Direct Proton Research Articles

Light acclimation interacts with thylakoid ion transport to govern the dynamics of photosynthesis in Arabidopsis.

Understanding photosynthesis in natural, dynamic light environments requires knowledge of long-term acclimation, short-term responses, and their mechanistic interactions. To approach the latter, we systematically determined and characterized light-environmental effects on thylakoid ion transport-mediated short-term responses during light fluctuations. For this, Arabidopsis thaliana wild-type and mutants of the Cl- channel VCCN1 and the K+ exchange antiporter KEA3 were grown under eight different light environments and characterized for photosynthesis-associated parameters and factors in steady state and during light fluctuations. For a detailed characterization of selected light conditions, we monitored ion flux dynamics at unprecedented high temporal resolution by a modified spectroscopy approach. Our analyses reveal that daily light intensity sculpts photosynthetic capacity as a main acclimatory driver with positive and negative effects on the function of KEA3 and VCCN1 during high-light phases, respectively. Fluctuations in light intensity boost the accumulation of the photoprotective pigment zeaxanthin (Zx). We show that KEA3 suppresses Zx accumulation during the day, which together with its direct proton transport activity accelerates photosynthetic transition to lower light intensities. In summary, both light-environment factors, intensity and variability, modulate the function of thylakoid ion transport in dynamic photosynthesis with distinct effects on lumen pH, Zx accumulation, photoprotection, and photosynthetic efficiency.

Counting the Acid Sites in a Commercial ZSM-5 Zeolite Catalyst.

This work investigates the acid sites in a commercial ZSM-5 zeolite catalyst by a combination of spectroscopic and physical methods. The Brønsted acid sites in such catalysts are associated with the aluminum substituted into the zeolite lattice, which may not be identical to the total aluminum content of the zeolite. Inelastic neutron scattering spectroscopy (INS) directly quantifies the concentrations of Brønsted acid protons, silanol groups, and hydroxyl groups associated with extra-framework aluminum species. The INS measurements show that ∼50% of the total aluminum content of this particular zeolite is extra framework, a conclusion supported by solid-state NMR and ammonia temperature-programmed desorption (TPD) measurements. Evidence for the presence of extra-framework aluminum oxide species is also seen in neutron powder diffraction data from proton- and deuterium-exchanged samples. The differences between results from the different analytical methods are discussed, and the novelty of direct proton counting by INS in this typical commercial catalyst is emphasized.

Mechanisms of Reactions between HOI and HY (Y = Cl, Br, I) on a Water Nanodroplet Surface.

Iodine chemistry has a broad range of implications for atmospheric processes including new particle formation. Hypoiodous acid (HOI) is a major iodine reservoir species. Its heterogeneous recycling in marine aerosols influences the lifetime of ozone in the troposphere. One important step of such recycling is the reaction between HOI and HY (Y = Cl, Br, I). In this article, we employ ab initio molecular dynamics (AIMD) and quantum chemistry to investigate these reactions at the surface of atmospheric aerosols. Di-halogen (XY) can be formed in a picosecond time scale, with the formation of a loop structure connected by hydrogen and halogen bonds. The photolysis of XY at the surface of an aerosol is faster than in the gas phase. In addition to the formation of di-halogen, a new pathway to forming a [H2O···I···OH2]+ complex by the direct or indirect proton transition is identified. Results presented in this study deepen our understanding of the faster iodine-heterogeneous recycling at the surface of aerosols.

Brønsted Acid Catalyzed Carbocyclizations Involving Electrophilic Activation of Alkynes

