Proton Transfer Step Research Articles

Ab initio study of ligand dissociation/exchange and the hydrogen production process of the Co(dmgH)2(py)Cl cobaloxime in the acetonitrile-water solvent

Density functional theory (DFT) calculations and Car-Parrinello molecular dynamics (CPMD) simulations in the explicit acetonitrile-water solvent were carried out to study the ligand dissociation/exchange process and hydrogen production pathway of a common cobaloxime complex, Co(dmgH)2(py)Cl (py = pyridine). Our results show that the axial Cl− is readily replaced by a water molecule which is a key step for the subsequent proton transfer in the hydrogen production cycle. Moreover, the py ligand also dissociates readily from the complex at a later stage. The alternate two electrons and two protons addition pathway was identified to be the favorable one for hydrogen production. The rate determining step of the hydrogen production by Co(dmgH)2(py)Cl is the first protonation of the Co ion, which competes with the proton transfer to the O of the side group of the complex.

Photoreceptors Take Charge: Emerging Principles for Light Sensing.

The first stage in biological signaling is based on changes in the functional state of a receptor protein triggered by interaction of the receptor with its ligand(s). The light-triggered nature of photoreceptors allows studies on the mechanism of such changes in receptor proteins using a wide range of biophysical methods and with superb time resolution. Here, we critically evaluate current understanding of proton and electron transfer in photosensory proteins and their involvement both in primary photochemistry and subsequent processes that lead to the formation of the signaling state. An insight emerging from multiple families of photoreceptors is that ultrafast primary photochemistry is followed by slower proton transfer steps that contribute to triggering large protein conformational changes during signaling state formation. We discuss themes and principles for light sensing shared by the six photoreceptor families: rhodopsins, phytochromes, photoactive yellow proteins, light-oxygen-voltage proteins, blue-light sensors using flavin, and cryptochromes.

Reaction Coordinate, Free Energy, and Rate of Intramolecular Proton Transfer in Human Carbonic Anhydrase II.

The role of structure and dynamics of an enzyme has been investigated at three different stages of its function including the chemical event it catalyzes. A one-pot computational method has been designed for each of these stages on the basis of classical and/or quantum mechanical-molecular mechanical molecular dynamics and transition path sampling simulations. For a pair of initial and final states A and B separated by a high free-energy barrier, using a two-stage selection process, several collective variables (CVs) are identified that can delineate A and B. However, these CVs are found to exhibit strong cross-coupling over the transition paths. A set of mutually orthogonal order parameters is then derived from these CVs and an optimal reaction coordinate, r, determined applying half-trajectory likelihood maximization along with a Bayesian information criterion. The transition paths are also used to project the multidimensional free energy surface and barrier crossing dynamics along r. The proposed scheme has been applied to the rate-determining intramolecular proton transfer reaction of the well-known enzyme human carbonic anhydrase II. The potential of mean force, F( r), in the absence of the chemical step is found to reproduce earlier results on the equilibrium population of two side-chain orientations of key residue His-64. Estimation of rate constants, k, from mean first passage times for the three different stages of catalysis shows that the rate-determining step of intramolecular proton transfer occurs with k ≃ 1.0 × 106 s-1, in close agreement with known experimental results.

Thermodynamic Acidity Studies of 6,6′-Dihydroxy-2,2′-bipyridine: A Combined Experimental and Computational Approach

The organic ligand 6,6'-dihydroxy-2,2'-bipyridine (6,6'-dhbp) is frequently used to bind transition metals in order to form catalysts for many organic and inorganic transformations. 6,6'-dhbp exists in two tautomeric forms, the pyridinol tautomer and the amide (lactam) tautomer with each tautomer having two rotational conformers: cis or trans. Only the cis-pyridinol tautomer has the proper configuration to bind transition metals. The pendant OH (or O- groups when deprotonated) in 6,6'-dhbp typically do not bind the metal when forming the metal catalyst but can facilitate the proton transfer steps in the catalysis process. Electronic structure calculations were used to predict the stability of all possible isomers (including conformers and protonation states) in the gas phase and aqueous solution. These results have been compared to experimental data including UV-vis and NMR spectra as a function of pH. The pKa values for the 6,6'-dhbp ligand in the -2 to +2 structures were predicted, and these ligands show different behavior in the gas phase versus in aqueous solution.

