Insight into catalytic mechanism of papain-like cysteine proteinases

We studied the role of D158 in papain-like cysteine proteinases by using subtilisin Carlsberg, and its chemically modified analog thiolsubtilisin, by applying the proton inventory (PI) method and also by taking into account the pH profiles of the kcat/Km parameter. In the case of thiolsubtilisin, we estimated large inverse solvent isotope effects for kcat/Km, as in papain, whereas for subtilisin we found "dome-shaped" PI, suggesting a completely different mechanism. Finally, the kinetic behavior of thiolsubtilisin presented similarities as well as differences, compared to papain, suggesting a possible role for D158 as part of a catalytic triad in papain-like cysteine proteinases.     

Insight into the inversion mechanism of an inverse polymer emulsion

A study of the mechanism of inversion of inverse polymer emulsions showed that the likely key step in the inversion process is the swelling of polymer particles caused by added water diffusing through the oil phase. Therefore, we propose that inversion occurs as a result of polymer particle crowding caused by water diffusion and subsequent droplet rupture that results in the release of the polymer into the water phase.     

Insight into the catalytic thermal decomposition mechanism of ammonium perchlorate

Journal of Thermal Analysis and Calorimetry -     

Insight into the mechanism of transient trapping in micellar electrokinetic chromatography

Transient trapping is a new mechanism of on-line sample concentration and separation that has recently been presented. It involves the injection of a short length of micellar solution in front of the sample, making it similar to sweeping in partial-filling MEKC. Here, we examine the mechanism of transient trapping by the use of computer simulations and compare it to sweeping in MEKC for the two analytes, sulforhodamine B and 101. The simulation results confirm the mechanism for concentration and separation originally proposed. The mechanism for concentration is similar to sweeping since the analytes are picked and accumulated by the micelles that penetrate the sample zone. The mechanism for separation is however quite unique since the concentrated analytes are trapped for a few seconds on the sample/micelle boundary before they are released as the concentration of micelle is reduced as it undergoes electromigration dispersion and the analytes separate down a micelle gradient. Simulation results suggested that a significant contribution of band broadening arises from the micelle gradient, with shallower gradients resulting in broader peaks. However, this is offset by an increase in selectivity, such that resolution was enhanced even though the peaks are broader. Transient trapping analysis with similar resolution to those obtained by sweeping MEKC could be achieved in 1/10 of the time and 1/4 of the capillary length, which results in a 2-3 times increase in sensitivity.     

Insight into the mechanism of three component condensation leading to aminomethylenebisphosphonates

Three-component reaction of a primary amine, diethyl phosphite and triethyl orthoformate followed by acid hydrolysis of the adduct provides N-substituted aminomethylenebisphosphonic acids in good yields. Being extremely versatile, it is commonly utilized for preparation of compounds possessing potential antiosteoporotic, antibacterial, anticancer, antiparasitic or herbicidal activity. However, the mechanism of the reaction remains unknown. p-Nitroaniline has been found an interesting tool to shed light on this matter. Its use allowed to separate and identify four intermediates, both non-phosphorus and phosphorus containing, and subsequently suggest the mechanism of the whole process. The acquired knowledge was helpful in explanation the route and the final product structure obtained for more complex reaction proceeding with the use of 4-aminopyridine. Additional alkylation of the pyridine nitrogen atom, leading to unexpected N-(1-alkylpyridinium-4-amino)methylenebisphosphonic acids was unambiguously proved.     

Insight into the reaction mechanism of the conversion of methylbutynol on silica-alumina

The conversion of methylbutynol (MBOH) over commercially available silicaalumina solids was studied. The formation of 3-methyl-3-butene-2-one (MIPK) was explained in terms of the cooperative action of both Br?nsted acidic and coordinatively unsaturated surface sites. With increasing silica content the number of defect sites decreases and well ordered silica-alumina is formed.     

