Proton Motion Research Articles

Forward-backward electron–proton asymmetry from a two-photon crossing of diabatic states of H[formula omitted] in linearly polarized intense laser field

Controlling spatial–temporal overlap between nuclear wave packets propagating on the coupled electronic states with opposite parity by intense laser field leads to a π periodic modulation in the symmetry breaking of the coupled forward–backward electron and proton motions. The most probable directionality of electron and proton moving simultaneously in opposite directions with total electron–proton asymmetry parameter Ae−ptot=0.62 occurs at fixed carrier-envelope phases of ϑ=15° and 195°. Analysis of the time evolution of the nuclear and the electronic-nuclear wave packets on the field-dressed potentials gives rise to newly insightful images of the nonlinear nonperturbative processes for the asymmetrical localization.

Proton transfer reactions: From photochemistry to biochemistry and bioenergetics

The present Review is an attempt by projecting the basic knowledge on photochemical proton transfer to achieve consistent understanding of proton motions in biocatalysis, photobiocatalysis, operation of selective proton channels and systems of photosynthesis and cellular respiration. The basic mechanisms of proton transfer are in active research in the electronic excited states of organic molecules. This allows observing the reactions directly in real time, providing their dynamic and thermodynamic description and coupling with structural and energetic variables. These achievements lay the background for understanding the proton transfers in biochemical reactions, where such ultrafast events are not only ‘optically silent’ but are hidden under much slower rate-limiting steps, such as protein conformational changes, substrate binding and product release. The mechanistic description of biocatalytic and transmembrane proton transport is shown as a multi-step proton migration that is available for modeling in photochemical reactions. For explaining the formation of transmembrane proton gradients, a simple ‘proton lift’ concept is presented that may be the basis of further research and analysis.

Dielectric ordering of water molecules in the dipole lattice of potassium hexacyanoferrate(II) trihydrate

The structure of potassium hexacyanoferrate(II) trihydrate (yellow prussiate) contains layers of water molecules between the layers of potassium and ferrocyanide octahedra. When the temperature drops down to 120 K, the water molecules have a tendency to rearrange. The movement of protons in molecular and individual rings occurs in a coordinated manner. The asymmetry of the ring environment leads to a significant decrease of the double-well potential barrier. The theory of coherent correlated motions of protons allows to explain the discreteness of the observed temperature anomalies of dielectric permittivity ε, thermally stimulated depolarization current j, and pyroelectric coefficient γ.

Ultrafast Charge Relocation Dynamics in Enol-Keto Tautomerization Monitored with a Local Soft-X-ray Probe.

Proton-coupled electron transfer (PCET) is the underlying mechanism governing important reactions ranging from water splitting in photosynthesis to oxygen reduction in hydrogen fuel cells. The interplay of proton and electronic charge distribution motions can vary from sequential to concerted schemes, with elementary steps occurring on ultrafast time scales. We demonstrate with a simulation study that femtosecond soft-X-ray spectroscopy provides key insights into the PCET mechanism of a photoinduced intramolecular enol* → keto* tautomerization reaction. A full quantum treatment of the electronic and nuclear dynamics of 2-(2′-hydroxyphenyl)benzothiazole upon electronic excitation reveals how spectral signatures of local excitations from core to frontier orbitals display the distinctly different stages of charge relocation for the H atom, donating, and accepting sites. Our findings indicate that ultraviolet/X-ray pump-probe spectroscopy provides a unique way to probe ultrafast electronic structure rearrangements in photoinduced chemical reactions essential to understanding the mechanism of PCET.

ДРЕЙФОВЫЕ ЭФФЕКТЫ ГЕОМАГНИТНЫХ ПУЛЬСАЦИЙ УЛЬТРАНИЗКОЧАСТНОГО ДИАПАЗОНА

Previously, when analyzing ULF variations of the natural electromagnetic fi according to observations in the Borok and Mondy observatories, separated by 60 degrees of longitude, longitudinal effects of geomagnetic Pc1 pulsations («pearls») were revealed. The effects were manifested themselves as a delay or advance of the beginning of the coherent Pc1 series in Borok in relation to their observation at the Mondy observatory. In 63% and 37% of cases, pulsations in Borok began later and before their detection at the Mondy observatory, respectively. The delay-advance time varied in the range from few minutes to one hour. A hypothesis is proposed about the nature of the revealed phenomenon, which directly associates these longitudinal effects with the drift motion of ring current particles, protons and antiprotons, as the source of pulsations, in the western and eastern direction, respectively. Examples illustrating the revealed effects are given. The assumption is qualitatively and quantitatively assessed.

