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Nicastri KA, Zappia SA, Pratt JC, Duncan JM, Guzei IA, Fernández I, Schomaker JM. Tunable Aziridinium Ylide Reactivity: Non-covalent Interactions Enable Divergent Product Outcomes. ACS Catal 2022; 12:1572-1580. [PMID: 35291380 DOI: 10.1021/acscatal.1c05413] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Methods for rapid preparation of densely functionalized and stereochemically complex N-heterocyclic scaffolds are in demand for exploring potential bioactive chemical space. This work describes experimental and computational studies to better understand the features of aziridinium ylides as intermediates for the synthesis of highly substituted dehydromorpholines. The development of this chemistry has enabled the extension of aziridinium ylide chemistry to the concomitant formation of both a C-N and a C-O bond in a manner that preserves the stereochemical information embedded in the substrate. Additionally, we have uncovered several key insights that describe the importance of steric effects, rotational barriers around the C-N bond of the aziridinium ylide, and non-covalent interactions (NCIs) on the ultimate reaction outcome. These critical insights will assist in the further development of this chemistry to generate N-heterocycles that will further expand complex amine chemical space.
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77
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Zhao J, Zheng X. Progress on Exploring the Luminescent Properties of Organic Molecular Aggregates by Multiscale Modeling. Front Chem 2022; 9:808957. [PMID: 35096770 PMCID: PMC8790572 DOI: 10.3389/fchem.2021.808957] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Accepted: 12/03/2021] [Indexed: 11/20/2022] Open
Abstract
Luminescent molecular aggregates have attracted worldwide attention because of their potential applications in many fields. The luminescent properties of organic aggregates are complicated and highly morphology-dependent, unraveling the intrinsic mechanism behind is urgent. This review summarizes recent works on investigating the structure-property relationships of organic molecular aggregates at different environments, including crystal, cocrystal, amorphous aggregate, and doped systems by multiscale modeling protocol. We aim to explore the influence of intermolecular non-covalent interactions on molecular packing and their photophysical properties and then pave the effective way to design, synthesize, and develop advanced organic luminescent materials.
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78
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Jian J, Hammink R, McKenzie CJ, Bickelhaupt FM, Poater J, Mecinovic J. Probing the Lewis Acidity of Boronic Acids through Interactions with Arene Substituents. Chemistry 2021; 28:e202104044. [PMID: 34958482 PMCID: PMC9306523 DOI: 10.1002/chem.202104044] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Indexed: 11/23/2022]
Abstract
Boronic acids are Lewis acids that exist in equilibrium with boronate forms in aqueous solution. Here we experimentally and computationally investigated the Lewis acidity of 2,6‐diarylphenylboronic acids; specially designed phenylboronic acids that possess two flanking aromatic rings with tunable aromatic character. Hammett analysis of 2,6‐diarylphenylboronic acids reveals that their Lewis acidity remains unchanged upon the introduction of EWG/EDG at the distant para position of the flanking aromatic rings. Structural and computational studies demonstrate that polar‐π interactions and solvation effects contribute to the stabilization of boronic acids and boronate forms by aromatic rings. Our physical‐organic chemistry work highlights that boronic acids and boronates can be stabilized by aromatic systems, leading to an important molecular knowledge for rational design and development of boronic acid‐based catalysts and inhibitors of biomedically important proteins.
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79
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Clustering of Aromatic Amino Acid Residues around Methionine in Proteins. Biomolecules 2021; 12:biom12010006. [PMID: 35053154 PMCID: PMC8774105 DOI: 10.3390/biom12010006] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 12/14/2021] [Accepted: 12/18/2021] [Indexed: 12/31/2022] Open
Abstract
Short-range, non-covalent interactions between amino acid residues determine protein structures and contribute to protein functions in diverse ways. The interactions of the thioether of methionine with the aromatic rings of tyrosine, tryptophan, and/or phenylalanine has long been discussed and such interactions are favorable on the order of 1–3 kcal mol−1. Here, we carry out a new bioinformatics survey of known protein structures where we assay the propensity of three aromatic residues to localize around the [-CH2-S-CH3] of methionine. We term these groups “3-bridge clusters”. A dataset consisting of 33,819 proteins with less than 90% sequence identity was analyzed and such clusters were found in 4093 structures (or 12% of the non-redundant dataset). All sub-classes of enzymes were represented. A 3D coordinate analysis shows that most aromatic groups localize near the CH2 and CH3 of methionine. Quantum chemical calculations support that the 3-bridge clusters involve a network of interactions that involve the Met-S, Met-CH2, Met-CH3, and the π systems of nearby aromatic amino acid residues. Selected examples of proposed functions of 3-bridge clusters are discussed.
