Internal Proton Research Articles

Remarkable difference between five- and six- number-membered ring transition states for intramolecular proton transfer in excited state

Abstract In this study, a range of organic dyes were prepared to investigate difference between five- and six- number-membered ring transition states for internal proton transfer in excited state. Different strength intramolecular hydrogen bond in the target dyes was demonstrated by X-ray crystallography, 1 H NMR spectroscopy and ultraviolet/visible spectroscopy. The fluorescence measurement suggested excited state intramolecular proton transfer occurred via six number-membered ring transition state, while it could not occur through five number-membered ring transition state. The molecular geometry optimization of the target dyes further accounted for the difference of internal proton transfer in excited state occurred by five- or six- number-membered ring transition state.

Dynamics of the KB Proton Pathway in Cytochrome ba3 from Thermus thermophilus

AbstractThe ba3 cytochrome c oxidase from Thermus thermophilus is a B‐type oxygen‐reducing heme‐copper oxidase and a proton pump. It uses only one proton pathway for transfer of protons to the catalytic site, the KB pathway. It was previously shown that the ba3 oxidase has an overall similar reaction sequence to that in mitochondrial‐like A‐type oxidases. However, the timing of loading the pump site, and formation and decay of catalytic intermediates is different in the two types of oxidases. In the present study, we have investigated variants in which two amino acids of the KB proton pathway leading to the catalytic site were exchanged; Tyr‐248 (located ∼23 Å below the active site towards the cytoplasm) in subunit I (Y248T) and Glu‐15 (∼26 Å below the active site, ∼16 Å from Tyr‐248) in subunit II (E15IIQ). Even though the overall catalytic turnover in these two variants is similar and very low (<1 % of wildtype), the substitutions had distinctly different effects on the kinetics of proton transfer to the catalytic site. The results indicate that the Glu‐15II is the only essentially crucial residue of the KB pathway, but that the Tyr‐248 also plays a distinct role in defining an internal proton donor and controlling the dynamics of proton transfer to the pump site and the catalytic site.

Two intensified fluorescence colors' switching achieved by branched dye nanoaggregates.

In this study, a variety of branched target dyes containing double internal proton transfer segments were synthesized. For comparison, some linear analogs including a single internal proton transfer part were synthesized. The corresponding reference molecules lacking proton transfer segments were also prepared. The properties and aggregation modes of these dye aggregates were investigated on the basis of scanning electron microscopy images, transmission electron microscopy images, dynamic light scattering, X-ray diffraction, UV/visible absorption spectra and fluorescence emission spectra. The results showed that molecular aggregates with the morphologies of nano-scaled rounded or cubic particles of the target branched dyes could be yielded in mixed organic solvent/H2O solution. A remarkable emission enhancement and fluorescence switching process (from bright yellow to luminous pure blue) under 365 nm lamp irradiation was observed for these target branched dye nanoaggregates. However, no aggregates of the reference branched dyes free of hydroxyl groups were formed and no obvious spectral variations were found. In contrast, all the studied linear dyes yielded molecular nanoaggregates in mixed organic solvent/H2O solution, and only intensified single normal blue fluorescence emission was presented. This study provided real examples of some branched organic dye aggregates which were capable of displaying naked-eye enhanced fluorescence color switching under an UV lamp.

A three-dimensional movie of structural changes in bacteriorhodopsin.

Bacteriorhodopsin (bR) is a light-driven proton pump and a model membrane transport protein. We used time-resolved serial femtosecond crystallography at an x-ray free electron laser to visualize conformational changes in bR from nanoseconds to milliseconds following photoactivation. An initially twisted retinal chromophore displaces a conserved tryptophan residue of transmembrane helix F on the cytoplasmic side of the protein while dislodging a key water molecule on the extracellular side. The resulting cascade of structural changes throughout the protein shows how motions are choreographed as bR transports protons uphill against a transmembrane concentration gradient.