The cytochrome b6f complex: DFT modeling of the first step of plastoquinol oxidation by the iron-sulfur protein

In chloroplasts, the cytochrome (Cyt) b6f complex (plastoquinol-plastocyanin-oxidoreductase) provides connectivity between photosystems (PS) II and I, oxidizing plastoquinol (PQH2) formed in PSII and reducing plastocyanin (electron donor to PSI). The overall rate of the intersystem electron transport is determined by PQH2 oxidation by the Cyt b6f complex. In this work, using the DFT method, we have modeled the first step of PQH2 oxidation by the iron-sulfur protein (ISP) of the Cyt b6f complex. The model system contained the iron–sulfur cluster [Fe2S2], surrounding amino acid residues, and 2,3,5-trimethylbenzoquinol (TMBQH2), the tailless analog of PQH2. The energy profiles of the H atom transfer from TMBQH2 to the iron-sulfur protein (ISP) were calculated for two modes of the H-transfer, “diabatic” and “adiabatic”. The energies of transient states were estimated as 18.4 and 14.4 kcal mol−1. The energy effects of the reaction were evaluated as 7.7 and −0.2 kcal mol−1, respectively. The analysis of partial spin densities and electric charges on the atoms of the model system supports the bidirectional mechanism of the H-transfer reaction: an electron is directed to the Fe(1) atom of the [Fe2S2] cluster of the ISP, and a proton is accepted by the Nε atom of the His155 residue liganding the Fe(1) atom. Using the results of DFT computations of the energy profiles for the H-transfer reaction, we estimated the rate constants of quinol oxidation within the framework of the Marcus-Dutton-Crofts approach. Our analysis supports the diabatic model of the H-transfer, which implies that the elementary steps of electron and proton transfer occur much more rapidly than the concomitant changes in the system geometry. The rate constants estimated for this mode of H-transfer are in reasonable agreement with experimental data on the intersystem electron transport in chloroplasts.

Choreography of the Reductase and P450BM3 Domains Toward Electron Transfer Is Instigated by the Substrate.

The driving force for the electron transfer (ET) step in the catalytic cycle of cytochrome P450BM3 is investigated using three sets of 1 μs molecular dynamic simulations for the resting state of P450 in complex with the flavin (FMN) in the reductase domain. These sets involve the following: (i) substrate-free (SF), (ii) substrate (N-palmitoyl glycine, i.e., NPG)-bound (SB), and (iii) SB with the semiquinone radical anion (SQ-) of FMN. Starting from the X-ray structure of the SF heme domain, we observe that the α1-helix (of the reductase) and the C-helix (of the heme) undergo reorientation to a parallel orientation, which is the thermochemically stable form. The reorientation of the helices pushes away the FMN to a distance of 18.4 Å from the heme's center. When the substrate binds it causes the I-helix of the heme domain to kink and push the C-helix toward the α1-helix, thereby locking the latter two into a stabilized perpendicular conformation, wherein the FMN-heme distance is 12 Å. The distance drops further in the SQ- form, and upon QM/MM geometry optimization the two moieties approach 8.8 Å, which enhances the ET rate (by 104-106 fold) to the heme's Fe3+ ion. These motions are driven by hydrogen bond strengthening between the C- and the α1-helices. Finally, substrate binding leads to formation of an organized water chain connecting the FMN and heme moieties. The water channel assists the ET and couples it to the proton transfer steps that should activate O2 and create the oxo-iron active species.

The mechanism of the triple aryne-tetrazine reaction cascade: theory and experiment.

This article describes an experimental and computational investigation on the possible aryne reactivity modes in the course of the reaction of two highly energetic molecules, an aryne and a 1,2,4,5-tetrazine. Beyond the triple aryne-tetrazine (TAT) reaction, it was observed that combinations of several reactivity modes afford several heterocyclic compounds. Density Functional Theory (DFT) calculations of competition between a second Diels-Alder reaction and the nucleophilic addition pathways indicates the latter to be more favorable. Crossover experiments and computational study of the proton transfer step reveal that the reaction proceeds intermolecularly with the assistance of a water molecule, rather than intramolecularly. The resulting enamine intermediate was found to undergo either a stepwise formal [2 + 2] or [4 + 2] cycloaddition, and their energetic profiles were compared against each other. Isolation of an ene-product and a rearranged product shows the potential competition with oxidation/desaturation. These studies show how multiple arynes react with a highly reactive starting material and provide guidance for future applications of aryne-based multicomponent cascade reactions.

