1
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Meddeb-Limem S, Ben Fredj A. Computational study of the dimerization of glyphosate: mechanism and effect of solvent. RSC Adv 2024; 14:23184-23203. [PMID: 39045405 PMCID: PMC11264236 DOI: 10.1039/d4ra04300f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2024] [Accepted: 07/09/2024] [Indexed: 07/25/2024] Open
Abstract
A computational study on the structure and stability of different series of glyphosate (Glyph) dimers comprising nonionized (N) and zwitterionic structures (Z) for neutral monomers, followed by an analysis of energetics of Glyph dimerization process have been performed by means of quantum chemical calculations in different media. Optimized geometries for energy minima, as well as relative potential and free energies of the possible various conformers of each series of Glyph dimer were computed as a function of the medium at B3LYP-D3/6-311++G(2d,2p) level. The solvation model based on density (SMD) is employed for all solution phase computations. Non-ionized dimers (DN), anion-cation (AC) and either zwitterion-zwitterion (DZP and DZC) or non-ionized-phosphonate zwitterion (NZP) ionized neutral forms of Glyph dimer are predicted to exist in the gas phase and in solution in large contrast to Glyph monomers. The DZC dimer form exhibiting a centrosymmetric arrangement of two carboxylate zwitterion units was found to be the most stable dimer structure in all media. In aqueous solution, the DZP and AC dimer type structures are significantly stabilized by hydration. The tautomerisms between DZC, DZP and AC dimer type structures have been investigated in the gas phase and in solution. The DZC type structures are more prone to experience proton transfer in water than in the gas phase and in cyclohexane. The mechanism for the tautomerization process in neutral ionized Glyph dimers proceeds via two direct proton transfer paths: DZP ⇋ AC ⇋ DZC. Results show that solvents play a key role in modulating the energetics of the dimerization process of Glyph. Solvation in cyclohexane, favors the dimerization process however, hydration opposed it. In aqueous solution, the mechanism of the dimerization of Glyph from its phosphonate zwitterionic monomer form (ZP) could be described by a set of equilibria including direct proton transfer paths as follows: 2ZP ⇋ DZP ⇋ AC ⇋ DZC. According to our results, in aqueous solution, DZC Glyph dimers and their corresponding DZP and AC tautomers should be present in higher concentration than phosphonate zwitterionic Glyph monomers for high Glyph concentration, a fact that seems controversial in the literature.
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Affiliation(s)
- Sondes Meddeb-Limem
- Unité de recherche de Modélisation en Sciences Fondamentales et Didactiques, équipe de Chimie Théorique et Réactivité UR14ES10, Institut Préparatoire aux études d'Ingénieurs d'El Manar, Université de Tunis El Manar B. P. 244 El Manar II 2092 Tunis Tunisia +216 72 593 450 +216 72 593 450 + 216 54744256
| | - Arij Ben Fredj
- Unité de recherche de Modélisation en Sciences Fondamentales et Didactiques, équipe de Chimie Théorique et Réactivité UR14ES10, Institut Préparatoire aux études d'Ingénieurs d'El Manar, Université de Tunis El Manar B. P. 244 El Manar II 2092 Tunis Tunisia +216 72 593 450 +216 72 593 450 + 216 54744256
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2
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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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3
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Zhang J, Shao Y, Zheng H, Xue XS. Transition State Stabilization by SCF 2 -H⋅⋅⋅O Bifurcated Hydrogen Bond. Chem Asian J 2023; 18:e202201244. [PMID: 36635229 DOI: 10.1002/asia.202201244] [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: 12/14/2022] [Revised: 01/10/2023] [Accepted: 01/12/2023] [Indexed: 01/14/2023]
Abstract
The difluoromethylthio group (SCF2 H), which is generally considered a highly lipophilic weak hydrogen bonding donor, has attracted special interest from the pharmaceutical and agrochemical industry. Remarkably, there have been relatively few literature investigations of SCF2 H hydrogen bonding interactions. Here, we report the determination of the hydrogen bond acidity parameter A of the SCF2 H in the most popularly used electrophilic difluoromethylthiolating reagent. We present kinetic and computational evidence of the RSCF2 -H⋅⋅⋅O2 bifurcated hydrogen bond for stabilizing the SCF2 H-transferring transition state, which could cause a reversal of apparent electrophilic reactivity of difluoromethylthiolating and trifluoromethylthiolating reagents. Solvent effects on the RSCF2 -H⋅⋅⋅O2 bifurcated hydrogen bonds will also be discussed.
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Affiliation(s)
- Jingjing Zhang
- Center of Basic Molecular Science, Department of Chemistry, Tsinghua University, Beijing, 100084, China
| | - Yingbo Shao
- College of Chemistry, Nankai University, Tianjin, 300071, P. R. China
| | - Hanliang Zheng
- College of Chemistry, Nankai University, Tianjin, 300071, P. R. China
| | - Xiao-Song Xue
- College of Chemistry, Nankai University, Tianjin, 300071, P. R. China.,Key Laboratory of Organofluorine Chemistry, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences Chinese Academy of Sciences, 345 Lingling Road, Shanghai, 200032, P. R. China.,School of Chemistry and Materials Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, 1 Sub-lane Xiangshan, Hangzhou, 310024, P. R. China
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4
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Scheiner S. Competition Between the Two σ-Holes in the Formation of a Chalcogen Bond. Chemphyschem 2023; 24:e202200936. [PMID: 36744997 DOI: 10.1002/cphc.202200936] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 02/01/2023] [Accepted: 02/06/2023] [Indexed: 02/07/2023]
Abstract
A chalcogen atom Y contains two separate σ-holes when in a R1 YR2 molecular bonding pattern. Quantum chemical calculations consider competition between these two σ-holes to engage in a chalcogen bond (ChB) with a NH3 base. R groups considered include F, Br, I, and tert-butyl (tBu). Also examined is the situation where the Y lies within a chalcogenazole ring, where its neighbors are C and N. Both electron-withdrawing substituents R1 and R2 act cooperatively to deepen the two σ-holes, but the deeper of the two holes consistently lies opposite to the more electron-withdrawing group, and is also favored to form a stronger ChB. The formation of two simultaneous ChBs in a triad requires the Y atom to act as double electron acceptor, and so anti-cooperativity weakens each bond relative to the simple dyad. This effect is such that some of the shallower σ-holes are unable to form a ChB at all when a base occupies the other site.
