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Naz A, Asif S, Alwutayd KM, Sarfaraz S, Abbasi SW, Abbasi A, Alenazi AM, Hasan ME. Repurposing FIASMAs against Acid Sphingomyelinase for COVID-19: A Computational Molecular Docking and Dynamic Simulation Approach. Molecules 2023; 28:molecules28072989. [PMID: 37049752 PMCID: PMC10096053 DOI: 10.3390/molecules28072989] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 03/16/2023] [Accepted: 03/24/2023] [Indexed: 03/30/2023] Open
Abstract
Over the past few years, COVID-19 has caused widespread suffering worldwide. There is great research potential in this domain and it is also necessary. The main objective of this study was to identify potential inhibitors against acid sphingomyelinase (ASM) in order to prevent coronavirus infection. Experimental studies revealed that SARS-CoV-2 causes activation of the acid sphingomyelinase/ceramide pathway, which in turn facilitates the viral entry into the cells. The objective was to inhibit acid sphingomyelinase activity in order to prevent the cells from SARS-CoV-2 infection. Previous studies have reported functional inhibitors against ASM (FIASMAs). These inhibitors can be exploited to block the entry of SARS-CoV-2 into the cells. To achieve our objective, a drug library containing 257 functional inhibitors of ASM was constructed. Computational molecular docking was applied to dock the library against the target protein (PDB: 5I81). The potential binding site of the target protein was identified through structural alignment with the known binding pocket of a protein with a similar function. AutoDock Vina was used to carry out the docking steps. The docking results were analyzed and the inhibitors were screened based on their binding affinity scores and ADME properties. Among the 257 functional inhibitors, Dutasteride, Cepharanthine, and Zafirlukast presented the lowest binding affinity scores of −9.7, −9.6, and −9.5 kcal/mol, respectively. Furthermore, computational ADME analysis of these results revealed Cepharanthine and Zafirlukast to have non-toxic properties. To further validate these findings, the top two inhibitors in complex with the target protein were subjected to molecular dynamic simulations at 100 ns. The molecular interactions and stability of these compounds revealed that these inhibitors could be a promising tool for inhibiting SARS-CoV-2 infection.
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Affiliation(s)
- Aliza Naz
- National Center for Bioinformatics, Quaid-i-Azam University, Islamabad 45320, Pakistan
- Department of Bioinformatics and Biotechnology, International Islamic University, Islamabad 44000, Pakistan
| | - Sumbul Asif
- Department of Bioinformatics and Biotechnology, International Islamic University, Islamabad 44000, Pakistan
- School of Interdisciplinary Engineering and Sciences, National University of Sciences and Technology, Islamabad 44000, Pakistan
| | - Khairiah Mubarak Alwutayd
- Department of Biology, College of Science, Princess Nourah bint Abdulrahman University, P.O. Box 84428, Riyadh 11671, Saudi Arabia
| | - Sara Sarfaraz
- Department of Bioinformatics, Kohsar University Murree, Murree 47150, Pakistan
- Correspondence:
| | - Sumra Wajid Abbasi
- Department of Biological Sciences, National University of Medical Sciences, Rawalpindi 46000, Pakistan
| | - Asim Abbasi
- Department of Environmental Sciences, Kohsar University Murree, Murree 47150, Pakistan
| | - Abdulkareem M. Alenazi
- Pediatric Senior Registrar, King Salman Armed Forces Hospital in Northwestern Region (KSAFH), Tabuk 47512, Saudi Arabia
| | - Mohamed E. Hasan
- Bioinformatic Department, Genetic Engineering and Biotechnology Research Institute, University of Sadat City, Sadat City 32897, Egypt
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Zhang Y, Li Y, Zhang Y, Liu L, Zou D, Sun W, Li J, Feng Y, Geng Y, Cheng G. Improved solubility and hygroscopicity of enoxacin by pharmaceutical salts formation with hydroxybenzonic acids via charge assisted hydrogen bond. J Mol Struct 2023. [DOI: 10.1016/j.molstruc.2022.134272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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3
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A stability analysis of choline chloride: urea deep eutectic solvent using density functional theory. COMPUT THEOR CHEM 2022. [DOI: 10.1016/j.comptc.2022.113921] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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Sengupta A, Li B, Svatunek D, Liu F, Houk KN. Cycloaddition Reactivities Analyzed by Energy Decomposition Analyses and the Frontier Molecular Orbital Model. Acc Chem Res 2022; 55:2467-2479. [PMID: 36007242 DOI: 10.1021/acs.accounts.2c00343] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
This Account describes our quest to understand and predict organic reactivity, a principal goal of physical and theoretical organic chemistry. The focus is on the development and testing of models for the prediction of cycloaddition reactivities and selectivities. We describe the involvement of the Houk group, and other groups, in the evolution of theoretical models that can achieve ever greater accuracy as well as provide practical heuristic models for understanding and prediction.Is the venerable frontier molecular orbital (FMO) model, the basis of Kenichi Fukui's 1981 Nobel Prize, still useful, or must it be replaced with more advanced models? In particular, models such as Conceptual Density Functional, the Pauli Exclusion Model, and the recent popularity of Electrostatic Potential Plots and Dispersion Energies have not only added to our understanding, but they have also created uncertainty about whether the simple FMO heuristic model has a place in 21st century discussions. This Account addresses this issue and asserts the value of the FMO model.Beginning with brief descriptions of selected models for cycloaddition reactivity starting with early donor-acceptor (nucleophile-electrophile) charge-transfer concepts, this Account reviews Fukui's frontier molecular orbital model, Salem and Klopman's orbital, electrostatic and Pauli repulsion model, the conceptual DFT model by Parr and later by Domingo and others, the recent Houk and Bickelhaupt Distortion/Interaction Activation Strain model, and the Bickelhaupt-Hamlin's Pauli-repulsion lowering model.Computations and analyses of four well-studied Diels-Alder cycloadditions, both normal and inverse electron-demand types, are presented. Most were studied earlier in our published work but are presented here with new insights from calculations with modern methods. Depending on the types of substrates (cycloaddends), the dominant factors controlling reactivity can be orbital interactions, electrostatics and polarization, or Pauli repulsion and dispersion effects, or a combination of all of these.By comparing orbital interactions, especially the frontier molecular orbital interactions, with the other factors that influence reactivity, we show why the FMO model is such a powerful─and theoretically meaningful─heuristic for understanding and predicting reactivity. We also present a method to understand Pauli repulsion effects on activation barriers, ρ(1.1). The use of a new reaction coordinate, the extent of Pauli repulsion along the reaction path, is advocated to emphasize the role of repulsive occupied orbital interactions on reactivity.Fukui's frontier molecular orbital model is effective because FMO interactions parallel all the quantities that influence reactivity. The FMO model continues to provide a practical model to understand and guide experiments.
