Proton Dynamics Research Articles

Exploring non-equilibrium molecular dynamics of mobile protons in the solid acid CsH2PO4 at the micrometer and microsecond scale.

We explicitly compute the non-equilibrium molecular dynamics of protons in the solid acid CsH2PO4 on the micrometer length scale via a multiscale Markov model: The molecular dynamics/matrix propagation (MDM) method. Within the MDM approach, the proton dynamics information of an entire molecular dynamics simulation can be condensed into a single M × M matrix (M is the number of oxygen atoms in the simulated system). Due to this drastic reduction in the complexity, we demonstrate how to increase the length and time scales in order to enable the simulation of inhomogeneities of CsH2PO4 systems at the nanometer scale. We incorporate explicit correlation of protonation dynamics with the protonation state of the neighboring proton sites and illustrate that this modification conserves the Markov character of the MDM method. We show that atomistic features such as the mean square displacement and the diffusion coefficient of the protons can be computed quantitatively from the matrix representation. Furthermore, we demonstrate the application potential of the scheme by computing the explicit dynamics of a non-equilibrium process in an 8 μm CsH2PO4 system during 5 ms.

A closer look at superionic phase transition in (NH4)4H2(SeO4)3: impedance spectroscopy under pressure.

The proton-conducting material (NH4)4H2(SeO4)3 is examined to check whether its conductivity spectra are sensitive to subtle changes in the crystal structure and proton dynamics caused by external pressure. The AC conductivity was measured using impedance spectroscopy, in the frequency range from 100 Hz to 1 MHz, at temperatures 260 K < T < 400 K and pressures 0.1 MPa < p < 500 MPa. On the basis of the impedance spectra, carefully analyzed at different thermodynamic conditions, the p-T phase diagram of the crystal is constructed. It is found to be linear in the pressure range of the experiment, with the pressure coefficient value dTs/dp = -0.023 K MPa-1. The hydrostatic pressure effect on proton conductivity is also presented and discussed. Measurements of the electrical conductivity versus time were performed at a selected temperature T = 352.3 K and at pressures 0.1 MPa < p < 360 MPa. At fixed thermodynamic conditions (p = 302 MPa, T = 352.3 K), the sluggish solid-solid transformation from low conducting to superionic phase was induced. It is established that the kinetics of this transformation can be described by the Avrami model with an effective Avrami index value of about 4, which corresponds to the classical value associated with the homogeneous nucleation and three-dimensional growth of a new phase.

Local Coordination Environments and Vibrational Dynamics of Protons in Hexagonal and Cubic Sc-Doped BaTiO3 Proton-Conducting Oxides

The proton local coordination environments and vibrational dynamics associated with the two order of magnitude change in proton conductivity in hydrated forms of hexagonal and cubic structured BaTi...

Discriminating High-Pressure Water Phases Using Rare-Event Determined Ionic Dynamical Properties* *Supported by the National Basic Research Program of China under Grant Nos. 2016YFA0300900 and 2017YFA0205003, the National Science Foundation of China under Grant Nos. 11774003, 11634001, 11934003, and 11774072. D. Pan also acknowledges the support from Hong Kong Research Grands Council (Nos. ECS-26305017 and GRF-16307618), the Alfred R. Sloan Foundation

Recent discoveries of dynamic ice VII and superionic ice highlight the importance of ionic diffusions in discriminating high-pressure (P) water phases. The rare event nature and the chemical bond breaking associated with these diffusions, however, make extensive simulations of these processes unpractical to ab initio and inappropriate for force field based methods. Using a first-principles neural network potential, we performed a theoretical study of water at 5–70 GPa and 300–3000 K. Long-time dynamics of protons and oxygens were found indispensable in discriminating several subtle states of water, characterized by proton’s and oxygen ion’s diffusion coefficients and the distribution of proton’s displacements. Within dynamic ice VII, two types of proton transfer mechanisms, i.e., translational and rotational transfers, were identified to discriminate this region further into dynamic ice VII T and dynamic ice VII R. The triple point between ice VII, superionic ice (SI), and liquid exists because the loosening of the bcc oxygen skeleton is prevented by the decrease of interatomic distances at high P’s. The melting of ice VII above ∼40 GPa can be understood as a process of two individual steps: the melting of protons and the retarded melting of oxygens, responsible for the forming of SI. The boundary of the dynamic ice VII and SI lies on the continuation line ice VII’s melting curve at low P’s. Based on these, a detailed phase diagram is given, which may shed light on studies of water under P’s in a wide range of interdisciplinary sciences.

