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  • 1
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    Substituent Effects in Tetrel Bonds Involving Aromatic Silane Derivatives: An ab initio Study
    MDPI AG ; 2023
    In:  Molecules Vol. 28, No. 5 ( 2023-03-05), p. 2385-
    Details
    In: Molecules, MDPI AG, Vol. 28, No. 5 ( 2023-03-05), p. 2385-
    Abstract: In this manuscript substituent effects in several silicon tetrel bonding (TtB) complexes were investigated at the RI-MP2/def2-TZVP level of theory. Particularly, we have analysed how the interaction energy is influenced by the electronic nature of the substituent in both donor and acceptor moieties. To achieve that, several tetrafluorophenyl silane derivatives have been substituted at the meta and para positions by several electron donating and electron withdrawing groups (EDG and EWG, respectively), such as –NH2, –OCH3, –CH3, –H, –CF3 and –CN substituents. As electron donor molecules, we have used a series of hydrogen cyanide derivatives using the same EDGs and EWGs. We have obtained the Hammett’s plots for different combinations of donors and acceptors and in all cases we have obtained good regression plots (interaction energies vs. Hammet’s σ parameter). In addition, we have used the electrostatic potential (ESP) surface analysis as well as the Bader’s theory of atoms in molecules (AIM) and noncovalent interaction plot (NCI plot) techniques to further characterize the TtBs studied herein. Finally, a Cambridge Structural Database (CSD) inspection was carried out, retrieving several structures where halogenated aromatic silanes participate in tetrel bonding interactions, being an additional stabilization force of their supramolecular architectures.
    Type of Medium: Online Resource
    ISSN: 1420-3049
    URL: Article
    DOI: 10.3390/molecules28052385
    Language: English
    Publisher: MDPI AG
    Publication Date: 2023
    detail.hit.zdb_id: 2008644-1
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  • 2
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    The Copper(II)-Thiodiacetate (tda) Chelate as Efficient Receptor of N9-(2-Hydroxyethyl)Adenine (9heade): Synthesis, Molecular and Crystal Structures, Physical Properties and DFT Calculations of [Cu(tda)(9heade)(H2O)]·2H2O
    MDPI AG ; 2023
    In:  Molecules Vol. 28, No. 15 ( 2023-08-02), p. 5830-
    Details
    In: Molecules, MDPI AG, Vol. 28, No. 15 ( 2023-08-02), p. 5830-
    Abstract: Considering that Cu(tda) chelate (tda: dithioacetate) is a receptor for adenine and related 6-aminopurines, this study reports on the synthesis, molecular and crystal structures, thermal stability, spectral properties and DFT calculations related to [Cu(tda)(9heade)(H2O)]·2H2O (1) [9heade: N9-(2-hydroxyethyl)adenine] . Concerning the molecular recognition of (metal chelate)-(adenine synthetic nucleoside), 1 represents an unprecedented metal binding pattern (MBP) for 9heade. However, unprecedentedly, the Cu(tda)-9heade molecular recognition in 1 is essentially featured in the Cu-N1(9heade) bond, without any N6-H⋯O(carboxyl tda) interligand interaction. Nevertheless, N1 being the most basic donor for N9-substituted adenines, this Cu-N1 bond is now assisted by an O2–water-mediated interaction (N6-H⋯O2 and O2⋯Cu weak contact). Also, in the crystal packing, the O-H(ol) of 9heade interacts with its own adenine moiety as a result of an O3–water-mediated interaction (O(ol)-H⋯O3 plus O3-H36⋯π(adenine moiety)). Both water-mediated interactions seem to be responsible for serious alterations in the physical properties of crystalline or grounded samples. Density functional theory calculations were used to evaluate the interactions energetically. Moreover, the quantum theory of atoms-in-molecules (QTAIM), in combination with the noncovalent interaction plot (NCIPlot), was used to analyze the interactions and rationalize the existence and relative importance of hydrogen bonding, chalcogen bonding and π-stacking interactions. The novelty of this work resides in the discovery of a novel binding mode for N9-(2-hydroxyethyl)adenine. Moreover, the investigation of the important role of water in the solid state of 1 is also relevant, along with the chalcogen bonding interactions demonstrated by the density functional theory (DFT) study.
