Proton Exchange Mechanism Research Articles

Emergence of a proton exchange-based isomerization and lactonization mechanism in the plant coumarin synthase COSY

Plants contain rapidly evolving specialized enzymes that support the biosynthesis of functionally diverse natural products. In coumarin biosynthesis, a BAHD acyltransferase-family enzyme COSY was recently discovered to accelerate coumarin formation as the only known BAHD enzyme to catalyze an intramolecular acyl transfer reaction. Here we investigate the structural and mechanistic basis for COSY’s coumarin synthase activity. Our structural analyses reveal an unconventional active-site configuration adapted to COSY’s specialized activity. Through mutagenesis studies and deuterium exchange experiments, we identify a unique proton exchange mechanism at the α-carbon of the o-hydroxylated trans-hydroxycinnamoyl-CoA substrates during the catalytic cycle of COSY. Quantum mechanical cluster modeling and molecular dynamics further support this key mechanism for lowering the activation energy of the rate-limiting trans-to-cis isomerization step in coumarin production. This study unveils an unconventional catalytic mechanism mediated by a BAHD-family enzyme, and sheds light on COSY’s evolutionary origin and its recruitment to coumarin biosynthesis in eudicots.

Preferential Recovery of Rare-Earth Elements from Coal Fly Ash Using a Recyclable Ionic Liquid.

Recent global geopolitical tensions have exacerbated the scarcity of rare-earth elements (REEs), which are critical across many industries. REE-rich coal fly ash (CFA), a coal combustion residual, has been proposed as a potential source. Conventional REE-CFA recovery methods are energy- and material-intensive and leach elements indiscriminately. This study has developed a new valorization process based on the ionic liquid (IL) betainium bis(trifluoromethylsulfonyl)imide ([Hbet][Tf2N]) for preferential extraction of REEs from different CFAs. Efficient extraction relies on [Hbet][Tf2N]'s thermomorphic behavior with water: upon heating, water and the IL form a single liquid phase, and REEs are leached from CFA via a proton-exchange mechanism. Upon cooling, the water and IL separate, and leached elements partition between the two phases. REEs were preferentially extracted over bulk elements from CFAs into the IL phase and then recovered in a subsequent mild-acid stripping step, regenerating the IL. Alkaline pretreatment significantly improved REE leaching efficiency from recalcitrant Class-F CFAs, and additional betaine improved REE and bulk element separation. Weathered CFA showed slightly higher REE leaching efficiency than unweathered CFA, and Class-C CFA demonstrated higher leaching efficiency but less selective partitioning than Class-F CFAs. Significantly, this method consistently exhibits a particularly high extraction efficiency for scandium across different CFAs.

Gas-phase and aqueous-surface reaction mechanism of Criegee radicals with serine and nucleation of products: A theoretical study

Criegee intermediates (CIs) are short-lived carbonyl oxides, which can affect the budget of OH radicals, ozone, ammonia, organic/inorganic acids in the troposphere. This study investigated the reaction of CIs with serine (Ser) in the gas phase by using density functional theory (DFT) calculations and at the gas-liquid interface by using Born-Oppenheimer molecular dynamics (BOMD). The results reveal that the reactivity of the three functional groups of Ser can be ordered as follows: COOH > NH2 > OH. Water-mediated reactions of CIs with NH2 and OH groups of Ser on the droplet follow the proton exchange mechanism. The products, sulfuric acids, ammonia, and water molecules form stable clusters within 20 ns. This study shows that hydroperoxide products can contribute to new particle formation (NPF). The result deepens the understanding of the reaction of CIs with multifunctional pollutants and atmospheric behavior of CIs in polluted areas.

Construction of unimpeded proton-conducting pathways in solution-processed nanoporous polymer membranes.