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Affiliation(s)
- Steve Scheiner
- Department of Chemistry and Biochemistry, Utah State University, 84322-0300, Logan, Utah, USA
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5
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Lo R, Mašínová A, Lamanec M, Nachtigallová D, Hobza P. The unusual stability of H-bonded complexes in solvent caused by greater solvation energy of complex compared to those of isolated fragments. J Comput Chem 2023; 44:329-333. [PMID: 35616117 DOI: 10.1002/jcc.26928] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 04/25/2022] [Accepted: 04/28/2022] [Indexed: 01/03/2023]
Abstract
Here, the effect of solvent on the stability of non-covalent complexes, was studied. These complexes were from previously published S22, S66, and X40 datasets, which include hydrogen-, halogen- and dispersion-bonded complexes. It was shown that the charge transfer in the complex determines whether the complex is stabilized or destabilized in solvent.
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Affiliation(s)
- Rabindranath Lo
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Prague, Czech Republic
| | - Anna Mašínová
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Prague, Czech Republic
| | - Maximilián Lamanec
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Prague, Czech Republic.,Regional Centre of Advanced Technologies and Materials, Czech Advanced Technology and Research Institute, Palacký University Olomouc, Olomouc, Czech Republic
| | - Dana Nachtigallová
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Prague, Czech Republic.,Regional Centre of Advanced Technologies and Materials, Czech Advanced Technology and Research Institute, Palacký University Olomouc, Olomouc, Czech Republic
| | - Pavel Hobza
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Prague, Czech Republic.,Regional Centre of Advanced Technologies and Materials, Czech Advanced Technology and Research Institute, Palacký University Olomouc, Olomouc, Czech Republic
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6
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Daniecki NJ, Bhatt MR, Yap GPA, Zondlo NJ. Proline C-H Bonds as Loci for Proline Assembly via C-H/O Interactions. Chembiochem 2022; 23:e202200409. [PMID: 36129371 DOI: 10.1002/cbic.202200409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 09/20/2022] [Indexed: 01/25/2023]
Abstract
Proline residues within proteins lack a traditional hydrogen bond donor. However, the hydrogens of the proline ring are all sterically accessible, with polarized C-H bonds at Hα and Hδ that exhibit greater partial positive character and can be utilized as alternative sites for molecular recognition. C-H/O interactions, between proline C-H bonds and oxygen lone pairs, have been previously identified as modes of recognition within protein structures and for higher-order assembly of protein structures. In order to better understand intermolecular recognition of proline residues, a series of proline derivatives was synthesized, including 4R-hydroxyproline nitrobenzoate methyl ester, acylated on the proline nitrogen with bromoacetyl and glycolyl groups, and Boc-4S-(4-iodophenyl)hydroxyproline methyl amide. All three derivatives exhibited multiple close intermolecular C-H/O interactions in the crystallographic state, with H⋅⋅⋅O distances as close as 2.3 Å. These observed distances are well below the 2.72 Å sum of the van der Waals radii of H and O, and suggest that these interactions are particularly favorable. In order to generalize these results, we further analyzed the role of C-H/O interactions in all previously crystallized derivatives of these amino acids, and found that all 26 structures exhibited close intermolecular C-H/O interactions. Finally, we analyzed all proline residues in the Cambridge Structural Database of small-molecule crystal structures. We found that the majority of these structures exhibited intermolecular C-H/O interactions at proline C-H bonds, suggesting that C-H/O interactions are an inherent and important mode for recognition of and higher-order assembly at proline residues. Due to steric accessibility and multiple polarized C-H bonds, proline residues are uniquely positioned as sites for binding and recognition via C-H/O interactions.
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Affiliation(s)
- Noah J Daniecki
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, USA
| | - Megh R Bhatt
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, USA
| | - Glenn P A Yap
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, USA
| | - Neal J Zondlo
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, USA
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7
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Asghar S, Hameed S, Tahir MN, Naseer MM. Molecular duplexes featuring NH···N, CH···O and CH···π interactions in solid-state self-assembly of triazine-based compounds. ROYAL SOCIETY OPEN SCIENCE 2022; 9:220603. [PMID: 36397969 PMCID: PMC9626258 DOI: 10.1098/rsos.220603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/07/2022] [Accepted: 09/09/2022] [Indexed: 06/16/2023]
Abstract
Synthetic supramolecular structures constructed through the cooperative action of numerous non-covalent forces are highly desirable as models to unravel and understand the complexity of systems created in nature via self-assembly. Taking advantage of the low cost of 2,4,6-trichloro-1,3,5-triazine (cyanuric chloride) and the sequential nucleophilic substitution reactions with almost all types of nucleophiles, a series of six structurally related novel s-triazine derivatives 1-6 were synthesized and structurally characterized based on their physical, spectral and crystallographic data. The solid-state structures of all the six compounds showed intriguing and unique molecular duplexes featuring NH···N, CH···O and CH···π interactions. Careful analysis of different geometric parameters of the involved H-bonds indicates that they are linear, significant and are therefore responsible for guiding the three-dimensional structure of these compounds in the solid state. The prevalence of sextuple hydrogen bond array-driven molecular duplexes and the possibility of structural modifications on the s-triazine ring render these novel triazine derivatives 1-6 attractive as a platform to create heteroduplex constructs and their subsequent utility in the field of supramolecular chemistry and crystal engineering.
