Metal-catalyzed Hydrolysis Research Articles

Metal-Catalyzed Hydrolysis of RNA in Aqueous Environments.

The stability of RNA in aqueous systems is critical for multiple environmental applications including evaluating the environmental fate of RNA interference pesticides and interpreting viral genetic marker abundance for wastewater-based epidemiology. In addition to biological processes, abiotic reactions may also contribute to RNA loss. In particular, some metals are known to dramatically accelerate rates of RNA hydrolysis under certain conditions (i.e., 37 °C or higher temperatures, 0.15-100 mM metal concentrations). In this study, we investigated the extent to which metals catalyze RNA hydrolysis under environmentally relevant conditions. At ambient temperature, neutral pH, and ∼10 μM metal concentrations, we determined that metals that are stronger Lewis acids (i.e., lead, copper) catalyzed single-stranded (ss)RNA, whereas metals that are weaker Lewis acids (i.e., zinc, nickel) did not. In contrast, double-stranded (ds)RNA resisted hydrolysis by all metals. While lead and copper catalyzed ssRNA hydrolysis at ambient temperature and neutral pH values, other factors such as lowering the solution pH and including inorganic and organic ligands reduced the rates of these reactions. Considering these factors along with sub-micromolar metal concentrations typical of environmental systems, we determined that both ssRNA and dsRNA are unlikely to undergo significant metal-catalyzed hydrolysis in most environmental aqueous systems.

Role of Pyridine Nitrogen in Palladium-Catalyzed Imine Hydrolysis: A Case Study of (E)-1-(3-bromothiophen-2-yl)-N-(4-methylpyridin-2-yl)methanimine

In the present study, 4-methylpyridin-2-amine was reacted with 3-bromothiophene-2-carbaldehyde and the Schiff base (E)-1-(3-bromothiophen-2-yl)-N-(4-methylpyridin-2-yl)methanimine was obtained in a 79% yield. Coupling of the Schiff base with aryl/het-aryl boronic acids under Suzuki coupling reaction conditions, using Pd(PPh3)4 as catalyst, yielded products with the hydrolysis of the imine linkages (5a–5k, 6a–6h) in good to moderate yields. To gain mechanistic insight into the transition metal-catalyzed hydrolysis of the compounds, density functional theory (DFT) calculations were performed. The theoretical calculations strongly supported the experiment and provided an insight into the transition metal-catalyzed hydrolysis of imines.

Catalytic Chemosensing Assay for Selective Detection of Methyl Parathion Organophosphate Pesticide.

Herein, a catalytic chemosensing assay (CCA), based on a bimetallic complex, [RuII (bpy)2 (CN)2 ]2 (CuI I)2 (bpy=2,2'-bipyridine), is described. This complex integrates a task-specific catalyst (CuI -catalyst) and a signaling unit ([RuII (bpy)2 (CN)2 ]) to specifically hydrolyze methyl parathion, a highly toxic organophosphate (OP) pesticide. The bimetallic complex catalyzed the hydrolysis of the phosphate ester to generate o,o-dimethyl thiophosphate (DTP) anion and 4-nitrophenolate. Intrinsically, 4-nitrophenolate absorbed UV/Vis light at λmax =400 nm, creating the first level of the chemosensing signal. DTP interacted with the original complex to displace the chromophore, [RuII (bpy)2 (CN)2 ], which was monitored by spectrofluorometry; this was classified as the second level of chemosensing signal. By integrating both spectroscopic and spectrofluorometric signals with a simple AND logic gate, only methyl parathion was able to provide a positive response. Other aromatic and aliphatic OP pesticides (diazinon, fenthion, meviphos, terbufos, and phosalone) and 4-nitrophenyl acetate provided negative responses. Furthermore, owing to the metal-catalyzed hydrolysis of methyl parathion, the CCA system led to the detoxification of the pesticide. The CCA system also demonstrated its catalytic chemosensing properties in the detection of methyl parathion in real samples, including tap water, river water, and underground water.

