Conformational study by CD of chirally tethered naphthalene moieties: toward an understanding of the asymmetric intramolecular coupling reaction?

The carbonate (R,R)-1 and the diester (R,R)-2, precursors of optically active 1,1'-binaphthyl derivatives through asymmetric intramolecular coupling, were prepared and fully characterized. The absorption and CD spectra, together with the cholesteric induction measurement of (R,R)-1, indicate that it assumes a conformation in which the naphthalene rings are M-skewed. Since the intramolecular coupling of (R,R)-1 affords a P-twisted (S) binaphthyl derivative, a change of twist from M to P must occur during the reaction. Moreover, this conformation allows the coupling to occur along only one pathway, thus explaining the high stereoselectivity. The CD analysis of (R,R)-2 indicates that it assumes a rigid conformation as well, with the naphthalene rings fixed relative to each other. However, in this compound the naphthalene moieties can give rise to a coupling reaction following two different pathways, leading to oppositely configured binaphthyls with almost the same probability so that low stereoselectivity results. Copyright 2000 Wiley-Liss, Inc.     

Effect of the cross-linker on the general performance and temperature dependent behaviour of a molecularly imprinted polymer catalyst of a Diels–Alder reaction

Here we present a series of molecularly imprinted polymers capable of catalysing the Diels–Alder reaction between benzyl 1,3-butadienylcarbamate (1) and N,N-dimethyl acrylamide (2). The polymer systems studied here demonstrated an unusual cross-linker and temperature dependent behaviour, namely that polymer catalysis of the Diels–Alder reaction was lower at elevated temperature, in contrast to the solution reaction. Furthermore, not only was the catalytic activity significantly influenced by the choice of cross-linker, but in a similar fashion also the extent of the temperature effect, indicating a close relationship between catalysis and the observed inhibition. Molecular dynamics simulations of both the polymer systems studied were used to provide insight into the molecular background of transition state stabilisation, and differences in properties of the systems based on different cross-linkers.     

Computational study of one-step polar Diels–Alder reactions using the NEB method for the minimum energy paths search

The Nudged Elastic Band (NEB) method is an algorithm to search the minimum energy path (MEP), which has been successfully applied for studying several processes that involve solid-state models; however, it has not been widely tested in discrete molecular systems. Performing density functional theory calculations, this method was employed in NWChem to find the MEP of reactions between cyclopentadiene and cyano-substituted ethylenes. Results suggest that the reaction mechanism is concerted in all systems. Also, kinetics and thermodynamics analysis were done: With respect to experimental data, energetic parameters are computed better at the M06-2X/6-31++G** level; entropy and frequency factors were poorly predicted. This is a simple methodology, where the NEB method is evaluated to find the MEP in some prototypical Diels–Alder reactions.     

Calorimetric studies of the haemoglobin–haptoglobin reaction

Haptoglobin binds haemoglobin so firmly that there is practically no dissociation. It would be expected that the heat of the reaction would be relatively large. The development of the microcalorimeter by Benzinger offered the opportunity to measure the heat of reaction. The experiments were carried out in the Beckman 190B Microcalorimeter in two ways: (1) a constant amount of haptoglobin (Kabi; 65mg.) with different amounts of haemoglobin, and (2) a constant amount of haemoglobin (32.5mg.) with different amounts of haptoglobin. The proteins, each in 5ml. of 0.15m-phosphate buffer, pH7.4, were placed in equal-volume calorimeter cells. The heat produced/mg. of haemoglobin was calculated from the slope of the curve for a constant amount of haptoglobin and from the maximum heat for a constant amount of haemoglobin. This heat is about 70kcal./mole at 37 degrees . DeltaH varies with temperature, being -70.2 at 37 degrees , -29.7 at 20 degrees and 7.2 at 4 degrees . From the amount of haptoglobin required to attain maximum heat with 32.5mg. of haemoglobin and the amount of haemoglobin required to attain maximum heat with 65mg. of haptoglobin, it appears that at excess of haptoglobin there is competition between the reactions of 2moles of haptoglobin with 1mole of haemoglobin (or 2 alphabeta-chains) and 1mole of haptoglobin with 1mole of haemoglobin.     

