The novel noncovalent interactions between the charged and neutral aromatic rings and with anions are utilized to design the solid-state assembly of triply protonated PTPH3 (PTP = ...4′-(4-pyridyl)-3,2′:6′,3″-terpyridine) with H2O and three ClO4 –, which is synthesized and characterized by single-crystal X-ray diffraction analysis. Crystallography reveals that the π+–π+, π+–π, and various anion···π interactions are the major driving forces in the stabilization of the self-assembled structure. In the title complex, a layered assembly is formed through the mutual influence of π+–π+ and π+–π interactions. The anions are interacting with the charged π-acceptors, which are again stabilized through π+–π interactions. Therefore, the overall stabilization is governed through π+–π/π–π+, (π+–π+) n , and anion···π+/π+–π/π–π+ networks in the solid state. The interaction energies of the main driving forces observed in the crystal structure have been calculated using density functional theory. In addition, the short O···O contact between ClO4 – anions has been analyzed in detail both computationally and exploring the Cambridge Structural Database.
In this article, ab initio calculations have been combined with a search in the Protein Data Bank (PDB) to demonstrate the importance of σ-hole tetrel bonding interactions in biological systems. In ...particular, we focus our attention on the ability of the −CF3 group to participate in noncovalent interactions as Lewis acids, and we show the importance of this interaction in the inhibition mechanism of a NADP+-dependent isocitrate dehydrogenase (IDH) enzyme that converts isocitrate to α-ketoglutarate. IDH mutations are found in multiple hematologic and solid tumors, inducing premalignant disorders. A potent triazine-based inhibitor of the mutant IDH (enasidenib) presents two −CF3 groups in the structure. One establishes a tetrel bonding interaction with an aspartate residue that contributes to the binding and selectivity of the inhibitor to the active site.
Carboxylato (R = tBu and Et) and carbonato bridges have been utilized for nickel(II)-based aggregates Ni4(μ-H2L)2(μ3-OH)2(μ1,3-O2CBut)2(NO3)2·H2O·2DMF (1·H2O·2DMF), ...Ni4(μ-hyHL)2(μ3-OMe)2(μ1,1-N3)2(μ1,3-O2CEt)2·4H2O (2·4H2O), and Ni6(μ4-L)(μ3-L)2(μ6-CO3)(H2O)8(ClO4)·9H2O (3·9H2O). Building blocks Ni2(μ-H2L)3+, Ni2(μ-hyHL)3+, and Ni2(μ-L)+ originating from Ni2(μ-H2L)3+ have been trapped in these complexes. The complexes have been characterized by X-ray crystallography, magnetic measurements, and density functional theory (DFT) analysis. In 1, the magnetic interactions are transmitted through the μ3-phenoxido/μ3-hydroxido/syn–syn-tBuCO2 –, μ3-phenoxido/μ3- hydroxido, and double μ3-phenoxido/double μ3-hydroxido bridges with J = +11.4 cm–1, J 1 = −2.1 cm–1, and J 2 = −2.8 cm–1, respectively. In 2, the interactions are ferromagnetic, with J 1 = +27.5 cm–1, J 2 = +20.62 cm–1, and J 3 = +1.52 cm–1 describing the magnetic couplings through the μ-phenoxidoo/μ3-methoxido, μ-azido/μ3-methoxido, and μ3-methoxido/μ3-methoxido exchange pathways, respectively. Complex 3 gives J 1 = −3.30 cm–1, J 2 = +1.7 cm–1, and J 3 = −12.8 cm–1 for exchange pathways mediated by μ-phenoxido/μ-carbonato, μ-alkoxido/μ-alkooxido/μ-syn–syn-carbonato, and the μ-phenoxido/μ-carbonato, respectively. Interestingly, 1 and 3 below 20 K and 35 K, respectively, show an abrupt increase of the χM T product to reach a magnetic-field-dependent maximum, which is associated with a slightly frequency-dependent out-of-phase alternating-current peak. DFT calculations have also been performed on 1–3 to explain the exchange interaction mechanisms and to support the magnitude and sign of the magnetic coupling constants between the NiII ions.
In this manuscript, we combine high-level ab initio calculations on some model systems (XCH3 σ-hole/H-bond donors) and a Protein Data Bank (PDB) survey to distinguish between trifurcated H-bonds and ...noncovalent carbon bonds in XCH3···O complexes (X = any atom or group). Recently, it has been demonstrated both experimentally and theoretically the importance of noncovalent carbon bonds in the solid state. When an electron-rich atom interacts with a methyl group, the role of the methyl group is commonly viewed as a weak H-bond donor. However, if the electron-rich atom is located equidistant from the three H atoms, the directionality of each individual H-bond in the trifurcated binding mode is poor. Therefore, the XCH3···O interaction could be also defined as a tetrel bond (C···O interaction). In this manuscript, we shed light into this matter and demonstrate the importance of XCH3···O noncovalent carbon bonding interactions in two relevant protein-substrate complexes retrieved from the PDB.
Regium−π Bonds Are Involved in Protein–Gold Binding Piña, María de las Nieves; Frontera, Antonio; Bauzá, Antonio
The journal of physical chemistry letters,
10/2020, Letnik:
11, Številka:
19
Journal Article
Recenzirano
The regium−π interaction is an attractive noncovalent force between group 11 elements (Cu, Ag, and Au) acting as Lewis acids and aromatic surfaces. Herein, we report for the first time experimental ...(Protein Data Bank analysis) and theoretical (RI-MP2/def2-TZVP level of theory) evidence of regium−π bonds involving Au(I) and aromatic amino acids (Phe, Tyr, Trp, and His). These findings might be important in the field of drug design and for retrospectively understanding the role of gold in proteins.
