Stretching the α-helix: a direct measure of the hydrogen-bond energy of a single-peptide molecule

Atomic force microscopy was used to measure the force required to stretch individual molecules of the peptide cysteine₃–lysine₃₀–cysteine from the α-helical state into a linear chain (approximately 200 pN). The measured force versus peptide elongation was used to calculate the work done in breaking the hydrogen bonds which give rise to the helical structure. The average experimental value of the hydrogen-bond energy (20.2 kJ/mol) is in good agreement with reported theoretical calculations. In addition, the stiffness of individual peptides was measured directly using a force modulation technique and found to vary from approximately 0.005–0.012 N/m during elongation.     

Is the dynamical polarization a significant part of the contribution of the triples to the correlation energy?

One may call dynamical polarization of doubly excited configurations the energy lowering of these configurations under the response of the other electrons to the so-created fluctuation of the electric field. This contribution of triply excited configurations may be identified and calculated through a computation that only requires a computation time proportional to the sixth power of the number of molecular orbitals (MOs), instead of the seventh power for the total contribution of the triples. Its amplitude depends on the choice of the MOs and becomes important when localized MOs are used.     

The cuticle of the cactusCereus peruvianus as a source of a homo-α-d-galacturonan

The waxy pecto-cellulosic cuticle of cladodes of the columnar cactusCereus peruvianus (19% of the whole phytobiomass; dry wt) is a source of an α-d-polygalacturonic or pectic acid (35–40% yield, on a dry wt based on the wax-free pectocellulose layer). Warm EDTA/oxalate or room temperature strong acid/alkali cycles are efficient for pectic acid extraction, since divalent cation (mainly Ca²⁺) is a barrier to be removed within the native and compact architecture of the cuticle. Despite some molecular dispersion arising from the application of strong mineral acid in the first extraction step, the pectic material appears to be quite homogeneous and, on acid or enzymatic analyses, was shown to contain onlyd-galacturonic acid as its monomer.Cereus cuticle pectate (sodium salt) tends to gel above a concentration of 1%, a useful property that can be more easily obtained by the inclusion of sucrose, light addition of calcium salt, and/or mild acidification.     

Effect of the State of a Surface Layer on the Properties of Pd–P Catalysts in the Hydrogenation of Alkylanthraquinones

Kinetics and Catalysis - X-ray photoelectron spectroscopy (XPS) was used to study the state of the surface layer of a Pd–P catalyst, which exhibits high selectivity in the hydrogenation of...     

Adsorption-Induced Segregation as a Method for the Target-Oriented Modification of the Surface of a Bimetallic Pd–Ag Catalyst

The effect of palladium segregation was studied which resulted from the effect of CO and O₂ on the surface structure and catalytic characteristics of the Pd–Ag₂/Al₂O₃ catalyst. The IR-spectroscopic study of adsorbed CO showed that Pd₁ centers isolated from each other by silver atoms predominated on the surface of reduced Pd–Ag₂/Al₂O₃, as evidenced by the almost complete absence of absorption bands typical for the multicentred CO adsorption. In the course of catalyst treatment with CO and O₂, the intensity of absorption bands characteristic of the multicenter CO adsorption considerably increased due to the transformation of a portion of monatomic Pd₁ centers into multiatomic Pd_n ones as a result of the surface segregation of Pd. In this case, a substantial increase in the catalyst activity in the liquid-phase hydrogenation of diphenylacetylene was observed. It was established that, after treatment with CO, the catalyst selectivity for the formation of a target olefin (stilbene) remained almost constant, whereas the treatment with O₂ led to a decrease in the selectivity because of more considerable surface modification.     

Is there a scaffolding domain within the structure of the immunosuppressive agent cyclosporin a (CsA)? Studies of the cyclophilin binding domain of CsA

The synthesis of a peptide that approximates the critical binding/immunosuppressive domain within CsA but which is lacking any form of molecular scaffolding is described. The analysis of the conformation and cyclophilin binding properties of this synthetic analogue provides further evidence for the existence of a scaffolding domain within the natural product.     

