Proton Transfer In Catalysis Research Articles

Benchmarking Cationic Monolayer Protected Nanoparticles and Micelles for Phosphate-Mediated and Nucleotide-Selective Proton Transfer Catalysis.

Both micelles and self-assembled monolayer (SAM)-protected nanoparticles are capable of efficiently hosting water-immiscible substrates to carry out organic reactions in aqueous media. Herein, we have analyzed the different catalytic effect of SAM-protected cationic nanoparticles and cationic surfactants of varying chain length towards base-catalyzed proton transfer mediated ring-opening reaction of 5-nitrobenzisoxazole (NBI) (also known as Kemp Elimination (KE) reaction). We use inorganic phosphate ion or different nucleotide (phosphate-ligated different nucleoside) as base to promote the reaction on micellar or nanoparticle interface. We find almost 2-3 orders of magnitude higher concentration of surfactants of comparable hydrophobicity required to reach the similar activity which attained by low cationic head group concentration bound on nanoparticle. Additionally, at low concentration of nanoparticle-bound surfactant or with high surfactant in micellar form, nucleotide-selectivity has been observed in activating KE reaction unlike free surfactant at low concentration. Finally, we showed enzyme-mediated nucleotide hydrolysis to generate phosphate ion which in situ upregulate the KE activity much more in GNP-based system compared to CTAB. Notably, we show a reasonable superiority of SAM-protected nanoparticles in activating chemical reaction in micromolar concentration of headgroup which certainly boost up application of SAM-based nanoparticles not only for selective recognition but also as eco-friendly catalyst.

Specific base catalysis by yeast alcohol dehydrogenase I with substitutions of histidine-48 by glutamate or serine residues in the proton relay system

His-48 in yeast alcohol dehydrogenase I (His 51 in horse liver alcohol dehydrogenase) is a highly conserved residue in the active sites of many alcohol dehydrogenases. The imidazole group of His-48 may participate in base catalysis of proton transfer as it is linked by hydrogen bonds through the 2′-hydroxyl group of the nicotinamide ribose and the hydroxyl group of Thr-45 to the hydroxyl group of the alcohol bound to the catalytic zinc. In this study, His-48 was substituted with a glutamic acid residue to determine if a carboxylate could replace imidazole or to a serine residue to determine if the exposure of the 2′-hydroxyl group of the ribose to solvent would allow proton transfer to water without base catalysis. At pH 7.3, the H48E substitution increases affinity for NAD+ and NADH 17- or 2.6-fold, but decreases catalytic efficiency (V/Km) on ethanol by 70-fold and on acetaldehyde by 6-fold relative to wild-type enzyme. The H48S substitution increases affinity for coenzymes by 2-fold and decreases (V/Km) on ethanol and acetaldehyde only by ∼3-fold. The substituted enzymes show substrate deuterium isotope (H/D) effects of 3–4 for turnover number (V1) and catalytic efficiency (V1/Kb) for ethanol oxidation, indicating that hydrogen transfer is partially rate-limiting and suggesting a somewhat more random mechanism for binding of ethanol and NAD+. For reduction of acetaldehyde, the deuterium isotope effects are small, and the kinetic mechanism appears to be ordered for binding of NADH first and acetaldehyde next. The pH dependencies for H48E and H48S ADHs can be described by a mechanism with pK values of about 6–7 and 9. However, the pH dependencies for oxidation of ethanol and butanol by the H48S enzyme are also simply described by a straight line, with slopes of log V1/Kb against pH of 0.37 or 0.43, respectively. The linear dependence apparently represents catalysis by hydroxide that has a low activity coefficient due to the protein environment, or to a kinetically complex proton transfer. The effects of the substitutions of His-48 show that this residue contributes to catalysis, although many dehydrogenases also have other residues.

