Excess Proton Research Articles

How many methanol molecules effectively solvate an excess proton in the gas phase? Infrared spectroscopy of H+(methanol)n-benzene clusters.

An excess proton in a hydrogen-bonded system enhances the strength of hydrogen bonds of the surrounding molecules. The extent of this influence can be a measure of the number of molecules effectively solvating the excess proton. Such extent in methanol has been discussed by the observation of the π-hydrogen-bonded OH stretch bands of the terminal sites of protonated methanol clusters, H+(methanol)n, in benzene solutions, and it has been concluded that ∼8 molecules effectively solvate the excess proton (Stoyanov et al., Chem. Eur. J. 2008, 14, 3596-3604). In the present study, we performed infrared spectroscopy of H+(methanol)n-benzene clusters in the gas phase. The cluster size and hydrogen-bonded network structure are identified by the tandem mass spectrometric technique and the comparison of the observed infrared spectra with density functional theory calculations. Though changes of the preferred hydrogen bond network type occur with the increase of cluster size in the gas phase clusters, the observed size dependence of the π-hydrogen bonded OH frequency agrees well with that in the benzene solutions. This means that the observations in both the gas and condensed phases catch the same physical essence of the excess proton solvation by methanol.

Dynamical Behavior of Water; Fluctuation, Reactions and Phase Transitions

Abstract Water dynamical and thermodynamical properties in molecular scale were theoretically investigated in a wide range of temperatures to clarify the physical origin of anomalous water properties. It was found in water that there exist intermittent and collective motions that arise from hydrogen bond network rearrangement. These intermittent motions become more distinctive with temperature decrease and diminish at the glass transition. In a deeply supercooled region, water dynamics shows that a new (“the third”) branch exists in its relaxation and in this branch special defects, H2O1, play a critical role. These defects make water glass transition temperature remarkably low. The intermittent collective motions have significant effects on water phase transitions and chemical reactions. The detailed dynamical mechanisms of the water freezing and the ice melting processes were analyzed. It was found how the embryos of nuclei for these processes are created and grow. The fast proton transfer mechanism in ice was also investigated to find its physical origin. Due to a strong geometrical constraint in ice, the excess proton is not trapped in a deep energy minimum and makes a facile transfer on the small energy barrier surface. As for the auto-dissociation process of water molecules, non-monotonic temperature dependence was theoretically clarified in a wide range of temperatures from ambient to supercritical region. On water roles in biomolecular functions, ion/proton transports and concomitant molecular relaxations were examined in ion-channel, photoactive yellow protein and reaction center.

Resolving the Structural Debate for the Hydrated Excess Proton in Water.

It has long been proposed that the hydrated excess proton in water (aka the solvated "hydronium" cation) likely has two limiting forms, that of the Eigen cation (H9O4+) and that of the Zundel cation (H5O2+). There has been debate over which of these two is the more dominant species and/or whether intermediate (or "distorted") structures between these two limits are the more realistic representation. Spectroscopy experiments have recently provided further results regarding the excess proton. These experiments show that the hydrated proton has an anisotropy reorientation time scale on the order of 1-2 ps. This time scale has been suggested to possibly contradict the picture of the more rapid "special pair dance" phenomenon for the hydrated excess proton, which is a signature of a distorted Eigen cation. The special pair dance was predicted from prior computational studies in which the hydrated central core hydronium structure continually switches (O-H···O)* special pair hydrogen-bond partners with the closest three water molecules, yielding on average a distorted Eigen cation with three equivalent and dynamically exchanging distortions. Through state-of-art simulations it is shown here that anisotropy reorientation time scales of the same magnitude are obtained that also include structural reorientations associated with the special pair dance, leading to a reinterpretation of the experimental results. These results and additional analyses point to a distorted and dynamic Eigen cation as the most prevalent hydrated proton species in aqueous acid solutions of dilute to moderate concentration, as opposed to a stabilized or a distorted (but not "dancing") Zundel cation.

Towards complete assignment of the infrared spectrum of the protonated water cluster H+(H2O)21

The spectroscopic features of protonated water species in dilute acid solutions have been long sought after for understanding the microscopic behavior of the proton in water with gas-phase water clusters H+(H2O)n extensively studied as bottom-up model systems. We present a new protocol for the calculation of the infrared (IR) spectra of complex systems, which combines the fragment-based Coupled Cluster method and anharmonic vibrational quasi-degenerate perturbation theory, and demonstrate its accuracy towards the complete and accurate assignment of the IR spectrum of the H+(H2O)21 cluster. The site-specific IR spectral signatures reveal two distinct structures for the internal and surface four-coordinated water molecules, which are ice-like and liquid-like, respectively. The effect of inter-molecular interaction between water molecules is addressed, and the vibrational resonance is found between the O-H stretching fundamental and the bending overtone of the nearest neighboring water molecule. The revelation of the spectral signature of the excess proton offers deeper insight into the nature of charge accommodation in the extended hydrogen-bonding network underpinning this aqueous cluster.

