Distance-dependent proton transfer along water wires connecting acid-base pairs

Mechanism of proton-powered c-ring rotation in a mitochondrial ATP synthase

Proton-powered c-ring rotation in mitochondrial ATP synthase is crucial to convert the transmembrane protonmotive force into torque to drive the synthesis of adenosine triphosphate (ATP). Capitalizing on recent cryo-EM structures, we aim at a structural and energetic understanding of how functional directional rotation is achieved. We performed multi-microsecond atomistic simulations to determine the free energy profiles along the c-ring rotation angle before and after the arrival of a new proton. Our results reveal that rotation proceeds by dynamic sliding of the ring over the a-subunit surface, during which interactions with conserved polar residues stabilize distinct intermediates. Ordered water chains line up for a Grotthuss-type proton transfer in one of these intermediates. After proton transfer, a high barrier prevents backward rotation and an overall drop in free energy favors forward rotation, ensuring the directionality of c-ring rotation required for the thermodynamically disfavored ATP synthesis. The essential arginine of the a-subunit stabilizes the rotated configuration through a salt bridge with the c-ring. Overall, we describe a complete mechanism for the rotation step of the ATP synthase rotor, thereby illuminating a process critical to all life at atomic resolution.

Energy Dissipation into the Solvent during Proton Transfer Occurs via Acoustic Phonons

In photochemistry, rapid energy dissipation into the solvent is mandatory to prevent radiation damages. By optical pump THz spectroscopy, we are able to follow the details of the energy dissipation mechanism upon photoexcitation of the photoacid to the hydrogen-bonded network of water: Based on the frequency maps subsequent to photoexcitation, we propose that energy transfer takes place via propagation of an acoustic phonon. The dissipation into the solvent can be rationalized by an initial first hydration shell response followed by energy dissipation via an acoustic phonon. Surprisingly, for the first 10 ps, the propagation in the water network can be described by a wave packet with a constant group velocity, indicating a long-range correlation. After 300 ps, thermalization in the liquid jet is reached and the THz spectrum reflects a Boltzmann population, corresponding a temperature increase of ΔT = 0.5 °C.

Ultrafast Proton Transfer Pathways Mediated by Amphoteric Imidazole

Imidazole, being an amphoteric molecule, can act both as an acid and as a base. This property enables imidazole, as an essential building block, to effectively facilitate proton transport in high-temperature proton exchange membrane fuel cells and in proton channel transmembrane proteins, enabling those systems to exhibit high energy conversion yields and optimal biological function. We explore the amphoteric properties of imidazole by following the proton transfer exchange reaction dynamics with the bifunctional photoacid 7-hydroxyquinoline (7HQ). We show with ultrafast ultraviolet-mid-infrared pump-probe spectroscopy how for imidazole, in contrast to expectations based on textbook knowledge of acid-base reactivity, the preferential reaction pathway is that of an initial proton transfer from 7HQ to imidazole, and only at a later stage a transfer from imidazole to 7HQ, completing the 7HQ tautomerization reaction. An assessment of the molecular distribution functions and first-principles calculations of proton transfer reaction barriers reveal the underlying reasons for our observations.

Observing Aqueous Proton-Uptake Reactions Triggered by Light

Proton-transfer reactions in water are essential to chemistry and biology. Earlier studies reported on aqueous proton-transfer mechanisms by observing light-triggered reactions of strong (photo)acids and weak bases. Similar studies on strong (photo)base-weak acid reactions would also be of interest because earlier theoretical works found evidence for mechanistic differences between aqueous H⁺ and OH^- transfer. In this work, we study the reaction of actinoquinol, a water-soluble strong photobase, with the water solvent and the weak acid succinimide. We find that in aqueous solutions containing succinimide, the proton-transfer reaction proceeds via two parallel and competing reaction channels. In the first channel, actinoquinol extracts a proton from water, after which the newly generated hydroxide ion is scavenged by succinimide. In the second channel, succinimide forms a hydrogen-bonded complex with actinoquinol and the proton is transferred directly. Interestingly, we do not observe proton conduction in water-separated actinoquinol-succinimide complexes, which makes the newly studied strong base-weak acid reaction essentially different from previously studied strong acid-weak base reactions.