Developing proton-conducting membranes with three-dimensional conductivity and expedited interfacial contact is requested in the field of fuel cells. Here, we present a design strategy by combining solution processing and material flexibility into amorphous and porous polymers. We design a nanoporous polymer whose skeleton contains dihydrophenazine as a proton-accepting site, and subsequently protonate these sites to produce abundant charges on the polymer skeletons, which enables ionic polymers to be well dispersed in organic solvents and guarantees that they can be fabricated into uniform and amorphous membranes in a solution-processed manner. Importantly, after protonation, the dihydrophenazines change to proton-donating sites, which exhibit dynamic local motions that assist proton exchange on the polymer skeletons and thus construct three-dimensional and unimpeded proton-conduction pathways, with a striking proton conductivity of 0.30 S cm-1 (298 K and 90% relative humidity), a low resistance of 3.02 Ω, and a H+ transport number of 0.98 that was very close to the upper limitation of 1.0.

Synergy of mercaptosilane monolayer embedding and extremely dilute cobalt alloying for metallization of copper without a conventional metallic barrier

TaN/Ta bilayer is the standard barrier for the metallization of copper interconnects of current integrated circuit devices. However, thickness reduction of the barrier becomes a major bottleneck for the successful metallization of the downsizing copper interconnects in sub-7-nm technology nodes. Hence, the feasibility of a mercaptosilane self-assembled monolayer (SAM) as a barrier, as well as a seed adsorber for electroless copper metallization, is investigated. The mercaptosilane SAM after proper functionalization in a RCA-1 aqueous solution has the capacity to adsorb 3-nm-sized nickel particles, subsequently catalyzing the plating of extremely dilute Cu(Co) films with only 0.13 at.% of Co. Using the adhesion strength (13.1 MPa) and threshold temperature for thermal failure (450 °C) of pristine Cu/SiO2 as a control, Cu/SAM/SiO2 (pristine state) yields markedly enhanced adhesion strength and threshold temperature of 39.4 MPa and 500 °C, respectively. Cu(Co)/SAM/Cu exhibits even a much higher adhesion of 53.8 MPa (pristine state) and 74.6 MPa (annealed state). Seeding of the nickel particles by the functionalized mercaptosilane monolayer is clarified from the viewpoints of solution chemistry and proton exchange mechanism, and why only a tiny amount of cobalt is incorporated onto copper matrix is explained. The synergetic effect of the mercaptosilane monolayer embedding and extreme dilution of cobalt alloying on enhancing the adhesion and thermal stability of copper films is discussed considering the context of previous studies.

Understanding the chemistry of cation leaching in illite/water interfacial system using reactive molecular dynamics simulations and hydrothermal experiments

Despite long standing pursuit, fundamental questions concerning the chemical pathways of leaching of ions in minerals, a phenomenon crucial to energy extraction, hydrometallurgy, metal recovery, and agriculture remain unanswered. Here we use large-scale ReaxFF reactive molecular dynamics (MD) simulations in combination with hydrothermal experiments to understand the chemistry of leaching in illite exposed to aqueous environment. Our simulations show that potassium counterions leach out into the solution much earlier and in higher concentration when compared with aluminum and silicon, which form the structural network of illite. Upon analyzing the chemical pathway from the trajectory of MD simulations, water molecules supply protons near the illite surface that binds with the non-bridging oxygen (NBO) of the Al-O-Si linkage forming an [Al-O-Si]—H transition state that later converts to silanol group upon Al-O bond dissociation. Proton addition also weakens the interlayer K-O bonds, resulting in the diffusion of K+ ions to illite surface, where they combine with the hydroxyl group formed from water dissociation, to form KOH molecules. KOH molecules diffuse out reactively to bulk water via proton exchange mechanism. Furthermore, we also find that continued protonation results in the formation of Al(OH)3 and Si(OH)4 groups predominantly at the surface, which diffuse out into water resulting in the leaching of Al and Si cations. We also estimated the kinetics of surface reactivity from the MD simulations and explored its effectiveness as a surrogate model for leaching kinetics. However, surface reaction kinetics and experimentally measured leaching kinetics seemed to be off by several orders of magnitude. We also analyzed the effects of leaching on structural distortion and found that more than 20% leaching is required for a notable structural distortion in illite crystal.

Acid-catalyzed proton exchange as a novel approach for relaxivity enhancement in Gd-HPDO3A-like complexes.