Effect of Different Cooking Methods on Proton Dynamics and Physicochemical Attributes in Spanish Mackerel Assessed by Low-Field NMR.

The states of protons within food items are highly related to their physical attributes. In this study, the effect of cooking methods including boiling, steaming, roasting and frying on proton dynamics, physicochemical parameters and microstructure of Spanish mackerel was assessed by low-field nuclear magnetic resonance (LF-NMR) and magnetic resonance imaging (MRI) techniques. The treatment of cooking resulted in a significant reduction of proton mobility and declined freedom of protons. The state changes of protons can be monitored easily in an intuitive and non-destructive manner during various cooking process. The treatments of boiling, steaming, roasting and frying resulted in different cooking loss and similar water-holding capability. A significant increase of total carbonyl content and thiobarbituric acid reactive substances was found, while a decrease of the values for free thiols and surface hydrophobicity was observed. The analysis of circular dichroism spectroscopy and cryo-scanning electron microscopy showed significant structural change. The correlation coefficients of Rcal2 and Rcv2 from partial least squares (PLS) regression models were more than 0.980, suggesting good correlation between LF-NMR data and hardness, resilience, springiness, chewiness, gumminess, and adhesiveness. Good recoveries and a relatively small coefficient of variation (CV) were obtained from the PLS regression models, indicating good reliability and accuracy in predicting texture parameters for mackerel samples.

Dynamical matrix propagator scheme for large-scale proton dynamics simulations.

We derive a matrix formalism for the simulation of long range proton dynamics for extended systems and timescales. On the basis of an ab initio molecular dynamics simulation, we construct a Markov chain, which allows us to store the entire proton dynamics in an M × M transition matrix (where M is the number of oxygen atoms). In this article, we start from common topology features of the hydrogen bond network of good proton conductors and utilize them as constituent constraints of our dynamic model. We present a thorough mathematical derivation of our approach and verify its uniqueness and correct asymptotic behavior. We propagate the proton distribution by means of transition matrices, which contain kinetic data from both ultra-short (sub-ps) and intermediate (ps) timescales. This concept allows us to keep the most relevant features from the microscopic level while effectively reaching larger time and length scales. We demonstrate the applicability of the transition matrices for the description of proton conduction trends in proton exchange membrane materials.

Proton motive function of the terminal antiporter-like subunit in respiratory complex I

In the aerobic respiratory chains of many organisms, complex I functions as the first electron input. By reducing ubiquinone (Q) to ubiquinol, it catalyzes the translocation of protons across the membrane as far as ~200 Å from the site of redox reactions. Despite significant amount of structural and biochemical data, the details of redox coupled proton pumping in complex I are poorly understood. In particular, the proton transfer pathways are extremely difficult to characterize with the current structural and biochemical techniques. Here, we applied multiscale computational approaches to identify the proton transfer paths in the terminal antiporter-like subunit of complex I. Data from combined classical and quantum chemical simulations reveal for the first time structural elements that are exclusive to the subunit, and enables the enzyme to achieve coupling between the spatially separated Q redox reactions and proton pumping. By studying long time scale protonation and hydration dependent conformational dynamics of key amino acid residues, we provide novel insights into the proton pumping mechanism of complex I.

Temperature Dependence of X-ray-Induced Auger Processes in Liquid Water.

Auger spectroscopy has previously been used to study changes in the hydrogen bond network in liquid water, but to the best of our knowledge it has not been used to track such changes as a function of temperature. We show Auger spectroscopy to reflect the weakening of the hydrogen bond network upon heating. This shows that the radiation response of water, i.e., the relative propensity of the different processes occurring after radiation exposure, including femtosecond proton dynamics, depends on the temperature of the system. This proof-of-principle study further demonstrates the suitability of the technique to help elucidate information on the intermolecular structure of liquids such as water, opening the door to further temperature-dependent studies.

Shedding Light on Proton and Electron Dynamics in [FeFe] Hydrogenases.