Engineering the hydrogen transfer pathway of an alcohol dehydrogenase to increase activity by rational enzyme design

The reduction catalyzed by an alcohol dehydrogenase (ADH) consists of two steps, hydride transfer (HT) from the NAD(P)H cofactor to the substrate followed by proton transfer (PT) originating from the aqueous solvent. We report a rational enzyme design strategy in the quest to improve the catalytic efficiency of an ADH by targeting appropriately chosen remote residues that function in PT. An ADH from Thermoanaerobacter brockii (TbSADH) was selected as the catalyst involving the enantioselective reduction of a bulky prochiral ketone (4-chlorophenyl)(pyridin-2-yl)-methanone (CPMK). Previous studies demonstrated that the protonated histidine residue H42 in TbSADH plays a key role in PT. In order to explore any change of the HT mechanism possibly affecting enzyme activity, the residue H42 was rationally mutated to other amino acids. After experimental validation, the substitution H42T was found to confer enhanced reduction ability in the transformation of CPMK to the corresponding (S)-configured product with a high activity (kcat/Km = 787.38 s−1 mM−1), a 9-fold increase relative to that of the starting enzyme. We performed molecular dynamics (MD) simulations together with quantum mechanical (QM) calculations which shed light on the origin of the improved activity. It revealed that the enlarged volume of the substrate-binding pocket brought by mutation H42T appears to be the main reason for the increase of activity. QM calculations displayed that the water-linked hydrogen bond network through H42T lead to lower activate energy. Our study indicates that the key residues participating in the catalytic proton transfer process may also serve as hotspots for engineering the activity of ADHs. The detailed information that we have learned about the mechanism can be exploited in the study of other NAD(P)H-dependent dehydrogenases.

Asymmetric Proton Transfer Catalysis by Stereocomplementary Old Yellow Enzymes for C═C Bond Isomerization Reaction

Native and promiscuous catalytic activities of flavin-dependent Old Yellow Enzymes (OYEs) reported to date are initiated by the reduced flavin upon electron transfer. As a rare exception, the isomerization of a nonactivated C═C bond was shown to be hydride-independent with two nonstereoselective yeast OYEs. Here, we report the asymmetric isomerization of a prochiral model substrate, γ-methyl β,γ-butenolide, to the corresponding (R)- and (S)-enantiomers of the γ-methyl α,β-butenolide in up to >99% ee by two stereocomplementary OYEs of algal and fungal origin, respectively, which operate by asymmetric proton transfer. Mechanistic studies based on two newly solved crystal structures, along with soaking experiments and site-directed mutagenesis, support the crucial role of partially nonconserved tyrosine residues for the activity and stereoselectivity of both (R)- and (S)-isomerases. This study offers a unique view on the potential of flavoproteins in nonredox catalysis and provides hints for scouting olefin isomerases in likely stereodivergent classes of OYEs.

Solvent-Mediated Proton-Transfer Catalysis of the Gas-Phase Isomerization of Ciprofloxacin Protomers.

Understanding how neutral molecules become protonated during positive-ion electrospray ionization (ESI) mass spectrometry is critically important to ensure analytes can be efficiently ionized, detected, and unambiguously identified. The ESI solvent is one of several parameters that can alter the dominant site of protonation in polyfunctional molecules and thus, in turn, can significantly change the collision-induced dissociation (CID) mass spectra relied upon for compound identification. Ciprofloxacin─a common fluoroquinolone antibiotic─is one such example whereby positive-ion ESI can result in gas-phase [M + H]+ ions protonated at either the keto-oxygen or the piperazine-nitrogen. Here, we demonstrate that these protonation isomers (or protomers) of ciprofloxacin can be resolved by differential ion mobility spectrometry and give rise to distinctive CID mass spectra following both charge-directed and charge-remote mechanisms. Interaction of mobility-selected protomers with methanol vapor (added via the throttle gas supply) was found to irreversibly convert the piperazine N-protomer to the keto-O-protomer. This methanol-mediated proton-transport catalysis is driven by the overall exothermicity of the reaction, which is computed to favor the O-protomer by 93 kJ mol-1 (in the gas phase). Conversely, gas phase interactions of mobility-selected ions with acetonitrile vapor selectively depletes the N-protomer ion signal as formation of stable [M + H + CH3CN]+ cluster ions skews the apparent protomer population ratio, as the O-protomer is unaffected. These findings provide a mechanistic basis for tuning protomer populations to ensure faithful characterization of multifunctional molecules by tandem mass spectrometry.

