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Chemical Kinetics in Metal Complexes
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Chemical Kinetics in Metal Complexes

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

Deadline for manuscript submissions: closed (28 February 2023) | Viewed by 17850

Special Issue Editors

Dr. Girolamo Casella

E-Mail Website
Guest Editor
Dipartimento di Scienze della Terra e del Mare (DiSTeM), Università degli Studi di Palermo, Palermo, Italy
Interests: DFT computational methods; spectroscopy; bond analysis; chemical kinetics; inorganic complexes
Special Issues, Collections and Topics in MDPI journals
Dr. Silvia Carlotto

E-Mail Website
Guest Editor
Department of Chemical Sciences (DiSC), University of Padova, Via F. Marzolo 1, 35131 Padova, Italy
Interests: chemical modelling
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Metal complexes are widely used as intermediates and/or catalysts in a huge area of applications, from industry to the “lab”, with a continuous growing interest in their wide use in always new branches.

Molecules is pleased to announce a Special Issue focused on the “Chemical Kinetics in Metal Complexes”. The Issue will cover both experimental and theoretical contributions concerning the properties of metal complexes as catalysts and/or reaction intermediates, from inorganic to bioinorganic.

It is a pleasure to invite you to submit manuscript to this Special Issue. Regular articles, communications, as well as reviews are all welcome.

Dr. Girolamo Casella
Dr. Silvia Carlotto
Guest Editor

Manuscript Submission Information

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Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Molecules is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • Metal complexes
  • Kinetics
  • Inorganic
  • Bioinorganic
  • DFT
  • Post-HF
  • Catalysis
  • Chemical Reactivity

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Published Papers (7 papers)

