Electrochemical and FTIRS characterisation of NO adlayers on cyanide-modified Pt(111) electrodes: the mechanism of nitric oxide electroreduction on Pt

We report here a study, using cyclic voltammetry and FTIRS, of NO irreversibly adsorbed on a cyanide-modified Pt(111) electrode. NO adlayers were formed by immersion of the cyanide-modified Pt(111) electrode in an acidic solution of KNO(2). The behaviour of NO adsorbed on the cyanide-modified electrode is very similar to that of NO on the clean Pt(111) surface, suggesting that adsorbed cyanide (saturation coverage theta(CN) = 0.5) behaves simply as a third body, blocking some of the surface sites but leaving the free Pt sites unaffected. Comparison of the voltammetric profile for NO electroreduction on Pt(111) and on cyanide-modified Pt(111) electrodes has allowed us: (i) to confirm that the reduction of three-fold hollow NO and atop NO on Pt(111) electrodes occurs in two distinct reduction peaks, as previously proposed by Rosca et al. (Langmuir, 2005, 21, 1448); (ii) to suggest that the reduction of irreversibly adsorbed NO layers on Pt electrodes can proceed through two possible paths, one involving an EE mechanism in which the rate-determining step (rds) is an Eley-Rideal reaction, with a direct proton transfer from the solution to adsorbed NO, and the other involving an EC mechanism in which the rds is a Langmuir-Hinshelwood reaction of adsorbed NO with adsorbed H. The availability of adsorbed hydrogen determines which path is followed by the reaction; (iii) to identify the smallest atomic ensemble for the reduction of NO on Pt as being composed of two adjacent Pt atoms.     

Kinetic analysis of a slow electron transfer coupled with a father—son reaction

The electrode reaction mechanism involving interaction of the products of a slow, rate-determining electron transfer with the parent molecule (father—son reaction) has been examined theoretically under the conditions of cyclic voltammetry. The kinetic analysis indicates how to determine the correct values of the kinetic parameters for both the heterogeneous charge transfer and the homogeneous chemical step. The irreversible cathodic reaction of diphenylmethylphenylsulphide in anhydrous DMF provides a good example of this mechanism, since the diphenylmethyl carbanion resulting from the irreversible two-electron reduction undergoes proton transfer from the parent molecule (self-protonation mechanism).     

Pathways of diffusion mixed with subsequent reactions with examples of hydrogen extraction from hydride-forming electrode and oxygen reduction at gas diffusion electrode

This paper covers the role of the rate-determining step (RDS) in anodic hydrogen extraction from hydride-forming electrode. In general, hydrogen extraction from the electrode proceeds through the following steps: (1) hydrogen diffusion within the electrode, (2) hydrogen transfer from absorbed state to adsorbed state, (3) electrochemical oxidation of hydrogen to hydrogen ion involving charge transfer, and (4) hydrogen ion conduction through the electrolyte. In most theoretical and experimental investigations, it has been assumed that the RDS of anodic hydrogen extraction is hydrogen diffusion through the electrode. In real situation, however, the overall rate of hydrogen extraction is simultaneously determined by the rates of two or more reaction steps including hydrogen diffusion. The present work provides the overview of anodic hydrogen extraction in case that diffusion is coupled with interfacial charge transfer, interfacial hydrogen transfer, and hydrogen ion conduction through the electrolyte as well as the purely diffusion-controlled hydrogen extraction. In addition, the mixed controlled diffusion model was also exemplified with oxygen reduction at gas diffusion electrode of fuel cell system.     

Pathways of diffusion mixed with subsequent reactions with examples of hydrogen extraction from hydride-forming electrode and oxygen reduction at gas diffusion electrode

This paper covers the role of the rate-determining step (RDS) in anodic hydrogen extraction from hydride-forming electrode. In general, hydrogen extraction from the electrode proceeds through the following steps: (1) hydrogen diffusion within the electrode, (2) hydrogen transfer from absorbed state to adsorbed state, (3) electrochemical oxidation of hydrogen to hydrogen ion involving charge transfer, and (4) hydrogen ion conduction through the electrolyte. In most theoretical and experimental investigations, it has been assumed that the RDS of anodic hydrogen extraction is hydrogen diffusion through the electrode. In real situation, however, the overall rate of hydrogen extraction is simultaneously determined by the rates of two or more reaction steps including hydrogen diffusion. The present work provides the overview of anodic hydrogen extraction in case that diffusion is coupled with interfacial charge transfer, interfacial hydrogen transfer, and hydrogen ion conduction through the electrolyte as well as the purely diffusion-controlled hydrogen extraction. In addition, the mixed controlled diffusion model was also exemplified with oxygen reduction at gas diffusion electrode of fuel cell system.