Correlation between the properties of a compound and the polynomial coefficients of a molecular Graph’s adjacency matrix

An additive scheme with 11 constants is derived from the coefficients of characteristic polynomials (CCPs) of adjacency matrix A of irregular molecular graphs (IMG) for molecules that contain a bivalent heteroatom -SH or -OH at the beginning of the chain. The structural significance of the CCPs to adjacency matrix A′ is established. Our formula is used to calculate the enthalpies of formation Δ_f H _{liq 298K} ^○ of liquid alkanethiols (mercaptanes) C _n H_{2n + 1}SH and Δ_f H _{liq 298K} ^○ of liquid saturated monoalcohols C _n H_{2n + 1}OH that remain unstudied experimentally.     

State of the Art for the Biosorption Process—a Review

In recent years, biosorption process has become an economic and eco-friendly alternative treatment technology in the water and wastewater industry. In this light, a number of biosorbents were developed and are successfully employed for treating various pollutants including metals, dyes, phenols, fluoride, and pharmaceuticals in solutions (aqueous/oil). However, still there are few technical barriers in the biosorption process that impede its commercialization and thus to overcome these problems there has been a steadily growing interest in this research field. This resulted in large numbers of publications and patents each year. This review reports the state of the art in biosorption research. In this review, we provide a compendium of know-how in laboratory methodology, mathematical modeling of equilibrium and kinetics, identification of the biosorption mechanism. Various mathematical models of biosorption were discussed: the process in packed-bed column arrangement, as well as by suspended biomass. Particular attention was paid to patents in biosorption and pilot-scale systems. In addition, we provided future aspects in biosorption research.     

Exploration on the Biotechnological Aspect of the Ureolytic Bacteria for the Production of the Cementitious Materials—a Review

Biomineralization is a process that leads to the formation of minerals using the biologically or biotechnologically mediated route. Calcium carbonate is one such biomineral that is secreted by the ureolytic bacteria which contributes for the strengthening and improvement of cementitious and sandy materials. It is a new and innovative area in the geotechnological engineering and structural engineering due to its wide range of implications in strengthening of soil, sand, stone, and cementitious materials. The shape and size of the calcium carbonate particle vary with the strain of the bacterium used, and it is species specific. This paper aims in the critical review of the mechanism of calcium carbonate precipitation by the bacterium, various bacteria involved, and the useful outputs of the technique of biomineralization. Based on the critical review, it also recommends the future development and research in the field to develop a technology that can strengthen the existing and the proposed structures.     

Development of a scalable palladium-catalyzed α-arylation process for the synthesis of a CGRP antagonist

The Pd-catalyzed α-arylation of cycloheptapyridyl ketone is a key complexity-building step in the synthesis of BMS-846372, a CGRP antagonist. A first-generation process utilized Pd(OAc)₂/P^tBu₃·HBF₄ catalyst system with a strong base NaO^tBu. Although this process was demonstrated on multi-kilo scale, the harsh conditions led to non-selective metal catalyzed processes, which generated several operational, quality, and throughput issues. By acquiring detailed knowledge around several important process parameters, we were able to design an efficient and scalable second-generation α-arylation process using a Pd(OAc)₂/RuPhos catalyst system with the weaker base, K₃PO₄ in tert-amyl alcohol. This new weak base process was high yielding, efficient, and superior in several respects compared to the strong base process. The strategy behind the reaction and isolation development and the process considerations important to scaling a catalytic reaction from laboratory to manufacturing scale will be discussed.     

Measurement of the Bulk Modulus of a Liquid Using a Pump–Probe Laser Technique

We describe an undergraduate laboratory experiment that uses a time-resolved laser technique. Using pump-probe in a novel way, students determined the bulk modulus of a liquid. Employing the fourth harmonic from a pulsed Nd:YAG laser, an elastic wave is generated in an aqueous solution of N-acetyltryptophan, and the wave propagation is probed by a He-Ne laser. This experiment serves as a rare example of how a bulk property of a condensed phase can be measured using time-resolved optical measurements having relevance to undergraduate physical chemistry or material science laboratory.     