A current challenge in medical diagnostics is how to obtain high MRI relaxation enhancement using GdIII-based contrast agents (CAs) containing the minimum concentration of GdIII ions. We report that in GdHPDO3A-like complexes a primary amide group located in close proximity to the coordinated hydroxyl group can provide a strong relaxivity enhancement at slightly acidic pH. A maximum relaxivity of r1 = 9.8 mM−1 s−1 (20 MHz, 298 K) at acidic pH was achieved, which is more than double that of clinically approved MRI contrast agents under identical conditions. This effect was found to strongly depend on the number of amide protons, i.e. it decreases with a secondary amide group and almost completely vanishes with a tertiary amide. This relaxivity enhancement is attributed to an acid-catalyzed proton exchange process between the metal-coordinated OH group, the amide protons and second sphere water molecules. The mechanism and kinetics of the corresponding H+ assisted exchange process are discussed in detail and a novel simultaneous double-site proton exchange mechanism is proposed. Furthermore, 1H and 17O NMR relaxometry, Chemical Exchange Saturation Transfer (CEST) on the corresponding EuIII complexes, and thermodynamic and kinetic studies are reported. These highlight the optimal physico-chemical properties required to achieve high relaxivity with this series of GdIII-complexes. Thus, proton exchange provides an important opportunity to enhance the relaxivity of contrast agents, providing that labile protons close to the paramagnetic center can contribute.

A facile method to graphene oxide/polyaniline nanocomposite with sandwich-like structure for enhanced electrical properties of humidity detection

In this paper, a novel graphene oxide (GO)/polyaniline (PANI) sandwich-like nanocomposite has been synthesized by in-situ chemical oxidative polymerization. The GO/PANI is then fabricated onto the interdigitated transducers as sensor for humidity detection. The electrical properties of the thin films are investigated in various relative humidity (RH), including conduction mechanism, sensitivity, reproducibility and humidity hysteresis. The conduction mechanism of the GO/PANI for humidity response is discussed in detail, and the total resistance of GO/PANI is mainly depending on the bulk resistance of PANI. At the lower (60%) RH, the proton hopping transfer plays a very important role for the proton exchange mechanism of GO/PANI thin film. At the higher RH, ionic conduction is not only main conduction process, but also with the proton hopping partially exists for the proton exchange mechanism. Besides, the humidity sensitivity of the thin films enhances with increasing the mass ratio of GO (0, 5, and 50 mg) to PANI due to its larger surface area, hydrophilic functional groups and synergistic effect of π–π* conjugation system, which is also supported by adsorption of QCM humidity response. Meanwhile, the morphology and structure of the thin films are analyzed by fourier transform infrared spectroscopy (FTIR), ultraviolet–visible spectroscopy (UV–vis), scanning electron microscopy (SEM) and transmission electron microscope (TEM), respectively.

Tannic acid-based adsorbent with superior selectivity for lead(II) capture: Adsorption site and selective mechanism

Rational design and directed synthesis of an adsorbent with superior selectivity is challenging but of utmost importance for the remediation of heavy metal-laden actual wastewater. In this work, a novel tannic acid (TA)-based adsorbent (TA@Zr) was synthesized by a simple coordination reaction. Adsorption isotherm experiments exhibited the TA@Zr had a high capacity for Pb2+ capture. Impressively, an outstanding selectivity with extremely high selective coefficient (40–170) can be achieved by the TA@Zr. With decrease of Zr precursor, the selectivity of as-synthesized TA@Zr remained unchanged, implying that the Zr species played a negligible role in the selectivity of TA@Zr. Even the Zr species were completely replaced by Ti precursor, the resultant adsorbent still possessed a remarkable selectivity. All these results revealed that it was the TA, rather than the Zr species, made a substantial contribution to the selectivity of TA@Zr. Further, based on the results of XPS, DFT and batch adsorption experiments, it can be deduced that the phenolic hydroxyl groups on TA functioned as the dominant adsorption sites in which the hydroxyl groups’ oxygen atoms coordinated with Pb2+ while hydrogen atoms of hydroxyl groups were replaced and released as hydrogen ions, thus extending a proton exchange mechanism for the selective adsorption of Pb2+ ions.