Nitrogen Reduction to Ammonia on a Biomimetic Mononuclear Iron Centre: Insights into the Nitrogenase Enzyme.

Nitrogenases catalyse nitrogen fixation to ammonia on a multinuclear Fe‐Mo centre, but their mechanism and particularly the order of proton and electron transfer processes that happen during the catalytic cycle is still unresolved. Recently, a unique biomimetic mononuclear iron model was developed using tris(phosphine)borate (TPB) ligands that was shown to convert N2 into NH3. Herein, we present a computational study on the [(TPB)FeN2]− complex and describe its conversion into ammonia through the addition of electrons and protons. In particular, we tested the consecutive proton transfer on only the distal nitrogen atom or alternated protonation of the distal/proximal nitrogen. It is found that the lowest energy pathway is consecutive addition of three protons to the same site, which forms ammonia and an iron‐nitrido complex. In addition, the proton transfer step of complexes with the metal in various oxidation and spin states were tested and show that the pK a values of biomimetic mononuclear nitrogenase intermediates vary little with iron oxidation states. As such, the model gives several possible NH3 formation pathways depending on the order of electron/proton transfer, and all should be physically accessible in the natural system. These results may have implications for enzymatic nitrogenases and give insight into the catalytic properties of mononuclear iron centres.

PH-sensitive vibrational probe reveals a cytoplasmic protonated cluster in bacteriorhodopsin

Infrared spectroscopy has been used in the past to probe the dynamics of internal proton transfer reactions taking place during the functional mechanism of proteins but has remained mostly silent to protonation changes in the aqueous medium. Here, by selectively monitoring vibrational changes of buffer molecules with a temporal resolution of 6 µs, we have traced proton release and uptake events in the light-driven proton-pump bacteriorhodopsin and correlate these to other molecular processes within the protein. We demonstrate that two distinct chemical entities contribute to the temporal evolution and spectral shape of the continuum band, an unusually broad band extending from 2,300 to well below 1,700 cm-1 The first contribution corresponds to deprotonation of the proton release complex (PRC), a complex in the extracellular domain of bacteriorhodopsin where an excess proton is shared by a cluster of internal water molecules and/or ionic E194/E204 carboxylic groups. We assign the second component of the continuum band to the proton uptake complex, a cluster with an excess proton reminiscent to the PRC but located in the cytoplasmic domain and possibly stabilized by D38. Our findings refine the current interpretation of the continuum band and call for a reevaluation of the last proton transfer steps in bacteriorhodopsin.

Charging through the looking glass

Organic Chemistry Asymmetric catalysis is a commonly applied technique to prepare just one of two mirror-image products in a chemical reaction. But what if you already have the compound you want, stuck in a mixture of left- and right-handed enantiomers? Shin et al. now show that light-induced electron transfer can trigger a favorable succession of proton and hydrogen-atom transfer steps, both of which are susceptible to biasing by catalysts, to preferentially convert a mixture of cyclic urea enantiomers into just one (see the Perspective by Wendlandt). Science , this issue p. [364][1]; see also p. [304][2] [1]: /lookup/doi/10.1126/science.aay2204 [2]: /lookup/doi/10.1126/science.aay6919

Ab Initio QM/MM Modeling of the Rate-Limiting Proton Transfer Step in the Deamination of Tryptamine by Aromatic Amine Dehydrogenase.

