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John EA, Riel AMS, Wieske LHE, Ray D, Decato DA, Boller M, Takacs Z, Erdélyi M, Bryantsev VS, Berryman OB. Taming Molecular Folding: Anion-Templated Foldamers with Tunable Quaternary Structures. J Am Chem Soc 2024. [PMID: 38842125 DOI: 10.1021/jacs.3c14820] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2024]
Abstract
Higher-order foldamers represent a unique class of supramolecules at the forefront of molecular design. Herein we control quaternary folding using a novel approach that combines halogen bonding (XBing) and hydrogen bonding (HBing). We present the first anion-templated double helices induced by halogen bonds (XBs) and stabilized by "hydrogen bond enhanced halogen bonds" (HBeXBs). Our findings demonstrate that the number and orientation of hydrogen bond (HB) and XB donors significantly affect the quaternary structure and guest selectivity of two similar oligomers. This research offers new design elements to engineer foldamers and tailor their quaternary structure for specific guest binding.
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Affiliation(s)
- Eric A John
- Department of Chemistry and Biochemistry, University of Montana, Missoula, Montana 59812, United States
| | - Asia Marie S Riel
- Department of Chemistry and Biochemistry, University of Montana, Missoula, Montana 59812, United States
| | - Lianne H E Wieske
- Department of Chemistry─BMC, Organic Chemistry, Uppsala University, Husargatan 3, 752 37 Uppsala, Sweden
| | - Debmalya Ray
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Daniel A Decato
- Department of Chemistry and Biochemistry, University of Montana, Missoula, Montana 59812, United States
| | - Madeleine Boller
- Department of Chemistry and Biochemistry, University of Montana, Missoula, Montana 59812, United States
| | - Zoltan Takacs
- Swedish NMR Center, University of Gothenburg, Gothenburg SE-405 30, Sweden
| | - Máté Erdélyi
- Department of Chemistry─BMC, Organic Chemistry, Uppsala University, Husargatan 3, 752 37 Uppsala, Sweden
| | - Vyacheslav S Bryantsev
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Orion B Berryman
- Department of Chemistry and Biochemistry, University of Montana, Missoula, Montana 59812, United States
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2
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Devore DP, Ellington TL, Shuford KL. Elucidating the Role of Electron-Donating Groups in Halogen Bonding. J Phys Chem A 2024; 128:1477-1490. [PMID: 38373286 DOI: 10.1021/acs.jpca.3c06894] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/21/2024]
Abstract
Computational quantum chemical techniques were utilized to systematically examine how electron-donating groups affect the electronic and spectroscopic properties of halogen bond donors and their corresponding complexes. Unlike the majority of studies on halogen bonding, where electron-withdrawing groups are utilized, this work investigates the influence of electron-donating substituents within the halogen bond donors. Statistical analyses were performed on the descriptors of halogen bond donors in a prescribed set of archetype, halo-alkyne, halo-benzene, and halo-ethynyl benzene halogen bond systems. The σ-hole magnitude, binding and interaction energies, and the vibrational X···N local force constant (where X = Cl, Br, I, and At) were found to correlate very well in a monotonic and linear manner with all other properties studied. In addition, enhanced halogen bonds were found when the systems contained electron-donating groups that could form intramolecular hydrogen bonds with the electronegative belt of the halogen atom and adjacent linker features.
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Affiliation(s)
- Daniel P Devore
- Department of Chemistry and Biochemistry, Baylor University, One Bear Place #97348, Waco, Texas 76798-7348, United States
| | - Thomas L Ellington
- Department of Chemistry and Biochemistry, Baylor University, One Bear Place #97348, Waco, Texas 76798-7348, United States
| | - Kevin L Shuford
- Department of Chemistry and Biochemistry, Baylor University, One Bear Place #97348, Waco, Texas 76798-7348, United States
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3
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Sun J, Decato DA, Bryantsev VS, John EA, Berryman OB. The interplay between hydrogen and halogen bonding: substituent effects and their role in the hydrogen bond enhanced halogen bond. Chem Sci 2023; 14:8924-8935. [PMID: 37621436 PMCID: PMC10445465 DOI: 10.1039/d3sc02348f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Accepted: 07/20/2023] [Indexed: 08/26/2023] Open
Abstract
The hydrogen bond enhanced halogen bond (HBeXB) has recently been used to effectively improve anion binding, organocatalysis, and protein structure/function. In this study, we present the first systematic investigation of substituent effects in the HBeXB. NMR analysis confirmed intramolecular HBing between the amine and the electron-rich belt of the XB donor (N-H⋯I). Gas-phase density functional theory studies showed that the influence of HBing on the halogen atom is more sensitive to substitution on the HB donor ring (R1). The NMR studies revealed that the intramolecular HBing had a significant impact on receptor performance, resulting in a 50-fold improvement. Additionally, linear free energy relationship (LFER) analysis was employed for the first time to study the substituent effect in the HBeXB. The results showed that substituents on the XB donor ring (R2) had a competing effect where electron donating groups strengthened the HB and weakened the XB. Therefore, selecting an appropriate substituent on the adjacent HB donor ring (R1) could be an alternative and effective way to enhance an electron-rich XB donor. X-ray crystallographic analysis demonstrated that intramolecular HBing plays an important role in the receptor adopting the bidentate conformation. Taken together, the findings imply that modifying distal substituents that affect neighboring noncovalent interactions can have a similar impact to conventional para substitution substituent effects.
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Affiliation(s)
- Jiyu Sun
- Department of Chemistry and Biochemistry, University of Montana, 32 Campus Drive Missoula MT 59812 USA
| | - Daniel A Decato
- Department of Chemistry and Biochemistry, University of Montana, 32 Campus Drive Missoula MT 59812 USA
| | | | - Eric A John
- Department of Chemistry and Biochemistry, University of Montana, 32 Campus Drive Missoula MT 59812 USA
| | - Orion B Berryman
- Department of Chemistry and Biochemistry, University of Montana, 32 Campus Drive Missoula MT 59812 USA
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4
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Amonov A, Scheiner S. Competition between Binding to Various Sites of Substituted Imidazoliums. J Phys Chem A 2023. [PMID: 37490696 DOI: 10.1021/acs.jpca.3c04097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/27/2023]
Abstract
The imidazolium cation has a number of different sites that can interact with a nucleophile. Adding a halogen atom (X) or a chalcogen (YH) group introduces the possibility of an NX···nuc halogen or NY···nuc chalcogen bond, which competes against the various H-bonds (NH and CH donors) as well as the lone pair···π interaction wherein the nucleophile lies above the plane of the cation. Substituted imidazoliums are paired with the NH3 base, and the various different complexes are evaluated by density functional theory (DFT) calculations. The strength of XB and YB increases quickly along with the size and polarizability of the X/Y atom, and this sort of bond is the strongest for the heavier Br, I, Se, and Te atoms, followed by the NH···N H-bond, but this order reverses for Cl and S. The various CH···N H-bonds are comparable to one another and to the lone pair···π bond, all with interaction energies of 10-13 kcal/mol, values which show very little dependence upon the substituent placed on the imidazolium.
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Affiliation(s)
- Akhtam Amonov
- Department of Optics and Spectroscopy, Engineering Physics Institute, Samarkand State University, University blv. 15, Samarkand 140104, Uzbekistan
| | - Steve Scheiner
- Department of Chemistry and Biochemistry, Utah State University, Logan, Utah 84322-0300, United States
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5
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Abstract
Quantum calculations study the potential of an intramolecular H-bond between the halogen atom (X) of a halobenzene and a substituent placed ortho to it, to amplify the ability of X to engage in a halogen bond (XB) with a Lewis base. H-bonding substituents NH2, CH2CH2OH, CH2OH, OH, and COOH were added to halobenzenes (X = Cl, Br, I). The amino group had little effect, but those containing OH increased the CX···N XB energy to a NH3 nucleophile by about 0.5 kcal/mol; the increment associated with COOH is larger, nearly 2 kcal/mol. These energy increments were approximately doubled if two such H-bonding substituents are present. Combining a pair of ortho COOH groups with an electron-withdrawing NO2 group in the para position has a particularly large effect, raising the XB energy by about 4 kcal/mol, which can amount to as much as a 4-fold magnification.
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Affiliation(s)
- Steve Scheiner
- Department of Chemistry and Biochemistry, Utah State University, Logan, Utah 84322-0300, United States
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6
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Gao M, Zhang Y, Wang B, Guo N, Shao L, Zhai W, Jiang L, Wang Q, Qian H, Yan L. Novel dual-target μ‑opioid and TRPV1 ligands as potential pharmacotherapeutics for pain management. Bioorg Chem 2023; 131:106335. [PMID: 36603243 DOI: 10.1016/j.bioorg.2022.106335] [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: 10/05/2022] [Revised: 12/16/2022] [Accepted: 12/20/2022] [Indexed: 12/24/2022]
Abstract
Currently, the development of effective analgesic drugs with few side effects remains a great challenge. Studies have suggested that multi-target drug treatments show high efficacy and reduced side effects compared to single-target drug therapies. In this work, we designed and synthesized two series of novel MOR/TRPV1 dual active ligands in which the phenylpiperidine group or the N-phenyl-N-(piperidin-4-yl) propionamide group as the MOR pharmacophore was fused to the benzylpiperazinyl urea-based TRPV1 pharmacophore. In particular, compound 5a exhibited promising dual pharmacological activity for MOR (EC50 = 53.7 nM) and TRPV1 (IC50 = 32.9 nM) in vitro. In formalin tests, compound 5a showed potent, dose-dependent in vivo analgesic activity in both the 1st and 2nd phases. Gratifyingly, compound 5a did not cause the side effects of hyperthermia and analgesic tolerance. Consistent with its in vitro activity, compound 5a also simultaneously agonized MOR and antagonized TRPV1 in vivo. Further studies on compound 5a showed acceptable pharmacokinetic properties and brain permeability. Furthermore, molecular docking studies showed that compound 5a tightly bound to the active pockets of hMOR and hTRPV1, respectively. Overall, this work shows the promise in discovering new analgesic treatments through the strategy of simultaneously targeting MOR and TRPV1 with a single molecule.