    Type of Medium: Online Resource
    ISSN: 1420-3049
    URL: Article
    DOI: 10.3390/molecules28155830
    Language: English
    Publisher: MDPI AG
    Publication Date: 2023
    detail.hit.zdb_id: 2008644-1
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  • 3
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    A Tetranuclear Ni(II)-Cubane Cluster Molecule Build by Four µ3-O-Methanolate (MeO) Ligands, Externally Cohesive by Four Unprecedented Bridging µ2-N7,O6-Acyclovirate (acv-H) Anions
    MDPI AG ; 2022
    In:  Crystals Vol. 13, No. 1 ( 2022-12-21), p. 7-
    Details
    In: Crystals, MDPI AG, Vol. 13, No. 1 ( 2022-12-21), p. 7-
    Abstract: Metal ion interactions with nuclei acids and their constituents represent a multi-faceted and growing research field. This contribution deals with molecular recognition between synthetic purine 17 nucleosides and first-row transition metal complexes, with O- and/or N-amino chelators which are able to 18 engage in intra-molecular N-H···(N or O) and O-H···(N or O) interligand interactions. Crystals of these complexes can also display inter-molecular aromatic π-stacking and/or other non-conventional interactions. In this manuscript, we used 2-(2-aminoethoxy)ethanol (2aee) as a potential N,O(e),O(ol)-chelator for nickel(II). However, unexpectedly, the reaction between NiCl2, acyclovir (acv), and 2aee in methanol afforded parallelepiped apple-green crystals of [Ni(acv-H)(MeO)(H2O)] 4·8H2O, (1) a tetranuclear molecule with an equimolar Ni(II):µ3-methanolate(1-):µ2-N7,O6-acyclovirate(1-) (acv-H) ratio. The µ2-N7,O6-(acv-H) metal-binding pattern (MBP) is unprecedented in terms of both its anionic and bridging roles. The single-crystal X-ray diffraction structure as well as thermogravimetric analysis and the (FT-IR +Vis-UV) spectra of 1 are reported. Theoretical density functional theory (DFT) calculations are used to analyse the antiparallel π-stacking interactions that govern the formation of self-assembled dimers in the solid state.
    Type of Medium: Online Resource
    ISSN: 2073-4352
    URL: Article
    DOI: 10.3390/cryst13010007
    Language: English
    Publisher: MDPI AG
    Publication Date: 2022
    detail.hit.zdb_id: 2661516-2
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  • 4
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    Novel Pb(II) Complexes: X-Ray Structures, Hirshfeld Surface Analysis and DFT Calculations
    MDPI AG ; 2020
    In:  Crystals Vol. 10, No. 7 ( 2020-07-02), p. 568-
    Details
    In: Crystals, MDPI AG, Vol. 10, No. 7 ( 2020-07-02), p. 568-
    Abstract: Herein we report the synthesis and detailed structural characterization of two new centrosymmetric dinuclear coordination compounds of Pb(II) [Pb2L2(NCS)4] (1) and [Pb2L2(NO3)4] ∙2MeOH (2), using the organic ligand 1,2-diphenyl-1,2-bis((methyl(pyridin-2-yl)methylene)hydrazono)ethane (L). In both complexes, each subunit [PbLX2 (X = NO3 or NCS)] adopts a quasi-aromatic Möbius metal chelate structure. Each ligand L is coordinated in a tetradentate coordination mode to Pb(II), yielding the 12π electron chelate ring via two pyridyl-imine units. In compound (1), the coordination sphere is completed by one disordered N,S-coordinated thiocyanate anion and two μ1,1-bridging N-coordinated thiocyanate anions. In compound (2), the coordination sphere of Pb(II) is completed by two monodentate and two bidentate nitrato ligands (two of them acting as bridging ligands). Crystal packing of both compounds is stabilized by intermolecular hydrogen bonds, intra- and intermolecular C–H∙∙∙π interactions. The Hirshfeld molecular surfaces of (1) and (2) demonstrate that their packing is dominated by C–H∙∙∙O/N/S interactions as well as by far less favored H∙∙∙H contacts.