Understanding the Chemistry of Cation Leaching in Illite/Water Interfacial System Using Reactive Molecular Dynamics Simulations and Hydrothermal Experiments

Despite long standing pursuit, fundamental questions concerning the chemical pathways of leaching of ions in minerals, a phenomenon crucial to energy extraction, hydrometallurgy, metal recovery, and agriculture remain unanswered. Here we use large-scale ReaxFF reactive molecular dynamics (MD) simulations in combination with hydrothermal experiments to understand the chemistry of leaching in illite in contact with water. Our simulations under equilibrium conditions show that 12.58% of potassium cations leach out to the solution. On the other hand, aluminum and silicon, which form the structural network of illite, are far less leachable as only 0.51% and 2.86% respectively of Al and Si leach out. Upon analyzing the chemical pathway from the trajectory of MD simulations, water molecules supply protons near the illite surface that binds with the non-bridging oxygen (NBO) of the Al-O-Si linkage forming an [Al-O-Si]---H transition state that later converts to silanol group upon Al-O bond dissociation. Proton addition also weakens the interlayer K-O bonds, resulting in the diffusion of K+ ions to illite surface, where they combine with the hydroxyl group formed from water dissociation, to form KOH molecules. KOH molecules diffuse out reactively to bulk water via proton exchange mechanism. Furthermore, we also find that continued protonation results in the formation of Al(OH)3 and Si(OH)4 groups predominantly at the surface, which diffuse out into water resulting in the leaching of Al and Si cations. We observe excellent agreement in the equilibrium cation concentrations of ReaxFF simulations and hydrothermal experiments. Reactive MD methodology with reliable, ab-initio based forcefields is, therefore, a promising approach to understand chemistry of water dynamics and ion transport and can be extended to similar mineral/water interfacial systems.

QM/MM study of the stereospecific proton exchange of glutathiohydroxyacetone by glyoxalase I

We have performed quantum mechanics (QM), molecular mechanics (MM) and hybrid QM/MM calculations to study the stereospecific proton exchange of glutathiohydroxyacetone (HOC-SG) by glyoxalase I (GlxI). We did the QM/MM calculations with a large QM system (246 atoms) to investigate the proton-exchange mechanism. Moreover, single-point big-QM energies with 1303 atoms in the big QM system and 22,412 atoms in the MM system were used to compare the energy difference of the stationary structures. GlxI catalyzes the exchange of the pro-S, but not the pro-R hydroxymethyl proton of HOC-SG with a deuterium from the D2O solvent. Classical molecular dynamics simulations with different protonation states of Glu99, Glu172 and HOC-SG led to the determination of most stable species (Glu-172 is protonated and the alcoholic oxygen of HOC-SG is deprotonated). The QM/MM results showed that before binding of HOC-SG, both active-site glutamates are charged, whereas HOC-SG is protonated. When HOC-SG binds, its alcoholic proton (HO) can point toward either Glu-99 or Glu-172. However, if the substrate binds so that HO is directed toward Glu-99, it is not transferred, whereas if it is directed toward Glu-172, the latter abstracts HO. The results showed that transferring HO to the glutamates from the reactant states is the key step to make the proton exchange reaction possible. Our calculations show that order of basicity of the glutamates and HOC-SG inside the enzyme is: Glu-172 > HOC-SG > Glu-99. The calculations allow us to propose a reaction mechanism for the stereospecific proton exchange of HOC-SG by GlxI with an overall barrier of 14.1 kcal/mol.

Ab Initio Prediction of Proton Exchange Barriers for Alkanes at Brønsted Sites of Zeolite H-MFI.