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Affiliation(s)
- Mengkang Gao
- School of Pharmacy, Henan University, N. Jinming Ave., Kaifeng, Henan 475004, China; State Key Laboratory of Natural Medicines, Center of Drug Discovery, China Pharmaceutical University, 24 Tongjiaxiang, Nanjing, Jiangsu 210009, China
| | - Yang Zhang
- State Key Laboratory of Natural Medicines, Center of Drug Discovery, China Pharmaceutical University, 24 Tongjiaxiang, Nanjing, Jiangsu 210009, China; Department of Life Sciences, Changzhi University, 73 East Chengbei Street, Changzhi, Shanxi 046011, China
| | - Bingxin Wang
- School of Pharmacy, Henan University, N. Jinming Ave., Kaifeng, Henan 475004, China
| | - Ning Guo
- School of Pharmacy, Henan University, N. Jinming Ave., Kaifeng, Henan 475004, China
| | - Lulian Shao
- School of Pharmacy, Henan University, N. Jinming Ave., Kaifeng, Henan 475004, China
| | - Weibin Zhai
- School of Pharmacy, Henan University, N. Jinming Ave., Kaifeng, Henan 475004, China
| | - Lei Jiang
- School of Pharmacy, Henan University, N. Jinming Ave., Kaifeng, Henan 475004, China
| | - Qiang Wang
- School of Pharmaceutical Sciences, South-Central University for Nationalities, 182 Minyuan road, Wuhan, Hubei 430074, China
| | - Hai Qian
- State Key Laboratory of Natural Medicines, Center of Drug Discovery, China Pharmaceutical University, 24 Tongjiaxiang, Nanjing, Jiangsu 210009, China.
| | - Lin Yan
- School of Pharmacy, Henan University, N. Jinming Ave., Kaifeng, Henan 475004, China.
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7
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Scheiner S. Ability of Peripheral H Bonds to Strengthen a Halogen Bond. J Phys Chem A 2022; 126:9691-9698. [PMID: 36520542 DOI: 10.1021/acs.jpca.2c07611] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Quantum calculations study the manner in which the involvement of a halogen atom as a proton acceptor in one or more H bonds (HBs) affects the strength of the halogen bond (XB) it can form with a nucleophile aligned with the X σ-hole. A variety of Lewis acids wherein X = F, Cl, Br, and I are attached to a tetrel atom C or Ge engaged in a XB with nucleophile NH3. One, two, and three HF molecules were positioned perpendicular to the XB axis so that they could form a HB to the X atom. Each such HB strengthened the XB by an increment of 1 kcal/mol or more that does not attenuate as each new HB is added, potentially increasing the interaction energy manyfold. Additionally, the presence of one or more HBs facilitates the formation of a XB by molecules which are reluctant to engage in such a bond in the absence of these auxiliary interactions. Even the F atom, which avoids such a XB, can be coaxed to participate in a XB of moderate strength by one or more of these external HBs.
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Affiliation(s)
- Steve Scheiner
- Department of Chemistry and Biochemistry, Utah State University, Logan, Utah 84322-0300, United States
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8
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Bogado ML, Villafañe RN, Gómez Chavez JL, Angelina EL, Sosa GL, Peruchena NM. Targeting Protein Pockets with Halogen Bonds: The Role of the Halogen Environment. J Chem Inf Model 2022; 62:6494-6507. [PMID: 36044012 DOI: 10.1021/acs.jcim.2c00475] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Protein pockets that form a halogen bond (X-bond) with a halogenated ligand molecule simultaneously form other (mainly hydrophobic) interactions with the halogen atom that can be considered as its "X-bond environment" (XBenv). Most studies in the field have focused on the X-bond, with the properties of the XBenv usually overlooked. In this work, we derived a protocol that evaluates the XBenv strength as a measure of the propensity of a protein pocket to host an X-bond. The charge density-based topological descriptors in combination with machine learning tools were employed to predict formation and strength of the interactions that conform the XBenv as a function of their geometrical parameters. On the basis of these results, we propose that the XBenv can be used as a footprint to judge the chance of a protein pocket to form an X-bond.
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Affiliation(s)
- María Lucrecia Bogado
- Lab. Estructura Molecular y Propiedades, IQUIBA-NEA, Universidad Nacional del Nordeste, CONICET, FaCENA, Av. Libertad 5470, Corrientes 3400, Argentina
| | - Roxana Noelia Villafañe
- Lab. Estructura Molecular y Propiedades, IQUIBA-NEA, Universidad Nacional del Nordeste, CONICET, FaCENA, Av. Libertad 5470, Corrientes 3400, Argentina
| | - José Leonardo Gómez Chavez
- Lab. Estructura Molecular y Propiedades, IQUIBA-NEA, Universidad Nacional del Nordeste, CONICET, FaCENA, Av. Libertad 5470, Corrientes 3400, Argentina
| | - Emilio Luis Angelina
- Lab. Estructura Molecular y Propiedades, IQUIBA-NEA, Universidad Nacional del Nordeste, CONICET, FaCENA, Av. Libertad 5470, Corrientes 3400, Argentina
| | - Gladis Laura Sosa
- Lab. Estructura Molecular y Propiedades, IQUIBA-NEA, Universidad Nacional del Nordeste, CONICET, FaCENA, Av. Libertad 5470, Corrientes 3400, Argentina
| | - Nélida María Peruchena
- Lab. Estructura Molecular y Propiedades, IQUIBA-NEA, Universidad Nacional del Nordeste, CONICET, FaCENA, Av. Libertad 5470, Corrientes 3400, Argentina
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9
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Qiao G, Xing J, Luo X, Zhang C, Yi J. Integrated bioinformatics analysis and screening of hub genes in polycystic ovary syndrome. Endocrine 2022; 78:615-627. [PMID: 36068422 DOI: 10.1007/s12020-022-03181-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Accepted: 08/23/2022] [Indexed: 11/03/2022]
Abstract
PURPOSE Polycystic ovary syndrome (PCOS) is one of the most common endocrine and metabolic disorders, posing a serious threat to the health of women. Herein, we aimed to explore new biomarkers and potential therapeutic targets for PCOS by employing integrated bioinformatics tools. METHODS Three gene expression profile datasets (GSE138518, GSE155489, GSE106724) were obtained from the Gene Expression Omnibus database and the differentially expressed genes in PCOS and normal groups with an adjusted p-value < 0.05 and a |log fold change (FC) | > 1.2 were first identified using the DESeq package. The weighted correlation network analysis (WGCNA) R package was used to identify clusters of highly correlated genes or modules associated with PCOS. Protein-protein interaction (PPI) network analysis and visualization of genes in the key module were performed using the STRINGdb database and the NetworkX package (edge > 5), respectively. The genes overlapping among the key module genes and PCOS-associated genes were further analyzed. Ligand molecules with strong binding energy < -10 kJ/mol to GNB3 were screened in the drug library using MTiOpenScreen. AutoDock, ChimeraX, and BIOVIA Discovery Studio Visualizer were further used to elucidate the mechanism of ligand interaction with GNB3. Finally, the relationship between GNB3 and PCOS was verified using experimental models in vivo and in vitro. RESULTS Of the 11 modules identified by WGCNA, the black module had the highest correlation with PCOS (correlation = 0.96, P = 0.00016). The PPI network of 351 related genes revealed that VCL, GNB3, MYH11, LMNA, MLLT4, EZH2, PAK3, and CHRM1 have important roles in PCOS. The hub gene GNB3 was identified by taking the intersection of PCOS-related gene sets. MTiOpenScreen revealed that five compounds interacted with GNB3. Of these five, compound 1 had the strongest binding ability and can bind amino acids in the WD40 motif of GNB3, which in turn affects the function of the G protein-coupled receptor β subunit. GNB3 was also significantly downregulated in PCOS models. CONCLUSION We identified the hub gene GNB3 as the most important regulatory gene in PCOS. We suggest that compound 1 can target the WD40 motif of GNB3 to affect related functions and must be considered as a lead compound for drug development. This study will provide new insights into the development of PCOS-related drugs.
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Affiliation(s)
- Gan Qiao
- Department of Pharmacology, School of Pharmacy, Nucleic Acid Medicine of Luzhou Key Laboratory, Central Nervous System Drug Key Laboratory of Sichuan Province, Southwest Medical University, Luzhou, 646000, Sichuan, China
| | - Jinshan Xing
- Department of Neurosurgery, The Affiliated Traditional Chinese Medicine Hospital of Southwest Medical University, Luzhou, 646000, Sichuan, China
| | - Xin Luo
- Department of Pharmacology, School of Pharmacy, Nucleic Acid Medicine of Luzhou Key Laboratory, Central Nervous System Drug Key Laboratory of Sichuan Province, Southwest Medical University, Luzhou, 646000, Sichuan, China
| | - Chunxiang Zhang
- Nucleic Acid Medicine of Luzhou Key Laboratory, Key Laboratory of Medical Electrophysiology, Ministry of Education & Medical Electrophysiological Key Laboratory of Sichuan Province, (Collaborative Innovation Center for Prevention of Cardiovascular Diseases), Institute of Cardiovascular Research, Southwest Medical University, Luzhou, 646000, Sichuan, China.
| | - Jingyan Yi
- Department of Medical Cell Biology and Genetics, School of Basic Medical Sciences, Nucleic Acid Medicine of Luzhou Key Laboratory, Key Laboratory of Medical Electrophysiology, Ministry of Education & Medical Electrophysiological Key Laboratory of Sichuan Province, (Collaborative Innovation Center for Prevention of Cardiovascular Diseases), Institute of Cardiovascular Research, Southwest Medical University, Luzhou, 646000, Sichuan, China.
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10
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An S, Hao A, Xing P. [N···I···N] + Type Halogen-Bonding-Driven Supramolecular Helical Polymers with Modulated Chirality. ACS NANO 2022; 16:19220-19228. [PMID: 36286252 DOI: 10.1021/acsnano.2c08506] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
The [N···I···N]+ type halogen bond has been utilized to synthesize supramolecular architectures, while the applications in constructing helical motifs and modulating supramolecular chirality have been unexplored so far. In this work, the [N···I···N]+ halogen bond was introduced to drive the formation of supramolecular helical polymers via a Ag(I) coordination intermediate, showing tunable supramolecular chirality. Pyridine segments were conjugated to the asymmetric ferrocene skeleton, which show "open" and "closed" geometry depending on the sp2 N positions. Coordination with Ag(I) generated one-dimensional (1D) double helices and 2D helicates featured the [Ag(O)···I···Ag(O)]+ bond, which further stacked into 3D porous frameworks with chiral channels and adjustable pore sizes. Ionic exchange afforded 1D supramolecular helical polymers in solution phases driven by the [N···I···N]+ type halogen bonds, which was evidenced by the experimental results and density functional theory calculation. Fc2 exclusively demonstrated tunable supramolecular chirality in the formation of coordinated and halogen bonded polymers. In addition, solvent change would further inverse the helicity of halogen bonded supramolecular helical polymers depending on the rotation of the ferrocenyl core whose "closed" and "open" states were accompanied by the breakage of intramolecular hydrogen bonds. This work introduces a [N···I···N]+ type ionic halogen bond to prepare supramolecular helical polymers, providing multiple protocols in regulating helicity by ion exchange and solvent environments.