    Type of Medium: Online Resource
    ISSN: 2073-4352
    URL: Article
    DOI: 10.3390/cryst10070568
    Language: English
    Publisher: MDPI AG
    Publication Date: 2020
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  • 5
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    Metal Coordination Enhances Chalcogen Bonds: CSD Survey and Theoretical Calculations
    MDPI AG ; 2022
    In:  International Journal of Molecular Sciences Vol. 23, No. 8 ( 2022-04-10), p. 4188-
    Details
    In: International Journal of Molecular Sciences, MDPI AG, Vol. 23, No. 8 ( 2022-04-10), p. 4188-
    Abstract: In this study the ability of metal coordinated Chalcogen (Ch) atoms to undergo Chalcogen bonding (ChB) interactions has been evaluated at the PBE0-D3/def2-TZVP level of theory. An initial CSD (Cambridge Structural Database) inspection revealed the presence of square planar Pd/Pt coordination complexes where divalent Ch atoms (Se/Te) were used as ligands. Interestingly, the coordination to the metal center enhanced the σ-hole donor ability of the Ch atom, which participates in ChBs with neighboring units present in the X-ray crystal structure, therefore dictating the solid state architecture. The X-ray analyses were complemented with a computational study (PBE0-D3/def2-TZVP level of theory), which shed light into the strength and directionality of the ChBs studied herein. Owing to the new possibilities that metal coordination offers to enhance or modulate the σ-hole donor ability of Chs, we believe that the findings presented herein are of remarkable importance for supramolecular chemists as well as for those scientists working in the field of solid state chemistry.
    Type of Medium: Online Resource
    ISSN: 1422-0067
    URL: Article
    DOI: 10.3390/ijms23084188
    Language: English
    Publisher: MDPI AG
    Publication Date: 2022
    detail.hit.zdb_id: 2019364-6
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  • 6
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    Nitropyridine-1-Oxides as Excellent π-Hole Donors: Interplay between σ-Hole (Halogen, Hydrogen, Triel, and Coordination Bonds) and π-Hole Interactions
    MDPI AG ; 2019
    In:  International Journal of Molecular Sciences Vol. 20, No. 14 ( 2019-07-12), p. 3440-
    Details
    In: International Journal of Molecular Sciences, MDPI AG, Vol. 20, No. 14 ( 2019-07-12), p. 3440-
    Abstract: In this manuscript, we use the primary source of geometrical information, i.e., Cambridge Structural Database (CSD), combined with density functional theory (DFT) calculations (PBE0-D3/def2-TZVP level of theory) to demonstrate the relevance of π-hole interactions in para-nitro substituted pyridine-1-oxides. More importantly, we show that the molecular electrostatic potential (MEP) value above and below the π–hole of the nitro group is largely influenced by the participation of the N-oxide group in several interactions like hydrogen-bonding (HB) halogen-bonding (XB), triel bonding (TrB), and finally, coordination-bonding (CB) (N+–O− coordinated to a transition metal). The CSD search discloses that p-nitro-pyridine-1-oxide derivatives have a strong propensity to participate in π-hole interactions via the nitro group and, concurrently, N-oxide group participates in a series of interactions as electron donor. Remarkably, the DFT calculations show from strong to moderate cooperativity effects between π–hole and HB/XB/TrB/CB interactions (σ-bonding). The synergistic effects between π-hole and σ-hole bonding interactions are studied in terms of cooperativity energies, using MEP surface analysis and the Bader’s quantum theory of atoms in molecules (QTAIM).
    Type of Medium: Online Resource
    ISSN: 1422-0067
    URL: Article
    DOI: 10.3390/ijms20143440
    Language: English
    Publisher: MDPI AG
    Publication Date: 2019
    detail.hit.zdb_id: 2019364-6
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  • 7
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    Dicopper(II)-EDTA Chelate as a Bicephalic Receptor Model for a Synthetic Adenine Nucleoside
    MDPI AG ; 2021
    In:  Pharmaceuticals Vol. 14, No. 5 ( 2021-05-02), p. 426-
    Details
    In: Pharmaceuticals, MDPI AG, Vol. 14, No. 5 ( 2021-05-02), p. 426-
    Abstract: In the extensive field of metal ions, their interactions with nucleic acids, and their constituents, the main aim of this work is to develop a metal chelate suitable to recognize two molecules of an adenine nucleoside. For this purpose, the dinuclear chelate Cu2 (µ-EDTA) (ethylenediaminetetraacetate(4-) ion (EDTA)) is chosen as a bicephalic receptor model for N9-(2-hydroxyethyl)adenine (9heade). A one-pot synthesis is reported to obtain the compound [Cu2(µ2-EDTA)(9heade)2(H2O)4]·3H2O, which has been characterized by single-crystal X-ray diffraction and various spectral, thermal, and magnetic methods. The complex unit is a centro-symmetric molecule, where each Cu (II) center is chelated by a half-EDTA, and is further surrounded by an N7-dentate 9heade nucleoside and two non-equivalent trans-O-aqua molecules. The metal chelate-nucleoside molecular recognition is referred to as an efficient cooperation between the Cu-N7(9heade) coordination bond and a (9heade)N6-H···O(carboxyl, EDTA) interligand interaction. Theoretical calculations are also made to account for the relevance of this interaction. The extreme weakness with which each water molecule binds to the metal center disturbs the thermal stability and the infrared (FT-IR) and electron spin resonance (ESR) spectra of the compound.