Theoretical studies on the mechanism of the thermal decarboxylation and decarbonylation of a number of α-keto-acids

Both processes of decarboxylation and decarbonylation of a number of acids including RCOCO2H,R=H,CH3,CH2F,CF3,CH=CH2,Ph,OH have been studied by semi-empirical MO theory AMI method to verify the reaction mechanism of each process and the effect of different substituents on them.The calculated results are consistent with the experimental reports and can be summed up as follows:(1) The decarboxylation of these acids to form aldehydes and carbon dioxide is concerted and takes place through a 4-membered ring transition state in which a partial negative charge develops on the carbon of the α-carbonyl group,so that the inductive effect of some substituents is favourable for this process.(2) Their decarbonylation into carboxylic acids and carbon monoxide however is the attack of the OH on the carbon of the alkyl portion of the acid,forming a 3-membered ring transition state.(3) The activation energy of decarbonylation is lower than that of decarboxylation,since oxygen is more nucleophilic than hydrogen and als     

A chemoenzymatic approach to the synthesis of the stereoisomers of a β-adrenergic receptor antagonist

The four stereoisomers of Δ²-isoxazoline 2, a β-adrenergic receptor antagonist structurally related to Falintolol 1, were prepared by an enzyme-catalyzed kinetic resolution of the unsaturated secondary alcohol (±)-7 followed by its cycloaddition to pyruvonitrile oxide. Through this strategy, diastereomeric aminoalcohols (+)-2a/(−)-2b and (−)-2a/(+)-2b were obtained in 99 and 92% enantiomeric excess, respectively. The absolute configuration to the target compounds was assigned via chemical correlation to the enantiomers of epoxides 4a and 4b, whose stereochemistry had been previously established.     

Crowding alters the folding kinetics of a β-hairpin by modulating the stability of intermediates

Crowded environments inside cells exert significant effects on protein structure, stability, and function, but their effects on (pre)folding dynamics and kinetics, especially at molecular levels, remain ill-understood. Here, we examine the latter for, as an initial candidate, a small de novo β-hairpin using extensive all-atom molecular dynamics simulations for crowder volume fractions φ up to 40%. We find that crowding does not introduce new folding intermediates or misfolded structures, although, as expected, it promotes compact structures and reduces the accessible conformational space. Furthermore, while hydrophobic-collapse-mediated folding is slightly enhanced, the turn-directed zipper mechanism (dominant in crowder-free situations) increases many-fold, becoming even more dominant. Interestingly, φ influences the stability of the folding intermediates (FI(1) and FI(2)) in an apparently counterintuitive manner, which can be understood only by considering specific intrachain interactions and intermediate (and hierarchical) structural transitions. For φ values <20%, native-turn formation is enhanced, and FI(1), characterized by a hairpin structure but slightly mismatched hydrophobic contacts, increases in frequency, thus enhancing eventual folding. However, higher φ values impede native-turn formation, and FI(2), which lacks native turns, re-emerges and increasingly acts as a kinetic trap. The change in the stability of these intermediates with φ strongly correlates with the hierarchical folding stages and their kinetics. The results show that crowding assists intermediate structural changes more by impeding backward transitions than by promoting forward transitions and that a delicate competition between reduction in configuration space and introduction of kinetic traps along the folding route is key to understanding folding kinetics under crowded conditions.     

Copper trimer: a revised assignment of the upper state of the 5397 Å system

In light of recent fluorescence spectra obtained for the 5397 Å system of Cu₃, this system is reassigned as à ²A₁-X̃ ²E'. This assignment explains the observed bands without the need to invoke vibronic or Coriolis perturbations. It also accounts for the anomalous pattern of linewidths observed for the higher vibronic levels of the à ²A₁ state as unresolved splittings of the multiply excited doubly degenerate bending mode. The implications for the analysis of the ground state potential energy surfaces are discussed.     

