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1. Imaging active site chemistry and protonation states: NMR crystallography of the tryptophan synthase α-aminoacrylate intermediate

   https://doi.org/10.1073/pnas.2109235119  

   Holmes, Jacob B.; Liu, Viktoriia; Caulkins, Bethany G.; Hilario, Eduardo; Ghosh, Rittik K.; Drago, Victoria N.; Young, Robert P.; Romero, Jennifer A.; Gill, Adam D.; Bogie, Paul M.; et al (January 2022, Proceedings of the National Academy of Sciences)

   NMR-assisted crystallography—the integrated application of solid-state NMR, X-ray crystallography, and first-principles computational chemistry—holds significant promise for mechanistic enzymology: by providing atomic-resolution characterization of stable intermediates in enzyme active sites, including hydrogen atom locations and tautomeric equilibria, NMR crystallography offers insight into both structure and chemical dynamics. Here, this integrated approach is used to characterize the tryptophan synthase α-aminoacrylate intermediate, a defining species for pyridoxal-5′-phosphate–dependent enzymes that catalyze β-elimination and replacement reactions. For this intermediate, NMR-assisted crystallography is able to identify the protonation states of the ionizable sites on the cofactor, substrate, and catalytic side chains as well as the location and orientation of crystallographic waters within the active site. Most notable is the water molecule immediately adjacent to the substrate β-carbon, which serves as a hydrogen bond donor to the ε-amino group of the acid–base catalytic residue βLys87. From this analysis, a detailed three-dimensional picture of structure and reactivity emerges, highlighting the fate of the L-serine hydroxyl leaving group and the reaction pathway back to the preceding transition state. Reaction of the α-aminoacrylate intermediate with benzimidazole, an isostere of the natural substrate indole, shows benzimidazole bound in the active site and poised for, but unable to initiate, the subsequent bond formation step. When modeled into the benzimidazole position, indole is positioned with C3 in contact with the α-aminoacrylate C β and aligned for nucleophilic attack. Here, the chemically detailed, three-dimensional structure from NMR-assisted crystallography is key to understanding why benzimidazole does not react, while indole does. 

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2. Hydrogen bonding in duplex DNA probed by DNP enhanced solid-state NMR N-H bond length measurements

   https://doi.org/10.3389/fmolb.2023.1286172  

   Bhai, Lakshmi; Thomas, Justin K; Conroy, Daniel W; Xu, Yu; Al-Hashimi, Hashim M; Jaroniec, Christopher P (December 2023, Frontiers in Molecular Biosciences)

   Numerous biological processes and mechanisms depend on details of base pairing and hydrogen bonding in DNA. Hydrogen bonds are challenging to quantify by X-ray crystallography and cryo-EM due to difficulty of visualizing hydrogen atom locations but can be probed with site specificity by NMR spectroscopy in solution and the solid state with the latter particularly suited to large, slowly tumbling DNA complexes. Recently, we showed that low-temperature dynamic nuclear polarization (DNP) enhanced solid-state NMR is a valuable tool for distinguishing Hoogsteen base pairs (bps) from canonical Watson-Crick bps in various DNA systems under native-like conditions. Here, using a model 12-mer DNA duplex containing two central adenine-thymine (A-T) bps in either Watson-Crick or Hoogsteen confirmation, we demonstrate DNP solid-state NMR measurements of thymine N3-H3 bond lengths, which are sensitive to details of N-H···N hydrogen bonding and permit hydrogen bonds for the two bp conformers to be systematically compared within the same DNA sequence context. For this DNA duplex, effectively identical TN3-H3 bond lengths of 1.055 ± 0.011 Å and 1.060 ± 0.011 Å were found for Watson-Crick A-T and Hoogsteen A (syn)-T base pairs, respectively, relative to a reference amide bond length of 1.015 ± 0.010 Å determined for N-acetyl-valine under comparable experimental conditions. Considering that prior quantum chemical calculations which account for zero-point motions predict a somewhat longer effective peptide N-H bond length of 1.041 Å, in agreement with solution and solid-state NMR studies of peptides and proteins at ambient temperature, to facilitate direct comparisons with these earlier studies TN3-H3 bond lengths for the DNA samples can be readily scaled appropriately to yield 1.083 Å and 1.087 Å for Watson-Crick A-T and Hoogsteen A (syn)-T bps, respectively, relative to the 1.041 Å reference peptide N-H bond length. Remarkably, in the context of the model DNA duplex, these results indicate that there are no significant differences in N-H···N A-T hydrogen bonds between Watson-Crick and Hoogsteen bp conformers. More generally, high precision measurements of N-H bond lengths by low-temperature DNP solid-state NMR based methods are expected to facilitate detailed comparative analysis of hydrogen bonding for a range of DNA complexes and base pairing environments. 

