Proton solvation and transport in aqueous and biomolecular systems: insights from computer simulations

Solid-State Glass Nanopipettes: Functionalization and Applications

Solid-state glass nanopipettes provide a promising confined space that offers several advantages such as controllable size, simple preparation, low cost, good mechanical stability, and good thermal stability. These advantages make them an ideal choice for various applications such as biosensors, DNA sequencing, and drug delivery. In this review, we first delve into the functionalized nanopipettes for sensing various analytes and the methods used to develop detection means with them. Next, we provide an in-depth overview of the advanced functionalization methodologies of nanopipettes based on diversified chemical kinetics. After that, we present the latest state-of-the-art achievements and potential applications in detecting a wide range of targets, including ions, molecules, biological macromolecules, and single cells. We examine the various challenges that arise when working with these targets, as well as the innovative solutions developed to overcome them. The final section offers an in-depth overview of the current development status, newest trends, and application prospects of sensors. Overall, this review provides a comprehensive and detailed analysis of the current state-of-the-art functionalized nanopipette perception sensing and development of detection means and offers valuable insights into the prospects for this exciting field.

Femtosecond Electron-Transfer Dynamics across the D2O/Cs+/Cu(111) Interface: The Impact of Hydrogen Bonding

Hydrogen bonding is essential in electron-transfer processes at water-electrode interfaces. We study the impact of the H-bonding of water as a solvent molecule on real-time electron-transfer dynamics across a Cs+-Cu(111) ion-metal interface using femtosecond time-resolved two-photon photoelectron spectroscopy. We distinguish in the formed water-alkali aggregates two regimes below and above two water molecules per ion. Upon crossing the boundary of these regimes, the lifetime of the excess electron localized transiently at the Cs+ ion increases from 40 to 60 fs, which indicates a reduced alkali-metal interaction. Furthermore, the energy transferred to a dynamic structural rearrangement due to hydration is reduced from 0.3 to 0.2 eV concomitantly. These effects are a consequence of H-bonding in the water-water interaction and the beginning formation of a nanoscale water network. This finding is supported by real-space imaging of the solvatomers and vibrational frequency shifts of the OH stretching and bending modes calculated for these specific interfaces.

Electrophoresis of ions and electrolyte conductivity: From bulk to nanochannels

When electrolyte solutions are confined in micro- and nanochannels their conductivity is significantly different from those in a bulk phase. Here we revisit the theory of this phenomenon by focusing attention on the reduction in the ion mobility with the concentration of salt and a consequent impact to the conductivity of a monovalent solution, from bulk to confined in a narrow slit. We first give a systematic treatment of electrophoresis of ions and obtain equations for their zeta potentials and mobilities. The latter are then used to obtain a simple expression for a bulk conductivity, which is valid in a concentration range up to a few molars and more accurate than prior analytic theories. By extending the formalism to the electrolyte solution in the charged channel the equations describing the conductivity in different modes are presented. They can be regarded as a generalization of prior work on the channel conductivity to a more realistic case of a nonzero reduction of the electrophoretic mobility of ions with salt concentration. Our analysis provides a framework for interpreting measurements on the conductivity of electrolyte solutions in the bulk and in narrow channels.

Understanding the Multifaceted Mechanism of Compound I Formation in Unspecific Peroxygenases through Multiscale Simulations

Unspecific peroxygenases (UPOs) can selectively oxyfunctionalize unactivated hydrocarbons by using peroxides under mild conditions. They circumvent the oxygen dilemma faced by cytochrome P450s and exhibit greater stability than the latter. As such, they hold great potential for industrial applications. A thorough understanding of their catalysis is needed to improve their catalytic performance. However, it remains elusive how UPOs effectively convert peroxide to Compound I (CpdI), the principal oxidizing intermediate in the catalytic cycle. Previous computational studies of this process primarily focused on heme peroxidases and P450s, which have significant differences in the active site from UPOs. Additionally, the roles of peroxide unbinding in the kinetics of CpdI formation, which is essential for interpreting existing experiments, have been understudied. Moreover, there has been a lack of free energy characterizations with explicit sampling of protein and hydration dynamics, which is critical for understanding the thermodynamics of the proton transport (PT) events involved in CpdI formation. To bridge these gaps, we employed multiscale simulations to comprehensively characterize the CpdI formation in wild-type UPO from Agrocybe aegerita (AaeUPO). Extensive free energy and potential energy calculations were performed in a quantum mechanics/molecular mechanics setting. Our results indicate that substrate-binding dehydrates the active site, impeding the PT from H2O2 to a nearby catalytic base (Glu196). Furthermore, the PT is coupled with considerable hydrogen bond network rearrangements near the active site, facilitating subsequent O-O bond cleavage. Finally, large unbinding free energy barriers kinetically stabilize H2O2 at the active site. These findings reveal a delicate balance among PT, hydration dynamics, hydrogen bond rearrangement, and cosubstrate unbinding, which collectively enable efficient CpdI formation. Our simulation results are consistent with kinetic measurements and offer new insights into the CpdI formation mechanism at atomic-level details, which can potentially aid the design of next-generation biocatalysts for sustainable chemical transformations of feedstocks.