Electrogenic steps of light-driven proton transport in ESR, a retinal protein from Exiguobacterium sibiricum

A retinal protein from Exiguobacterium sibiricum (ESR) functions as a light-driven proton pump. Unlike other proton pumps, it contains Lys96 instead of a usual carboxylic residue in the internal proton donor site. Nevertheless, the reprotonation of the Schiff base occurs fast, indicating that Lys96 facilitates proton transfer from the bulk. In this study we examined kinetics of light-induced transmembrane electrical potential difference, ΔΨ, generated in proteoliposomes reconstituted with ESR. We show that total magnitude of ΔΨ is comparable to that produced by bacteriorhodopsin but its kinetic components and their pH dependence are substantially different. The results are in agreement with the earlier finding that proton uptake precedes reprotonation of the Schiff base in ESR, suggesting that Lys96 is unprotonated in the initial state and gains a proton transiently in the photocycle. The electrogenic phases and the photocycle transitions related to proton transfer from the bulk to the Schiff base are pH dependent. At neutral pH, they occur with τ 0.5ms and 4.5ms. At alkaline pH, the fast component ceases and Schiff base reprotonation slows. At pH8.4, a spectrally silent electrogenic component with τ 0.25ms is detected, which can be attributed to proton transfer from the bulk to Lys96. At pH5.1, the amplitude of ΔΨ decreases 10 fold, reflecting a decreased yield and rate of proton transfer, apparently from protonation of the acceptor (Asp85-His57 pair) in the initial state. The features of the photoelectric potential generation correlate with the ESR structure and proposed mechanism of proton transfer.

Multiscale simulations reveal key features of the proton-pumping mechanism in cytochrome c oxidase

Cytochrome c oxidase (CcO) reduces oxygen to water and uses the released free energy to pump protons across the membrane. We have used multiscale reactive molecular dynamics simulations to explicitly characterize (with free-energy profiles and calculated rates) the internal proton transport events that enable proton pumping during first steps of oxidation of the fully reduced enzyme. Our results show that proton transport from amino acid residue E286 to both the pump loading site (PLS) and to the binuclear center (BNC) are thermodynamically driven by electron transfer from heme a to the BNC, but that the former (i.e., pumping) is kinetically favored whereas the latter (i.e., transfer of the chemical proton) is rate-limiting. The calculated rates agree with experimental measurements. The backflow of the pumped proton from the PLS to E286 and from E286 to the inside of the membrane is prevented by large free-energy barriers for the backflow reactions. Proton transport from E286 to the PLS through the hydrophobic cavity and from D132 to E286 through the D-channel are found to be strongly coupled to dynamical hydration changes in the corresponding pathways and, importantly, vice versa.

New ESIPT-Inspired Photostabilizers of Two-Photon Absorption Coumarin–Benzotriazole Dyads: From Experiments to Molecular Modeling

In this work, a variety of new coumarin–benzotriazole dyads are synthesized to study the photostabilities under the irradiation of broad UV light as well as near-infrared (near-IR) laser respectively inspired by efficient excited state intramolecular proton transfer (ESIPT). The corresponding esterified dyads and the coumarin dyes are prepared as the references. The intramolecular hydrogen bond in the target dyads is confirmed by 1H NMR spectra and UV/visible absorption spectra. The internal proton transfer in the excited states of the target dyads under single photon excitation and near-IR laser irradiation is demonstrated by the measurements of one-photon fluorescence spectra and two-photon upconverted fluorescence spectra, respectively. The photostabilities of the target dyads under broad UV light irradiation and near-IR laser irradiation in various organic solvents with saturated air, oxygen, or argon are studied. The theoretical evidence of ESIPT of the target dyads is provided by the molecular geome...

New AB2 type two-photon absorption dyes for well-separated dual-emission: molecular preorganization based approach to photophysical properties

A variety of AB2 type new target dyes containing two proton transfer segments (o-hydroxy-phenyl-imino) are presented in this study. Furthermore, the corresponding reference molecules absent of hydroxy or imino groups are provided as well. Dual intramolecular hydrogen bonds in the target dyes are demonstrated by 1H NMR spectra, X-ray single crystal analysis as well as one-photon absorption spectra. Linear emission properties (static and transient emission nature) and two-photon absorption optical properties of these target and reference dyes are determined in various media such as organic solvents, solid phase state as well as PMMA substrate. The results show that the new AB2 type target dyes can efficiently undergo internal proton transfer in the excited states under one-photon irradiation and near-infrared femtosecond laser two-photon irradiation, respectively, and thus they exhibit well-separated dual-emission. The molecular geometry optimization is performed for the analysis of the occurrence of internal proton transfer in the excited states of the target AB2 chromophores.