     

Hydrogen bonding pathways in human dihydroorotate dehydrogenase

Dihydroorotate dehydrogenase (DHOD) catalyzes the only redox reaction in the pathway for pyrimidine biosynthesis. In this reaction, a proton is transferred from a carbon atom of the substrate to a serine residue, and a hydride is transferred from another carbon atom of the substrate to a cofactor. The deprotonation of the substrate is postulated to involve a proton relay mechanism along a hydrogen bonding pathway in the active site. In this paper, molecular dynamics simulations are used to identify and characterize potential hydrogen bonding pathways that could facilitate the redox reaction catalyzed by human DHOD. The observed pathways involve hydrogen bonding of the active base serine to a water molecule, which is hydrogen bonded to the substrate carboxylate group or a threonine residue. The threonine residue is positioned to enable proton transfer to another water molecule leading to the bulk solvent. The impact of mutating the active base serine to cysteine is also investigated. This mutation is found to increase the average donor-acceptor distances for proton and hydride transfer and to disrupt the hydrogen bonding pathways observed for the wild-type enzyme. These effects could lead to a significant decrease in enzyme activity, as observed experimentally for the analogous mutant in Escherichia coli DHOD.     

Calculation of proton transfers in hydrogen bonding interactions with semi-empirical MNDO/H

A method for calculating proton transfer enthalpies by a proper modification of the recent H-bonding version of MNDO is presented. This method perceives the proton as being both “bonded” and “hydrogen bonded” to the two electronegative atoms involved in the hydrogen bond: as it moves from one potential minimum at X-H---Y to the other at X---H-Y, a hydrogen bonding function is attached to the proportion of the distance that is to be traversed. The method is applied to two proton transfers within anionic oxygen H-bonded complexes and is shown to reduce the previously calculated barriers which were too high. Gas phase results for the single step of proton transfer over a barrier are required to evaluate the results obtained by this method.     

Insights on the mechanism of proton transfer reactions in amino acids

In the present work, the joint use of the potential energy, the reaction electronic flux profiles and NBO analysis along the intrinsic reaction coordinate within the framework of the reaction force analysis allows us to gain insights into the mechanism of the proton transfer process in amino acids. The reaction was studied in alanine and phenylalanine in the presence of a continuum and with addition of one water molecule acting as a bridge, the results were compared to those of tryptophan. The bridging water molecule stabilizes the zwitterionic form and increases the reaction barriers by a factor of two. This result is interpreted in terms of the energy required to bring the amino acid and the water molecule closer to each other and to promote the proton transfer through the reordering of the electron density. Furthermore, the bridging water molecule induces a concerted asynchronous double proton transfer, where the transfer of the carboxyl hydrogen atom is followed by the second proton transfer to the ammonium group. In addition, a second not intervening water molecule was added, which changes the proton acceptor and donor properties of the reactive water molecule modulating the reaction mechanism. The aforementioned methods allow us to identify the order of the transferred protons and the asynchronicity, thereby, evolving as promising tools to not only characterize but also manipulate reaction mechanisms.     

Mechanistic study on the gold-catalyzed C-S bond formation of α-thioallenes to form 2,5-dihydrothiophenes

The reaction mechanism of the AuCl-catalyzed reaction of the α-thioallenes to give 2,5-dihydrothiophenes has been computationally studied using DFT (B3LYP/6-31G*, SDD for Au). Calculations indicate the complexation of α-thioallene with AuCl occurs preferentially at the distal double bond, followed by the C-S bond formation, the proton transfer from the sulfur to the carbon "b", and the [1,2]-hydride shift to give the 2,5-dihydrothiophene gold complex. The proton transfer is the rate-limiting step with very high activation energy in the gas phase. In the presence of one water molecule, the activation free energy of the proton transfer was lowered by as much as 19.9 kcal/mol. Furthermore, one dichloromethane molecule stabilized all of the transition structures by its hydrogen bonds.     