Highly efficient method for 125I-radiolabeling of biomolecules using inverse-electron-demand Diels–Alder reaction

In this report, we present a rapid and highly efficient method for radioactive iodine labeling of trans-cyclooctene group conjugated biomolecules using inverse-electron-demand Diels–Alder reaction. Radioiodination reaction of the tetrazine structure was carried out using the stannylated precursor 2 to give ¹²⁵I-labeled product ([¹²⁵I]1) with high radiochemical yield (65 ± 8%) and radiochemical purity (>99%). For radiolabeling application of [¹²⁵I]1, trans-cyclooctene derived cRGD peptide and human serum albumin were prepared. These substrates were reacted with [¹²⁵I]1 under mild condition to provide the radiolabeled products [¹²⁵I]6 and [¹²⁵I]8, respectively, with excellent radiochemical yields. The biodistribution study of [¹²⁵I]8 in normal ICR mice showed significantly lower thyroid uptake values than that of ¹²⁵I-labeled human serum albumin prepared by a traditional radiolabeling method. Therefore [¹²⁵I]8 will be a useful radiolabeled tracer in various molecular imaging and biological studies. Those results clearly demonstrate that [¹²⁵I]1 will be used as a valuable prosthetic group for radiolabeling of biomolecules.     

Kinetic study on the β-glucosidase-catalysed reaction of Trichoderma viride cellulase

A kinetic study of the -glucosidase-catalysed reaction of a commercial cellulase preparation from Trichoderma viride is described. The K _m and V _max values of the -glucosidase system were: (a) 0.5 mm and 6.6 mol/min, respectively, using p-nitrophenyl -d-glucopyranoside (pNPG) as substrate; and (b) 2.5 mm and 8.1 mol/min, respectively, using cellobiose as subtrate. The glucose effect on initial reaction velocity agrees with a mixed-inhibition pattern. The inhibition constant (K _i) values were, 0.53 and 0.39 mm with nNPG and cellobiose as substrates, respectively. The temperature and pH optima were determined. Correspondence to: A. Romeu     

Reductive activation of the heme iron–nitrosyl intermediate in the reaction mechanism of cytochrome c nitrite reductase: a theoretical study

Cytochrome c nitrite reductase catalyzes the six-electron, seven-proton reduction of nitrite to ammonia without release of any detectable reaction intermediate. This implies a unique flexibility of the active site combined with a finely tuned proton and electron delivery system. In the present work, we employed density functional theory to study the recharging of the active site with protons and electrons through the series of reaction intermediates based on nitrogen monoxide [Fe(II)-NO(+), Fe(II)-NO·, Fe(II)-NO(-), and Fe(II)-HNO]. The activation barriers for the various proton and electron transfer steps were estimated in the framework of Marcus theory. Using the barriers obtained, we simulated the kinetics of the reduction process. We found that the complex recharging process can be accomplished in two possible ways: either through two consecutive proton-coupled electron transfers (PCETs) or in the form of three consecutive elementary steps involving reduction, PCET, and protonation. Kinetic simulations revealed the recharging through two PCETs to be a means of overcoming the predicted deep energetic minimum that is calculated to occur at the stage of the Fe(II)-NO· intermediate. The radical transfer role for the active-site Tyr(218), as proposed in the literature, cannot be confirmed on the basis of our calculations. The role of the highly conserved calcium located in the direct proximity of the active site in proton delivery has also been studied. It was found to play an important role in the substrate conversion through the facilitation of the proton transfer steps.     