Protons in Gating the Kv1.2 Channel: A Calculated Set of Protonation States in Response to Polarization/Depolarization of the Channel, with the Complete Proposed Proton Path from Voltage Sensing Domain to Gate.

We have in the past proposed that proton motion constitutes the gating current in the potassium channel Kv1.2 and is responsible for the gating mechanism. For this to happen, there must be a proton path between the voltage-sensing domain (VSD) and the channel gate, and here we present quantum calculations that lead to a specific pair of proton paths, defined at the molecular level, with well-defined water molecule linkages, and with hydrogen bonding between residues; there is also at least one interpath crossover, where protons can switch paths. Quantum calculations on the entire 563-atom system give the complete geometry, the energy, and atomic charges. Calculations show that three specific residues (in the pdb 3Lut numbering, H418, E327, R326), and the T1 intracellular moiety, all of which have been shown experimentally to be involved in gating, would necessarily be protonated or deprotonated in the path between the VSD and the gate. Hydroxyl reorientation of serine and threonine residues are shown to provide a means of adjusting proton directions of motion. In the deprotonated state for K312, a low energy state, our calculations come close to reproducing the X-ray structure. The demonstration of the existence of a double proton path between VSD and gate supports the proposed proton gating mechanism; when combined with our earlier demonstration of proton generation in the VSD, and comparison with other systems that are known to move protons, we are close to achieving the definition of a complete gating mechanism in molecular detail. The coupling of the paths to the VSD, and to the PVPV section that essentially forms the gate, can be easily seen from the results of the calculation. The gate itself remains for further computations.

Some differences in turnover kinetics of penams and cephems catalyzed by classes A and C ?-lactamases

The differences in the kinetic mechanism of catalysis of class A and class C ?-lactamases are shown by the manner by which these enzymes catalyze the hydrolyses of the penicillins and the cephalosporins. The hydrolysis of cephalosporins that are good substrates of the class C P99 ?-lactamase, where deacylation of an acyl-enzyme intermediate is rate-determining, has been shown to involve a free enzyme isoform (Adediran et al, 2021). We describe here how reconversion of this isoform to the native enzyme is accelerated by bases (e.g. imidazole) and salts (e. g. sodium chloride). The hydrolysis of penicillins by the P99 enzyme, where deacylation is also rate-determining, is not affected by imidazole and sodium chloride, a result that suggests that an enzyme isoform does not accumulate as an intermediate in turnover of this class of substrate. In support of these conclusions, solvent deuterium kinetic isotope effects on kcat values were changed by the presence of imidazole for turnover of cephalothin by the P99 enzyme but unaffected for benzylpenicillin turnover. The hydrolyses of cephalosporins and penicillins by the class A TEM-2 ?-lactamase were not affected by imidazole and sodium chloride and thus also may not involve an accumulating free enzyme isoform. Solvent deuterium kinetic isotope effects and proton inventories on the class A PC1 and P99 ?-lactamase-catalyzed hydrolyses of benzylpenicillin at saturating concentrations showed the deacylation transition states of these two classes of enzymes to be different with respect to proton motion.

Ultrafast charge transfer coupled to quantum proton motion at molecule/metal oxide interface.

