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Non-covalent Interactions in Coordination and Organometallic Chemistry

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Biochemistry".

Deadline for manuscript submissions: closed (28 February 2024) | Viewed by 6562

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Guest Editor
Institute of Chemistry, Saint Petersburg State University, Universitetskii pr., 26, Petergof, 198504 St. Petersburg, Russia
Interests: quantum and computational chemistry; inorganic and coordination chemistry; organometallic chemistry; organic chemistry; catalysis; non-covalent interactions; machine learning and artificial intelligence in chemistry
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Special Issue Information

Dear Colleagues,

Non-covalent interactions are one of the key topics in the fields of coordination and organometallic chemistry. Examples of such weak interactions are hydrogen, halogen, and chalcogen bonds; stacking interactions; and metallophilic contacts. Non-covalent interactions control the structure of solids (mainly molecular crystals), as well as the properties of supramolecular systems in liquid and gas phases; in addition, the elementary stages of chemical reactions are caused by such weak inter- and intramolecular contacts. In the context of bio(organic/inorganic)chemistry, non-covalent interactions are necessary for the formation and folding of the three-dimensional structure of proteins and nucleic acids, as well as their metal complexes and ligand–protein binding process. These inter- and intramolecular interactions have a significant effect on the properties of polymers, gels, and membranes, and on the dissolving abilities of liquids and their boiling points. Non-covalent interactions play an important role in materials science, catalysis, and medicinal chemistry. Finally, the processing of large amounts of data (quantitative indicators of the properties and energy characteristics of various supramolecular contacts in coordination and organometallic compounds), machine learning, and artificial intelligence (building predictive models using mathematical statistics, numerical methods, mathematical analysis, optimization methods, probability theory, graph theory, and various techniques for working with data in digital form) is a very promising goal for data scientists. The aim of this Special Issue in the International Journal of Molecular Sciences, entitled “Non-covalent Interactions in Coordination and Organometallic Chemistry”, is to address the most recent progress in the rapidly growing field of non-covalent interactions in coordination and organometallic chemistry. Both experimental and theoretical studies, fundamental and applied research, and any forms of manuscripts (for example, reviews, mini-reviews, full papers, short communications, technical notes, and highlights) are welcome for consideration.

This Special Issue will address the following topics: experimental studies of non-covalent interactions; theoretical modeling of supramolecular systems; 1-, 2-, and 3-D coordination polymers; weak contacts in bio(organic/inorganic)chemistry; non-covalent interactions in material science; and the application of machine learning and artificial intelligence in studies of non-covalent interactions.

We welcome researchers to contribute their research to our Special Issue.

Dr. Alexander S. Novikov
Guest Editor

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Keywords

  • non-covalent interactions
  • supramolecular systems
  • coordination chemistry
  • organometallic chemistry
  • material science
  • machine learning
  • artificial intelligence
  • computer modeling

Published Papers (6 papers)

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Editorial

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2 pages, 157 KiB  
Editorial
Plethora of Non-Covalent Interactions in Coordination and Organometallic Chemistry Are Modern Smart Tool for Materials Science, Catalysis, and Drugs Design
by Alexander S. Novikov
Int. J. Mol. Sci. 2022, 23(23), 14767; https://doi.org/10.3390/ijms232314767 - 25 Nov 2022
Cited by 1 | Viewed by 916
Abstract
Non-covalent interactions are one of the key topics in coordination and organometallic chemistry. Examples of such weak interactions are hydrogen, halogen, and chalcogen bonds, stacking interactions, metallophilic contacts, etc. Non-covalent interactions play an important role in materials science, catalysis, and medicinal chemistry. The [...] Read more.
Non-covalent interactions are one of the key topics in coordination and organometallic chemistry. Examples of such weak interactions are hydrogen, halogen, and chalcogen bonds, stacking interactions, metallophilic contacts, etc. Non-covalent interactions play an important role in materials science, catalysis, and medicinal chemistry. The aim of this Special Issue of International Journal of Molecular Sciences, entitled “Non-Covalent Interactions in Coordination and Organometallic Chemistry”, is to cover the most recent progress in the rapidly growing field of non-covalent interactions in coordination and organometallic chemistry. Both experimental and theoretical studies, fundamental and applied research and any types of manuscripts are welcome for consideration. Full article