Advantages of Multidimensional Biasing in Accelerated Dynamics: Application to the Calculation of the Acid pKa for Acetic Acid

The use of accelerated sampling methods such as metadynamics has shown a significant advantage in calculations that involve infrequent events, which would otherwise require sampling a prohibitive number of configurations to determine the difference in free energies between two or more chemically distinct states such as in the calculation of acid dissociation constants Ka. In this case, the most common method is to bias the system via a single collective variable (CV) representing the coordination number of the proton donor group, which yields results in reasonable agreement with experiments. Here we study the deprotonation of acetic acid using the reactive force field ReaxFF and observe a significant dependence of Ka on the simulation box size when biasing only the coordination number CV, which is due to incomplete sampling of the deprotonated state for small simulation systems and inefficient sampling for larger ones. Incorporating a second CV representing the distance between the H3O+ cation and the acetate anion results in substantially more efficient sampling, both accelerating the dynamics and virtually eliminating the computational box size dependence.

Search for a Grotthuss mechanism through the observation of proton transfer

The transport of protons is critical in a variety of bio- and electro-chemical processes and technologies. The Grotthuss mechanism is considered to be the most efficient proton transport mechanism, generally implying a transfer of protons between 'chains' of host molecules via elementary reactions within the hydrogen bonds. Although Grotthuss proposed this concept more than 200 years ago, only indirect experimental evidence of the mechanism has been observed. Here we report the first experimental observation of proton transfer between the molecules in pure and 85% aqueous phosphoric acid. Employing dielectric spectroscopy, quasielastic neutron, and light scattering, and ab initio molecular dynamic simulations we determined that protons move by surprisingly short jumps of only ~0.5-0.7 Å, much smaller than the typical ion jump length in ionic liquids. Our analysis confirms the existence of correlations in these proton jumps. However, these correlations actually reduce the conductivity, in contrast to a desirable enhancement, as is usually assumed by a Grotthuss mechanism. Furthermore, our analysis suggests that the expected Grotthuss-like enhancement of conductivity cannot be realized in bulk liquids where ionic correlations always decrease conductivity.

Ab initio molecular dynamics study of proton transport in imidazolium-based ionic liquids with added imidazole

Development of efficient anhydrous proton-conducting materials would expand the operational temperature ranges of hydrogen fuels cells (HFCs) and eliminate their dependence on maintaining sufficient hydration levels to function efficiently. Protic ionic liquids (PILs), which have high ionic densities and low vapor pressures, have emerged as a potential material for proton conducting layers in HFCs. In this work, we investigate proton transport via the Grotthuss mechanism in 1-ethylimidazolium bis-(trifluoromethanesulfonyl)imide ([C₂HIm][TFSI]) protic ionic liquids with added imidazole (Im⁰) using ab initio molecular dynamics. In particular, we vary the composition of the systems studied from pure [C₂HIm][TFSI] to those where the mole fraction of Im⁰ is 0.67. Given the large difference in pK_a between C₂HIm⁺ and HTFSI, TFSI^- does not accept acidic protons from C₂HIm⁺; conversely, imidazolium (HIm⁺) and C₂HIm⁺ have very similar pK_a values, and thus Im⁰ can readily accept protons. We find that the unprotonated nitrogen on Im⁰ dominates solvation of the labile protons on C₂HIm⁺ and other Im⁰ species, resulting in formation of robust imidazole wires. Given the amphoteric nature of Im⁰, i.e. its ability to accept and donate protons, these wires provide conduits along which protons can rapidly traverse via the Grotthuss mechanism, thereby greatly increasing the proton coefficient of self-diffusion. We find that the average length of the wires increases with added Im⁰, and thus as the mole fraction of Im⁰ increases so too does the proton diffusion constant. Lastly, we analyze our trajectories to determine the energy and time scales associated with proton transfer.

Accurate pKa Calculations in Proteins with Reactive Molecular Dynamics Provide Physical Insight Into the Electrostatic Origins of Their Values

Classical molecular dynamics simulations are a versatile tool in the study of biomolecular systems, but they usually rely on a fixed bonding topology, precluding the explicit simulation of chemical reactivity. Certain modifications can permit the modeling of reactions. One such method, multiscale reactive molecular dynamics, makes use of a linear combination approach to describe condensed-phase free energy surfaces of reactive processes of biological interest. Before these simulations can be performed, models of the reactive moieties must first be parametrized using electronic structure data. A recent study demonstrated that gas-phase electronic structure data can be used to derive parameters for glutamate and lysine which reproduce experimental pKa values in both bulk water and the staphylococcal nuclease protein with remarkable accuracy and transferability between the water and protein environments. In this work, we first present a new model for aspartate derived in similar fashion and demonstrate that it too produces accurate pKa values in both bulk and protein contexts. We also describe a modification to the prior methodology, involving refitting some of the classical force field parameters to density functional theory calculations, which improves the transferability of the existing glutamate model. Finally and most importantly, this reactive molecular dynamics approach, based on rigorous statistical mechanics, allows one to specifically analyze the fundamental physical causes for the marked pKa shift of both aspartate and glutamate between bulk water and protein and also to demonstrate that local steric and electrostatic effects largely explain the observed differences.