Improved indicator algorithms for tracking a hydrated proton as a local structural defect in Grotthuss diffusion in aqueous solutions

Keeping track of a hydrated proton in dynamics simulations is important and nontrivial. Here, we report two revised algorithms for the proton indicator, a pseudo-atom whose position approximates the location of an excess proton diffusing via the Grotthuss mechanism in aqueous solution. The new methods describe the delocalized proton as a structural defect. Encouragingly, in test simulations of a hydrated proton in bulk water, the new algorithms substantially outperform the original scheme by significantly reducing large displacements in the indicator positions upon donor switch, yielding smoother trajectories that effectively track the movement of the solvated proton.

Anomalous interfacial dynamics of single proton charges in binary aqueous solutions.

Our understanding of the dynamics of charge transfer between solid surfaces and liquid electrolytes has been hampered by the difficulties in obtaining interface, charge, and solvent-specific information at both high spatial and temporal resolution. Here, we measure at the single charge scale the dynamics of protons at the interface between an hBN crystal and binary mixtures of water and organic amphiphilic solvents (alcohols and acetone), evidencing a marked influence of solvation on interfacial dynamics. Applying single-molecule localization microscopy to emissive crystal defects, we observe correlated activation between adjacent ionizable surface defects, mediated by the transport of single excess protons along the solid/liquid interface. Solvent content has a nontrivial effect on interfacial dynamics, leading at intermediate water fraction to an increased surface diffusivity, as well as an increased affinity of the proton charges to the solid surface. Our measurements evidence the notable role of solvation on interfacial proton charge transport.

Quantum-Mechanical Molecular Dynamics Simulations on Secondary Proton Transfer in Bacteriorhodopsin Using Realistic Models.

Bacteriorhodopsin (BR) transports a proton from intracellular to extracellular (EC) sites through five proton transfers. The second proton transfer is the release of an excess proton stored in BR into the EC medium, and an atomistic understanding of this whole process has remained unexplored due to its ubiquitous environment. Here, fully quantum mechanical (QM) molecular dynamics (MD) and metadynamics (MTD) simulations for this process were performed at the divide-and-conquer density-functional tight-binding level using realistic models (∼50000 and ∼20000 atoms) based on the time-resolved photointermediate structures from an X-ray free electron laser. Regarding the proton storage process, the QM-MD/MTD simulations confirmed the Glu-shared mechanism, in which an excess proton is stored between Glu194 and Glu204, and clarified that the activation occurs by localizing the proton at Glu204 in the photocycle. Furthermore, the QM-MD/MTD simulations elucidated a release pathway from Glu204 through Ser193 to the EC water molecules and clarified that the proton release starts at ∼250 μs. In the ubiquitous proton diffusion in the EC medium, the transient proton receptors predicted experimentally were assigned to carboxylates in Glu9 and Glu74. Large-scale QM-MD/MTD simulations beyond the conventional sizes, which provided the above findings and confirmations, were possible by adopting our Dcdftbmd program.

Using Constrained Density Functional Theory to Track Proton Transfers and to Sample Their Associated Free Energy Surface.

Ab initio molecular dynamics (AIMD) and quantum mechanics/molecular mechanics (QM/MM) methods are powerful tools for studying proton solvation, transfer, and transport processes in various environments. However, due to the high computational cost of such methods, achieving sufficient sampling of rare events involving excess proton motion—especially when Grotthuss proton shuttling is involved—usually requires enhanced free energy sampling methods to obtain informative results. Moreover, an appropriate collective variable (CV) that describes the effective position of the net positive charge defect associated with an excess proton is essential both for tracking the trajectory of the defect and for the free energy sampling of the processes associated with the resulting proton transfer and transport. In this work, such a CV is derived from first principles using constrained density functional theory (CDFT). This CV is applicable to a broad array of proton transport and transfer processes as studied via AIMD and QM/MM simulations.