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80
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Belhocine Y, Rahali S, Allal H, Assaba IM, Ghoniem MG, Ali FAM. A Dispersion Corrected DFT Investigation of the Inclusion Complexation of Dexamethasone with β-Cyclodextrin and Molecular Docking Study of Its Potential Activity against COVID-19. Molecules 2021; 26:molecules26247622. [PMID: 34946702 PMCID: PMC8708408 DOI: 10.3390/molecules26247622] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2021] [Revised: 12/09/2021] [Accepted: 12/10/2021] [Indexed: 12/23/2022] Open
Abstract
The encapsulation mode of dexamethasone (Dex) into the cavity of β-cyclodextrin (β-CD), as well as its potential as an inhibitor of the COVID-19 main protease, were investigated using density functional theory with the recent dispersion corrections D4 and molecular docking calculations. Independent gradient model and natural bond orbital approaches allowed for the characterization of the host–guest interactions in the studied systems. Structural and energetic computation results revealed that hydrogen bonds and van der Waals interactions played significant roles in the stabilization of the formed Dex@β-CD complex. The complexation energy significantly decreased from −179.50 kJ/mol in the gas phase to −74.14 kJ/mol in the aqueous phase. A molecular docking study was performed to investigate the inhibitory activity of dexamethasone against the COVID-19 target protein (PDB ID: 6LU7). The dexamethasone showed potential therapeutic activity as a SARS CoV-2 main protease inhibitor due to its strong binding to the active sites of the protein target, with predicted free energy of binding values of −29.97 and −32.19 kJ/mol as calculated from AutoDock4 and AutoDock Vina, respectively. This study was intended to explore the potential use of the Dex@β-CD complex in drug delivery to enhance dexamethasone dissolution, thus improving its bioavailability and reducing its side effects.
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81
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Inoue H, Yamashita Y, Ozawa Y, Ono T, Abe M. Solid-State Structures and Photoluminescence of Lamellar Architectures of Cu(I) and Ag(I) Paddlewheel Clusters with Hydrogen-Bonded Polar Guests. Molecules 2021; 26:molecules26216731. [PMID: 34771140 PMCID: PMC8587135 DOI: 10.3390/molecules26216731] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 11/01/2021] [Accepted: 11/03/2021] [Indexed: 11/16/2022] Open
Abstract
Two hexanuclear paddlewheel-like clusters appending six carboxylic-acid pendants have been isolated with the inclusion of polar solvent guests: [Cu6(Hmna)6]·7DMF (1·7DMF) and [Ag6(Hmna)6]·8DMSO (2·8DMSO), where H2mna = 2-mercaptonicotininc acid, DMF = N,N’-dimethylformamide, and DMSO = dimethyl sulfoxide. The solvated clusters, together with their fully desolvated forms 1 and 2, have been characterized by FTIR, UV–Vis diffuse reflectance spectroscopy, TG-DTA analysis, and DFT calculations. Crystal structures of two solvated clusters 1·7DMF and 2·8DMSO have been unambiguously determined by single-crystal X-ray diffraction analysis. Six carboxylic groups appended on the clusters trap solvent guests, DMF or DMSO, through H-bonds. As a result, alternately stacked lamellar architectures comprising of a paddlewheel cluster layer and H-bonded solvent layer are formed. Upon UV illumination (λex = 365 nm), the solvated hexasilver(I) cluster 2·8DMSO gives intense greenish-yellow photoluminescence in the solid state (λPL = 545 nm, ΦPL = 0.17 at 298 K), whereas the solvated hexacopper(I) cluster 1·7DMF displays PL in the near-IR region (λPL = 765 nm, ΦPL = 0.38 at 298 K). Upon complete desolvation, a substantial bleach in the PL intensity (ΦPL < 0.01) is observed. The desorption–sorption response was studied by the solid-state PL spectroscopy. Non-covalent interactions in the crystal including intermolecular H-bonds, CH⋯π interactions, and π⋯π stack were found to play decisive roles in the creation of the lamellar architectures, small-molecule trap-and-release behavior, and guest-induced luminescence enhancement.