Gas-Phase External Solvation of Protonated Benzonitrile by Eight Methanol Molecules

The gas-phase sequential association of methanol onto protonated benzonitrile (C₆H₅CNH⁺) and the proton-bound dimer (C₆H₅CN)₂H⁺ have been examined experimentally by equilibrium thermochemical measurements and computationally by density functional theory (DFT). The bonding enthalpy (ΔH°) for the association of methanol with protonated benzonitrile (25.2 kcal mol^-1) reflects the strong electrostatic interaction provided by the formation of an ionic hydrogen bond in the C₆H₅CNH⁺OHCH₃ cluster in excellent agreement with a DFT-calculated binding energy of 24.9 kcal mol^-1. The sequential bonding enthalpy within the (C₆H₅CN)H⁺(OHCH₃)_n clusters decreases from 25.2 to 10.6 kcal mol^-1 for the eighth solvation step (n = 8), which remains more than 25% above the enthalpy of vaporization of liquid methanol (8.4 kcal mol^-1). The nonbulk convergence of ΔH°_n-1,n with eight solvent molecules is attributed to the external solvation of a benzonitrile molecule by an extended hydrogen bonding network of protonated methanol clusters H⁺(CH₃OH)_n. In the external solvation of protonated benzonitrile by methanol, the proton resides on the methanol subcluster and the neutral benzonitrile molecule remains outside and bonded to the surface of the protonated methanol cluster. The bonding enthalpy of methanol to the proton-bound benzonitrile dimer (C₆H₅CN)H⁺(NCC₆H₅) is measured to be 18.0 kcal mol^-1, in good agreement with a DFT-calculated value of 17.1 kcal mol^-1, which reflects the association of the proton with the lower proton affinity methanol molecule, thus forming a highly stable structure of protonated methanol terminated by two ionic hydrogen bonds to the two benzonitrile molecules. The external solvation of benzonitrile by methanol ices in space allows benzonitrile to remain on the ice grain surface rather than being isolated inside the ice. This could provide accessibility for reactions with incoming ions and molecules or for photochemical processes by UV irradiation, leading to the formation of complex organics on the surface of ice grains.

Water-Assisted Proton Transfer in the Sequential Hydration of Benzonitrile Radical Cation C6H5CN•+(H2O)n: Transition to Hydrated Distonic Cation •C6H4CNH+(H2O)n with n ≥ 4

The stepwise hydration of the benzonitrile^•+ radical cation with one-seven H₂O molecules was investigated experimentally and computationally with density functional theory in C₆H₅CN^•+(H₂O)_n clusters. The stepwise binding energies (ΔH_n-1,n^°) were determined by equilibrium measurements for C₆H₅CN^•+(H₂O) and for ^•C₆H₄CNH⁺(H₂O)_n with n = 5, 6, and 7 to be 8.8 and 11.3, 11.0, and 10.0 kcal/mol, respectively. The populations of n = 2 and 3 of the C₆H₅CN^•+(H₂O)_n clusters were observed only in trace abundance due to fast depletion processes leading to the formation of the hydrated distonic cations ^•C₆H₄CNH⁺(H₂O)_n with n = 4-7. The observed transition occurs between conventional radical cations hydrated on the ring in C₆H₅CN^•+(H₂O)_n clusters with n = 1-3 and the protonated radical ^•C₆H₄CNH⁺ (distonic ion) formed by a proton transfer to the CN nitrogen and ionic hydrogen bonding to water molecules in ^•C₆H₄CNH⁺(H₂O)_n clusters with n = 4-7. The measured binding energy of the hydrated ion C₆H₅CN^•+(H₂O) (8.8 kcal/mol) is similar to that of the hydrated benzene radical cation (8.5 kcal/mol) that involves a relatively weak CH^δ+···O hydrogen bonding interaction. Also, the measured binding energies of the ^•C₆H₄CNH⁺(H₂O)_n clusters with n = 5-7 are similar to those of the protonated benzonitrile (methanol)_n clusters [C₆H₅CNH⁺(CH₃OH)_n, n = 5-7] that involve CNH⁺···O ionic hydrogen bonds. The proton shift from the para-^•C ring carbon to the nitrogen of the benzonitrile radical cation is endothermic without solvent but thermoneutral for n = 1 and exothermic for n = 2-4 in C₆H₅CN^•+(H₂O)_n clusters to form the distonic ^•C₆H₄CN···H⁺(OH₂)_n clusters. The distonic clusters ^•C₆H₄CN···H⁺(OH₂)_n constitute a new class of structures in radical ion/solvent clusters.

Comparison of proton transfer paths to the QA and QB sites of the Rb. sphaeroides photosynthetic reaction centers

The photosynthetic bacterial reaction centers from purple non-sulfur bacteria use light energy to drive the transfer of electrons from cytochrome c to ubiquinone. Ubiquinone bound in the Q_A site cycles between quinone, Q_A, and anionic semiquinone, Q_A^·-, being reduced once and never binding protons. In the Q_B site, ubiquinone is reduced twice by Q_A^·-, binds two protons and is released into the membrane as the quinol, QH₂. The network of hydrogen bonds formed in a molecular dynamics trajectory was drawn to investigate proton transfer pathways from the cytoplasm to each quinone binding site. Q_A is isolated with no path for protons to enter from the surface. In contrast, there is a complex and tangled network requiring residues and waters that can bring protons to Q_B. There are three entries from clusters of surface residues centered around HisH126, GluH224, and HisH68. The network is in good agreement with earlier studies, Mutation of key nodes in the network, such as SerL223, were previously shown to slow proton delivery. Mutational studies had also shown that double mutations of residues such as AspM17 and AspL210 along multiple paths in the network presented here slow the reaction, while single mutations do not. Likewise, mutation of both HisH126 and HisH128, which are at the entry to two paths reduce the rate of proton uptake.

