Quantifying the kinetic paths of flexible biomolecular recognition

Biomolecular recognition often involves large conformational changes, sometimes even local unfolding. The identification of kinetic pathways has become a central issue in understanding the nature of binding. A new approach is proposed here to study the dynamics of this binding-folding process through the establishment of a path-integral framework on the underlying energy landscape. The dominant kinetic paths of binding and folding can be determined and quantified. The significant coupling between the binding and folding of biomolecules often exists in many important cellular processes. In this case, the corresponding kinetic paths of binding are shown to be intimately correlated with those of folding and the dynamics becomes quite cooperative. This implies that binding and folding happen concurrently. When the coupling between binding and folding is weak (strong), the kinetic process usually starts with significant folding (binding) first, with the binding (folding) later proceeding to the end. The kinetic rate can be obtained through the contributions from the dominant paths. The rate is shown to have a bell-shaped dependence on temperature in the concentration-saturated regime consistent with experiment. The changes of the kinetics that occur upon changing the parameters of the underlying binding-folding energy landscape are studied.

Bronsted guanidine acid-base ionic liquids: Novel reaction media for the palladium-catalyzed Heck reaction

Bronsted acid-base ionic liquids (GILs) based on guanidine and acetic acid are efficient reaction media for palladium-catalyzed Heck reactions. They offer the advantages of high activity and reusability. GIL2 plays multiple roles in the reaction: it could act as solvent, as a strong base to facilitate beta-hydride elimination, and as a ligand to stabilize activated Pd species.

CE coupling with end-column electrochemiluminescence detection for chiral separation of disopyramide

CE with electrochemiluminescence, (ECL) detection technique was successfully applied for the chiral separation of a kind of class IA antiarrhythmic racemic drug. To the best of our knowledge, this is the first report of ECL detection used in chiral CE. To get better detection sensitivity and good enantioresolution at the same time, the conditions of capillary inlet and outlet buffer were systematically optimized. Unlike the traditional chiral separation method, the buffers we used in the capillary inlet and outlet differed from each other in terms of buffer pH, ionic strength, type of BGE as well as buffer composition. Under the optimum conditions, baseline enantioseparation and highly sensitive detection of the enantiomers were achieved. Wide linear relationship of each enantiomer was achieved in the range of 5 x 10(-7) to 2 x 10(-5) mol/L with relative coefficients of 0.996 and 0.997, respectively. The detection limits were estimated to be 8 x 10(-8) and 1.0 X 10(-7) mol/L (S/N = 3) for the enantiomers, respectively. In addition, a successful application of this new method to the chiral separation of the racemic drug in spiked plasma samples confirmed the validity and applicability of the chiral CE-ECL method.

Synthesis of fluorene-based oligomeric organoboron reagents via Kumada, Heck, and stille cross-coupling reactions

Boronic pinacol ester group is not reactive in Kumada, Heck and Stille coupling reaction conditions. Fluorene-based sophisticated organoboron compounds were synthesized by means of Palladium catalyzed Kumada, Heck and Stille cross-coupling reactions from halofluorenyl boronic esters.

Dewetting and phase behaviors for ultrathin films of polymer blend

Dynamics of dewetting and phase separation in ultrathin films (thickness is ca. one radius of gyration, approximate to 1 R-g) of poly(methyl methacrylate) (PMMA) and poly(styrene-ran-acrylonitrile) (SAN) blends on Si substrate has been studied by in situ atomic force microscopy (AFM). In the miscible region, a "spinodal-like" dewetting driven by a composition fluctuation recently predicted by Wensink and Jerome (Langmuir 2002, 18, 413) occurs. In the two-phase region, the dewetting of the whole film is followed by phase separation in the droplets, coupling with the wetting of the substrate by the PMMA extracted by the strong attractive interaction between them.

