Stochastic kinetic study of protein aggregation and molecular crowding effects of Aβ40 and Aβ42

Two isoforms of β-amyloid peptides, Aβ40 and Aβ42, differ from each other only in the last two amino acids, IA, at the end of Aβ42. They, however, differ significantly in their ability in inducing Alzheimer's disease (AD). The rate curves of fibril growth of Aβ40 and Aβ42 and the effects of molecular crowding have been measured in in vitro experiments. These experimental curves, on the other hand, have been fitted in terms of rate constants for elementary reaction steps using rate equation approaches. Several sets of such rate parameters have been reported in the literature. Employing a recently developed stochastic kinetic method, implemented in a browser-based simulator, popsim, we study to reveal the differences in the kinetic behaviors implied by these sets of rate parameters. In particular, the stochastic method is used to distinguish the kinetic behaviors between Aβ40 and Aβ42 isoforms. As a result, we make general comments on the usefulness of these sets of rate parameters.     

Oxidation of aniline and some para-substituted anilines by benzimidazolium fluorochromate in aqueous acetic acid medium – A kinetic and mechanistic study

The oxidation kinetics of some para-substituted anilines by benzimidazolium fluorochromate (BIFC) have been studied in aqueous acetic acid media in the presence of perchloric acid. The reaction is first order with respect to both aniline and BIFC and is catalysed by a hydrogen ion. The rate data obey Hammett relationship. The products of oxidation are the corresponding azo benzenes. Based on the kinetic results and product analysis, a suitable mechanism has been proposed for the reaction of BIFC with anilines.     

The solvent effect in obtaining of acid–base multicomponent systems: thermal,structural and luminescence study

Journal of Thermal Analysis and Calorimetry - Acid–base multicomponent systems based on active pharmaceutical ingredients 2-chloro-5-nitrobenzoic acid (2Cl5NBH) and monoethanolamine were...     

A structural study of the naringin-β-cyclodextrin complex

The structure of the inclusion complex formed between naringin (naringenin-7-O--neohesperidoside) and-cyclodextrin (BCD) was studied in detail by UV and NMR spectroscopic techniques and potentiometry. A binding constant value of 1016±150M^–1 was arrived at from UV studies. Potentiometric studies showed that pK values of 4-OH and 5-OH were affected by and-cyclodextrins. One-dimensional difference NOE and spin-lattice relaxation time (T ₁) measurements indicated that the aglycone protion was affected more than the neohesperidoside portion. TheT ₁ values analysed for local motions indicated that _c values of complexed naringin was higher than that of free naringin. The internal rotation calculated for different groups showed _i values for the phenolic and dihydrobenzopyran portion decrease by a factor of 2. Also a value of 0.12–0.17 observed for the aglycone portion indicated that the coupling between guest and host is weak. All the studies have shown that the disposition in which the phenol group at 2 is inside the BCD cavity with 4-keto and 5-OH hydrogen bonded to the secondary hydroxyl groups at the rim of the wider end of the BCD cavity is the most probable one.     

Thermal behavior and kinetic analysis of halloysite–stearic acid complex

Journal of Thermal Analysis and Calorimetry - Kraft lignin has been widely proposed as a renewable raw material for bio-based polyurethane (PU) synthesis. Drawbacks related to direct use of...     

Synthesis and structural study of novel dimethylcyclobutyl β-peptides

The synthesis of some representative compounds of a new class of cyclobutane-containing β-peptides starting from (?)-verbenone as a chiral precursor is presented. In these products, the cyclobutane moiety is not a part of the peptide backbone but a bulky substituent at the β³-position. These compounds have been carefully characterized and studied on the basis of the combined use of several experimental techniques together with molecular modeling by means of theoretical calculations. In the solid state, the non-cyclic β-peptides adopt a hairpin-like molecular folding ruled by intermolecular hydrogen bonds in the crystal packing.     