AbstractThis review focuses on the carbocyclization reactions of alkyne-containing substrates catalyzed by Brønsted acids. The electrophilic activation occurs either by direct protonation of the alkyne or by formation of an intermediate cation that further reacts with the alkyne to give a key vinyl cation intermediate. Specific focus is placed on the selectivity of the various methodologies described herein and on mechanistic rationales.1 Introduction2 Brønsted Acid Catalyzed Alkyne Carbocyclization Involving C(sp) Reaction Partners2.1 Brønsted Acid Catalyzed Cyclization of Diynes2.2 Brønsted Acid Catalyzed Cyclization of Allenynes3 Brønsted Acid Catalyzed Alkyne Carbocyclization Involving C(sp2) Reaction Partners3.1 Brønsted Acid Catalyzed Cycloisomerization of Enynes3.1.1 Initial Protonation of the Alkene Function3.1.2 Initial Protonation of the Alkyne Function3.1.3 A Conia-Ene Reaction3.2 Electrophile-Induced Carbocyclization Involving Other C(sp2)-Based Reaction Partners3.2.1 Iminium Electrophiles3.2.2 Oxonium Electrophiles3.2.3 Isocyanate and Thioisocyanate Electrophiles3.3 Brønsted Acid Catalyzed Cycloisomerization of Aryl-alkynes3.3.1 Reactions Using Excess or Stoichiometric Amounts of Brønsted Acid3.3.2 Reactions Using Substoichiometric Amounts of Brønsted Acid3.3.3 Heteroatom-Substituted Alkynes3.3.4 Enantioselective Brønsted Acid Catalyzed Cycloisomerization of Aryl-alkynes4 Brønsted Acid Catalyzed Alkyne Carbocyclization Involving C(sp3) Reaction Partners: Alkyne-alkane Cycloisomerization5 Conclusion and Outlook

A TD-DFT-Based Study on the Attack of the OH· Radical on a Guanine Nucleotide.

Heavy charged particles induce severe damage in DNA, which is a radiobiological advantage when treating radioresistant tumors. However, these particles can also induce cancer in humans exposed to them, such as astronauts in space missions. This damage can be directly induced by the radiation or indirectly by the attack of free radicals mainly produced by water radiolysis. We previously studied the impact of a proton on a DNA base pair, using the Time Dependent-Density Functional Theory (TD-DFT). In this work, we go a step further and study the attack of the OH· radical on the Guanine nucleotide to unveil how this molecule subsequently dissociates. The OH· attack on the H1′, H2′, H3′, and H5′ atoms in the guanine was investigated using the Ehrenfest dynamics within the TD-DFT framework. In all cases, the hydrogen abstraction succeeded, and the subsequent base pair dissociation was observed. The DNA dissociates in three major fragments: the phosphate group, the deoxyribose sugar, and the nitrogenous base, with slight differences, no matter which hydrogen atom was attacked. Hydrogen abstraction occurs at about 6 fs, and the nucleotide dissociation at about 100 fs, which agrees with our previous result for the direct proton impact on the DNA. These calculations may be a reference for adjusting reactive force fields so that more complex DNA structures can be studied using classical molecular dynamics, including both direct and indirect DNA damage.

Respiratory complex I with charge symmetry in the membrane arm pumps protons

Energy-converting NADH:ubiquinone oxidoreductase, respiratory complex I, is essential for cellular energy metabolism coupling NADH oxidation to proton translocation. The mechanism of proton translocation by complex I is still under debate. Its membrane arm contains an unusual central axis of polar and charged amino acid residues connecting the quinone binding site with the antiporter-type subunits NuoL, NuoM, and NuoN, proposed to catalyze proton translocation. Quinone chemistry probably causes conformational changes and electrostatic interactions that are propagated through these subunits by a conserved pattern of predominantly lysine, histidine, and glutamate residues. These conserved residues are thought to transfer protons along and across the membrane arm. The distinct charge distribution in the membrane arm is a prerequisite for proton translocation. Remarkably, the central subunit NuoM contains a conserved glutamate residue in a position that is taken by a lysine residue in the two other antiporter-type subunits. It was proposed that this charge asymmetry is essential for proton translocation, as it should enable NuoM to operate asynchronously with NuoL and NuoN. Accordingly, we exchanged the conserved glutamate in NuoM for a lysine residue, introducing charge symmetry in the membrane arm. The stably assembled variant pumps protons across the membrane, but with a diminished H+/e- stoichiometry of 1.5. Thus, charge asymmetry is not essential for proton translocation by complex I, casting doubts on the suggestion of an asynchronous operation of NuoL, NuoM, and NuoN. Furthermore, our data emphasize the importance of a balanced charge distribution in the protein for directional proton transfer.

