H-bonding interactions in networks are stabilised by cooperativity, but the relationship between the chemical structures of the interacting functional groups and the thermodynamic consequences is not well-understood. We have used compounds with an intramolecular H-bond between a pyridine H-bond acceptor and an amide NH group to quantify cooperative effects on the H-bond acceptor properties of the amide carbonyl group. H NMR experiments in -octane confirm the presence of the intramolecular H-bond and show that this interaction is intact in the 1 : 1 complex formed with perfluoro--butanol (PFTB). UV-vis absorption titrations were used to measure the relationship between the association constant for formation of this complex and the H-bond acceptor properties of the pyridine involved in the intramolecular H-bond. Electron-donating substituents on the pyridine increase the strength of the intermolecular H-bond between PFTB and the amide. There is a linear relationship between the H-bond acceptor parameter measured for the amide carbonyl group and the H-bond acceptor parameter for the pyridine. The cooperativity parameter determined from this relationship is 0.2, for an amide carbonyl group is increased by one fifth of the value of of an acceptor that interacts with the NH group. This result is reproduced by DFT calculations of H-bond parameters for the individual molecules in the gas phase, which implies that the observed cooperativity can be understood as polarisation of the electron density in the amide π-system in response to formation of a H-bond. The cooperativity parameter measured for the secondary amide H-bond donor and H-bond acceptor is identical, which implies that polarisation of an amide mediates the interaction between an external donor or acceptor in a reciprocal manner.
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http://dx.doi.org/10.1039/d3sc03823h | DOI Listing |
Angew Chem Int Ed Engl
January 2025
RIKEN: Rikagaku Kenkyujo, Center for Sustainable Resource Science, 2-1 Hirosawa, 351-0198, Wako, JAPAN.
Transition-metal-catalyzed selective and efficient activation of an inert C-H bond in an organic substrate is of importance for the development of streamlined synthetic methodologies. An attractive approach is the design of a metal catalyst capable of recognizing an organic substrate through noncovalent interactions to control reactivity and selectivity. We report here a spirobipyridine ligand that bears a hydroxy group that recognizes pyridine and quinoline substrates through hydrogen bonding, and in combination with an iridium catalyst enables site-selective C-H borylation.
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December 2024
State Key Laboratory of Anti-Infective Drug Discovery and Development, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, China.
The faithful charging of amino acids to cognate tRNAs by aminoacyl-tRNA synthetases (AARSs) determines the fidelity of protein translation. Isoleucyl-tRNA synthetase (IleRS) distinguishes tRNA from tRNA solely based on the nucleotide at wobble position (N34), and a single substitution at N34 could exchange the aminoacylation specificity between two tRNAs. Here, we report the structural and biochemical mechanism of N34 recognition-based tRNA discrimination by Saccharomyces cerevisiae IleRS (ScIleRS).
View Article and Find Full Text PDFBiochemistry
January 2025
Department of Applied Chemistry, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8654, Japan.
Photosystem I (PSI) from utilizes chlorophyll (Chl) with a formyl group as its primary pigment, which is more red-shifted than chlorophyll (Chl) in PSI from . Using the cryo-electron microscopy structure and solving the linear Poisson-Boltzmann equation, here we report the redox potential () values in PSI. The (Chl) values at the paired chlorophyll site, [PP], are nearly identical to the corresponding (Chl) values in PSI, despite Chl having a 200 mV lower reduction power.
View Article and Find Full Text PDFPhys Chem Chem Phys
December 2024
Department of Chemistry, Malaviya National Institute of Technology, Jaipur, J L N Marg, Jaipur-302017, India.
H-bonded complexes between CHCl and HS have been studied in a cold and inert argon matrix using IR spectroscopy. Both molecules were found to act as both a H-bond donor and acceptor, resulting in two different conformers. The more stable one (binding energy 3.
View Article and Find Full Text PDFACS Phys Chem Au
November 2024
Department of Chemistry, Faculty of Science, University of Zagreb, Horvatovac 102a, 10000 Zagreb, Croatia.
In this work, we developed (thio)ureido-calix[4]arene derivatives and thoroughly explored their anion-binding properties in acetonitrile. A series of anions, including important inorganic ones (Cl, HSO , HPO , and HPO ) and several ever-present carboxylates (acetate, benzoate, and fumarate), were studied. All systems were investigated by several methods (NMR, ITC, and UV) used in a synergistic fashion, providing their comprehensive thermodynamic description.
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