Aromatic amine dehydrogenase (AADH) and related enzymes are at the heart of debates on the roles of quantum tunneling and protein dynamics in catalysis. The reaction of tryptamine in AADH involves significant quantum tunneling in the rate-limiting proton transfer step, shown by large H/D primary kinetic isotope effects (KIEs), with unusual temperature dependence. We apply correlated ab initio combined quantum mechanics/molecular mechanics (QM/MM) methods, at levels up to local coupled cluster theory (LCCSD(T)/(aug)-cc-pVTZ), to calculate accurate potential energy surfaces for this reaction, which are necessary for quantitative analysis of tunneling contributions and reaction dynamics. Different levels of QM/MM treatment are tested. Multiple pathways are calculated with fully flexible transition state optimization by the climbing-image nudged elastic band method at the density functional QM/MM level. The average LCCSD(T) potential energy barriers to proton transfer are 16.7 and 14.0 kcal/mol for proton transfer to the two carboxylate atoms of the catalytic base, Asp128β. The results show that two similar, but distinct pathways are energetically accessible. These two pathways have different barriers, exothermicity and curvature, and should be considered in analyses of the temperature dependence of reaction and KIEs in AADH and other enzymes. These results provide a benchmark for this prototypical enzyme reaction and will be useful for developing empirical models, and analyzing experimental data, to distinguish between different conceptual models of enzyme catalysis.

Temperature Dependence of the Catalytic Two- versus Four-Electron Reduction of Dioxygen by a Hexanuclear Cobalt Complex.

The synthesis and characterization of a hexanuclear cobalt complex 1 involving a nonheme ligand system, L1, supported on a Sn6O6 stannoxane core are reported. Complex 1 acts as a unique catalyst for dioxygen reduction, whose selectivity can be changed from a preferential 4e-/4H+ dioxygen-reduction (to water) to a 2e-/2H+ process (to hydrogen peroxide) only by increasing the temperature from -50 to 25 °C. A variety of spectroscopic methods (119Sn-NMR, magnetic circular dichroism (MCD), electron paramagnetic resonance (EPR), SQUID, UV-vis absorption, and X-ray absorption spectroscopy (XAS)) coupled with advanced theoretical calculations has been applied for the unambiguous assignment of the geometric and electronic structure of 1. The mechanism of the O2-reduction reaction has been clarified on the basis of kinetic studies on the overall catalytic reaction as well as each step in the catalytic cycle and by low-temperature detection of intermediates. The reason why the same catalyst can act in either the two- or four-electron reduction of O2 can be explained by the constraint provided by the stannoxane core that makes the O2-binding to 1 an entropically unfavorable process. This makes the end-on μ-1,2-peroxodicobalt(III) intermediate 2 unstable against a preferential proton-transfer step at 25 °C leading to the generation of H2O2. In contrast, at -50 °C, the higher thermodynamic stability of 2 leads to the cleavage of the O-O bond in 2 in the presence of electron and proton donors by a proton-coupled electron-transfer (PCET) mechanism to complete the O2-to-2H2O catalytic conversion in an overall 4e-/4H+ step. The present study provides deep mechanistic insights into the dioxygen reduction process that should serve as useful and broadly applicable principles for future design of more efficient catalysts in fuel cells.

Insights into chemoselective fluorination reaction of alkynals via N-heterocyclic carbene and Brønsted base cooperative catalysis

A systematically theoretical study has been carried out to understand the mechanism and chemoselectivity of N-heterocyclic carbene (NHC)-catalyzed fluorination reaction of alkynals using density functional theory calculations. The calculated results reveal that the reaction contains several steps, i.e., formation of the actual catalyst NHC, the nucleophilic attack of NHC on the carbonyl carbon atom of a formyl group, the formation of Breslow intermediate, the removal of methyl carbonate group to afford cumulative allenol intermediate, C–F bond formation coupled with generation of (SO2Ph)2N− anion, esterification accompanied with formation of (SO2Ph)2NH, and dissociation of NHC from product. For the formation of Breslow intermediate via the [1,2]-proton transfer process, apart from the direct proton transfer mechanism, the H2O- and EtOH-mediated proton transfer mechanisms were also investigated, and the free energy barriers for the crucial proton transfer steps can be significantly lowered by explicit inclusion of the protic media EtOH. Furthermore, multiple analyses have also been performed to explore the roles of catalysts and origin of chemoselectivity. Noteworthily, the in situ formed Bronsted base (BB) (SO2Ph)2N− anion was found to play an indispensable role in the esterification process, indicating that the reaction undergoes NHC-BB cooperatively catalytic mechanism, which is remarkably different from the direct esterification pathway proposed in the experimental references. This theoretical work provides a case on the exploration of the dual catalysis in NHC chemistry, which is valuable for rational design on newly cooperative organocatalysis in future.