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Affiliation(s)
- Shuguo An
- School of Chemistry and Chemical Engineering, Shandong University, Jinan 250100, People's Republic of China
| | - Aiyou Hao
- School of Chemistry and Chemical Engineering, Shandong University, Jinan 250100, People's Republic of China
| | - Pengyao Xing
- School of Chemistry and Chemical Engineering, Shandong University, Jinan 250100, People's Republic of China
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11
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Docker A, Tse YC, Tay HM, Taylor AJ, Zhang Z, Beer PD. Anti‐Hofmeister Anion Selectivity via a Mechanical Bond Effect in Neutral Halogen‐Bonding [2]Rotaxanes. Angew Chem Int Ed Engl 2022; 61:e202214523. [PMID: 36264711 PMCID: PMC10100147 DOI: 10.1002/anie.202214523] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Indexed: 11/18/2022]
Abstract
Exceptionally strong halogen bonding (XB) donor-chloride interactions are exploited for the chloride anion template synthesis of neutral XB [2]rotaxane host systems which contain perfluoroaryl-functionalised axle components, including a remarkably potent novel 4,6-dinitro-1,3-bis-iodotriazole motif. Halide anion recognition properties in aqueous-organic media, determined via extensive 1 H NMR halide anion titration experiments, reveal the rotaxane host systems exhibit dramatically enhanced affinities for hydrophilic Cl- and Br- , but conversely diminished affinities for hydrophobic I- , relative to their non-interlocked axle counterparts. Crucially, this mechanical bond effect induces a binding selectivity which directly opposes Hofmeister bias. Free-energy analysis of this mechanical bond enhancement demonstrates anion recognition by neutral XB interlocked host systems as a rare and general strategy to engineer anti-Hofmeister bias anion selectivity in synthetic receptor design.
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Affiliation(s)
- Andrew Docker
- Department of Chemistry University of Oxford Chemistry Research Laboratory 12 Mansfield Road Oxford OX1 3TA UK
| | - Yuen Cheong Tse
- Department of Chemistry University of Oxford Chemistry Research Laboratory 12 Mansfield Road Oxford OX1 3TA UK
| | - Hui Min Tay
- Department of Chemistry University of Oxford Chemistry Research Laboratory 12 Mansfield Road Oxford OX1 3TA UK
| | - Andrew J. Taylor
- Department of Chemistry University of Oxford Chemistry Research Laboratory 12 Mansfield Road Oxford OX1 3TA UK
| | - Zongyao Zhang
- Department of Chemistry University of Oxford Chemistry Research Laboratory 12 Mansfield Road Oxford OX1 3TA UK
| | - Paul D. Beer
- Department of Chemistry University of Oxford Chemistry Research Laboratory 12 Mansfield Road Oxford OX1 3TA UK
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12
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Docker A, Marques I, Kuhn H, Zhang Z, Félix V, Beer PD. Selective Potassium Chloride Recognition, Sensing, Extraction, and Transport Using a Chalcogen-Bonding Heteroditopic Receptor. J Am Chem Soc 2022; 144:14778-14789. [PMID: 35930460 PMCID: PMC9394446 DOI: 10.1021/jacs.2c05333] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
![]()
Chalcogen bonding (ChB) is rapidly rising to prominence
in supramolecular
chemistry as a powerful sigma (σ)-hole-based noncovalent interaction,
especially for applications in the field of molecular recognition.
Recent studies have demonstrated ChB donor strength and potency to
be remarkably sensitive to local electronic environments, including
redox-switchable on/off anion binding and sensing capability. Influencing
the unique electronic and geometric environment sensitivity of ChB
interactions through simultaneous cobound metal cation recognition,
herein, we present the first potassium chloride-selective heteroditopic
ion-pair receptor. The direct conjugation of benzo-15-crown-5 ether
(B15C5) appendages to Te centers in a bis-tellurotriazole framework
facilitates alkali metal halide (MX) ion-pair binding through the
formation of a cofacial intramolecular bis-B15C5 M+ (M+ = K+, Rb+, Cs+) sandwich
complex and bidentate ChB···X– formation.
Extensive quantitative 1H NMR ion-pair affinity titration
experiments, solid–liquid and liquid–liquid extraction,
and U-tube transport studies all demonstrate unprecedented KCl selectivity
over all other group 1 metal chlorides. It is demonstrated that the
origin of the receptor’s ion-pair binding cooperativity and
KCl selectivity arises from an electronic polarization of the ChB
donors induced by the cobound alkali metal cation. Importantly, the
magnitude of this switch on Te-centered electrophilicity, and therefore
anion-binding affinity, is shown to correlate with the inherent Lewis
acidity of the alkali metal cation. Extensive computational DFT investigations
corroborated the experimental alkali metal cation–anion ion-pair
binding observations for halides and oxoanions.
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Affiliation(s)
- Andrew Docker
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Mansfield Road, Oxford OX1 3TA, U. K
| | - Igor Marques
- CICECO─Aveiro Institute of Materials, Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal
| | - Heike Kuhn
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Mansfield Road, Oxford OX1 3TA, U. K
| | - Zongyao Zhang
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Mansfield Road, Oxford OX1 3TA, U. K
| | - Vítor Félix
- CICECO─Aveiro Institute of Materials, Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal
| | - Paul D Beer
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Mansfield Road, Oxford OX1 3TA, U. K
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13
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Peluso P, Chankvetadze B. Recognition in the Domain of Molecular Chirality: From Noncovalent Interactions to Separation of Enantiomers. Chem Rev 2022; 122:13235-13400. [PMID: 35917234 DOI: 10.1021/acs.chemrev.1c00846] [Citation(s) in RCA: 54] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
It is not a coincidence that both chirality and noncovalent interactions are ubiquitous in nature and synthetic molecular systems. Noncovalent interactivity between chiral molecules underlies enantioselective recognition as a fundamental phenomenon regulating life and human activities. Thus, noncovalent interactions represent the narrative thread of a fascinating story which goes across several disciplines of medical, chemical, physical, biological, and other natural sciences. This review has been conceived with the awareness that a modern attitude toward molecular chirality and its consequences needs to be founded on multidisciplinary approaches to disclose the molecular basis of essential enantioselective phenomena in the domain of chemical, physical, and life sciences. With the primary aim of discussing this topic in an integrated way, a comprehensive pool of rational and systematic multidisciplinary information is provided, which concerns the fundamentals of chirality, a description of noncovalent interactions, and their implications in enantioselective processes occurring in different contexts. A specific focus is devoted to enantioselection in chromatography and electromigration techniques because of their unique feature as "multistep" processes. A second motivation for writing this review is to make a clear statement about the state of the art, the tools we have at our disposal, and what is still missing to fully understand the mechanisms underlying enantioselective recognition.
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Affiliation(s)
- Paola Peluso
- Istituto di Chimica Biomolecolare ICB, CNR, Sede secondaria di Sassari, Traversa La Crucca 3, Regione Baldinca, Li Punti, I-07100 Sassari, Italy
| | - Bezhan Chankvetadze
- Institute of Physical and Analytical Chemistry, School of Exact and Natural Sciences, Tbilisi State University, Chavchavadze Avenue 3, 0179 Tbilisi, Georgia
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14
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Torii H, Kimura A, Sakai T. Nature of hydrogen-bond-enhanced halogen bonding viewed through electron density changes. Phys Chem Chem Phys 2022; 24:17951-17955. [PMID: 35861167 DOI: 10.1039/d2cp02845j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Elucidating the mechanism of how we can achieve fine tuning of intermolecular interaction strength will be helpful for designing functionally important molecules. In the present study, a theoretical analysis is conducted, by examining the electron density changes, for two halogen-bonding iodinated systems whose halogen-bond strengths have been considered to be enhanced by the presence of a hydrogen-bond donating group (termed hydrogen-bond-enhanced halogen bonding). It is shown that, contrary to the expectation obtained from the enhancement of electrostatic potential along the line extended from the C-I bond, the anisotropy of electron distribution on the iodine atom remains nearly the same. This means that the hydrogen bond and halogen bond contribute almost independently and additively to the enhancement of electrostatic potential, indicating the nature of this enhancement and, in a more general sense, the relationship between the strength and the extent of directionality of halogen bonding.
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Affiliation(s)
- Hajime Torii
- Applied Chemistry and Biochemical Engineering Course, Department of Engineering, Graduate School of Integrated Science and Technology, Shizuoka University, 3-5-1 Johoku, Naka-ku, Hamamatsu 432-8561, Japan. .,Department of Optoelectronics and Nanostructure Science, Graduate School of Science and Technology, Shizuoka University, 3-5-1 Johoku, Naka-ku, Hamamatsu 432-8561, Japan
| | - Akari Kimura
- Applied Chemistry and Biochemical Engineering Course, Department of Engineering, Graduate School of Integrated Science and Technology, Shizuoka University, 3-5-1 Johoku, Naka-ku, Hamamatsu 432-8561, Japan.
| | - Takanori Sakai
- Applied Chemistry and Biochemical Engineering Course, Department of Engineering, Graduate School of Integrated Science and Technology, Shizuoka University, 3-5-1 Johoku, Naka-ku, Hamamatsu 432-8561, Japan.