Acoustic Modulation Enables Proton Detection With Nanodroplets at Body Temperature.

Superheated nanodroplet (ND) vaporization by proton radiation was recently demonstrated, opening the door to ultrasound-based in vivo proton range verification. However, at body temperature and physiological pressures, perfluorobutane nanodroplets (PFB-NDs), which offer a good compromise between stability and radiation sensitivity, are not directly sensitive to primary protons. Instead, they are vaporized by infrequent secondary particles, which limits the precision for range verification. The radiation-induced vaporization threshold (i.e., sensitization threshold) can be reduced by lowering the pressure in the droplet such that ND vaporization by primary protons can occur. Here, we propose to use an acoustic field to modulate the pressure, intermittently lowering the proton sensitization threshold of PFB-NDs during the rarefactional phase of the ultrasound wave. Simultaneous proton irradiation and sonication with a 1.1 MHz focused transducer, using increasing peak negative pressures (PNPs), were applied on a dilution of PFB-NDs flowing in a tube, while vaporization was acoustically monitored with a linear array. Sensitization to primary protons was achieved at temperatures between [Formula: see text] and 40 °C using acoustic PNPs of relatively low amplitude (from 800 to 200 kPa, respectively), while sonication alone did not lead to ND vaporization at those PNPs. Sensitization was also measured at the clinically relevant body temperature (i.e., 37 °C) using a PNP of 400 kPa. These findings confirm that acoustic modulation lowers the sensitization threshold of superheated NDs, enabling a direct proton response at body temperature.

Femtosecond-to-millisecond mid-IR spectroscopy of photoactive yellow protein uncovers structural micro-transitions of the chromophore's protonation mechanism.

Protein structural dynamics can span many orders of magnitude in time. Photoactive yellow protein's (PYP) reversible photocycle encompasses picosecond isomerization of the light-absorbing chromophore as well as large scale protein backbone motions occurring on a millisecond timescale. Femtosecond-to-millisecond time-resolved mid-infrared spectroscopy is employed here to uncover structural details of photocycle intermediates up to chromophore protonation and the first structural changes leading to the formation of the partially unfolded signaling state pB. The data show that a commonly thought stable transient photocycle intermediate is actually formed after a sequence of several smaller structural changes. We provide residue-specific spectroscopic evidence that protonation of the chromophore on a few hundreds of microseconds timescale is delayed with respect to deprotonation of the nearby E46 residue. That implies that the direct proton donor is not E46 but most likely a water molecule. Such details may assist the ongoing photocycle and protein folding simulation efforts on the complex and wide time-spanning photocycle of the model system PYP.

Theoretical Insights into Enantioselective [3 + 2] Cycloaddition between Cinnamaldehyde and Cyclic N-Sulfonyl Trifluoromethylated Ketimine Catalyzed by N-Heterocyclic Carbene.

The density functional theory (DFT) method was used to investigate the mechanism and the origin of stereoselectivity of N-heterocyclic carbene (NHC)-catalyzed [3 + 2] cycloaddition between enals and cyclic imine N-sulfonyl trifluoromethyl ketimines at the M06-2X/SMD/6-311+G(d,p)//M06-2X/SMD/6-31G (d,p) level. The results show that the favorable reaction path consists of five steps: nucleophilic attack, proton transfer, the formation of the C-C bond, the tautomerism of the enol intermediate, the formation of the five-membered ring, and the regeneration of the catalyst. For the process of proton transfer, the base-assisted reaction can reduce the activation free energy and make the reaction easier to occur compared with the direct proton transfer process. The formation of the C-C bond is the crucial step of stereoselectivity, in which two chiral centers and four configurations of intermediates (RR/RS/SR/SS) were generated. The free energy barriers obtained and the noncovalent interaction analysis confirm that the dominant configuration is SS, becoming the final trans-type product observed in experiment. Furthermore, through the analyses of the conceptual DFT and natural atomic charges, it is revealed that NHC acts as a double catalyst, which can not only increase the nucleophilicity of reactants by Lewis base but also activate the C-H bond and promote the proton transfer process. The understanding of the mechanism obtained in this study should be helpful to the other organic catalytic reactions with high stereoselectivity.