The Solvation-Induced Onsager Reaction Field Rather than the Double-Layer Field Controls CO2 Reduction on Gold

The selectivity and activity of the carbon dioxide reduction (CO₂R) reaction are sensitive functions of the electrolyte cation. By measuring the vibrational Stark shift of in situ-generated CO on Au in the presence of alkali cations, we quantify the total electric field present at catalytic active sites and deconvolute this field into contributions from (1) the electrochemical Stern layer and (2) the Onsager (or solvation-induced) reaction field. Contrary to recent theoretical reports, the CO₂R kinetics does not depend on the Stern field but instead is closely correlated with the strength of the Onsager reaction field. These results show that in the presence of adsorbed (bent) CO₂, the Onsager field greatly exceeds the Stern field and is primarily responsible for CO₂ activation. Additional measurements of the cation-dependent water spectra using vibrational sum frequency generation spectroscopy show that interfacial solvation strongly influences the CO₂R activity. These combined results confirm that the cation-dependent interfacial water structure and its associated electric field must be explicitly considered for accurate understanding of CO₂R reaction kinetics.

A quantitative paradigm for water-assisted proton transport through proteins and other confined spaces

Water-assisted proton transport through confined spaces influences many phenomena in biomolecular and nanomaterial systems. In such cases, the water molecules that fluctuate in the confined pathways provide the environment and the medium for the hydrated excess proton migration via Grotthuss shuttling. However, a definitive collective variable (CV) that accurately couples the hydration and the connectivity of the proton wire with the proton translocation has remained elusive. To address this important challenge-and thus to define a quantitative paradigm for facile proton transport in confined spaces-a CV is derived in this work from graph theory, which is verified to accurately describe water wire formation and breakage coupled to the proton translocation in carbon nanotubes and the Cl^-/H⁺ antiporter protein, ClC-ec1. Significant alterations in the conformations and thermodynamics of water wires are uncovered after introducing an excess proton into them. Large barriers in the proton translocation free-energy profiles are found when water wires are defined to be disconnected according to the new CV, even though the pertinent confined space is still reasonably well hydrated and-by the simple measure of the mere existence of a water structure-the proton transport would have been predicted to be facile via that oversimplified measure. In this paradigm, however, the simple presence of water is not sufficient for inferring proton translocation, since an excess proton itself is able to drive hydration, and additionally, the water molecules themselves must be adequately connected to facilitate any successful proton transport.

C-Graphs Tool with Graphical User Interface to Dissect Conserved Hydrogen-Bond Networks: Applications to Visual Rhodopsins

Dynamic hydrogen-bond networks provide proteins with structural plasticity required to translate signals such as ligand binding into a cellular response or to transport ions and larger solutes across membranes and, thus, are of central interest to understand protein reaction mechanisms. Here, we present C-Graphs, an efficient tool with graphical user interface that analyzes data sets of static protein structures or of independent numerical simulations to identify conserved, vs unique, hydrogen bonds and hydrogen-bond networks. For static structures, which may belong to the same protein or to proteins with different sequences, C-Graphs uses a clustering algorithm to identify sites of the hydrogen-bond network where waters are conserved among the structures. Using C-Graphs, we identify an internal protein-water hydrogen-bond network common to static structures of visual rhodopsins and adenosine A2A G protein-coupled receptors (GPCRs). Molecular dynamics simulations of a visual rhodopsin indicate that the conserved hydrogen-bond network from static structure can recruit dynamic hydrogen bonds and extend throughout most of the receptor. We release with this work the code for C-Graphs and its graphical user interface.

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.

The Effect of the Osmotically Active Compound Concentration Difference on the Passive Water and Proton Fluxes across a Lipid Bilayer

The molecular details of the passive water flux across the hydrophobic membrane interior are still a matter of debate. One of the postulated mechanisms is the spontaneous, water-filled pore opening, which facilitates the hydrophilic connection between aqueous phases separated by the membrane. In the paper, we provide experimental evidence showing that the spontaneous lipid pore formation correlates with the membrane mechanics; hence, it depends on the composition of the lipid bilayer and the concentration of the osmotically active compound. Using liposomes as an experimental membrane model, osmotically induced water efflux was measured with the stopped-flow technique. Shapes of kinetic curves obtained at low osmotic pressure differences are interpreted in terms of two events: the lipid pore opening and water flow across the aqueous channel. The biological significance of the dependence of the lipid pore formation on the concentration difference of an osmotically active compound was illustrated by the demonstration that osmotically driven water flow can be accompanied by the dissipation of the pH gradient. The application of the Helfrich model to describe the probability of lipid pore opening was validated by demonstrating that the probability of pore opening correlates with the membrane bending rigidity. The correlation was determined by experimentally derived bending rigidity coefficients and probabilities of lipid pores opening.