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15
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Gallagher JF, Hehir N, Mocilac P, Violin C, O’Connor BF, Aubert E, Espinosa E, Guillot B, Jelsch C. Probing the Electronic Properties and Interaction Landscapes in a Series of N-(Chlorophenyl)pyridinecarboxamides. CRYSTAL GROWTH & DESIGN 2022; 22:3343-3358. [PMID: 35547941 PMCID: PMC9074230 DOI: 10.1021/acs.cgd.2c00153] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 03/29/2022] [Indexed: 06/15/2023]
Abstract
A 3 × 3 isomer grid of nine N-(chlorophenyl)pyridinecarboxamides (NxxCl) is reported with physicochemical studies and single crystal structures (Nx = pyridinoyl moiety; xCl = aminochlorobenzene ring; x = para-/meta-/ortho-), as synthesized by the reaction of the substituted p-/m-/o-pyridinecarbonyl chlorides (Nx) with p-/m-/o-aminochlorobenzenes (xCl). Several of the nine NxxCl crystal structures display structural similarities with their halogenated NxxX and methylated NxxM relatives (x = p-/m-/o-substitutions; X = F, Br; M = methyl). Indeed, five of the nine NxxCl crystal structures are isomorphous with their NxxBr analogues as the NpmCl/Br, NpoCl/Br, NmoCl/NmoBr, NopCl/Br, and NooCl/Br pairs. In the NxxCl series, the favored hydrogen bonding mode is aggregation by N-H···Npyridine interactions, though amide···amide intermolecular interactions are noted in NpoCl and NmoCl. For the NoxCl triad, intramolecular N-H···Npyridine interactions influence molecular planarity, whereas NppCl·H2O (as a monohydrate) exhibits O-H···O, N-H···O1W, and O1W-H···N interactions as the primary hydrogen bonding. Analysis of chlorine-containing compounds on the CSD is noted for comparisons. The interaction environments are probed using Hirshfeld surface analysis and contact enrichment studies. The melting temperatures (T m) depend on both the lattice energy and molecular symmetry (Carnelley's rule), and the melting points can be well predicted from a linear regression of the two variables. The relationships of the T m values with the total energy, the electrostatic component, and the strongest hydrogen bond components have been analyzed.
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Affiliation(s)
- John F. Gallagher
- School
of Chemical Sciences, Dublin City University, Dublin D09 DXA0, Ireland
| | - Niall Hehir
- School
of Chemical Sciences, Dublin City University, Dublin D09 DXA0, Ireland
| | - Pavle Mocilac
- School
of Chemical Sciences, Dublin City University, Dublin D09 DXA0, Ireland
| | - Chloé Violin
- School
of Chemical Sciences, Dublin City University, Dublin D09 DXA0, Ireland
| | | | - Emmanuel Aubert
- CRM, CNRS UMR 7036, Faculté
des Sciences et Technologies, Université
de Lorraine, BP 70239, Boulevard des Aiguillettes, 54506 Vandoeuvre-lès-Nancy, France
| | - Enrique Espinosa
- CRM, CNRS UMR 7036, Faculté
des Sciences et Technologies, Université
de Lorraine, BP 70239, Boulevard des Aiguillettes, 54506 Vandoeuvre-lès-Nancy, France
| | - Benoît Guillot
- CRM, CNRS UMR 7036, Faculté
des Sciences et Technologies, Université
de Lorraine, BP 70239, Boulevard des Aiguillettes, 54506 Vandoeuvre-lès-Nancy, France
| | - Christian Jelsch
- CRM, CNRS UMR 7036, Faculté
des Sciences et Technologies, Université
de Lorraine, BP 70239, Boulevard des Aiguillettes, 54506 Vandoeuvre-lès-Nancy, France
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16
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Il'in MV, Sysoeva AA, Novikov AS, Bolotin DS. Diaryliodoniums as Hybrid Hydrogen- and Halogen-Bond-Donating Organocatalysts for the Groebke-Blackburn-Bienaymé Reaction. J Org Chem 2022; 87:4569-4579. [PMID: 35176856 DOI: 10.1021/acs.joc.1c02885] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Dibenziodolium and diphenyliodonium triflates display high catalytic activity for the multicomponent reaction that leads to a series of imidazopyridines. Density functional theory (DFT) calculations indicate that both the salts can play the role of hybrid hydrogen- and halogen-bond-donating organocatalysts, which electrophilically activate the carbonyl and imine groups during the reaction process. The ortho-H atoms in the vicinal position to the I atom play a dual role: forming additional noncovalent bonds with the ligated substrate and increasing the maximum electrostatic potential on the σ-hole at the iodine atom owing to the effects of polarization. Dibenziodolium triflate exhibits higher catalytic activity, and the results obtained from 1H nuclear magnetic resonance (NMR) titrations, in conjunction with those from DFT calculations, indicate that this could be explained in terms of the additional energy required for the rotation of the phenyl ring in the diphenyliodonium cation during ligation of the substrate.
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Affiliation(s)
- Mikhail V Il'in
- Institute of Chemistry, Saint Petersburg State University, Universitetskaya Nab. 7/9, Saint Petersburg 199034, Russian Federation
| | - Alexandra A Sysoeva
- Institute of Chemistry, Saint Petersburg State University, Universitetskaya Nab. 7/9, Saint Petersburg 199034, Russian Federation
| | - Alexander S Novikov
- Institute of Chemistry, Saint Petersburg State University, Universitetskaya Nab. 7/9, Saint Petersburg 199034, Russian Federation
| | - Dmitrii S Bolotin
- Institute of Chemistry, Saint Petersburg State University, Universitetskaya Nab. 7/9, Saint Petersburg 199034, Russian Federation
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17
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Riel AMS, Decato DA, Sun J, Berryman OB. Halogen bonding organocatalysis enhanced through intramolecular hydrogen bonds. Chem Commun (Camb) 2022; 58:1378-1381. [PMID: 34989732 PMCID: PMC8919959 DOI: 10.1039/d1cc05475a] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Recent results indicate a halogen bond donor is strengthened through direct interaction with a hydrogen bond to the electron-rich belt of the halogen. Here, this Hydrogen Bond enhanced Halogen Bond (HBeXB) plays a clear role in a catalyst. Our HBeXB catalyst improves product conversion in a halide abstraction reaction over a traditional halogen bonding derivative.
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Affiliation(s)
| | - Daniel A. Decato
- Address University of Montana, 32 Campus Drive, Missoula, MT, USA
| | - Jiyu Sun
- Address University of Montana, 32 Campus Drive, Missoula, MT, USA
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18
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Affiliation(s)
- Yunying Xu
- School of Chemistry and Chemical Engineering Shandong University Jinan 250100 P. R. China
| | - Aiyou Hao
- School of Chemistry and Chemical Engineering Shandong University Jinan 250100 P. R. China
| | - Pengyao Xing
- School of Chemistry and Chemical Engineering Shandong University Jinan 250100 P. R. China
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19
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Decato DA, Sun J, Boller MR, Berryman OB. Pushing the Limits of the Hydrogen Bond Enhanced Halogen Bond —The Case of the C–H Hydrogen Bond. Chem Sci 2022; 13:11156-11162. [PMID: 36320486 PMCID: PMC9516949 DOI: 10.1039/d2sc03792k] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Accepted: 08/31/2022] [Indexed: 11/21/2022] Open
Abstract
C–H hydrogen bonds have remarkable impacts on various chemical systems. Here we consider the influence of C–H hydrogen bonds to iodine atoms. Positioning a methyl group between two iodine halogen bond donors of the receptor engendered intramolecular C–H hydrogen bonding (HBing) to the electron-rich belt of both halogen bond donors. When coupled with control molecules, the role of the C–H hydrogen bond was evaluated. Gas-phase density functional theory studies indicated that methyl C–H hydrogen bonds help bias a bidentate binding conformation. Interaction energy analysis suggested that the charged C–H donors augment the halogen bond interaction—producing a >10 kcal mol−1 enhancement over a control lacking the C–H⋯I–C interaction. X-ray crystallographic analysis demonstrated C–H hydrogen bonds and bidentate conformations with triflate and iodide anions, yet the steric bulk of the central functional group seems to impact the expected trends in halogen bond distance. In solution, anion titration data indicated elevated performance from the receptors that utilize C–H Hydrogen Bond enhanced Halogen Bonds (HBeXBs). Collectively, the results suggest that even modest hydrogen bonds between C–H donors and iodine acceptors can influence molecular structure and improve receptor performance. C–H hydrogen bonds to iodine halogen bond donors are shown to improve halogen bonding and molecular preorganization.![]()
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Affiliation(s)
| | - Jiyu Sun
- University of Montana 32 Campus Drive Missoula MT USA
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20
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Fotović L, Bedeković N, Stilinović V. Evaluation of Halogenopyridinium Cations as Halogen Bond Donors. CRYSTAL GROWTH & DESIGN 2021; 21:6889-6901. [PMID: 34880714 PMCID: PMC8641392 DOI: 10.1021/acs.cgd.1c00805] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 10/26/2021] [Indexed: 06/13/2023]
Abstract
We have performed a database survey and a structural and computational study of the potential and the limitations of halogenopyridinium cations as halogen bond donors. The database survey demonstrated that adding a positive charge on a halogenopyridine ring increases the probability that the halogen atom will participate in a halogen bond, although for chloropyridines it remains below 60%. Crystal structures of both protonated and N-methylated monohalogenated pyridinium cations revealed that the iodo- and bromopyridinium cations always form halogen-bonding contacts with the iodide anions shorter than the sum of the vdW radii, while chloropyridinium cations mostly participate in longer contacts or fail to form halogen bonds. Although a DFT study of the electrostatic potential has shown that both protonation and N-methylation of halogenopyridines leads to a considerable increase in the ESP of the halogen σ-hole, it is generally not the most positive site on the cation, allowing for alternate binding sites.
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Affiliation(s)
- Luka Fotović
- Department of Chemistry,
Faculty of Science, University of Zagreb, Horvatovac 102a, 10000 Zagreb, Croatia
| | - Nikola Bedeković
- Department of Chemistry,
Faculty of Science, University of Zagreb, Horvatovac 102a, 10000 Zagreb, Croatia
| | - Vladimir Stilinović
- Department of Chemistry,
Faculty of Science, University of Zagreb, Horvatovac 102a, 10000 Zagreb, Croatia
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21
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Xu Y, Hao A, Xing P. X⋅⋅⋅X Halogen Bond-Induced Supramolecular Helices. Angew Chem Int Ed Engl 2021; 61:e202113786. [PMID: 34729878 DOI: 10.1002/anie.202113786] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Indexed: 12/28/2022]
Abstract
The halogen bond is the attractive interaction between the electrophilic region of a halogen atom and the nucleophilic region of another molecular entity, emerging as a favorable manner to manipulate supramolecular chirality in self-assemblies. Engineering halogen bonded helical structures remains a challenge due to its sensitivity to solvent polarity and competitive forces like hydrogen bonds. Herein, we report a X⋅⋅⋅X (X=Cl, Br, I) type weak halogen bond that induces the formation and evolution of supramolecular helical structures both in solid and solution state. The π-conjugated phenylalanine derivatives with F, Cl, Br and I substitution self-assembled into 21 helical packing driven by hydrogen bond and halogen bond, respectively. The specific molecular geometries of π-conjugated amino acids gave rise to multiple noncovalent forces to stabilize the X⋅⋅⋅X halogen bond with small bond energies ranging from -0.69 to -1.49 kcal mol-1 . Halogen bond induced an opposite helicity compared to the fluorinated species, accompanied by the inversed circularly polarized luminescence.