Highly active, hexabutylguanidinium salt/zinc bromide binary catalyst for the coupling reaction of carbon dioxide and epoxides

An experimentally simple and inexpensive catalyst system based on hexabutylguanidinium/ZnBr, has been developed for the coupling of carbon dioxide and epoxides to form cyclic carbonates with significant catalytic activity under mild reaction conditions without using additional organic solvents (e.g. the turnover frequencies (TOF, h(-1)) values as high as 6.6 x 10(3) h(-1) for styrene oxide and 1.01 x 10(4) h(-1) for epichlorohydrin). This catalyst system also offers the advantages of recyclability and reusability. Therefore, it is a very effective, environmentally benign, and simple catalytic process. The special steric and electrophilic characteristics of hexabutylguanidinium bromide ionic liquid result in the prominent performance of this novel catalyst system.

Studies of electron-transfer and charge-transfer coupling processes at a liquid/liquid interface by double-barrel micropipet technique

Investigation of a heterogeneous electron-transfer (ET) reaction at the water/1,2-dichloroethane interface employing a double-barrel micropipet technique is reported. The chosen system was the reaction between Fe(CN)(6)(3-) in the aqueous phase (W) and ferrocene in 1,2-dichloroethane (DCE). According to the generation and the collection currents as well as collection efficiency, the ET-ion-transfer (IT) coupling process at such an interface and competing reactions with the organic supporting electrolyte in the organic phase can be studied. In addition, this technique has been found to be an efficient method to distinguish and measure the charge-transfer coupling reaction between two ions (IT-IT) processes occurring simultaneously at a liquid/liquid interface. On this basis, the formal Gibbs energies of transfer of some ions across the W/DCE interface, such as NO3-, NO2-, Cl-, COO-, TBA(+), IPAs+, Cs+, Rb+, K+, Na+, and Li+, for which their direct transfers are usually difficult to obtain because of the IT-IT coupling processes, were quantitatively evaluated.

Syntheses of biphenyl polyimides via nickel-catalyzed coupling polymerization of bis(chlorophthalimide)s

A facile method for the synthesis of biphenyl polyimides, which involves the nickel-catalyzed coupling of aromatic dichlorides containing imide structure in the presence of zinc and triphenylphosphine, has been developed. The polymerizations proceeded smoothly under mild conditions and produced biphenyl polyimides with inherent viscosities of 0.13-0.98 dL/g. The polymerizations of bis(4-chlorophthalimide)s with bulky side substituents gave high molecular weight polymers. Low molecular weight polymers from bis(4-chlorophthalimide)s containing rigid diamine moieties and bis(3-chlorophthalimide)s were obtained because of the formations of polymer precipitate and cyclic oligoimides, respectively. The effects of various factors, such as amount of catalyst, solvent volume, ligand, reaction temperature, and time, on the polymerization were studied. The random copolymerization of two bis(chlorophthalimide)s in varying proportions produced medium molecular weight material. The TgS of prepared polyimides were observed at 245-311 degreesC, and the thermogravimetry of polymers showed 10% weight loss in nitrogen at 470-530 degreesC.

Effect of configuration and conformation on the spin multiplicity in xylylene type biradicals

The singlet-triplet splitting energy gap DeltaE(S.T) = E-S - E-T is calculated for the ortho-, meta-, and para-xylylenes and their heteroatomic analogous by means of AM1-CI approach. It is shown that when the radical centers R-.(R-.=H2C.-,H2N.+- or HN.-) are twisted sufficiently Tar out of conjugation with the benzene ring, DeltaE(S.T) tends to zero or is negative, i.e, ortho-, meta-, and para-phenylenes turn into weak ferromagnetic or antiferromagnetic coupling unit, while they are strong ferromagnetic (meta-isomers) or antiferromagnetic (ortho-, para-isomers) coupling units under planar conformation. It is suggested that serious twisted conformation is not recommended candidate for the design of novel high-spin molecules with stable high-spin ground states by ortho- or para-phenylene coupling unit.