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Affiliation(s)
- Shazia Asghar
- Department of Chemistry, Quaid-i-Azam University, Islamabad 45320, Pakistan
| | - Shahid Hameed
- Department of Chemistry, Quaid-i-Azam University, Islamabad 45320, Pakistan
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8
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Zondlo NJ. Solvation stabilizes intercarbonyl n→π* interactions and polyproline II helix. Phys Chem Chem Phys 2022; 24:13571-13586. [PMID: 35635541 DOI: 10.1039/d2cp00857b] [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
n→π* interactions between consecutive carbonyls stabilize the α-helix and polyproline II helix (PPII) conformations in proteins. n→π* interactions have been suggested to provide significant conformational biases to the disordered states of proteins. To understand the roles of solvation on the strength of n→π* interactions, computational investigations were conducted on a model n→π* interaction, the twisted-parallel-offset formaldehyde dimer, as a function of explicit solvation of the donor and acceptor carbonyls, using water and HF. In addition, the effects of urea, thiourea, guanidinium, and monovalent cations on n→π* interaction strength were examined. Solvation of the acceptor carbonyl significantly strengthens the n→π* interaction, while solvation of the donor carbonyl only modestly weakens the n→π* interaction. The n→π* interaction strength was maximized with two solvent molecules on the acceptor carbonyl. Urea stabilized the n→π* interaction via simultaneous engagement of both oxygen lone pairs on the acceptor carbonyl. Solvent effects were further investigated in the model peptides Ac-Pro-NMe2, Ac-Ala-NMe2, and Ac-Pro2-NMe2. Solvent effects in peptides were similar to those in the formaldehyde dimer, with solvation of the acceptor carbonyl increasing n→π* interaction strength and resulting in more compact conformations, in both the proline endo and exo ring puckers, as well as a reduction in the energy difference between these ring puckers. Carbonyl solvation leads to an energetic preference for PPII over both the α-helix and β/extended conformations, consistent with experimental data that protic solvents and protein denaturants both promote PPII. Solvation of the acceptor carbonyl weakens the intraresidue C5 hydrogen bond that stabilizes the β conformation.
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Affiliation(s)
- Neal J Zondlo
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, USA.
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9
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Stereoselective synthesis, structural determination, computational studies and antimicrobial activity of novel class of spiropyrroloquinoxaline engrafted ferrocenoindole hybrid heterocycle. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2021.132131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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10
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Abstract
At the heart of drug design is the discovery of molecules that bind with high affinity to their drug targets. Biotin forms the strongest known noncovalent ligand-protein interactions with avidin and streptavidin, achieving femtomolar and picomolar affinities, respectively. This is made even more exceptional because biotin achieves this with a meagre molecular weight of 240 Da. Surprisingly, the approaches by which biotin achieves this are not in the standard repertoire of current medicinal chemistry practice. Biotin's biggest lesson is the importance of nonclassical H-bonds in protein-ligand complexes. Most of biotin's affinity stems from its flexible valeric acid side chain that forms CH-π, CH-O, and classical H-bonds with the lipophilic region of the binding pocket. Biotin also utilizes an oxyanion hole, a sulfur-centered H-bond, and water solvation in the bound state to achieve its potency. The facets and advantages of biotin's approach to binding should be more widely adopted in drug design.
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Affiliation(s)
- Darryl B McConnell
- Discovery Research, Boehringer Ingelheim Regional Center Vienna GmbH & Co KG, 1120 Vienna, Austria
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11
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Xu QQ, Liu R, Mu WH, Chen R, Huang B, Yang Z, Kou JF. Robust nickel, manganese, and iron imidazole carboxylic acid catalysts for efficient visible-light driven reduction of CO2 to CO. INORG CHEM COMMUN 2020. [DOI: 10.1016/j.inoche.2020.108269] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
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12
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Lasri J, Al-Rasheed HH, El-Faham A, Haukka M, Abutaha N, Soliman SM. Synthesis, structure and in vitro anticancer activity of Pd(II) complexes of mono- and bis-pyrazolyl-s-triazine ligands. Polyhedron 2020. [DOI: 10.1016/j.poly.2020.114665] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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13
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Soliman SM, Elsilk SE, El-Faham A. Syntheses, structure, Hirshfeld analysis and antimicrobial activity of four new Co(II) complexes with s-triazine-based pincer ligand. Inorganica Chim Acta 2020. [DOI: 10.1016/j.ica.2020.119753] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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14
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Soliman SM, El‐Faham A, El Silk SE. Novel one‐dimensional polymeric Cu(II) complexes via Cu(II)‐assisted hydrolysis of the 2,4‐
bis
(3,5‐dimethyl‐1
H
‐pyrazol‐1‐yl)‐6‐methoxy‐1,3,5‐triazine pincer ligand: Synthesis, structure, and antimicrobial activities. Appl Organomet Chem 2020. [DOI: 10.1002/aoc.5941] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Saied M. Soliman
- Department of Chemistry, Faculty of Science Alexandria University PO Box 426, Ibrahimia Alexandria 21321 Egypt
| | - Ayman El‐Faham
- Department of Chemistry, Faculty of Science Alexandria University PO Box 426, Ibrahimia Alexandria 21321 Egypt
- Department of Chemistry College of Science King Saud University, PO Box 2455 Riyadh 11451 Saudi Arabia
| | - Sobhy E. El Silk