Understanding how the nuclear quantum effects (NQEs) in the hydrogen bond (H-bond) network influence the photoexcited charge transfer at semiconductor/molecule interface is a challenging problem. By combining two kinds of emerging molecular dynamics methods at the ab initio level, the path integral-based molecular dynamics and time-dependent nonadiabatic molecular dynamics, and choosing CH3OH/TiO2 as a prototypical system to study, we find that the quantum proton motion in the H-bond network is strongly coupled with the ultrafast photoexcited charge dynamics at the interface. The hole trapping ability of the adsorbed methanol molecule is notably enhanced by the NQEs, and thus, it behaves as a hole scavenger on titanium dioxide. The critical role of the H-bond network is confirmed by in situ scanning tunneling microscope measurements with ultraviolet light illumination. It is concluded the quantum proton motion in the H-bond network plays a critical role in influencing the energy conversion efficiency based on photoexcitation.

Ab Initio Study of the Mechanism of Proton Migration in Perovskite LaScO3

The mechanism of proton motion in a LaScO3 perovskite crystal was studied by ab initio molecular dynamics. The calculations were performed at different temperatures, locations, and initial velocity of the proton. Different magnitudes and directions of the external electric field were also considered. It is shown that initial location and interaction between proton and its nearest environment are of great importance to the character of the proton movement, while the magnitude and direction of the initial velocity and electric field strength are secondary factors characterizing its movement through the LaScO3 crystal. Four types of proton-jumping between oxygen atoms are determined and the probability of each of them is established. Energy barriers and characteristic times of these jumps are determined. The probable distances from a proton to other types of atoms present in perovskite are calculated. It is shown that the temperature determines, to a greater extent, the nature of the motion of a proton in a perovskite crystal than the magnitude of the external electric field. The distortion of the crystal lattice and its polarization provoke the formation of a potential well, which determines the path for the proton to move and its mobility in the perovskite crystal.

Effect of density gradients on the generation of a highly energetic and strongly collimated proton beam from a laser-irradiated Gaussian-shaped hydrogen microsphere

An investigation is made on the influence of the sharpness of the density gradients on the generation of energetic protons in a radially Gaussian density profile of a spherical hydrogen plasma. It is possible to create such density gradients by impinging a solid density target with a secondary lower intensity pulse, which ionizes the target and explodes it to create an expanded plasma target of lower effective density for the high-intensity main pulse to hit on. The density gradients are scanned in the near-critical regime, and separate regimes of proton motion are identified based on the density sharpness. An intermediate-density gradient [npeak≈(1.5–2.5)γnc] favors the generation of high energetic protons with narrow energy spectra that are emitted with better collimation from the target rear surface. Protons with energies exceeding 100 MeVs could be achieved using such modified plasma targets with circularly polarized lasers of peak intensities I0∼1020 W cm−2 and peak energy ∼10 J.

The reorientation of protonic defects in barium zirconate: Low-temperature tunneling regime and transition to the adiabatic regime

In most proton-conducting oxides, proton conductivity is mediated by a Grotthuss-like mechanism, i.e. the succession of transfers, in which the proton jumps from an oxygen onto another (breaking, and then reforming an ionocovalent hydroxyl bond OH), and reorientations, in which the OH bond simply rotates without breaking. We focus in this work on this second step, i.e. the reorientation of the protonic defect, in barium zirconate, one of the most promising proton-conducting oxides. Considered alone, the rotations of a proton are responsible for a rotational diffusion of this proton around a given oxygen atom. The reorientation of the protonic defect, like transfer, is strongly affected by the quantum effects associated with the protonic motions, and can only take place thanks to two specific lattice vibrations: (i) a reorganization, that symmetrizes the proton potential and puts the proton levels in the initial and final wells in coincidence, and (ii) the increase of the separation between the protonated oxygen and the nearest neighbor barium atom (that forms an obstacle to the reorientation of the protonic defect). The former (necessary step) mostly consists in rotations of the two oxygen octahedra sharing the protonated oxygen, while the latter (facilitating step) helps to overcome the proton‑barium electrostatic repulsion and lowers the proton barrier. We show that the reorientation of the protonic defect in barium zirconate undergoes a transition at about 220 K between a low-temperature and a high-temperature regime. Below ∼ 220 K, it is governed by tunneling, with a reorientation rate having an activation energy of 0.09 eV and a prefactor of ∼ 0.4 THz, due to quasi-non-adiabatic transitions between coincident protonic ground states (GS → GS), and involving an effective proton coupling of 5.7 meV. Above 220 K, two additional contributions, corresponding to transitions between the first excited protonic state (1st) in one of the two wells, and the protonic ground state (GS) in the other well, become dominant. These asymmetric transitions (1st → GS and GS → 1st) are quasi-adiabatic, and their rates are associated with an activation energy of 0.14 eV and a prefactor of 1.7 THz. The contribution due to adiabatic symmetric transitions between first excited protonic states (1st → 1st) should become equivalent to each of the asymmetric ones only at high temperature (above 900 K).