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.

Protein Motifs for Proton Transfers That Build the Transmembrane Proton Gradient

Biological membranes are barriers to polar molecules, so membrane embedded proteins control the transfers between cellular compartments. Protein controlled transport moves substrates and activates cellular signaling cascades. In addition, the electrochemical gradient across mitochondrial, bacterial and chloroplast membranes, is a key source of stored cellular energy. This is generated by electron, proton and ion transfers through proteins. The gradient is used to fuel ATP synthesis and to drive active transport. Here the mechanisms by which protons move into the buried active sites of Photosystem II (PSII), bacterial RCs (bRCs) and through the proton pumps, Bacteriorhodopsin (bR), Complex I and Cytochrome c oxidase (CcO), are reviewed. These proteins all use water filled proton transfer paths. The proton pumps, that move protons uphill from low to high concentration compartments, also utilize Proton Loading Sites (PLS), that transiently load and unload protons and gates, which block backflow of protons. PLS and gates should be synchronized so PLS proton affinity is high when the gate opens to the side with few protons and low when the path is open to the high concentration side. Proton transfer paths in the proteins we describe have different design features. Linear paths are seen with a unique entry and exit and a relatively straight path between them. Alternatively, paths can be complex with a tangle of possible routes. Likewise, PLS can be a single residue that changes protonation state or a cluster of residues with multiple charge and tautomer states.

Pseudo Jahn-Teller Origin of the Proton-transfer Energy Barrier in the Hydrogen-bonded [FHF]-System

The results of ab initio calculations of the adiabatic potential energy surfaces for the proton-bound [FHF]- system at different F-F distances have been rationalized in the framework of the vibronic theory. It is shown that the instability of the symmetric D∞h structure at increased F∙∙∙F distances and the proton displacement to one of the fluorine atoms is due to the pseudo Jahn–Teller mixing of the ground 1Σg electronic state with the lowest excited state of 1Σu symmetry through the asymmetric σu vibrational mode.

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.

Ionosomes: Observation of Ionic Bilayer Water Clusters

Emulsification of immiscible two-phase fluids, i.e., one condensed phase dispersed homogeneously as tiny droplets in an outer continuous medium, plays a key role in medicine, food, chemical separations, cosmetics, fabrication of micro- and nanoparticles and capsules, and dynamic optics. Herein, we demonstrate that water clusters/droplets can be formed in an organic phase via the spontaneous assembling of ionic bilayers. We term these clusters ionosomes, by analogy with liposomes where water clusters are encapsulated in a bilayer of lipid molecules. The driving force for the generation of ionosomes is a unique asymmetrical electrostatic attraction at the water/oil interface: small and more mobile hydrated ions reside in the inner aqueous side, which correlate tightly with the lipophilic bulky counterions in the adjacent outer oil side. These ionosomes can be formed through electrochemical (using an external power source) or chemical (by salt distribution) polarization at the liquid-liquid interface. The charge density of the cations, the organic solvent, and the synergistic effects between tetraethylammonium and lithium cations, all affecting the formation of ionosomes, were investigated. These results clearly prove that a new emulsification strategy is developed providing an alternative and generic platform, besides the canonical emulsification procedure with either ionic or nonionic surfactants as emulsifiers. Finally, we also demonstrate the detection of individual ionosomes via single-entity electrochemistry.

Structural Basis for the Function of the C-Terminal Proton Release Pathway in the Calcium Pump

The calcium pump (sarco/endoplasmic reticulum Ca²⁺-ATPase, SERCA) plays a major role in calcium homeostasis in muscle cells by clearing cytosolic Ca²⁺ during muscle relaxation. Active Ca²⁺ transport by SERCA involves the structural transition from a low-Ca²⁺ affinity E2 state toward a high-Ca²⁺ affinity E1 state of the pump. This structural transition is accompanied by the countertransport of protons to stabilize the negative charge and maintain the structural integrity of the transport sites and partially compensate for the positive charges of the two Ca²⁺ ions passing through the membrane. X-ray crystallography studies have suggested that a hydrated pore located at the C-terminal domain of SERCA serves as a conduit for proton countertransport, but the existence and function of this pathway have not yet been fully characterized. We used atomistic simulations to demonstrate that in the protonated E2 state and the absence of initially bound water molecules, the C-terminal pore becomes hydrated in the nanosecond timescale. Hydration of the C-terminal pore is accompanied by the formation of water wires that connect the transport sites with the cytosol. Water wires are known as ubiquitous proton-transport devices in biological systems, thus supporting the notion that the C-terminal domain serves as a conduit for proton release. Additional simulations showed that the release of a single proton from the transport sites induces bending of transmembrane helix M5 and the interaction between residues Arg762 and Ser915. These structural changes create a physical barrier against full hydration of the pore and prevent the formation of hydrogen-bonded water wires once proton transport has occurred through this pore. Together, these findings support the notion that the C-terminal proton release pathway is a functional element of SERCA and also provide a mechanistic model for its operation in the catalytic cycle of the pump.