Catalytic methanolysis and hydrolysis of hydrazine-borane with monodisperse Ru NPs@nano-CeO2 catalyst for hydrogen generation at room temperature

Abstract Herein, we report metal catalyzed methanolysis and hydrolysis of hydrazine-borane as a fast hydrogen generation system under mild conditions. To the best of our knowledge, this is the first report that a monodisperse Ru NPs@nano-CeO2 catalyst can achieve a complete conversion of N2H4BH3 to H2 with the assistance of both methanolysis and hydrolysis reactions. In order to achieve hydrolysis and methanolysis effectively, monodisperse Ru NPs@nano-CeO2 catalyst have been prepared by modifying the chemical reduction method which is a very simple and efficient method in room conditions. The synthesized Ru NPs@nano-CeO2 catalyst showed excellent catalytic activity, stability, and selectivity in the production of hydrogen by both hydrolysis and methanolysis of the hydrazine-borane. The results reported here also includes (i) identification of the prepared catalyst by using analytical techniques such as XRD, XPS, TEM, HR-TEM, (ii) determination of stoichiometry for methanolysis and hydrolysis reactions, (iii) determination of rate constants and laws for methanolysis and hydrolysis reactions, (iv) determination of kinetic parameters such as enthalpy, entropy and activation energy for methanolysis and hydrolysis reactions.

Liquid phase in situ hydrodeoxygenation of biomass-derived phenolic compounds to hydrocarbons over bifunctional catalysts

The objective of this study was to find an effective method for converting renewable biomass-derived phenolic compounds into hydrocarbons bio-fuel via in situ catalytic hydrodeoxygenation. The in situ hydrodeoxygenation of biomass-derived phenolic compounds was carried out in methanol-water solvent over bifunctional catalysts of Raney Ni and HZSM-5 or H-Beta. In the in situ hydrodeoxygenation, the hydrogen was donated by aqueous phase reforming of methanol without external hydrogen gas. This reaction pathway for liquid-phase in situ hydrodeoxygenation of phenolic monomers was based on methanol-water as a solvent, stepwise metal-catalyzed hydrogenation, acid-catalyzed dehydration, and metal-catalyzed hydrolysis. The three-step conversion process can be achieved by a one-pot procedure. When HZSM-5 (Si/Al ratio of 25) and Raney Ni were used as the bifunctional catalysts of in situ hydrodeoxygenation, more than 90% conversion of phenolic monomers and dimers, approximately 70–90% selectivity of cyclohexanes and hydrocarbons could be obtained at 220°C with a reaction time of 7h. The bifunctional catalysts combined Raney Ni with HZSM-5 can achieve the aqueous-phase reforming of methanol, which coupled with the in situ hydrodeoxygenation of phenolic compounds. Therefore, this in situ hydrodeoxygenation process with bifunctional catalysts provided an efficient route for upgrading bio-oil containing large amounts of phenolic compounds into renewable hydrocarbon products.

Structural insights into the coordination chemistry and reactivity of a 3,3′-bis-imine-2,2′-bipyridine ligand

The coordination chemistry of the bis-salicyl-appended Schiff-base ligand L8 with Lewis acidic metal ions affords the mononuclear complex [Sn(L9)Cl4] (1) and two paramagnetic dimers [Cu(L9)(sal)]2(ClO4)2, (2) and [Mn(L9)Cl2(EtOH)]2] (3). The X-ray crystal structures of 1–3 reveal a propensity for L8 to undergo metal catalyzed hydrolysis and cyclization to the diazepine ligand L9. Theoretical calculations on L8 and a model Sn(IV) complex reveal that coordination to a metal ion weakens the imine bonds, rendering them more susceptible to hydrolysis reactions and/or attack by nucleophiles. In contrast, reaction of L8 with FeCl3 in the presence of base affords the partial hydrolysis product [Fe(L10)2]Cl·CH3CN (4). Tuning the reaction conditions via the addition of a second base slows down the hydrolysis of the ligand sufficiently to afford a few crystals of the μ2-oxo diferric complex (μ-O)[Fe(L8)]2·2CH3CN (5) in which intact L8 coordinates to the Fe(III) in a bis-bidentate manner through a deprotonated salicyl oxygen and a bis-imine nitrogen lone pair, with the nitrogen atoms of its 2,2′-bipyridine remaining uncoordinated.