Effects of ZrO_2 on the Microstructure of a Mica Glass-ceramic

1 INTRODUCTION Glass-ceramic technology is based on the controlled nucleation and crystallization of glass, and glass-ceramics have several advantages over the conventional powder-processed ceramics. In addition to the easy flexibility of formation in t…     

The Effect of a Covalent and a Noncovalent Small-Molecule Inhibitor on the Structure of Abg β-Glucosidase in the Gas-Phase

The effects of binding two small-molecule inhibitors to Agrobacterium sp. strain ATCC 21400 (Abg) β-glucosidase on the conformations and stability of gas-phase ions of Abg have been investigated. Biotin-iminosugar conjugate (BIC) binds noncovalently to Abg while 2,4-dinitro-2-deoxy-2-fluoro-β-d-glucopyranoside (2FG-DNP) binds covalently with loss of DNP. In solution, Abg is a dimer. Mass spectra show predominantly dimer ions, provided care is taken to avoid dissociation of dimers in solution and dimer ions in the ion sampling interface. When excess inhibitor, either covalent or noncovalent, is added to solutions of Abg, mass spectra show peaks almost entirely from 2:2 inhibitor-enzyme dimer complexes. Tandem mass spectrometry experiments show similar dissociation channels for the apo-enzyme and 2FG-enzyme dimers. The +21 dimer produces +10 and +11 monomers. The internal energy required to dissociate the +21 2FG-enzyme to its monomers (767?±?30 eV) is about 36 eV higher than that for the apo-enzyme dimer (731?±?6 eV), reflecting the stabilization of the free enzyme dimer by the 2FG inhibitor. The primary dissociation channels for the noncovalent BIC-enzyme dimer are loss of neutral and charged BIC. The internal energy required to induce loss of BIC is 482?±?8 eV, considerably less than that required to dissociate the dimers. For a given charge state, ions of the covalent and noncovalent complexes have about 15 % and 25 % lower cross sections, respectively, compared with the apo-enzyme. Thus, binding the inhibitors causes the gas-phase protein to adopt more compact conformations. Noncovalent binding surprisingly produces the greatest change in protein ion conformation, despite the weaker inhibitor binding.

Kinetics of the Oxidative Dehydrogenation of Propane over a VMgO Catalyst

The reaction kinetics of the oxidative dehydrogenation of propane was studied at 475-550℃ over a VMgO catalyst. Vanadium-magnesium-oxides are among the most selective and active catalysts for the dehydrogenation of propane to propylene. Selectivity to propylene up to about 60% was obtained at 10% conversion, but the selectivity decreased with increasing conversion. No oxygenates were detected, the only by-products were CO and CO2. The reaction rate of propane was found to be first order in propane and close to zero order in oxygen, which is in agreement with a Mars van Krevelen mechanism with the activation of the hydrocarbon as the rate determining step. The activation energy of the conversion of propane was found to be 122±6 kJ/mol.     

On the preparation of bilirubins of the natural α series substituted with a propionic acid residue and a hydroxypropyl group

Summary The reduction of mesobiliverdin XIII propan-1,3-diyl diester with NaBH₄ affords mesobilirubin XIII propan-1,3-diyl diester. The same reduction of mesobiliverdin XIII methylen diester. The same reduction of mesobiliverdin XIII methylen diester affords 8-(2-carboxyethyl)-3,17-diethyl-12-(3-hydroxypropyl)-2,7,13,17-tetramethylbiladien-ac-1,19-(21H, 24H)-dione (MBR-mc). The UV/Vis and¹H NMR spectra ofMBR-mc show that its structure in solution is similar to that of the natural bilirubins of the series.

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Zur Herstellung von Bilirubinen der natürlichen -Reihe mit Propionsäure- und Hydroxypropylsubstituenten

Zusammenfassung Reduktion von Mesobiliverdin-XIII-propan-1,3-diyl-diester mit NaBH₄ liefert Mesobilirubin-XIII-propan-1,4-diyl-diester. Die analoge Reaktion des Mesobiliverdin-XIII-methylen-diesters führt zu 8-(2-Carboxyäthyl)-3,17-diäthyl-12-(3-hydroxypropyl)-2,7,13,17-tetramethylbiladien-ac-1,19-(21H,24H)-dion (MBR-mc).MBR-mc weist in Lösung (UV/Vis und 1H-NMR Spektren) eine ähnliche Struktur auf wie die der natürlichen Bilirubine der -Serie.