Characterizing the Water Wire in the Gramicidin Channel Found by Monte Carlo Sampling Using Continuum Electrostatics and in Molecular Dynamics Trajectories with Conventional or Polarizable Force Fields

Water molecules play a key role in all biochemical processes. They help define the shape of proteins, and they are reactant or product in many reactions and are released as ligands are bound. They facilitate the transfer of protons through transmembrane proton channel, pump and transporter proteins. Continuum electrostatics (CE) force fields used by program Multiconformation CE (MCCE) capture electrostatic interactions in biomolecules with an implicit solvent, which captures the averaged solvent water equilibrium properties. Hybrid CE methods can use explicit water molecules within the protein surrounded by implicit solvent. These hybrid methods permit the study of explicit hydrogen bond networks within the protein and allow analysis of processes such as proton transfer reactions. Yet hybrid CE methods have not been rigorously tested. Here, we present an explicit treatment of water molecules in the Gramicidin A (gA) channel using MCCE and compare the resulting distributions of water molecules and key hydration features against those obtained with explicit solvent Molecular Dynamics (MD) simulations with the nonpolarizable CHARMM36 and polarizable Drude force fields. CHARMM36 leads to an aligned water wire in the channel characterized by a large absolute net water dipole moment; the MCCE and Drude analysis lead to a small net dipole moment as the water molecules change orientation within the channel. The correct orientation is not as yet known, so these calculations identify an open question.

Decoupling between the translation and rotation of water in the proximity of a protein molecule

The interaction between water and biomacromolecules is of fundamental interest in biophysics, biochemistry and physical chemistry. By combining neutron scattering and molecular dynamics simulations on a perdeuterated protein at a series of hydration levels, we demonstrated that the translational motion of water is slowed down more significantly than its rotation, when water molecules approach the protein molecule. Further analysis of the simulation trajectories reveals that the observed decoupling results from the fact that the translational motion of water is more correlated over space and more retarded by the charged/polar residues and spatial confinement on the protein surface, than the rotation. Moreover, around the stable protein residues (with smaller atomic fluctuations), water exhibits more decoupled dynamics, indicating a connection between the observed translation-rotation decoupling in hydration water and the local stability of the protein molecule.

Molecular Origins of the Barriers to Proton Transport in Acidic Aqueous Solutions

The self-consistent iterative multistate empirical valence bond (SCI-MS-EVB) method is used to analyze the structure, thermodynamics, and dynamics of hydrochloric acid solutions. The reorientation time scales of irreversible proton transport are elucidated by simulating 0.43, 0.85, 1.68, and 3.26 M HCl solutions at 270, 285, 300, 315, and 330 K. The results indicate increased counterion pairing with increasing concentration, which manifests itself via a reduced hydronium oxygen-chloride (O*-Cl) structuring in the radial distribution functions. Increasing ionic concentration also reduces the diffusion of the hydrated excess protons, principally by reducing the contribution of the Grotthuss proton hopping (shuttling) mechanism to the overall diffusion process. In agreement with prior experimental findings, a decrease in the activation energy of reorientation time scales was also observed, which is explicitly explained by using activated rate theory and an energy-entropy decomposition of the state-averaged radial distribution functions. These results provide atomistic verification of suggestions from recent two-dimensional infrared spectroscopy experiments that chloride anions (as opposed to hydrated excess protons) create entropic barriers to proton transport.

Slowing Down of the Molecular Reorientation of Water in Concentrated Alkaline Solutions

It is generally accepted that the hydroxide ion (OH^-) is a strong hydrogen bond acceptor and that its anomalously high diffusion constant in water results from a Grotthuss-like structural diffusion mechanism. However, the spatial extent over which OH^- ions influence the dynamics of the hydrogen-bond network of water remained largely unclear. Here, we measure the ultrafast dynamics of OH groups of HDO molecules interacting with the deuterated hydroxide ion OD^-. For solutions with OD^- concentrations up to 4 M, we find that HDO molecules that are not directly interacting with the ions have a reorientation time constant of ∼2.7 ps, similar to that of pure liquid water. When the concentration of OD^- ions is increased, the reorientation time constant increases, indicating a strong slowing down of the structural dynamics of the solution.

Reactive Molecular Dynamics at Constant Pressure via Nonreactive Force Fields: Extending the Empirical Valence Bond Method to the Isothermal-Isobaric Ensemble

The Empirical Valence Bond (EVB) method offers a suitable framework to obtain reactive potentials through the coupling of nonreactive force fields. In this formalism, most of the implemented coupling terms are built using functional forms that depend on spatial coordinates, while parameters are fitted against reference data to model the change of chemistry between the participating nonreactive states. In this work, we demonstrate that the use of such coupling terms precludes the computation of the stress tensor for condensed phase systems and prevents the possibility to carry out EVB molecular dynamics in the isothermal-isobaric (NPT) ensemble. Alternatively, we make use of coupling terms that depend on the energy gaps, defined as the energy differences between the participating nonreactive force fields, and derive a general expression for the EVB stress tensor suitable for computation. Implementation of this new methodology is tested for a model of a single reactive malonaldehyde solvated in nonreactive water. Mass densities and probability distributions for the values of the energy gaps computed in the NPT ensemble reveal a negligible role of the reactive potential in the limit of low concentrated solutions, thus corroborating for the first time the validity of approximations based on the canonical NVT ensemble, customarily adopted for EVB simulations. The presented formalism also aims to contribute to future implementations and extensions of the EVB method to research the limit of highly concentrated solutions.