    Type of Medium: Online Resource
    ISSN: 1424-8247
    URL: Article
    DOI: 10.3390/ph14050426
    Language: English
    Publisher: MDPI AG
    Publication Date: 2021
    detail.hit.zdb_id: 2193542-7
    SSG: 15,3
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  • 8
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    Square Planar Pt(II) Ion as Electron Donor in Pnictogen Bonding Interactions
    MDPI AG ; 2023
    In:  Inorganics Vol. 11, No. 2 ( 2023-02-15), p. 80-
    Details
    In: Inorganics, MDPI AG, Vol. 11, No. 2 ( 2023-02-15), p. 80-
    Abstract: It has been proposed that late transition metals with low coordination numbers (square planar or linear) can act as nucleophiles and participate in σ-hole interactions as electron donors. This is due to the existence, in this type of metal complexes, of a pair of electrons located at high energy d-orbitals (dz2 or dx2-y2), which are adequate for interacting with antibonding σ-orbitals [σ*(X–Y)] where Y is usually an electron withdrawing element and X an element of the p-block. This type of d[M] →σ*(X–Y) interaction has been reported for metals of groups 9–11 in oxidation states +1 and +2 (d8 and d10) as electron donors and σ-holes located in halogen and chalcogen atoms as electron acceptors. To our knowledge, it has not been described for σ-holes located in pnictogen atoms. In this manuscript, evidence for the existence of pnictogen bonding involving the square planar Pt(II) metal as the electron donor and Sb as the electron acceptor is provided by using an X-ray structure retrieved from the Cambridge Structural Database (CSD) and theoretical calculations. In particular, the quantum theory of atoms in molecules (QTAIM), the noncovalent interaction plot (NCIPlot) and molecular electrostatic potential (MEP) methods were used. Moreover, to further confirm the nature of the Sb···Pt(II) contact, a recently developed method was used where the electron density (ED) and electrostatic potential (ESP) distribution were compared along the Sb···Pt(II) bond path.
    Type of Medium: Online Resource
    ISSN: 2304-6740
    URL: Article
    DOI: 10.3390/inorganics11020080
    Language: English
    Publisher: MDPI AG
    Publication Date: 2023
    detail.hit.zdb_id: 2735043-5
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  • 9
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    Reconciling Experiment and Theory in the Use of Aryl-Extended Calix[4]pyrrole Receptors for the Experimental Quantification of Chloride–π Interactions in Solution
    MDPI AG ; 2015
    In:  International Journal of Molecular Sciences Vol. 16, No. 12 ( 2015-04-22), p. 8934-8948
    Details
    In: International Journal of Molecular Sciences, MDPI AG, Vol. 16, No. 12 ( 2015-04-22), p. 8934-8948
    Type of Medium: Online Resource
    ISSN: 1422-0067
    URL: Article
    DOI: 10.3390/ijms16048934
    Language: English
    Publisher: MDPI AG
    Publication Date: 2015
    detail.hit.zdb_id: 2019364-6
    SSG: 12
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  • 10
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    On the Importance of Pnictogen and Chalcogen Bonding Interactions in Supramolecular Catalysis
    MDPI AG ; 2021
    In:  International Journal of Molecular Sciences Vol. 22, No. 22 ( 2021-11-21), p. 12550-
    Details
    In: International Journal of Molecular Sciences, MDPI AG, Vol. 22, No. 22 ( 2021-11-21), p. 12550-
    Abstract: In this review, several examples of the application of pnictogen (Pn) (group 15) and chalcogen (Ch) bonding (group 16) interactions in organocatalytic processes are gathered, backed up with Molecular Electrostatic Potential surfaces of model systems. Despite the fact that the use of catalysts based on pnictogen and chalcogen bonding interactions is taking its first steps, it should be considered and used by the scientific community as a novel, promising tool in the field of organocatalysis.
    Type of Medium: Online Resource
    ISSN: 1422-0067
    URL: Article
    DOI: 10.3390/ijms222212550
    Language: English
    Publisher: MDPI AG
    Publication Date: 2021
    detail.hit.zdb_id: 2019364-6
    SSG: 12
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