- Bacteriology Unit, Botany Department, Faculty of Science Tanta University Tanta 31527 Egypt
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15
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16
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Su H, Wu H, Wang H, Wang H, Ni Y, Lu Y, Zhu Z. A comparative study of S···π chalcogen bonds between SF2 or SFH and C C multiple bonds. J Mol Struct 2019. [DOI: 10.1016/j.molstruc.2019.03.085] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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18
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Chopra N, Chopra G, Kaur D. Exploring the Role of Consecutive Addition of Nitrogen Atoms on Stability and Reactivity of Hydrogen-Bonded Azine-Water Complexes. ACS OMEGA 2019; 4:8112-8121. [PMID: 31459902 PMCID: PMC6648882 DOI: 10.1021/acsomega.8b03496] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Accepted: 04/09/2019] [Indexed: 06/10/2023]
Abstract
The second-order Møller-Plesset perturbation theory (MP2) and density functional theory with dispersion function calculations have been applied to investigate the hydrogen-bonding interaction between azines and water. The study suggests that the ability of nitrogen present in azine to act as a hydrogen-bond acceptor decreases in the order of pyridine (PY) > diazine (DZ) > triazine (TZ) > tetrazine (TTZ) > pentazine (PZ) > hexazine (HZ). Natural bond orbital (NBO) analysis, atoms in molecules, symmetry-adapted perturbation theory (SAPT), and molecular electrostatic potential studies reflect the factors important for hydrogen-bond strength as well as for the structural, electronic, and vibrational changes occurring during complexation. NBO analysis reflects that upon gradual addition of nitrogen atoms, hyperconjugation leads to an increase in the population of antibonding O-H bond, thus causing elongation and weakening of O-H bond in complexes incorporating N···H-OW interaction, whereas rehybridization leads to an increase in the s character of the carbon hybrid orbital in C-H bond, thus causing contraction and shortening of C-H bond in complexes having C-H···OW interactions. From the topological analysis, an excellent linear correlation is found to exist between stabilization energy (ΔE BSSE), electron density (ρc), and its Laplacian (∇2ρc) at the bond critical points.
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19
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Soliman SM, El-Faham A. Synthesis and structure diversity of high coordination number Cd(II) complexes of large s-triazine bis-Schiff base pincer chelate. Inorganica Chim Acta 2019. [DOI: 10.1016/j.ica.2019.01.018] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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20
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Soliman SM, El-Faham A, Elsilk SE, Farooq M. Two heptacoordinated manganese(II) complexes of giant pentadentate s -triazine bis -Schiff base ligand: Synthesis, crystal structure, biological and DFT studies. Inorganica Chim Acta 2018. [DOI: 10.1016/j.ica.2018.04.043] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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21
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Soliman SM, El-Faham A. Synthesis, characterization, and structural studies of two heteroleptic Mn(II) complexes with tridentate N,N,N-pincer type ligand. J COORD CHEM 2018. [DOI: 10.1080/00958972.2018.1475660] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
Affiliation(s)
- Saied M. Soliman
- Department of Chemistry, Rabigh College of Science and Art, King Abdulaziz University, Jeddah, Saudi Arabia
- Faculty of Science, Department of Chemistry, Alexandria University, Alexandria, Egypt
| | - Ayman El-Faham
- Faculty of Science, Department of Chemistry, Alexandria University, Alexandria, Egypt
- Department of Chemistry, College of Science, King Saud University, Riyadh, Saudi Arabia
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22
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Komati R, Spadoni D, Zheng S, Sridhar J, Riley KE, Wang G. Ligands of Therapeutic Utility for the Liver X Receptors. Molecules 2017; 22:molecules22010088. [PMID: 28067791 PMCID: PMC5373669 DOI: 10.3390/molecules22010088] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Revised: 12/29/2016] [Accepted: 12/30/2016] [Indexed: 12/21/2022] Open
Abstract
Liver X receptors (LXRs) have been increasingly recognized as a potential therapeutic target to treat pathological conditions ranging from vascular and metabolic diseases, neurological degeneration, to cancers that are driven by lipid metabolism. Amidst intensifying efforts to discover ligands that act through LXRs to achieve the sought-after pharmacological outcomes, several lead compounds are already being tested in clinical trials for a variety of disease interventions. While more potent and selective LXR ligands continue to emerge from screening of small molecule libraries, rational design, and empirical medicinal chemistry approaches, challenges remain in minimizing undesirable effects of LXR activation on lipid metabolism. This review provides a summary of known endogenous, naturally occurring, and synthetic ligands. The review also offers considerations from a molecular modeling perspective with which to design more specific LXRβ ligands based on the interaction energies of ligands and the important amino acid residues in the LXRβ ligand binding domain.
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Affiliation(s)
- Rajesh Komati
- Department of Chemistry and RCMI Cancer Research Center, Xavier University of Louisiana, New Orleans, LA 70125, USA.
| | - Dominick Spadoni
- Department of Chemistry and RCMI Cancer Research Center, Xavier University of Louisiana, New Orleans, LA 70125, USA.
| | - Shilong Zheng
- Department of Chemistry and RCMI Cancer Research Center, Xavier University of Louisiana, New Orleans, LA 70125, USA.
| | - Jayalakshmi Sridhar
- Department of Chemistry and RCMI Cancer Research Center, Xavier University of Louisiana, New Orleans, LA 70125, USA.
| | - Kevin E Riley
- Department of Chemistry and RCMI Cancer Research Center, Xavier University of Louisiana, New Orleans, LA 70125, USA.
| | - Guangdi Wang
- Department of Chemistry and RCMI Cancer Research Center, Xavier University of Louisiana, New Orleans, LA 70125, USA.