A comparative MP2 study between water- and acid-assisted proton transfer: allophanic acid as a case of study

Electronic structures of allophanic acid were studied using MP2/6-311++G(d,p) level of theory. Five most stable tautomers were selected and stability of them was studied in detail. Obtained data showed that tautomer 1 having hydrogen atom in the central nitrogen N3 and also in a trans conformation of carbonyl and amino functional groups becomes the most stable one. Then, interconversion of these tautomers to each other was investigated step by step through internal rotation and proton transfer routes. Results indicated that movement of protons determines rate-determining step of all paths A–E. Effects of different solvents were carefully surveyed for each tautomer, and among investigated solvents, water made slight stabilization. Activation barrier for proton exchange assisted by one water molecule and one formic acid molecule was also studied, separately. Both molecules had a great influence on lowering barrier especially for proton transfer routes. Comparative MP2 study showed that the barrier will be lowered much more when acid-assisted proton exchange takes place.

Multiscale Simulations Reveal Key Aspects of the Proton Transport Mechanism in the ClC-ec1 Antiporter

Multiscale reactive molecular dynamics simulations are used to study proton transport through the central region of ClC-ec1, a widely studied ClC transporter that enables the stoichiometric exchange of 2 Cl– ions for 1 proton (H+). It has long been known that both Cl– and proton transport occur through partially congruent pathways, and that their exchange is strictly coupled. However, the nature of this coupling and the mechanism of antiporting remain topics of debate. Here multiscale simulations have been used to characterize proton transport between E203 (Gluin) and E148 (Gluex), the internal and external intermediate proton binding sites, respectively. Free energy profiles are presented, explicitly accounting for the binding of Cl– along the central pathway, the dynamically coupled hydration changes of the central region, and conformational changes of Gluin and Gluex. We find that proton transport between Gluin and Gluex is possible in both the presence and absence of Cl– in the central binding site, although it is facilitated by the anion presence. These results support the notion that the requisite coupling between Cl– and proton transport occurs elsewhere (e.g., during proton uptake or release). In addition, proton transport is explored in the E203K mutant, which maintains proton permeation despite the substitution of a basic residue for Gluin. This collection of calculations provides for the first time, to our knowledge, a detailed picture of the proton transport mechanism in the central region of ClC-ec1 at a molecular level.

Fluorescence and phosphorescence of tryptophan in peptides of different length and sequence

To interpret accurately protein fluorescence and phosphorescence, it is essential to achieve a better understanding of the luminescence properties of tryptophan (Trp, or W) in peptides. In published literature data on luminescence of peptides of varied length are scarce. This article describes studies of fluorescence and phosphorescence properties of the eight Trp-containing synthetic peptides: WAK, AWK, SWA, KYLWE, AVSWK, WVSWAK, WAKLAWE, and AVSWAKLARE. The aim was to investigate which factors influence the fluorescence yield and phosphorescence-spectra and lifetimes. Absorption spectra, room temperature fluorescence emission and corresponding excitation spectra and time-resolved phosphorescence spectra (77K) have been recorded; the dependence of the fluorescence quantum yield on the specific peptide and its variation with the wavelength of excitation has been studied. The changes in fluorescence yield and shape of phosphorescence spectra are explained in terms of internal electron and proton transfer. The structured phosphorescence spectrum originates from proton transfer occurring upon excitation of Trp, while electron transfer gives rise to a non-structured luminescence spectrum. There is also electron transfer from higher vibronic S1 states. In the peptides there is higher probability of electron transfer than in Trp alone. The obtained data are interpreted in light of the peptides' sequence, length and conformation.

Proton reduction by a nickel complex with an internal quinoline moiety for proton relay.

The complex Ni(DQPD) (where DQPD = deprotonated N(2),N(6)-di(quinolin-8-yl)pyridine-2,6-dicarboxamide (DQPDH2)) behaves as a visible light driven active catalyst to reduce protons from water when employed with the photosensitizer fluorescein (Fl) and triethylamine (TEA) as the sacrificial electron donor. The photocatalytic system shows very high activity, attaining 2160 turnovers and an initial turnover rate of 0.032 s(-1) with respect to the catalyst. The proposed electrocatalytic mechanism is of the CECE type (C is a chemical step protonation and E is the electrochemical step reduction), where the Ni(DQPD) catalyst undergoes rapid protonation at the non-coordinating nitrogen atom of the quinoline before undergoing reduction. The location of the pendant base is a key factor such that the N-H resulting from the protonation of the non-coordinating nitrogen atom of the quinoline is properly located to interact with the Ni-H hydride leading to heterocoupling between protons and hydrides. Theoretical calculations for the catalytic system were carried out using the density functional level of theory (DFT) and are consistent with a mechanism for catalysis in a polypyridine nickel system. This is the first report of a polypyridine based nickel catalyst where the pendant base is responsible for the internal proton relay towards the metal center through the heterocoupling between protons and hydrides to generate hydrogen.