Ultrafast transient absorption and solvation of a super-photoacid in acetoneous environments

The phenomenon of photoacidity, i.e., an increase in acidity by several orders of magnitude upon electronic excitation, is frequently encountered in aromatic alcohols capable of transferring a proton to a suitable acceptor. A promising new class of neutral super-photoacids based on pyranine derivatives has been shown to exhibit pronounced solvatochromic effects. To disclose the underlying mechanisms contributing to excited-state proton transfer (ESPT) and the temporal characteristics of solvation and ESPT, we scrutinize the associated ultrafast dynamics of the strongest photoacid of this class, namely tris(1,1,1,3,3,3-hexafluoropropan-2-yl)8-hydroxypyrene-1,3,6-trisulfonate, in acetoneous environment, thereby finding experimental evidence for ESPT even under these adverse conditions for proton transfer. Juxtaposing results from time-correlated single-photon counting and femtosecond transient absorption measurements combined with a complete decomposition of all signal components, i.e., absorption of ground and excited states as well as stimulated emission, we disclose dynamics of solvation, rotational diffusion, and radiative relaxation processes in acetone and identify the relevant steps of ESPT along with the associated time scales.

Suitable acid groups and density in electrolytes to facilitate proton conduction

Proton conducting materials suffer from low proton conductivity under low-relative humidity (RH) conditions. Previously, it was reported that acid-acid interactions, where acids interact with each other at close distances, can facilitate proton conduction without water movement and are promising for overcoming this drawback [T. Ogawa, H. Ohashi, T. Tamaki and T. Yamaguchi, Chem. Phys. Lett., 2019, 731, 136627]. However, acid groups have not been compared to find a suitable acid group and density for the interaction, which is important to experimentally synthesize the material. Here, we performed ab initio calculations to identify acid groups and acid densities as a polymer design that effectively causes acid-acid interactions. The evaluation method employed parameters based on several different optimized coordination interactions of acids and water molecules. The results show that the order of the abilities of polymer electrolytes to readily induce acid-acid interactions is hydrocarbon-based phosphonated polymers > phosphonated aromatic hydrocarbon polymers > perfluorosulfonic acid polymers ≈ perfluorophosphonic acid polymers > sulfonated aromatic hydrocarbon polymers. The acid-acid interaction becomes stronger as the distance between acids decreases. The preferable distance between phosphonate moieties is within 13 Å.

Structural Origin and Vibrational Fingerprints of the Ultrafast Excited State Proton Transfer of the Pyranine-Acetate Complex in Aqueous Solution

The excited state proton transfer (ESPT) reaction from the photoacid 8-hydroxypyrene-1,3,6-trisulfonic acid (HPTS or pyranine) to an acetate molecule has been investigated in explicit aqueous solution via excited state ab initio molecular dynamics simulations based on hybrid quantum/molecular mechanics (QM/MM) potentials. In all the trajectories, the direct proton transfer has been observed in the excited state within 1 ps. We find that the initial structural configuration extracted from the ground state distribution strongly affects the ESPT kinetics. Indeed, the relative orientation of the proton donor-acceptor pair and the presence of a water molecule hydrogen bonded to the phenolic acid group of the pyranine are the key factors to facilitate the ESPT. Furthermore, we analyze the vibrational fingerprints of the ESPT reaction, reproducing the blue shift of the acetate CO stretching (CO_ac), from 1666 to 1763 cm^-1 testifying the transformation of acetate to acetic acid. Finally, our findings suggest that the acetate CC stretching (CC_ac) is also sensitive to the progress of the ESPT reaction. The CC_ac stretching is indeed ruled by the two vibrational modes (928 and 1426 cm^-1), that in the excited state are alternately activated when the proton is shared or bound to the donor/acceptor, respectively.