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82
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Rama Krishna VS, Adak S, Jana P, Bheemireddy V, Bandyopadhyay S. Mimicking the Energy Funnel of the Photosynthetic Unit Using a Dendrimer-Dye Supramolecular Assembly. Chem Asian J 2021; 16:3481-3486. [PMID: 34487427 DOI: 10.1002/asia.202100886] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 09/01/2021] [Indexed: 11/10/2022]
Abstract
Photosynthesis involves light-harvesting complexes where an array of antenna pigment channels the absorbed solar energy to the reaction centre of a photosystem. This work reports a supramolecular dendrimer-dye assembly that mimics the natural light-harvesting mechanism. A dendrimeric molecule based on two-fluorophores has been constructed with three coumarin units at the end of three long arms and a 7-diethylaminocoumarin unit at the interior. The molecule self-aggregates in water into spherical micelles, which can encapsulate a rose-bengal dye (RB). On excitation, peripheral coumarin units shuttled the energy to the loaded RB dye reaction center via a two-step cascade resonance energy transfer (RET). The energy absorbed in the periphery is funnelled efficiently, resulting in a strong emission from the dye that resembles an energy funnel. The energy transfer cascade has been studied with both steady-state and time-resolved fluorescence spectroscopy. Molecular dynamics simulations of the self-assembled aggregates in water were also in agreement with the experimental observations.
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83
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Zhang W, Nafady A, Shan C, Wojtas L, Chen YS, Cheng Q, Zhang XP, Ma S. Functional Porphyrinic Metal-Organic Framework as a New Class of Heterogeneous Halogen-Bond-Donor Catalyst. Angew Chem Int Ed Engl 2021; 60:24312-24317. [PMID: 34496141 DOI: 10.1002/anie.202111893] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Indexed: 11/12/2022]
Abstract
Biomimetic metal-organic frameworks have attracted great attention as they can be used as bio-inspired models, allowing us to gain important insights into how large biological molecules function as catalysts. In this work, we report the synthesis and utilization of such a metal-metalloporphyrin framework (MMPF) that is constructed from a custom-designed ligand as an efficient halogen bond donor catalyst for Diels-Alder reactions under ambient conditions. The implementation of fabricated halogen bonding capsule as binding pocket with high-density C-Br bonds enabled the use of halogen bonding to facilitate organic transformations in their three-dimensional cavities. Through combined experimental and computational studies, we showed that the substrate molecules diffuse through the pores of the MMPF, establishing a host-guest system via the C-Br⋅⋅⋅π interaction. The formation of halogen bonds is a plausible explanation for the observed boosted catalytic efficiency in Diels-Alder reactions. Moreover, the unique capability of MMPF highlights new opportunities in using artificial non-covalent binding pockets as highly tunable and selective catalytic materials.
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84
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Bravin C, Piękoś JA, Licini G, Hunter CA, Zonta C. Dissection of the Polar and Non-Polar Contributions to Aromatic Stacking Interactions in Solution. Angew Chem Int Ed Engl 2021; 60:23871-23877. [PMID: 34472177 PMCID: PMC8596670 DOI: 10.1002/anie.202110809] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Indexed: 11/19/2022]
Abstract
Aromatic stacking interactions have been a matter of study and debate due to their crucial role in chemical and biological systems. The strong dependence on orientation and solvent together with the relatively small interaction energies have made evaluation and rationalization a challenge for experimental and theoretical chemists. We have used a supramolecular cage formed by two tris(pyridylmethyl)amines units to build chemical Double Mutant Cycles (DMC) for the experimental measurement of the free energies of π-stacking interactions. Extrapolating the substituent effects to remove the contribution due to electrostatic interactions reveals that there is a substantial contribution to the measured stacking interaction energies which is due to non-polar interactions (-3 to -6 kJ mol-1 ). The perfectly flat nature of the surface of an aromatic ring gives π-stacking an inherent advantage over non-polar interactions with alkyl groups and accounts for the wide-spread prevalence of stacking interactions in Nature.