Characterizing Protein Protonation Microstates Using Monte Carlo Sampling.

Proteins are polyelectrolytes with acidic and basic amino acids Asp, Glu, Arg, Lys, and His, making up ≈25% of the residues. The protonation state of residues, cofactors, and ligands defines a "protonation microstate". In an ensemble of proteins some residues will be ionized and others neutral, leading to a mixture of protonation microstates rather than in a single one as is often assumed. The microstate distribution changes with pH. The protein environment also modifies residue proton affinity so microstate distributions change in different reaction intermediates or as ligands are bound. Particular protonation microstates may be required for function, while others exist simply because there are many states with similar energy. Here, the protonation microstates generated in Monte Carlo sampling in MCCE are characterized in HEW lysozyme as a function of pH and bacterial photosynthetic reaction centers (RCs) in different reaction intermediates. The lowest energy and highest probability microstates are compared. The ΔG, ΔH, and ΔS between the four protonation states of Glu35 and Asp52 in lysozyme are shown to be calculated with reasonable precision. At pH 7 the lysozyme charge ranges from 6 to 10, with 24 accepted protonation microstates, while RCs have ≈50,000. A weighted Pearson correlation analysis shows coupling between residue protonation states in RCs and how they change when the quinone in the QB site is reduced. Protonation microstates can be used to define input MD parameters and provide insight into the motion of protons coupled to reactions.

Unveiling the two-proton halo character of 17Ne: Exclusive measurement of quasi-free proton-knockout reactions

The proton drip-line nucleus 17Ne is investigated experimentally in order to determine its two-proton halo character. A fully exclusive measurement of the 17Ne(p,2p)16F→15⁎O+p quasi-free one-proton knockout reaction has been performed at GSI at around 500 MeV/nucleon beam energy. All particles resulting from the scattering process have been detected. The relevant reconstructed quantities are the angles of the two protons scattered in quasi-elastic kinematics, the decay of 16F into 15O (including γ decays from excited states) and a proton, as well as the 15O+p relative-energy spectrum and the 16F momentum distributions. The latter two quantities allow an independent and consistent determination of the fractions of l=0 and l=2 motion of the valence protons in 17Ne. With a resulting relatively small l=0 component of only around 35(3)%, it is concluded that 17Ne exhibits a rather modest halo character only. The quantitative agreement of the two values deduced from the energy spectrum and the momentum distributions supports the theoretical treatment of the calculation of momentum distributions after quasi-free knockout reactions at high energies by taking into account distortions based on the Glauber theory. Moreover, the experimental data allow the separation of valence-proton knockout and knockout from the 15O core. The latter process contributes with 11.8(3.1) mb around 40% to the total proton-knockout cross section of 30.3(2.3) mb, which explains previously reported contradicting conclusions derived from inclusive cross sections.

Universal trend of charge radii of even-even Ca–Zn nuclei

Radii of nuclear charge distributions carry information about the strong and electromagnetic forces acting inside the atomic nucleus. While the global behavior of nuclear charge radii is governed by the bulk properties of nuclear matter, their local trends are affected by quantum motion of proton and neutron nuclear constituents. The measured differential charge radii $\delta\langle r^2_c\rangle$ between neutron numbers $N=28$ and $N=40$ exhibit a universal pattern as a function of $n=N-28$ that is independent of the atomic number. Here we analyze this remarkable behavior in even-even nuclei from calcium to zinc using two state-of-the-art theories based on quantified nuclear interactions: the ab-initio coupled cluster theory and nuclear density functional theory. Both theories reproduce the smooth rise of differential charge radii and their weak dependence on the atomic number. By considering a large set of isotopic chains, we show that this trend can be captured by just two parameters: the slope and curvature of ${\delta\langle r^2_c\rangle(n)}$. We demonstrate that these parameters show appreciable model dependence, and the statistical analysis indicates that they are not correlated with any single model property, i.e., they are impacted by both bulk nuclear properties as well as shell structure.