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Affiliation(s)
- Arkajyoti Sengupta
- Department of Chemistry and Biochemistry, University of California, Los Angeles 90095, California, United States
| | - Bo Li
- Department of Chemistry, School of Science, Tianjin University, Tianjin 300072, China
| | - Dennis Svatunek
- Department of Chemistry and Biochemistry, University of California, Los Angeles 90095, California, United States
| | - Fang Liu
- College of Sciences, Nanjing Agricultural University, Nanjing 210024, Jiangsu, China
| | - K N Houk
- Department of Chemistry and Biochemistry, University of California, Los Angeles 90095, California, United States
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Kaupp M, Schattenberg CJ, Müller R, Reimann M. Unusually Large Effects of Charge-assisted C-H⋅⋅⋅F Hydrogen Bonds to Anionic Fluorine in Organic Solvents: Computational Study of 19 F NMR Shifts versus Thermochemistry. Chemistry 2022; 11:e202200146. [PMID: 35984672 PMCID: PMC9716039 DOI: 10.1002/open.202200146] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 07/26/2022] [Indexed: 01/31/2023]
Abstract
A comparison of computed 19 F NMR chemical shifts and experiment provides evidence for large specific solvent effects for fluoride-type anions interacting with the σ*(C-H) orbitals in organic solvents like MeCN or CH2 Cl2 . We show this for systems ranging from the fluoride ion and the bifluoride ion [FHF]- to polyhalogen anions [ClFx ]- . Discrepancies between computed and experimental shifts when using continuum solvent models like COSMO or force-field-based descriptions like the 3D-RISM-SCF model show specific orbital interactions that require a quantum-mechanical treatment of the solvent molecules. This is confirmed by orbital analyses of the shielding constants, while less negatively charged fluorine atoms (e. g., in [EF4 ]- ) do not require such quantum-mechanical treatments to achieve reasonable accuracy. The larger 19 F solvent shift of fluoride in MeCN compared to water is due to the larger coordination number in the former. These observations are due to unusually strong charge-assisted C-H⋅⋅⋅F- hydrogen bonds, which manifest beyond some threshold negative natural charge on fluorine of ca. < -0.6 e. The interactions are accompanied by sizable free energies of solvation, in the order F- ≫[FHF]- >[ClF2 ]- >[ClF4 ]- . COSMO-RS solvation free energies tend to moderately underestimate those from the micro-solvated cluster treatment. Red-shifted and intense vibrational C-H stretching bands, potentially accessible in bulk solution, are further spectroscopic finger prints.
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Affiliation(s)
- Martin Kaupp
- Technische Universität BerlinInstitut für Chemie, Theoretische Chemie/QuantenchemieSekr. C7, Strasse des 17. Juni 13510623BerlinGermany
| | - Caspar J. Schattenberg
- Technische Universität BerlinInstitut für Chemie, Theoretische Chemie/QuantenchemieSekr. C7, Strasse des 17. Juni 13510623BerlinGermany
| | - Robert Müller
- Technische Universität BerlinInstitut für Chemie, Theoretische Chemie/QuantenchemieSekr. C7, Strasse des 17. Juni 13510623BerlinGermany
| | - Marc Reimann
- Technische Universität BerlinInstitut für Chemie, Theoretische Chemie/QuantenchemieSekr. C7, Strasse des 17. Juni 13510623BerlinGermany
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Jenepha Mary SJ, Pradhan S, James C. Molecular structure, NBO analysis of the hydrogen-bonded interactions, spectroscopic (FT-IR, FT-Raman), drug likeness and molecular docking of the novel anti COVID-2 molecule (2E)-N-methyl-2-[(4-oxo-4H-chromen-3-yl)methylidene]-hydrazinecarbothioamide (Dimer) - quantum chemical approach. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2021; 251:119388. [PMID: 33503560 PMCID: PMC7834302 DOI: 10.1016/j.saa.2020.119388] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2020] [Revised: 12/04/2020] [Accepted: 12/24/2020] [Indexed: 05/14/2023]
Abstract
Prospective antiviral molecule (2E)-N-methyl-2-[(4-oxo-4H-chromen-3-yl)methylidene]-hydrazinecarbothioamide has been probed using Fourier transform infrared (FTIR), FT-Raman and quantum chemical computations. The geometry equilibrium and natural bond orbital analysis have been carried out with density functional theory employing Becke, 3-parameter, Lee-Yang-Parr method with the 6-311G++(d,p) basis set. The vibrational assignments pertaining to different modes of vibrations have been augmented by normal coordinate analysis, force constant and potential energy distributions. Drug likeness and oral activity have been carried out based on Lipinski's rule of five. The inhibiting potency of 2(2E)-methyl-2-[(4-oxo-4H-chromen-3-yl)methylidene]-hydrazinecarbothioamide has been investigated by docking simulation against SARS-CoV-2 protein. The optimized geometry shows a planar structure between the chromone and the side chain. Differences in the geometries due to the substitution of the electronegative atom and intermolecular contacts due to the chromone and hydrazinecarbothioamide were analyzed. NBO analysis confirms the presence of two strong stable hydrogen bonded NH⋯O intermolecular interactions and two weak hydrogen bonded CH⋯O interactions. The red shift in NH stretching frequency exposed from IR substantiates the formation of NH⋯O intermolecular hydrogen bond and the blue shift in CH stretching frequency substantiates the formation of CH⋯O intermolecular hydrogen bond. Drug likeness, absorption, distribution, metabolism, excretion and toxicity property gives an idea about the pharmacokinetic properties of the title molecule. The binding energy of the nonbonding interaction with Histidine 41 and Cysteine 145, present a clear view that 2(2E)-methyl-2-[(4-oxo-4H-chromen-3-yl)methylidene]-hydrazinecarbothioamide can irreversibly interact with SARS-CoV-2 protease.
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Affiliation(s)
- S J Jenepha Mary
- Department of Physics and Research Centre, Scott Christian College (Autonomous), Nagercoil 629003, Tamil Nadu, Affiliated to Manonmaniam Sundarnar University, Abishekapatti, Tirunelveli 627012, India
| | - Sayantan Pradhan
- Department of Chemistry, Jadavpur University, Kolkata 700 032, West Bengal, India
| | - C James
- Department of Physics and Research Centre, Scott Christian College (Autonomous), Nagercoil 629003, Tamil Nadu, Affiliated to Manonmaniam Sundarnar University, Abishekapatti, Tirunelveli 627012, India.
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Zhang Y, Duan Y, Su J, Liu L, Feng Y, Wu L, Zhang L, Zhang Y, Zou D, Liu Y. Inspiration for revival of old drugs: improving solubility and avoiding hygroscopicity of pipemidic acid by forming two pharmaceutical salts based on charge-assisted hydrogen bond recognitions. NEW J CHEM 2021. [DOI: 10.1039/d1nj03314j] [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
Improving solubility and avoiding hygroscopicity of pipemidic acid by forming pharmaceutical salts based on CAHBs.
