Copper-induced oligomerization of peptides: a model study

In this work, copper-binding of the tetraglycine peptide (Gly-Gly-Gly-Gly) was studied by electrospray ionization mass spectrometry. Experiments were performed under alkaline conditions, in the presence of ethanolamine (pH 10.95). We observed that the presence of copper(II) ions induces the aggregation of the peptide and the formation of copper-bound complexes with higher molecular mass is favored, such as the oligomer complexes [3M+2Cu-3H](+) and [4M+3Cu-5H](+). At 1:1 peptide-copper(II) ion ratio, the singly charged [3M+2Cu-3H](+) oligomer complex is the base peak in the mass spectrum. Metal ion-induced oligomer-ization of neurotoxic peptides is well known in the literature; however, there are very few examples in which such oligomerization was directly observed by mass spectrometry. Our results show that application of short peptides can be useful to study the -mechanism of metal ion binding and metal ion-induced oligomerization of peptides.     

Reaction mechanism of deoxyribonucleotidase: a theoretical study

The reaction mechanism of human deoxyribonucleotidase (dN) is studied using high-level quantum-chemical methods. dN catalyzes the dephosphorylation of deoxyribonucleoside monophosphates (dNMPs) to their nucleoside form in human cells. Large quantum models are employed (99 atoms) based on a recent X-ray crystal structure. The calculations support the proposed mechanism in which Asp41 performs a nucleophilic attack on the phosphate to form a phospho-enzyme intermediate. Asp43 acts in the first step as an acid, protonating the leaving nucleoside, and in the second step as a base, deprotonating the lytic water. No pentacoordinated intermediates could be located.     

A thermodynamic surface model for caesium sorption on bentonite

Caesium sorption on Wyoming bentonite MX-80 has been studied in solutions of NaCl, KCl, MgCl(2), CaCl(2), NaNO(3) and Ca (NO(3))(2) of concentrations varying between 0.025 and 1 mol/L, as well as in a weakly saline (I=0.004 ml/L) and a strongly saline (I=0.46 mol/L) natural groundwater. These experiments have been used to derive a thermodynamic model for the interaction of caesium with the bentonite surface in accordance with a surface chemical model, including acid/base reactions developed recently for montmorillonite. The sorption behaviour of caesium on bentonite can be described, within the experimental and model uncertainties, in terms of a one-site ion exchange model. The ion exchange constant obtained for the reaction NaX+Cs(+) left arrow over right arrow CsX+Na(+) (where X represents the ion exchange sites on montmorillonite) is log(10) K(0)(ex)=1.6. Impurities in the bentonite, influencing the concentrations of competing cations, such as Na(+), K(+), Mg(2+) and Ca(2+), have a crucial impact on the sorption of caesium. This impact can be adequately quantified with the present model. The model predictions compare well with sorption data published in the open literature on both Wyoming bentonite MX-80 and other types of bentonite. Distribution coefficients from the literature obtained from both batch and diffusion experiments and varying over four orders of magnitude are reproduced and explained successfully by the model.     

Catalytic mechanism of glyoxalase I: a theoretical study

Hybrid density functional theory is used to study the catalytic mechanism of human glyoxalase I (GlxI). This zinc enzyme catalyzes the conversion of the hemithioacetal of toxic methylglyoxal and glutathione to nontoxic (S)-D-lactoylglutathione. GlxI can process both diastereomeric forms of the substrate, yielding the same form of the product. As a starting point for the calculations, we use a recent crystal structure of the enzyme in complex with a transition-state analogue, where it was found that the inhibitor is bound directly to the zinc by its hydroxycarbamoyl functions. It is shown that the Zn ligand Glu172 can abstract the substrate C1 proton from the S enantiomer of the substrate, without being displaced from the Zn ion. The calculated activation barrier is in excellent agreement with experimental rates. Analogously, the Zn ligand Glu99 can abstract the proton from the R form of the substrate. To account for the stereochemical findings, it is argued that the S and R reactions cannot be fully symmetric. A detailed mechanistic scheme is proposed.     