Study of the alkylation of isobutane with n-butene over WO3/ZrO2 strong solid acid. 1. Effect of the preparation method, WO3 loading, and calcination temperature

A series of strong solid acids composed of WO3/ZrO2 were prepared. Their crystal structure, surface state, and acidity were determined by the methods of X-ray diffraction, thermal gravimetric and differential thermal analysis, temperature-programmed reduction, laser Raman, and acidity measurement. The results revealed that ZrO2 in WO3/ZrO2 existed mainly in the tetragonal phase, the addition of WO3 plays an important role in stabilizing the tetragonal phase of ZrO2, and all of the samples possessed large surface areas. WO3 in WO3/ZrO2 is mainly monolayer dispersed, and a small amount crystallized on the ZrO2 surface and partly reacted with ZrO2 to form the bond of Zr-O-W, acting as the strong solid acid center. The catalytic properties of WO3/ZrO2 strong solid;acids for alkylation of isobutane with butene at different conditions were investigated. They had a better reaction performance than other strong solid acids; a parallel relationship could be drawn between the catalytic activity and the acid amounts as well as the acidic strength of the catalysts.

Studies on the alkylation of isobutane with butene over WO3/ZrO2 strong solid acid (I) - Effect of preparation, load of WO3 and calcination temperature

A series of WO3/ZrO2 strong solid acid prepared under different conditions were studied. Their crystal structures, surface properties and acidities were determined by means of XRD, DTA-TG, H-2- TPR, Laser Raman and acidity measurements. The results revealed that ZrO2 in WO3/ZrO2 existed mainly in tetragonal phase, the addition of WO3 plays an important role to stabilize tetragonal phase of ZrO2 and thus the catalyst had a considerable surface area. WO3 in WO3/ZrO2 was dispersed and crystalized in WO3 crystalite on ZrO2 surface and partly reacted with ZrO2 to form the bond of Zr-O-W, which acts as the strong solid acid site. The catalytic properties of WO3/ZrO2 strong solid acid for alkylation of iso-butane with butene under the different conditions were investigated. They had a better reaction performance than other strong solid acids, a parallel relationship could be drawn between the catalytic activity and the amount of acid sites as well as the acidic strength of the catalysts.

Melt crystallization of poly(ether ether ketone ketone) under strong electric field

In this paper, melt crystallization of poly(ether ether ketone ketone) (PEEKK) under strong electric field was investigated. In the crystal structure of PEEKK, the length of c axis was found to he 1.075 nm, increasing by 7% compared to that of PEEKK crystallized without strong electric field. The molecule chains might take a more extended conformation through the opening of the bridge bond angles by increasing from 124 degrees to 144 degrees under strong electric field in the crystal structure.

Studies on the morphology transition of micro-crystal growth in polymer films in high vacuum and strong electrostatic field

The morphology of films of isotactic polypropylene poly (3-dodecylthiophene) and iPP/P3DDT blend formed in electrostatic fields has been investigated by using scanning electron microscope. The experiment results show that the micro-crystal morphology of polymer films was strongly dependent on electrostatic fields. It was found that the effect of the electrostatic field led to the formation of dendrite crystals aligned in the field direction, and some branches of P3DDT ruptured. However, the micro-crystals in these films grew into spherulites without electrostatic field,and have no crystal orientation.

Using triazine as coupling unit for intramolecular ferromagnetic coupling of multiradicals

Novel high spin tri-, tetra-, pentaradicals, composed of triazine coupling units and cationic amino radical spin centers (+ . NH) under various configurations and linkages, are predicted from AM1-CI calculations. It is found that for charged planar multiradicals the stability of high spin ground states depends on both the molecular configuration and the number of end groups. Generally, cyclic 1,3-bridged charged multiradicals (S less than or equal to 5/2) possess more stable high spin ground states than their isomers under the branched 1,3,5,-bridged configuration. Therefore, it is suggested that in the design of planar high spin molecules with stable high spin ground states, less end groups and all the supposed spin centers and/or the coupling units should be under the same structural situation. (C) 1999 Elsevier Science B.V. All rights reserved.