vs. DFT potential energy surfaces were observed. Employing MP2, addition was followed by either a 180° rotation through an eclipsed conformation of vicinal bromine atoms or by an opposite rotation avoiding that conformation, with 5 kcal mol⁻¹ of elimination activation energy. Within B3LYP, the addition and rotation proceeded simultaneously, with a 9 (7) kcal mol⁻¹ barrier for rotation involving (avoiding) eclipsed conformation of vicinal bromines. For weakly bound complexes, ZPE corrections with MP2 revealed significant artifacts when diffuse bases were included, which must be considered in the Gibbs free energy profile interpretation. Full article

(This article belongs to the Special Issue Reactivity and Properties of Radicals and Radical Ions)

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16 pages, 1504 KiB

Open AccessArticle

Stochastic Modelling of ¹³C NMR Spin Relaxation Experiments in Oligosaccharides

by Sergio Rampino, Mirco Zerbetto and Antonino Polimeno

Molecules 2021, 26(9), 2418; https://doi.org/10.3390/molecules26092418 - 21 Apr 2021

Cited by 1 | Viewed by 2049

Abstract

A framework for the stochastic description of relaxation processes in flexible macromolecules including dissipative effects has been recently introduced, starting from an atomistic view, describing the joint relaxation of internal coordinates and global degrees of freedom, and depending on parameters recoverable from classic force fields (energetics) and medium modelling at the continuum level (friction tensors). The new approach provides a rational context for the interpretation of magnetic resonance relaxation experiments. In its simplest formulation, the semi-flexible Brownian (SFB) model has been until now shown to reproduce correctly correlation functions and spectral densities related to orientational properties obtained by direct molecular dynamics simulations of peptides. Here, for the first time, we applied directly the SFB approach to the practical evaluation of high-quality ¹³C nuclear magnetic resonance relaxation parameters,

T_{1}

and

T_{2}

, and the heteronuclear NOE of several oligosaccharides, which were previously interpreted on the basis of refined ad hoc modelling. The calculated NMR relaxation parameters were in agreement with the experimental data, showing that this general approach can be applied to diverse classes of molecular systems, with the minimal usage of adjustable parameters. Full article

(This article belongs to the Special Issue Reactivity and Properties of Radicals and Radical Ions)

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