The Evolution of Research on Abundances of Solar Energetic Particles

Sixty years of study of energetic particle abundances have made a major contribution to our understanding of the physics of solar energetic particles (SEPs) or solar cosmic rays. An early surprise was the observation in small SEP events of huge enhancements in the isotope 3He from resonant wave–particle interactions, and the subsequent observation of accompanying enhancements of heavy ions, later found to increase 1000-fold as a steep power of the mass-to-charge ratio A/Q, right across the elements from H to Pb. These “impulsive” SEP events have been related to magnetic reconnection on open field lines in solar jets; similar processes occur on closed loops in flares, but those SEPs are trapped and dissipate their energy in heat and light. After early controversy, it was established that particles in the large “gradual” SEP events are accelerated at shock waves driven by wide, fast coronal mass ejections (CMEs) that expand broadly. On average, gradual SEP events give us a measure of element abundances in the solar corona, which differ from those in the photosphere as a classic function of the first ionization potential (FIP) of the elements, distinguishing ions and neutrals. Departures from the average in gradual SEPs are also power laws in A/Q, and fits of this dependence can determine Q values and thus estimate source plasma temperatures. Complications arise when shock waves reaccelerate residual ions from the impulsive events, but excess protons and the extent of abundance variations help to resolve these processes. Yet, specific questions about SEP abundances remain.

Protonation-Induced B-Site Deficiency in Perovskite-Type Oxides: Fully Hydrated BaSc0.67O(OH)2 as a Proton Conductor

One of the concepts for the design of a highly proton-conductive perovskite-type oxide is to increase the proton concentration. In this study, we focused on Ba–Sc oxide known for its brownmillerite-type structure and great potential for a high proton concentration. To achieve the highly hydrated phase, high-pressure synthesis was conducted using hydroxide as the H2O source. Although the expectation was that perovskite-type BaScO2(OH) would simply be a hydrated phase, the formation of Sc vacancies increased resulting in the greater hydration of the Ba–Sc oxide. It was likely that the fully hydrated phase was perovskite-type BaSc0.67O(OH)2. One third of the Sc sites were vacant, and the effective charge of Sc vacancies were compensated by the excess protons. First principles calculation revealed that the protons residing in the Sc vacancies were orientated toward a Sc vacancy and compensated the B-site charge in a manner similar to that of hydrogarnet substitution. This B-site deficiency caused by the extensive hydration condition is a novel mechanism to increase the proton concentration of perovskite-type proton conductors. The electrical conductivity, 10–2 S·cm–1 at 450–500 °C, was comparable to that of acceptor-doped BaZrO3, although the conductivity discontinuously changed at dehydration temperature.

Proton Transport and Related Chemical Processes of Ice.

Excess protons play a key role in the chemical reactions of ice because of their exceptional mobility, even when the diffusion of atoms and molecules is suppressed in ice at low temperatures. This article reviews the current state of knowledge on the properties of excess protons in ice, with a focus on the involvement of protons in chemical reactions. The mechanism of efficient proton transport in ice, which involves a proton-hopping relay along the hydrogen-bond ice network and the reorientation of water, is discussed and compared with the inefficient transport of hydroxide in ice. Distinctly different properties of protons residing in the ice interior and on the ice surface are emphasized. Recent observations of the spontaneous occurrence of reactions in ice at low temperatures, which include the dissociation of protic acids and the hydrolysis of acidic oxides, are discussed with regard to the kinetic and thermodynamic effects of mobile protons on the promotion of unique chemical processes of ice.

Structural Characterization of Protonated Water Clusters Confined in HZSM-5 Zeolites.

A molecular description of the structure and behavior of water confined in aluminosilicate zeolite pores is a crucial component for understanding zeolite acid chemistry under hydrous conditions. In this study, we use a combination of ultrafast two-dimensional infrared (2D IR) spectroscopy and ab initio molecular dynamics (AIMD) to study H2O confined in the pores of highly hydrated zeolite HZSM-5 (∼13 and ∼6 equivalents of H2O per Al atom). The 2D IR spectrum reveals correlations between the vibrations of both terminal and H-bonded O-H groups and the continuum absorption of the excess proton. These data are used to characterize the hydrogen-bonding network within the cluster by quantifying single-, double-, and non-hydrogen-bond donor water molecules. These results are found to be in good agreement with the statistics calculated from an AIMD simulation of an H+(H2O)8 cluster in HZSM-5. Furthermore, IR spectral assignments to local O-H environments are validated with DFT calculations on clusters drawn from AIMD simulations. The simulations reveal that the excess charge is detached from the zeolite and resides near the more highly coordinated water molecules in the cluster. When they are taken together, these results unambiguously assign the complex IR spectrum of highly hydrated HZSM-5, providing quantitative information on the molecular environments and hydrogen-bonding topology of protonated water clusters under extreme confinement.

The hopping mechanism of the hydrated excess proton and its contribution to proton diffusion in water.