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Affiliation(s)
- Yunan Zhang
- College of pharmacy, Jiamusi University, Jiamusi 154007, China
| | - Yu Duan
- College of pharmacy, Jiamusi University, Jiamusi 154007, China
| | - Jin Su
- College of pharmacy, Jiamusi University, Jiamusi 154007, China
| | - Lixin Liu
- College of pharmacy, Jiamusi University, Jiamusi 154007, China
| | - Yanru Feng
- College of pharmacy, Jiamusi University, Jiamusi 154007, China
| | - Lili Wu
- College of pharmacy, Jiamusi University, Jiamusi 154007, China
| | - Lei Zhang
- College of pharmacy, Jiamusi University, Jiamusi 154007, China
| | - Yunjie Zhang
- College of pharmacy, Jiamusi University, Jiamusi 154007, China
| | - Dongyu Zou
- College of pharmacy, Jiamusi University, Jiamusi 154007, China
| | - Yingli Liu
- College of pharmacy, Jiamusi University, Jiamusi 154007, China
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Itoh Y, Kurohara T, Suzuki T. N<sup>+</sup>-C-H…O Hydrogen Bonds in Protein-Ligand Complexes and their Application to Drug Design. J SYN ORG CHEM JPN 2020. [DOI: 10.5059/yukigoseikyokaishi.78.1151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
| | | | - Takayoshi Suzuki
- The Institute of Scientific and Industrial Research, Osaka University
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11
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To T, Mizusaki H, Murai A, Matsugami M, Takamuku T. Conformational change of L-phenylalanine in fluorinated alcohol-water mixed solvents studied by IR, NMR, and MD simulations. J Mol Liq 2019. [DOI: 10.1016/j.molliq.2019.111192] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Costantini NV, Ganguly HK, Martin MI, Wenzell NA, Yap GPA, Zondlo NJ. The Distinct Conformational Landscapes of 4S-Substituted Prolines That Promote an endo Ring Pucker. Chemistry 2019; 25:11356-11364. [PMID: 31237705 PMCID: PMC6710147 DOI: 10.1002/chem.201902382] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Revised: 06/20/2019] [Indexed: 12/28/2022]
Abstract
4-Substitution on proline directly impacts protein main chain conformational preferences. The structural effects of N-acyl substitution and of 4-substitution were examined by NMR spectroscopy and X-ray crystallography on minimal molecules with a proline 4S-nitrobenzoate. The effects of N-acyl substitution on conformation were attenuated in the 4S-nitrobenzoate context, due to the minimal role of the n→π* interaction in stabilizing extended conformations. By X-ray crystallography, an extended conformation was observed for most molecules. The formyl derivative adopted a δ conformation that is observed at the i+2 position of β-turns. Computational analysis indicated that the structures observed crystallographically represent the inherent conformational preferences of 4S-substituted prolines with electron-withdrawing 4-position substituents. The divergent conformational preferences of 4R- and 4S-substituted prolines suggest their wider structure-specific application in molecular design. In particular, the proline endo ring pucker favored by 4S-substituted prolines uniquely promotes the δ conformation [(ϕ, ψ) ≈(-80°, 0°)] found in β-turns. In contrast to other acyl capping groups, the pivaloyl group strongly promoted trans amide bond and polyproline II helix conformation, with a close n→π* interaction in the crystalline state, despite the endo ring pucker, suggesting its special capabilities in promoting compact conformations in ϕ due to its strongly electron-donating character.
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Affiliation(s)
- Nicholas V. Costantini
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, United States
| | - Himal K. Ganguly
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, United States
| | - Maxwell I. Martin
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, United States
| | - Nicole A. Wenzell
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, United States
| | - Glenn P. A. Yap
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, United States
| | - Neal J. Zondlo
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, United States
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Rajakovich LJ, Pandelia ME, Mitchell AJ, Chang WC, Zhang B, Boal AK, Krebs C, Bollinger JM. A New Microbial Pathway for Organophosphonate Degradation Catalyzed by Two Previously Misannotated Non-Heme-Iron Oxygenases. Biochemistry 2019; 58:1627-1647. [PMID: 30789718 PMCID: PMC6503667 DOI: 10.1021/acs.biochem.9b00044] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
The assignment of biochemical functions to hypothetical proteins is challenged by functional diversification within many protein structural superfamilies. This diversification, which is particularly common for metalloenzymes, renders functional annotations that are founded solely on sequence and domain similarities unreliable and often erroneous. Definitive biochemical characterization to delineate functional subgroups within these superfamilies will aid in improving bioinformatic approaches for functional annotation. We describe here the structural and functional characterization of two non-heme-iron oxygenases, TmpA and TmpB, which are encoded by a genomically clustered pair of genes found in more than 350 species of bacteria. TmpA and TmpB are functional homologues of a pair of enzymes (PhnY and PhnZ) that degrade 2-aminoethylphosphonate but instead act on its naturally occurring, quaternary ammonium analogue, 2-(trimethylammonio)ethylphosphonate (TMAEP). TmpA, an iron(II)- and 2-(oxo)glutarate-dependent oxygenase misannotated as a γ-butyrobetaine (γbb) hydroxylase, shows no activity toward γbb but efficiently hydroxylates TMAEP. The product, ( R)-1-hydroxy-2-(trimethylammonio)ethylphosphonate [( R)-OH-TMAEP], then serves as the substrate for the second enzyme, TmpB. By contrast to its purported phosphohydrolytic activity, TmpB is an HD-domain oxygenase that uses a mixed-valent diiron cofactor to enact oxidative cleavage of the C-P bond of its substrate, yielding glycine betaine and phosphate. The high specificities of TmpA and TmpB for their N-trimethylated substrates suggest that they have evolved specifically to degrade TMAEP, which was not previously known to be subject to microbial catabolism. This study thus adds to the growing list of known pathways through which microbes break down organophosphonates to harvest phosphorus, carbon, and nitrogen in nutrient-limited niches.
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Affiliation(s)
- Lauren J. Rajakovich
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
- Present address: Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States
| | - Maria-Eirini Pandelia
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
- Present address: Department of Biochemistry, Brandeis University, Waltham, Massachusetts 02453, United States
| | - Andrew J. Mitchell
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
- Present address: Whitehead Institute for Biomedical Research, Cambridge, Massachusetts 02142
| | - Wei-chen Chang
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
- Present address: Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Bo Zhang
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
- Present address: REG Life Sciences, LLC, South San Francisco, California 94080
| | - Amie K. Boal
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Carsten Krebs
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - J. Martin Bollinger
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
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Itoh Y, Nakashima Y, Tsukamoto S, Kurohara T, Suzuki M, Sakae Y, Oda M, Okamoto Y, Suzuki T. N +-C-H···O Hydrogen bonds in protein-ligand complexes. Sci Rep 2019; 9:767. [PMID: 30683882 PMCID: PMC6347603 DOI: 10.1038/s41598-018-36987-9] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Accepted: 11/28/2018] [Indexed: 12/03/2022] Open
Abstract
In the context of drug design, C-H···O hydrogen bonds have received little attention so far, mostly because they are considered weak relative to other noncovalent interactions such as O-H···O hydrogen bonds, π/π interactions, and van der Waals interactions. Herein, we demonstrate the significance of hydrogen bonds between C-H groups adjacent to an ammonium cation and an oxygen atom (N+-C-H···O hydrogen bonds) in protein-ligand complexes. Quantum chemical calculations revealed details on the strength and geometrical requirements of these N+-C-H···O hydrogen bonds, and a subsequent survey of the Protein Data Bank (PDB) based on these criteria suggested that numerous protein-ligand complexes contain such N+-C-H···O hydrogen bonds. An ensuing experimental investigation into the G9a-like protein (GLP)-inhibitor complex demonstrated that N+-C-H···O hydrogen bonds affect the activity of the inhibitors against the target enzyme. These results should provide the basis for the use of N+-C-H···O hydrogen bonds in drug discovery.