Dehydrogenative Aza-[4 + 2] Cycloaddition of Amines with 1,3-Dienes via Dual Catalysis.

We describe a synergistic utilization of copper catalysis and proton-transfer catalysis that enables an atom- and step-economical aza-[4 + 2] cycloaddition reaction of readily available N-arylamino carbonyl compounds with simple 1,3-dienes. The reaction proceeds smoothly under an air atmosphere and produces water as the sole side product. Whereas the amines can directly serve as the C- and N-atom donors, this operationally simple protocol provides green, rapid, and efficient access to 1,2,3,6-tetrahydropyridines with a broad scope.

An Iron Porphyrin Complex with Pendant Pyridine Substituents Facilitates Electrocatalytic CO2Reduction via Second Coordination Sphere Effects

AbstractA bispyridylamine‐based hanging unit within the ligand framework of a newly synthesized iron porphyrin complex (Py2XPFe) can act, on the one hand, as a hydrogen bonding site to facilitate proton transfer in catalysis and, on the other hand, as coordination site for a second Lewis acidic metal center. The bispyridylamine group in close proximity of the iron porphyrin center is able to mediate electrocatalytic CO2reduction in anhydrous MeCN. The hydrogen bonding interactions within the hanging group affect the kinetics of catalysis likely through stabilization of the [FeI(CO2H)]−intermediate, increasing the overall rate of catalysis when compared to the non‐functionalized analog,TMPFe(TMP=tetramesitylporphyrin). The rate constants (kapp) of the reduction reaction were calculated using the FOWA method which resulted in a higher TOFmaxfor the complexPy2XPFecompared withTMPFein neat MeCN (1.7×102vs. 1.1×101 s−1). The addition of weak Brønsted acids to the reaction mixture (TFE or PhOH) shows an increase in the rate of catalysis for both complexes, yet thePy2XPFeanalog displays higher TOFmaxat each relative acid concentration, suggesting the hanging group beneficially impacts the rate of catalysis in the presence of these proton sources. The addition of Lewis acidic Sc3+toPy2XPFealso results in an increase in current density of the CO2reduction reaction. Resonance Raman as well as1H‐NMR spectroscopy indicates coordination to the pyridine substituents.

Rational engineering of the Plasmodium falciparuml-lactate dehydrogenase loop involved in catalytic proton transfer to improve chiral 2-hydroxybutyric acid production

l-lactate dehydrogenases (LDHs) has been widely studied for their ability to reduce 2-keto acids for the production of 2-hydroxy acids, whereby 2-hydroxybutyric acids (2-HBA) is among the most important fundamental building blocks for synthesizing pharmaceuticals and biodegradable materials. However, LDHs usually show low activity towards 2-keto acids with longer side chain such as 2-oxobutyric acid (2-OBA). Here rational engineering of the Plasmodium falciparum LDH loop with residue involved in the catalytic proton transfer was initially studied. By combining homology alignment and structure-based design approach, we found that changing the charge characteristics or hydrogen bond network interactions of this loop could improve enzymatic catalytic activities and stabilities towards 2-OBA. Compared with wild type, variant N197Dldh showed 1.15 times higher activity and 2.73 times higher Kcat/Km. The half-life of variant N197Dldh at 40 °C increased to 77.9 h compared with 50.4 h of wild type. Furthermore, asymmetric synthesis of (S)-2-HBA with coenzyme regeneration revealed 95.8 g/L production titer within 12 h for variant N197Dldh, 2.05 times higher than using wild type. Our study indicated the importance of loop with residues involved in the catalytic proton transfer process, and the engineered LDH would be more suitable for (S)-2-HBA production.