Water-Mediated Excited State Proton Transfer of Pyranine-Acetate in Aqueous Solution: Vibrational Fingerprints from Ab Initio Molecular Dynamics

In this work, we simulate the excited state proton transfer (ESPT) reaction involving the pyranine photoacid and an acetate molecule as proton acceptor, connected by a bridge water molecule. We employ ab initio molecular dynamics combined with an hybrid quantum/molecular mechanics (QM/MM) framework. Furthermore, a time-resolved vibrational analysis based on the wavelet-transform allows one to identify two low frequency vibrational modes that are fingerprints of the ESPT event: a ring wagging and ring breathing. Their composition suggests their key role in optimizing the structure of the proton donor–acceptor couple and promoting the ESPT event. We find that the choice of the QM/MM partition dramatically affects the photoinduced reactivity of the system. The QM subspace was gradually extended including the water molecules directly interacting with the pyranine–water–acetate system. Indeed, the ESPT reaction takes place when the hydrogen bond network around the reactive system is taken into account at full QM level.

Ab initio metadynamics calculations of dimethylamine for probing pKb variations in bulk vs. surface environments

Free energy landscape obtained from ab initio metadynamics calculations for dimethylamine protonation at the air–water interface.

Excited-State Proton Transfer on the Surface of a Therapeutic Protein, Protamine

Proton transfer reactions on biosurfaces play an important role in a myriad of biological processes. Herein, the excited-state proton transfer reaction of 8-hydroxypyrene-1,3,6-trisulfonate (HPTS) has been investigated in the presence of an important therapeutic protein, Protamine (PrS), using ground-state absorption, steady-state, and detailed time-resolved emission measurements. HPTS forms a 1:1 complex with Protamine with a high association constant of 2.6 × 10⁴ M^-1. The binding of HPTS with Protamine leads to a significant modulation in the ground-state prototropic equilibrium causing a downward shift of 1.1 unit in the acidity constant (pK_a). In contrast to a large number of reports of slow proton transfer of HPTS on biosurfaces, interestingly, HPTS registers a faster proton transfer event in the presence of Protamine as compared to that of even the bulk aqueous buffer medium. Furthermore, the dimensionality of the proton diffusion process is also significantly reduced on the surface of Protamine that is in contrast to the behavior of HPTS in the bulk aqueous buffer medium, where the proton diffusion process is three-dimensional. The effect of ionic strength on the binding of HPTS toward PrS suggests a predominant role of electrostatic interaction between anionic HPTS and cationic Protamine, which is further supported by molecular docking simulations which predict that the most preferable binding site for HPTS on the surface of Protamine is surrounded by multiple cationic arginine residues.

Special Pairs Are Decisive in the Autoionization and Recombination of Water

Although water's chemical properties are no less important than its exceptional physical properties, its acid-base behavior is relatively poorly understood. In fact, the Grotthus trajectories for ion recombination predicted by density functional theory do not comport well with the almost 100-fold slower diffusive trajectories observed in time-resolved spectroscopy. And, in the reverse reaction, the barrier to autoionization is not well characterized. Here we develop a self-consistent picture of both processes based on the occurrence and role of ultrashort hydrogen bonds. The predicted populations of these special pairs in bulk water are consistent with the high frequency electrodynamics of water and its pressure dependence. The rate-limiting role of the special pairs manifests in autoionization as a two-stage barrier, first to form a contact ion pair and then to separate it by one water molecule. From this configuration, similar frequencies are observed for further separation vs recombination. The requirement of ultrashort hydrogen bonds for proton transfer in autoionization is consistent with the rise in K_w with increasing pressure and points to a role for density fluctuations in autoionization events. In neutralization, the manifestation of the role of special pairs is the prolonged diffusional process observed in time-resolved spectroscopy experiments. The requirement of special pairs as transition states for proton transfer is less obvious for neutralization in isolated water chains than in the bulk liquid only because an unbroken sequence of ultrashort H-bonds is more easily formed in a 1D H-bonded chain than in a 3D H-bonded network.