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85
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López JC, Macario A, Maris A, Alkorta I, Blanco S. How Aromatic Fluorination Exchanges the Interaction Role of Pyridine with Carbonyl Compounds: The Formaldehyde Adduct. Chemistry 2021; 27:13870-13878. [PMID: 34347915 PMCID: PMC8518414 DOI: 10.1002/chem.202102163] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Indexed: 11/11/2022]
Abstract
The rotational spectrum of the weakly bound complex pentafluoropyridine⋅⋅⋅formaldehyde has been investigated using Fourier transform microwave spectroscopy. From the analysis of the rotational parameters of the parent species and of the 13 C and 15 N isotopologues, the structural arrangement of the adduct has been unambiguously established. The full ring fluorination of pyridine has a dramatic effect on its binding properties: It alters the electron density distribution at the π-cloud of pyridine creating a π-hole and changing its electron donor-acceptor capabilities. In the complex, formaldehyde lies above the aromatic ring with one of the oxygen lone pairs, as conventionally envisaged, pointing toward its centre. This lone pair⋅⋅⋅π-hole interaction, reinforced by a weak C-H⋅⋅⋅N interaction, indicates an exchange of the electron-acceptor roles of both molecules when compared to the pyridine⋅⋅⋅formaldehyde adduct. Tunnelling doublets due to the internal rotation of formaldehyde have also been observed and analysed leading to a discussion on the competition between lone pair⋅⋅⋅π-hole and π⋅⋅⋅π stacking interactions.
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86
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Balónová B, Blight BA. Elucidation of Charge Contribution in Iridium-Chelated Hydrogen-Bonding Systems. Front Chem 2021; 9:712698. [PMID: 34504832 PMCID: PMC8421767 DOI: 10.3389/fchem.2021.712698] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Accepted: 07/20/2021] [Indexed: 11/13/2022] Open
Abstract
We present two iridium complexes 1H+ and 2H+ that contain cationic ligands to extend the knowledge of charge-assisted hydrogen bonding (CAHB), which counts among the strongest non-covalent bonding interactions. Upon protonation, both complexes were converted into new hydrogen-bonding arrays with various selectivity for respective H-bonding partners. This study compares the association strengths of four hydrogen-bonding co-systems, emphasizing the roles of CAHB in supramolecular systems. We determined that the cationic charge in these systems contributed up to 2.7 kJ mol−1 in the H-bonding complexation processes.
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87
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Weiss R, Aubert E, Pale P, Mamane V. Chalcogen-Bonding Catalysis with Telluronium Cations. Angew Chem Int Ed Engl 2021; 60:19281-19286. [PMID: 34166563 DOI: 10.1002/anie.202105482] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Revised: 06/04/2021] [Indexed: 11/08/2022]
Abstract
Chalcogen bonding results from non-covalent interactions occurring between electrodeficient chalcogen atoms and Lewis bases. Among the chalcogens, tellurium is the strongest Lewis acid, but Te-based compounds are scarcely used as organocatalysts. For the first time, telluronium cations demonstrated impressive catalytic properties at low loadings in three benchmark reactions: the Friedel-Crafts bromination of anisole, the bromolactonization of ω-unsaturated carboxylic acids and the aza-Diels-Alder between Danishefsky's diene and imines. The ability of telluronium cations to interact with a Lewis base through chalcogen bonding was demonstrated on the basis of multi-nuclear (17 O, 31 P, and 125 Te) NMR analysis and DFT calculations.
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88
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Shenderovich IG, Denisov GS. Modeling of the Response of Hydrogen Bond Properties on an External Electric Field: Geometry, NMR Chemical Shift, Spin-Spin Scalar Coupling. Molecules 2021; 26:molecules26164967. [PMID: 34443575 PMCID: PMC8399935 DOI: 10.3390/molecules26164967] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 08/10/2021] [Accepted: 08/16/2021] [Indexed: 12/15/2022] Open
Abstract
The response of the geometric and NMR properties of molecular systems to an external electric field has been studied theoretically in a wide field range. It has been shown that this adduct under field approach can be used to model the geometric and spectral changes experienced by molecular systems in polar media if the system in question has one and only one bond, the polarizability of which significantly exceeds the polarizability of other bonds. If this requirement is met, then it becomes possible to model even extreme cases, for example, proton dissociation in hydrogen halides. This requirement is fulfilled for many complexes with one hydrogen bond. For such complexes, this approach can be used to facilitate a detailed analysis of spectral changes associated with geometric changes in the hydrogen bond. For example, in hydrogen-bonded complexes of isocyanide C≡15N-1H⋯X, 1J(15N1H) depends exclusively on the N-H distance, while δ(15N) is also slightly influenced by the nature of X.