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23
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Assessment of the Presence and Strength of H-Bonds by Means of Corrected NMR. Molecules 2016; 21:molecules21111426. [PMID: 27801801 PMCID: PMC6274571 DOI: 10.3390/molecules21111426] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Revised: 10/19/2016] [Accepted: 10/21/2016] [Indexed: 11/30/2022] Open
Abstract
The downfield shift of the NMR signal of the bridging proton in a H-bond (HB) is composed of two elements. The formation of the HB causes charge transfer and polarization that lead to a deshielding. A second factor is the mere presence of the proton-accepting group, whose electron density and response to an external magnetic field induce effects at the position of the bridging proton, exclusive of any H-bonding phenomenon. This second positional shielding must be subtracted from the full observed shift in order to assess the deshielding of the proton caused purely by HB formation. This concept is applied to a number of H-bonded systems, both intramolecular and intermolecular. When the positional shielding is removed, the remaining chemical shift is in much better coincidence with other measures of HB strength.
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24
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Xing L, Lin K, Zhou X, Liu S, Luo Y. Multistate Mechanism of Lysozyme Denaturation through Synchronous Analysis of Raman Spectra. J Phys Chem B 2016; 120:10660-10667. [DOI: 10.1021/acs.jpcb.6b07900] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
| | - Ke Lin
- School
of Physics and Optoelectronic Engineering, Xidian University, Xi’an, Shanxi 710071, China
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25
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A DFT study on electronic and optical properties of aspirin-functionalized B12N12 fullerene-like nanocluster. Struct Chem 2016. [DOI: 10.1007/s11224-016-0858-y] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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26
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Kasende OE, Nziko VDPN, Scheiner S. Interactions of Nucleic Acid Bases with Temozolomide. Stacked, Perpendicular, and Coplanar Heterodimers. J Phys Chem B 2016; 120:9347-61. [DOI: 10.1021/acs.jpcb.6b06150] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Okuma Emile Kasende
- Faculty of Science University of Kinshasa, B.P. 190 Kinshasa XI, D. R. Congo
| | - Vincent de Paul N. Nziko
- Department of Chemistry & Biochemistry, Utah State University, Logan, Utah 84322-0300, United States
| | - Steve Scheiner
- Department of Chemistry & Biochemistry, Utah State University, Logan, Utah 84322-0300, United States
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27
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Kozlowska M, Goclon J, Rodziewicz P. Intramolecular Hydrogen Bonds in Low-Molecular-Weight Polyethylene Glycol. Chemphyschem 2016; 17:1143-53. [DOI: 10.1002/cphc.201501182] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Indexed: 11/06/2022]
Affiliation(s)
- Mariana Kozlowska
- Institute of Chemistry; University of Bialystok; Ciolkowskiego Str. 1K 15-245 Bialystok Poland
| | - Jakub Goclon
- Institute of Chemistry; University of Bialystok; Ciolkowskiego Str. 1K 15-245 Bialystok Poland
- Interdisciplinary Center for Molecular Materials (ICMM) and Computer-Chemistry-Center (CCC); Friedrich-Alexander-University Erlangen-Nürnberg; Nägelsbachstr. 25 91052 Erlangen Germany
| | - Pawel Rodziewicz
- Institute of Chemistry; University of Bialystok; Ciolkowskiego Str. 1K 15-245 Bialystok Poland
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28
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29
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Dissection of the Factors Affecting Formation of a CH∙∙∙O H-Bond. A Case Study. CRYSTALS 2015. [DOI: 10.3390/cryst5030327] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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30
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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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31
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Nziko VDPN, Scheiner S. S···π Chalcogen Bonds between SF2 or SF4 and C–C Multiple Bonds. J Phys Chem A 2015; 119:5889-97. [DOI: 10.1021/acs.jpca.5b03359] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- Vincent de Paul N. Nziko
- 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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32
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Yesselman JD, Horowitz S, Brooks CL, Trievel RC. Frequent side chain methyl carbon-oxygen hydrogen bonding in proteins revealed by computational and stereochemical analysis of neutron structures. Proteins 2015; 83:403-410. [PMID: 25401519 DOI: 10.1002/prot.24724] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2014] [Revised: 10/19/2014] [Accepted: 11/10/2014] [Indexed: 11/11/2022]
Abstract
The propensity of backbone Cα atoms to engage in carbon-oxygen (CH · · · O) hydrogen bonding is well-appreciated in protein structure, but side chain CH · · · O hydrogen bonding remains largely uncharacterized. The extent to which side chain methyl groups in proteins participate in CH · · · O hydrogen bonding is examined through a survey of neutron crystal structures, quantum chemistry calculations, and molecular dynamics simulations. Using these approaches, methyl groups were observed to form stabilizing CH · · · O hydrogen bonds within protein structure that are maintained through protein dynamics and participate in correlated motion. Collectively, these findings illustrate that side chain methyl CH · · · O hydrogen bonding contributes to the energetics of protein structure and folding.