In this work, a series of analyses are performed on ab initio molecular dynamics simulations of a hydrated excess proton in water to quantify the relative occurrence of concerted hopping events and "rattling" events and thus to further elucidate the hopping mechanism of proton transport in water. Contrary to results reported in certain earlier papers, the new analysis finds that concerted hopping events do occur in all simulations but that the majority of events are the product of proton rattling, where the excess proton will rattle between two or more waters. The results are consistent with the proposed "special-pair dance" model of the hydrated excess proton wherein the acceptor water molecule for the proton transfer will quickly change (resonate between three equivalent special pairs) until a decisive proton hop occurs. To remove the misleading effect of simple rattling, a filter was applied to the trajectory such that hopping events that were followed by back hops to the original water are not counted. A steep reduction in the number of multiple hopping events is found when the filter is applied, suggesting that many multiple hopping events that occur in the unfiltered trajectory are largely the product of rattling, contrary to prior suggestions. Comparing the continuous correlation function of the filtered and unfiltered trajectories, we find agreement with experimental values for the proton hopping time and Eigen-Zundel interconversion time, respectively.

The Triple Salt 2(C7H9N4O2)[MoOCl4(H2O)] ⋅ 2(C7H9N4O2)Cl ⋅ (H17O8)Cl Containing a C2‐symmetrical Unbranched H+(H2O)8Zundel type Species in a Framework Composed of Theophyllinium, Aquatetrachloridooxidomolybdate and Chloride Ions

AbstractFrom a concentrated hydrochloric acid solution of molybdenum‐(V) chloride and theophylline octaaquahydrogen(1+) tetrakis(theophyllinium) bis[aquatetrachloridooxidomolybdate(1−)] tri‐chloride, C7H9N4O2)4(H17O8)[MoOCl4(H2O)]2Cl3, (1) was obtained. The light emerald green inorganic‐organic hybrid material can be rationalized as a triple salt according to the formula 2(C7H9N4O2)[MoOCl4(H2O)] ⋅ 2(C7H9N4O2)Cl ⋅ (H17O8)Cl. The ions involved are connected by charge‐supported hydrogen bonds to form a 3D framework. The unique H17O8+ moiety features a chain of eight hydrogen bonded water molecules, with the excess proton defining a H5O2+ Zundel‐ion (O⋅⋅⋅O distance 240.3(6) pm) in the middle of the chain, and is placed with crystallographic site symmetry 2. Although engaged in strong O−H⋅⋅⋅O bonding to the neighboring water molecules in the chain (O⋅⋅⋅O distance 262.9(4) pm) and in hydrogen bonding to a carbonyl group of a theophyllinium ion, both the conformation of the H5O2+ unit and the geometry of the very strong central O−H−O bond fit to the C2‐symmetrical global minimum structure of an isolated H5O2+ species. The outer water molecules of the H17O8+ moiety are further engaged in N−H⋅⋅⋅O, O−H⋅⋅⋅Cl and O−H⋅⋅⋅O=C bonds.

Switching between Proton Vacancy and Excess Proton Transfer Pathways in the Reaction between 7-Hydroxyquinoline and Formate.

Bifunctional or amphoteric photoacids simultaneously present donor (acidic) and acceptor (basic) properties making them useful tools to analyze proton transfer reactions. In protic solvents, the proton exchange between the acid and the base is controlled by the acidity or basicity strength and typically occurs on two different pathways known as protolysis and hydrolysis. We report here how the addition of a formate base will alter the relative importance of the possible reaction pathways of the bifunctional photoacid 7-hydroxyquinoline (7HQ), which has been recently understood to predominantly involve a hydroxide/methoxide transport mechanism between the basic proton-accepting quinoline nitrogen site toward the proton-donating OH group with a time constant of 360 ps in deuterated methanol (CD3OD). We follow the reaction dynamics by probing the IR-active marker modes of the different charged forms of photoexcited 7HQ, and of formic acid (HCOOD) in CD3OD solution. A comparison of the transient IR spectra as a function of formate concentration, and classical molecular dynamics simulations enables us to identify distinct contributions of “tight” (meaning “contact”) and “loose” (i.e., “solvent-separated”) 7HQ–formate reaction pairs in our data. Our results suggest that depending on the orientation of the OH group with respect to the quinoline aromatic ring system, the presence of the formate molecule in a proton relay pathway facilitates a net proton transfer from the proton-donating OH group of 7HQ-N* via the methanol/formate bridge toward the quinoline N site.