Arylhydrazones of α-keto esters via methanolysis of dichlorodiazabutadienes: synthesis and structural study

Novel approach to methyl 2-aryl-2-(arylhydrazono) acetates via methanolysis of dichlorodiazabutadienes was developed. Hydrogen bonding in methyl Z-2-phenyl-2-(phenyl-hydrazono) acetate was explored by DFT calculations and topological analysis of the electron density distribution within the framework of Bader’s theory (QTAIM method).     

Mechanistic and kinetic study of CF3CH═CH2 + OH reaction

The potential energy surfaces of the CF(3)CH═CH(2) + OH reaction have been investigated at the BMC-CCSD level based on the geometric parameters optimized at the MP2/6-311++G(d,p) level. Various possible H (or F)-abstraction and addition/elimination pathways are considered. Temperature- and pressure-dependent rate constants have been determined using Rice-Ramsperger-Kassel-Marcus theory with tunneling correction. It is shown that IM1 (CF(3)CHCH(2)OH) and IM2 (CF(3)CHOHCH(2)) formed by collisional stabilization are major products at 100 Torr pressure of Ar and in the temperature range of T < 700 K (at P = 700 Torr with N(2) as bath gas, T ≤ 900 K), whereas CH(2)═CHOH and CF(3) produced by the addition/elimination pathway are the dominant end products at 700-2000 K. The production of CF(3)CHCH and CF(3)CCH(2) produced by hydrogen abstractions become important at T ≥ 2000 K. The calculated results are in good agreement with available experimental data. The present theoretical study is helpful for the understanding the characteristics of the reaction of CF(3)CH═CH(2) + OH.     

A radiation-chemical and quantum-chemical study of ascorbic acid interaction with α-hydroxyethyl radicals

The effect of ascorbic acid and its analogue 5,6-O-isopropylidenyl-2,3-O-dimethylascorbic acid (I), which has been synthesized for the purpose and does not contain mobile hydrogen atoms, on the formation of the products of continuous radiolysis of deaerated ethanol and its aqueous solutions has been studied. The ionization potentials, the molecular orbital energies, the enthalpies of homolytic dissociation of C-H and O-H bonds, and the enthalpies of H atom addition to the C=O group of the test compounds have been calculated by ab initio methods. The array of the experimental and calculated theoretical data suggests that both ascorbic acid in the undissociated form and compound I can oxidize α-hydroxyethyl radicals, whereas the monoanion of ascorbic acid acts as a reducing agent in the reactions with these transient radicals. The reduction of α-hydroxyethyl radicals in aqueous solutions by the ascorbic acid monoanion can follow both the hydrogen transfer and electron transfer mechanisms.     

Shift of reaction pathway by added chloride ions in the oxidation of aromatic ketones by dichloroisocyanuric acid—A kinetic study

Role of added chloride ions on the shift of reaction pathway of oxidation of aromatic ketones (acetophenone, desoxybenzoin) by dichloroisocyanuric acid (DCICA) was studied in aqueous acetic acid—perchloric acid medium. Participation of enolic and protonated forms of ketones in the rate determining steps is manifested from zero and first orders with respect to the oxidant in absence and presence of added chloride ions, respectively. Positive and negative effects of acid and dielectric constant on the reaction rate were observed. The observations deduce plausible mechanisms involving (i) rate-determining formation of enol from the conjugate acid of the ketone (SH⁺) in the absence of added chloride ions and (ii) rapid formation of molecular chlorine species from HOCl (hydrolytic species of DCICA) in the presence of added chloride ions, which then interacts with SH⁺ in a rate-determining step prior to the rapid steps of product formation. The order of Arrhenius parameters substantiate the proposed plausible mechanisms based on order of reactants both in presence and absence of added chloride ions.     