A thermodynamic surface model for caesium sorption on bentonite

Caesium sorption on Wyoming bentonite MX-80 has been studied in solutions of NaCl, KCl, MgCl₂, CaCl₂, NaNO₃ and Ca (NO₃)₂ of concentrations varying between 0.025 and 1 mol/L, as well as in a weakly saline (I=0.004 ml/L) and a strongly saline (I=0.46 mol/L) natural groundwater. These experiments have been used to derive a thermodynamic model for the interaction of caesium with the bentonite surface in accordance with a surface chemical model, including acid/base reactions developed recently for montmorillonite. The sorption behaviour of caesium on bentonite can be described, within the experimental and model uncertainties, in terms of a one-site ion exchange model. The ion exchange constant obtained for the reaction NaX+Cs⁺CsX+Na⁺ (where X represents the ion exchange sites on montmorillonite) is log₁₀K⁰_ex=1.6. Impurities in the bentonite, influencing the concentrations of competing cations, such as Na⁺, K⁺, Mg²⁺ and Ca²⁺, have a crucial impact on the sorption of caesium. This impact can be adequately quantified with the present model. The model predictions compare well with sorption data published in the open literature on both Wyoming bentonite MX-80 and other types of bentonite. Distribution coefficients from the literature obtained from both batch and diffusion experiments and varying over four orders of magnitude are reproduced and explained successfully by the model.     

Synthesis of 3-methoxyazetidines via an aziridine to azetidine rearrangement and theoretical rationalization of the reaction mechanism

The synthetic utility of N-alkylidene-(2,3-dibromo-2-methylpropyl)amines and N-(2,3-dibromo-2-methylpropylidene)benzylamines was demonstrated by the unexpected synthesis of 3-methoxy-3-methylazetidines upon treatment with sodium borohydride in methanol under reflux through a rare aziridine to azetidine rearrangement. These findings stand in contrast to the known reactivity of the closely related N-alkylidene-(2,3-dibromopropyl)amines, which are easily converted into 2-(bromomethyl)aziridines under the same reaction conditions. A thorough insight into the reaction mechanism was provided by both experimental study and theoretical rationalization.     

A model developed for acid dissolution thermodynamics of a Turkish bentonite

A model was proposed to calculate some thermodynamic parameters for the acid dissolution process of a bentonite containing a calcium-rich smectite as clay mineral along with quartz, opal and feldspar as impurities. The bentonite sample was treated with H₂SO₄ by applying dry method in the temperature range 50–150°C for 24 h. The acid content in the dry bentonite-sulphuric acid mixture was 45 mass%. The total content (x) of Al₂O₃, Fe₂O₃ and MgO remained in the undissolved sample after treatment was taken as an equilibrium parameter. An apparent equilibrium constant, K _a, was calculated for each temperature by assuming K _a=(x _m−x)/x where x _m is the total oxide content of the natural bentonite. Also, an apparent change in Gibbs free energy, ΔG _a^o, was calculated for each temperature by using the K _a value. The graphs of lnK _a vs. 1/T and ΔG _a^o vs. T were drawn and then the real change in both the enthalpy, ΔH ^o and the entropy, ΔS ^o, values were calculated from the slopes of the straight lines, respectively. Inversely, real ΔG ^o and K values were calculated from the real ΔH ^o and ΔS ^o values through ΔG ^o = −RT ln K = ΔH ^o − TΔS ^o equation. The best ΔH ^o and ΔS ^o fittings to this relation were found to be 65687 J mol⁻¹ and 164 J mol⁻¹K⁻¹, respectively.     

Insights into the mechanism of BN generation via boron triazide precursor: theoretical study

Potential-energy surfaces for unimolecular decomposition of B(N3)(3) have been studied to understand the possible mechanism for BN generation. The decomposition of B(N3)(3) takes place on either the singlet and triplet surface, and both processes are high exothermic and obey sequential mechanisms. For the singlet reaction, the rate-determining step corresponds to cleavage of the first azide bond and linear (1)NBNN instead of (1)BN was suggested as the dominant product at room temperature. For the triplet surface, a fragment process from (3)BN(7) to (3)BN(5) is predicted to be the rate-determining step; once this barrier is counteracted, the subsequent decomposition processes could easily occur to form final product (3)BN. In addition, the possible mechanism for generating BN film via B(N3)(3) was discussed based on MC-SCF calculation results. These findings might be helpful in understanding the controllable decomposition of B(N3)(3) as well as its application in generating BN films.     