A hybrid of high level and low level quantum mechanics (QM) methods has been employed to predict intrinsic and apparent energy barriers for the direct proton exchange mechanism of methane, ethane, propane, n-butane, and i-butane on Brønsted sites of H-MFI. The specific hybrid MP2:PBE+D2 + ΔCC implementation used is known to yield the so-called "chemical accuracy" (±4 kJ/mol). Whereas the apparent enthalpy barriers decrease with increasing C number from 104 to 63 kJ/mol, in line with the decreasing heat of adsorption, the intrinsic enthalpy barriers are constant within 124-127 kJ/mol at 500 K. For methane, ethane, propane, and n-butane, we find the expected agreement of apparent barriers with activation energies from batch recirculation reactor experiments. The activation energies derived from NMR experiments (103-113 kJ/mol) are similarly constant as the predicted intrinsic barriers but systematically lower. For i-butane the predicted intrinsic and apparent barriers for the direct proton exchange step are the same as for n-butane with deviations of 2-5 kJ/mol, while the experiments yield values that are 50-60 kJ/mol lower, far outside the estimated range of combined experimental and computational uncertainty (±14 kJ/mol). A change to the indirect proton exchange mechanism, in which a hydride ion is transferred between the alkane and a tert-butyl carbenium ion can be excluded, because we confirm previous findings that the barrier for dehydrogenation that would create a tert-butyl cation from i-butane is much too high, 188 and 132 kJ/mol for the intrinsic and apparent enthalpy barriers, respectively, at 500 K. The possible role of extraframework- and framework-bound alumina species is discussed.

In Ukrainian

Despite the large number of experimental and theoretical works devoted to the structure and properties of silica surface known in the literature, as well as the extensive research on the structure of hydrated ionic pairs, the mechanism of adsorption of hydrated ions of electrolytes on silica surface has not yet been studied sufficiently. The paper presents a review of experimental works devoted to this problem, as well as their analysis at the atomic-molecular level. In order to study the interface "the silica surface - a solution of electrolyte", a number of papers used a method of density functional theory (DFT) using the exchange-correlation functional В3LYP and the basis set 6-31++G(d,p). The environmental impact modeling was taken into account within the framework of the supermolecular approach using a continuum solvent exposure model (PCM). The structure of the double electric layer and the mechanism of proton exchange in the near-surface layer of the silica surface are considered, as well as the value of the Gibbs energy of the silanol group deprotonation reaction, from which, in turn, the value of pK a2 was obtained. The results of calculations have shown that, with increasing size of oligomer molecules of silicic acid, the degree of localization of charges on hydrogen atoms and oxygen of the silanol group increases, the length of the O-H bond increases and the pK a2 decreases. It is shown that when adsorbed on a silica surface, alkali metal cations, in contact with silanol groups, can change the protolytic equilibrium of surface groups, due to redistribution of electron density, thereby increasing their acidity. The processes of ion exchange on silica surface and the dependence of the pK Me value on the size of ions and pH are considered. In a strongly acidic medium on silica surface, the formation of a cationic form of the silanol group is probable due to the proton transfer from the ion of hydroxonium to the oxygen atom of the silanol group. The deprotonation constant pK a1 of the cationic form of the silanol group depends on the nature of the anion and increases as an absolute value with anion radius increase. The models considered allow us to find the theoretical value of the point of zero charge of silica surface, which corresponds to the experimental data. Calculations using the constructed models of adsorption complexes of alkali hydroxides for the molecular state and for the state with separated charges with the participation of water molecules and silanol groups of silica surface indicate a possibility of ionization of the silanol group. The calculated Gibbs free energy changes are used to determine the values of pK Me , which increase in the series Li<Na<K, which correlates with the experimentally found adsorption values.

Quantum molecular dynamics study on the proton exchange, ionic structures, and transport properties of warm dense hydrogen-deuterium mixtures.

Comprehensive knowledge of physical properties such as equation of state (EOS), proton exchange, dynamic structures, diffusion coefficients, and viscosities of hydrogen-deuterium mixtures with densities from 0.1 to 5g/cm^{3} and temperatures from 1 to 50 kK has been presented via quantum molecular dynamics (QMD) simulations. The existing multi-shock experimental EOS provides an important benchmark to evaluate exchange-correlation functionals. The comparison of simulations with experiments indicates that a nonlocal van der Waals density functional (vdW-DF1) produces excellent results. Fraction analysis of molecules using a weighted integral over pair distribution functions was performed. A dissociation diagram together with a boundary where the proton exchange (H_{2}+D_{2}⇌2HD) occurs was generated, which shows evidence that the HD molecules form as the H_{2} and D_{2} molecules are almost 50% dissociated. The mechanism of proton exchange can be interpreted as a process of dissociation followed by recombination. The ionic structures at extreme conditions were analyzed by the effective coordination number model. High-order cluster, circle, and chain structures can be founded in the strongly coupled warm dense regime. The present QMD diffusion coefficient and viscosity can be used to benchmark two analytical one-component plasma (OCP) models: the Coulomb and Yukawa OCP models.