We report evidence of the favorable noncovalent interaction between a covalently bonded atom of Group 18 (known as noble gases or aerogens) and a negative site, for example, a lone pair of a Lewis ...base or an anion. It involves a region of positive electrostatic potential (σ‐hole), therefore it is a totally new and unexplored σ‐hole‐based interaction, namely aerogen bonding. We demonstrate for the first time the existence of σ‐hole regions in aerogen derivatives by means of high‐level ab initio calculations. In addition, several crystal structures retrieved from the Cambridge Structural Database (CSD) give reliability to the calculations. Energetically, aerogen bonds are comparable to hydrogen bonds and other σ‐hole‐based interactions but less directional. They are expected to be important in xenon chemistry.
A new noncovalent interaction between a covalently bonded atom of Group 18 and a negative site, for example, a lone pair of a Lewis base or an anion, is called an aerogen bonding. It involves a region of positive electrostatic potential (σ‐hole). Energetically, aerogen bonds are comparable to hydrogen bonds and other σ‐hole‐based interactions but less directional. They might be important in xenon chemistry.
Five heterobimetallic copper(II)–uranium(VI) complexes (CuL1)UO2(NO3)2 (1), {CuL1(CH3CN)}UO2(NO3)2 (2), {CuL1(CH3COCH3)}UO2(NO3)2 (3), {CuL2(CH3CN)}UO2(NO3)2(4), and ...{CuL2(CH3COCH3)}UO2(NO3)2{CuL2}UO2(NO3)2 (5) have been synthesized by reacting the Cu(II)-derived metalloligands CuL1 and CuL2 (where, H2L1 = N,N′-bis(α-methylsalicylidene)-1,3-propanediamine and H2L2 = N,N′-bis(salicylidene)-1,3-propanediamine) with UO2(NO3)2·6H2O in 1:1 ratio by varying the reaction temperature and solvents. Absorption and fluorescence quenching experiments (steady-state and time-resolved) indicate the formation of 1:1 ground-state charge transfer copper(II)–uranium(VI) complexes in solution. X-ray single-crystal structure reveals that each complex contains diphenoxido bridged Cu(II)–U(VI) dinuclear core with two chelated nitrato coligands. The complexes are solvated (acetonitrile or acetone) in the axial position of the Cu(II) in different manner or desolvated. The supramolecular interactions that depend upon the co-ordinating metalloligands seem to control the solvation. In complexes 2 and 3 a rare NO3 –···NO3 – weak interaction plays an important role in forming supramolecular network whereas an uncommon UO···NO3 – weak interaction helps to self-assemble heterobinuclear units in complex 5. The significance of the noncovalent interactions in terms of energies and geometries has been analyzed using theoretical calculations.
Unraveling the binding preferences involved in the formation of a supramolecular complex is key to properly understand molecular recognition and aggregation phenomena, which are of pivotal importance ...to biology. The halogenation of nucleic acids has been routinely carried out for decades to assist in their X-ray diffraction analysis. The incorporation of a halogen atom on a DNA/RNA base not only affected its electronic distribution, but also expanded the noncovalent interactions toolbox beyond the classical hydrogen bond (HB) by incorporating the halogen bond (HalB). In this regard, an inspection of the Protein Data Bank (PDB) revealed 187 structures involving halogenated nucleic acids (either unbound or bound to a protein) where at least 1 base pair (BP) exhibited halogenation. Herein, we were interested in disclosing the strength and binding preferences of halogenated A···U and G···C BPs, which are predominant in halogenated nucleic acids. To achieve that, computations at the RI-MP2/def2-TZVP level of theory together with state of the art theoretical modeling tools (including the computation of molecular electrostatic potential (MEP) surfaces, the quantum theory of "Atoms in Molecules" (QTAIM) and the non-covalent interactions plot (NCIplot) analyses) allowed for the characterization of the HB and HalB complexes studied herein.
•Noble gas bonding interactions: theoretical insights.•Cooperativity effects between Noble gas bonding and other noncovalent interactions.•Noble gas bonding interactions: A CSD survey of xenon ...compounds.
Following the systematic nomenclature recommended by the IUPAC for other π,σ-hole interactions, a nobel gas (or aerogen) bond (NgB) is defined as the attractive interaction between an electron rich atom or group of atoms and any element of Group-18 acting as electron acceptor. Investigations on π,σ-hole interactions and their applications in crystal engineering, molecular recognition and catalysis have exponentially grown in recent years. For obvious reasons, investigations on noncovalent Ng bonding interactions are less abundant compared to their sisters (halogen, chalcogen, pnictogen and tetrel bonding, namely XB, ChB, PnB and TrB, respectively). In this review, we put into perspective the available theoretical and experimental investigations on σ-hole and π-hole interactions involving noble gas atoms. We describe a number of theoretical works revealing that NgB follows the typical behavior already described for XB, ChB, PnB and TrB, where stronger interactions occur moving the whole group down. A search the Cambridge Structural Database (CSD) and Inorganic Crystal Structure Database (ICSD) reveals that there are several X-ray structures of xenon derivatives where NgB interaction is crucial for the crystal packing stability. This taking is sub-divided into three sections subject to the oxidation state of xenon. The crystallographic search evidences that interactions between Xe and electron rich atoms are frequent and directional.
The w(hole) picture: A tetrel bond is a directional noncovalent interaction between a covalently bonded atom of Group IV and a negative site, for example, the lone pair of a Lewis base or an anion. ...It involves a region of positive electrostatic potential (σ hole), and energetically, they are comparable to hydrogen bonds and other σ‐hole‐based interactions.
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