Search results for "Isotope Effects"
showing 10 items of 11 documents
Opposite Trends in Holocene Speleothem Proxy Records From Two Neighboring Caves in Germany: A Multi-Proxy Evaluation
2021
Holocene climate in Central Europe was characterized by variations on millennial to decadal time scales. Speleothems provide the opportunity to study such palaeoclimate variability using high temporal resolution proxy records, and offer precise age models by U-series dating. However, the significance of proxy records from an individual speleothem is still a matter of debate, and limited sample availability often hampers the possibility to reproduce proxy records or to resolve spatial climate patterns. Here we present a palaeoclimate record based on four stalagmites from the Hüttenbläserschachthöhle (HBSH), western Germany. Two specimens cover almost the entire Holocene, with a short hiatus …
Study of the benzene⋅N2 intermolecular potential-energy surface
2003
The intermolecular potential-energy surface pertaining to the interaction between benzene and N2 is investigated theoretically and experimentally. Accurate intermolecular interaction energies are evaluated for the benzene–N2 van der Waals complex using the coupled cluster singles and doubles including connected triples [CCSD(T)] method and the aug-cc-pVDZ basis set extended with a set of 3s3p2d1f1g midbond functions. After fitting the energies to an analytic function, the intermolecular Schrödinger equation is solved to yield energies, rotational constants, and Raman-scattering coefficients for the lowest intermolecular levels of several benzene–N2 isotopomers. Experimentally, intermolecula…
Carboxylate catalyzed isomerization of β,γ‐unsaturated N-acetylcysteamine thioesters
2022
We demonstrate herein the capacity of simple carboxylate salts – tetrametylammonium and tetramethylguanidinium pivalate – to act as catalysts in the isomerization of β,γ-unsaturated thioesters to α,β-unsaturated thioesters. The carboxylate catalysts gave reaction rates comparable to those obtained with DBU, but with fewer side reactions. The reaction exhibits a normal secondary kinetic isotope effect ( k 1H / k 1D = 1.065±0.026) with a β,γ−deuterated substrate. Computational analysis of the mechanism provides a similar value ( k 1H / k 1D = 1.05) with a mechanism where γ-reprotonation of the enolate intermediate is rate determining. peerReviewed
Computational and experimental investigation of intermolecular states and forces in the benzene-helium van der Waals complex
2003
A study of the intermolecular potential-energy surface (IPS) and the intermolecular states of the perprotonated and perdeuterated benzene–He complex is reported. From a fit to ab initio data computed within the coupled cluster singles and doubles including connected triples model for 280 interaction geometries, an analytic IPS including two- to four-body atom–atom terms is obtained. This IPS, and two other Lennard-Jones atom–atom surfaces from the literature, are each employed in dynamically exact (within the rigid-monomer approximation) calculations of J = 0 intermolecular states of the isotopomers. Rotational constants and Raman-scattering coefficients for intermolecular vibrational trans…
Heavy enzymes and the rational redesign of protein catalysts
2019
Abstract An unsolved mystery in biology concerns the link between enzyme catalysis and protein motions. Comparison between isotopically labelled “heavy” dihydrofolate reductases and their natural‐abundance counterparts has suggested that the coupling of protein motions to the chemistry of the catalysed reaction is minimised in the case of hydride transfer. In alcohol dehydrogenases, unnatural, bulky substrates that induce additional electrostatic rearrangements of the active site enhance coupled motions. This finding could provide a new route to engineering enzymes with altered substrate specificity, because amino acid residues responsible for dynamic coupling with a given substrate present…
Why Are Some Enzymes Dimers? Flexibility and Catalysis in Thermotoga maritima Dihydrofolate Reductase
2019
[Image: see text] Dihydrofolate reductase from Thermotoga maritima (TmDFHFR) is a dimeric thermophilic enzyme that catalyzes the hydride transfer from the cofactor NADPH to dihydrofolate less efficiently than other DHFR enzymes, such as the mesophilic analogue Escherichia coli DHFR (EcDHFR). Using QM/MM potentials, we show that the reduced catalytic efficiency of TmDHFR is most likely due to differences in the amino acid sequence that stabilize the M20 loop in an open conformation, which prevents the formation of some interactions in the transition state and increases the number of water molecules in the active site. However, dimerization provides two advantages to the thermophilic enzyme: …
Binding isotope effects as a tool for distinguishing hydrophobic and hydrophilic binding sites of HIV-1 RT.
2014
The current treatment for HIV-1 infected patients consists of a cocktail of inhibitors, in an attempt to improve the potency of the drugs by adding the possible effects of each supplied compound. In this contribution, nine different inhibitors of HIV-1 RT, one of the three key proteins responsible for the virus replication, have been selected to develop and test a computational protocol that allows getting a deep insight into the inhibitors’ binding mechanism. The interaction between the inhibitors and the protein have been quantified by computing binding free energies through FEP calculations, while a more detailed characterization of the kind of inhibitor–protein interactions is based on …
Chemical Ligation and Isotope Labeling to Locate Dynamic Effects during Catalysis by Dihydrofolate Reductase.
2015
Abstract Chemical ligation has been used to alter motions in specific regions of dihydrofolate reductase from E. coli and to investigate the effects of localized motional changes on enzyme catalysis. Two isotopic hybrids were prepared; one with the mobile N‐terminal segment containing heavy isotopes (2H, 13C, 15N) and the remainder of the protein with natural isotopic abundance, and the other one with only the C‐terminal segment isotopically labeled. Kinetic investigations indicated that isotopic substitution of the N‐terminal segment affected only a physical step of catalysis, whereas the enzyme chemistry was affected by protein motions from the C‐terminal segment. QM/MM studies support th…
Convergence of Theory and Experiment on the Role of Preorganization, Quantum Tunneling, and Enzyme Motions into Flavoenzyme-Catalyzed Hydride Transfer
2017
Hydride transfer is one of the most common reactions catalyzed by enzymatic systems, and it has become an object of study because of possible significant quantum tunneling effects. In the present work, we provide a combination of theoretical QM/MM simulations and experimental measurements of the rate constants and kinetic isotopic effects (KIEs) for the hydride transfer reaction catalyzed by morphinone reductase, MR. Quantum mechanical tunneling coefficients, computed in the framework of variational transition-state theory, play a significant role in this reaction, reaching values of 23.8 ± 5.5 for the lightest isotopologue—one of the largest values reported for enzymatic systems. This pred…
Theoretical Study of Primary Reaction of Pseudozyma antarctica Lipase B as the Starting Point To Understand Its Promiscuity
2014
Pseudozyma antarctica lipase B (PALB) is a serine hydrolase that catalyzes the hydrolysis of carboxylic acid esters in aqueous medium but it has also shown catalytic activity for a plethora of reactions. This promiscuous activity has found widespread applications. In the present paper, the primary reaction of PALB, its native hydrolytic activity, has been studied using hybrid quantum mechanical/molecular mechanical (QM/MM) potentials. Free energy surfaces, obtained from QM/MM Molecular Dynamics (MD) simulations, show that the reaction takes place by means of a multi-step mechanism where the first step, the activation of the carbonyl group of the substrate and the nucleophilic attack of Ser1…