Catalytic Enantioselective Proton Transfer Reactions

AbstractEnantioselective proton transfer refers to the process of enantioselective introduction of protons to carbanions through the recognition of prochiral faces. Enantioselective proton transfer can easily construct tertiary carbon stereocenters, which widely exist in natural products and bioactive compounds. However, catalytic enantioselective proton transfer has been a long-lasting challenge in asymmetric synthesis because the proton is the smallest ion and the proton transfer process of active intermediates is generally fast with complicated pathways and strong background reaction. In recent years, a series of new catalysts and catalytic strategies have been developed for stereocontrol of proton transfer processes in various organic reactions. At the same time, more in-depth mechanism studies have revealed detailed information and regulations of proton transfer in catalytic reactions. This paper reviews the recent progress on catalytic enantioselective proton transfer reactions according reaction types. At the end of this paper, the stereocontrol strategies of catalytic proton transfer are classified and the prospects of this field are also presented.

Temperature Dependence of Structural Dynamics at the Catalytic Cofactor of [FeFe]-hydrogenase.

[FeFe]-hydrogenases are nature's blueprint for efficient hydrogen turnover. Understanding their enzymatic mechanism may improve technological H2 fuel generation. The active-site cofactor (H-cluster) consists of a [4Fe-4S] cluster ([4Fe]H), cysteine-linked to a diiron site ([2Fe]H) carrying an azadithiolate (adt) group, terminal cyanide and carbon monoxide ligands, and a bridging carbon monoxide (μCO) in the oxidized protein (Hox). Recently, the debate on the structure of reduced H-cluster states was intensified by the assignment of new species under cryogenic conditions. We investigated temperature effects (4-280 K) in infrared (IR) and X-ray absorption spectroscopy (XAS) data of [FeFe]-hydrogenases using fit analyses and quantum-chemical calculations. IR data from our laboratory and literature sources were evaluated. At ambient temperatures, reduced H-cluster states with a bridging hydride (μH-, in Hred and Hsred) or with an additional proton at [4Fe]H (Hred') or at the distal iron of [2Fe]H (Hhyd) prevail. At cryogenic temperatures, these species are largely replaced by states that hold a μCO, lack [4Fe]H protonation, and bind an additional proton at the adt nitrogen (HredH+ and HsredH+). XAS revealed the atomic coordinate dispersion (i.e., the Debye-Waller parameter, 2σ2) of the iron-ligand bonds and Fe-Fe distances in the oxidized and reduced H-cluster. 2σ2 showed a temperature dependence typical for the so-called protein-glass transition, with small changes below ∼200 K and a pronounced increase above this "breakpoint". This behavior is attributed to the freezing-out of larger-scale anharmonic motions of amino acid side chains and water species. We propose that protonation at [4Fe]H as well as ligand rearrangement and μH- binding at [2Fe]H are impaired because of restricted molecular mobility at cryogenic temperatures so that protonation can be biased toward adt. We conclude that a H-cluster with a μCO, selective [4Fe]H or [2Fe]H protonation, and catalytic proton transfer via adt facilitates efficient H2 conversion in [FeFe]-hydrogenase.

How [FeFe]-Hydrogenase Facilitates Bidirectional Proton Transfer.

Hydrogenases are metalloenzymes that catalyze the conversion of protons and molecular hydrogen, H2. [FeFe]-hydrogenases show particularly high rates of hydrogen turnover and have inspired numerous compounds for biomimetic H2 production. Two decades of research on the active site cofactor of [FeFe]-hydrogenases have put forward multiple models of the catalytic proceedings. In comparison, our understanding of proton transfer is poor. Previously, residues were identified forming a hydrogen-bonding network between active site cofactor and bulk solvent; however, the exact mechanism of catalytic proton transfer remained inconclusive. Here, we employ in situ infrared difference spectroscopy on the [FeFe]-hydrogenase from Chlamydomonas reinhardtii evaluating dynamic changes in the hydrogen-bonding network upon photoreduction. While proton transfer appears to be impaired in the oxidized state (Hox), the presented data support continuous proton transfer in the reduced state (Hred). Our analysis allows for a direct, molecular unique assignment to individual amino acid residues. We found that transient protonation changes of glutamic acid residue E141 and, most notably, arginine R148 facilitate bidirectional proton transfer in [FeFe]-hydrogenases.

Nucleophilic Iron Complexes in Proton-Transfer Catalysis: An Iron-Catalyzed Dimroth Cyclocondensation.