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89
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Landeros-Rivera B, Jancik V, Moreno-Esparza R, Martínez Otero D, Hernández-Trujillo J. Non-Covalent Interactions in the Biphenyl Crystal: Is the Planar Conformer a Transition State? Chemistry 2021; 27:11912-11918. [PMID: 34043851 DOI: 10.1002/chem.202101490] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Indexed: 11/09/2022]
Abstract
A combined experimental and theoretical study of the biphenyl (BP) crystal is presented. The X-ray diffraction data collected at 100 K were subjected to Hirshfeld atom and multipole refinements of the electron density, ρ(r). A theoretical exploration of the potential energy surface (PES) of the crystal was also carried out. This investigation challenges the common assumption that the planar structure of BP in the phase I crystal is an average of two twisted configurations in a double-well potential. The theoretical computations provide compelling evidence that this structure corresponds to a minimum on the PES hence to a stable molecular arrangement. Consistently, the experiment showed no evidence of positional or dynamic disorder. The intramolecular hydrogen-hydrogen bonds detected are not repulsive. The topological analysis of the experimental and theoretical ρ(r) reveals that both the intra- and intermolecular H⋅⋅⋅H and the C-H⋅⋅⋅π contacts stabilize the BP crystal.
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90
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Sureshan KM, Madhusudhanan MC, Balan H, Werz DB. Azide···Oxygen Interaction: A Crystal Engineering Tool for Conformational Locking. Angew Chem Int Ed Engl 2021; 60:22797-22803. [PMID: 34399025 DOI: 10.1002/anie.202106614] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 08/15/2021] [Indexed: 11/09/2022]
Abstract
We have designed, synthesized and crystallized 36 compounds, each containing an azide group and an oxygen atom separated by three bonds. Crystal structure analysis revealed that each of these molecules adopts a conformation in which the azide and oxygen groups orient syn to each other with a short O ··· N b contact. Geometry-optimized structures [using M06-2X/6-311G(d,p) level of theory ] also showed the syn conformation in all 36 of these cases, suggesting that this not merely a crystal packing effect. Quantum topological analysis using Bader's Atoms in Molecules (AIM) theory revealed bond paths and bond critical points (BCP) in these structures suggesting its nature and energetics to be similar to weak hydrogen bonding. The NCI-RDG plot clearly revealed the attractive interaction consisting of electrostatic or dispersive components in all the 36 systems. NBO analysis suggested a weak orbital-relaxation (charge-transfer) contribution of energy for a few (sp2) O-donor systems. Natural population analysis (NPA) and molecular electrostatic potential mapping (MESP) of these crystal structures further revealed the existence of favorable azide-oxygen interaction. A CSD search indicated the frequent and consistent occurrence of this interaction and its role dictating the syn conformation of azide and oxygen in molecules where these groups are separated by 2-4 bonds.
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91
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Czernek J, Brus J. On the Many-Body Expansion of an Interaction Energy of Some Supramolecular Halogen-Containing Capsules. Molecules 2021; 26:4431. [PMID: 34361581 PMCID: PMC8347495 DOI: 10.3390/molecules26154431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 07/18/2021] [Accepted: 07/19/2021] [Indexed: 11/16/2022] Open
Abstract
A tetramer model was investigated of a remarkably stable iodine-containing supramolecular capsule that was most recently characterized by other authors, who described emergent features of the capsule's formation. In an attempt to address the surprising fact that no strong pair-wise interactions between any of the respective components were experimentally detected in condensed phases, the DFT (density-functional theory) computational model was used to decompose the total stabilization energy as a sum of two-, three- and four-body contributions. This model considers complexes formed between either iodine or bromine and the crucial D4d-symmetric form of octaaryl macrocyclic compound cyclo[8](1,3-(4,6-dimethyl)benzene that is surrounded by arenes of a suitable size, namely, either corannulene or coronene. A significant enthalpic gain associated with the formation of investigated tetramers was revealed. Furthermore, it is shown that the total stabilization of these complexes is dominated by binary interactions. Based on these findings, comments are made regarding the experimentally observed behavior of related multicomponent mixtures.
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92
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Skopinska-Wisniewska J, De la Flor S, Kozlowska J. From Supramolecular Hydrogels to Multifunctional Carriers for Biologically Active Substances. Int J Mol Sci 2021; 22:7402. [PMID: 34299020 PMCID: PMC8307912 DOI: 10.3390/ijms22147402] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2021] [Revised: 07/05/2021] [Accepted: 07/07/2021] [Indexed: 01/04/2023] Open
Abstract
Supramolecular hydrogels are 3D, elastic, water-swelled materials that are held together by reversible, non-covalent interactions, such as hydrogen bonds, hydrophobic, ionic, host-guest interactions, and metal-ligand coordination. These interactions determine the hydrogels' unique properties: mechanical strength; stretchability; injectability; ability to self-heal; shear-thinning; and sensitivity to stimuli, e.g., pH, temperature, the presence of ions, and other chemical substances. For this reason, supramolecular hydrogels have attracted considerable attention as carriers for active substance delivery systems. In this paper, we focused on the various types of non-covalent interactions. The hydrogen bonds, hydrophobic, ionic, coordination, and host-guest interactions between hydrogel components have been described. We also provided an overview of the recent studies on supramolecular hydrogel applications, such as cancer therapy, anti-inflammatory gels, antimicrobial activity, controlled gene drug delivery, and tissue engineering.