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Affiliation(s)
- Joseph D Yesselman
- Departments of Biophysics and Molecular, Cellular, University of Michigan, Ann Arbor, MI 48109, USA.,Departments of Biochemistry & Physics, Stanford University, Stanford, CA 94305
| | - Scott Horowitz
- Departments of Biophysics and Molecular, Cellular, University of Michigan, Ann Arbor, MI 48109, USA.,Department of Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA.,Department of Biological Chemistry, Howard Hughes Medical Institute, University of Michigan, Ann Arbor MI 48109 USA
| | - Charles L Brooks
- Departments of Biophysics and Molecular, Cellular, University of Michigan, Ann Arbor, MI 48109, USA.,Department of Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
| | - Raymond C Trievel
- Department of Biological Chemistry, Howard Hughes Medical Institute, University of Michigan, Ann Arbor MI 48109 USA
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33
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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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34
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Angelina EL, Andujar SA, Tosso RD, Enriz RD, Peruchena NM. Non-covalent interactions in receptor-ligand complexes. A study based on the electron charge density. J PHYS ORG CHEM 2013. [DOI: 10.1002/poc.3250] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Affiliation(s)
- Emilio L. Angelina
- Lab. Estructura Molecular y Propiedades, Área de Química Física, Departamento de Química, Facultad de Ciencias Exactas y Naturales y Agrimensura; Universidad Nacional del Nordeste; Av. Libertad 5470 Corrientes 3400 Argentina
- Instituto Multidiciplinario de Investigaciones Biológicas (IMIBIO-SL, CONICET); Chacabuco y Pedrenera (5700) San Luis Argentina
| | - Sebastián A. Andujar
- Departamento de Química, Facultad de Química, Bioquímica y Farmacia; Universidad Nacional de San Luis; Chacabuco 917, San Luis (5700) San Luis Argentina
- Instituto Multidiciplinario de Investigaciones Biológicas (IMIBIO-SL, CONICET); Chacabuco y Pedrenera (5700) San Luis Argentina
| | - Rodrigo D. Tosso
- Departamento de Química, Facultad de Química, Bioquímica y Farmacia; Universidad Nacional de San Luis; Chacabuco 917, San Luis (5700) San Luis Argentina
- Instituto Multidiciplinario de Investigaciones Biológicas (IMIBIO-SL, CONICET); Chacabuco y Pedrenera (5700) San Luis Argentina
| | - Ricardo D. Enriz
- Departamento de Química, Facultad de Química, Bioquímica y Farmacia; Universidad Nacional de San Luis; Chacabuco 917, San Luis (5700) San Luis Argentina
- Instituto Multidiciplinario de Investigaciones Biológicas (IMIBIO-SL, CONICET); Chacabuco y Pedrenera (5700) San Luis Argentina
| | - Nélida M. Peruchena
- Lab. Estructura Molecular y Propiedades, Área de Química Física, Departamento de Química, Facultad de Ciencias Exactas y Naturales y Agrimensura; Universidad Nacional del Nordeste; Av. Libertad 5470 Corrientes 3400 Argentina
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35
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Adhikari U, Scheiner S. Magnitude and Mechanism of Charge Enhancement of CH··O Hydrogen Bonds. J Phys Chem A 2013; 117:10551-62. [DOI: 10.1021/jp4081788] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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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36
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Dragelj JL, Janjić GV, Veljković DŽ, Zarić SD. Crystallographic and ab initio study of pyridine CH–O interactions: linearity of the interactions and influence of pyridine classical hydrogen bonds. CrystEngComm 2013. [DOI: 10.1039/c3ce40759d] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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37
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Jones CR, Baruah PK, Thompson AL, Scheiner S, Smith MD. Can a C-H···O interaction be a determinant of conformation? J Am Chem Soc 2012; 134:12064-71. [PMID: 22789294 DOI: 10.1021/ja301318a] [Citation(s) in RCA: 98] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Whether nonconventional hydrogen bonds, such as the C-H···O interaction, are a consequence or a determinant of conformation is a long-running and unresolved issue. Here we outline a solid-state and quantum mechanical study designed to investigate whether a C-H···O interaction can override the significant trans-planar conformational preferences of α-fluoroamide substituents. A profound change in dihedral angle from trans-planar((OCCF)) to cis-planar((OCCF)) observed on introducing an acceptor group for a C-H···O hydrogen bond is consistent with this interaction functioning as a determinant of conformation in certain systems. This testifies to the potential influence of the C-H···O hydrogen bond and is consistent with the assignment of this interaction as a contributor to overall conformation in both model and natural systems.
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Affiliation(s)
- Christopher R Jones
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, UK
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38
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Vibhute AM, Gonnade RG, Swathi RS, Sureshan KM. Strength from weakness: opportunistic CH⋯O hydrogen bonds differentially dictate the conformational fate in solid and solution states. Chem Commun (Camb) 2012; 48:717-9. [DOI: 10.1039/c1cc15051k] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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39
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Engle JM, Lakshminarayanan PS, Carroll CN, Zakharov LN, Haley MM, Johnson DW. Molecular Self Assembly: Solvent Guests Tune the Conformation of a Series of 2,6-Bis(2-anilinoethynyl)pyridine-Based Ureas. CRYSTAL GROWTH & DESIGN 2011; 11:5144-5152. [PMID: 22102795 PMCID: PMC3216052 DOI: 10.1021/cg201074v] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
The conformations of 2,6-bis(2-anilinoethynyl)pyridine-based urea receptors were studied by single crystal X-ray diffraction methods and revealed a rich conformational flexibility influenced by solvents. Whereas receptor L(1) in DMSO prefers an "S" conformation, receptor L(1) crystallizes in an "O" conformation from DMSO/CH(3)OH binary solvent system, and a "W" conformation in the ternary solvent mixture DMSO/toluene/1,4-dioxane. In the case of L(2), the molecule adopts an "S" conformation where water molecules are sandwiched between two molecules of L(2) to form a dimer. Similar to L(2), L(3) also forms a dimer where water molecules are sandwiched between L(3) molecules, which are capped with two molecules of DMSO. Such a capping DMSO solvate is lacking in the case of L(2). Taken together, these results demonstrate that the conformation of 2,6-bis(2-anilinoethynyl) pyridine-based urea receptors can be dramatically manipulated and tuned by the choice of crystallization solvents.