Nickel phlorin intermediate formed by proton-coupled electron transfer in hydrogen evolution mechanism

The development of more effective energy conversion processes is critical for global energy sustainability. The design of molecular electrocatalysts for the hydrogen evolution reaction is an important component of these efforts. Proton-coupled electron transfer (PCET) reactions, in which electron transfer is coupled to proton transfer, play an important role in these processes and can be enhanced by incorporating proton relays into the molecular electrocatalysts. Herein nickel porphyrin electrocatalysts with and without an internal proton relay are investigated to elucidate the hydrogen evolution mechanisms and thereby enable the design of more effective catalysts. Density functional theory calculations indicate that electrochemical reduction leads to dearomatization of the porphyrin conjugated system, thereby favoring protonation at the meso carbon of the porphyrin ring to produce a phlorin intermediate. A key step in the proposed mechanisms is a thermodynamically favorable PCET reaction composed of intramolecular electron transfer from the nickel to the porphyrin and proton transfer from a carboxylic acid hanging group or an external acid to the meso carbon of the porphyrin. The C-H bond of the active phlorin acts similarly to the more traditional metal-hydride by reacting with acid to produce H2. Support for the theoretically predicted mechanism is provided by the agreement between simulated and experimental cyclic voltammograms in weak and strong acid and by the detection of a phlorin intermediate through spectroelectrochemical measurements. These results suggest that phlorin species have the potential to perform unique chemistry that could prove useful in designing more effective electrocatalysts.

The Role of Alloying Elements on the Crevice Corrosion Behavior of Ni-Cr-Mo Alloys

The roles of the alloying elements Mo, Cr, and W in resisting crevice corrosion of UNS N06022, UNS N06625, and UNS N10362 have been studied under galvanostatic conditions in 5 mol/L NaCl at 150°C. Corrosion damage patterns were investigated using surface analytical techniques such as scanning electron microscopy and optical imaging, and the corrosion products characterized by energy dispersive x-ray spectroscopy. While the Cr content of the alloy is critical in controlling initiation of crevice corrosion, the rate of activation (passive-to-active transition) is influenced by both the Cr and the Mo (and W) contents. The alloy’s Mo content also determines the distribution of corrosion damage within the crevice. In alloys with high Mo content, corrosion propagates laterally across the surface, while in alloys with low Mo content, it penetrates into the alloy. This can be attributed to the accumulation of molybdates (and tungstates), which stifle alloy dissolution at active sites. Thus, as the Mo content of the alloy increases in the order N06625 (9 wt% Mo) < N06022 (13 wt% Mo [3 wt% W]) < N10362 (22 wt% Mo), the depth of corrosion penetration decreases. In addition, once crevice corrosion initiates and the crevice acidifies, metal oxidation can also couple to proton reduction inside the crevice. The role of internal proton reduction in driving the crevice corrosion of these Ni alloys was found to be quite significant; greater than 50% of the corrosion damage is caused by proton reduction inside the crevice.

Patterned Poly(acrylic acid) Brushes Containing Gold Nanoparticles for Peptide Detection by Surface-Assisted Laser Desorption/Ionization Mass Spectrometry.

Patterned poly(acrylic acid) (PAA) brushes was successfully generated via photolithography and surface-initiated reversible addition-fragmentation chain transfer (RAFT) polymerization of acrylic acid as verified by water contact angle measurements and FT-IR analysis. The carboxyl groups of PAA brushes can act as reducing moieties for in situ synthesis of gold nanoparticles (AuNPs), without the use of additional reducing agent. The formation of AuNPs was confirmed by transmission electron microscopy and X-ray photoelectron spectroscopy. The glass surface-modified by PAA brushes and immobilized with AuNPs (AuNPs-PAA) can be used as a substrate for SALDI-MS analysis, which is capable of detecting both small peptides having m/z ≤ 600 (glutathione) and large peptides having m/z ≥ 1000 (bradykinin, ICNKQDCPILE) without the interference from matrix signal suggesting that AuNPs were stably trapped within the PAA brushes and the carboxyl groups of PAA can serve as internal proton source. By employing AuNPs as the capture probe, the AuNPs-PAA substrate can selectively identify thiol-containing peptides from the peptide mixtures with LOD as low as 0.1 and 0.05 nM for glutathione and ICNKQDCPILE, respectively. An ability to selectively detect ICNKQDCPILE in a diluted human serum is also demonstrated. The patterned format together with its high sensitivity and selectivity render this newly developed substrate a potential platform for high-throughput analysis of other biomarkers, especially those with low molecular weight in complex biological samples.