On the anomalous diffusion of proton in Y-doped BaZrO3 perovskite oxide

Proton transport in perovskite oxides (ABO3) is a complex dynamical process involving hydroxide ion rotation and proton transfer. Combining ab initio molecular dynamics (AIMD) and machine-learning molecular dynamics (MLMD) simulations of proton dynamics in Y-doped BaZrO3 perovskite oxide, we systematically illustrate the anomalous characteristics of proton motion. At short times, proton performs superdiffusion through the OH wag and proton transfer. At intermediate times, the larger rotation angle results in the larger plateau value. At longer times, proton diffusion first becomes subdiffusive due to the hydroxide ion rotations then gradually turns to normal diffusion. A theoretical model is also offered to quantitatively describe this abnormal proton diffusion. In all, this work provides a more complete understanding of proton dynamics in perovskite oxides.

Determinants of Directionality and Efficiency of the ATP Synthase Fo Motor at Atomic Resolution.

Fo subcomplex of ATP synthase is a membrane-embedded rotary motor that converts proton motive force into mechanical energy. Despite a rapid increase in the number of high-resolution structures, the mechanism of tight coupling between proton transport and motion of the rotary c-ring remains elusive. Here, using extensive all-atom free energy simulations, we show how the motor’s directionality naturally arises from the interplay between intraprotein interactions and energetics of protonation of the c-ring. Notably, our calculations reveal that the strictly conserved arginine in the a-subunit (R176) serves as a jack-of-all-trades: it dictates the direction of rotation, controls the protonation state of the proton-release site, and separates the two proton-access half-channels. Therefore, arginine is necessary to avoid slippage between the proton flux and the mechanical output and guarantees highly efficient energy conversion. We also provide mechanistic explanations for the reported defective mutations of R176, reconciling the structural information on the Fo motor with previous functional and single-molecule data.

Relationship between apparent diffusion coefficient value of the bone marrow and cortical width of the mandible in the healthy patients

ObjectivesDiffusion-weighted imaging (DWI) is a technique reflecting motion of water proton within the tissue. Studies have investigated the apparent diffusion coefficient (ADC) of bone marrow in musculoskeletal lesions. This study assessed the correlation between the ADC of bone marrow in the mandible and the mandibular cortical width (MCW) in the healthy patients. MethodsThis research was a retrospective cohort study. The patient underwent echo planar (EPI)-DWI and panoramic X-ray at the Nihon University School of Dentistry between April 2020 and October 2020. The predictor variable was mean MCW. The primary outcome variable was the mean ADC of mandibular bone marrow. The other variable was age. Data were analyzed using a Mann-Whitney U test, Spearman’s correlation coefficient. Statistical significance was set at p < 0.05. ResultsWe analyzed the records of 18 men (mean age, 44.94, age range 20–73 years) and 40 women (mean age, 47.98, age range 21–78 years). There was not significant difference between sex and mean ADC value, mean MCW (p = 0.853 and p= 0.43, respectively). There was a significant positive correlation between MCW and the ADC of the mandibular bone marrow (r = .493, p < 0.001). ConclusionsThis suggests that in addition to evaluating the MCW, which is currently used for bone quality evaluation, measuring the ADC of bone marrow in the mandible could contribute toward the examination of bone quality and diseases.

Elucidating Inner Workings of Naturally Sourced Organic Optoelectronic Materials with Ultrafast Spectroscopy.