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Research

18 pages, 5166 KiB  
Article
Challenges for Kinetics Predictions via Neural Network Potentials: A Wilkinson’s Catalyst Case
by Ruben Staub, Philippe Gantzer, Yu Harabuchi, Satoshi Maeda and Alexandre Varnek
Molecules 2023, 28(11), 4477; https://doi.org/10.3390/molecules28114477 - 31 May 2023
Cited by 4 | Viewed by 2757
Abstract
Ab initio kinetic studies are important to understand and design novel chemical reactions. While the Artificial Force Induced Reaction (AFIR) method provides a convenient and efficient framework for kinetic studies, accurate explorations of reaction path networks incur high computational costs. In this article, [...] Read more.
Ab initio kinetic studies are important to understand and design novel chemical reactions. While the Artificial Force Induced Reaction (AFIR) method provides a convenient and efficient framework for kinetic studies, accurate explorations of reaction path networks incur high computational costs. In this article, we are investigating the applicability of Neural Network Potentials (NNP) to accelerate such studies. For this purpose, we are reporting a novel theoretical study of ethylene hydrogenation with a transition metal complex inspired by Wilkinson’s catalyst, using the AFIR method. The resulting reaction path network was analyzed by the Generative Topographic Mapping method. The network’s geometries were then used to train a state-of-the-art NNP model, to replace expensive ab initio calculations with fast NNP predictions during the search. This procedure was applied to run the first NNP-powered reaction path network exploration using the AFIR method. We discovered that such explorations are particularly challenging for general purpose NNP models, and we identified the underlying limitations. In addition, we are proposing to overcome these challenges by complementing NNP models with fast semiempirical predictions. The proposed solution offers a generally applicable framework, laying the foundations to further accelerate ab initio kinetic studies with Machine Learning Force Fields, and ultimately explore larger systems that are currently inaccessible. Full article
(This article belongs to the Special Issue Chemical Kinetics in Metal Complexes)
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21 pages, 5896 KiB  
Article
DNA Binding and Cleavage, Stopped-Flow Kinetic, Mechanistic, and Molecular Docking Studies of Cationic Ruthenium(II) Nitrosyl Complexes Containing “NS4” Core
by Hadeer A. Shereef, Yasmine S. Moemen, Fawzia I. Elshami, Ahmed M. El-Nahas, Shaban Y. Shaban and Rudi van Eldik
Molecules 2023, 28(7), 3028; https://doi.org/10.3390/molecules28073028 - 28 Mar 2023
Cited by 5 | Viewed by 2127
Abstract
This work aimed to evaluate in vitro DNA binding mechanistically of cationic nitrosyl ruthenium complex [RuNOTSP]+ and its ligand (TSPH2) in detail, correlate the findings with cleavage activity, and draw conclusions about the impact of the metal center. Theoretical studies [...] Read more.
This work aimed to evaluate in vitro DNA binding mechanistically of cationic nitrosyl ruthenium complex [RuNOTSP]+ and its ligand (TSPH2) in detail, correlate the findings with cleavage activity, and draw conclusions about the impact of the metal center. Theoretical studies were performed for [RuNOTSP]+, TSPH2, and its anion TSP−2 using DFT/B3LYP theory to calculate optimized energy, binding energy, and chemical reactivity. Since nearly all medications function by attaching to a particular protein or DNA, the in vitro calf thymus DNA (ctDNA) binding studies of [RuNOTSP]+ and TSPH2 with ctDNA were examined mechanistically using a variety of biophysical techniques. Fluorescence experiments showed that both compounds effectively bind to ctDNA through intercalative/electrostatic interactions via the DNA helix’s phosphate backbone. The intrinsic binding constants (Kb), (2.4 ± 0.2) × 105 M−1 ([RuNOTSP]+) and (1.9 ± 0.3) × 105 M−1 (TSPH2), as well as the enhancement dynamic constants (KD), (3.3 ± 0.3) × 104 M−1 ([RuNOTSP]+) and (2.6 ± 0.2) × 104 M−1 (TSPH2), reveal that [RuNOTSP]+ has a greater binding propensity for DNA compared to TSPH2. Stopped-flow investigations showed that both [RuNOTSP]+ and TSPH2 bind through two reversible steps: a fast second-order binding, followed by a slow first-order isomerization reaction via a static quenching mechanism. For the first and second steps of [RuNOTSP]+ and TSPH2, the detailed binding parameters were established. The total binding constants for [RuNOTSP]+ (Ka = 43.7 M−1, Kd = 2.3 × 10−2 M−1, ΔG0 = −36.6 kJ mol−1) and TSPH2 (Ka = 15.1 M−1, Kd = 66 × 10−2 M, ΔG0 = −19 kJ mol−1) revealed that the relative reactivity is approximately ([RuNOTSP]+)/(TSPH2) = 3/1. The significantly negative ΔG0 values are consistent with a spontaneous binding reaction to both [RuNOTSP]+ and TSPH2, with the former being very favorable. The findings showed that the Ru(II) center had an effect on the reaction rate but not on the mechanism and that the cationic [RuNOTSP]+ was a more highly effective DNA binder than the ligand TSPH2 via strong electrostatic interaction with the phosphate end of DNA. Because of its higher DNA binding affinity, cationic [RuNOTSP]+ demonstrated higher cleavage efficiency towards the minor groove of pBR322 DNA via the hydrolytic pathway than TSPH2, revealing the synergy effect of TSPH2 in the form of the complex. Furthermore, the mode of interaction of both compounds with ctDNA has also been supported by molecular docking. Full article