Quantum-mechanical model of thermally stimulated depolarization in layered dielectrics at low temperatures

Built the quantum-mechanical scheme for investigating the spectrum of thermally stimulated currents of depolarization (TCDP), which allows to study the processes of relaxation of hetero-and homo-charge in hydrogen bonded crystals (HBC) with complex crystalline structure (layered silicates, crystal-hydrates), taking into account the distribution of relaxers (protons) over the energy levels of the quasi-discrete spectrum in potential image of the crystal lattice, and allows us to calculate the parameters of low-temperature relaxers by the Klinger method in the quadratic approximation over the external electric field. However, the calculation of the excess proton concentration operator was carried out in the quasi-classical approximation on the basis of the Fokker-Planck operator equation, which is solved together with the Poisson operator equation. By method of density matrix in the quadratic approximation in the external field calculated thermally stimulated depolarization currents on the basis of which the investigated size effects in the nanometer size layers associated with the shift of the maximum current of thermo-depolarization to low temperatures while reducing the thickness of the crystal layer.

Demystifying the Diffuse Vibrational Spectrum of Aqueous Protons Through Cold Cluster Spectroscopy.

The ease with which the pH is routinely determined for aqueous solutions masks the fact that the cationic product of Arrhenius acid dissolution, the hydrated proton, or H+(aq), is a remarkably complex species. Here, we review how results obtained over the past 30 years in the study of H+⋅(H2O)n cluster ions isolated in the gas phase shed light on the chemical nature of H+(aq). This effort has also revealed molecular-level aspects of the Grotthuss relay mechanism for positive-charge translocation in water. Recently developed methods involving cryogenic cooling in radiofrequency ion traps and the application of two-color, infrared-infrared (IR-IR) double-resonance spectroscopy have established a clear picture of how local hydrogen-bond topology drives the diverse spectral signatures of the excess proton. This information now enables a new generation of cluster studies designed to unravel the microscopic mechanics underlying the ultrafast relaxation dynamics displayed by H+(aq).

Quantum-Classical Path Integral Simulation of Excess Proton Dynamics in a Water Dimer Embedded in the Gramicidin Channel.

We use the quantum-classical path integral (QCPI) methodology to investigate the relaxation dynamics of an excess proton that has been inserted in a water dimer embedded in the gramicidin A channel at room temperature. We obtain one-dimensional potential slices for the quantum degree of freedom through a proper transformation to internal coordinates. Our results indicate that the proton transfer is driven by the oscillation of the oxygen pair, and that the transfer occurs primarily at single-well or nearby low-barrier configurations. Yet, we find that tunneling and zero-point energy lead to a significant acceleration of the proton transfer dynamics.

Delivery of Electrons by Proton-Hole Transfer in Ice at 10 K: Role of Surface OH Radicals

Although water ice has been widely accepted to carry a positive charge via the transfer of excess protons through a hydrogen-bonded system, ice was recently found to be a negative charge conductor upon simultaneous exposure to electrons and ultraviolet photons at temperatures below 50 K. In this work, the mechanism of electron delivery was confirmed experimentally by both measuring currents through ice and monitoring photodissociated OH radicals on ice by using a novel method. The surface OH radicals significantly decrease upon the appearance of negative current flow, indicating that the electrons are delivered by proton-hole (OH-) transfer in ice triggered by OH- production on the surface. The mechanism of proton-hole transfer was rationalized by density functional theory calculations.

Ab initio molecular dynamics simulations and experimental speciation study of levofloxacin under different pH conditions.

Levofloxacin is an extensively employed broad-spectrum antibiotic belonging to the fluoroquinolone class. Despite the extremely wide usage of levofloxacin for a plethora of diseases, the molecular characterization of this antibiotic appears quite poor in the literature. Moreover, the acid-base properties of levofloxacin - crucial for the design of efficient removal techniques from wastewaters - have never extensively been investigated so far. Here we report on a study on the behavior of levofloxacin under standard and diverse pH conditions in liquid water by synergistically employing static quantum-mechanical calculations along with experimental speciation studies. Furthermore, with the aim of characterizing the dynamics of the water solvation shells as well as the protonation and deprotonation mechanisms, here we present the unprecedented quantum-based simulation of levofloxacin in aqueous environments by means of state-of-the-art density-functional-theory-based molecular dynamics. This way, we prove the cooperative role played by the aqueous hydration shells in assisting the proton transfer events and, more importantly, the key place held by the nitrogen atom binding the methyl group of levofloxacin in accepting excess protons eventually present in water. Finally, we also quantify the energetic contribution associated with the presence of a H-bond internal to levofloxacin which, on the one hand, stabilizes the ground-state molecular structure of this antibiotic and, on the other, hinders the first deprotonation step of this fluoroquinolone. Among other things, the synergistic employment of quantum-based calculations and speciation experiments reported here paves the way toward the development of targeted removal approaches of drugs from wastewaters.