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Non-covalent Interactions in Coordination and Organometallic Chemistry

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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 6724

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Special Issue Editor

Dr. Alexander S. Novikov

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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

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

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. International Journal of Molecular Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

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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

Open AccessEditorial

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 949

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 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

(This article belongs to the Special Issue Non-covalent Interactions in Coordination and Organometallic Chemistry)

Research

Jump to: Editorial

12 pages, 1685 KiB

Open AccessArticle

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 774

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 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

(This article belongs to the Special Issue Non-covalent Interactions in Coordination and Organometallic Chemistry)

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14 pages, 1300 KiB

Open AccessArticle

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 654

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 = 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 R_agg values previously introduced in investigations with the participation of the author were used (R_agg 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: R_F = 1.57, R_Cl = 1.90, R_Br = 1.99, and R_I = 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 R_I (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 ≤ R_agg. Full article

(This article belongs to the Special Issue Non-covalent Interactions in Coordination and Organometallic Chemistry)

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Figure 1

21 pages, 3045 KiB

Open AccessArticle

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 6 | Viewed by 1459

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). The structures of 1–3 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 E_1/2 = 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 μ_B (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 g_xx = g_yy = 2.393 and g_zz = 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

(This article belongs to the Special Issue Non-covalent Interactions in Coordination and Organometallic Chemistry)

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Graphical abstract

17 pages, 4312 KiB

Open AccessArticle

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 1039

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.

^{'}

-(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

(This article belongs to the Special Issue Non-covalent Interactions in Coordination and Organometallic Chemistry)

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Graphical abstract

18 pages, 5065 KiB

Open AccessArticle

Halogen Bond to Experimentally Significant N-Heterocyclic Carbenes (I, IMe₂, IⁱPr₂, I^tBu₂, 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 1166

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 (IR

_{2}

) 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 (IR

_{2}

) with experimentally significant and systematically increased R substituents at both nitrogen atoms: methyl = Me, iso-propyl =

^{i}

Pr, tert-butyl =

^{t}

Bu, 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, IMes

_{2}

forms the strongest and also the shortest halogen bonds with an apogee for complex IMes

_{2} \dots

ICN for which

D_{0}

= 18.71 kcal/mol and

d_{C \dots I}

= 2.541 Å. In many cases, IDipp

_{2}

forms as strong halogen bonds as IMes

_{2}

. Quite the opposite, although characterized by the greatest nucleophilicity, I

^{t}

_{2}

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 IAd