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3. Interfacial acidity on the strontium titanate surface: a scaling paradigm and the role of the hydrogen bond

   https://doi.org/10.1039/D1CP03587H  

   Chapleski, Robert C.; Chowdhury, Azhad U.; Mason, Kyle R.; Sacci, Robert L.; Doughty, Benjamin; Roy, Sharani (October 2021, Physical Chemistry Chemical Physics)

   A fundamental understanding of acidity at an interface, as mediated by structure and molecule–surface interactions, is essential to elucidate the mechanisms of a range of chemical transformations. While the strength of an acid in homogeneous gas and solution phases is conceptually well understood, acid–base chemistry at heterogeneous interfaces is notoriously more complicated. Using density functional theory and nonlinear vibrational spectroscopy, we present a method to determine the interfacial Brønsted–Lowry acidity of aliphatic alcohols adsorbed on the (100) surface of the model perovskite, strontium titanate. While shorter and less branched alkanols are known to be less acidic in the gas phase and more acidic in solution, here we show that shorter alcohols are less acidic whereas less substituted alkanols are more acidic at the gas–oxide interface. Hydrogen bonding plays a critical role in defining acidity, whereas structure–acidity relationships are dominated by van der Waals interactions between the alcohol and the surface. 

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4. Light‐Driven Hydrodefluorination of Electron‐Rich Aryl Fluorides by an Anionic Rhodium‐Gallium Photoredox Catalyst

   https://doi.org/10.1002/anie.202205575  

   Moore, James T.; Dorantes, Michael J.; Pengmei, Zihan; Schwartz, Timothy M.; Schaffner, Jacob; Apps, Samantha L.; Gaggioli, Carlo A.; Das, Ujjal; Gagliardi, Laura; Blank, David A.; et al (September 2022, Angewandte Chemie International Edition)

   Abstract An anionic Rh−Ga complex catalyzed the hydrodefluorination of challenging C−F bonds in electron‐rich aryl fluorides and trifluoromethylarenes when irradiated with violet light in the presence of H₂, a stoichiometric alkoxide base, and a crown‐ether additive. Based on theoretical calculations, the lowest unoccupied molecular orbital (LUMO), which is delocalized across both the Rh and Ga atoms, becomes singly occupied upon excitation, thereby poising the Rh−Ga complex for photoinduced single‐electron transfer (SET). Stoichiometric and control reactions support that the C−F activation is mediated by the excited anionic Rh−Ga complex. After SET, the proposed neutral Rh⁰intermediate was detected by EPR spectroscopy, which matched the spectrum of an independently synthesized sample. Deuterium‐labeling studies corroborate the generation of aryl radicals during catalysis and their subsequent hydrogen‐atom abstraction from the THF solvent to generate the hydrodefluorinated arene products. Altogether, the combined experimental and theoretical data support an unconventional bimetallic excitation that achieves the activation of strong C−F bonds and uses H₂and base as the terminal reductant. 

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5. An Investigation of the Effect of pH on Micelle Formation by a Glutamic Acid-Based Biosurfactant

   https://doi.org/10.3390/colloids8030038  

   Mayer, Jacob D; Rauscher, Robert M; Fritz, Shayden R; Fang, Yayin; Billiot, Eugene J; Billiot, Fereshteh H; Morris, Kevin F (June 2024, Colloids and Interfaces)

   NMR spectroscopy, molecular modeling, and conductivity experiments were used to investigate micelle formation by the amino acid-based surfactant tridecanoic L-glutamic acid. Amino acid-based biosurfactants are green alternatives to surfactants derived from petroleum. NMR titrations were used to measure the monomeric surfactant’s primary and gamma (γ) carboxylic acid pKa values. Intramolecular hydrogen bonding within the surfactant’s headgroup caused the primary carboxylic acid to be less acidic than the corresponding functional group in free L-glutamic acid. Likewise, intermolecular hydrogen bonding caused the micellar surfactant’s γ carboxylic functional group to be less acidic than the corresponding monomer value. The binding of four positive counterions to the anionic micelles was also investigated. At pH levels below 7.0 when the surfactant headgroup charge was −1, the micelle hydrodynamic radii were larger (~30 Å) and the mole fraction of micelle-bound counterions was in the 0.4–0.7 range. In the pH range of 7.0–10.5, the micelle radii decreased with increasing pH and the mole fraction of micelle bound counterions increased. These observations were attributed to changes in the surfactant headgroup charge with pH. Above pH 10.5, the counterions deprotonated and the mole fraction of micelle-bound counterions decreased further. Finally, critical micelle concentration measurements showed that the micelles formed at lower concentrations at pH 6 when the headgroup charge was predominately −1 and at higher concentrations at pH 7 where headgroups had a mixture of −1 and −2 charges in solution. 

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