Isokinetic Temperature and Size-Controlled Activation of Ruthenium-Catalyzed Ammonia Borane Hydrolysis

Metal-catalyzed hydrolysis is an important reaction for releasing hydrogen stored in ammonia borane, a promising fuel form for the future hydrogen economy, under ambient conditions. A variety of catalysts made of different transition metals have been investigated to improve the efficiency of hydrogen generation; however, little attention has been given to the possible influence of the compensation effect on catalyst design. Using face-centered cubic (FCC) packed ruthenium (Ru) nanoparticles supported on layered double oxide nanodisks, we show that the compensation effect produces an isokinetic temperature at Ti = 17.5(±1.6) °C within the operational range of hydrogen generation. We further show that the turnover frequency (TOF) of the reaction can be maximized for operations performed below Ti by reducing the size of Ru-FCC nanoparticles, which increases the fraction of edge and corner atoms and lowers the activation energy. At 15 °C, TOF can reach more than 90% of the theoretical maximum (0.72 mol m–2 h–...

Octarepeat region flexibility impacts prion function, endoproteolysis and disease manifestation.

The cellular prion protein (PrPC) comprises a natively unstructured N-terminal domain, including a metal-binding octarepeat region (OR) and a linker, followed by a C-terminal domain that misfolds to form PrPSc in Creutzfeldt-Jakob disease. PrPC β-endoproteolysis to the C2 fragment allows PrPSc formation, while α-endoproteolysis blocks production. To examine the OR, we used structure-directed design to make novel alleles, ‘S1’ and ‘S3’, locking this region in extended or compact conformations, respectively. S1 and S3 PrP resembled WT PrP in supporting peripheral nerve myelination. Prion-infected S1 and S3 transgenic mice both accumulated similar low levels of PrPSc and infectious prion particles, but differed in their clinical presentation. Unexpectedly, S3 PrP overproduced C2 fragment in the brain by a mechanism distinct from metal-catalysed hydrolysis reported previously. OR flexibility is concluded to impact diverse biological endpoints; it is a salient variable in infectious disease paradigms and modulates how the levels of PrPSc and infectivity can either uncouple or engage to drive the onset of clinical disease.

Understanding the hydrolysis mechanism of ethyl acetate catalyzed by an aqueous molybdocene: a computational chemistry investigation.

A thoroughly mechanistic investigation on the [Cp2Mo(OH)(OH2)](+)-catalyzed hydrolysis of ethyl acetate has been performed using density functional theory methodology together with continuum and discrete-continuum solvation models. The use of explicit water molecules in the PCM-B3LYP/aug-cc-pVTZ (aug-cc-pVTZ-PP for Mo)//PCM-B3LYP/aug-cc-pVDZ (aug-cc-pVDZ-PP for Mo) computations is crucial to show that the intramolecular hydroxo ligand attack is the preferred mechanism in agreement with experimental suggestions. Besides, the most stable intermediate located along this mechanism is analogous to that experimentally reported for the norbornenyl acetate hydrolysis catalyzed by molybdocenes. The three most relevant steps are the formation and cleavage of the tetrahedral intermediate immediately formed after the hydroxo ligand attack and the acetic acid formation, with the second one being the rate-determining step with a Gibbs energy barrier of 36.7 kcal/mol. Among several functionals checked, B3LYP-D3 and M06 give the best agreement with experiment as the rate-determining Gibbs energy barrier obtained only differs 0.2 and 0.7 kcal/mol, respectively, from that derived from the experimental kinetic constant measured at 296.15 K. In both cases, the acetic acid elimination becomes now the rate-determining step of the overall process as it is 0.4 kcal/mol less stable than the tetrahedral intermediate cleavage. Apart from clarifying the identity of the cyclic intermediate and discarding the tetrahedral intermediate formation as the rate-determining step for the mechanism of the acetyl acetate hydrolysis catalyzed by molybdocenes, the small difference in the Gibbs energy barrier found between the acetic acid formation and the tetrahedral intermediate cleavage also uncovers that the rate-determining step could change when studying the reactivity of carboxylic esters other than ethyl acetate substrate specific toward molybdocenes or other transition metal complexes. Therefore, in general, the information reported here could be of interest in designing new catalysts and understanding the reaction mechanism of these and other metal-catalyzed hydrolysis reactions.