Coherent intermolecular proton transfer in the acid–base reaction of excited state pyranine

The acidic proton in pyranine is transferred coherently to acetate through the stretching motion of the whole molecule.

Proton Wire Dynamics in the Green Fluorescent Protein

Inside proteins, protons move on proton wires (PWs). Starting from the highest resolution X-ray structure available, we conduct a 306 ns molecular dynamics simulation of the (A-state) wild-type (wt) green fluorescent protein (GFP) to study how its PWs change with time. We find that the PW from the chromophore via Ser205 to Glu222, observed in all X-ray structures, undergoes rapid water molecule insertion between Ser205 and Glu222. Sometimes, an alternate Ser205-bypassing PW exists. Side chain rotations of Thr203 and Ser205 play an important role in shaping the PW network in the chromophore region. Thr203, with its bulkier side chain, exhibits slower transitions between its three rotameric states. Ser205 experiences more frequent rotations, slowing down when the Thr203 methyl group is close by. The combined states of both residues affect the PW probabilities. A random walk search for PWs from the chromophore reveals several exit points to the bulk, one being a direct water wire (WW) from the chromophore to the bulk. A longer WW connects the "bottom" of the GFP barrel with a "water pool" (WP1) situated below Glu222. These two WWs were not observed in X-ray structures of wt-GFP, but their analogues have been reported in related fluorescent proteins. Surprisingly, the high-resolution X-ray structure utilized herein shows that Glu222 is protonated at low temperatures. At higher temperatures, we suggest ion pairing between anionic Glu222 and a proton hosted in WP1. Upon photoexcitation, these two recombine, while a second proton dissociates from the chromophore and either exits the protein using the short WW or migrates along the GFP-barrel axis on the long WW. This mechanism reconciles the conflicting experimental and theoretical data on proton motion within GFP.

Protons and Hydroxide Ions in Aqueous Systems

Understanding the structure and dynamics of water's constituent ions, proton and hydroxide, has been a subject of numerous experimental and theoretical studies over the last century. Besides their obvious importance in acid-base chemistry, these ions play an important role in numerous applications ranging from enzyme catalysis to environmental chemistry. Despite a long history of research, many fundamental issues regarding their properties continue to be an active area of research. Here, we provide a review of the experimental and theoretical advances made in the last several decades in understanding the structure, dynamics, and transport of the proton and hydroxide ions in different aqueous environments, ranging from water clusters to the bulk liquid and its interfaces with hydrophobic surfaces. The propensity of these ions to accumulate at hydrophobic surfaces has been a subject of intense debate, and we highlight the open issues and challenges in this area. Biological applications reviewed include proton transport along the hydration layer of various membranes and through channel proteins, problems that are at the core of cellular bioenergetics.

Deprotonation of formic acid in collisions with a liquid water surface studied by molecular dynamics and metadynamics simulations

Formic acid has a lower barrier to deprotonation at the air–water interface than in bulk liquid water.

Solvation-Dependent Latency of Photoacid Dissociation and Transient IR Signatures of Protonation Dynamics

We elucidate the characteristic proton pathways and the transient infrared signatures of intermediate complexes during the first picoseconds of photoinduced protonation dynamics of a photoacid (N-methyl-6-hydroxyquinolinium) in aqueous solution from first-principles molecular dynamics simulations. Our results indicate that the typical latency time between photoexcitation and proton dissociation ranges from 1 ps to longer time time scales (∼100 ps). The rate-limiting step for the actual dissociation of the proton into the solvent is the solvation structure of the first accepting water molecule. The nature of the proton pathway in water (stepwise or concerted) is not unique but determined by the coordination number of the accepting water molecules along the hydrogen bond chain. We find a characteristic uncommon infrared mode at ∼1300 cm(-1) of the transient photobase-Eigen cation complex immediately after photodissociation that we predict to be observable experimentally in time-resolved IR spectroscopy. A broad continuous absorption band from 1500 to 2000 cm(-1) arises from the acidic proton imminently before dissociation.