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93
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Explanation of the Formation of Complexes between Representatives of Oxazolidinones and HDAS-β-CD Using Molecular Modeling as a Complementary Technique to cEKC and NMR. Int J Mol Sci 2021; 22:ijms22137139. [PMID: 34281189 PMCID: PMC8268345 DOI: 10.3390/ijms22137139] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 06/21/2021] [Accepted: 06/26/2021] [Indexed: 12/17/2022] Open
Abstract
Molecular modeling (MM) results for tedizolid and radezolid with heptakis-(2,3-diacetyl-6-sulfo)-β-cyclodextrin (HDAS-β-CD) are presented and compared with the results previously obtained for linezolid and sutezolid. The mechanism of interaction of chiral oxazolidinone ligands belonging to a new class of antibacterial agents, such as linezolid, tedizolid, radezolid, and sutezolid, with HDAS-β-CD based on capillary electrokinetic chromatography (cEKC), nuclear magnetic resonance (NMR) spectroscopy, and MM methods was described. Principles of chiral separation of oxazolidinone analogues using charged single isomer derivatives of cyclodextrin by the cEKC method were presented, including the selection of the optimal chiral selector and separation conditions, complex stoichiometry, and binding constants, which provided a comprehensive basis for MM studies. In turn, NMR provided, where possible, direct information on the geometry of the inclusion complexes and also provided the necessary structural information to validate the MM calculations. Consequently, MM contributed to the understanding of the structure of diastereomeric complexes, the thermodynamics of complexation, and the visualization of their structures. The most probable mean geometries of the studied supramolecular complexes and their dynamics (geometry changes over time) were determined by molecular dynamics methods. Oxazolidinone ligands have been shown to complex mainly the inner part of cyclodextrin, while the external binding is less privileged, which is consistent with the conclusions of the NMR studies. Enthalpy values of binding of complexes were calculated using long-term molecular dynamics in explicit water as well as using molecular mechanics, the Poisson-Boltzmann or generalized Born, and surface area continuum solvation (MM/PBSA and MM/GBSA) methods. Computational methods predicted the effect of changes in pH and composition of the solution on the strength and complexation process, and it adapted the conditions selected as optimal during the cEKC study. By changing the dielectric constant in the MM/PBSA and MM/GBSA calculations, the effect of changing the solution to methanol/acetonitrile was investigated. A fairly successful attempt was made to predict the chiral separation of the oxazolidinones using the modified cyclodextrin by computational methods.
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94
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Shanker G, Paul B, Ganjiwale A. Amino Acid and Peptide-Based Liquid Crystals: An Overview. Curr Org Synth 2021; 18:333-351. [PMID: 32938353 DOI: 10.2174/1570179417666200916092109] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Revised: 08/08/2020] [Accepted: 08/09/2020] [Indexed: 11/22/2022]
Abstract
The role of amino acids and peptides has found remarkable usage in both living systems and nonliving materials, which have enabled its utility by virtue of crafting molecular architectures through covalent bonds and non-covalent interactions. In material chemistry, the role of peptides in Liquid Crystals (LCs) is profound, especially in the rapid construction of supramolecular hierarchical networks. The importance of LCs for a variety of societal needs leads to the synthesis of innumerable LCs by conventional mesogenic strategy and nonconventional molecular design principles. For example, electronic appliances, including flat panel TV displays, electronic notebooks, digital cameras, domestic devices, use LCs as an integral component for such applications. In addition, LCs are useful in biological systems, including stem cell research, sensors for bacteria, virus, and proteins. These accomplishments are possible mostly due to the non-conventional molecular design principles for crafting LCs using smaller molecular motifs. The usage of amino acids and peptides in LCs facilitates many intrinsic characteristics, including side-chain diversity, chirality, directionality, reversibility, electro-optical, columnar axis, stimuli-responsive complex molecular architectures. The next essential criteria for any LCs design for useful applications are room temperature LC (RT-LC); therefore, the quest for such LCs system remains highly significant. Evidently, there are around half a million liquid crystalline molecules; only a handful of RTLCs has been found, as there is no simple, precise strategy or molecular design principles to obtain RT-LC systems. The smaller molecular motifs of amino acids and linear peptides as a structural part of mesogenic molecules led to many LC phases with properties, including lyotropic, thermotropic, and its applications in different realms. Therefore, this review serves as a compilation of Small Peptide-based LCs (SPLCs) exhibiting lyotropic and thermotropic phases with applications in the recent advancements.