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Affiliation(s)
- Yunying Xu
- School of Chemistry and Chemical Engineering, Shandong University, Jinan, 250100, P. R. China
| | - Aiyou Hao
- School of Chemistry and Chemical Engineering, Shandong University, Jinan, 250100, P. R. China
| | - Pengyao Xing
- School of Chemistry and Chemical Engineering, Shandong University, Jinan, 250100, P. R. China
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22
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Abstract
We performed a structural study of N-alkylated halogenopyridinium cations to examine whether choice of the N-substituent has any considerable effect on the halogen bonding capability of the cations. For that purpose, we prepared a series of N-ethyl-3-halopyridinium iodides and compared them with their N-methyl-3-halopyridinium analogues. Structural analysis revealed that N-ethylated halogenopyridinium cations form slightly shorter C−X⋯I− halogen bonds with iodide anion. We have also attempted synthesis of ditopic symmetric bis-(3-iodopyridinium) dications. Although successful in only one case, the syntheses have afforded two novel ditopic asymmetric monocations with an iodine atom bonded to the pyridine ring and another on the aliphatic N-substituent. Here, the C−I⋯I− halogen bond lengths involving pyridine iodine atom were notably shorter than those involving an aliphatic iodine atom as a halogen bond donor. This trend in halogen bond lengths is in line with the charge distribution on the Hirshfeld surfaces of the cations—the positive charge is predominantly located in the pyridine ring making the pyridine iodine atom σ-hole more positive than the one on the alkyl chan.
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23
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Lindblad S, Boróka Németh F, Földes T, von der Heiden D, Vang HG, Driscoll ZL, Gonnering ER, Pápai I, Bowling N, Erdelyi M. The Influence of Secondary Interactions on the [N-I-N] + Halogen Bond. Chemistry 2021; 27:13748-13756. [PMID: 34339075 PMCID: PMC8518683 DOI: 10.1002/chem.202102575] [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: 07/15/2021] [Indexed: 12/21/2022]
Abstract
[Bis(pyridine)iodine(I)]+ complexes offer controlled access to halonium ions under mild conditions. The reactivity of such stabilized halonium ions is primarily determined by their three-center, four-electron [N-I-N]+ halogen bond. We studied the importance of chelation, strain, steric hindrance and electrostatic interaction for the structure and reactivity of halogen bonded halonium ions by acquiring their 15 N NMR coordination shifts and measuring their iodenium release rates, and interpreted the data with the support of DFT computations. A bidentate ligand stabilizes the [N-I-N]+ halogen bond, decreasing the halenium transfer rate. Strain weakens the bond and accordingly increases the release rate. Remote modifications in the backbone do not influence the stability as long as the effect is entirely steric. Incorporating an electron-rich moiety close by the [N-I-N]+ motif increases the iodenium release rate. The analysis of the iodine(I) transfer mechanism highlights the impact of secondary interactions, and may provide a handle on the induction of stereoselectivity in electrophilic halogenations.
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Affiliation(s)
- Sofia Lindblad
- Department of Chemistry - BMC, Uppsala University, 751 23, Uppsala, Sweden
| | - Flóra Boróka Németh
- Institute of Organic Chemistry, Research Center for Natural Sciences, Budapest, Hungary
| | - Tamás Földes
- Institute of Organic Chemistry, Research Center for Natural Sciences, Budapest, Hungary
| | | | - Herh G Vang
- Department of Chemistry, University of Wisconsin-Stevens Point, 2001 Fourth Avenue, Stevens Point, Wisconsin, 54481, USA
| | - Zakarias L Driscoll
- Department of Chemistry, University of Wisconsin-Stevens Point, 2001 Fourth Avenue, Stevens Point, Wisconsin, 54481, USA
| | - Emily R Gonnering
- Department of Chemistry, University of Wisconsin-Stevens Point, 2001 Fourth Avenue, Stevens Point, Wisconsin, 54481, USA
| | - Imre Pápai
- Institute of Organic Chemistry, Research Center for Natural Sciences, Budapest, Hungary.,Department of Chemistry, University J. Selyeho, 94505, Komárno, Slovakia
| | - Nathan Bowling
- Department of Chemistry, University of Wisconsin-Stevens Point, 2001 Fourth Avenue, Stevens Point, Wisconsin, 54481, USA
| | - Mate Erdelyi
- Department of Chemistry - BMC, Uppsala University, 751 23, Uppsala, Sweden
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24
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Yang H, Tan CH, Wong MW. In silico characterization and prediction of thiourea-like neutral bidentate halogen bond catalysts. Org Biomol Chem 2021; 19:7051-7060. [PMID: 34341809 DOI: 10.1039/d1ob01092a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Preorganization is a common strategy to align halogen bond (XB) donors to form two or more halogen bonds simultaneously. Previous approaches have utilized various non-covalent interactions such as steric interactions, ππ stacking, and hydrogen bond interactions. However, some of the introduced aligning interactions may compete with halogen bond interactions if the donors are employed in catalysis. To achieve thiourea-like properties, we have designed in silico several neutral bidentate halogen bond donors in whose structures the donor moieties are connected via covalent bonds. Compared to previous XB catalyst designs, the new design does not involve other potentially competitive non-covalent interactions such as hydrogen bonds. One of the designed XB donors can deliver strong halogen bonds, with a O-I distance as short as 2.64 Å. Density functional theory (DFT) calculations predicted that our designed catalysts may catalyze important organic reactions on their own, particularly for those reactions that involve (developing) soft anions such as thiolates.
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Affiliation(s)
- Hui Yang
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore 117543.
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25
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Ford MC, Rappé AK, Ho PS. A Reduced Generalized Force Field for Biological Halogen Bonds. J Chem Theory Comput 2021; 17:5369-5378. [PMID: 34232642 DOI: 10.1021/acs.jctc.1c00362] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The halogen bond (or X-bond) is a noncovalent interaction that is increasingly recognized as an important design tool for engineering protein-ligand interactions and controlling the structures of proteins and nucleic acids. In the past decade, there have been significant efforts to characterize the structure-energy relationships of this interaction in macromolecules. Progress in the computational modeling of X-bonds in biological molecules, however, has lagged behind these experimental studies, with most molecular mechanics/dynamics-based simulation methods not properly treating the properties of the X-bond. We had previously derived a force field for biological X-bonds (ffBXB) based on a set of potential energy functions that describe the anisotropic electrostatic and shape properties of halogens participating in X-bonds. Although fairly accurate for reproducing the energies within biomolecular systems, including X-bonds engineered into a DNA junction, the ffBXB with its seven variable parameters was considered to be too unwieldy for general applications. In the current study, we have generalized the ffBXB by reducing the number of variables to just one for each halogen type and show that this remaining electrostatic variable can be estimated for any new halogenated molecule through a standard restricted electrostatic potential calculation of atomic charges. In addition, we have generalized the ffBXB for both nucleic acids and proteins. As a proof of principle, we have parameterized this reduced and more general ffBXB against the AMBER force field. The resulting parameter set was shown to accurately recapitulate the quantum mechanical landscape and experimental interaction energies of X-bonds incorporated into DNA junction and T4 lysozyme model systems. Thus, this reduced and generalized ffBXB is more readily adaptable for incorporation into classical molecular mechanics/dynamics algorithms, including those commonly used to design inhibitors against therapeutic targets in medicinal chemistry and materials in biomolecular engineering.
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Affiliation(s)
- Melissa Coates Ford
- Department of Biochemistry & Molecular Biology, Colorado State University, Fort Collins, Colorado 80523-1870, United States
| | - Anthony K Rappé
- Department of Chemistry, Colorado State University, Fort Collins, Colorado 80523, United States
| | - P Shing Ho
- Department of Biochemistry & Molecular Biology, Colorado State University, Fort Collins, Colorado 80523-1870, United States
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26
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van Terwingen S, Brüx D, Wang R, Englert U. Hydrogen-Bonded and Halogen-Bonded: Orthogonal Interactions for the Chloride Anion of a Pyrazolium Salt. Molecules 2021; 26:3982. [PMID: 34210096 PMCID: PMC8272125 DOI: 10.3390/molecules26133982] [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: 05/31/2021] [Revised: 06/25/2021] [Accepted: 06/25/2021] [Indexed: 11/21/2022] Open
Abstract
In the hydrochloride of a pyrazolyl-substituted acetylacetone, the chloride anion is hydrogen-bonded to the protonated pyrazolyl moiety. Equimolar co-crystallization with tetrafluorodiiodobenzene (TFDIB) leads to a supramolecular aggregate in which TFDIB is situated on a crystallographic center of inversion. The iodine atom in the asymmetric unit acts as halogen bond donor, and the chloride acceptor approaches the σ-hole of this TFDIB iodine subtending an almost linear halogen bond, with Cl···I = 3.1653(11) Å and Cl···I-C = 179.32(6)°. This contact is roughly orthogonal to the N-H···Cl hydrogen bond. An analysis of the electron density according to Bader's Quantum Theory of Atoms in Molecules confirms bond critical points (bcps) for both short contacts, with ρbcp = 0.129 for the halogen and 0.321eÅ-3 for the hydrogen bond. Our halogen-bonded adduct represents the prototype for a future class of co-crystals with tunable electron density distribution about the σ-hole contact.
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Affiliation(s)
- Steven van Terwingen
- Institute of Inorganic Chemistry, RWTH Aachen University, Landoltweg 1, 52074 Aachen, Germany; (S.v.T.); (D.B.); (R.W.)
| | - Daniel Brüx
- Institute of Inorganic Chemistry, RWTH Aachen University, Landoltweg 1, 52074 Aachen, Germany; (S.v.T.); (D.B.); (R.W.)
| | - Ruimin Wang
- Institute of Inorganic Chemistry, RWTH Aachen University, Landoltweg 1, 52074 Aachen, Germany; (S.v.T.); (D.B.); (R.W.)
- Institute of Molecular Science, Shanxi University, Taiyuan 030006, China
| | - Ulli Englert
- Institute of Inorganic Chemistry, RWTH Aachen University, Landoltweg 1, 52074 Aachen, Germany; (S.v.T.); (D.B.); (R.W.)