The nucleophilic iron complex Bu4 N[Fe(CO)3 (NO)] (TBA[Fe]) is an active catalyst in C-H-amination but also in proton-transfer catalysis. Herein, we describe the successful use of this complex as a proton-transfer catalyst in the cyclocondensation reaction between azides and ketones to the corresponding 1,2,3-triazoles. Cross-experiments indicate that the proton-transfer catalysis is significantly faster than the nitrene-transfer catalysis, which would lead to the C-H amination product. An example of a successful sequential Dimroth triazole-indoline synthesis to the corresponding triazole-substituted indolines is presented.

Freezing of Aqueous Solutions and Chemical Stability of Amorphous Pharmaceuticals: Water Clusters Hypothesis

Molecular mobility has been traditionally invoked to explain physical and chemical stability of diverse pharmaceutical systems. Although the molecular mobility concept has been credited with creating a scientific basis for stabilization of amorphous pharmaceuticals and biopharmaceuticals, it has become increasingly clear that this approach represents only a partial description of the underlying fundamental principles. An additional mechanism is proposed herein to address 2 key questions: (1) the existence of unfrozen water (i.e., partial or complete freezing inhibition) in aqueous solutions at subzero temperatures and (2) the role of water in the chemical stability of amorphous pharmaceuticals. These apparently distant phenomena are linked via the concept of water clusters. In particular, freezing inhibition is associated with the confinement of water clusters in a solidified matrix of an amorphous solute, with nanoscaled water clusters being observed in aqueous glasses using wide-angle neutron scattering. The chemical instability is suggested to be directly related to the catalysis of proton transfer by water clusters, considering that proton transfer is the key elementary reaction in many chemical processes, including such common reactions as hydrolysis and deamidation.

Hydrogen adsorption engineering by intramolecular proton transfer on 2D nanosheets

Proton transfer has been intensively researched in the catalysis of reactions involving hydrogen, such as the hydrogen evolution reaction (HER), oxygen evolution reaction, and carbon dioxide reduction. Recently, two-dimensional (2D) materials have gained attention as catalysts for these reactions, and their catalytic effect upon changing the size, shape, thickness, and phase has been studied. However, there are no reports on the role of proton transfer in catalysis by 2D materials. Here, a novel way to enhance the catalytic effect of 2D MoS2 was demonstrated via functionalization with four different organic moieties: phenyl–Me, phenyl–OMe, phenyl–OH, and phenyl–COOH groups. The role of proton transfer in 2D catalysis was carefully investigated via electrochemical kinetic analysis and electrical measurement. The best HER performance was observed with proton-donating COOH-functionalized active materials due to intramolecular proton transfer, which shows potential in hydrogen adsorption engineering using proton transfer. In addition, other molecularly functionalized 2D catalysts, including MoTe2 and graphene, also show proton transfer due to the incorporation of organic moieties, providing enhanced HER performance.

Enantioselective cooperative proton-transfer catalysis using chiral ammonium phosphates.

Chiral phosphorate anions are shown to be highly enantioselective templates for proton-transfer catalysis. A salt generated in situ from a bridgehead amine and a BINOL-derived chiral phosphoric acid serves as an effective proton-shuttle that exhibits remarkable enantioselectivity in a bioinspired, triple co-operative catalysis involving an achiral NHC. Thioesters with a β-chiral center can be prepared in a single step from substituted cinnamaldehyde derivatives, with up to 99% yield and 99% ee. Heteroaryl groups are well tolerated in these reactions, despite the presence of basic sites.