Research

Jump to: Editorial

12 pages, 1685 KiB  
Article
Molecular Modelling of Polychlorinated Dibenzo-p-Dioxins Non-Covalent Interactions with β and γ-Cyclodextrins
by Maria-Cristina Ghetu, Marian Virgolici, Alina Tirsoaga and Ioana Stanculescu
Int. J. Mol. Sci. 2023, 24(17), 13214; https://doi.org/10.3390/ijms241713214 - 25 Aug 2023
Viewed by 752
Abstract
Polychlorinated dibenzo-p-dioxins (PCDD) are persistent organic pollutants which result as byproducts in industrial or combustion processes and induce toxicity in both wildlife and humans. In this study, all seven PCDD, tetrachlorinated dibenzo-p-dioxins (TCDD), pentachlorinated dibenzo-p-dioxins (P5CDD), hexachlorinated dibenzo-p-dioxins (H6CDD), heptachlorinated dibenzo-p-dioxins (H7CDD), and [...] Read more.
Polychlorinated dibenzo-p-dioxins (PCDD) are persistent organic pollutants which result as byproducts in industrial or combustion processes and induce toxicity in both wildlife and humans. In this study, all seven PCDD, tetrachlorinated dibenzo-p-dioxins (TCDD), pentachlorinated dibenzo-p-dioxins (P5CDD), hexachlorinated dibenzo-p-dioxins (H6CDD), heptachlorinated dibenzo-p-dioxins (H7CDD), and octachlorinated dibenzo-p-dioxins (OCDD) were studied in interaction with two cyclodextrins, β-CD and γ-CD, resulting in a total of 40 host–guest complexes. The flexibility of the cyclodextrins was given by the number of glucose units, and the placement of the chlorine groups on the dioxins structure accounted for the different complex formed. Various geometries of interaction obtained by guided docking were studied, and the complexation and binding energy were calculated in the frame of MM+ and OPLS force fields. The results show that the recognition of the PCDD pollutants by the CD may be possible through the formation of PCDD:CD inclusion complexes. This recognition is based on the formation of Coulombic interactions between the chlorine atom of the PCDD and the primary and secondary hydroxyl groups of the CD and van der Waals interaction of the CD hydrophobic cavity with PCDD aromatic structures. Both MM+ and OPLS calculus resulted in close values for the complexation and binding energies. Molecular mechanics calculations offer a proper insight into the molecular recognition process between the PCDD compounds and CD molecules, proved by a good description of the C-H···O bonds formed between the guest and host molecules. It was shown for the first time that CD may efficiently trap PCCDs, opening the way for their tremendous potential use in environmental remediation. Full article
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14 pages, 1300 KiB  
Article
Comparison of Intermolecular Halogen...Halogen Distances in Organic and Organometallic Crystals
by Olga V. Grineva
Int. J. Mol. Sci. 2023, 24(15), 11911; https://doi.org/10.3390/ijms241511911 - 25 Jul 2023
Viewed by 640
Abstract
Statistical analysis of halogen...halogen intermolecular distances was performed for three sets of homomolecular crystals under normal conditions: C–Hal1...Hal2–C distances in crystals consisting of: (i) organic compounds (set Org); (ii) organometallic compounds (set Orgmet); and (iii) distances M1–Hal1...Hal2–M2 (set MHal) (in all cases Hal1 [...] Read more.
Statistical analysis of halogen...halogen intermolecular distances was performed for three sets of homomolecular crystals under normal conditions: C–Hal1...Hal2–C distances in crystals consisting of: (i) organic compounds (set Org); (ii) organometallic compounds (set Orgmet); and (iii) distances M1–Hal1...Hal2–M2 (set MHal) (in all cases Hal1 = Hal2, and in MHal M1 = M2, M is any metal). When analyzing C–Hal...Hal–C distances, a new method for estimating the values of van der Waals radii is proposed, based on the use of two subsets of distances: (i) the shortest distances from each substance less than a