Insight into selected reactions in low-temperature dimethyl ether combustion from Born-Oppenheimer molecular dynamics

Dimethyl ether is under consideration as an alternative diesel fuel. Its combustion chemistry is as yet ill-characterized. Here we use Born-Oppenheimer molecular dynamics (BOMD) based on DFT-B3LYP forces to investigate the short-time dynamics of selected features of the low-temperature dimethyl ether (DME) oxidation potential energy surface. Along the chain propagation pathway, we run BOMD simulations from the transition state involving the decomposition of (*)CH(2)OCH(2)OOH to two CH(2)=O and an (*)OH radical. We predict that formaldehyde C-O stretch overtones are excited, consistent with laser photolysis experiments. We also predict that O-H overtones are excited for the (*)OH formed from (*)CH(2)OCH(2)OOH dissociation. We also investigate short-time dynamics involved in chain branching. First, we examine the isomerization transition state of (*)OOCH(2)OCH(2)OOH --> HOOCH(2)OCHOOH. The latter species is predicted to be a short-lived metastable radical that decomposes within 500 fs to hydroperoxymethyl formate (HPMF; HOOCH(2)OC(=O)H) and the first (*)OH of chain branching. The dissociation of HOOCH(2)OCHOOH exhibits non-RRKM behavior in its lifetime profile, which may be due to conformational constraints or slow intramolecular vibrational energy transfer (IVR) from the nascent H-O bond to the opposite end of the radical, where O-O scission occurs to form HPMF and (*)OH. In a few trajectories, we see HOOCH(2)OCHOOH recross back to (*)OOCH(2)OCH(2)OOH because the isomerization is endothermic, with only an 8 kcal/mol barrier to recrossing. Therefore, some inhibition of chain-branching may be due to recrossing. Second, trajectories run from the transition state leading to the direct decomposition of HPMF (an important source of the second (*)OH radical in chain branching) to HCO, (*)OH, and HC(=O)OH show that these products can recombine to form many other possible products. These products include CH(2)OO + HC(=O)OH, H(2)O + CO + HC(=O)OH, HC(=O)OH + HC(=O)OH, and HC(=O)C(=O)H + H(2)O, which (save CH(2)OO + HC(=O)OH) are all more thermodynamically stable than the original HCO + (*)OH + HC(=O)OH products. Moreover, the multitude of extra products suggest that standard statistical rate theories cannot completely describe the reaction kinetics of significantly oxygenated compounds such as HPMF. These secondary products consume the second (*)OH required for explosive combustion, suggesting an inhibition of DME fuel combustion is likely.     

Insight into vulcanization mechanism of novel binary accelerators for natural rubber

A novel TU derivative, N-phenyl-N′-(у-triethoxysilane)-propyl thiourea(STU), is prepared and its binary accelerator system is investigated in detail. Compared to the control references, the optimum curing time of NR compounds with STU is the shortest, indicating a more nucleophilic reaction occurs. The Py-GC/MS results present that the phenyl isothiocyanate fragment still remains in the NR/STU compounds with or without extracting treatment, but no silane segment can be found in the vulcanizate with extracting treatment. Vibrations of C=S, NH and aromatic ring in FTIR experiments and a new methyne carbon peak, as well as the peaks of phenyl group of STU, in the solid state 13C-NMR experiments are found in the NR/STU vulcanizate with extracting treatment. Moreover, the crosslinking density of vulcanizates with STU evolves to lower level, indicating the sulfur atom of STU does not contribute to the sulfur crosslinking. Therefore, a new vulcanization kinetic mechanism of STU is propounded that the thiourea groups can graft to the rubber main chains as pendant groups by chemical bonds during the vulcanization process, which is in accordance with the experimental observations quite well.     

