On the possibility of detecting low barrier hydrogen bonds with UV spectroscopy and kinetic measurements

Recent Experimental evidence has pointed that in many enzyme-catalyzed biochemical pathways a short, strong hydrogen bond between an enzyme and substrate leads to an important contribution to enzyme catalysis. These bonds are termed low barrier hydrogen bonds. In this paper we show that the presence of low barrier hydrogen bonds can be determined in systems by UV spectroscopy and kinetic measurements. In using the time-dependent view of UV spectroscopy, we apply several different UV spectra: photoabsorption, photodissociation, and emission, on systems containing a low barrier hydrogen bond. We find several distinguishing features in the UV spectra for systems that possess a low barrier hydrogen bond. In using kinetic measurements, we find non-trivial differences among rate constant ratios of protonated to deuterated hydrogen bonds between strong and weak hydrogen bonds of proton transfer between donor and acceptor sites. This kinetic isotope effect is determined by performing full dynamic calculations of these rate constants by computing reactive flux through a dividing surface. This reactive flux is computed by evolving classical trajectories on an effective quantum mechanical potential energy surface

Detection techniques for tenuous planetary atmospheres Fifth six-month report, 1 Jul. - 30 Dec. 1965

Physical methods description for detection and analysis of tenuous planetary atmospheric component gases, especially water vapo

Vibrational spectroscopy of NO^+(H_2O)_n: Evidence for the intracluster reaction NO^+(H_2O)_n→H_3O^+(H_2O)_(n-2)(HONO) at n≥4

Infrared spectra of mass‐selected clusters NO^+(H_2O)_n for n=1 to 5 were recorded from 2700 to 3800 cm^(−1) by vibrational predissociation spectroscopy. Vibrational frequencies and intensities were also calculated for n=1 and 2 at the second‐order Møller–Plesset (MP2) level, to aid in the interpretation of the spectra, and at the singles and doubles coupled cluster (CCSD) level energies of n=1 isomers were computed at the MP2 geometries. The smaller clusters (n=1 to 3) were complexes of H_2O ligands bound to a nitrosonium ion NO^+ core. They possessed perturbed H_2O stretch bands and dissociated by loss of H_2O. The H_2O antisymmetric stretch was absent in n=1 and gradually increased in intensity with n. In the n=4 clusters, we found evidence for the beginning of a second solvation shell as well as the onset of an intracluster reaction that formed HONO. These clusters exhibited additional weak, broad bands between 3200 and 3400 cm^(−1) and two new minor photodissociation channels, loss of HONO and loss of two H_2O molecules. The reaction appeared to go to completion within the n=5 clusters. The primary dissociation channel was loss of HONO, and seven vibrational bands were observed. From an analysis of the spectrum, we concluded that the n=5 cluster rearranged to form H_3O^+(H_2O)_3(HONO), i.e., an adduct of the reaction products

The loops facing the active site of prolyl oligopeptidase are crucial components in substrate gating and specificity

Prolyl oligopeptidase (POP) has emerged as a drug target for neurological diseases. A flexible loop structure comprising loop A (res. 189–209) and loop B (res. 577–608) at the domain interface is implicated in substrate entry to the active site. Here we determined kinetic and structural properties of POP with mutations in loop A, loop B, and in two additional flexible loops (the catalytic His loop, propeller Asp/Glu loop). POP lacking loop A proved to be an inefficient enzyme, as did POP with a mutation in loop B (T590C). Both variants displayed an altered substrate preference profile, with reduced ligand binding capacity. Conversely, the T202C mutation increased the flexibility of loop A, enhancing the catalytic efficiency beyond that of the native enzyme. The T590C mutation in loop B increased the preference for shorter peptides, indicating a role in substrate gating. Loop A and the His loop are disordered in the H680A mutant crystal structure, as seen in previous bacterial POP structures, implying coordinated structural dynamics of these loops. Unlike native POP, variants with a malfunctioning loop A were not inhibited by a 17-mer peptide that may bind non-productively to an exosite involving loop A. Biophysical studies suggest a predominantly closed resting state for POP with higher flexibility at the physiological temperature. The flexible loop A, loop B and His loop system at the active site is the main regulator of substrate gating and specificity and represents a new inhibitor target

Kinetics and mechanism of the hydrogen peroxide reduction reaction on a graphite carbon ntride sensor

The kinetics and mechanism of the hydrogen peroxide reduction reaction (HPRR) on a recently proposed carbon-based electrode is studied by means of experiments and simulations. The electrode is highly oriented pyrolytic graphite (HOPG) modified by the deposition of a graphite carbon nitride (g-C3N4) film. Current transients obtained from chronoamperometry measurements allow us to propose a kinetic model for the HPRR on the surface. The model produces excellent fits of current transients, providing sensible rate constants for each electrocatalytic step. The rate constants obtained are consistent with low energy barriers for each step, suggesting outstanding electrocatalytic activity of the g-C3N4/HOPG electrode. Moreover, different trends are found for low and high analyte concentrations, evidencing a change in the reaction mechanism. To clarify the mechanisms involved in the reaction, first-principles atomistic simulations were performed. The different reaction steps were modeled at the substrate/water interface, including solvent environment through continuum embedding approaches. The simulated thermodynamics and kinetics of the different processes show that a significant role in the electrocatalytic activity of the system is associated with the geometrical rearrangements of the interface, with a critical role played by the corrugation/decorrugation processes of the outermost sheet of the electrode.Fil: Rojas, Mariana Isabel. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Instituto de Investigaciones en Físico-química de Córdoba. Universidad Nacional de Córdoba. Facultad de Ciencias Químicas. Instituto de Investigaciones en Físico-química de Córdoba; ArgentinaFil: Andreussi, Oliviero. University of North Texas; Estados UnidosFil: Gomez, Cesar Gerardo. Universidad Nacional de Córdoba. Instituto de Investigación y Desarrollo en Ingeniería de Procesos y Química Aplicada. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Instituto de Investigación y Desarrollo en Ingeniería de Procesos y Química Aplicada; ArgentinaFil: Avalle, Lucia Bernardita. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Instituto de Física Enrique Gaviola. Universidad Nacional de Córdoba. Instituto de Física Enrique Gaviola; Argentin

Electron scattering from molecules and molecular aggregates of biological relevance

In this Topical Review we survey the current state of the art in the study of low energy electron collisions with biologically relevant molecules and molecular clusters. We briefly describe the methods and techniques used in the investigation of these processes and summarise the results obtained so far for DNA constituents and their model compounds, amino acids, peptides and other biomolecules. The applications of the data obtained is briefly described as well as future required developments