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Affiliation(s)
- Yukihiro Itoh
- Department of Chemistry, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, 1-5 Shimogamohangi-cho, Sakyo-ku, Kyoto, 606-0823, Japan
| | - Yusuke Nakashima
- Department of Chemistry, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, 1-5 Shimogamohangi-cho, Sakyo-ku, Kyoto, 606-0823, Japan
| | - Shuichiro Tsukamoto
- Department of Physics, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8602, Japan
| | - Takashi Kurohara
- Department of Chemistry, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, 1-5 Shimogamohangi-cho, Sakyo-ku, Kyoto, 606-0823, Japan
| | - Miki Suzuki
- Department of Chemistry, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, 1-5 Shimogamohangi-cho, Sakyo-ku, Kyoto, 606-0823, Japan
| | - Yoshitake Sakae
- Department of Physics, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8602, Japan
| | - Masayuki Oda
- Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, Kyoto, 1-5 Shimogamohangi-cho, Sakyo-ku, Kyoto, 606-8522, Japan
| | - Yuko Okamoto
- Department of Physics, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8602, Japan.,CREST, Japan Science and Technology Agency (JST), 4-1-8 Honcho, Kawaguchi, Saitama, 332-0012, Japan
| | - Takayoshi Suzuki
- Department of Chemistry, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, 1-5 Shimogamohangi-cho, Sakyo-ku, Kyoto, 606-0823, Japan. .,CREST, Japan Science and Technology Agency (JST), 4-1-8 Honcho, Kawaguchi, Saitama, 332-0012, Japan.
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Crystallographic and Computational Characterization of Methyl Tetrel Bonding in S-Adenosylmethionine-Dependent Methyltransferases. Molecules 2018; 23:molecules23112965. [PMID: 30428636 PMCID: PMC6278250 DOI: 10.3390/molecules23112965] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Revised: 10/19/2018] [Accepted: 10/20/2018] [Indexed: 11/17/2022] Open
Abstract
Tetrel bonds represent a category of non-bonding interaction wherein an electronegative atom donates a lone pair of electrons into the sigma antibonding orbital of an atom in the carbon group of the periodic table. Prior computational studies have implicated tetrel bonding in the stabilization of a preliminary state that precedes the transition state in SN2 reactions, including methyl transfer. Notably, the angles between the tetrel bond donor and acceptor atoms coincide with the prerequisite geometry for the SN2 reaction. Prompted by these findings, we surveyed crystal structures of methyltransferases in the Protein Data Bank and discovered multiple instances of carbon tetrel bonding between the methyl group of the substrate S-adenosylmethionine (AdoMet) and electronegative atoms of small molecule inhibitors, ions, and solvent molecules. The majority of these interactions involve oxygen atoms as the Lewis base, with the exception of one structure in which a chlorine atom of an inhibitor functions as the electron donor. Quantum mechanical analyses of a representative subset of the methyltransferase structures from the survey revealed that the calculated interaction energies and spectral properties are consistent with the values for bona fide carbon tetrel bonds. The discovery of methyl tetrel bonding offers new insights into the mechanism underlying the SN2 reaction catalyzed by AdoMet-dependent methyltransferases. These findings highlight the potential of exploiting these interactions in developing new methyltransferase inhibitors.
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Kurczab R, Śliwa P, Rataj K, Kafel R, Bojarski AJ. Salt Bridge in Ligand-Protein Complexes-Systematic Theoretical and Statistical Investigations. J Chem Inf Model 2018; 58:2224-2238. [PMID: 30351056 DOI: 10.1021/acs.jcim.8b00266] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Although the salt bridge is the strongest among all known noncovalent molecular interactions, no comprehensive studies have been conducted to date to examine its role and significance in drug design. Thus, a systematic study of the salt bridge in biological systems is reported herein, with a broad analysis of publicly available data from Protein Data Bank, DrugBank, ChEMBL, and GPCRdb. The results revealed the distance and angular preferences as well as privileged molecular motifs of salt bridges in ligand-receptor complexes, which could be used to design the strongest interactions. Moreover, using quantum chemical calculations at the MP2 level, the energetic, directionality, and spatial variabilities of salt bridges were investigated using simple model systems mimicking salt bridges in a biological environment. Additionally, natural orbitals for chemical valence (NOCV) combined with the extended-transition-state (ETS) bond-energy decomposition method (ETS-NOCV) were analyzed and indicated a strong covalent contribution to the salt bridge interaction. The present results could be useful for implementation in rational drug design protocols.
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Affiliation(s)
- Rafał Kurczab
- Department of Medicinal Chemistry, Institute of Pharmacology , Polish Academy of Sciences , Smetna 12 , 31-343 Cracow , Poland
| | - Paweł Śliwa
- Faculty of Chemical Engineering and Technology , Cracow University of Technology , Warszawska 24 , 31-155 Cracow , Poland
| | - Krzysztof Rataj
- Department of Medicinal Chemistry, Institute of Pharmacology , Polish Academy of Sciences , Smetna 12 , 31-343 Cracow , Poland
| | - Rafał Kafel
- Department of Medicinal Chemistry, Institute of Pharmacology , Polish Academy of Sciences , Smetna 12 , 31-343 Cracow , Poland
| | - Andrzej J Bojarski
- Department of Medicinal Chemistry, Institute of Pharmacology , Polish Academy of Sciences , Smetna 12 , 31-343 Cracow , Poland
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18
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Isaev AN. syn- and anti-H Bonds in Ammonia and Phosphine Complexes with Proton Donors. RUSSIAN JOURNAL OF PHYSICAL CHEMISTRY A 2018. [DOI: 10.1134/s0036024418100096] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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19
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Isaev AN. Ammonia and phosphine complexes with proton donors. Hydrogen bonding from the backside of the N(P) lone pair. COMPUT THEOR CHEM 2018. [DOI: 10.1016/j.comptc.2018.08.021] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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20
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Sengupta A, Liu Y, Flood AH, Raghavachari K. Anion‐Binding Macrocycles Operate Beyond the Electrostatic Regime: Interaction Distances Matter. Chemistry 2018; 24:14409-14417. [PMID: 30036449 DOI: 10.1002/chem.201802657] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Indexed: 12/22/2022]
Affiliation(s)
- Arkajyoti Sengupta
- Department of Chemistry Indiana University 800 E. Kirkwood Avenue Bloomington Indiana 47405 USA
- Current Address: Department of Chemistry Michigan State University East Lansing Michigan 48824 USA
| | - Yun Liu
- Department of Chemistry Indiana University 800 E. Kirkwood Avenue Bloomington Indiana 47405 USA
- Current Address: Beckman Institute for Advanced Science and Technology University of Illinois at Urbana-Champaign Urbana Illinois 61801 USA
| | - Amar H. Flood
- Department of Chemistry Indiana University 800 E. Kirkwood Avenue Bloomington Indiana 47405 USA
| | - Krishnan Raghavachari
- Department of Chemistry Indiana University 800 E. Kirkwood Avenue Bloomington Indiana 47405 USA
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21
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Fick RJ, Clay MC, Vander Lee L, Scheiner S, Al-Hashimi H, Trievel RC. Water-Mediated Carbon–Oxygen Hydrogen Bonding Facilitates S-Adenosylmethionine Recognition in the Reactivation Domain of Cobalamin-Dependent Methionine Synthase. Biochemistry 2018; 57:3733-3740. [DOI: 10.1021/acs.biochem.8b00375] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- Robert J. Fick
- Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Mary C. Clay
- Department of Biochemistry, Duke University, Durham, North Carolina 27710, United States
| | - Lucas Vander Lee
- Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Steve Scheiner
- Department of Chemistry and Biochemistry, Utah State University, Logan, Utah 84322, United States
| | - Hashim Al-Hashimi
- Department of Biochemistry, Duke University, Durham, North Carolina 27710, United States
| | - Raymond C. Trievel
- Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
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22
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Xu J, Liu J, Li Z, Xu S, Wang H, Guo T, Gao Y, Zhang L, Zhang C, Guo K. Opposite-charge repulsive cation and anion pair cooperative organocatalysis in ring-opening polymerization. Polym Chem 2018. [DOI: 10.1039/c8py00338f] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
A new strained ion pair catalysis was proposed in ring-opening polymerization.