Insight into the C-F bond mechanism of molecular analogs for antibacterial drug design

The activities of biological molecules usually rely on both of intra-molecular and intermolecular interactions between their function groups. These interactions include interonic attraction theory, Van der Waal’s forces and the function of geometry on the individual molecules, whether they are naturally or synthetic. The purpose of this study was to evaluate the antibacterial activity of C-F bond compound using combination of experiments verification and theoretical calculation. We target on the insect natural products from the maggots of Chrysomyis megacephala Fabricius. Based on density functional theory(DFT) and B3LYP method, a theoretical study of the C-F bond on fluoride was designed to explore compounds 2 and 4 antibacterial structure–activity relationship. With the progress in DFT, first-principle calculation based on DFT has gradually become a routine method for drug design, quantum chemistry and other science fields.     

Insight into the formation mechanism of levoglucosenone in phosphoric acid-catalyzed fast pyrolysis of cellulose

The catalytic fast pyrolysis of cellulose impregnated with phosphoric acid (H_3PO_4) offers a promising method for the selective production of levoglucosenone (LGO),a valuable anhydrosugar product.However,the fundamental mechanism for selective LGO formation is unclear.Herein,quantum chemistry calculations and catalytic fast pyrolysis experiments were performed to reveal the formation mechanism of LGO in H3_PO_4-catalyzed cellulose pyrolysis.H_3PO_4 significantly decreased the energy barriers of the pyrolytic reactions and altered the competitiveness of the LGO formation pathways,promoting LGO formation.Through different pathways in the non-catalytic and H3P04-catalyzed conditions,LGO is mainly produced from the primary decomposition of glucose units of cellulose and secondary conversion of levoglucosan.The major catalytic formation pathways of LGO comprise similar reactions,with dehydration at the 3-OH+2-H site as the rate-determining step.Importantly,secondary conversion of 1,4;3,6-dianhydro-α-D-glucopyranose is not feasible for LGO formation,in contrast to previous reports.In addition,a high degree of polymerization is beneficial for the selectivity of LGO formation in the catalytic process,because the glycosidic bond is important for the formation of the bicyclic structure (1,5-and1,6-acetal rings).     

Insight into the deamination mechanism of 6-cyclopropylamino guanosine analogs for anti-HIV drug design

Deamination is a crucial step in the transformation of 6-cyclopropylamino guanosine prodrug to its active form. A convenient method using capillary electrophoresis (CE) without sample labeling was developed to analyze the deamination of a series of D-/L-6-cyclopropylamino guanosine analogs by mouse liver homogenate, mouse liver microsome, and adenosine deaminase (ADA). A two-step process involving a 6-amino guanosine intermediate formed by oxidative N-dealkylation was demonstrated in the metabolism of 6-cyclopropylamino guanosine to 6-hydroxy guanosine. The results indicated that the transformation rates of different prodrugs to the active form varied greatly, which were closely correlated with the configuration of nucleosides and the structure of glycosyl groups. Most importantly, D-form analogs were metabolized much faster than their L-counterparts, thus clearly pointed out that compared to guanine, modification of glycosyl part might be a better choice for the development of L-guanosine analogs for the treatment of HIV.     

Insight into the catalytic mechanism of vanadium haloperoxidases. DFT investigation of vanadium cofactor reactivity

Density functional theory (DFT) has been used to investigate the catalytic properties of the isolated vanadium cofactor found in vanadium haloperoxidases, with a particular emphasis on the steps going from the resting form of the cofactor to the peroxo complex. Computation of transition states, intermediate species, and UV-vis spectra, as well as comparison of reaction energies, demonstrated the important role of protonation in cofactor activation. This illustrates that the resting form of the vanadium cofactor reacts with hydrogen peroxide according to a mechanism that implies formation of an aqua complex, release of the apical water molecule according to a dissociative pathway, and binding of hydrogen peroxide to vanadium. This process leads to a side-on peroxo species corresponding to the peroxo form observed in the enzyme. In addition, it appears that an acid-base catalysts strongly accelerates the conversion to the side-on peroxo form. The comparison of computed and experimental UV-vis spectra corroborated the proposed reaction pathway and allowed us to explain the effects of the vanadium ligands on the electronic properties of the cofactor.     