[FeFe] hydrogenases are highly efficient catalysts for reversible dihydrogen evolution. H2 turnover involves different catalytic intermediates including a recently characterized hydride state of the active site (H-cluster). Applying cryogenic infrared and electron paramagnetic resonance spectroscopy to an [FeFe] model hydrogenase from Chlamydomonas reinhardtii (CrHydA1), we have discovered two new hydride intermediates and spectroscopic evidence for a bridging CO ligand in two reduced H-cluster states. Our study provides novel insights into these key intermediates, their relevance for the catalytic cycle of [FeFe] hydrogenase, and novel strategies for exploring these aspects in detail.

Global Prompt Proton Sensor Network: Monitoring Solar Energetic Protons Based on GPS Satellite Constellation

AbstractEnergetic particle instruments on board Global Positioning System (GPS) satellites form a powerful global prompt proton sensor network (GPPSn) that provides an unprecedented opportunity to monitor and characterize solar energetic protons targeting the Earth. The medium‐Earth orbits of the GPS constellation have the unique advantage of allowing solar energetic protons to be simultaneously measured from multiple points in both open‐ and closed‐field line regions. Examining two example intervals of solar proton events, we showcase in this study how GPS proton data are prepared, calibrated, and utilized to reveal important features of solar protons, including their source, acceleration/scattering by interplanetary shocks, the relative position of Earth when impinged by these shocks, the shape of solar particle fronts, the access of solar protons inside the dynamic geomagnetic field, and temporally varying proton distributions in both energy and space. By comparing to Van Allen Probes data, GPS proton observations are further demonstrated not only to be useful for qualitatively monitoring the dynamics of solar protons but also for quantitative scientific research including determining cutoff L‐shells. Our results establish that this GPPSn can join forces with other existing solar proton monitors and contribute to observing, warning, understanding, and ultimately forecasting the incoming solar energetic proton events.

Proton dynamics in antiferroelectric CsH3(SeO3)2 single crystal investigated by 1H NMR measurements

1H nuclear magnetic resonance (NMR) measurements have been performed to study the proton dynamics associated with the antiferroelectric transition of a hydrogen-bonded single crystal of CsH3(SeO3)2. Herein, 1H NMR spectrum, shift, linewidth, and spin-lattice relaxation rate 1/T1 are measured in the temperature range of 80–296 K with the c-axis parallel to a magnetic field of ~4.85 T. The spectrum exhibits a composite structure with two narrow peaks at 296 K; at a low temperature, this structure evolves into a single broad shape with three humps. This complex shape and evolution are deconvoluted into five or six components based on the number of inequivalent and disordered hydrogen sites. By estimating the chemical shift and linewidth for each proton site, we identify all peaks. The spin-lattice relaxation recovery exhibits a double-exponential behavior with two relaxation times, short T1S and extremely large T1L. Both T1S and T1L follow Arrhenius behavior. From the respective 1/T1(T), the activation energies for proton motion are measured to be small: 1.16 ± 0.1 and 0.83 ± 0.06 kJ/mol for T1S and T1L, respectively. While the static NMR data, chemical shift and linewidth, show no evidence for the transition, the dynamic data 1/T1L highlights a clear increase across TN = 145 K, which is possibly a signature of the transition.

Ultrafast Backbone Protonation in Channelrhodopsin-1 Captured by Polarization Resolved Fs Vis-pump-IR-Probe Spectroscopy and Computational Methods.

Channelrhodopsins (ChR) are light-gated ion-channels heavily used in optogenetics. Upon light excitation an ultrafast all-trans to 13-cis isomerization of the retinal chromophore takes place. It is still uncertain by what means this reaction leads to further protein changes and channel conductivity. Channelrhodopsin-1 in Chlamydomonas augustae exhibits a 100 fs photoisomerization and a protonated counterion complex. By polarization resolved ultrafast spectroscopy in the mid-IR we show that the initial reaction of the retinal is accompanied by changes in the protein backbone and ultrafast protonation changes at the counterion complex comprising Asp299 and Glu169. In combination with homology modelling and quantum mechanics/molecular mechanics (QM/MM) geometry optimization we assign the protonation dynamics to ultrafast deprotonation of Glu169, and transient protonation of the Glu169 backbone, followed by a proton transfer from the backbone to the carboxylate group of Asp299 on a timescale of tens of picoseconds. The second proton transfer is not related to retinal dynamics and reflects pure protein changes in the first photoproduct. We assume these protein dynamics to be the first steps in a cascade of protein-wide changes resulting in channel conductivity.