Mechanistic study of the electrochemical oxygen reduction reaction on Pt(111) using density functional theory

Density functional theory (DFT) was used to study the electrolyte solution effects on the oxygen reduction reaction (ORR) on Pt(111). To model the acid electrolyte, an H(5)O(2)(+) cluster was used. The vibrational proton oscillation modes for adsorbed H(5)O(2)(+) computed at 1711 and 1010 cm(-1), in addition to OH stretching and H(2)O scissoring modes, agree with experimental vibrational spectra for proton formation on Pt surfaces in ultrahigh vacuum. Using the H(5)O(2)(+) model, protonation of adsorbed species was found to be facile and consistent with the activation barrier of proton transfer in solution. After protonation, OOH dissociates with an activation barrier of 0.22 eV, similar to the barrier for O(2) dissociation. Comparison of the two pathways suggests that O(2) protonation precedes dissociation in the oxygen reduction reaction. Additionally, an OH diffusion step following O protonation inhibits the reaction, which may lead to accumulation of oxygen on the electrode surface.     

Calculation of vibronic couplings for phenoxyl/phenol and benzyl/toluene self-exchange reactions: implications for proton-coupled electron transfer mechanisms

The vibronic couplings for the phenoxyl/phenol and the benzyl/toluene self-exchange reactions are calculated with a semiclassical approach, in which all electrons and the transferring hydrogen nucleus are treated quantum mechanically. In this formulation, the vibronic coupling is the Hamiltonian matrix element between the reactant and product mixed electronic-proton vibrational wavefunctions. The magnitude of the vibronic coupling and its dependence on the proton donor-acceptor distance can significantly impact the rates and kinetic isotope effects, as well as the temperature dependences, of proton-coupled electron transfer reactions. Both of these self-exchange reactions are vibronically nonadiabatic with respect to a solvent environment at room temperature, but the proton tunneling is electronically nonadiabatic for the phenoxyl/phenol reaction and electronically adiabatic for the benzyl/toluene reaction. For the phenoxyl/phenol system, the electrons are unable to rearrange fast enough to follow the proton motion on the electronically adiabatic ground state, and the excited electronic state is involved in the reaction. For the benzyl/toluene system, the electrons can respond virtually instantaneously to the proton motion, and the proton moves on the electronically adiabatic ground state. For both systems, the vibronic coupling decreases exponentially with the proton donor-acceptor distance for the range of distances studied. When the transferring hydrogen is replaced with deuterium, the magnitude of the vibronic coupling decreases and the exponential decay with distance becomes faster. Previous studies designated the phenoxyl/phenol reaction as proton-coupled electron transfer and the benzyl/toluene reaction as hydrogen atom transfer. In addition to providing insights into the fundamental physical differences between these two types of reactions, the present analysis provides a new diagnostic for differentiating between the conventionally defined hydrogen atom transfer and proton-coupled electron transfer reactions.     

Role of protein flexibility in enzymatic catalysis: quantum mechanical-molecular mechanical study of the deacylation reaction in class A beta-lactamases

We present a theoretical study of a mechanism for the hydrolysis of the acyl-enzyme complex formed by a class A beta-lactamase (TEM1) and an antibiotic (penicillanate), as a part of the process of antibiotic's inactivation by this type of enzymes. In the presented mechanism the carboxylate group of a particular residue (Glu166) activates a water molecule, accepting one of its protons, and afterward transfers this proton directly to the acylated serine residue (Ser70). In our study we employed a quantum mechanics (AM1)-molecular mechanics partition scheme (QM/MM) where all the atoms of the system were allowed to relax. For this purpose we used the GRACE procedure in which part of the system is used to define the Hessian matrix while the rest is relaxed at each step of the stationary structures search. By use of this computational scheme, the hydrolysis of the acyl-enzyme is described as a three-step process: The first step corresponds to the proton transfer from the hydrolytic water molecule to the carboxylate group of Glu166 and the subsequent formation of a tetrahedral adduct as a consequence of the attack of this activated water molecule to the carbonyl carbon atom of the beta-lactam. In the second step, the acyl-enzyme bond is broken, obtaining a negatively charged Ser70. In the last step this residue is protonated by means of a direct proton transfer from Glu166. The large mobility of Glu166, a residue that is placed in a Ohms-loop, is essential to facilitate this mechanism. The geometry of the acyl-enzyme complex shows a large distance between Glu166 and Ser70 and thus, if protein coordinates were kept frozen during the reaction path, it would be difficult to get a direct proton transfer between these two residues. This computational study shows how a flexible treatment suggests the feasibility of a mechanism that could have been discounted on the basis of crystallographic positions.     