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Affiliation(s)
- Jiaxi Xu
- College of Biotechnology and Pharmaceutical Engineering
- Nanjing Tech University
- Nanjing
- China
| | - Jingjing Liu
- College of Biotechnology and Pharmaceutical Engineering
- Nanjing Tech University
- Nanjing
- China
| | - Zhenjiang Li
- College of Biotechnology and Pharmaceutical Engineering
- Nanjing Tech University
- Nanjing
- China
- State Key Laboratory of Materials-Oriented Chemical Engineering
| | - Songquan Xu
- College of Biotechnology and Pharmaceutical Engineering
- Nanjing Tech University
- Nanjing
- China
| | - Haixin Wang
- College of Biotechnology and Pharmaceutical Engineering
- Nanjing Tech University
- Nanjing
- China
| | - Tianfo Guo
- College of Biotechnology and Pharmaceutical Engineering
- Nanjing Tech University
- Nanjing
- China
| | - Yu Gao
- College of Biotechnology and Pharmaceutical Engineering
- Nanjing Tech University
- Nanjing
- China
| | - Lei Zhang
- College of Biotechnology and Pharmaceutical Engineering
- Nanjing Tech University
- Nanjing
- China
| | - Chan Zhang
- College of Biotechnology and Pharmaceutical Engineering
- Nanjing Tech University
- Nanjing
- China
| | - Kai Guo
- College of Biotechnology and Pharmaceutical Engineering
- Nanjing Tech University
- Nanjing
- China
- State Key Laboratory of Materials-Oriented Chemical Engineering
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23
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Two kinds of X H⋯C(sp 3 ) hydrogen bond formed by the methide anion: Syn- and anti- orientation of monomers. COMPUT THEOR CHEM 2017. [DOI: 10.1016/j.comptc.2017.08.013] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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24
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Backman LRF, Funk MA, Dawson CD, Drennan CL. New tricks for the glycyl radical enzyme family. Crit Rev Biochem Mol Biol 2017; 52:674-695. [PMID: 28901199 DOI: 10.1080/10409238.2017.1373741] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Glycyl radical enzymes (GREs) are important biological catalysts in both strict and facultative anaerobes, playing key roles both in the human microbiota and in the environment. GREs contain a backbone glycyl radical that is post-translationally installed, enabling radical-based mechanisms. GREs function in several metabolic pathways including mixed acid fermentation, ribonucleotide reduction and the anaerobic breakdown of the nutrient choline and the pollutant toluene. By generating a substrate-based radical species within the active site, GREs enable C-C, C-O and C-N bond breaking and formation steps that are otherwise challenging for nonradical enzymes. Identification of previously unknown family members from genomic data and the determination of structures of well-characterized GREs have expanded the scope of GRE-catalyzed reactions as well as defined key features that enable radical catalysis. Here, we review the structures and mechanisms of characterized GREs, classifying members into five categories. We consider the open questions about each of the five GRE classes and evaluate the tools available to interrogate uncharacterized GREs.
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Affiliation(s)
- Lindsey R F Backman
- a Department of Chemistry , Massachusetts Institute of Technology , Cambridge , MA , USA
| | - Michael A Funk
- a Department of Chemistry , Massachusetts Institute of Technology , Cambridge , MA , USA.,b Department of Chemistry , University of Illinois at Urbana-Champaign , Urbana , IL , USA
| | - Christopher D Dawson
- c Department of Biology , Massachusetts Institute of Technology , Cambridge , MA , USA
| | - Catherine L Drennan
- a Department of Chemistry , Massachusetts Institute of Technology , Cambridge , MA , USA.,c Department of Biology , Massachusetts Institute of Technology , Cambridge , MA , USA.,d Howard Hughes Medical Institute , Massachusetts Institute of Technology , Cambridge , MA , USA
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25
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Maji R, Wheeler SE. Importance of Electrostatic Effects in the Stereoselectivity of NHC-Catalyzed Kinetic Resolutions. J Am Chem Soc 2017; 139:12441-12449. [DOI: 10.1021/jacs.7b01796] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Rajat Maji
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Steven E. Wheeler
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
- Center
for Computational Quantum Chemistry, Department of Chemistry, University of Georgia, Athens, Georgia 30602, United States
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26
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Hunt PA. Quantum Chemical Modeling of Hydrogen Bonding in Ionic Liquids. Top Curr Chem (Cham) 2017; 375:59. [PMID: 28523638 PMCID: PMC5480408 DOI: 10.1007/s41061-017-0142-7] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2017] [Accepted: 04/16/2017] [Indexed: 01/18/2023]
Abstract
Hydrogen bonding (H-bonding) is an important and very general phenomenon. H-bonding is part of the basis of life in DNA, key in controlling the properties of water and ice, and critical to modern applications such as crystal engineering, catalysis applications, pharmaceutical and agrochemical development. H-bonding also plays a significant role for many ionic liquids (IL), determining the secondary structuring and affecting key physical parameters. ILs exhibit a particularly diverse and wide range of traditional as well as non-standard forms of H-bonding, in particular the doubly ionic H-bond is important. Understanding the fundamental nature of the H-bonds that form within ILs is critical, and one way of accessing this information, that cannot be recovered by any other computational method, is through quantum chemical electronic structure calculations. However, an appropriate method and basis set must be employed, and a robust procedure for determining key structures is essential. Modern generalised solvation models have recently been extended to ILs, bringing both advantages and disadvantages. QC can provide a range of information on geometry, IR and Raman spectra, NMR spectra and at a more fundamental level through analysis of the electronic structure.
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Affiliation(s)
- Patricia A Hunt
- Imperial College of Science, Technology and Medicine, London, UK.