A Computational Study on the Photochemical O-H Functionalization of Alcohols with Diazoacetates.

In this computational study, we provide a detailed analysis of the underlying reaction mechanism and show that a singlet carbene is initially formed. Depending on the pKA of the alcohol, this singlet carbene can engage in direct protonation or enol formation to yield the O-H functionalization product. On the contrary, propargylic alcohols take up a dual role and form a complex with the carbene intermediate that leads to facile cyclopropenation reactions.

A density functional theory study on the mechanism of simultaneous trifluoromethylation and oximation of aryl-substituted ethylenes

The effects of different substituents, located at the para position of the aromatic ring and at the β-carbon atom of styrenes, on difunctionalizations involving trifluoromethylation and oxime formation are investigated, showing that the difunctionalization reaction has a good adaptability to such reactants containing a range of substituents. This is important in the actual production process. It was found that proton transfer in the final tautomerism step involving transformation of a nitroso intermediate into an oxime is the rate-limiting step. The solvent effect did not influence the rate-limiting step significantly. Compared with direct proton transfer in a vacuum, the energy barrier of the final tautomerism step decreased from 57.80 kcal mol−1 in vacuum to 12.98 kcal mol−1 in water occurring via mediated proton transfer, which declines by 77.5%. When water participates in the rate-limiting steps in organic solvents, the energy barrier also decreases significantly, which indicates that a small amount of water in the organic solvent is conducive to the reaction.

Generation of polarized proton beams with gaseous targets from CO2-laser-driven collisionless shock acceleration

We propose obtaining polarized proton beams based on CO2-laser-driven collisionless shock acceleration (CSA) of the pre-polarized HCl gas. By tailoring the density profile of the pre-polarized HCl gas, the intense CO2 laser pulse heats the plasma target and forms a strong shock that reflects the polarized protons to high energy. According to particle-in-cell simulations implemented with the spin dynamics, directional proton beams of several MeV were generated at a total beam polarization of over 80%. Simulations showed that proton spin precession occurred in the azimuthal magnetic fields generated by the Biermann effect and plasma currents. The latter was the main depolarization mechanism in the early stage of shock wave formation. For CSA at CO2 laser intensities around 1017–1018 W/cm2, the proton depolarization was insignificant and the beam polarization purity was preserved. As pre-polarized hydrogen targets were available at gaseous densities in-state-of-art facilities, CSA driven by relatively long wavelength lasers provided a feasible solution for obtaining ultra-fast polarized proton sources.

Enhanced In Vitro Antiviral Activity of Hydroxychloroquine Ionic Liquids against SARS-CoV-2.

The development of effective antiviral drugs against SARS-CoV-2 is urgently needed and a global health priority. In light of the initial data regarding the repurposing of hydroxychloroquine (HCQ) to tackle this coronavirus, herein we present a quantitative synthesis and spectroscopic and thermal characterization of seven HCQ room temperature ionic liquids (HCQ-ILs) obtained by direct protonation of the base with two equivalents of organic sulfonic, sulfuric and carboxylic acids of different polarities. Two non-toxic and hydrophilic HCQ-ILs, in particular, [HCQH2][C1SO3]2 and [HCQH2][GlcCOO]2, decreased the virus-induced cytopathic effect by two-fold in comparison with the original drug, [HCQH2][SO4]. Despite there being no significant differences in viral RNA production between the three compounds, progeny virus production was significantly affected (p < 0.05) by [HCQH2][GlcCOO]2. Overall, the data suggest that the in vitro antiviral activities of the HCQ-ILs are most likely the result of specific intra- and intermolecular interactions and not so much related with their hydrophilic or lipophilic character. This work paves the way for the development of future novel ionic formulations of hydroxychloroquine with enhanced physicochemical properties.

Interdisciplinary Methods for Zoonotic Tissue Acellularization for Natural Heart Valve Substitute of Biomimetic Materials.