Excited-State Proton Transfer in Resveratrol and Proposed Mechanism for Plant Resistance to Fungal Infection

Steady-state and time-resolved fluorescence techniques were employed to study the photophysics and photochemistry of trans-resveratrol. trans-Resveratrol is found in large quantities in fungi-infected grapevine-leaf tissue and plays a direct role in the resistance to plant disease. We found that trans-resveratrol in liquid solution undergoes a trans-cis isomerization process in the excited state at a rate that depends partially on the solvent viscosity, as was found in previous studies on trans-stilbene. The hydroxyl groups of the phenol moieties in resveratrol are weak photoacids. In water and methanol solutions containing weak bases such as acetate, a proton is transferred to the base within the lifetime of the excited state. When resveratrol is adsorbed on cellulose (also a component of the plant's cell wall), the cis-trans process is slow and the lifetime of the excited state increases from several tens of picoseconds in ethanol to about 1.5 ns. Excited-state proton transfer occurs when resveratrol is adsorbed on cellulose and acetate ions are in close proximity to the phenol moieties. We propose that proton transfer from excited resveratrol to the fungus acid-sensing chemoreceptor is one of the plant's resistance mechanisms to fungal infection.

Deciphering the infrared spectrum of the protonated water pentamer and the hybrid Eigen-Zundel cation

Traditionally, infrared band assignment for the protonated water clusters, such as H(+)(H2O)5, is based on their lowest energy isomer. Recent experiments extend the observation spectral window to lower frequencies, for which such assignment appears to be inadequate. Because this hydrogen-bonded system is highly anharmonic, harmonic spectral calculations are insufficient for reliable interpretation. Consequently, we have calculated the IR spectrum of several isomers of the protonated water pentamer using an inherently anharmonic methodology, utilizing dipole and velocity autocorrelation functions computed from ab initio molecular dynamic trajectories. While the spectrum of H(+)(H2O)5 is universally assumed to represent the branched Eigen isomer, we find a better agreement for a mixture of a ring and linear isomers. The first has an Eigen core and contributes at high frequencies, whereas the latter accounts for all prominent low-frequency bands. Interestingly, its core is neither a classical Eigen nor a Zundel cation, but rather has hybrid geometry. Such an isomer may play a role in proton conductance along short proton wires.

Excited state structural events of a dual-emission fluorescent protein biosensor for Ca²⁺ imaging studied by femtosecond stimulated Raman spectroscopy

Fluorescent proteins (FPs) are luminescent biomolecules that emit characteristic hues upon irradiation. A group of calmodulin (CaM)-green FP (GFP) chimeras have been previously engineered to enable the optical detection of calcium ions (Ca(2+)). We investigate one of these genetically encoded Ca(2+) biosensors for optical imaging (GECOs), GEM-GECO1, which fluoresces green without Ca(2+) but blue with Ca(2+), using femtosecond stimulated Raman spectroscopy (FSRS). The time-resolved FSRS data (<800 cm(-1)) reveal that initial structural evolution following 400 nm photoexcitation involves small-scale coherent proton motions on both ends of the chromophore two-ring system with a <250 fs time constant. Upon Ca(2+) binding, the chromophore adopts a more twisted conformation in the protein pocket with increased hydrophobicity, which inhibits excited-state proton transfer (ESPT) by effectively trapping the protonated chromophore in S1. Both the chromophore photoacidity and local environment form the ultrafast structural dynamics basis for the dual-emission properties of GEM-GECO1. Its photochemical transformations along multidimensional reaction coordinates are evinced by distinct stages of FSRS spectral evolution, particularly related to the ∼460 and 504 cm(-1) modes. The direct observation of lower frequency modes provides crucial information about the nuclear motions preceding ESPT, which enriches our understanding of photochemistry and enables the rational design of new biosensors.