First-principles study of structural,elastic, electronic and optical properties of rutile GeO2 and α-quartz GeO2

Structural parameters, elastic, electronic, bonding and optical properties of rutile GeO₂ and α-quartz GeO₂ have been investigated using the plane-wave ultrasoft pseudopotential technique based on the first-principles density functional theory (DFT). The ground-state properties obtained by minimizing the total energy are in favorable agreement with the previous work. Two phases of GeO₂ are found to be elastically stable and we have derived the bulk, shear and Young’s modulus, Poisson coefficient for rutile GeO₂ and α-quartz GeO₂. We estimated the Debye temperature of rutile GeO₂ and α-quartz GeO₂ from the acoustic velocity. Electronic and chemical bonding properties have been studied from the calculation of band structure, density of states and charge densities. Furthermore, in order to clarify the mechanism of optical transitions for rutile GeO₂ and α-quartz GeO₂, the complex dielectric function, refractive index, extinction coefficient, optical reflectivity, absorption coefficient, energy-loss spectrum and the complex conductivity function are calculated, which show the significant optical anisotropy in the components of polarization directions (100) and (001) for rutile GeO₂ and α-quartz GeO₂.     

Polymerization of spiro-orthoesters—2. A kinetic approach

The polymerization behaviour of a typical spiro-orthoester, 2-Phenoxymethyl-1,4,6-trioxaspiro(4,4)-nonane, was investigated. The polymerization rate decreases abnormally with conversion; the effect is explained by a mechanism involving deactivation of the active centres by the polymer.     

The kinetic and thermodynamic study of KNiPO4·H2O from DSC and TG data

The DSC and TG data showed the dehydration process occurring over the range of 160?C300?°C. The XRD patterns of the synthesized KNiPO₄·H₂O and the calcined product at 350?°C with exposing in the air over 8?h are indexed as the KNiPO₄·H₂O structure, whereas at 600?°C is indexed as KNiPO₄ structure. Hence, these data confirmed that the water molecule was eliminated from the structure at 300?°C, after that the spontaneously reversible hydration?Crehydration process was observed. The activation energy and pre-exponential factor were calculated by Kissinger, Ozawa, and KAS equations. According to the DSC curves, the enthalpy change (??H) of dehydration process can be calculated and was found to be 100.12?kJ?mol^?1. Besides, we suggested another new method to determine the isokinetic temperature value using spectroscopic data. The surface area of synthesized hydrate and its calcined product at 350?°C with exposing in the air at over 8?h were found to be 21.48 and 134.3?m²?g^?1, respectively. The reversible hydration?Crehydration process was observed, and the surface area of final product at 350?°C (aging time over 8?h) is higher than that of the synthesized compound. This behavior is important to develop alternative desiccant materials or other process based on the rehydration mechanism with increasing the surface area.     

Synthesis of trifluoromethyl-group-containing cyclopentadienones by the palladium-catalyzed [2 + 2 + 1] cycloaddition of aryl- and trifluoromethyl-group substituted internal alkynes and carbon monoxide

We investigated the palladium-catalyzed [2?+?2?+?1] cycloaddition of aryl- and trifluoromethyl-group-substituted internal alkynes and carbon monoxide, and revealed that the PdBr₂ effectively catalyzed the intended reaction. The PdBr₂-catalyzed reaction smoothly proceeded and provided aryl- and trifluoromethyl-group-containing cyclopentadienone derivatives in up to 92% yield.     

Oxidation of aliphatic alcohols by triethylammonium chlorochromate in non-aqueous medium – A kinetic and mechanistic study

The oxidation of some aliphatic alcohols by triethylammonium chlorochromate (TriEACC) in dimethyl sulfoxide leads to the formation of the corresponding carbonyl compounds. The reaction is first order with respect to TriEACC. The reaction exhibited Michaelis–Menten type kinetics with respect to alcohol. The reaction is catalyzed by hydrogen ions. The hydrogen-ion dependence has the form: k_obs = a + b[H⁺]. The oxidation of [1,1-²H₂] ethanol (MeCD₂OH) exhibits a substantial primary kinetic isotope effect. Oxidation of aliphatic alcohol was studied in 19 different organic solvents. The solvent effect has been analysed using Kamlet’s and Swain’s multi-parametric equation. A suitable mechanism has been proposed.     