Higher Flexibility of Glu-172 Explains the Unusual Stereospecificity of Glyoxalase I.

Despite many studies during the latest two decades, the reason for the unusual stereospecificity of glyoxalase I (GlxI) is still unknown. This metalloenzyme converts both enantiomers of its natural substrate to only one enantiomer of its product. In addition, GlxI catalyzes reactions involving some substrate and product analogues with a stereospecificity similar to that of its natural substrate reaction. For example, the enzyme exchanges the pro- S, but not the pro- R, hydroxymethyl proton of glutathiohydroxyacetone (HOC-SG) with a deuterium from D2O. To find some clues to the unusual stereospecificity of GlxI, we have studied the stereospecific proton exchange of the hydroxymethyl proton of HOC-SG by this enzyme. We employed density functional theory and molecular dynamics (MD) simulations to study the proton exchange mechanism and origin of the stereospecificity. The results show that a rigid cluster model with the same flexibility for the two active-site glutamate residues cannot explain the unusual stereospecificity of GlxI. However, using a cluster model with full flexibility of Glu-172 or a larger model with the entire glutamates, extending the backbone into the neighboring residues, the results showed that there is no way for HOC-SG to exchange its protons if the alcoholic proton is directed toward Glu-99. However, if the hydroxymethyl proton instead is directed toward the more flexible Glu-172, we find a catalytic reaction mechanism for the exchange of the HS proton by a deuterium, in accordance with experimental findings. Thus, our results indicate that the special stereospecificity of GlxI is caused by the more flexible environment of Glu-172 in comparison to that of Glu-99. This higher flexibility of Glu-172 is also confirmed by MD simulations. We propose a reaction mechanism for the stereospecific proton exchange of the hydroxymethyl proton of HOC-SG by GlxI with an overall energy barrier of 15 kcal/mol.

Fluorescence-based monitoring of electronic state and ion exchange kinetics with FCS and related techniques: from T-jump measurements to fluorescence fluctuations

In this review, we give a historical view of how our research in the development and use of fluorescence correlation spectroscopy (FCS) and related techniques has its roots and how it originally evolved from the pioneering work of Manfred Eigen, his colleagues, and coworkers. Work on temperature-jump (T-jump) experiments, conducted almost 50 years ago, led on to the development of the FCS technique. The pioneering work in the 1970s, introducing and demonstrating the concept for FCS, in turn formed the basis for the breakthrough use of FCS more than 15 years later. FCS can be used for monitoring reaction kinetics, based on fluctuations at thermodynamic equilibrium, rather than on relaxation measurements following perturbations. In this review, we more specifically discuss FCS measurements on photodynamic, electronic state transitions in fluorophore molecules, and on proton exchange dynamics in solution and on biomembranes. In the latter case, FCS measurements have proven capable of casting new light on the mechanisms of proton exchange at biological membranes, of central importance to bioenergetics and signal transduction. Finally, we describe the transient-state (TRAST) spectroscopy/imaging technique, sharing features with both relaxation (T-jump) and equilibrium fluctuation (FCS) techniques. TRAST is broadly applicable for cellular and molecular studies, and we briefly outline how TRAST can provide unique information from fluorophore blinking kinetics, reflecting e.g., cellular metabolism, rare molecular encounters, and molecular stoichiometries.

Proton-Exchange-Induced Configuration Rearrangement in a Poly(ionic liquid) Solution: A NMR Study.

Polymeric ionic liquids have emerged recently as a promising alternative to traditional polymers as the polymer electrolyte membrane materials of choice because of their strongly decoupled dynamics between the polymer backbone and the counterions. Knowledge of proton exchange and transport mechanism in such materials is critical to the design and development of new poly(ionic liquid) materials with improved electrochemical properties. Our NMR results show that the proton exchange between the labile proton of the diethylmethylammonium (NH122) cation and H2O molecules is accompanied by a concerted configuration rearrangement of the ammonium. Through a combination of PFG-NMR and proton relaxation (line width) analysis, we demonstrate that at lower temperatures the labile proton diffuses along with the NH122 ammonium cation as an integral unit, whereas at higher temperatures the NH/H2O proton exchange sets in gradually, and the PFG-NMR measured diffusion coefficient is a population-averaged value between the two exchanging sites.