Anomalous sub-diffusion of water in biosystems: From hydrated protein powders to concentrated protein solution to living cells

Water is essential to life and its translational motion in living systems mediates various biological processes, including transportation of function-required ingredients and facilitating the interaction between biomacromolecules. By combining neutron scattering and isotopic labeling, the present work characterizes translational motion of water on a biomolecular surface, in a range of systems: a hydrated protein powder, a concentrated protein solution, and in living Escherichia coli (E. coli) cells. Anomalous sub-diffusion of water is observed in all samples, which is alleviated upon increasing the water content. Complementary molecular dynamics simulations and coarse-grained numerical modeling demonstrated that the sub-diffusive behavior results from the heterogeneous distribution of microscopic translational mobility of interfacial water. Moreover, by comparing the experimental results measured on E. coli cells with those from a concentrated protein solution with the same amount of water, we show that water in the two samples has a similar average mobility, however the underlying distribution of motion is more heterogeneous in the living cell.

Understanding and Tracking the Excess Proton in Ab Initio Simulations; Insights from IR Spectra

Proton transport in aqueous media is ubiquitously important in chemical and biological processes. Although ab initio molecular dynamics (AIMD) simulations have made great progress in characterizing proton transport, there has been a long-standing challenge in defining and tracking the excess proton, or more properly, the center of excess charge (CEC) created when a hydrogen nucleus distorts the electron distributions of water molecules in a delocalized and highly dynamic nature. Yet, defining (and biasing) such a CEC is essential when combining AIMD with enhanced sampling methods to calculate the relevant macroscopic properties via free-energy landscapes, which is the standard practice for most processes of interest. Several CEC formulas have been proposed and used, but none have yet been systematically tested or rigorously derived. In this paper, we show that the CEC can be used as a computational tool to disentangle IR features of the solvated excess proton from its surrounding solvent, and in turn, how correlating the features in the excess charge spectrum with the behavior of CEC in simulations enables a systematic evaluation of various CEC definitions. We present a new definition of CEC and show how it overcomes the limitations of those currently available both from a spectroscopic point of view and from a practical perspective of performance in enhanced sampling simulations.

Kohn-Sham Density Functional Calculations Reveal Proton Wires in the Enolization and Carboxylase Reactions Catalyzed by Rubisco

Ribulose 1,5-bisphosphate (RuBP) carboxylase-oxygenase (Rubisco) plays a fundamental role in the carbon cycle by fixing the atmospheric CO₂ used in photosynthesis. Rubisco is all the more remarkable because it must catalyze some difficult multistep reaction chemistry involving proton transfers within the one active site. In the present study, we have used Kohn-Sham density functional theory at the B3LYP/6-31G* level with basis set superposition error and dispersion corrections (B3LYP-gCP-D3) to examine the possibility that the proton transfers can take place through molecular wires (including active-site water molecules) via the classical Grotthuss proton-shuttle mechanism. The results support an essential role for water molecules found in the crystal structures of Rubisco complexes as facilitators of proton transport in all the rate-limiting (catalytic) reaction steps through a network of short proton wires within the Rubisco active site. We suggest that completion of the initial product turnover (cycle) requires two excess protons produced in the initial carbamylation that is required for Rubisco activation. By use of proton wires, a large number of reaction steps may be accommodated within a single active site without necessitating the input of excessive conformational strain energy arising from the movement of residue side chains into positions where direct protonation of substrates can occur. The involvement of the identified types of proton wires in the kinetic mechanism is capable of providing a unique explanation for various experimental observations, including deuterium isotope effects and the results of site-directed mutagenesis experiments, and may thus provide a realistic solution to the problem of Rubisco's challenging chemistry.

Hydration interactions beyond the first solvation shell in aqueous phenolate solution

We investigate the orientational dynamics of water molecules solvating phenolate ions using ultrafast vibrational spectroscopy and density functional theory-based molecular dynamics simulations.

Ion Pairing in HCl-Water Clusters: From Electronic Structure Investigations to Multiconfigurational Force-Field Development

In the bulk, condensed-phase HCl exists as a dissociated Cl^- ion and a proton that is delocalized over solvating water molecules. However, in the gas phase, HCl is covalent, and even on the introduction of hydrating water molecules, the HCl covalent state dominates small clusters and is relevant at larger clusters including 21 water molecules. Electronic structure calculations (at the MP2 level) and ab initio metadynamics simulations (at the DFT level) have been carried out on HCl-(H₂O)_n clusters with n = 2-22 to investigate distinct solvation environments in clusters from covalent HCl structure, to contact ion pairs and solvent-separated ion pairs. The data were further used to train and validate a multiconfigurational force-field for HCl-water clusters that incorporates covalent HCl states into the MS-EVB3.2 formalism. Additionally, the many-body interaction of the Cl^- ion with water and the excess proton was modeled by the introduction of two geometric three-body terms that incorporates the dominant many-body interaction in an efficient noniterative manner.