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Mewes J, Hansen A, Grimme S. Comment on "The Nature of Chalcogen-Bonding-Type Tellurium-Nitrogen Interactions": Fixing the Description of Finite-Temperature Effects Restores the Agreement Between Experiment and Theory. Angew Chem Int Ed Engl 2021; 60:13144-13149. [PMID: 33960596 PMCID: PMC8252449 DOI: 10.1002/anie.202102679] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Indexed: 12/14/2022]
Abstract
Mitzel and co-workers recently presented an intriguing molecule displaying a tellurium-nitrogen interaction. Structural data obtained in the solid and in gas phase indicated a large increase of the Te-N equilibrium distance re from 2.64 to 2.92 Å, respectively. Although some DFT calculations appear to support the large re in gas phase, we argue that the lions share of the increase is due to an incomplete description of finite-temperature effects in the back-corrected experimental data. This hypothesis is based on high-level coupled-cluster (CC) and periodic DFT calculations, which consistently point towards a much smaller re in the isolated molecule. Further support comes through MD simulations with a tuned GFN2-xTB Hamiltonian: Calibrated against a CC reference, these show a six-times larger influence of temperature than with the originally used GFN1-xTB. Taking this into account, the back-corrected re in gas phase becomes 2.67±0.08 Å, in good agreement with high-level CC theory and most DFT methods.
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96
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I-Ting T, Montero-Campillo MM, Alkorta I, Elguero J, Yáñez M. Large Stabilization Effects by Intramolecular Beryllium Bonds in Ortho-Benzene Derivatives. Molecules 2021; 26:molecules26113401. [PMID: 34199746 PMCID: PMC8199991 DOI: 10.3390/molecules26113401] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Revised: 05/31/2021] [Accepted: 06/01/2021] [Indexed: 11/16/2022] Open
Abstract
Intramolecular interactions are shown to be key for favoring a given structure in systems with a variety of conformers. In ortho-substituted benzene derivatives including a beryllium moiety, beryllium bonds provide very large stabilizations with respect to non-bound conformers and enthalpy differences above one hundred kJ·mol−1 are found in the most favorable cases, especially if the newly formed rings are five or six-membered heterocycles. These values are in general significantly larger than hydrogen bonds in 1,2-dihidroxybenzene. Conformers stabilized by a beryllium bond exhibit the typical features of this non-covalent interaction, such as the presence of a bond critical point according to the topology of the electron density, positive Laplacian values, significant geometrical distortions and strong interaction energies between the donor and acceptor quantified by using the Natural Bond Orbital approach. An isodesmic reaction scheme is used as a tool to measure the strength of the beryllium bond in these systems in terms of isodesmic energies (analogous to binding energies), interaction energies and deformation energies. This approach shows that a huge amount of energy is spent on deforming the donor–acceptor pairs to form the new rings.
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97
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Zn(II) Heteroleptic Halide Complexes with 2-Halopyridines: Features of Halogen Bonding in Solid State. Molecules 2021; 26:molecules26113393. [PMID: 34205151 PMCID: PMC8199927 DOI: 10.3390/molecules26113393] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Revised: 05/28/2021] [Accepted: 06/02/2021] [Indexed: 12/29/2022] Open
Abstract
Reactions between Zn(II) dihalides and 2-halogen-substituted pyridines 2-XPy result in a series of heteroleptic molecular complexes [(2-XPy)2ZnY2] (Y = Cl, X = Cl (1), Br (2), I (3); Y = Br, X = Cl (4), Br (5), I (6), Y = I, X = Cl (7), Br (8), and I (9)). Moreover, 1-7 are isostructural (triclinic), while 8 and 9 are monoclinic. In all cases, halogen bonding plays an important role in formation of crystal packing. Moreover, 1-9 demonstrate luminescence in asolid state; for the best emitting complexes, quantum yield (QY) exceeds 21%.