(This article belongs to the Special Issue Chemical Kinetics in Metal Complexes)
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15 pages, 3731 KiB  
Article
Kinetics and Mechanism of In(III) Ions Electroreduction on Cyclically Renewable Liquid Silver Amalgam Film Electrode: Significance of the Active Complexes of In(III)—Acetazolamide
by Agnieszka Nosal-Wiercińska, Marlena Martyna, Alicja Pawlak, Aleksandra Bazan-Woźniak, Robert Pietrzak, Selehatin Yilmaz, Sultan Yağmur Kabaş and Anna Szabelska
Molecules 2023, 28(7), 2942; https://doi.org/10.3390/molecules28072942 - 25 Mar 2023
Cited by 2 | Viewed by 1556
Abstract
The results of kinetic measurements revealed an accelerating effect of acetazolamide (ACT) on the multistep In(III) ions electroreduction in chlorates(VII) on a novel, cyclically renewable liquid silver amalgam film electrode (R–AgLAFE). The kinetic and thermodynamic parameters were determined by applying the DC polarography, [...] Read more.
The results of kinetic measurements revealed an accelerating effect of acetazolamide (ACT) on the multistep In(III) ions electroreduction in chlorates(VII) on a novel, cyclically renewable liquid silver amalgam film electrode (R–AgLAFE). The kinetic and thermodynamic parameters were determined by applying the DC polarography, square-wave (SWV) and cyclic voltammetry (CV), as well as electrochemical impedance spectroscopy (EIS). It was shown that ACT catalyzed the electrode reaction (“cap-pair” effect) by adsorbing on the surface of the R–AgLAFE electrode. The catalytic activity of ACT was explained as related to its ability to form active In(III)- acetazolamide complexes on the electrode surface, facilitating the electron transfer process. The active complexes constitute a substrate in the electroreduction process and their different structures and properties are responsible for differences in the catalytic activity. The determined values of the activation energy ΔH≠ point to the catalytic activity of ACT in the In(III) ions electroreduction process in chlorates(VII). Analysis of the standard entropy values ΔS0 confirm changes in the dynamics of the electrode process. Full article
(This article belongs to the Special Issue Chemical Kinetics in Metal Complexes)
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22 pages, 70055 KiB  
Article
Kinetic Study of the Oxidative Addition Reaction between Methyl Iodide and [Rh(imino-β-diketonato)(CO)(PPh)3] Complexes, Utilizing UV–Vis, IR Spectrophotometry, NMR Spectroscopy and DFT Calculations
by Hendrik Ferreira, Marrigje Marianne Conradie and Jeanet Conradie
Molecules 2022, 27(6), 1931; https://doi.org/10.3390/molecules27061931 - 16 Mar 2022
Cited by 1 | Viewed by 2331
Abstract
The oxidative addition of methyl iodide to [Rh(β-diketonato)(CO)(PPh)3] complexes, as modal catalysts of the first step during the Monsanto process, are well-studied. The β-diketonato ligand is a bidentate (BID) ligand that bonds, through two O donor atoms (O,O-BID ligand), to rhodium. [...] Read more.
The oxidative addition of methyl iodide to [Rh(β-diketonato)(CO)(PPh)3] complexes, as modal catalysts of the first step during the Monsanto process, are well-studied. The β-diketonato ligand is a bidentate (BID) ligand that bonds, through two O donor atoms (O,O-BID ligand), to rhodium. Imino-β-diketones are similar to β-diketones, though the donor atoms are N and O, referred to as an N,O-BID ligand. In this study, the oxidative addition of methyl iodide to [Rh(imino-β-diketonato)(CO)(PPh)3] complexes, as observed on UV–Vis spectrophotometry, IR spectrophotometry and NMR spectrometry, are presented. Experimentally, one isomer of [Rh(CH3COCHCNPhCH3)(CO)(PPh3)] and two isomers of [Rh(CH3COCHCNHCH3)(CO)(PPh3)] are observed—in agreement with density functional theory (DFT) calculations. Experimentally the [Rh(CH3COCHCNPhCH3)(CO)(PPh3)] + CH3I reaction proceeds through one reaction step, with a rhodium(III)-alkyl as the final reaction product. However, the [Rh(CH3COCHCNHCH3)(CO)(PPh3)] + CH3I reaction proceeds through two reaction steps, with a rhodium(III)-acyl as the final reaction product. DFT calculations of all the possible reaction products and transition states agree with experimental findings. Due to the smaller electronegativity of N, compared to O, the oxidative addition reaction rate of CH3I to the two [Rh(imino-β-diketonato)(CO)(PPh)3] complexes of this study was 7–11 times faster than the oxidative addition reaction rate of CH3I to [Rh(CH3COCHCOCH3)(CO)(PPh3)]. Full article
(This article belongs to the Special Issue Chemical Kinetics in Metal Complexes)
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15 pages, 7488 KiB  
Article
Trans–Cis Kinetic Study of Azobenzene-4,4′-dicarboxylic Acid and Aluminium and Zirconium Based Azobenzene-4,4′-dicarboxylate MOFs
by Refilwe Mogale, Jeanet Conradie and Ernst H. G. Langner
Molecules 2022, 27(4), 1370; https://doi.org/10.3390/molecules27041370 - 17 Feb 2022
Cited by 5 | Viewed by 3441
Abstract
Metal organic frameworks (MOFs) are porous hybrid crystalline materials that consist of organic linkers coordinated to metal centres. The trans–cis isomerisation kinetics of the azobenzene-4,4′-dicarboxylic acid (AZB(COOH)2) precursor, as well as the Al3+ (Al-AZB)- and Zr4+ (Zr-AZB)-based [...] Read more.