Structure and function of Aspergillus niger laccase McoG

AbstractThe ascomycete Aspergillus niger produces several multicopper oxidases, but their biocatalytic properties remain largely unknown. Elucidation of the crystal structure of A. niger laccase McoG at 1.7 Å resolution revealed that the C-terminal tail of this glycoprotein blocks the T3 solvent channel and that a peroxide ion bridges the two T3 copper atoms. Remarkably, McoG contains a histidine (His253) instead of the common aspartate or glutamate expected to be involved in catalytic proton transfer with phenolic compounds. The crystal structure of H253D at 1.5 Å resolution resembles the wild type structure. McoG and the H253D, H253A and H253N variants have similar activities with 2,2’-azino-bis(3- ethylbenzothiazoline-6-sulphonic acid or N,N-dimethyl-p-phenylenediamine sulphate. However, the activities of H253A and H253N with 2-amino-4-methylphenol and 2-amino-4-methoxyphenol are strongly reduced compared to that of wild type. The redox potentials and electron transfer rates (k

Cinchonium Betaines as Efficient Catalysts for Asymmetric Proton Transfer Catalysis: The Development of a Practical Enantioselective Isomerization of Trifluoromethyl Imines.

We have developed a new class of cinchonium betaine catalysts bearing both a base moiety and an aromatic moiety as an N-substituent of the quinuclidine motif. These cinchonium betaines were found to promote proton transfer catalysis with 1000-5000 turnovers per 24 h, thereby enabling us to realize highly efficient enantioselective isomerization of trifluoromethyl imines to provide a practical access to optically active trifluoromethylated amines.

Protonation of silylenol ether via excited state proton transfer catalysis.

We demonstrate the photocatalytic protonation of a silylenol ether using 7-bromo-2-naphthol as an ESPT catalyst with phenol as the sacrificial proton source. Greater than 95% conversion is achieved with 1 mol% catalyst. The reaction cycle is dependent on the significantly increased acidity of the catalyst in the excited state as well as the long lifetime for the triplet excited state of 7-bromo-2-naphthol. The reaction does not occur in the absence of light (367 nm) and can readily be controlled by light intensity modulation. We also demonstrate that a 72% reaction yield can be obtained with unsubstituted naphthol as the catalyst by coupling triplet energy transfer, via a visible light absorbing (445 nm) sensitizer, into the catalytic cycle. These results open the door to an entirely new class of sensitized photocatalytic reactions that harness the excited state acidity of ESPT dyes.

Nonadiabatic Dynamics in Atomistic Environments: Harnessing Quantum-Classical Theory with Generalized Quantum Master Equations.

The development of methods that can efficiently and accurately treat nonadiabatic dynamics in quantum systems coupled to arbitrary atomistic environments remains a significant challenge in problems ranging from exciton transport in photovoltaic materials to electron and proton transfer in catalysis. Here we show that our recently introduced MF-GQME approach, which combines Ehrenfest mean field theory with the generalized quantum master equation framework, is able to yield quantitative accuracy over a wide range of charge-transfer regimes in fully atomistic environments. This is accompanied by computational speed-ups of up to 3 orders of magnitude over a direct application of Ehrenfest theory. This development offers the opportunity to efficiently investigate the atomistic details of nonadiabatic quantum relaxation processes in regimes where obtaining accurate results has previously been elusive.

A theoretical study of 3,5-diazido-1,2,4-triazole: the role of the hydrogen bonding interaction in stabilizing the molecular system

3,5-Diazido-1, 2, 4-triazole (DATZ) is a compound that has a good thermal stability and can be used to produce high energetic ionic salts. The conformations of DATZ were searched by the molecular dynamics simulations and optimized by the molecular mechanics and dispersion-corrected density functional theory methods. The dimer and trimer of DATZ were constructed from the most stable monomer. The hydrogen bonding interactions, which were found to be critically important in increasing the stability of the dimer and trimer, were investigated with the help of the natural bond orbital and the quantum theory of atoms in molecules analyses. The changes in thermodynamic functions, stabilization interaction energies, and hydrogen-bonding energies show that the trimer is most likely the existing form of DATZ. The intramolecular, intermolecular, and water catalytic proton transfer processes were simulated to investigate the proton transfer mechanism. The intermolecular transfer process requires the lowest activation energy (42.56 kJ mol−1) and is the most likely process of proton transfer. DATZ is not only a proton acceptor but also a proton donor. Its weak acidity was quantified as pKa = 10.16. The solvation energy estimated using the conductor-like polarizable continuum model in water is the largest (−99.96 kJ mol−1), revealing that DATZ is more stable in water than in another seven solvents.