- Institute of Molecular Science, Shanxi University, Taiyuan 030006, China
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27
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Czarny RS, Ho AN, Shing Ho P. A Biological Take on Halogen Bonding and Other Non-Classical Non-Covalent Interactions. CHEM REC 2021; 21:1240-1251. [PMID: 33886153 DOI: 10.1002/tcr.202100076] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2021] [Revised: 04/07/2021] [Indexed: 01/23/2023]
Abstract
Classical hydrogen bonds have, for many decades, been the dominant non-covalent interaction in the toolbox that chemists and chemical engineers have used to design and control the structures of compounds and molecular assemblies as novel materials. Recently, a set of non-classical non-covalent (NC-NC) interactions have emerged that exploit the properties of the Group IV, V, VI, and VII elements of the periodic table (the tetrel, pnictogen, chalcogen, and halogen bonds, respectively). Our research group has been characterizing the prevalence, geometric constraints, and structure-function relationship specifically of the halogen bond in biological systems. We have been particularly interested in exploiting the biological halogen bonds (or BXBs) to control the structures, stabilities, and activities of biomolecules, including the DNA Holliday junction and enzymes. In this review, we first provide a set of criteria for how to determine whether BXBs or any other NC-NC interactions would have biological relevance. We then navigate the trail of studies that had led us from an initial, very biological question to our current point in the journey to establish BXBs as a tool for biomolecular engineering. Finally, we close with a perspective on future directions for this line of research.
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Affiliation(s)
- Ryan S Czarny
- Department of Biochemistry & Molecular Biology, Colorado State University, Fort Collins, CO, 80523-1870, USA
| | - Alexander N Ho
- Department of Biochemistry & Molecular Biology, Colorado State University, Fort Collins, CO, 80523-1870, USA
| | - P Shing Ho
- Department of Biochemistry & Molecular Biology, Colorado State University, Fort Collins, CO, 80523-1870, USA
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Guagnini F, Pedrini A, Dalcanale E, Massera C. Multidentate, V-Shaped Pyridine Building Blocks as Tectons for Crystal Engineering. Chemistry 2021; 27:4660-4669. [PMID: 33350008 DOI: 10.1002/chem.202004918] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Revised: 12/18/2020] [Indexed: 01/13/2023]
Abstract
The formation of supramolecular structural units through self-assembly is a powerful method to design new architectures and materials endowed with specific properties. With the aim of adding a group of versatile tectons to the toolkit of crystal engineers, we have devised and synthesised four new V-shaped building blocks characterised by an aryl acetylene scaffold comprising three substituted pyridine rings connected by two triple bonds. The judicious choice of different substituents on the pyridine rings provides these tectons with distinctive steric, electrostatic and self-assembly properties, which influence their crystal structures and their ability to form co-crystals. Co-crystals of the tectons with tetraiododifluorobenzene were obtained both via traditional and mechanochemical crystallisation strategies, proving their potential use in crystal engineering. The energetic contributions of the supramolecular interactions at play in the crystal lattice have also been evaluated to better understand their nature and strength and to rationalise their role in designing molecular crystals.
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Affiliation(s)
- Francesca Guagnini
- Dipartimento di Scienze Chimiche, della Vita e della Sostenibilità, Ambientale and INSTM UdR Parma, Università di Parma, Parco Area delle Scienze 17/A, 43123, Parma (PR), Italy
| | - Alessando Pedrini
- Dipartimento di Scienze Chimiche, della Vita e della Sostenibilità, Ambientale and INSTM UdR Parma, Università di Parma, Parco Area delle Scienze 17/A, 43123, Parma (PR), Italy
| | - Enrico Dalcanale
- Dipartimento di Scienze Chimiche, della Vita e della Sostenibilità, Ambientale and INSTM UdR Parma, Università di Parma, Parco Area delle Scienze 17/A, 43123, Parma (PR), Italy
| | - Chiara Massera
- Dipartimento di Scienze Chimiche, della Vita e della Sostenibilità, Ambientale and INSTM UdR Parma, Università di Parma, Parco Area delle Scienze 17/A, 43123, Parma (PR), Italy
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29
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Decato DA, Riel AMS, May JH, Bryantsev VS, Berryman OB. Theoretical, Solid‐State, and Solution Quantification of the Hydrogen Bond‐Enhanced Halogen Bond. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202012262] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Daniel A. Decato
- Department of Chemistry and Biochemistry University of Montana 32 Campus Drive Missoula MT 59812 USA
| | - Asia Marie S. Riel
- Department of Chemistry and Biochemistry University of Montana 32 Campus Drive Missoula MT 59812 USA
| | - James H. May
- Department of Chemistry and Biochemistry University of Montana 32 Campus Drive Missoula MT 59812 USA
| | | | - Orion B. Berryman
- Department of Chemistry and Biochemistry University of Montana 32 Campus Drive Missoula MT 59812 USA
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30
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Sutar RL, Erochok N, Huber SM. Mukaiyama aldol reaction catalyzed by (benz)imidazolium-based halogen bond donors. Org Biomol Chem 2021; 19:770-774. [PMID: 33432958 DOI: 10.1039/d0ob02503h] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A series of cationic monodentate and bidentate iodo(benz)imidazolium-based halogen bond (XB) donors were employed as catalysts in a Mukaiyama aldol reaction. While 5 mol% of a monodentate variant showed noticeable activity, a syn-preorganized bidentate XB donor provided a strong performance even with 0.5 mol% loading. In contrast to the very active BArF4 salts, PF6 or OTf salts were either inactive or showed background reaction through Lewis base catalysis. Repetition experiments clearly ruled out a potential hidden catalysis by elemental iodine and demonstrated the stability of our catalyst over three consecutive cycles.
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Affiliation(s)
- Revannath L Sutar
- Fakultät für Chemie und Biochemie, Ruhr-Universität Bochum, Universitätsstraße 150, 44801 Bochum, Germany.
| | - Nikita Erochok
- Fakultät für Chemie und Biochemie, Ruhr-Universität Bochum, Universitätsstraße 150, 44801 Bochum, Germany.
| | - Stefan M Huber
- Fakultät für Chemie und Biochemie, Ruhr-Universität Bochum, Universitätsstraße 150, 44801 Bochum, Germany.
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31
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Decato DA, Riel AMS, May JH, Bryantsev VS, Berryman OB. Theoretical, Solid-State, and Solution Quantification of the Hydrogen Bond-Enhanced Halogen Bond. Angew Chem Int Ed Engl 2020; 60:3685-3692. [PMID: 33150716 DOI: 10.1002/anie.202012262] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 10/20/2020] [Indexed: 01/02/2023]
Abstract
Proximal noncovalent forces are commonplace in natural systems and understanding the consequences of their juxtaposition is critical. This paper experimentally quantifies for the first time a Hydrogen Bond-Enhanced Halogen Bond (HBeXB) without the complexities of protein structure or preorganization. An HBeXB is a halogen bond that has been strengthened when the halogen donor simultaneously accepts a hydrogen bond. Our theoretical studies suggest that electron-rich halogen bond donors are strengthened most by an adjacent hydrogen bond. Furthermore, stronger hydrogen bond donors enhance the halogen bond the most. X-ray crystal structures of halide complexes (X- =Br- , I- ) reveal that HBeXBs produce shorter halogen bonds than non-hydrogen bond analogues. 19 F NMR titrations with chloride highlight that the HBeXB analogue exhibits stronger binding. Together, these results form the foundation for future studies concerning hydrogen bonds and halogen bonds in close proximity.
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Affiliation(s)
- Daniel A Decato
- Department of Chemistry and Biochemistry, University of Montana, 32 Campus Drive, Missoula, MT, 59812, USA
| | - Asia Marie S Riel
- Department of Chemistry and Biochemistry, University of Montana, 32 Campus Drive, Missoula, MT, 59812, USA
| | - James H May
- Department of Chemistry and Biochemistry, University of Montana, 32 Campus Drive, Missoula, MT, 59812, USA
| | | | - Orion B Berryman
- Department of Chemistry and Biochemistry, University of Montana, 32 Campus Drive, Missoula, MT, 59812, USA
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32
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Abula A, Xu Z, Zhu Z, Peng C, Chen Z, Zhu W, Aisa HA. Substitution Effect of the Trifluoromethyl Group on the Bioactivity in Medicinal Chemistry: Statistical Analysis and Energy Calculations. J Chem Inf Model 2020; 60:6242-6250. [DOI: 10.1021/acs.jcim.0c00898] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Amina Abula
- The Key Laboratory of Plant Resources and Chemistry in Arid Regions and Key Laboratory of Xinjiang Indigenous Medicinal Plants Resource Utilization, Xinjiang Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, South Beijing Road 40-1, Urumqi, Xinjiang 830011, People’s Republic of China
- University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, People’s Republic of China
- CAS Key Laboratory of Receptor Research; Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
| | - Zhijian Xu
- University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, People’s Republic of China
- CAS Key Laboratory of Receptor Research; Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
| | - Zhengdan Zhu
- University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, People’s Republic of China
- CAS Key Laboratory of Receptor Research; Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
| | - Cheng Peng
- University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, People’s Republic of China
- CAS Key Laboratory of Receptor Research; Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
| | - Zhaoqiang Chen
- University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, People’s Republic of China
- CAS Key Laboratory of Receptor Research; Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
| | - Weiliang Zhu
- University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, People’s Republic of China
- CAS Key Laboratory of Receptor Research; Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
| | - Haji Akber Aisa
- The Key Laboratory of Plant Resources and Chemistry in Arid Regions and Key Laboratory of Xinjiang Indigenous Medicinal Plants Resource Utilization, Xinjiang Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, South Beijing Road 40-1, Urumqi, Xinjiang 830011, People’s Republic of China
- University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, People’s Republic of China
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33
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Mammadova F, Hamarat B, Ahmadli D, Şahin O, Bozkaya U, Türkmen YE. Polarization‐Enhanced Hydrogen Bonding in 1,8‐Dihydroxynaphthalene: Conformational Analysis, Binding Studies and Hydrogen Bonding Catalysis. ChemistrySelect 2020. [DOI: 10.1002/slct.202002960] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Flora Mammadova
- Department of Chemistry, Faculty of Science Bilkent University Ankara 06800 Turkey
| | - Büşra Hamarat
- Department of Chemistry Hacettepe University Ankara 06800 Turkey
| | - Dilgam Ahmadli
- Department of Chemistry, Faculty of Science Bilkent University Ankara 06800 Turkey
| | - Onur Şahin
- Scientific and Technological Research Application and Research Center Sinop University Sinop 57000 Turkey
| | - Uğur Bozkaya
- Department of Chemistry Hacettepe University Ankara 06800 Turkey
| | - Yunus E. Türkmen
- Department of Chemistry, Faculty of Science Bilkent University Ankara 06800 Turkey
- UNAM-National Nanotechnology Research Center, Institute of Materials Science and Nanotechnology Bilkent University Ankara 06800 Turkey
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Amsaraj C, Bharathikannan R, Muthuraja P, Rajkumar M. Chlorine directed C–Cl … π and C–H⋯Cl interactions in acridinium 3,5-dichlorosalicylate: Synthesis, X-ray diffraction and theoretical analysis. J Mol Struct 2020. [DOI: 10.1016/j.molstruc.2020.128759] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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35
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Zhang Q, Smalley A, Zhu Z, Xu Z, Peng C, Chen Z, Yao G, Shi J, Zhu W. Computational study of the substituent effect of halogenated fused-ring heteroaromatics on halogen bonding. J Mol Model 2020; 26:270. [PMID: 32930882 DOI: 10.1007/s00894-020-04534-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Accepted: 09/03/2020] [Indexed: 10/23/2022]
Abstract
Halogen bonding (XB) has been applied in many fields from crystal engineering to medicinal chemistry. Compared with the well-studied XB of simple halogenated aromatics, little research has been done on the XB of halogenated fused-ring heteroaromatics, a prevalent substructure in organic compounds. With 1H-pyrrolo[3,2-b]pyridines (PPs) as examples of novel fused-ring heteroaromatics with hydrogen bond donor and acceptor and XB donor, the XB formed by the halogenated heteroaromatics was explored in this study. With 4 different substituents, viz., -CH3, -NH2, -F, and -CONH2, at different positions, 339 derivatives of brominated PP (Br-PP) were designed for calculating their electrostatic potential of the σ-hole of the halogen atom (VS,max) and binding energy with ammonia as XB acceptor (Eint) at M06-2X/6-311++G(d,p) level by PCM model in dichloromethane. The calculated VS,max values ranging from -1.3 to 35.1 kcal/mol and the calculated Eint ranging from -0.82 to -2.37 kcal/mol demonstrated that the XB is complicated and highly tunable. Noticeably, the electron-withdrawing substituents, especially at ortho-position, do not always increase the values of VS,max, while the electron-donating substituents do not always decrease VS,max. Similar results were observed from the calculation on 339 iodinated PPs at M06-2X/6-311++G(d,p) level. The complexity of the XB formed by the halogenated fused ring heteroaromatics indicated a great potential of tuning its strength by different substituents at different positions and revealed a necessity of quantum chemistry calculation for predicting the XB.Graphical abstract.