Excited-state structural dynamics of a dual-emission calmodulin-green fluorescent protein sensor for calcium ion imaging

Fluorescent proteins (FPs) have played a pivotal role in bioimaging and advancing biomedicine. The versatile fluorescence from engineered, genetically encodable FP variants greatly enhances cellular imaging capabilities, which are dictated by excited-state structural dynamics of the embedded chromophore inside the protein pocket. Visualization of the molecular choreography of the photoexcited chromophore requires a spectroscopic technique capable of resolving atomic motions on the intrinsic timescale of femtosecond to picosecond. We use femtosecond stimulated Raman spectroscopy to study the excited-state conformational dynamics of a recently developed FP-calmodulin biosensor, GEM-GECO1, for calcium ion (Ca(2+)) sensing. This study reveals that, in the absence of Ca(2+), the dominant skeletal motion is a ∼ 170 cm(-1) phenol-ring in-plane rocking that facilitates excited-state proton transfer (ESPT) with a time constant of ∼ 30 ps (6 times slower than wild-type GFP) to reach the green fluorescent state. The functional relevance of the motion is corroborated by molecular dynamics simulations. Upon Ca(2+) binding, this in-plane rocking motion diminishes, and blue emission from a trapped photoexcited neutral chromophore dominates because ESPT is inhibited. Fluorescence properties of site-specific protein mutants lend further support to functional roles of key residues including proline 377 in modulating the H-bonding network and fluorescence outcome. These crucial structural dynamics insights will aid rational design in bioengineering to generate versatile, robust, and more sensitive optical sensors to detect Ca(2+) in physiologically relevant environments.

Proton transfer through the water gossamer

The diffusion of protons through water is understood within the framework of the Grotthuss mechanism, which requires that they undergo structural diffusion in a stepwise manner throughout the water network. Despite long study, this picture oversimplifies and neglects the complexity of the supramolecular structure of water. We use first-principles simulations and demonstrate that the currently accepted picture of proton diffusion is in need of revision. We show that proton and hydroxide diffusion occurs through periods of intense activity involving concerted proton hopping followed by periods of rest. The picture that emerges is that proton transfer is a multiscale and multidynamical process involving a broader distribution of pathways and timescales than currently assumed. To rationalize these phenomena, we look at the 3D water network as a distribution of closed directed rings, which reveals the presence of medium-range directional correlations in the liquid. One of the natural consequences of this feature is that both the hydronium and hydroxide ion are decorated with proton wires. These wires serve as conduits for long proton jumps over several hydrogen bonds.

Some conceptual thoughts toward nanoscale oriented friction in a model of articular cartilage

This work presents a conceptual framework as to how a deficit in the synovial-fluid content, exemplified by hyaluronan or any other amphiphilic species, is capable of decisively altering the complex lubrication and wear conditions observed clinically in articular cartilage. The effect is revealed in (non)stationary regimes if the cartilage is subjected to some normal periodic load, revealing over its exploitation time increasingly dissipative, in general entropy-addressing, characteristics. It can be hypothesized that a Grotthuss-type proton transport physiology-concerning mechanism in channel-like, phospholipid-water cartilage's articulating nanospaces will be responsible for the expression of the lubrication mode. The corresponding wear involving overall change is then manifested adequately in the stationary regime, and in a viable system-parametric correlation with its lubrication counterpart. Certain analytic formulae for the nanoscale oriented coefficient of friction, involving generically H-bonds breaking mechanism, and pointing to some local-viscosity context, have been proposed for fitting the experimental data and clinical observations involving proton management at articular cartilage surfaces.