Time-resolved FTIR difference spectroscopy for the study of quinones in the A1 binding site in photosystem I: Identification of neutral state quinone bands

Infrared absorption bands associated with the neutral state of quinones in the A1 binding site in photosystem I (PSI) have been difficult to identify in the past. This problem is addressed here, where time-resolved step-scan FTIR difference spectroscopy at 77 K has been used to study PSI with six different quinones incorporated into the A1 binding site. (P700+A1− – P700A1) and (A1− – A1) FTIR difference spectra (DS) were obtained for PSI with the different quinones incorporated, and several double-difference spectra (DDS) were constructed from the DS. From analysis of the DS and DDS, in combination with density functional theory based vibrational frequency calculations of the quinones, the neutral state bands of the incorporated quinones are identified and assigned. For neutral PhQ in the A1 binding site, infrared absorption bands were identified near 1665 and 1635 cm−1, that are due to the C1O and C4O stretching vibrations of the incorporated PhQ, respectively. These assignments indicate a 30 cm−1 separation between the C1O and C4O modes, considerably less than the ~80 cm−1 found for similar modes of PhQ−. The C4O mode downshifts due to hydrogen bonding, so the suggestion is that hydrogen bonding is weaker for the neutral state compared to the anion state, indicating radical-induced proton dynamics associated with the quinone in the A1 binding site in PSI.

CMOS-based bio-image sensor spatially resolves neural activity-dependent proton dynamics in the living brain

Recent studies have shown that protons can function as neurotransmitters in cultured neurons. To further investigate regional and neural activity-dependent proton dynamics in the brain, the development of a device with both wide-area detectability and high spatial-ltemporal resolution is necessary. Therefore, we develop an image sensor with a high spatial-temporal resolution specifically designed for measuring protons in vivo. Here, we demonstrate that spatially deferent neural stimulation by visual stimulation induced distinct patterns of proton changes in the visual cortex. This result indicates that our biosensor can detect micrometer and millisecond scale changes of protons across a wide area. Our study demonstrates that a CMOS-based proton image sensor with high spatial and temporal precision can be used to detect pH changes associated with biological events. We believe that our sensor may have broad applicability in future biological studies.

The effects of beam proportion on electromagnetic proton/proton instability and associated ion heating: 2D hybrid simulation

In this paper, the effects of beam proportion on the electromagnetic proton/proton instability and involved proton dynamics have been investigated with a two-dimensional hybrid simulation model. The beam proportion is defined as the number density ratio between the beam and all protons. The simulation results show that the saturation amplitude of excited oblique Alfvén waves becomes larger with the increasing proportion of beam protons. Besides, the polarization of oblique Alfvén waves generated by beam protons with a higher proportion tends to be more linear. Moreover, with the increase in the beam proportion, the peak frequencies of excited waves will move toward higher values even exceed the proton gyrofrequency. This will result in more efficient heating of core protons in the perpendicular direction through the cyclotron resonance with Alfvén waves. Our study may provide some new insights into the heating mechanism of the solar wind.

Theoretical study of intramolecular hydrogen bond in selected symmetric "proton sponges" on the basis of DFT and CPMD methods.

"Proton sponges," derivatives of prototypic 1,8-bis(dimethylamino)naphthalene (DMAN), exhibit remarkable basicity, which made them interesting for various experimental and theoretical studies. The details of bridged proton dynamics in protonated DMAN and its derivative denoted as TMGN (1,8-bis(tetramethylguanidino)naphthalene) were investigated on the basis of density functional theory (DFT) and Car-Parrinello molecular dynamics (CPMD) methods. Special attention was paid to the effects of symmetry of the molecular skeleton and the type of substituent on the bridged proton neighborhood statistics and dynamics. The metric parameter analyses of hydrogen bridge provided us with a conclusion that proton migration events in TMGNH+ are less numerous than in DMANH+, which can be rationalized by noticing the slower dynamics of large substituents of TMGN with respect to the smaller -N(Me)2 groups of DMAN. The atomic velocity power spectra served as computational models of the vibrational signatures associated with the presence of the intramolecular hydrogen bond. A broad feature was registered for hydrogen bonds present in both compounds. The computations were verified by experimental data available.