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40
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Liu Y, Gallo AA, Xu W, Bajpai R, Florián J. CH···π Interactions Do Not Contribute to Hydrogen Transfer Catalysis by Glycerol Dehydratase. J Phys Chem A 2011; 115:11162-6. [DOI: 10.1021/jp202687g] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Yuemin Liu
- Department of Chemistry, University of Louisiana at Lafayette, Lafayette, Louisiana 70504, United States
| | - August A. Gallo
- Department of Chemistry, University of Louisiana at Lafayette, Lafayette, Louisiana 70504, United States
| | - Wu Xu
- Department of Chemistry, University of Louisiana at Lafayette, Lafayette, Louisiana 70504, United States
| | - Rakesh Bajpai
- Department of Chemical Engineering, University of Louisiana at Lafayette, Lafayette, Louisiana 70504, United States
| | - Jan Florián
- Department of Chemistry, Loyola University Chicago, Chicago, Illinois 60626, United States
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41
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Scheiner S. Weak H-bonds. Comparisons of CH···O to NH···O in proteins and PH···N to direct P···N interactions. Phys Chem Chem Phys 2011; 13:13860-72. [PMID: 21573303 DOI: 10.1039/c1cp20427k] [Citation(s) in RCA: 153] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Whereas CH···O H-bonds are usually weaker than interpeptide NH···O H-bonds, this is not necessarily the case within proteins. The nominally weaker CH···O are surprisingly strong, comparable to, and in some cases stronger than, the NH···O H-bonds in the context of the forces that hold together the adjacent strands in protein β-sheets. The peptide NH is greatly weakened as proton donor in certain conformations of the protein backbone, particularly extended structures, and forms correspondingly weaker H-bonds. The PH group is a weak proton donor, but will form PH···N H-bonds. However, there is a stronger interaction in which P can engage, in which the P atom, not the H, directly approaches the N electron donor to establish a direct P···N interaction. This approach is stabilized by the same sort of electron transfer from the N lone pair to the P-H σ* antibond that characterizes the PH···N H-bond.
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Affiliation(s)
- Steve Scheiner
- Department of Chemistry and Biochemistry, Utah State University, Logan, UT 84322-0300, USA.
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42
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Lu Y, Li H, Zhu X, Zhu W, Liu H. How Does Halogen Bonding Behave in Solution? A Theoretical Study Using Implicit Solvation Model. J Phys Chem A 2011; 115:4467-75. [DOI: 10.1021/jp111616x] [Citation(s) in RCA: 104] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Yunxiang Lu
- Key Laboratory for Advanced Material and Department of Chemistry, East China University of Science and Technology, Shanghai 200237, China
| | - Haiying Li
- Key Laboratory for Advanced Material and Department of Chemistry, East China University of Science and Technology, Shanghai 200237, China
| | - Xiang Zhu
- Key Laboratory for Advanced Material and Department of Chemistry, East China University of Science and Technology, Shanghai 200237, China
| | - Weiliang Zhu
- Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Honglai Liu
- Key Laboratory for Advanced Material and Department of Chemistry, East China University of Science and Technology, Shanghai 200237, China
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43
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Riley KE, Hobza P. Noncovalent interactions in biochemistry. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2011. [DOI: 10.1002/wcms.8] [Citation(s) in RCA: 157] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Kevin E. Riley
- Department of Chemistry, University of Puerto Rico, Rio Piedras, Puerto Rico
| | - Pavel Hobza
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic and Center for Biomolecules and Complex Molecular Systems, Prague, Czech Republic
- Department of Physical Chemistry, Palacky University, Olomouc, Czech Republic
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44
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Maerz AK, Fowler DA, Mossine AV, Mistry M, Kumari H, Barnes CL, Deakyne CA, Atwood JL. Solvent mediated self-assembly of organic nanostructures. NEW J CHEM 2011. [DOI: 10.1039/c1nj00005e] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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45
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Veljković DŽ, Janjić GV, Zarić SD. Are C–H⋯O interactions linear? The case of aromatic CH donors. CrystEngComm 2011. [DOI: 10.1039/c1ce05065f] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
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46
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Scheiner S, Kar T. Analysis of the Reactivities of Protein C−H Bonds to H Atom Abstraction by OH Radical. J Am Chem Soc 2010; 132:16450-9. [DOI: 10.1021/ja105204v] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Steve Scheiner
- Department of Chemistry & Biochemistry, Utah State University, Logan, Utah 84322, United States
| | - Tapas Kar
- Department of Chemistry & Biochemistry, Utah State University, Logan, Utah 84322, United States
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47
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Rossetti G, Magistrato A, Pastore A, Carloni P. Hydrogen Bonding Cooperativity in polyQ β-Sheets from First Principle Calculations. J Chem Theory Comput 2010; 6:1777-82. [DOI: 10.1021/ct900476e] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Giulia Rossetti
- Statistical and Biological Physics Sector, International School for Advanced Studies (SISSA-ISAS) and CNR-IOM-DEMOCRITOS National Simulation Center, Trieste, Italy, Via Beirut 2-4, Trieste, Italy, German Research School for Simulation Science, FZ-Juelich and RWTH, Germany, Italian Institute of Technology—SISSA Unit, Via Beirut 2-4, Trieste, Italy, and National Institute for Medical Research, The Ridgeway London, NW71AA, United Kingdom