Recent advances in sustainable optoelectronics including photovoltaics, light-emitting diodes, transistors, and semiconductors have been enabled by π-conjugated organic molecules. A fundamental understanding of light-matter interactions involving these materials can be realized by time-resolved electronic and vibrational spectroscopies. In this Minireview, the photoinduced mechanisms including charge/energy transfer, electronic (de)localization, and excited-state proton transfer are correlated with functional properties encompassing optical absorption, fluorescence quantum yield, conductivity, and photostability. Four naturally derived molecules (xylindein, dimethylxylindein, alizarin, indigo) with ultrafast spectral insights showcase efficient energy dissipation involving H-bonding networks and proton motions, which yield high photostability. Rational design principles derived from such investigations could increase the efficiency for light harvesting, triplet formation, and photosensitivity for improved and versatile optoelectronic performance.

Graph-Theory-Based Molecular Fragmentation for Efficient and Accurate Potential Surface Calculations in Multiple Dimensions.

We present a multitopology molecular fragmentation approach, based on graph theory, to calculate multidimensional potential energy surfaces in agreement with post-Hartree-Fock levels of theory but at the density functional theory cost. A molecular assembly is coarse-grained into a set of graph-theoretic nodes that are then connected with edges to represent a collection of locally interacting subsystems up to an arbitrary order. Each of the subsystems is treated at two levels of electronic structure theory, the result being used to construct many-body expansions that are embedded within an ONIOM scheme. These expansions converge rapidly with the many-body order (or graphical rank) of subsystems and capture many-body interactions accurately and efficiently. However, multiple graphs, and hence multiple fragmentation topologies, may be defined in molecular configuration space that may arise during conformational sampling or from reactive, bond breaking and bond formation, events. Obtaining the resultant potential surfaces is an exponential scaling proposition, given the number of electronic structure computations needed. We utilize a family of graph-theoretic representations within a variational scheme to obtain multidimensional potential surfaces at a reduced cost. The fast convergence of the graph-theoretic expansion with increasing order of many-body interactions alleviates the exponential scaling cost for computing potential surfaces, with the need to only use molecular fragments that contain a fewer number of quantum nuclear degrees of freedom compared to the full system. This is because the dimensionality of the conformational space sampled by the fragment subsystems is much smaller than the full molecular configurational space. Additionally, we also introduce a multidimensional clustering algorithm, based on physically defined criteria, to reduce the number of energy calculations by orders of magnitude. The molecular systems benchmarked include coupled proton motion in protonated water wires. The potential energy surfaces and multidimensional nuclear eigenstates obtained are shown to be in very good agreement with those from explicit post-Hartree-Fock calculations that become prohibitive as the number of quantum nuclear dimensions grows. The developments here provide a rigorous and efficient alternative to this important chemical physics problem.

1H NMR Study of the HCa2Nb3O10 Photocatalyst with Different Hydration Levels.

The photocatalytic activity of layered perovskite-like oxides in water splitting reaction is dependent on the hydration level and species located in the interlayer slab: simple or complex cations as well as hydrogen-bonded or non-hydrogen-bonded H2O. To study proton localization and dynamics in the HCa2Nb3O10·yH2O photocatalyst with different hydration levels (hydrated—α-form, dehydrated—γ-form, and intermediate—β-form), complementary Nuclear Magnetic Resonance (NMR) techniques were applied. 1H Magic Angle Spinning NMR evidences the presence of different proton containing species in the interlayer slab depending on the hydration level. For α-form, HCa2Nb3O10·1.6H2O, 1H MAS NMR spectra reveal H3O+. Its molecular motion parameters were determined from 1H spin-lattice relaxation time in the rotating frame (T1ρ) using the Kohlrausch-Williams-Watts (KWW) correlation function with stretching exponent β = 0.28: eV, s. For the β-form, HCa2Nb3O10·0.8H2O, the only 1H NMR line is the result of an exchange between lattice and non-hydrogen-bonded water protons. T1ρ(1/T) indicates the presence of two characteristic points (224 and 176 K), at which proton dynamics change. The γ-form, HCa2Nb3O10·0.1H2O, contains bulk water and interlayer H+ in regular sites. 1H NMR spectra suggest two inequivalent cation positions. The parameters of the proton motion, found within the KWW model, are as follows: eV, s.