Structural studies of copper(II) complexes derived from di-2-pyridyl-ketone, (py)2CO

Reaction of ArSNC(py)2 [Ar=2,4-dinitrophenyl, (O2N)2C6H3] with CuCl2·2H2O in DMF yielded the tetranuclear complex [Me2NH2][Cu4Cl6{py2CO2}{py2C(OH)O}] (1) through metal-catalysed hydrolysis of both DMF and the thiazyl chain. Notably direct reaction of dipyridylketone (py2CO) with CuCl2·2H2O in DMF yielded the mononuclear pseudo-octahedral complex [CuCl2(py2C(OH)2)(DMF)]·DMF (2) in which the 1,1-gem diol, py2C(OH)2 acts as a tripodal ligand. Heating of 2 in DMF/MeOH promoted aggregation and formation of the polymer [Cu2Cl3{py2(OMe)O}]∞ (3). The structures of 1–3 were determined by X-ray diffraction.

Hydrogen Generation from Hydrolysis and Methanolysis of Guanidinium Borohydride

Metal-catalyzed hydrolysis and methanolysis of guanidinium borohydride (C(NH2)3BH4 or GBH) for hydrogen generation are reported. GBH is comparatively stable in water with only 0.3 equiv of H2 liberated in 24 h at 25 °C while it reacts vigorously with methanol, releasing more than 3.2 equiv of H2 within only 17 min. Even at 0 °C, there was still nearly 2.0 equiv of H2 released after 2 h, but no H2 liberation was observed for hydrolysis under the same conditions. Various metal chlorides were adopted to enhance the reaction kinetics of the hydrolysis and methanolysis, of which CoCl2 exhibits the highest activity in both cases. With the addition of 2.0 mol % CoCl2 at 25 °C, the methanolysis of GBH could generate 4 equiv of H2 within 10 min with a maximum hydrogen generation rate of 9961.5 mL·min–1·g–1 while only 1.8 equiv of H2 was obtained under the same conditions at a maximum hydrogen generation rate of 692.3 mL·min–1·g–1 for hydrolysis. Compared with hydrolysis, methanolysis of GBH possesses much faster r...

Chemical hydrogen storage using polynuclear borane anion salts

The polynuclear borane anions nido-B 11H 14 −, closo-B 10H 10 2− and closo-B 12H 12 2− undergo heterogeneous transition metal-catalyzed hydrolysis to generate hydrogen. The rate of hydrolysis is dependent upon the concentration of polynuclear borane anions and surface area of the metallic catalyst. The aqueous solutions of polynuclear borane anions, especially the closo-B 10H 10 2− and closo-B 12H 12 2− dianions, are very stable for an extended period of time (years) in the absence of catalyst and spontaneously generate hydrogen in the presence of a rhodium metal catalyst. These polynuclear borane anions have a high potential for use in portable hydrogen storage systems without requiring high pH aqueous media for storage as in the case of NaBH 4.