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Affiliation(s)
- Qihua Zhang
- School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China.,CAS Key Laboratory of Receptor Research; Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | | | - Zhengdan Zhu
- CAS Key Laboratory of Receptor Research; Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Zhijian Xu
- CAS Key Laboratory of Receptor Research; Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Cheng Peng
- CAS Key Laboratory of Receptor Research; Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Zhaoqiang Chen
- CAS Key Laboratory of Receptor Research; Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Guangmin Yao
- School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China.
| | - Jiye Shi
- UCB Pharma, 208 Bath Road, Slough, SL1 3WE, UK
| | - Weiliang Zhu
- CAS Key Laboratory of Receptor Research; Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China.
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36
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Kutus B, Zhu J, Luo J, Wang Q, Lupan A, Attia AAA, Wang D, Hunger J. Enhancement of Ion Pairing of Sr(II) and Ba(II) Salts by a Tritopic Ion-Pair Receptor in Solution. Chemphyschem 2020; 21:1957-1965. [PMID: 32643260 PMCID: PMC7540308 DOI: 10.1002/cphc.202000507] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 07/04/2020] [Indexed: 12/12/2022]
Abstract
Tritopic ion-pair receptors can bind bivalent salts in solution; yet, these salts have a tendency to form ion-pairs even in the absence of receptors. The extent to which such receptors can enhance ion pairing has however remained elusive. Here, we study ion pairing of M2+ (Ba2+ , Sr2+ ) and X- (I- , ClO4- ) in acetonitrile with and without a dichlorooxacalix[2]arene[2]triazine-related receptor containing a pentaethylene-glycol moiety. We find marked ion association already in receptor-free solutions. When present, most of the MX+ ion-pairs are bound to the receptor and the overall degree of ion association is enhanced due to coordinative, hydrogen-bonding, and anion-π interactions. The receptor shows higher selectivity for iodides but also stabilizes perchlorates, despite the latter are often considered as weakly coordinating anions. Our results show that ion-pair binding is strongly correlated to ion pairing in these solutions, thereby highlighting the importance of taking ion association in organic solvents into account.
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Affiliation(s)
- Bence Kutus
- Department of Molecular SpectroscopyMax Planck Institute for Polymer Research55128MainzGermany
| | - Jun Zhu
- Beijing National Laboratory for Molecular SciencesCAS Key Laboratory of Molecular Recognition and FunctionInstitute of ChemistryUniversity of Chinese Academy of SciencesChinese Academy of SciencesBeijing100190China
| | - Jian Luo
- Beijing National Laboratory for Molecular SciencesCAS Key Laboratory of Molecular Recognition and FunctionInstitute of ChemistryUniversity of Chinese Academy of SciencesChinese Academy of SciencesBeijing100190China
| | - Qi‐Qiang Wang
- Beijing National Laboratory for Molecular SciencesCAS Key Laboratory of Molecular Recognition and FunctionInstitute of ChemistryUniversity of Chinese Academy of SciencesChinese Academy of SciencesBeijing100190China
| | - Alexandru Lupan
- Faculty of Chemistry and Chemical EngineeringBabeş-Bolyai University400028Cluj-NapocaRomania
| | - Amr A. A. Attia
- Faculty of Chemistry and Chemical EngineeringBabeş-Bolyai University400028Cluj-NapocaRomania
| | - De‐Xian Wang
- Beijing National Laboratory for Molecular SciencesCAS Key Laboratory of Molecular Recognition and FunctionInstitute of ChemistryUniversity of Chinese Academy of SciencesChinese Academy of SciencesBeijing100190China
| | - Johannes Hunger
- Department of Molecular SpectroscopyMax Planck Institute for Polymer Research55128MainzGermany
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38
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39
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Preorganization-enhanced halogen bonding via intramolecular hydrogen bonding: a theoretical study. Struct Chem 2020. [DOI: 10.1007/s11224-020-01559-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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40
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Pizzi A, Pigliacelli C, Bergamaschi G, Gori A, Metrangolo P. Biomimetic engineering of the molecular recognition and self-assembly of peptides and proteins via halogenation. Coord Chem Rev 2020. [DOI: 10.1016/j.ccr.2020.213242] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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41
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Smithen D, Leung LMH, Challinor M, Lawrence R, Tang H, Niculescu-Duvaz D, Pearce SP, Mcleary R, Lopes F, Aljarah M, Brown M, Johnson L, Thomson G, Marais R, Springer C. 2-Aminomethylene-5-sulfonylthiazole Inhibitors of Lysyl Oxidase (LOX) and LOXL2 Show Significant Efficacy in Delaying Tumor Growth. J Med Chem 2020; 63:2308-2324. [PMID: 31430136 PMCID: PMC7073924 DOI: 10.1021/acs.jmedchem.9b01112] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Indexed: 12/11/2022]
Abstract
The lysyl oxidase (LOX) family of extracellular proteins plays a vital role in catalyzing the formation of cross-links in fibrillar elastin and collagens leading to extracellular matrix (ECM) stabilization. These enzymes have also been implicated in tumor progression and metastatic disease and have thus become an attractive therapeutic target for many types of invasive cancers. Following our recently published work on the discovery of aminomethylenethiophenes (AMTs) as potent, orally bioavailable LOX/LOXL2 inhibitors, we report herein the discovery of a series of dual LOX/LOXL2 inhibitors, as well as a subseries of LOXL2-selective inhibitors, bearing an aminomethylenethiazole (AMTz) scaffold. Incorporation of a thiazole core leads to improved potency toward LOXL2 inhibition via an irreversible binding mode of inhibition. SAR studies have enabled the discovery of a predictive 3DQSAR model. Lead AMTz inhibitors exhibit improved pharmacokinetic properties and excellent antitumor efficacy, with significantly reduced tumor growth in a spontaneous breast cancer genetically engineered mouse model.
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Affiliation(s)
- Deborah
A. Smithen
- Drug
Discovery Unit, Cancer Research UK Manchester Institute, University of Manchester, Alderley Park, Macclesfield SK10 4TG, United Kingdom
- Cancer
Research UK Centre for Cancer Therapeutics, The Institute of Cancer Research, 15 Cotswold Road, London SM2 5NG, United Kingdom
| | - Leo M. H. Leung
- Drug
Discovery Unit, Cancer Research UK Manchester Institute, University of Manchester, Alderley Park, Macclesfield SK10 4TG, United Kingdom
- Cancer
Research UK Centre for Cancer Therapeutics, The Institute of Cancer Research, 15 Cotswold Road, London SM2 5NG, United Kingdom
| | - Mairi Challinor
- Drug
Discovery Unit, Cancer Research UK Manchester Institute, University of Manchester, Alderley Park, Macclesfield SK10 4TG, United Kingdom
| | - Rae Lawrence
- Drug
Discovery Unit, Cancer Research UK Manchester Institute, University of Manchester, Alderley Park, Macclesfield SK10 4TG, United Kingdom
| | - HaoRan Tang
- Molecular
Oncology Team, Cancer Research UK Manchester Institute, University of Manchester, Alderley Park, Macclesfield SK10 4TG, United Kingdom
| | - Dan Niculescu-Duvaz
- Drug
Discovery Unit, Cancer Research UK Manchester Institute, University of Manchester, Alderley Park, Macclesfield SK10 4TG, United Kingdom
- Cancer
Research UK Centre for Cancer Therapeutics, The Institute of Cancer Research, 15 Cotswold Road, London SM2 5NG, United Kingdom
| | - Simon P. Pearce
- Clinical
and Experimental Pharmacology, Cancer Research UK Manchester Institute, University of Manchester, Alderley Park, Macclesfield SK10 4TG, United Kingdom
| | - Robert Mcleary
- Drug
Discovery Unit, Cancer Research UK Manchester Institute, University of Manchester, Alderley Park, Macclesfield SK10 4TG, United Kingdom
- Cancer
Research UK Centre for Cancer Therapeutics, The Institute of Cancer Research, 15 Cotswold Road, London SM2 5NG, United Kingdom
| | - Filipa Lopes
- Drug
Discovery Unit, Cancer Research UK Manchester Institute, University of Manchester, Alderley Park, Macclesfield SK10 4TG, United Kingdom
- Cancer
Research UK Centre for Cancer Therapeutics, The Institute of Cancer Research, 15 Cotswold Road, London SM2 5NG, United Kingdom
| | - Mohammed Aljarah
- Drug
Discovery Unit, Cancer Research UK Manchester Institute, University of Manchester, Alderley Park, Macclesfield SK10 4TG, United Kingdom
- Cancer
Research UK Centre for Cancer Therapeutics, The Institute of Cancer Research, 15 Cotswold Road, London SM2 5NG, United Kingdom
| | - Michael Brown
- Drug
Discovery Unit, Cancer Research UK Manchester Institute, University of Manchester, Alderley Park, Macclesfield SK10 4TG, United Kingdom
- Cancer
Research UK Centre for Cancer Therapeutics, The Institute of Cancer Research, 15 Cotswold Road, London SM2 5NG, United Kingdom
| | - Louise Johnson
- Cancer
Research UK Centre for Cancer Therapeutics, The Institute of Cancer Research, 15 Cotswold Road, London SM2 5NG, United Kingdom
| | - Graeme Thomson
- Drug
Discovery Unit, Cancer Research UK Manchester Institute, University of Manchester, Alderley Park, Macclesfield SK10 4TG, United Kingdom
| | - Richard Marais
- Molecular
Oncology Team, Cancer Research UK Manchester Institute, University of Manchester, Alderley Park, Macclesfield SK10 4TG, United Kingdom
| | - Caroline Springer
- Drug
Discovery Unit, Cancer Research UK Manchester Institute, University of Manchester, Alderley Park, Macclesfield SK10 4TG, United Kingdom
- Cancer
Research UK Centre for Cancer Therapeutics, The Institute of Cancer Research, 15 Cotswold Road, London SM2 5NG, United Kingdom
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Abstract
Sulfur is a widely used halogen bond (XB) acceptor, but only a limited number of neutral XB acceptors with bifurcated sp3-S sites have been reported. In this work a new bidentate XB acceptor, 1-(4-pyridyl)-4-thiopyridine (PTP), which combines sp3-S and sp2-N acceptor sites, is introduced. Three halogen bonded cocrystals were obtained by using 1,4-diiodobenzene (DIB), 1,4-diiodotetrafluorobenzene (DIFB), and iodopentafluorobenzene (IPFB) as XB donors and PTP as acceptor. The structures of the cocrystals showed some XB selectivity between the S and N donors in PTP. However, the limited contribution of XB to the overall molecular packing in these three cocrystals and the results from DSC measurements clearly point out the synergetic influence and interplay of all noncovalent interactions in crystal packing of these compounds.