threshold; and (ii) all C–Hal...Hal–C distances less than the same threshold. As initial approximations for these thresholds for different Hal, the Ragg values previously introduced in investigations with the participation of the author were used (Ragg values make it possible to perform a statistical assessment of the presence of halogen aggregates in crystals). The following values are recommended in this work to be used as universal values for crystals of organic and organometallic compounds: RF = 1.57, RCl = 1.90, RBr = 1.99, and RI = 2.15 Å. They are in excellent agreement with the results of some other works but significantly (by 0.10–0.17 Å) greater than the commonly used values. For the Orgmet set, slightly lower values for RI (2.11–2.09 Å) were obtained, but number of the C–I...I–C distances available for analysis was significantly smaller than in the other subgroups, which may be the reason for the discrepancy with value for the Org set (2.15 Å). Statistical analysis of the M–Hal...Hal–M distances was performed for the first time. A Hal-aggregation coefficient for M–Hal bonds is proposed, which allows one to estimate the propensity of M–Hal groups with certain M and Hal to participate in Hal-aggregates formed by M–Hal...Hal–M contacts. In particular, it was found that, for the Hg–Hal groups (Hal = Cl, Br, I), there is a high probability that the crystals have Hg–Hal...Hal–Hg distances with length ≤ Ragg. Full article
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21 pages, 3045 KiB  
Article
Iridium Complexes with BIAN-Type Ligands: Synthesis, Structure and Redox Chemistry
by Nikolai F. Romashev, Ivan V. Bakaev, Veronika I. Komlyagina, Pavel A. Abramov, Irina V. Mirzaeva, Vladimir A. Nadolinny, Alexander N. Lavrov, Nikolai B. Kompan’kov, Artem A. Mikhailov, Iakov S. Fomenko, Alexander S. Novikov, Maxim N. Sokolov and Artem L. Gushchin
Int. J. Mol. Sci. 2023, 24(13), 10457; https://doi.org/10.3390/ijms241310457 - 21 Jun 2023
Cited by 5 | Viewed by 1414
Abstract
A series of iridium complexes with bis(diisopropylphenyl)iminoacenaphtene (dpp-bian) ligands, [Ir(cod)(dpp-bian)Cl] (1), [Ir(cod)(NO)(dpp-bian)](BF4)2 (2) and [Ir(cod)(dpp-bian)](BF4) (3), were prepared and characterized by spectroscopic techniques, elemental analysis, X-ray diffraction analysis and cyclic voltammetry (CV). [...] Read more.
A series of iridium complexes with bis(diisopropylphenyl)iminoacenaphtene (dpp-bian) ligands, [Ir(cod)(dpp-bian)Cl] (1), [Ir(cod)(NO)(dpp-bian)](BF4)2 (2) and [Ir(cod)(dpp-bian)](BF4) (3), were prepared and characterized by spectroscopic techniques, elemental analysis, X-ray diffraction analysis and cyclic voltammetry (CV). The structures of 13 feature a square planar backbone consisting of two C = C π-bonds of 1,5-cyclooctadiene (cod) and two nitrogen atoms of dpp-bian supplemented with a chloride ion (for 1) or a NO group (for 2) to complete a square-pyramidal geometry. In the nitrosyl complex 2, the Ir-N-O group has a bent geometry (the angle is 125°). The CV data for 1 and 3 show two reversible waves between 0 and -1.6 V (vs. Ag/AgCl). Reversible oxidation was also found at E1/2 = 0.60 V for 1. Magnetochemical measurements for 2 in a range from 1.77 to 300 K revealed an increase in the magnetic moment with increasing temperature up to 1.2 μB (at 300 K). Nitrosyl complex 2 is unstable in solution and loses its NO group to yield [Ir(cod)(dpp-bian)](BF4) (3). A paramagnetic complex, [Ir(cod)(dpp-bian)](BF4)2 (4), was also detected in the solution of 2 as a result of its decomposition. The EPR spectrum of 4 in CH2Cl2 is described by the spin Hamiltonian Ĥ = gβHŜ with S = 1/2 and gxx = gyy = 2.393 and gzz = 1.88, which are characteristic of the low-spin 5d7-Ir(II) state. DFT calculations were carried out in order to rationalize the experimental results. Full article