| | - Alessandra Magistrato
- Statistical and Biological Physics Sector, International School for Advanced Studies (SISSA-ISAS) and CNR-IOM-DEMOCRITOS National Simulation Center, Trieste, Italy, Via Beirut 2-4, Trieste, Italy, German Research School for Simulation Science, FZ-Juelich and RWTH, Germany, Italian Institute of Technology—SISSA Unit, Via Beirut 2-4, Trieste, Italy, and National Institute for Medical Research, The Ridgeway London, NW71AA, United Kingdom
| | - Annalisa Pastore
- Statistical and Biological Physics Sector, International School for Advanced Studies (SISSA-ISAS) and CNR-IOM-DEMOCRITOS National Simulation Center, Trieste, Italy, Via Beirut 2-4, Trieste, Italy, German Research School for Simulation Science, FZ-Juelich and RWTH, Germany, Italian Institute of Technology—SISSA Unit, Via Beirut 2-4, Trieste, Italy, and National Institute for Medical Research, The Ridgeway London, NW71AA, United Kingdom
| | - Paolo Carloni
- Statistical and Biological Physics Sector, International School for Advanced Studies (SISSA-ISAS) and CNR-IOM-DEMOCRITOS National Simulation Center, Trieste, Italy, Via Beirut 2-4, Trieste, Italy, German Research School for Simulation Science, FZ-Juelich and RWTH, Germany, Italian Institute of Technology—SISSA Unit, Via Beirut 2-4, Trieste, Italy, and National Institute for Medical Research, The Ridgeway London, NW71AA, United Kingdom
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48
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Vallejos MM, Angelina EL, Peruchena NM. Bifunctional Hydrogen Bonds in Monohydrated Cycloether Complexes. J Phys Chem A 2010; 114:2855-63. [PMID: 20136161 DOI: 10.1021/jp906372t] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Margarita M. Vallejos
- Laboratorio de Estructura Molecular y Propiedades, Área de Química Física, Departamento de Química, Facultad de Ciencias Exactas y Naturales y Agrimensura, Universidad Nacional del Nordeste, Avenida Libertad 5460, (3400) Corrientes, Argentina, and Facultad Regional Resistancia, Universidad Tecnológica Nacional, French 414, (3500) Resistancia, Chaco, Argentina
| | - Emilio L. Angelina
- Laboratorio de Estructura Molecular y Propiedades, Área de Química Física, Departamento de Química, Facultad de Ciencias Exactas y Naturales y Agrimensura, Universidad Nacional del Nordeste, Avenida Libertad 5460, (3400) Corrientes, Argentina, and Facultad Regional Resistancia, Universidad Tecnológica Nacional, French 414, (3500) Resistancia, Chaco, Argentina
| | - Nélida M. Peruchena
- Laboratorio de Estructura Molecular y Propiedades, Área de Química Física, Departamento de Química, Facultad de Ciencias Exactas y Naturales y Agrimensura, Universidad Nacional del Nordeste, Avenida Libertad 5460, (3400) Corrientes, Argentina, and Facultad Regional Resistancia, Universidad Tecnológica Nacional, French 414, (3500) Resistancia, Chaco, Argentina
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49
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Scheiner S. Identification of spectroscopic patterns of CH...O H-bonds in proteins. J Phys Chem B 2009; 113:10421-7. [PMID: 19575539 DOI: 10.1021/jp9035138] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Ab initio calculations are used to identify characteristics of vibrational and NMR spectra that signal the involvement of a protein backbone in a CH...O H-bond and that distinguish this sort of interaction from other H-bonds in which a protein might participate. Glycine and alanine dipeptides, in both their C7 and C5 minimum-energy structures, are paired with formamide in a number of different H-bonding arrangements. The CH...O H-bond is characterized by a small contraction of the C-H bond length, along with a blue shift in its stretching frequency, accompanied by an intensification of this vibrational band. In the context of NMR spectra, the bridging CH proton's chemical shift is moved downfield by 1-2 ppm. The aforementioned features are not produced by other H-bonds in which the protein backbone might participate, such as NH proton donation or accepting a proton via the peptide C=O.
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Affiliation(s)
- Steve Scheiner
- Department of Chemistry & Biochemistry, Utah State University, Logan, Utah 84322-0300, USA.
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50
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Smith BC, Denu JM. Chemical mechanisms of histone lysine and arginine modifications. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2008; 1789:45-57. [PMID: 18603028 DOI: 10.1016/j.bbagrm.2008.06.005] [Citation(s) in RCA: 267] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2008] [Accepted: 06/09/2008] [Indexed: 10/21/2022]
Abstract
Histone lysine and arginine residues are subject to a wide array of post-translational modifications including methylation, citrullination, acetylation, ubiquitination, and sumoylation. The combinatorial action of these modifications regulates critical DNA processes including replication, repair, and transcription. In addition, enzymes that modify histone lysine and arginine residues have been correlated with a variety of human diseases including arthritis, cancer, heart disease, diabetes, and neurodegenerative disorders. Thus, it is important to fully understand the detailed kinetic and chemical mechanisms of these enzymes. Here, we review recent progress towards determining the mechanisms of histone lysine and arginine modifying enzymes. In particular, the mechanisms of S-adenosyl-methionine (AdoMet) dependent methyltransferases, FAD-dependent demethylases, iron dependent demethylases, acetyl-CoA dependent acetyltransferases, zinc dependent deacetylases, NAD(+) dependent deacetylases, and protein arginine deiminases are covered. Particular attention is paid to the conserved active-site residues necessary for catalysis and the individual chemical steps along the catalytic pathway. When appropriate, areas requiring further work are discussed.
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Affiliation(s)
- Brian C Smith
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
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