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27
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To T, Hatomoto Y, Umecky T, Takamuku T. Solvation power of HFIP for the hydrophilic and the hydrophobic moieties of l-leucine studied by MD, IR, and NMR techniques. J Mol Liq 2017. [DOI: 10.1016/j.molliq.2017.01.018] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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28
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Das B, Chakraborty A, Chakraborty S. Effect of ionic charge on O H⋯Se hydrogen bond: A computational study. COMPUT THEOR CHEM 2017. [DOI: 10.1016/j.comptc.2016.12.025] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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29
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Driver RW, Claridge TDW, Scheiner S, Smith MD. Torsional and Electronic Factors Control the C-H⋅⋅⋅O Interaction. Chemistry 2016; 22:16513-16521. [PMID: 27709689 PMCID: PMC5113693 DOI: 10.1002/chem.201602905] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2016] [Indexed: 01/07/2023]
Abstract
The precise role of non‐conventional hydrogen bonds such as the C−H⋅⋅⋅O interaction in influencing the conformation of small molecules remains unresolved. Here we survey a series of β‐turn mimetics using X‐ray crystallography and NMR spectroscopy in conjunction with quantum calculation, and conclude that favourable torsional and electronic effects are important for the population of states with conformationally influential C−H⋅⋅⋅O interactions. Our results also highlight the challenge in attempting to deconvolute a myriad of interdependent noncovalent interactions in order to focus on the contribution of a single one. Within a small molecule that is designed to resemble the complexity of the environment within peptides and proteins, the interplay of different steric burdens, hydrogen‐acceptor/‐donor properties and rotational profiles illustrate why unambiguous conclusions based solely on NMR chemical shift data are extremely challenging to rationalize.
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Affiliation(s)
- Russell W Driver
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK
| | - Timothy D W Claridge
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK
| | - Steve Scheiner
- Department of Chemistry and Biochemistry, Utah State University, Logan, Utah, 84322-0300, USA.
| | - Martin D Smith
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK.
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30
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Bodea S, Funk MA, Balskus EP, Drennan CL. Molecular Basis of C-N Bond Cleavage by the Glycyl Radical Enzyme Choline Trimethylamine-Lyase. Cell Chem Biol 2016; 23:1206-1216. [PMID: 27642068 DOI: 10.1016/j.chembiol.2016.07.020] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2016] [Revised: 07/07/2016] [Accepted: 07/25/2016] [Indexed: 01/16/2023]
Abstract
Deamination of choline catalyzed by the glycyl radical enzyme choline trimethylamine-lyase (CutC) has emerged as an important route for the production of trimethylamine, a microbial metabolite associated with both human disease and biological methane production. Here, we have determined five high-resolution X-ray structures of wild-type CutC and mechanistically informative mutants in the presence of choline. Within an unexpectedly polar active site, CutC orients choline through hydrogen bonding with a putative general base, and through close interactions between phenolic and carboxylate oxygen atoms of the protein scaffold and the polarized methyl groups of the trimethylammonium moiety. These structural data, along with biochemical analysis of active site mutants, support a mechanism that involves direct elimination of trimethylamine. This work broadens our understanding of radical-based enzyme catalysis and will aid in the rational design of inhibitors of bacterial trimethylamine production.
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Affiliation(s)
- Smaranda Bodea
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA 02138, USA
| | - Michael A Funk
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts, Avenue 68-680, Cambridge, MA 02139, USA
| | - Emily P Balskus
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA 02138, USA.
| | - Catherine L Drennan
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts, Avenue 68-680, Cambridge, MA 02139, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
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31
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Isaev AN. Intermolecular charge transfer as evidence for unusual O–H⋯C(sp3) hydrogen bond. COMPUT THEOR CHEM 2016. [DOI: 10.1016/j.comptc.2016.06.014] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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32
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Rusek M, Bendt G, Wölper C, Schulz S. Alternative Precursors for the Synthesis of Binary Sb2E3and Bi2E3(E = S, Se, Te) Nanoparticles by the Hot Injection Method. Eur J Inorg Chem 2016. [DOI: 10.1002/ejic.201600490] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Affiliation(s)
- Monika Rusek
- Faculty of Chemistry and Center for Nanointegration Duisburg-Essen (CENIDE); University of Duisburg-Essen (Campus Essen); Universitätsstrasse 7 45141 Essen Germany
| | - Georg Bendt
- Faculty of Chemistry and Center for Nanointegration Duisburg-Essen (CENIDE); University of Duisburg-Essen (Campus Essen); Universitätsstrasse 7 45141 Essen Germany
| | - Christoph Wölper
- Faculty of Chemistry and Center for Nanointegration Duisburg-Essen (CENIDE); University of Duisburg-Essen (Campus Essen); Universitätsstrasse 7 45141 Essen Germany
| | - Stephan Schulz
- Faculty of Chemistry and Center for Nanointegration Duisburg-Essen (CENIDE); University of Duisburg-Essen (Campus Essen); Universitätsstrasse 7 45141 Essen Germany
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33
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Fick RJ, Kroner GM, Nepal B, Magnani R, Horowitz S, Houtz RL, Scheiner S, Trievel RC. Sulfur-Oxygen Chalcogen Bonding Mediates AdoMet Recognition in the Lysine Methyltransferase SET7/9. ACS Chem Biol 2016; 11:748-54. [PMID: 26713889 DOI: 10.1021/acschembio.5b00852] [Citation(s) in RCA: 83] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Recent studies have demonstrated that carbon-oxygen (CH···O) hydrogen bonds have important roles in S-adenosylmethionine (AdoMet) recognition and catalysis in methyltransferases. Here, we investigate noncovalent interactions that occur between the AdoMet sulfur cation and oxygen atoms in methyltransferase active sites. These interactions represent sulfur-oxygen (S···O) chalcogen bonds in which the oxygen atom donates a lone pair of electrons to the σ antibonding orbital of the AdoMet sulfur atom. Structural, biochemical, and computational analyses of an asparagine mutation in the lysine methyltransferase SET7/9 that abolishes AdoMet S···O chalcogen bonding reveal that this interaction enhances substrate binding affinity relative to the product S-adenosylhomocysteine. Corroborative quantum mechanical calculations demonstrate that sulfonium systems form strong S···O chalcogen bonds relative to their neutral thioether counterparts. An inspection of high-resolution crystal structures reveals the presence of AdoMet S···O chalcogen bonding in different classes of methyltransferases, illustrating that these interactions are not limited to SET domain methyltransferases. Together, these results demonstrate that S···O chalcogen bonds contribute to AdoMet recognition and can enable methyltransferases to distinguish between substrate and product.