Insight into chain dimensions in PEO/water solutions

Small‐Angle Neutron Scattering has been performed from poly(ethylene oxide) in deuterated water at temperature ranging from 10 to 80 °C. A simple fitting model was used to obtain a correlation length and a Porod exponent. The correlation length L characterizes the average distance between entanglements in the semidilute region and is proportional to the individual coil sizes in the dilute region. L was found to increase with temperature in the semidilute region but it decreases with temperature in the dilute region. This decrease is the precursor to the single‐chain collapse which applies to very dilute polymer solutions. © 2007 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 45: 2196–2200, 2007     

Insight into the reaction mechanism of sulfur chains adjustable polymer cathode for high-loading lithium-organosulfur batteries

Small molecules with adjustable sulfur atoms in the confined structure were acted as precursor for the synthesis of polymer cathodes for lithium-organosulfur batteries.Among them,poly(diallyl tetrasulfide)(PDATtS)delivered a high capacity of 700 mAh g^-1,stable capacity retention of 85%after 300 cycles,high areal capacity~4 m Ah cm^-2 for electrode with up to 10.3 mg cm^-2 loading.New insight into the reaction mechanism of PDATtS electrode that radicals arisen from the homolytic cleavage of S-S bond in PDATtS reacted with Li+to generate thiolates(RSLi)and insoluble lithium sulfides(Li₂S)or lithium disulfide(Li₂S₂)was clearly verified by in-situ UV/Vis spectroscopy,nuclear magnetic resonance(NMR)studies and density-functional theory(DFT)calculations.Therefore,based on the unique reaction mechanism,problems of rapid capacity fading due to the formation of soluble polysulfide intermediates and their serious shuttle effect in conventional lithium-sulfur(Li-S)batteries was totally avoided,realizing the dendrite-free lithium sulfur batteries.This study sets new trends for avenues of further research to advance Li-S battery technologies.     

Insight into the construction of open-framework aluminophosphates

Over the past twenty five years, a class of open-framework aluminophosphates, denoted AlPOs, has been prepared with neutral zeolitic frameworks and anionic frameworks showing wonderfully complex structural and compositional diversity. An insight into the construction of open-framework AlPOs revealing their general structural features and topological chemistry is provided in this tutorial review, and the role of templating and the designed construction and synthesis of AlPOs are discussed.     

Semiconductor nanoparticle/polystyrene latex composite materials

Cadmium sulfide and cadmium selenide/cadmium sulfide core/shell nanoparticles stabilized with poly(cysteine acrylamide) have been bound to polystyrene (PS) latexes by three methods. First, anionic 5 nm diameter CdS particles were electrostatically attached to 130 nm surfactant-free cationic PS latexes to form stable dispersions when the amount of CdS particles was less than 10% of the amount required to form a monolayer on the surface of the PS particles or when the amount of CdS particles exceeded the amount required to form a monolayer on the PS particles. Transmission electron microscopy (TEM) showed nanoparticles on the surface of the latex particles. Fluorescence spectra showed unchanged emission from the nanoparticles. Second, anionic, surfactant-free PS latexes were synthesized in the presence of CdS and CdSe/CdS nanoparticles. TEM showed monodisperse latex particles with trapped nanoparticles. Third, surfactant-stabilized latexes were synthesized by copolymerization of styrene with vinylbenzyl(trimethyl)ammonium chloride electrostatically bound to the CdSe/CdS nanoparticle surface. Brownian motion of the submicroscopic composite particles in water was detected by fluorescence microscopy.     