The shape of the potential energy curves for NHN(+) hydrogen bonds and the influence of non-linearity

The potential energy curves for proton motion in NHN(+) hydrogen bonds have been calculated to investigate whether different methods of evaluation give different results: for linear H bonds most curves calculated along the NH direction are, as expected, identical with those along NN; for intramolecular H bonds it is very important to take into account the non-linearity and the potential energy curve calculated along the NH direction can be very far from the curve correctly describing the proton transfer. Other factors which influence the proton-transfer process are steric hindrance and presence of anions which modify the proton motion. In the analysis of the proton transfer process it is very important to take changes in the structure of the rest of the molecule into account, which is connected with exchange of energy with the surroundings. Comparison of adiabatic and non-adiabatic curves shows that they are significantly different for very bent hydrogen bonds and for hydrogen bonds with steric constraints for which the proton transfer process must be accompanied with relaxation of the whole molecule. Comparison of the potential-energy curves for compounds with very short H bonds emphasizes that the term 'strong H bond' needs to be qualified. For intermolecular H bonds shortening of the bond is connected with linearization. But for intramolecular H bonds the NN distance cannot be used as the only measure of H bond strength.     

Experimental study of the oxidation-reduction reaction on gold electrodes of the tungsten W(VI)/W(V) couple inside the dodecatungstosilicate anion

In this work we have proposed a qualitative mechanism for the first two steps of the reduction of the dodecatungstic anion on a gold electrode using measurements of faradaic impedance. Two types of supporting electrolyte were chosen—sulphate and perchlorate. The effect of competition with adsorbed SO₄^2? could be observed on the first reduction step. In both steps the charge transfer is related with homogeneous proton transfer reactions.     

Excited-state hydrogen relay along a blended-alcohol chain as a model system of a proton wire: deuterium effect on the reaction dynamics

The excited-state deuteron transfer (ESDT) of deuterated 7-hydroxyquinoline (7DQ) along a heterogeneous hydrogen (H)-bonded chain composed of two deuterated alcohol (ROD) molecules having different acidities, as a model system of a proton wire consisting of diverse amino acids, has been investigated. To understand dynamic differences between deuteron transfer and proton transfer, solvent-inventory experiments have been performed with variation of the combination as well as the composition of alcohols in a H-bonded mixed-alcohol chain. Deuteron transfer from the adjacent ROD molecule to the basic imino group of 7DQ via tunneling, which is the rate-determining step, initiates ESDT, and subsequent barrierless deuteron relay from the acidic enolic group of 7DQ to the alkoxide moiety along the H-bonded chain completes ESDT. Whereas the acceleration of the reaction has been observed in excited-state proton transfer because of the accumulated proton-donating abilities of two alcohol molecules in a H-bonded chain by a push-ahead effect, such acceleration is not observed in ESDT. Because the energy barrier of deuteron relay is much higher than that of proton relay due to the low zero-point energy of 7DQ·(ROD)(2) and a deuteron is twice as heavy as a proton, it is hard for a deuteron to pass through the barrier via tunneling. Moreover, both the H-bonding ability and the acidity of ROD molecules are so weak that their deuteron-donating abilities cannot be accumulated at the rate-determining step of ESDT. Consequently, the rate constant of ESDT is determined mostly by the acidity of the ROD molecule H-bonded directly to the imino group of 7DQ.     

Ab initio molecular dynamics simulations of the oxygen reduction reaction on a Pt(111) surface in the presence of hydrated hydronium (H3O)(+)(H2O)2: direct or series pathway?

Car-Parrinello molecular dynamics simulations have been performed to investigate the oxygen reduction reaction (ORR) on a Pt(111) surface at 350 K. By progressive loading of (H3O)(+)(H2O)(2,3) + e- into a simulation cell containing a Pt slab and O2 for the first reduction step, and either products or intermediate species for the subsequent reduction steps, the detailed mechanisms of the ORR are well illustrated via monitoring MD trajectories and analyzing Kohn-Sham electronic energies. A proton transfer is found to be involved in the first reduction step; depending on the initial proton-oxygen distance, on the degree of proton hydration, and on the surface charge, such transfer may take place either earlier or later than the O2 chemisorption, in all cases forming an adsorbed end-on complex H-O-O*. Decomposition of H-O-O* takes place with a rather small barrier, after a short lifetime of approximately 0.15 ps, yielding coadsorbed oxygen and hydroxyl (O + HO*). Formation of the one-end adsorbed hydrogen peroxide, HOO*H, is observed via the reduction of H-O-O*, which suggests that the ORR may also proceed via HOO*H, i.e., a series pathway. However, HOO*H readily dissociates homolytically into two coadsorbed hydroxyls (HO* + HO*) rather than forming a dual adsorbed HOOH. Along the direct pathway, the reduction of H-O* + O* yields two possible products, O* + H2O* and HO* + HO*. Of the three intermediates from the second electron-transfer step, HOO*H from the series pathway has the highest energy, followed by O* + H2O* and HO* + HO* from the direct pathway. It is therefore theoretically validated that the O2 reduction on a Pt surface may proceed via a parallel pathway, the direct and series occurring simultaneously, with the direct as the dominant step.     