Verification of a theoretical model for multicomponent condensation

In 1974, Taitel and Tamir presented a fully predictive model for the filmwise condensation of multicomponent mixtures. In the present work the predictions of the theoretical model were successfully verified. This was achieved by condensing several binary mixtures (acetone-methanol, acetone-ethanol, methanol-ethanol) and a ternary mixture (acetone-methanol-ethanol) onto a cooled vertical wall.     

Hydrolysis of a neonicotinoid: a theoretical study on the reaction mechanism of dinotefuran

Structural Chemistry - The possible hydrolysis mechanisms of dinotefuran with OH?, H2O, and H3O+ in the gas phase were systematically simulated by applying the M06-2X/6-311++G(d,p) and...     

Dissociative photoionization mechanism of 1,8-dihydroxyanthraquinone: an experimental and theoretical study

The photoionization and dissociative photoionization mechanism of 1,8-dihydroxyanthraquinone (1,8-DHAQ) have been investigated by infrared laser desorption/tunable synchrotron vacuum ultraviolet photoionization mass spectrometry (IR LD/VUV PIMS) technique and theoretical calculations. Consecutive losses of two carbon monoxides and elimination of hydroxyl group are found to be the major fragmentation channels in low photon energy range. Photoionization efficiency (PIE) spectrum of 1,8-DHAQ was measured in the photon energy range of 8.2-15.0 eV. Adiabatic ionization energy (IE) of 1,8-DAHQ (M) and appearance energies (AEs) of the major fragments (M-CO) (+), (M-C 2O 2) (+), and (M-OH) (+) are determined to be 8.54 +/- 0.05, 10.8 +/- 0.1, 11.0 +/- 0.1, and 13.1 +/- 0.1 eV, respectively, which are in fair agreement with calculated results. The B3LYP method with the 6-31+G(d) basis set was used to study fragmentation of 1,8-DHAQ. Theoretical calculations indicate that five lowest-energy isomers of 1,8-DHAQ cations can coexist by virtue of bond rotation and intramolecular proton transfer. A number of decarbonylation and dehydroxylation processes of 1,8-DHAQ cations are well established.     

Deoligomerization: a new route to lactams from unsaturated amides via radical oligomerization

[reaction: see text] Triethylborane-initiated atom transfer radical oligomerization of N-allyl or N-(3-butenyl)iodoacetamides followed by treatment with hydrochloric acid and subsequent neutralization with K(2)CO(3) led to the formation of the corresponding 5-hydroxyl-substituted delta-lactams or caprolactams, respectively. This oligomerization-deoligomerization sequence serves as an alternative to the corresponding intramolecular cyclization reactions.     

Reaction mechanism of methanol decomposition on Pt‐based model catalysts: A theoretical study

The decomposition mechanisms of methanol on five different Pt surfaces, the flat surface of Pt(111), Pt‐defect, Pt‐step, Pt(110)(1 × 1), and Pt(110)(2 × 1), have been studied with the DFT‐GGA method using the repeated slab model. The adsorption energies under the most stable configuration of the possible species and the activation energy barriers of the possible elementary reactions involved are obtained in this work. Through systematic calculations for the reaction mechanism of methanol decomposition on these surfaces, we found that such a reaction shows the same reaction mechanism on these Pt‐based model catalysts, that is, the final products are all H (H_ads) and CO (CO_ads) via O? H bond breaking in methanol and C? H bond scission in methoxy. These results are in general agreement with the previous experimental observations. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2010.     

Catalytic mechanism of 6-phosphogluconate dehydrogenase: a theoretical investigation