Insight into detailed mechanism of the atmospheric reaction of imidogen with hydroxyl: a computational study

The details of reaction mechanism of imidogen (NH) and hydroxyl radicals are explored at the UMP2(FC)/cc–pVDZ and PMP4(FC,SDTQ)/cc–pVQZ//UMP2 + ZPE levels, theoretically. The initial association between NH and OH radicals leads to the formation of the intermediates, NH…OH, HN…HO, cis HNOH, and trans HNOH, through the barrierless and exothermic processes. By starting from the initial intermediates, all possible paths for the formation of H + HNO, H₂ + NO, H₂O + ⁴N, H₂N + ³O, and H + ³HON products are investigated on potential energy surface. The results reveal that H₂O + ⁴N is the main product involved in the mechanism of hydrogen atom abstraction of NH by OH radical through the intermediate NH…OH.     

Insight into the Rydberg states of CH

Ab initio electronic structure calculations of a relatively large number of Rydberg states of the CH radical were carried out employing the multireference single and double excitation configuration interaction (MRD-CI) method. A Gaussian basis set of cc-pV5Z quality augmented with 12 diffuse functions was used together with an extensive treatment of electron correlation. The main focus of this contribution is to investigate the 3d Rydberg complex assigned by Watson [Astrophys. J. 555, 472 (2001)] to three unidentified interstellar bands. The authors' calculations reproduce quite well the absolute excitation energies of the three components of the 3d complex, i.e., 2Sigma+(3dsigma), 2Pi(3dpi), and 2Delta(3ddelta), but not the energy ordering inferred from a rotational assignment of the 3d<--X 2Pi laboratory spectrum. The computation of the 4d complex is reported for the first time along with a number of other higher lying Rydberg species with an X 1Sigma+ core. The lowest Rydberg states belonging to series converging to the a 3Pi and A 1Pi excited states of CH+ are also calculated.     

Insight into the mechanism of the asymmetric addition of alkyl groups to aldehydes catalyzed by titanium-BINOLate species

The asymmetric addition of alkyl groups to aldehydes catalyzed by BINOLate-titanium complexes has become the testing grounds to evaluate the potential of new BINOL-based ligands. We have investigated the mechanism of this reaction and report our findings here. Model systems for the open form of the catalyst, (BINOLate)[Ti(O-i-Pr)(3)](2), based on mono-oxygen-alkylated BINOL ligands have been examined. Comparison of the reactivity and enantioselectivity of the mono-alkyl BINOL derivatives with those of BINOL indicate that the open form of the catalyst, (BINOLate)[Ti(O-i-Pr)(3)](2), is not active in the asymmetric addition reaction. Several BINOLate-titanium complexes have been synthesized and characterized by X-ray crystallography. These include the dinuclear (BINOLate)Ti(O-i-Pr)(2).Ti(O-i-Pr)(4), which contains a bridging naphtholate and isopropoxy group, trinuclear (BINOLate)Ti(O-i-Pr)(2).[Ti(O-i-Pr)(4)](2), and trimeric [(BINOL)Ti(O-i-Pr)(2)](3). The solid-state and solution structures reported here indicate that (BINOLate)Ti(O-i-Pr)(2) prefers to bind to titanium tetraisopropoxide rather than to itself, explaining why no nonlinear effects are observed in the catalytic reaction. Additionally, experimental evidence suggests that the BINOLate-titanium species responsible for the catalytic and stoichiometric asymmetric addition reactions are different, indicating that the proposed intermediate, (BINOLate)Ti(R)(aldehyde)(O-i-Pr), is not involved in either of these processes. Reactions were examined using different sources of the alkyl group [ZnMe(2) or MeTi(O-i-Pr)(3)]. Under similar conditions, it was found that the product ee's were the same, independent of whether ZnMe(2) or Me-Ti(O-i-Pr)(3) was used as the source of the alkyl groups. This indicates that the role of the dialkylzinc is not to add the alkyl group to the carbonyl but rather to transfer the alkyl group to titanium. On the basis of these results, we hypothesize that the intermediate in the asymmetric addition involves (BINOLate)Ti(O-i-Pr)(2)(aldehyde).MeTi(O-i-Pr)(3).