Dynamic Protonation Dramatically Affects the Membrane Permeability of Drug-like Molecules

Permeability (P_m) across biological membranes is of fundamental importance and a key factor in drug absorption, distribution, and development. Although the majority of drugs will be charged at some point during oral delivery, our understanding of membrane permeation by charged species is limited. The canonical model assumes that only neutral molecules partition into and passively permeate across membranes, but there is mounting evidence that these processes are also facile for certain charged species. However, it is unknown whether such ionizable permeants dynamically neutralize at the membrane surface or permeate in their charged form. To probe protonation-coupled permeation in atomic detail, we herein apply continuous constant-pH molecular dynamics along with free energy sampling to study the permeation of a weak base propranolol (PPL), and evaluate the impact of including dynamic protonation on P_m. The simulations reveal that PPL dynamically neutralizes at the lipid-tail interface, which dramatically influences the permeation free energy landscape and explains why the conventional model overestimates the assigned intrinsic permeability. We demonstrate how fixed-charge-state simulations can account for this effect, and propose a revised model that better describes pH-coupled partitioning and permeation. Our results demonstrate how dynamic changes in protonation state may play a critical role in the permeation of ionizable molecules, including pharmaceuticals and drug-like molecules, thus requiring a revision of the standard picture.

Proton-Induced Conformational and Hydration Dynamics in the Influenza A M2 Channel

The influenza A M2 protein is an acid-activated proton channel responsible for acidification of the inside of the virus, a critical step in the viral life cycle. This channel has four central histidine residues that form an acid-activated gate, binding protons from the outside until an activated state allows proton transport to the inside. While previous work has focused on proton transport through the channel, the structural and dynamic changes that accompany proton flux and enable activation have yet to be resolved. In this study, extensive Multiscale Reactive Molecular Dynamics simulations with explicit Grotthuss-shuttling hydrated excess protons are used to explore detailed molecular-level interactions that accompany proton transport in the +0, + 1, and +2 histidine charge states. The results demonstrate how the hydrated excess proton strongly influences both the protein and water hydrogen-bonding network throughout the channel, providing further insight into the channel's acid-activation mechanism and rectification behavior. We find that the excess proton dynamically, as a function of location, shifts the protein structure away from its equilibrium distributions uniquely for different pH conditions consistent with acid-activation. The proton distribution in the xy-plane is also shown to be asymmetric about the channel's main axis, which has potentially important implications for the mechanism of proton conduction and future drug design efforts.

Direct Molecular Evidence of Proton Transfer and Mass Dynamics at the Electrode-Electrolyte Interface

Proton transfer has been widely regarded as a key step in many electrochemical and biological processes. However, direct molecular evidence has long been lacking. In this work, we chose the electrochemical oxidation of acetaminophen (APAP) as a model system and utilized in situ liquid time-of-flight secondary ion mass spectroscopy (ToF-SIMS) to molecularly examine proton solvation and transfer in this process. In addition, we successfully captured and identified the transient radical intermediate, providing solid molecular evidence to resolve an important debate in electron transfer-proton transfer oxidation mechanism of APAP. Moreover, the potential-dependent behaviors of both inert ions and electroactive species during the dynamic potential scanning were chemically monitored in real time and the mass diffusion mechanism regarding the electroactive and nonelectroactive species was revealed under polarized conditions. The results are consistent with our computer simulations. The observations in this work greatly improved our understanding of proton transfer and mass dynamics occurring at the electrode-electrolyte interface in complex electrochemical processes.

Intracluster proton transfer in protonated benzonitrile–(H2O)n≤6 nanoclusters: hydrated hydronium core for n ≥ 2

Infrared spectroscopy and density functional theory calculations of protonated benzonitrile–(H₂O)_n clusters reveal proton transfer to solvent for n ≥ 2 and the drastic effects of the aromatic dopant molecule on the network of H⁺(H₂O)_n+1.

Hydrated Excess Proton Raman Spectral Densities Probed in Floating Water Bridges

Excess proton structures in water remain unclear. The motion and nature of excess protons in water were probed using a supported water bridge structure in electric field (E) with an intensity of ∼10⁶ V/m. The experimental setup generated protons that exhibit a long lifetime. The effect of excess protons in water induced a ∼3% variation in the pH for a 300 V overvoltage at the cathode. The current versus voltage curves show a current space-charge-limited operation. By measuring the space-charge distribution in both the cathode and anode and by adjusting the Mott-Gurney law to the measured excess hydrated proton current and the voltage drop in the cationic space-charge region, the protonic mobility was determined to be ∼200 × 10^-8 m²/(V·s) (E ≈ 4 × 10⁶ V/m). This measured mobility, which is typically five times larger than the reported mobility for protons in water, is in agreement with the mechanism outlined by Grotthuss in 1805. The measured mid-Raman spectrum covering 1000-3800 cm^-1 range indicates the species character. The hydrated excess proton spectral response through the mid-Raman at 1760 and 3200 cm^-1 was attributed to the Zundel complex and the region at ∼2000 to ∼2600 cm^-1 response is attributed to the Eigen complex, indicating a core structure simultaneously with a Eigen-like and Zundel-like character, suggesting a rapid fluctuation between these two structures or a new specie.