The mechanism of the periodate–thiobarbituric acid reaction of sialic acids

1. The chromogen formation from N-acetylneuraminic acid in the periodate-thiobarbituric acid reaction was investigated. Measurement of periodate consumption showed an uptake of approx. 3moles/mole of substrate in neutral as well as in strongly acidic solution. Therefore the chromogen beta-formylpyruvic acid is not a direct product of the periodate oxidation; it is presumed to be formed from the true oxidation product, a hexos-5-uluronic acid, by aldol splitting during the reaction in hot acidic solution with thiobarbituric acid. 2. Methyl (methyl beta-l-threo-hexos-4-enepyranosid)uronate, an analogue of the pre-chromogen, has been shown to yield with thiobarbituric acid in acidic solution a pigment exhibiting an identical absorption spectrum and showing the same behaviour on paper chromatography as the pigment obtained from N-acetylneuraminic acid in the periodate-thiobarbituric acid assay. 3. The substitution at C-2 of methoxyneuraminic acid does not inhibit the periodate-thiobarbituric acid reaction. In neutral solution methoxyneuraminic acid is oxidized by periodate to a substance that reacts readily with thiobarbituric acid in acidic solution. When periodate oxidation is attempted in acidic solution, protonation of the amino group protects this group against oxidation, rendering methoxyneuraminic acid negative in the assay systems of Warren (1959a,b) and Aminoff (1959, 1961).     

Synthetic analogues of the histidine–chlorophyll complex: a NMR study to mimic structural features of the photosynthetic reaction center and the light-harvesting complex

Mg(II)–porphyrin–ligand and (bacterio)chlorophyl–ligand coordination interactions have been studied by solution and solid-state MAS NMR spectroscopy. ¹H, ¹³C and ¹⁵N coordination shifts due to ring currents, electronic perturbations and structural effects are resolved for imidazole (Im) and 1-methylimidazole (1-MeIm) coordinated axially to Mg(II)-OEP and (B)Chl a. As a consequence of a single axial coordination of Im or 1-MeIm to the Mg(II) ion, 0.9–5.2 ppm ¹H, 0.2–5.5 ppm ¹³C and 2.1–27.2 ppm ¹⁵N coordination shifts were measured for selectively labeled [1,3-¹⁵N]-Im, [1,3-¹⁵N,2-¹³C]-Im and [1,3-¹⁵N,1,2-¹³C]-1-MeIm. The coordination shifts depend on the distance of the nuclei to the porphyrin plane and the perturbation of the electronic structure. The signal intensities in the ¹H NMR spectrum reveal a five-coordinated complex, and the isotropic chemical shift analysis shows a close analogy with the electronic structure of the BChl a–histidine in natural light harvesting 2 complexes. The line broadening of the ligand responses support the complementary IR data and provide evidence for a dynamic coordination bond in the complex.Abbreviations (B)Chl a (bacterio)chlorophyll a - HMBC heteronuclear multiple bond correlation - Im imidazole - LH light-harvesting - 1-MeIm 1-methylimidazole - Mg(II)-Por Mg(II)-porphyrin macrocycle - OEP 2,3,7,8,12,13,17,18-octaethylporphyrin     

Advances in the study of protein–DNA interaction

Protein-DNA interaction plays an important role in many biological processes. The classical methods and the novel technologies advanced have been developed for the interaction of protein-DNA. Recent developments of these methods and research achievements have been reviewed in this paper.     

Isolation of some precursors of 2-methylpyrrole in the Elson–Morgan reaction

1-C-(1-Acetylacetonyl)-2-deoxy-2-(1-methyl-3-oxobut-1-enyl)amino -d-galactitol is obtained from the condensation of 2-amino-2-deoxy-d-galactose with pentane-2,4-dione in anhydrous solvent. On treatment with hot alkali it gives 2-methylpyrrole with 37% yield. By acid hydrolysis under mild conditions the compound loses the N substituent and from the resulting unstable derivative 2-methylpyrrole is obtained (52% yield). It is concluded that derivatives of aminohexoses substituted at C-1 with a dioxopentyl chain are the precursors of 2-methylpyrrole in the Cessi & Serafini-Cessi (1963) modification of the Elson-Morgan reaction. As demonstrated previously, products of condensation of aminohexoses with pentane-2,4-dione at the amino group are not converted directly into 2-methylpyrrole, but this step provides protection of the amino group during condensation at C-1.     

