A simple and convenient method is described to determine primary deuterium kinetic isotope effects (1°DKIEs) on reactions where the hydron incorporated into the reaction product is derived from solvent water. The 1°DKIE may be obtained by H NMR analyses as the ratio of the yields of H- and D-labeled products from a reaction in 50:50 (v/v) HOH/DOD. The procedures for these H NMR analyses are reviewed. This product deuterium isotope effect (PDIE) is defined as 1/ϕ for fractionation of hydrons between solvent and the transition state for the reaction examined. When the solvent is not the direct hydron donor, it is necessary to correct the PDIE for the fractionation factor ϕ for partitioning of the hydron between the solvent and the direct donor EL. This method was used to determine the 1°DKIE on decarboxylation reactions catalyzed by wild-type orotidine 5'-monophosphate decarboxylase (OMPDC) and by mutants of OMPDC, and then in the determination of the 1°DKIE on the decarboxylation reaction catalyzed by 5-carboxyvanillate decarboxylase. The experimental procedures used in studies on OMPDC and the rationale for these procedures are described.
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http://dx.doi.org/10.1016/bs.mie.2017.06.043 | DOI Listing |
Mol Cell Proteomics
January 2025
Broad Institute of MIT & Harvard, Cambridge, MA. Electronic address:
Despite the widespread use of MS for hydrogen/deuterium exchange measurements, no systematic, large-scale study has been conducted to compare the observed exchange rates in protein-derived, unstructured peptides measured by MS to the predicted exchange rates calculated from NMR-derived values and how neighboring residues and post-translational modifications influence those exchange rates. In this study, we sought to test the accuracy of predicted values by performing hydrogen exchange measurements on whole cell digests to generate an unbiased dataset of 563 unique peptides derived from naturally-occurring protein sequences. A remarkable 97% of observed exchange rates of peptides are within two-fold of predicted values.
View Article and Find Full Text PDFACS Chem Neurosci
January 2025
National Measurement Laboratory, LGC, Queens Road, TW11 0LY Teddington, U.K.
Neurofilament light chain (NfL) is an early nonspecific biomarker in neurodegenerative diseases and traumatic brain injury, indicating axonal damage. This work describes the detailed structural characterization of a selected primary calibrator with the potential to be used in future reference measurement procedure (RMP) development for the accurate quantification of NfL. As a part of the described workflow, the sequence, higher-order structure as well as solvent accessibility, and hydrogen-bonding profile were assessed under three different conditions in KPBS, artificial cerebrospinal fluid, and artificial cerebrospinal fluid in the presence of human serum albumin.
View Article and Find Full Text PDFJ Mass Spectrom
January 2025
Department of Chemical Engineering and Chemistry, Institute for Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, The Netherlands.
One critical issue in hydrogen/deuterium exchange mass spectrometry (HDX MS) analysis is the deleterious back exchange. Herein, we report that when matrix-assisted laser desorption/ionization (MALDI) is used, the MALDI process itself can also cause significant back exchange. The back exchange occurred inside the reactive MALDI plume was investigated by depositing a fully deuterated sample prepared in DO on top of a preloaded dried layer of matrix.
View Article and Find Full Text PDFJ Org Chem
January 2025
Department of Chemistry, Indian Institute of Science Education and Research (IISER) Tirupati, Tirupati 517619, India.
The development of efficient and robust catalytic systems based on earth-abundant transition metals for fundamentally new transformations is crucial for sustainable chemical synthesis. Herein, an effective and selective Ni-catalyzed dehydrogenative coupling of alcohols with hydrazines with the liberation of ammonia gas is reported. Although several methods were documented for the -alkylation reaction, the present strategy is conceptually novel, and the reaction proceeds through a pathway involving N-N bond cleavage of phenylhydrazine followed by hydrogen autotransfer.
View Article and Find Full Text PDFJ Am Chem Soc
January 2025
School of Chemical Science and Engineering, Tongji University, 1239 Siping Road, Shanghai, 200092 P.R. China.
A fine-tuning of enantioselective carbene insertion into primary C()-H bonds has been realized in challenging substrates, such as -methyl unblocked aromatic and non-deactivated aliphatic tertiary amines, in which sterically demanding β-axially chiral iridium porphyrin catalysts play a crucial role. This primary C()-H alkylation with diazo compounds affords a series of β-chiral tertiary amines in high yields with excellent enantioselectivities. Notably, the protocol was successfully applied to the postmodification of chiral bicuculline, yielding the desired derivative with high diastereoselectivity.
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