The goal of this work was to create a bioactive tissue-based scaffold using multi-disciplinary engineering materials and tissue engineering techniques. Materials & methods: Physical techniques such as direct laser interference lithography and proton radiation were selected as alternative methods of enzymatic and chemical decellularization to remove cells from a tissue without degradation of the extracellular matrix nor its protein structure. This study was an attempt to prepare a functional scaffold for cell culture from tissue of animal origin using new physical methods that have not been considered before. The work was carried out under full control of the histological and molecular analysis. Results & conclusions: The most important finding was that the physical methods used to obtain the decellularized tissue scaffold differed in the efficiency of cell removal from the tissue in favour of the laser method. Both the laser method and the proton method exhibited a destructive effect on tissue structure and the genetic material in cell nuclei. This effect was visible on histology images as blurred areas within the cell nucleus. The finite element 3D simulation of decellularization process of the three-layer tissue of animal origin sample reflected well the mechanical response of tissue described by hyperelastic material models and provided results comparable to the experimental ones.

Ultrahigh proton conductive nanofibrous composite membrane with an interpenetrating framework and enhanced acid-base interfacial layers for vanadium redox flow battery

Sulfonated poly(ether ether ketone)-based membranes containing amphoteric functionalized nanofibrous network (SP@f) with the three-dimensional interlaced structure were developed, and the acid-base interaction between SP@f and SPEEK constructs highly conductive proton channel and compatible interfaces. The large specific surface area and aspect ratio of nanofibers afford an orientated ion transmission channel along the fiber axis, bringing a high concentration of proton carriers and abundant hydrogen bonds to transfer proton. The S/SP@f-10 composite membrane displays superior proton conductivity (37.8 mS cm −1 ) to pristine SPEEK (16.4 mS cm −1 ) and Nafion 212 (28.0 mS cm −1 ). Owing to the interconnected network structure of SP@f and the acid-base interactions, ion selectivity and chemical stability of the S/SP@f-10 composite membranes improve seriously. VRFB single cell with S/SP@f-10 membrane shows better voltage efficiencies (VE: 93.0–74.0%) and energy efficiencies (EE: 87.5–73.0%) than that of pristine SPEEK (VE: 86.0–60.2%, EE: 82.1–58.0%) and Nafion 212 membrane (VE: 88.0–67.0%, EE: 80.0–63.9%) at 60–200 mA cm −2 . Meanwhile, S/SP@f-10 maintains a stable EE value of 80.0%, and no obvious decay after 500 cycles at 150 mA cm −2 appears, demonstrating its outstanding structural stability and durability. This opens a facile method to prepare the high-performance membrane by constructing the directional proton channels with functionalized nanofibers. To solve the tradeoffs between ion selectivity and conductivity, amphoteric functionalized nanofibrous network along with an orientated ion channel was constructed, and the interface layer occupied with acid-base pairs generates good structural stability, chemical stability and excellent VRFB performance. • Amphoteric functionalized nanofibrous network (SP@f) contains 3D interlaced structure. • Nanofiber interface layer formed by acid-base pairs provides high concentration of proton carriers. • Ultra-high proton conduction depends upon the long and continuous proton transport channel. • S/SP@f-10 membrane shows outstanding battery efficiencies and long-term cycle stability.

Low Voltage Voltammetry Probes Proton Dissociation Equilibria of Amino Acids and Peptides

Platinum-catalyzed electrochemical reduction of dissociable protons at low potentials was used to investigate proton dissociation equilibria of freely diffusing and peptide-incorporated charged amino acids. We first demonstrate with five charged essential amino acids and their analogs that the electrochemically induced deprotonation of each amino acid occurs at distinct formal reduction potential. Moreover, the observed direct reduction for all the charged species, excluding arginine, occurs at low potentials suitable for investigation under aqueous conditions (-0.4 to -0.9 V vs Ag/AgCl). The direct proton reduction was resolved via deconvolution of the observed differential pulse voltammogram (DPV) from background hydronium reduction and water electrolysis. A linear correlation was found between the formal reduction potentials and the pKa values of the dissociable protons hosted by various molecular moieties in the amino acids and their analogs and further verified with tripeptides. DPV of poly(l-lysine) decamer (Lys10) distinctively resolved the pKa values of the amino groups in the side chains and N-terminus, at a resolution not possible by conventional acid-base titration. This work demonstrates selective electrochemical titration of dissociable protons in charged amino acids in the free state and as residues in biomolecules, as well as the utility of DPV to indirectly interrogate local electrostatic environments that are essential to the stability and function of biomolecules.