Vertically Oriented Polymer Electrolyte Nanofiber Catalyst Support for Thin Film Proton‐Exchange Membrane Fuel Cell Electrodes

AbstractPolymer electrolyte fuel cells are highly efficient and offer high power density, but high precious‐metal loading and degradation of carbon‐supported platinum (Pt) catalysts still hinder commercialization. Ionomer binders in conventional electrodes also introduce undesirable, high oxygen‐transport resistance. This paper presents an alternative composite Nafion nanofiber catalyst support electrode, in which the nanofibers provide robust internal proton transport to a conformal Pt catalyst coating without impeding O2 transport. The high‐surface‐area electrodes are prepared by solution casting ionomer onto a sacrificial template to simultaneously fabricate the nanofibers and the membrane. Thin Pt films are deposited on the nanofibers using either physical vapor deposition or chemical vapor deposition. The electrochemical characterization of the nanofiber electrodes demonstrates the high current density and specific activity of this nanofiber approach relative to prior electrodes fabricated by depositing Pt directly onto other Nafion surfaces.

Molecular Design of Light-Responsive Hydrogels, For in Situ Generation of Fast and Reversible Valves for Microfluidic Applications

Reversible light-responsive hydrogel valves with response characteristics compatible for microfluidics have been obtained by optimization of molecular design of spiropyran photoswitches and gel composition. Self-protonating gel formulations were exploited, wherein acrylic acid was copolymerized in the hydrogel network as an internal proton donor, to achieve a swollen state of the hydrogel in water at neutral pH. Light-responsive properties were endowed upon the hydrogels by copolymerization of spiropyran chromophores, using electron withdrawing and donating groups to tune the gel-swelling and shrinkage behavior. In all cases, the shrinkage was determined by the water diffusion rate, while for the swelling the isomerization kinetics is the rate-determining step. For one hydrogel, reversible and reproducible volume changes were observed. Finally, gel-valves integrated within microfluidic channels were fabricated, allowing reversible and repeatable operation, with opening and closing of the valve in minutes.

Field - dipole interactions in L-cysteine-thiolate self assembled at p- and n-GaAs(100) electrodes

L-cysteine-thiolate monolayers spontaneously self-assembled on p- and n-GaAs(100) electrodes have been investigated by electrochemical impedance spectroscopy in H2SO4 solutions. On p-doped samples a potential-induced reversible proton transfer occurs within the L-cysteine-thiolate layer during both forward and backward potential scans; in contrast, on n-doped samples it is observed only in the reverse scan. The XPS data and the fractal analysis of the AFM images point to the field - dipole interactions operating distinctively in the L-cysteine-thiolate layer formed at p- and n-doped semiconducting substrates as the origin of the observed difference. The interaction of this small but highly polar molecule with the electrostatic field driven by the diffuse distribution of the excess charge in the semiconductor subsurface region both in equilibrium and under polarization conditions turned out to play a key role in determining the optimal orientation of the two polar groups. The latter one seems to be a prerequisite for the potential-induced internal proton transfer.

Responsive Polymer Photonics.

Responsive Polymer Photonics.

Complex formation and internal proton-transfer of hydroxyl-hydrogen anion complexes at low temperature

We have studied the three-body complex formation rate of the hydroxyl anion with molecular hydrogen at low temperatures. The formed cluster is found to quickly undergo internal proton transfer to a hydrogen anion–water complex. This is probed by photodetachment spectroscopy, which clearly distinguishes the two isomeric structures. The product cluster is the only isomer found to be stably formed at the temperature and densities employed in the experiment. The cluster then binds an additional hydrogen molecule by a second three-body collision, which appears at a rate comparable to the first formation process. This is followed by a rapid growth to larger clusters.