Hydrolysis of solid ammonia borane

Ammonia borane NH 3BH 3 is a promising hydrogen storage material by virtue of a theoretical gravimetric hydrogen storage capacity (GHSC) of 19.5 wt%. However, stored hydrogen has to be effectively released, one way of recovering this hydrogen being the metal-catalyzed hydrolysis. The present study focuses on CoCl 2-catalyzed hydrolysis of NH 3BH 3 with the concern of improving the effective GHSC of the system NH 3BH 3–H 2O. For that, NH 3BH 3 is stored as a solid and H 2O is provided in stoichiometric amount. By this way, an effective GHSC of 7.8 wt% has been reached at 25 °C. To our knowledge, it is the highest value ever reported. Besides, one of the highest hydrogen generation rates (HGRs, 21 ml(H 2) min −1) has been found. In parallel, the increases of the water amount and temperature have been studied and the reaction kinetics has been determined. Finally, it has been observed that some NH 3 release, what is detrimental for a fuel cell. To summarize, high performances in terms of GHSCs and HGRs can be reached with NH 3BH 3 and since research devoted to this boron hydride is at the beginning we may be confident in making it viable in a near future.

A hydridoirida-β-diketone as an efficient and robust homogeneous catalyst for the hydrolysis of ammonia–borane or amine–borane adducts in air to produce hydrogen

The first homogeneous metal-catalysed hydrolysis of ammonia-borane or amine-borane adducts for hydrogen generation, using a stable organometallic complex [IrHCl{(PPh(2)(o-C(6)H(4)CO))(2)H}], is reported.

Metal-Catalyzed Cleavage of tRNAPhe

This laboratory project is one component of a semester-long advanced biochemistry laboratory course that uses several complementary techniques to study tRNAPhe conformational changes induced by ligand binding. In this article we describe a set of experiments in which students assay metal-catalyzed hydrolysis of tRNAPhe using gel electrophoresis. tRNAPhe cleavage patterns are monitored in the presence of lead(II) and other metals cations. Small molecule ligands are also studied to determine their ability to enhance or inhibit lead(II)-catalyzed cleavage of tRNAPhe. Gel bands are quantified to determine ligand-binding equilibrium constants for the small molecule ligand–tRNAPhe adducts. By pooling class data from the metal and small molecule ligand experiments, students draw conclusions regarding how metal-catalyzed hydrolysis is affected by various parameters such as tRNAPhe structure, ligand charge, and inorganic chemistry of the metal ion complexes.

Probing Changes in the Conformation of tRNAPhe: An Integrated Biochemistry Laboratory Course

We have designed a new guided-inquiry laboratory for an advanced biochemistry course. This integrated laboratory focuses on the biomolecule tRNAPhe and combines elements of bioorganic and bioinorganic chemistry with biochemistry. Throughout the semester students work together to study tRNAPhe structure and ligand binding by (i) assaying metal-catalyzed hydrolysis using gel electrophoresis; (ii) probing thermal denaturation with UV–vis spectrophotometry; and (iii) characterizing ligand associated changes in conformation via fluorescence spectroscopy. Students begin the course with a common laboratory experience and then diverge into parallel projects, ending with a novel self-designed project. In their final report, students interpret experimental results from the entire class and draw conclusions regarding the effects of various ligands on the structure of tRNAPhe.

An integrated apparatus for production and measurement of molecular hydrogen

An integrated apparatus designed to carry out online accurate gas-volumetric (GV) measurements of chemicals generated in a reaction chamber is described here. In particular, such equipment is useful to quantify the molecular hydrogen produced into a small reactor via metal-catalysed hydrolysis of sodium borohydride. In its standard configuration the reactor is coupled to a hydrogenmeter relying on accurate weight measurements of water volumes displaced by the same hydrogen volumes produced during the reaction course. Both static (total gas evolved) and dynamic (rate of evolution) information on the analysed gas-mixture is accessible by such an apparatus. Finally, it can be easily interfaced with other quantitative techniques, such as gas-chromatographic (GC) or flow-measurement (FM) techniques. The apparatus is original in many technical solutions which have been adopted: (i) any kind of catalyst can be tested thanks to the insertion device (interchangeable sample plate, ISP), (ii) catalyst is dipped into solution in situ without system opening, (iii) work conditions are continuously monitored, and (iv) system control and data collection are completely automated. The apparatus has been designed to withstand rough usage, for easy and trouble-free manipulation, rapid and complete gas measurements and easy readability.