Single-molecule tautomerization tracking through space- and time-resolved fluorescence spectroscopy

Tautomerization, the interconversion between two constitutional molecular isomers, is ubiquitous in nature1, plays a major role in chemistry2 and is perceived as an ideal switch function for emerging molecular-scale devices3. Within free-base porphyrin4, porphycene5 or phthalocyanine6, this process involves the concerted or sequential hopping of the two inner hydrogen atoms between equivalent nitrogen sites of the molecular cavity. Electronic and vibronic changes6 that result from this NH tautomerization, as well as details of the switching mechanism, were extensively studied with optical spectroscopies, even with single-molecule sensitivity7. The influence of atomic-scale variations of the molecular environment and submolecular spatial resolution of the tautomerization could only be investigated using scanning probe microscopes3,8-11, at the expense of detailed information provided by optical spectroscopies. Here, we combine these two approaches, scanning tunnelling microscopy (STM) and fluorescence spectroscopy12-15, to study the tautomerization within individual free-base phthalocyanine (H2Pc) molecules deposited on a NaCl-covered Ag(111) single-crystal surface. STM-induced fluorescence (STM-F) spectra exhibit duplicate features that we assign to the emission of the two molecular tautomers. We support this interpretation by comparing hyper-resolved fluorescence maps15-18(HRFMs) of the different spectral contributions with simulations that account for the interaction between molecular excitons and picocavity plasmons19. We identify the orientation of the molecular optical dipoles, determine the vibronic fingerprint of the tautomers and probe the influence of minute changes in their atomic-scale environment. Time-correlated fluorescence measurements allow us to monitor the tautomerization events and to associate the proton dynamics to a switching two-level system. Finally, optical spectra acquired with the tip located at a nanometre-scale distance from the molecule show that the tautomerization reaction occurs even when the tunnelling current does not pass through the molecule. Together with other observations, this remote excitation indicates that the excited state of the molecule is involved in the tautomerization reaction path.

実空間におけるプロトンダイナミクス : トンネル反応をトンネル顕微鏡で観察する(最近の研究から)

実空間におけるプロトンダイナミクス : トンネル反応をトンネル顕微鏡で観察する(最近の研究から)

Understanding Li‐Ion Dynamics in Lithium Hydroxychloride (Li2OHCl) Solid State Electrolyte via Addressing the Role of Protons

AbstractLow‐melting‐point solid‐state electrolytes (SSE) are critically important for low‐cost manufacturing of all‐solid‐state batteries. Lithium hydroxychloride (Li2OHCl) is a promising material within the SSE domain due to its low melting point (mp &lt; 300 °C), cheap ingredients (Li, H, O, and Cl), and rapid synthesis. Another unique feature of this compound is the presence of Li vacancies and rotating hydroxyl groups which promote Li‐ion diffusion, yet the role of the protons in the ion transport remains poorly understood. To examine lithium and proton dynamics, a set of solid‐state NMR experiments are conducted, such as magic‐angle spinning 7Li NMR, static 7Li and 1H NMR, and spin‐lattice T1(7Li)/T1(1H) relaxation experiments. It is determined that only Li+ contributes to long‐range ion transport, while H+ dynamics is constrained to an incomplete isotropic rotation of the OH group. The results uncover detailed mechanistic understanding of the ion transport in Li2OHCl. It is shown that two distinct phases of ionic motions appear at low and elevated temperatures, and that the rotation of the OH group controls Li+ and H+ dynamics in both phases. The model based on the NMR experiments is fully consistent with crystallographic information, ionic conductivity measurements, and Born–Oppenheimer molecular dynamic simulations.

Collective exchange processes reveal an active site proton cage in bacteriorhodopsin

Proton translocation across membranes is vital to all kingdoms of life. Mechanistically, it relies on characteristic proton flows and modifications of hydrogen bonding patterns, termed protonation dynamics, which can be directly observed by fast magic angle spinning (MAS) NMR. Here, we demonstrate that reversible proton displacement in the active site of bacteriorhodopsin already takes place in its equilibrated dark-state, providing new information on the underlying hydrogen exchange processes. In particular, MAS NMR reveals proton exchange at D85 and the retinal Schiff base, suggesting a tautomeric equilibrium and thus partial ionization of D85. We provide evidence for a proton cage and detect a preformed proton path between D85 and the proton shuttle R82. The protons at D96 and D85 exchange with water, in line with ab initio molecular dynamics simulations. We propose that retinal isomerization makes the observed proton exchange processes irreversible and delivers a proton towards the extracellular release site.