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17 pages, 4312 KiB  
Article
Supramolecular Dimer as High-Performance pH Probe: Study on the Fluorescence Properties of Halogenated Ligands in Rigid Schiff Base Complex
by Jiajun Xu, Meifen Huang, Liang Jiao, Haijun Pang, Xia Wang, Rui Duan and Qiong Wu
Int. J. Mol. Sci. 2023, 24(11), 9480; https://doi.org/10.3390/ijms24119480 - 30 May 2023
Cited by 2 | Viewed by 1007
Abstract
The development of high-performance fluorescence probes has been an active area of research. In the present work, two new pH sensors Zn-3,5-Cl-saldmpn and Zn-3,5-Br-saldmpn based on a halogenated Schiff ligand (3,5-Cl-saldmpn = N, N-(3,3-dipropyhnethylamine) bis (3,5-chlorosalicylidene)) with linearity [...] Read more.
The development of high-performance fluorescence probes has been an active area of research. In the present work, two new pH sensors Zn-3,5-Cl-saldmpn and Zn-3,5-Br-saldmpn based on a halogenated Schiff ligand (3,5-Cl-saldmpn = N, N-(3,3-dipropyhnethylamine) bis (3,5-chlorosalicylidene)) with linearity and a high signal-to-noise ratio were developed. Analyses revealed an exponential intensification in their fluorescence emission and a discernible chromatic shift upon pH increase from 5.0 to 7.0. The sensors could retain over 95% of their initial signal amplitude after 20 operational cycles, demonstrating excellent stability and reversibility. To elucidate their unique fluorescence response, a non-halogenated analog was introduced for comparison. The structural and optical characterization suggested that the introduction of halogen atoms can create additional interaction pathways between adjacent molecules and enhance the strength of the interaction, which not only improves the signal-to-noise ratio but also forms a long-range interaction process in the formation of the aggregation state, thus enhancing the response range. Meanwhile, the above proposed mechanism was also verified by theoretical calculations. Full article
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18 pages, 5065 KiB  
Article
Halogen Bond to Experimentally Significant N-Heterocyclic Carbenes (I, IMe2, IiPr2, ItBu2, IPh2, IMes2, IDipp2, IAd2; I = Imidazol-2-ylidene)
by Mirosław Jabłoński
Int. J. Mol. Sci. 2023, 24(10), 9057; https://doi.org/10.3390/ijms24109057 - 21 May 2023
Viewed by 1151
Abstract
The subjects of the article are halogen bonds between either XCN or XCCH (X = Cl, Br, I) and the carbene carbon atom in imidazol-2-ylidene (I) or its derivatives (IR2) with experimentally significant and systematically increased R substituents at both nitrogen [...] Read more.
The subjects of the article are halogen bonds between either XCN or XCCH (X = Cl, Br, I) and the carbene carbon atom in imidazol-2-ylidene (I) or its derivatives (IR2) with experimentally significant and systematically increased R substituents at both nitrogen atoms: methyl = Me, iso-propyl = iPr, tert-butyl = tBu, phenyl = Ph, mesityl = Mes, 2,6-diisopropylphenyl = Dipp, 1-adamantyl = Ad. It is shown that the halogen bond strength increases in the order Cl < Br < I and the XCN molecule forms stronger complexes than XCCH. Of all the carbenes considered, IMes2 forms the strongest and also the shortest halogen bonds with an apogee for complex IMes2ICN for which D0 = 18.71 kcal/mol and dCI = 2.541 Å. In many cases, IDipp2 forms as strong halogen bonds as IMes2. Quite the opposite, although characterized by the greatest nucleophilicity, ItBu2 forms the weakest complexes (and the longest halogen bonds) if X ≠ Cl. While this finding can easily be attributed to the steric hindrance exerted by the highly branched tert-butyl groups, it appears that the presence of the four C-H⋯X hydrogen bonds may also be of importance here. Similar situation occurs in the case of complexes with IAd2. Full article
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