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98
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Vermeeren P, Wolters LP, Paragi G, Fonseca Guerra C. Cooperative Self-Assembly in Linear Chains Based on Halogen Bonds. Chempluschem 2021; 86:812-819. [PMID: 33905182 PMCID: PMC8252609 DOI: 10.1002/cplu.202100093] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 03/30/2021] [Indexed: 12/03/2022]
Abstract
Cooperative properties of halogen bonds were investigated with computational experiments based on dispersion-corrected relativistic density functional theory. The bonding mechanism in linear chains of cyanogen halide (X-CN), halocyanoacetylene (X-CC-CN), and 4-halobenzonitrile (X-C6 H4 -CN) were examined for X = H, Cl, Br, and I. Our energy decomposition and Kohn-Sham molecular-orbital analyses revealed the bonding mechanism of the studied systems. Cyanogen halide and halocyanoacetylene chains possess an extra stabilizing effect with increasing chain size, whereas the 4-halobenzonitrile chains do not. This cooperativity can be traced back to charge separation within the σ-electronic system by charge-transfer between the lone-pair orbital of the nitrogen (σHOMO ) on one unit and the acceptor orbital of the C-X (σ*LUMO ) on the adjacent unit. As such, the HOMO-LUMO gap in the σ-system decreases, and the cooperativity increases with chain length revealing the similarity in the bonding mechanisms of hydrogen and halogen bonds.
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Apátiga JL, del Castillo RM, del Castillo LF, Calles AG, Espejel-Morales R, Favela JF, Compañ V. Non-Covalent Interactions on Polymer-Graphene Nanocomposites and Their Effects on the Electrical Conductivity. Polymers (Basel) 2021; 13:1714. [PMID: 34073855 PMCID: PMC8197260 DOI: 10.3390/polym13111714] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 05/20/2021] [Accepted: 05/21/2021] [Indexed: 11/16/2022] Open
Abstract
It is well known that a small number of graphene nanoparticles embedded in polymers enhance the electrical conductivity; the polymer changes from being an insulator to a conductor. The graphene nanoparticles induce several quantum effects, non-covalent interactions, so the percolation threshold is accelerated. We studied five of the most widely used polymers embedded with graphene nanoparticles: polystyrene, polyethylene-terephthalate, polyether-ketone, polypropylene, and polyurethane. The polymers with aromatic rings are affected mainly by the graphene nanoparticles due to the π-π stacking, and the long-range terms of the dispersion corrections are predominant. The polymers with linear structure have a CH-π stacking, and the short-range terms of the dispersion corrections are the important ones. We used the action radius as a measuring tool to quantify the non-covalent interactions. This action radius was the main parameter used in the Monte-Carlo simulation to obtain the conductivity at room temperature (300 K). The action radius was the key tool to describe how the percolation transition works from the fundamental quantum levels and connect the microscopic study with macroscopic properties. In the Monte-Carlo simulation, it was observed that the non-covalent interactions affect the electronic transmission, inducing a higher mean-free path that promotes the efficiency in the transmission.
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100
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Maué D, Strebert PH, Bernhard D, Rösel S, Schreiner PR, Gerhards M. Dispersion-Bound Isolated Dimers in the Gas Phase: Observation of the Shortest Intermolecular CH⋅⋅⋅H-C Distance via Stimulated Raman Spectroscopy. Angew Chem Int Ed Engl 2021; 60:11305-11309. [PMID: 33709534 PMCID: PMC8252503 DOI: 10.1002/anie.202016020] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 02/13/2021] [Indexed: 11/30/2022]
Abstract
The triphenylmethane and all‐meta tert‐butyl triphenylmethane dimers, (TPM)2 and (T tBuPM)2, respectively, were studied with ionization loss stimulated Raman spectroscopy in molecular beam experiments to resolve structure sensitive vibrations. This answers the question whether the recently reported linear head‐to‐head arrangement in (T tBuPM)2 results from crystal packing or prevails also in the gas phase, and therefore must result from extraordinarily strong London dispersion (LD) interactions. Our study clearly demonstrates that the head‐to‐head arrangement is maintained even under isolated molecular beam conditions in the absence of crystal packing effects. The central Raman‐active aliphatic C−D vibration of appropriately deuterated (T tBuPM)2 associated with an unusually short C−D⋅⋅⋅D−C distance exhibits a strong blue‐shift compared to the undisturbed case. As the LD stabilizing tert‐butyl groups are absent in (TPM)2, it displays an approximately S6‐symmetric tail‐to‐tail arrangement.
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