Key role of active-site water molecules in bacteriorhodopsin proton-transfer reactions

The functional mechanism of the light-driven proton pump protein bacteriorhodopsin depends on the location of water molecules in the active site at various stages of the photocycle and on their roles in the proton-transfer steps. Here, free energy computations indicate that electrostatic interactions favor the presence of a cytoplasmic-side water molecule hydrogen bonding to the retinal Schiff base in the state preceding proton transfer from the retinal Schiff base to Asp85. However, the nonequilibrium nature of the pumping process means that the probability of occupancy of a water molecule in a given site depends both on the free energies of insertion of the water molecule in this and other sites during the preceding photocycle steps and on the kinetic accessibility of these sites on the time scale of the reaction steps. The presence of the cytoplasmic-side water molecule has a dramatic effect on the mechanism of proton transfer: the proton is channeled on the Thr89 side of the retinal, whereas the transfer on the Asp212 side is hindered. Reaction-path simulations and molecular dynamics simulations indicate that the presence of the cytoplasmic-side water molecule permits a low-energy bacteriorhodopsin conformer in which the water molecule bridges the twisted retinal Schiff base and the proton acceptor Asp85. From this low-energy conformer, proton transfer occurs via a concerted mechanism in which the water molecule participates as an intermediate proton carrier.     

Proton transfer in nanoconfined polar solvents. II. Adiabatic proton transfer dynamics

The reaction dynamics for a model phenol-amine proton transfer system in a confined methyl chloride solvent have been simulated by mixed quantum-classical molecular dynamics. In this approach, the proton vibration is treated quantum mechanically (and adiabatically), while the rest of the system is described classically. Nonequilibrium trajectories are used to determine the proton transfer reaction rate constant. The reaction complex and methyl chloride solvent are confined in a smooth, hydrophobic spherical cavity, and radii of 10, 12, and 15 A have been considered. The effects of the cavity radius and the heavy atom (hydrogen bond) distance on the reaction dynamics are considered, and the mechanism of the proton transfer is examined in detail by analysis of the trajectories.     

Reaction of 1,2-dibromobenzene with the Si(111)-7x7 surface, a DFT study

Reaction between 1,2-dibromobenzene and the Si(111)-7x7 surface has been studied theoretically on the DFT(B3LYP/6-31G(d)) level. A 12-atom silicon cluster, representing two adatoms and one rest atom of the faulted half of the unit cell, was used to model the silicon surface. The first step of the reaction was a covalent attachment (chemisorption) of an intact 1,2-dibromobenzene molecule to the silicon cluster. Binding energies were calculated to be between 1.04 and 1.14 eV, depending on the orientation of the molecule. A second step of the reaction was the transfer of the Br atom to the silicon cluster. Activation energies for the transfer of the Br atom were calculated to be between 0.4 and 0.6 eV, suggesting that the thermal bromination reaction occurs on a microsecond time scale at room temperature. A third step of the reaction could be the transfer of the second Br atom of the molecule, the desorption of the organic radical, or the change of the adsorption configuration of the radical, depending on the original orientation of the adsorbed intact molecule. A novel, aromatic, two-sigma-bound adsorbed configuration of the C6H4 radical, in which a carbon ring of the radical is perpendicular to the silicon surface, has been introduced to explain previous experimental observations (Surf. Sci. 2004, 561, 11).     

Quantum chemical investigation on the reaction mechanism of tertiary phosphines with unsaturated carboxylic acids: An insight into kinetic data

The structures of intermediates and transition states in the reaction of tertiary phosphines with unsaturated carboxylic acids have been calculated at the B3LYP level of theory using the 6‐31+G(d,p) basis set. Analysis of the results shows that [1,3]‐intramolecular migration of carboxylic proton to carbanionic center of generated zwitterionic intermediate is strongly kinetically unfavorable, and external proton‐donor source is essential to complete quaternization. A molecular cluster of the intermediate with one molecule of water has been modeled for intermolecular reaction pathway, but even in this case, the proton transfer remains to be the rate‐determining step that is in a good agreement with previous kinetic investigations on this reaction. The data obtained for this reaction have much in common with recent studies on the mechanisms of the Morita–Baylis–Hillman reaction and phosphine‐catalyzed [3+2] cycloaddition, which revealed paramount importance of proton‐transfer steps. © 2013 Wiley Periodicals, Inc.