Exploring the concept of interaction computing through the discrete algebraic analysis of the Belousov–Zhabotinsky reaction

Interaction computing (IC) aims to map the properties of integrable low-dimensional non-linear dynamical systems to the discrete domain of finite-state automata in an attempt to reproduce in software the self-organizing and dynamically stable properties of sub-cellular biochemical systems. As the work reported in this paper is still at the early stages of theory development it focuses on the analysis of a particularly simple chemical oscillator, the Belousov–Zhabotinsky (BZ) reaction. After retracing the rationale for IC developed over the past several years from the physical, biological, mathematical, and computer science points of view, the paper presents an elementary discussion of the Krohn–Rhodes decomposition of finite-state automata, including the holonomy decomposition of a simple automaton, and of its interpretation as an abstract positional number system. The method is then applied to the analysis of the algebraic properties of discrete finite-state automata derived from a simplified Petri net model of the BZ reaction. In the simplest possible and symmetrical case the corresponding automaton is, not surprisingly, found to contain exclusively cyclic groups. In a second, asymmetrical case, the decomposition is much more complex and includes five different simple non-abelian groups whose potential relevance arises from their ability to encode functionally complete algebras. The possible computational relevance of these findings is discussed and possible conclusions are drawn.     

Ab initio and DFT study on the electrophilic addition reaction of bromine to tetracyclo[5.3.0.02,6.03,10]deca–4,8–diene

The electronic and geometric structures of tetracyclo[5.3.0.0^2,6.0^3,10]deca-4,8-diene (hypostrophene) have been investigated by ab initio and DFT/B3LYP methods using the 6-31G* and 6-311G* basis sets. The double bonds of hypostrophene are endo-pyramidalized. The cationic intermediates and products formed in the addition reaction have been investigated using the HF/6-311G*, HF/6-311G**, and B3LYP/6-311G* methods. The bridged bromonium cation was more stable than the U-type cation. Considering that the bridged cation does not isomerize to the less stable U-type cation, it is not possible for the U-type product to be obtained in the reaction. The bridged bromonium cation transformed into the more stable N-type cation and the N-type product was obtained via this cation. The thermodynamic stability of the exo, exo and exo, endo isomers of the N-type dibromide molecule were almost identical. The N-type product was 16.6 kcal mol⁻¹ more stable than the U-type product. Figure General energy diagram of the hypostrophene–bromine (HS–Br₂) system (kcal mol⁻¹) (MP2/6-311G*//HF/6-311G*)     

A role for hydrophobicity in a Diels–Alder reaction catalyzed by pyridyl-modified RNA

New classes of RNA enzymes or ribozymes have been obtained by in vitro evolution and selection of RNA molecules. Incorporation of modified nucleotides into the RNA sequence has been proposed to enhance function. DA22 is a modified RNA containing 5-(4-pyridylmethyl) carboxamide uridines, which has been selected for its ability to promote a Diels–Alder cycloaddition reaction. Here, we show that DA_TR96, the most active member of the DA22 RNA sequence family, which was selected with pyridyl-modified nucleotides, accelerates a cycloaddition reaction between anthracene and maleimide derivatives with high turnover. These widely used reactants were not used in the original selection for DA22 and yet here they provide the first demonstration of DA_TR96 as a true multiple-turnover catalyst. In addition, the absence of a structural or essential kinetic role for Cu²⁺, as initially postulated, and nonsequence-specific hydrophobic interactions with the anthracene substrate have led to a reevaluation of the pyridine modification''s role. These findings broaden the catalytic repertoire of the DA22 family of pyridyl-modified RNAs and suggest a key role for the hydrophobic effect in the catalytic mechanism.     

Periodate oxidation of sperm-whale myoglobin and the role of the methionine residues in the antigen–antibody reaction