Examination of the Mechanism of the Yield of N2O from Nitroxyl (HNO) in the Solution Phase by Theoretical Calculations.

The dimerization of HNO and subsequent yield of N2O in aqueous solution are studied based on the theoretical calculations and kinetic simulations. The initial dimerization reactions were computed at various levels of theory, and large divergence was observed in the predictions of the gas-phase free energies. The T1 diagnostics at CCSD(T)/aug-cc-pVTZ suggests multireference characteristics of the HNO dimers and the transition states. The solution-phase free energies were obtained using the wB97XD method and the SMD solvation model. The pKa values of the (HNO)2 tautomers and their first protonated and deprotonated products were estimated using the cluster-continuum approach. The theoretical results confirmed the original conclusion that the favored cis-pathway is comprised of several rapid proton transfer steps leading to either cis-HONNOH or cis-HONNO¯ before decomposition. Several new water-catalyzed and H3O+/water catalyzed reactions are presented to explain the fast kinetics observed in the experiments. To validate the proposed mechanism, kinetic simulations with the consideration of diffusion-limited kinetics were implemented on several related systems, based on which the previously reported global rate constant was explained as the kinetics of the initial dimerization step and the global kinetics in very dilute HNO solutions.

Fenton's Reagent Catalyzed Release of Carbon Monooxide from 1,3-Dihydroxy Acetone.

Triose sugar, 1,3-dihydroxy acetone (DHA) on treatment with Fenton's reagent releases CO under physiological conditions. The release of CO has been demonstrated by myoglobin assay and quantum chemical studies. The mechanistic study has been carried out using B3LYP/6-311++G(d,p), M06-2X/6-311++G(d,p) and CCSD(T)//M06-2X/6-311++G(d,p) level of theories in aqueous medium with dielectric constant of 78.39 by employing the polarized continuum model (PCM). The theoretical investigation shows that DHA breaks down completely into 2 equiv of CO, 1 equiv of CO2, and 6 equiv of H2O without formation of toxic metabolites. The activation barriers of some steps are as high as ∼50 kcal mol-1 along with barrierless intermediate steps resulting from highly stabilized intermediates. The quantum tunneling mechanism of proton transfer steps has been confirmed through kinetic isotope effect study. The natural bond orbital analysis is consistent with the proposed mechanism. The present protocol does not require any photoactivation and thus it can serve as a promising alternative to transition metal CO-releasing molecules. The present work can initiate the study of carbohydrates as CO-releasing molecules for therapeutic applications and it could also be useful in generation of CO for laboratory applications.

Theoretical insights into the protonation states of active site cysteine and citrullination mechanism of Porphyromonas gingivalis peptidylarginine deiminase.

Porphyromonas gingivalis peptidylarginine deiminase (PPAD) catalyzes the citrullination of peptidylarginine, which plays a critical role in the rheumatoid arthritis (RA) and gene regulation. For a better understanding of citrullination mechanism of PPAD, it is required to establish the protonation states of active site cysteine, which is still a controversial issue for the members of guanidino-group-modifying enzyme superfamily. In this work, we first explored the transformation between the two states: State N (both C351 and H236 are neutral) and State I (both residues exist as a thiolate-imidazolium ion pair), and then investigated the citrullination reaction of peptidylarginine, using a combined QM/MM approach. State N is calculated to be more stable than State I by 8.46 kcal/mol, and State N can transform to State I via two steps of substrate-assisted proton transfer. Citrullination of the peptidylarginine contains deamination and hydrolysis. Starting from State N, the deamination reaction corresponds to an energy barrier of 18.82 kcal/mol. The deprotonated C351 initiates the nucleophilic attack to the substrate, which is the key step for deamination reaction. The hydrolysis reaction contains two chemical steps. Both the deprotonated D238 and H236 can act as the bases to activate the hydrolytic water, which correspond to similar energy barriers (∼17 kcal/mol). On the basis of our calculations, C351, D238, and H236 constitute a catalytic triad, and their protonation states are critical for both the deamination and hydrolysis processes. In view of the sequence similarity, these findings may be shared with human PAD1-PAD4 and other guanidino-group-modifying enzymes. Proteins 2017; 85:1518-1528. © 2017 Wiley Periodicals, Inc.