Early time excited-state structural evolution of pyranine in methanol revealed by femtosecond stimulated Raman spectroscopy

To understand chemical reactivity of molecules in condensed phase in real time, a structural dynamics technique capable of monitoring molecular conformational motions on their intrinsic time scales, typically on femtoseconds to picoseconds, is needed. We have studied a strong photoacid pyranine (8-hydroxypyrene-1,3,6-trisulfonic acid, HPTS, pK(a)* ≈ 0) in pure methanol and observed that excited-state proton transfer (ESPT) is absent, in sharp contrast with our previous work on HPTS in aqueous solutions wherein ESPT prevails following photoexcitation. Two transient vibrational marker bands at ~1477 (1454) and 1532 (1528) cm(-1) appear in CH3OH (CD3OD), respectively, rising within the instrument response time of ~140 fs and decaying with 390-470 (490-1400) fs and ~200 ps time constants in CH3OH (CD3OD). We attribute the mode onset to small-scale coherent proton motion along the pre-existing H-bonding chain between HPTS and methanol, and the two decay stages to the low-frequency skeletal motion-modulated Franck-Condon relaxation within ~1 ps and subsequent rotational diffusion of H-bonding partners in solution before fluorescence. The early time kinetic isotope effect (KIE) of ~3 upon methanol deuteration argues active proton motions particularly within the first few picoseconds when coherent skeletal motions are underdamped. Pronounced quantum beats are observed for high-frequency modes consisting of strong phenolic COH rocking (1532 cm(-1)) or H-out-of-plane wagging motions (952 cm(-1)) due to anharmonic coupling to coherent low-frequency modes impulsively excited at ca. 96, 120, and 168 cm(-1). The vivid illustration of atomic motions of HPTS in varying H-bonding geometry with neighboring methanol molecules unravels the multidimensional energy relaxation pathways immediately following photoexcitation, and provides compelling evidence that, in lieu of ESPT, the photoacidity of HPTS promptly activates characteristic low-frequency skeletal motions to search phase space mainly concerning the phenolic end and to efficiently dissipate vibrational energy via skeletal deformation and proton shuttling motions within the intermediate, relatively confined excited-state HPTS-methanol complex on a solvent-dependent dynamic potential energy surface.

Concerted and Sequential Proton Transfer Mechanisms in Water-Separated Acid-Base Encounter Pairs

The proton transfer mechanisms involved inside aqueous, solvent-separated encounter complexes between phenol and carboxyl moieties are studied using ab initio molecular dynamics and computational time-resolved vibrational spectroscopy. This model framework can be viewed as a ground-state analog of the excited-state proton transfer reactions that have been actively investigated using ultrafast spectroscopy. Three qualitatively distinct proton transfer pathways are observed in the simulations. These can be described as direct concerted, direct sequential, and through bulk transfers. The primary difference between the sequential and concerted mechanism is the involvement of a reaction intermediate in which the proton fluctuates for several picoseconds through the hydrogen bonds connecting donor and acceptor but resides primarily on an intervening water molecule in the encounter complex. These results contribute to our molecular level understanding of the diverse processes involved in proton transfer within water-separated encounter complexes.

Hydrogen-bonded networks along and bifurcation of the E-pathway in quinol:fumarate reductase

The E-pathway of transmembrane proton transfer has been demonstrated previously to be essential for catalysis by the diheme-containing quinol:fumarate reductase (QFR) of Wolinella succinogenes. Two constituents of this pathway, Glu-C180 and heme b(D) ring C (b(D)-C-) propionate, have been validated experimentally. Here, we identify further constituents of the E-pathway by analysis of molecular dynamics simulations. The redox state of heme groups has a crucial effect on the connectivity patterns of mobile internal water molecules that can transiently support proton transfer from the b(D)-C-propionate to Glu-C180. The short H-bonding paths formed in the reduced states can lead to high proton conduction rates and thus provide a plausible explanation for the required opening of the E-pathway in reduced QFR. We found evidence that the b(D)-C-propionate group is the previously postulated branching point connecting proton transfer to the E-pathway from the quinol-oxidation site via interactions with the heme b(D) ligand His-C44. An essential functional role of His-C44 is supported experimentally by site-directed mutagenesis resulting in its replacement with Glu. Although the H44E variant enzyme retains both heme groups, it is unable to catalyze quinol oxidation. All results obtained are relevant to the QFR enzymes from the human pathogens Campylobacter jejuni and Helicobacter pylori.