1. Oxidation of sperm-whale metmyoglobin and its apoprotein with periodate has been investigated under various conditions of pH and temperature to find those under which the reagent acted with specificity. 2. At pH6.8 and 22 degrees consumption of periodate ceased in 3(1/2)hr. at 43 moles of periodate/mole of myoglobin. The two methionine residues, the two tryptophan residues, the three tyrosine residues and two histidine residues were oxidized; serine increased in the hydrolysates from 6 to 9 residues/mol. 3. At pH5.0 and 22 degrees , consumption levelled off in 4(1/2)hr. at 26 moles of periodate/mole of myoglobin and resulted in the modification of the two methionine residues, the two tryptophan residues, the three tyrosine residues and two histidine residues; serine increased from 6 to 7 residues/mol. and, also, ferrihaem suffered considerable oxidation. 4. Oxidation at pH5.0 and 0 degrees resulted at completion (4hr.) in the consumption of 22 moles of periodate/mole of myoglobin and in the modification of the methionine, tyrosine and tryptophan residues. Spectral studies indicated oxidation of the haem group. This derivative reacted very poorly with rabbit antisera to MbX (the major component no. 10 obtained by CM-cellulose chromatography; Atassi, 1964). 5. Oxidation of apomyoglobin at pH5.0 and 0 degrees was complete in 4hr. with the consumption of 7.23 moles of periodate/mole of apoprotein. The rate of oxidation in decreasing order was: methionine; tryptophan; tyrosine; and after 7hr. of reaction the following residues/mol. were oxidized: methionine, 2.0; tryptophan, 1.6; tyrosine, 0.99. No peptide bonds were cleaved. Metmyoglobin prepared from the 7hr.-oxidized apoprotein showed that the reactivity with antisera to MbX had diminished considerably. 6. Milder oxidation of apoprotein (2 molar excess of periodate, pH5.0, 0 degrees , 2hr.) resulted in the modification of 1.66 residues of methionine/mol. Metmyoglobin prepared from this apoprotein was identical with native MbX spectrally, electrophoretically and immunochemically. It was concluded that the methionine residues at positions 55 and 131 were not essential parts of the antigenic sites of metmyoglobin.     

Determination of the number of degrees of freedom of the trapeziometacarpal joint–An in vitro study

ObjectiveMost of the studies about trapeziometacarpal joint assume that it exhibits only two independent degrees of freedom, but the experimental or theoretical support for considering a two-degrees of freedom model is not always clear.Materials and methodsTherefore, an in vitro kinematic study has been designed to demonstrate, from experimental data, that only two of the trapeziometacarpal degrees of freedom (i.e., flexion/extension and adduction/abduction) are non-null and independent. Several movements of maximal amplitude in flexion, abduction and circumduction have been realized and the relative position and orientation of the segment coordinate system embedded on the first metacarpal with respect to that embedded on the trapezium have been collected using electromagnetic sensors. The trapeziometacarpal rotations have been described using a joint coordinate system and the joint displacements have been evaluated on the axes of this coordinate system.ResultsThe root mean square (RMS) values of the joint displacement components have been found small enough to assume that the trapeziometacarpal joint has no translation degrees of freedom. A paraboloid coupling equation has been found between the internal/external rotation angle and the two other, flexion/extension and adduction/abduction, angles.ConclusionThus, this study demonstrates that the trapeziometacarpal joint has only two independent rotational degrees of freedom, and further, the described methodology could also be used to determine the coupling laws between degrees of freedom of various joints.     

Optimization of the Emerson–Trinder enzymatic reaction by response surface methodology

The Emerson–Trinder reaction has been optimized in this work using an initial rate spectrophotometric method and response surface methodology (RSM). In this investigation, the variation range of critical variables along with the fixed parameters were selected based on a preliminary ‘one at a time’ (OVAT) procedure for the subsequent RSM chemometric analysis as follows: pH (6–10), buffer concentration (50–250?mM), 4-aminoantipyrine (4-AAP) concentration (1–5?mM), temperature (25–45°C). The optimum values of fixed parameters were: 4-fluorophenol (4-FP, 30?mM), horseradish peroxidase (HRP) enzyme activity (0.12?U?mL^?1), and the fixed concentration of the H₂O₂ in the chemometric experiments was 11.4 µM. The non-linear nature of the experimental response of the reaction system was explained by a second-order polynomial equation, which revealed the impact of the experimental factors, their interactions and also their optimum values. The results of the reported RSM analysis proved to be quite appropriate for the design and optimization of this reaction, as illustrated by the relatively high value of the determination coefficient (R²=96.7%) for the fitting of quadratic model, along with the satisfactory results generated by the analysis of variance (ANOVA). All the evaluated analytical characteristics of this method: typical reaction progress curves, resulting linear calibration curve, within-day precisions at low and at high levels, and the upper and lower detection limits were, also, reported. In addition, to check the quality of the optimization and validity of the model, the assay of H₂O₂, in pooled serum matrix and in cosmetic samples, was performed.