A DFT-based mechanistic study on the formation of oximes

Oxime chemistry has been proven to be a reliable bioconjugation method for biomedical applications. Because of its stable and bio-orthogonal nature, a number of materials have been devised for in vitro and in vivo applications such as drug delivery, imaging, and biochemical assays. Polymers, synthetic molecules, nanoparticles, and biomolecules carrying alkoxyamine and aldehyde/ketone functional groups could be linked to each other through oxime bond, and a variety of modular platforms could be produced. Formation of oximes is catalyzed in acidic medium, and the proposed reaction mechanism follows classical imine formation pathways. Aniline has been found to accelerate the rate of oxime formation several orders of magnitude. In this computational study, we analyzed the proposed mechanism on model systems using DFT calculations including a solvation model. The energetics of the reaction steps in neutral and acidic conditions as well as in the presence of aniline was performed. Explicit water molecules were included in the calculations to study the energetics of solvent assisted proton transfer steps.

Dinitrogen Splitting Coupled to Protonation.

The coupling of electron- and proton-transfer steps provides a general concept to control the driving force of redox reactions. N2 splitting of a molybdenum dinitrogen complex into nitrides coupled to a reaction with Brønsted acid is reported. Remarkably, our spectroscopic, kinetic, and computational mechanistic analysis attributes N-N bond cleavage to protonation in the periphery of an amide pincer ligands rather than the {Mo-N2 -Mo} core. The strong effect on electronic structure and ultimately the thermochemistry and kinetic barrier of N-N bond cleavage is an unusual case of a proton-coupled metal-to-ligand charge transfer process, highlighting the use of proton-responsive ligands for nitrogen fixation.

Intramolecular Light-Driven Accumulation of Reduction Equivalents by Proton-Coupled Electron Transfer.

The photochemistry of a molecular pentad composed of a central anthraquinone (AQ) acceptor flanked by two Ru(bpy)32+ photosensitizers and two peripheral triarylamine (TAA) donors was investigated by transient IR and UV-vis spectroscopies in the presence of 0.2 M p-toluenesulfonic acid (TsOH) in deaerated acetonitrile. In ∼15% of all excited pentad molecules, AQ is converted to its hydroquinone form (AQH2) via reversible intramolecular electron transfer from the two TAA units (τ = 65 ps), followed by intermolecular proton transfer from TsOH (τ ≈ 3 ns for the first step). Although the light-driven accumulation of reduction equivalents occurs through a sequence of electron and proton transfer steps, the resulting photoproduct decays via concerted PCET (τ = 4.7 μs) with an H/D kinetic isotope effect of 1.4 ± 0.2. Moreover, the reoxidation of AQH2 seems to take place via a double electron transfer step involving both TAA+ units rather than sequential single electron transfer events. Thus, the overall charge-recombination reaction seems to involve a concerted proton-coupled two-electron oxidation of AQH2. The comparison of experimental data obtained in neat acetonitrile with data from acidic solutions suggests that the inverted driving-force effect can play a crucial role for obtaining long-lived photoproducts resulting from multiphoton, multielectron processes. Our pentad provides the first example of light-driven accumulation of reduction equivalents stabilized by PCET in artificial molecular systems without sacrificial reagents. Our study provides fundamental insight into how light-driven multielectron redox chemistry, for example the reduction of CO2 or the oxidation of H2O, can potentially be performed without sacrificial reagents.

Micellar control over tautomerization and photo-induced electron transfer of Lumichrome in the presence of aliphatic and aromatic amines: a transient absorption study

Lumichrome (Lc), a molecule consisting of a trinuclear alloxazine moiety is our present subject of interest. This molecule is subjected to tautomerization in the presence of pyridine, acetic acid, etc, through the formation of an eight-membered ring. In our present contribution, we have attempted to analyze the influence of the presence of an aliphatic amine, triethylamine (TEA) and an aromatic amine, N,N-dimethylaniline (DMA) in the double proton transfer step of the tautomerization as well as the photo-induced electron transfer (PET) from those amines to Lc. We have studied these phenomena within micelles, anionic and neutral, to observe the effect of confinement. Through our experiments, it could be stated that along with tautomerization and proton transfer, there is also evidence of PET in triplet excited state.