Oriented Nanoarchitectonics of Bacteriorhodopsin for Enhancing ATP Generation in a FoF1‐ATPase‐Based Assembly System

AbstractEnergy conversion plays an important role in the metabolism of photosynthetic organisms. Improving energy transformation by promoting a proton gradient has been a great challenge for a long time. In the present study, we realize a directional proton migration through the construction of oriented bacteriorhodopsin (BR) microcapsules coated by FoF1‐ATPase molecular motors through layer‐by‐layer (LBL) assembly. The changes in the conformation of BR under illumination lead to proton transfer in a radial direction, which generates a higher proton gradient to drive the synthesis of adenosine triphosphate (ATP) by FoF1‐ATPase. Furthermore, to promote the photosynthetic activity, optically matched quantum dots were introduced into the artificial coassembly system of BR and FoF1‐ATPase. Such a design creates a new path for the use of light energy.

Oriented Nanoarchitectonics of Bacteriorhodopsin for Enhancing ATP Generation in a Fo F1 -ATPase-Based Assembly System.

Energy conversion plays an important role in the metabolism of photosynthetic organisms. Improving energy transformation by promoting a proton gradient has been a great challenge for a long time. In the present study, we realize a directional proton migration through the construction of oriented bacteriorhodopsin (BR) microcapsules coated by Fo F1 -ATPase molecular motors through layer-by-layer (LBL) assembly. The changes in the conformation of BR under illumination lead to proton transfer in a radial direction, which generates a higher proton gradient to drive the synthesis of adenosine triphosphate (ATP) by Fo F1 -ATPase. Furthermore, to promote the photosynthetic activity, optically matched quantum dots were introduced into the artificial coassembly system of BR and Fo F1 -ATPase. Such a design creates a new path for the use of light energy.

Performance of proton exchange membrane fuel cell integrated with direct contact membrane distillation for electricity and fresh water productions

This paper develops a new hybrid system composed of direct contact membrane distillation (DCMD) and proton exchange membrane fuel cell (PEMFC), which generates fresh water from brine by utilizing waste heat from the PEMFC to improve the system energy efficiency. The mathematical model of the hybrid PEMFC-DCMD system is established to explore the influence of feed inlet temperature, feed and permeate inlet flow rates of DCMD on the hybrid system performance. To achieve the optimal system performance, the genetic algorithm (GA) is used to search for the optimal feed and permeate inlet flow rates of DCMD with the transmembrane water flux as the objective function. The optimization results illustrate that transmembrane water flux of DCMD is 15.24 kg/(m2·h), while feed and permeate inlet flow rates are 1.83 L/min and 8.98 L/min. In addition, the optimal overall energy efficiency of the proposed system is 72.96%, which is increased by 54.48% compared with a single PEMFC system.

Solvated Nuclear-Electronic Orbital Structure and Dynamics.

Nonadiabatic dynamical processes such as proton-coupled electron transfer and excited state intramolecular proton transfer have been the subject of much research. One of the promising theoretical methods to describe these processes is the nuclear-electronic orbital (NEO) approach. This approach inherently accounts for nuclear quantum effects within quantum chemistry calculations, and it has recently been extended to directly simulate nonadiabatic processes with the development of real-time NEO methods. These processes can also be significantly dependent on the surrounding chemical environment, however, and capturing the effects of the environment is often necessary for analyzing experimentally relevant systems. This work couples the NEO density functional theory and real-time time-dependent density functional theory approaches with solvation through the polarizable continuum model. The effects of this coupling are investigated for ground state properties, solvent-dependent vibrational frequencies, and direct excited state intramolecular proton transfer dynamics.