Metal-Catalyzed Phosphodiester Cleavage: Secondary 18O Isotope Effects as an Indicator of Mechanism

Information about the transition states of metal-catalyzed hydrolysis reactions of model phosphate compounds has been obtained through determination of isotope effects (IEs) on the hydrolysis reactions. Metal complexation has been found to significantly alter the transition state of the reaction from the alkaline hydrolysis reaction, and the transition state is quite dependent on the particular metal ion used. For the diester, ethyl p-nitrophenyl phosphate, the nonbridge 18O effect for the hydrolysis reactions catalyzed by Co(III) 1,5,9-triazacyclononane and Eu(III) were 1.0006 and 1.0016, respectively, indicative of a slightly associative transition state and little net change in bonding to the nonbridge oxygen. The reaction catalyzed by Zn(II) 1,4,7,10-tetraazacyclododecane had an 18O nonbridge IE of 1.0108, showing the reaction differs significantly from the reaction of the noncomplexed diester and resembles the reactions of triesters. Reaction with Co(III) 1,4,7,10-tetraazacyclododecane showed an inverse effect of 0.9948 reflecting the effects of bonding of the diester to the Co(III). Lanthanide-catalyzed hydrolysis has been observed to have unusually large 15N effects. To further investigate this effect, the 15N effect on the reaction catalyzed by Ce(IV) bis-Tris propane solutions at pH 8 was determined to be 1.0012. The 15N effects were also measured for the reaction of the monoester p-nitrophenyl phosphate by Ce(IV) bis-Tris propane (1.0014) and Eu(III) bis-Tris propane (1.0012). These smaller effects at pH 8 indicate that a smaller negative charge develops on the nitrogen during the hydrolysis reaction.

Different strategies for the direct determination of amoxicillin in human urine by second-order multivariate analysis of kinetic–spectrophotometric data

The kinetic evolution of UV–visible absorption spectra of amoxicillin in the presence of copper(II) ions has been processed by the second-order multivariate methods parallel factor analysis (PARAFAC) and also by a novel approach based on partial least-squares with residual bilinearization (PLS/RBL). The latter one is employed for the first time to evaluate kinetic–spectral information. The mechanism of the analyte metal-catalyzed hydrolysis involves a reaction intermediate and a final reaction product, both with spectra which may allow for the determination of amoxicillin in human urine, even in the presence of unsuspected sample components. This is possible thanks to the second-order advantage exploited by the employed chemometric algorithms, among which PARAFAC and PLS/RBL gave the best results. Amoxicillin was determined in a series of spiked and real urine samples, which allowed to perform, respectively, a recovery study and a comparison with the reference high-performance liquid chromatographic technique. The best figures of merit were obtained with PLS/RBL, namely sensitivity, 0.5 AU L mg −1 (AU = absorbance units), analytical sensitivity, 500 L mg −1 and limit of detection, 6 mg L −1. Relative advantages and disadvantages of the employed algorithms are discussed.

Inhibitory activity of thermal copolymers of amino acids for the metal-catalyzed hydrolysis of an RNA dinucleotide

It is well known that the hydrolysis of RNA is substantially catalyzed by several metal ions. Although this fact poses a problem for the RNA world hypothesis, there may have been unknown pathways for the protection of RNA molecules against the hydrolytic degradation under the primitive earth conditions. Thus, we have investigated whether or not thermal copolymers of amino acids (TCAA) inhibit the catalytic activity of metal ions for the RNA hydrolyses; TCAA is a suitable model material for prebiotic protein-like molecules since TCAA involving peptide bonding is readily prepared by heating amino acid mixtures under prebiotic conditions. The activities of metal ions that Fe(III) and Co(II) enhance somewhat the 3′,5′-cytidylylguanosine ( C 3 ′ pG ) hydrolysis and Ce(III) and Eu(III) accelerate greatly the C 3 ′ pG hydrolysis were notably reduced by TCAA. This fact indicates that protein-like molecules would have played important roles for the accumulation of RNA under the primitive earth conditions.