Density functional calculations are employed to theoretically explore the mechanism of all elementary reaction steps involved in the catalytic reaction of 6-phosphogluconate dehydrogenase (6PGDH). The model systems we choose for the enzyme contain the essential parts of the cofactor (NADP+), the substrate 6-phosphogluconate (6PG), and some key residues (Lys183 and Glu190) in the active site of sheep liver 6PGDH. The effect of the apoenzyme electrostatic environment on the studied reaction is treated by the self-consistent reaction-field method. Our calculations demonstrate that the first step of the catalytic reaction is the formation of a 3-keto 6PG intermediate, which proceeds through a concerted transition state involving a hydride transfer from 6PG to NADP+, and a proton transfer from 6PG to Lys183. The second step is the elimination of a CO2 molecule from 6-PG, concomitant with a proton transfer from Lys183 to 6-PG. In the final step, a concerted double proton transfer (one from Glu190 to the substrate, another from the substrate to Lys183) results in the final product, the keto form of ribulose 5-phosphate (Ru5P). The rate-limiting step is the formation of a 3-keto 6PG intermediate, with a free energy barrier of 22.7 kcal/mol at room temperature in the protein environment, and all three steps are calculated to be thermodynamically favorable. These results are in good agreement with the general acid/general base mechanism suggested from previous experiments for the 6PGDH reaction.     

Short-branch formation via the roedel mechanism in copolymers of ethylene and vinyl acetate

A realistic rotational isomeric state model has been used to estimate the relative probabilities of the formation of various types of short branches in ethylene–vinyl acetate copolymers that are rich in ethylene. Butyl is predicted to be the most common short branch in all of the copolymers examined, although it is less common in the copolymers than in low-density polyethylene. The major factor responsible for the suppression of the R₀₄ backbiting intrachain radical transfer is the increased preference for trans states at the mainchain bonds flanking the attachment site for an isolated acetoxy side chain.     

Biosynthesis via carbocations: theoretical studies on terpene formation

This review describes applications of quantum chemical calculations in the field of terpene biosynthesis, with a focus on insights into the mechanisms of terpene-forming carbocation rearrangements arising from theoretical studies.     

Fragmentation of ionized doped helium nanodroplets: theoretical evidence for a dopant ejection mechanism

We report a theoretical study of the effect induced by a helium nanodroplet environment on the fragmentation dynamics of a dopant. The dopant is an ionized neon cluster Ne(n) (+) (n=4-6) surrounded by a helium nanodroplet composed of 100 atoms. A newly designed mixed quantum/classical approach is used to take into account both the large helium cluster zero-point energy due to the light mass of the helium atoms and all the nonadiabatic couplings between the Ne(n) (+) potential-energy surfaces. The results reveal that the intermediate ionic dopant can be ejected from the droplet, possibly with some helium atoms still attached, thereby reducing the cooling power of the droplet. Energy relaxation by helium atom evaporation and dissociation, the other mechanism which has been used in most interpretations of doped helium cluster dynamics, also exhibits new features. The kinetic energy distribution of the neutral monomer fragments can be fitted to the sum of two Boltzmann distributions, one with a low kinetic energy and the other with a higher kinetic energy. This indicates that cooling by helium atom evaporation is more efficient than was believed so far, as suggested by recent experiments. The results also reveal the predominance of Ne(2) (+) and He(q)Ne(2) (+) fragments and the absence of bare Ne(+) fragments, in agreement with available experimental data (obtained for larger helium nanodroplets). Moreover, the abundance in fragments with a trimeric neon core is found to increase with the increase in dopant size. Most of the fragmentation is achieved within 10 ps and the only subsequent dynamical process is the relaxation of hot intermediate He(q)Ne(2) (+) species to Ne(2) (+) by helium atom evaporation. The dependence of the ionic fragment distribution on the parent ion electronic state reached by ionization is also investigated. It reveals that He(q)Ne(+) fragments are produced only from the highest electronic state, whereas He(q)Ne(2) (+) fragments originate from all the electronic states. Surprisingly, the highest electronic states also lead to fragments that still contain the original ionic dopant species. A mechanism is conjectured to explain this fragmentation inhibition.     

Palladium adsorption on MgO surface a theoretical model

The bonding energy of Pd atom with the MgO crystal surface has been calculated using semiempirical atomic potentials. The greatest energy for a perfect surface was found for the Pd atom placed over the Mg²⁺ ion (0.35 eV). The bonding energies for surfaces with Mg²⁺ or O^2- vacancies are 2.7 eV and 4.6 eV, respectively.

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Pd MgO. , Pd Mg⁺² (0,35 ). Pd O^–2 Mg⁺² , , 4,6, 2,7 .

     

On the adsorption mechanism of copper ions on bentonite clay

Russian Chemical Bulletin - The adsorption of copper ions on bentonite clay was studied as a function of the pH of the medium, contact time, and temperature. A comparative study of the...