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Affiliation(s)
| | | | - Binod Nepal
- Department
of Chemistry and Biochemistry, Utah State University, Logan, Utah 84322, United States
| | - Roberta Magnani
- Department
of Horticulture, University of Kentucky, Lexington, Kentucky 40546, United States
| | - Scott Horowitz
- Howard Hughes Medical Institute, Ann Arbor, Michigan 48109, United States
| | - Robert L. Houtz
- Department
of Horticulture, University of Kentucky, Lexington, Kentucky 40546, United States
| | - Steve Scheiner
- Department
of Chemistry and Biochemistry, Utah State University, Logan, Utah 84322, United States
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34
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Isaev AN. Hydrogen bonded С–H···Y (Y = O, S, Hal) molecular complexes: A natural bond orbital analysis. RUSSIAN JOURNAL OF PHYSICAL CHEMISTRY A 2016. [DOI: 10.1134/s0036024416030183] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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35
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Berg L, Mishra BK, Andersson CD, Ekström F, Linusson A. The Nature of Activated Non-classical Hydrogen Bonds: A Case Study on Acetylcholinesterase-Ligand Complexes. Chemistry 2016; 22:2672-81. [DOI: 10.1002/chem.201503973] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Indexed: 01/25/2023]
Affiliation(s)
- Lotta Berg
- Department of Chemistry; Umeå University; 901 87 Umeå Sweden
| | | | | | - Fredrik Ekström
- CBRN Defense and Security; Swedish Defense Research Agency; 906 21 Umeå Sweden
| | - Anna Linusson
- Department of Chemistry; Umeå University; 901 87 Umeå Sweden
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36
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Ashworth CR, Matthews RP, Welton T, Hunt PA. Doubly ionic hydrogen bond interactions within the choline chloride–urea deep eutectic solvent. Phys Chem Chem Phys 2016; 18:18145-60. [DOI: 10.1039/c6cp02815b] [Citation(s) in RCA: 221] [Impact Index Per Article: 27.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Computational analysis indicates flexibility and diversity in the hydrogen bonding, but limited charge delocalisation, within the choline chloride–urea eutectic.
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Affiliation(s)
| | | | - Tom Welton
- Department of Chemistry
- Imperial College London
- London
- UK
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37
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Loor M, Bendt G, Hagemann U, Wölper C, Assenmacher W, Schulz S. Synthesis of Bi2Te3and (BixSb1−x)2Te3nanoparticles using the novel IL [C4mim]3[Bi3I12]. Dalton Trans 2016; 45:15326-15335. [DOI: 10.1039/c6dt02361d] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
[C4mim]3[Bi3I12] is a promising Bi-source for the ionothermal synthesis of binary (Bi2Te3) and ternary tetradymite-type nanoparticles (BixSb1−x)2Te3(x= 0.25, 0.5, 0.75) in ionic liquid.
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Affiliation(s)
- M. Loor
- Institute of Inorganic Chemistry and Center for Nanointegration Duisburg-Essen (CENIDE)
- University of Duisburg-Essen
- D-45117 Essen
- Germany
| | - G. Bendt
- Institute of Inorganic Chemistry and Center for Nanointegration Duisburg-Essen (CENIDE)
- University of Duisburg-Essen
- D-45117 Essen
- Germany
| | - U. Hagemann
- Interdisciplinary Center for Analytics on the Nanoscale (ICAN)
- NETZ
- 47047 Duisburg
- Germany
| | - C. Wölper
- Institute of Inorganic Chemistry and Center for Nanointegration Duisburg-Essen (CENIDE)
- University of Duisburg-Essen
- D-45117 Essen
- Germany
| | - W. Assenmacher
- Institute of Inorganic Chemistry
- University of Bonn
- D-53117 Bonn
- Germany
| | - S. Schulz
- Institute of Inorganic Chemistry and Center for Nanointegration Duisburg-Essen (CENIDE)
- University of Duisburg-Essen
- D-45117 Essen
- Germany
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38
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39
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Katsyuba SA, Vener MV, Zvereva EE, Fei Z, Scopelliti R, Brandenburg JG, Siankevich S, Dyson PJ. Quantification of Conventional and Nonconventional Charge-Assisted Hydrogen Bonds in the Condensed and Gas Phases. J Phys Chem Lett 2015; 6:4431-4436. [PMID: 26496074 DOI: 10.1021/acs.jpclett.5b02175] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Charge-assisted hydrogen bonds (CAHBs) play critical roles in many systems from biology through to materials. In none of these areas has the role and function of CAHBs been explored satisfactorily because of the lack of data on the energy of CAHBs in the condensed phases. We have, for the first time, quantified three types of CAHBs in both the condensed and gas phases for 1-(2'-hydroxylethyl)-3-methylimidazolium acetate ([C2OHmim][OAc]). The energy of conventional OH···[OAc](-) CAHBs is ∼10 kcal·mol(-1), whereas nonconventional C(sp2)H···[OAc](-) and C(sp3)H···[OAc](-) CAHBs are weaker by ∼5-7 kcal·mol(-1). In the gas phase, the strength of the nonconventional CAHBs is doubled, whereas the conventional CAHBs are strengthened by <20%. The influence of cooperativity effects on the ability of the [OAc](-) anion to deprotonate the imidazolium cation is evaluated. The ability to quantify CAHBs in the condensed phase on the basis of easier accessible gas-phase estimates is highlighted.
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Affiliation(s)
- Sergey A Katsyuba
- A. E. Arbuzov Institute of Organic and Physical Chemistry, Kazan Scientific Centre of the Russian Academy of Sciences , Arbuzov Street 8, 420088 Kazan, Russia
| | - Mikhail V Vener
- Department of Quantum Chemistry, Mendeleev University of Chemical Technology , Miusskaya Square 9, 125047 Moscow, Russia
| | - Elena E Zvereva
- A. E. Arbuzov Institute of Organic and Physical Chemistry, Kazan Scientific Centre of the Russian Academy of Sciences , Arbuzov Street 8, 420088 Kazan, Russia
- Institut de Nanosciences et Cryogénie, SP2M/L_sim, CEA , 17 Rue des Martyrs, 38054 Grenoble, France
| | - Zhaofu Fei
- Institut des Sciences et Ingénierie Chimiques, Ecole Polytechnique Fédérale de Lausanne (EPFL) EPFL - BCH , CH-1015 Lausanne, Switzerland
| | - Rosario Scopelliti
- Institut des Sciences et Ingénierie Chimiques, Ecole Polytechnique Fédérale de Lausanne (EPFL) EPFL - BCH , CH-1015 Lausanne, Switzerland
| | - Jan Gerit Brandenburg
- Mulliken Center for Theoretical Chemistry, Institut für Physikalische und Theoretische Chemie der Universität Bonn , Beringstrasse 4, 53115 Bonn, Germany
| | - Sviatlana Siankevich
- Institut des Sciences et Ingénierie Chimiques, Ecole Polytechnique Fédérale de Lausanne (EPFL) EPFL - BCH , CH-1015 Lausanne, Switzerland
| | - Paul J Dyson
- Institut des Sciences et Ingénierie Chimiques, Ecole Polytechnique Fédérale de Lausanne (EPFL) EPFL - BCH , CH-1015 Lausanne, Switzerland
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Scheiner S. Comparison of CH···O, SH···O, Chalcogen, and Tetrel Bonds Formed by Neutral and Cationic Sulfur-Containing Compounds. J Phys Chem A 2015; 119:9189-99. [DOI: 10.1021/acs.jpca.5b06831] [Citation(s) in RCA: 83] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Steve Scheiner
- Department of Chemistry and
Biochemistry, Utah State University, Logan, Utah 84322-0300, United States
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Abstract
Ionic liquids (IL) and hydrogen bonding (H-bonding) are two diverse fields for which there is a developing recognition of significant overlap. Doubly ionic H-bonds occur when a H-bond forms between a cation and anion, and are a key feature of ILs. Doubly ionic H-bonds represent a wide area of H-bonding which has yet to be fully recognised, characterised or explored. H-bonds in ILs (both protic and aprotic) are bifurcated and chelating, and unlike many molecular liquids a significant variety of distinct H-bonds are formed between different types and numbers of donor and acceptor sites within a given IL. Traditional more neutral H-bonds can also be formed in functionalised ILs, adding a further level of complexity. Ab initio computed parameters; association energies, partial charges, density descriptors as encompassed by the QTAIM methodology (ρBCP), qualitative molecular orbital theory and NBO analysis provide established and robust mechanisms for understanding and interpreting traditional neutral and ionic H-bonds. In this review the applicability and extension of these parameters to describe and quantify the doubly ionic H-bond has been explored. Estimating the H-bonding energy is difficult because at a fundamental level the H-bond and ionic interaction are coupled. The NBO and QTAIM methodologies, unlike the total energy, are local descriptors and therefore can be used to directly compare neutral, ionic and doubly ionic H-bonds. The charged nature of the ions influences the ionic characteristics of the H-bond and vice versa, in addition the close association of the ions leads to enhanced orbital overlap and covalent contributions. The charge on the ions raises the energy of the Ylp and lowers the energy of the X-H σ* NBOs resulting in greater charge transfer, strengthening the H-bond. Using this range of parameters and comparing doubly ionic H-bonds to more traditional neutral and ionic H-bonds it is clear that doubly ionic H-bonds cover the full range of weak through to very strong H-bonds.