Metal organic frameworks (MOFs) are porous hybrid crystalline materials that consist of organic linkers coordinated to metal centres. The trans–cis isomerisation kinetics of the azobenzene-4,4′-dicarboxylic acid (AZB(COOH)2) precursor, as well as the Al3+ (Al-AZB)- and Zr4+ (Zr-AZB)-based MOFs with azobenzene-4,4′-dicarboxylate linkers, are presented. The photo-isomerization in the MOFs originates from singly bound azobenzene moieties on the surface of the MOF. The type of solvent used had a slight effect on the rate of isomerization and half-life, while the band gap energies were not significantly affected by the solvents. Photo-responsive MOFs can be classified as smart materials with possible applications in sensing, drug delivery, magnetism, and molecular recognition. In this study, the MOFs were applied in the dye adsorption of congo red (CR) in contaminated water. For both MOFs, the UV-irradiated cis isomer exhibited a slightly higher CR uptake than the ambient-light exposed trans isomer. Al-AZB displayed a dye adsorption capacity of over 95% for both the UV-irradiated and ambient light samples. The ambient light exposed Zr-AZB, and the UV irradiated Zr-AZB had 39.1% and 44.6% dye removal, respectively. Full article
(This article belongs to the Special Issue Chemical Kinetics in Metal Complexes)
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11 pages, 4207 KiB  
Article
In Situ Synchrotron X-ray Diffraction Studies of Hydrogen-Desorption Properties of 2LiBH4–Mg2FeH6 Composite
by Mohammad R. Ghaani, Michele Catti and Niall J. English
Molecules 2021, 26(16), 4853; https://doi.org/10.3390/molecules26164853 - 11 Aug 2021
Viewed by 2080
Abstract
Adding a secondary complex metal hydride can either kinetically or thermodynamically facilitate dehydrogenation reactions. Adding Mg2FeH6 to LiBH4 is energetically favoured, since FeB and MgB2 are formed as stable intermediate compounds during dehydrogenation reactions. Such “hydride destabilisation” enhances [...] Read more.
Adding a secondary complex metal hydride can either kinetically or thermodynamically facilitate dehydrogenation reactions. Adding Mg2FeH6 to LiBH4 is energetically favoured, since FeB and MgB2 are formed as stable intermediate compounds during dehydrogenation reactions. Such “hydride destabilisation” enhances H2-release thermodynamics from H2-storage materials. Samples of the LiBH4 and Mg2FeH6 with a 2:1 molar ratio were mixed and decomposed under three different conditions (dynamic decomposition under vacuum, dynamic decomposition under a hydrogen atmosphere, and isothermal decomposition). In situ synchrotron X-ray diffraction results revealed the influence of decomposition conditions on the selected reaction path. Dynamic decomposition of Mg2FeH6–LiBH4 under vacuum, or isothermal decomposition at low temperatures, was found to induce pure decomposition of LiBH4, whilst mixed decomposition of LiBH4 + Mg and formation of MgB2 were achieved via high-temperature isothermal dehydrogenation. Full article
(This article belongs to the Special Issue Chemical Kinetics in Metal Complexes)
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24 pages, 5576 KiB  
Article
Dramatic Effect of A Ring Size of Alicyclic α-Dioximate Ligand Synthons on Kinetics of the Template Synthesis and of the Acidic Decomposition of the Methylboron-Capped Iron(II) Clathrochelates
by Alexander L. Pomadchik, Alexander S. Belov, Ekaterina G. Lebed, Irina G. Belaya, Anna V. Vologzhanina and Yan Z. Voloshin
Molecules 2021, 26(13), 4019; https://doi.org/10.3390/molecules26134019 - 30 Jun 2021
Cited by 4 | Viewed by 2107
Abstract
Kinetics and thermodynamics of the template synthesis and of the acidic decomposition of the methylboron-capped iron(II) tris-1,2-dioximates—the clathrochelate derivatives of six (nioxime)- and eight (octoxime)-membered alicyclic ligand synthons—were compared. In the case of a macrobicyclic iron(II) tris-nioximate, the plausible pathway of its formation [...] Read more.
Kinetics and thermodynamics of the template synthesis and of the acidic decomposition of the methylboron-capped iron(II) tris-1,2-dioximates—the clathrochelate derivatives of six (nioxime)- and eight (octoxime)-membered alicyclic ligand synthons—were compared. In the case of a macrobicyclic iron(II) tris-nioximate, the plausible pathway of its formation contains a rate-determining stage and includes a reversible formation of an almost trigonal-antiprismatic (TAP) protonated tris-complex, followed by its monodeprotonation and addition of CH3B(OH)2. Thus, the formed TAP intermediate undergoes a multistep rate-determining stage of double cyclization with the elimination of two water molecules accompanied by a structural rearrangement, thus giving an almost trigonal-prismatic (TP) iron(FII) semiclathrochelate. It easily undergoes a cross-linking with CH3B(OH)2, resulting in the elimination of H+ ion and in the formation of a macrobicyclic structure. In contrast, the analogous scheme for its macrobicyclic tris-octoximate analog was found to contain up to three initial stages affecting the overall synthesis reaction rate. The rates of acidic decomposition of the above clathrochelates were found to be also affected by the nature of their ribbed substituents. Therefore, the single crystal XRD experiments were performed in order to explain these results. The difference in the kinetic schemes of a formation of the boron-capped iron(II) tris-nioximates and tris-octoximates is explained by necessity of the substantial changes in a geometry of the latter ligand synthon, caused by its coordination to the iron(II) ion, due to both the higher distortion of the FeN6-coordination polyhedra, and the intramolecular sterical clashes in the molecules of the macrobicyclic iron(II) tris-octoximates. Full article
(This article belongs to the Special Issue Chemical Kinetics in Metal Complexes)
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