Hydrogen-bond relays in concerted proton-electron transfers

Reaction mechanisms in which electron and proton transfers are coupled are central to a huge number of processes, both natural and synthetic. Moreover, most of the new approaches to address modern energy challenges involve proton-coupled electron transfer (PCET). Recent research has focused on the possibility that the two steps are concerted, that is, concerted proton-electron transfer (CPET) reactions, rather than stepwise pathways in which proton transfer precedes (PET) or follows (EPT) electron transfer. CPET pathways have the advantage of bypassing the high-energy intermediates of stepwise pathways, although this thermodynamic benefit may have a kinetic cost. Concerted processes require short distances between the group being oxidized and the proton acceptor (and vice versa for a reduction process), which usually involves the formation of a hydrogen bond. Unlike the electron in outer-sphere electron-transfer reactions, the distance a proton may travel in a CPET is therefore rather limited. The idea has recently emerged, however, that this distance may be substantially increased via a H-bond relay located between the electron-transfer-triggered proton source and the proton acceptor. Generally speaking, the relay is a group bearing a H atom able to accept a H-bond from the moiety being oxidized and, at the same time, to form a H-bond with the proton-accepting group without going through a protonated intermediate. Although these molecules do not retain all the properties of chains of water molecules engaged in Grotthuss-type transport of a proton, the OH group in these molecules does possess a fundamental property of water molecules: namely, it is both a hydrogen-bond acceptor and a hydrogen-bond donor. Despite centuries of study, the mechanisms of proton movement in water remain active experimental and theoretical research areas, but so far with no connection to CPET reactions. In this Account, we bring together recent results concerning (i) the oxidative response of molecules containing a H-bond relay and (ii) the oxidation of phenol with water (in water) as the proton acceptor. In the first case, a nondestructive electrochemical method (cyclic voltammetry) was used to investigate the oxidation of phenol molecules containing one H-bond relay and an amine proton acceptor compared with a similar amino phenol deprived of relay. In the second, the kinetics of phenol oxidation with water (in water) as proton acceptor is contrasted with that of conventional proton acceptors (such as hydrogen phosphate and pyridine) to afford evidence of the concerted nature of Grotthuss-type proton displacement with electron transfer. First indications were provided by the same electrochemical method, whereas a more complete kinetic characterization was obtained from laser flash photolysis. Older electrochemical results concerning the reduction of superoxide ion in the presence of water are also examined. The result is a timely picture of current insight into concerted mechanisms involving electron transfer coupled with proton transport over simple H-bond relays and over H-bond networks.

On the recombination of hydronium and hydroxide ions in water

The recombination of hydronium and hydroxide ions following water ionization is one of the most fundamental processes determining the pH of water. The neutralization step once the solvated ions are in close proximity is phenomenologically understood to be fast, but the molecular mechanism has not been directly probed by experiments. We elucidate the mechanism of recombination in liquid water with ab initio molecular dynamics simulations, and it emerges as quite different from the conventional view of the Grotthuss mechanism. The neutralization event involves a collective compression of the water-wire bridging the ions, which occurs in approximately 0.5 ps, triggering a concerted triple jump of the protons. This process leaves the neutralized hydroxide in a hypercoordinated state, with the implications that enhanced collective compressions of several water molecules around similarly hypercoordinated states are likely to serve as nucleation events for the autoionization of liquid water.