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von der Heiden D, Vanderkooy A, Erdélyi M. Halogen bonding in solution: NMR spectroscopic approaches. Coord Chem Rev 2020. [DOI: 10.1016/j.ccr.2019.213147] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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Abstract
Using anions to induce molecular structure is a rapidly growing area of dynamic and switchable supramolecular chemistry. The emphasis of this review is on helical anion foldamers in solution, and many of the beautiful complexes described herein are accentuated by their crystal structures. Anion foldamers are defined as single- or multistrand complexes-often helical-that incorporate one or more anions. The review begins by discussing foldamer structure and nomenclature and follows with discourse on the anions which are employed. Recent advances in functional foldamers that bind a single anion are examined, including: induced chirality, stimuli-responsive dynamics, fluorescence changes, organocatalysis, anion transport, and halogen bonding. The review then inspects multianion foldamers, and this section is organized by the number of strands within the foldamer-from single- to triple-strand foldamers. Finally, the review is punctuated by recent hydrogen- and halogen-bonding triple-strand anion foldamers.
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Affiliation(s)
- Eric A John
- Department of Chemistry and Biochemistry, University of Montana, 32 Campus Drive, Missoula, Montana 59812, United States
| | - Casey J Massena
- Department of Chemistry and Biochemistry, University of Montana, 32 Campus Drive, Missoula, Montana 59812, United States
| | - Orion B Berryman
- Department of Chemistry and Biochemistry, University of Montana, 32 Campus Drive, Missoula, Montana 59812, United States
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45
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Voelkel MHH, Wonner P, Huber SM. Preorganization: A Powerful Tool in Intermolecular Halogen Bonding in Solution. ChemistryOpen 2020; 9:214-224. [PMID: 32071831 PMCID: PMC7011185 DOI: 10.1002/open.201900355] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Revised: 01/21/2020] [Indexed: 11/25/2022] Open
Abstract
Preorganization is a powerful tool in supramolecular chemistry which has been utilized successfully in intra- and intermolecular halogen bonding. In previous work, we had developed a bidentate bis(iodobenzimidazolium)-based halogen bond donor which featured a central trifluoromethyl substituent. This compound showed a markedly increased catalytic activity compared to unsubstituted bis(iodoimidazolium)-based Lewis acids, which could be explained either by electronic effects (the electron withdrawal by the fluorinated substituent) or by preorganization (the hindered rotation of the halogen bonding moieties). Herein, we systematically investigate the origin of this increased Lewis acidity via a comparison of the two types of compounds and their respective derivatives with or without the central trifluoromethyl group. Calorimetric measurements of halide complexations indicated that preorganization is the main reason for the higher halogen bonding strength. The performance of the catalysts in a series of benchmark reactions corroborates this finding.
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Affiliation(s)
- Martin H. H. Voelkel
- Fakultät für Chemie und BiochemieRuhr-Universität BochumUniversitätsstraße 15044801BochumGermany
| | - Patrick Wonner
- Fakultät für Chemie und BiochemieRuhr-Universität BochumUniversitätsstraße 15044801BochumGermany
| | - Stefan Matthias Huber
- Fakultät für Chemie und BiochemieRuhr-Universität BochumUniversitätsstraße 15044801BochumGermany
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46
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Scheiner S, Michalczyk M, Zierkiewicz W. Coordination of anions by noncovalently bonded σ-hole ligands. Coord Chem Rev 2020. [DOI: 10.1016/j.ccr.2019.213136] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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Wonner P, Steinke T, Vogel L, Huber SM. Carbonyl Activation by Selenium- and Tellurium-Based Chalcogen Bonding in a Michael Addition Reaction. Chemistry 2020; 26:1258-1262. [PMID: 31729084 PMCID: PMC7027547 DOI: 10.1002/chem.201905057] [Citation(s) in RCA: 70] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Indexed: 11/20/2022]
Abstract
In the last years the use of chalcogen bonding—the noncovalent interaction involving electrophilic chalcogen centers—in noncovalent organocatalysis has received increased interest, particularly regarding the use of intermolecular Lewis acids. Herein, we present the first use of tellurium‐based catalysts for the activation of a carbonyl compound (and only the second such activation by chalcogen bonding in general). As benchmark reaction, the Michael‐type addition between trans‐crotonophenone and 1‐methylindole (and its derivatives) was investigated in the presence of various catalyst candidates. Whereas non‐chalcogen‐bonding reference compounds were inactive, strong rate accelerations of up to 1000 could be achieved by bidentate triazolium‐based chalcogen bond donors, with product yields of >90 % within 2 h of reaction time. Organotellurium derivatives were markedly more active than their selenium and sulphur analogues and non‐coordinating counterions like BArF4 provide the strongest dicationic catalysts.
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Affiliation(s)
- Patrick Wonner
- Fakultät für Chemie und Biochemie, Ruhr-Universität Bochum, Universitätsstraße 150, 44801, Bochum, Germany
| | - Tim Steinke
- Fakultät für Chemie und Biochemie, Ruhr-Universität Bochum, Universitätsstraße 150, 44801, Bochum, Germany
| | - Lukas Vogel
- Fakultät für Chemie und Biochemie, Ruhr-Universität Bochum, Universitätsstraße 150, 44801, Bochum, Germany
| | - Stefan M Huber
- Fakultät für Chemie und Biochemie, Ruhr-Universität Bochum, Universitätsstraße 150, 44801, Bochum, Germany
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Fotović L, Stilinović V. Halogenide anions as halogen and hydrogen bond acceptors in iodopyridinium halogenides. CrystEngComm 2020. [DOI: 10.1039/d0ce00534g] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Structures of iodopyridinium halogenides have demonstrated why iodide, the weakest halogen bond acceptor among the halogenides, preferentially forms halogen bonds.
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Affiliation(s)
- Luka Fotović
- Department of Chemistry
- Faculty of Science
- University of Zagreb
- HR-10002 Zagreb
- Croatia
| | - Vladimir Stilinović
- Department of Chemistry
- Faculty of Science
- University of Zagreb
- HR-10002 Zagreb
- Croatia
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Sandner A, Hüfner-Wulsdorf T, Heine A, Steinmetzer T, Klebe G. Strategies for Late-Stage Optimization: Profiling Thermodynamics by Preorganization and Salt Bridge Shielding. J Med Chem 2019; 62:9753-9771. [PMID: 31633354 DOI: 10.1021/acs.jmedchem.9b01196] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Structural fixation of a ligand in its bioactive conformation may, due to entropic reasons, improve affinity. We present a congeneric series of thrombin ligands with a variety of functional groups triggering preorganization prior to binding. Fixation in solution and complex formation have been characterized by crystallography, isothermal titration calorimetry (ITC), and molecular dynamics (MD) simulations. First, we show why these preorganizing modifications do not affect the overall binding mode and how key interactions are preserved. Next, we demonstrate how preorganization thermodynamics can be largely dominated by enthalpy rather than entropy because of the significant population of low-energy conformations. Furthermore, a salt bridge is shielded by actively reducing its surface exposure, thus leading to an enhanced enthalpic binding profile. Our results suggest that the consideration of the ligand solution ensemble by MD simulation is necessary to predict preorganizing modifications that enhance the binding behavior of already promising binders.
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Affiliation(s)
- Anna Sandner
- Institut für Pharmazeutische Chemie , Philipps-Universität Marburg , Marbacher Weg 6 , 35032 Marburg , Germany
| | - Tobias Hüfner-Wulsdorf
- Institut für Pharmazeutische Chemie , Philipps-Universität Marburg , Marbacher Weg 6 , 35032 Marburg , Germany
| | - Andreas Heine
- Institut für Pharmazeutische Chemie , Philipps-Universität Marburg , Marbacher Weg 6 , 35032 Marburg , Germany
| | - Torsten Steinmetzer
- Institut für Pharmazeutische Chemie , Philipps-Universität Marburg , Marbacher Weg 6 , 35032 Marburg , Germany
| | - Gerhard Klebe
- Institut für Pharmazeutische Chemie , Philipps-Universität Marburg , Marbacher Weg 6 , 35032 Marburg , Germany
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