Обмен протонами оксиметильного радикала с кислотами и основаниями: полуэмпирическое квантово-химические исследование

The reactions with proton participation are widely represented in the analytical, technological and biological chemistry. Quantum-chemical study of the exchange processes in hydrogen bonding complexes will allow us to achieve progress in the understanding of the elementary act mechanism of proton transfer in hydrogen bonding chain as well as the essence of the acid-base interactions. Oxymethyl radical •CH2ОН is small in size and comfortable as a model particle that well transmits protolytic properties of paramagnetic acids having more complex structure. Quantum-chemical modeling of proton exchange reaction oxymethyl radical ∙CH2OH and its diamagnetic analog CH3OH with amines, carboxylic acids and water was carried out using UAM1 method with the help of Gaussian-2009 program. QST2 method was used for the search of transition state, IRC procedure was applied for the calculation of descents along the reaction coordinate. The difference in the structure of transition states of ∙CH2OH/ CH3OH with bases and acids has been shown. It has been confirmed that in the case of bases, consecutive proton exchange mechanism was fixed, and in the case of complexes with carboxylic acids parallel proton exchange mechanism was fixed. The similarity in the reaction behavior of paramagnetic and diamagnetic systems in the proton exchange has been found. It was suggested that the mechanism of proton exchange reaction is determined by the structure of the hydrogen bonding cyclic complex, which is, in turn, depends from the nature of the acid-base interactions partners.

Protein-like proton exchange in a synthetic host cavity

The mechanism of proton exchange in a metal-ligand enzyme active site mimic (compound 1) is described through amide hydrogen-deuterium exchange kinetics. The type and ratio of cationic guest to host in solution affect the rate of isotope exchange, suggesting that the rate of exchange is driven by a host whose cavity is occupied by water. Rate constants for acid-, base-, and water-mediated proton exchange vary by orders of magnitude depending on the guest, and differ by up to 200 million-fold relative to an alanine polypeptide. These results suggest that the unusual microenvironment of the cavity of 1 can dramatically alter the reactivity of associated water by magnitudes comparable to that of enzymes.

Dynamics of proton exchange in a model phosphonic acid-functionalized polymer

The dynamics and mechanism of proton exchange in phosphonic acid-functionalized polymers were studied using poly(vinyl-phosphonic acid) (PVPA) as a model system along with quantum chemical calculations and Born–Oppenheimer molecular dynamics (BOMD) simulations at the B3LYP/TZVP level as model calculations. This theoretical study began with searching for the smallest, most active polymer segments and their intermediate conformations which could be involved in the local proton-exchange process. The B3LYP/TZVP results confirmed that a low local dielectric environment and excess proton conditions are required to generate the intermediate conformations, and the shapes of the potential energy curves of the proton exchange between the two phosphonic acid functional groups are sensitive to the local conformational changes. In contrast, a high local dielectric environment increases the energy barriers, thereby preventing the proton from returning to the original functional group. Based on the static results, a mechanism for the proton exchange between the two functional groups involving fluctuations in the local dielectric environment and a local conformational change was proposed. The BOMD results confirmed the proposed mechanism by showing that the activation energies for the proton exchange in the hydrogen bond between two immobilized phosphonic acid moieties, obtained from the exponential relaxation behaviors of the envelopes of the velocity autocorrelation functions and the 1H Nuclear Magnetic Resonance (NMR) line-shape analyses, are too low to be the rate-determining process. Instead, coupled librational motion in the backbone which leads to the interconversion between the two intermediate conformations possesses higher activation energy, and therefore represents one of the most important rate-determining processes. These findings suggested that the rate of the proton exchange in the model phosphonic acid-functionalized polymer is determined by the polymer mobility which, in this case, is the large-amplitude librational motion of the vinyl backbone. © 2015 Wiley Periodicals, Inc.