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Affiliation(s)
- Patricia A Hunt
- Department of Chemistry, Faculty of Natural Sciences, Imperial College London, London, SW7 2AZ, UK.
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Nepal B, Scheiner S. Anionic CH⋅⋅⋅X−Hydrogen Bonds: Origin of Their Strength, Geometry, and Other Properties. Chemistry 2014; 21:1474-81. [DOI: 10.1002/chem.201404970] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2014] [Indexed: 11/12/2022]
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Del Bene JE, Alkorta I, Elguero J. Pnicogen-Bonded Complexes HnF5–nP:N-Base, for n = 0–5. J Phys Chem A 2014; 118:10144-54. [DOI: 10.1021/jp509353a] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
- Janet E. Del Bene
- Department
of Chemistry, Youngstown State University, Youngstown, Ohio 44555, United States
| | - Ibon Alkorta
- Instituto de Química
Médica (IQM-CSIC), Juan de la
Cierva, 3, E-28006 Madrid, Spain
| | - José Elguero
- Instituto de Química
Médica (IQM-CSIC), Juan de la
Cierva, 3, E-28006 Madrid, Spain
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44
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Nepal B, Scheiner S. Effect of Ionic Charge on the CH···π Hydrogen Bond. J Phys Chem A 2014; 118:9575-87. [DOI: 10.1021/jp5070598] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- Binod Nepal
- Department of Chemistry and
Biochemistry, Utah State University, Logan, Utah 84322-0300, United States
| | - Steve Scheiner
- Department of Chemistry and
Biochemistry, Utah State University, Logan, Utah 84322-0300, United States
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Horowitz S, Adhikari U, Dirk LMA, Del Rizzo PA, Mehl RA, Houtz RL, Al-Hashimi HM, Scheiner S, Trievel RC. Manipulating unconventional CH-based hydrogen bonding in a methyltransferase via noncanonical amino acid mutagenesis. ACS Chem Biol 2014; 9:1692-7. [PMID: 24914947 DOI: 10.1021/cb5001185] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Recent studies have demonstrated that the active sites of S-adenosylmethionine (AdoMet)-dependent methyltransferases form strong carbon-oxygen (CH···O) hydrogen bonds with the substrate's sulfonium group that are important in AdoMet binding and catalysis. To probe these interactions, we substituted the noncanonical amino acid p-aminophenylalanine (pAF) for the active site tyrosine in the lysine methyltransferase SET7/9, which forms multiple CH···O hydrogen bonds to AdoMet and is invariant in SET domain enzymes. Using quantum chemistry calculations to predict the mutation's effects, coupled with biochemical and structural studies, we observed that pAF forms a strong CH···N hydrogen bond to AdoMet that is offset by an energetically unfavorable amine group rotamer within the SET7/9 active site that hinders AdoMet binding and activity. Together, these results illustrate that the invariant tyrosine in SET domain methyltransferases functions as an essential hydrogen bonding hub and cannot be readily substituted by residues bearing other hydrogen bond acceptors.
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Affiliation(s)
- Scott Horowitz
- Howard Hughes Medical Institute, Ann Arbor, Michigan 48109, United States
| | - Upendra Adhikari
- Department
of Chemistry and Biochemistry, Utah State University, Logan, Utah 84322, United States
| | - Lynnette M. A. Dirk
- Department
of Horticulture, University of Kentucky, Lexington, Kentucky 40546, United States
| | | | - Ryan A. Mehl
- Department
of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon 97331, United States
| | - Robert L. Houtz
- Department
of Horticulture, University of Kentucky, Lexington, Kentucky 40546, United States
| | | | - Steve Scheiner
- Department
of Chemistry and Biochemistry, Utah State University, Logan, Utah 84322, United States
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46
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Competition between lone pair–π, halogen bond, and hydrogen bond in adducts of water with perhalogenated alkenes C2ClnF4−n (n=0–4). Chem Phys 2014. [DOI: 10.1016/j.chemphys.2014.06.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
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47
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Reaction between [Ir(COD)(PMe3)3]Cl and 2-aminopent-4-enoic acid: Tridentate N, O and C bonding. J Organomet Chem 2014. [DOI: 10.1016/j.jorganchem.2014.01.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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48
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Adhikari U, Scheiner S. Effects of Charge and Substituent on the S···N Chalcogen Bond. J Phys Chem A 2014; 118:3183-92. [DOI: 10.1021/jp501449v] [Citation(s) in RCA: 133] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Upendra Adhikari
- Department
of Chemistry and
Biochemistry, Utah State University, Logan, Utah 84322-0300, United States
| | - Steve Scheiner
- Department
of Chemistry and
Biochemistry, Utah State University, Logan, Utah 84322-0300, United States
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49
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Veljković DŽ, Medaković VB, Andrić JM, Zarić SD. C–H/O interactions of nucleic bases with a water molecule: a crystallographic and quantum chemical study. CrystEngComm 2014. [DOI: 10.1039/c4ce00595c] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The C–H/O interactions of nucleic bases are substantially stronger than the C–H/O interactions of benzene and pyridine. These results can be very important for molecular recognition of DNA and RNA.
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Affiliation(s)
- D. Ž. Veljković
- Department of Chemistry
- University of Belgrade
- 11000 Belgrade, Serbia
| | - V. B. Medaković
- Department of Chemistry
- University of Belgrade
- 11000 Belgrade, Serbia
| | - J. M. Andrić
- Innovation Center
- Department of Chemistry
- 11000 Belgrade, Serbia
| | - S. D. Zarić
- Department of Chemistry
- University of Belgrade
- 11000 Belgrade, Serbia
- Department of Chemistry
- Texas A&M University at Qatar
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50
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Paton RS. Dissecting non-covalent interactions in oxazaborolidinium catalyzed cycloadditions of maleimides. Org Biomol Chem 2014; 12:1717-20. [DOI: 10.1039/c4ob00009a] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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