Halide ligand-more than just sigma-donors? A structural and spectroscopic study of homologous organonickel complexes

The isoleptic organonickel complexes [(bpy)Ni(Mes)X] (bpy ) 2,2'-bipyridine; Mes ) 2,4,6-trimethylphenyl; X ) F,Cl, Br, or I, and for comparison X ) OMe and SCN) have been investigated by multiple spectroscopic means.Their structures have been determined in part by single-crystal X-ray diffraction, the full series by extended X-ray absorption fine structure. The long-wavelength charge transfer absorptions (mainly metal-to-ligand charge transfer)obtain contributions from the mesityl coligand but are almost invariable upon variation of X. UV-vis spectroscopy allowed investigation of the solvolysis reaction [(bpy)Ni(Mes)X] + Solv a [(bpy)Ni(Mes)(Solv)]+ + X-, which occurs very fast for X ) I (k ) 0.176(4) M(-1) s(-1)) or Br but very slow for X ) Cl (k ) 5.18(5) x 10(-5) M(-1) cm(-1))or F. Quantum chemical (density functional theory) calculations on the geometry, electronic states, and electronic transitions (time-dependent density functional theory) are very helpful for detailed insight into the role the X coligands play in these complexes. The combination of methods reveals rather strong, highly covalent Ni-X bonds for all halide coligands but marginal pi-donation.     

Hydrolytic and redox transformations of chromium(III) bis-oxalato complexes with glutaminic acid and glutamine: a kinetic,UV–Vis and EPR,study

The title complexes have been synthesized, chromatographically isolated and characterized by their ligands to metal ratio determinations and spectroscopic analyses. The kinetics of the first aquation stage, i.e., the amino acid chelate ring opening via the Cr–N bond cleavage, has been studied spectrophotometrically in acidic and alkaline media. Hydrogen peroxide oxidizes the complexes in alkaline media to CrO ₄ ^2? anion and a relatively stable Cr(V) complex. Consecutive biphasic kinetics through two first-order steps were observed for the base hydrolysis and the oxidation process, whereas the acid-catalyzed aquation obeys a simple first-order pattern. Based on the kinetic and spectroscopic data, mechanisms of the coordinated amino acid liberation and chromium(III) oxidation are discussed.     

Absorptiometric and spectrofluorimetric study of the inclusion complexes of 2-naphthyloxyacetic acid and 1-naphthylacetic acid with β-cyclodextrin in aqueous solution

The inclusion complexes of 2-naphthyloxyacetic acid (NOA) and 1-naphthylacetic acid (NAA) with -cyclodextrin have been investigated in aqueous solution. It has been demonstrated that the naphthalene derivatives form 1:1 complexes when included in the cyclodextrin. A possible structure is proposed, having an axial inclusion of the naphthalene derivatives. In the case of the -CD: NOA complex, the naphthyl moiety is included in the cyclodextrin and the acetic acid group protrudes from the cavity, while NAA is only partially included because of the steric effect of the group in position 1. Association constants of 560±100 M^–1 and 100±50 M^–1 have been calculated for the -CD: NOA and -CD: NAA complexes, making use of the increment in the fluorescene emission produced in the inclusion process.     

Low-temperature structural behaviour of LaCoO3 – A high-resolution neutron study

We present the temperature evolution of the crystallographic structure of LaCoO₃ in the range 4–300 K. We observe no anomalies in the rhombohedral unit cell parameters at temperatures where electronic transitions are expected to occur. We also find no evidence of the monoclinic distortion of the unit cell proposed others. We parameterise the octahedral tilt and distortion as a function of temperature which show a linear evolution towards a more symmetric form.