Kinetic Barrier (kinetic + barrier)

Distribution by Scientific Domains

Selected Abstracts

Kinetic barriers and the role of topology in protein and RNA folding

Tobin R. Sosnick
Abstract This review compares the folding behavior of proteins and RNAs. Topics covered include the role of topology in the determination of folding rates, major folding events including collapse, properties of denatured states, pathway heterogeneity, and the influence of the mode of initiation on the folding pathway. [source]

Reactivity Pattern in the Room-Temperature Activation of NH3 by the Main-Group Atomic Ions Ga+, Ge+, As+ and Se+

Gregory K. Koyanagi
Abstract The activation of ammonia by the main-group cations Ga+, Ge+, As+ and Se+ has been explored both experimentally and theoretically. ICP/SIFT tandem mass spectrometer measurements of room-temperature kinetics have revealed a substantial variation in rates and product distributions across the Periodic Table of Elements. The main features of the observed primary chemistry include H-atom elimination, ammonia addition and a cation-assisted proton transfer to yield NH4+ that is second order in ammonia. These observations are shown to be completely consistent with computed potential energy surfaces for the reactions of each of the four atomic cations. Dehydrogenation by the elimination of molecular hydrogen, not observed experimentally, is shown by the calculations to be inhibited by the presence of a kinetic barrier. [source]

High-Performance Air-Stable n-Type Organic Transistors Based on Core-Chlorinated Naphthalene Tetracarboxylic Diimides

Joon Hak Oh
Abstract Core-chlorinated naphthalene tetracarboxylic diimides (NDIs) with fluoroalkyl chains are synthesized and employed for n-channel organic thin-film transistors (OTFTs). Structural analyses of the single crystals and thin films are performed and their charge-transport behavior is investigated in terms of structure,property relationships. NDIs with two chlorine substituents are shown to exhibit a herringbone structure with a very close ,-plane distance (3.3,3.4,), a large ,-stack overlap (slipping angle ca. 62), and high crystal densities (2.046,2.091,g,cm,3). These features result in excellent field-effect mobilities of up to 1.43,cm2,V,1,s,1 with minimal hysteresis and high on,off ratios (ca. 107) in air. This is similar to the highest n-channel mobilities in air reported so far. Despite the repulsive interactions of bulky Cl substituents, tetrachlorinated NDIs adopt a slip-stacked face-to-face packing with an interplanar distance of around 3.4,, resulting in a high mobility (up to 0.44,cm2,V,1,s,1). The air-stability of dichlorinated NDIs is superior to that of tetrachlorinated NDIs, despite of their higher LUMO levels. This is closely related to the denser packing of the fluorocarbon chains of dichlorinated NDIs, which serves as a kinetic barrier to the diffusion of ambient oxidants. Interestingly, these NDIs show an optimal performance either on bare SiO2 or on octadecyltrimethoxysilane (OTS)-treated SiO2, depending on the carbon number of the fluoroalkyl chains. Their synthetic simplicity and processing versatility combined with their high performance make these semiconductors highly promising for practical applications in flexible electronics. [source]

Cyclostreptin and Microtubules: Is a Low-Affinity Binding Site Required?

CHEMBIOCHEM, Issue 1 2010
Andrew J. Prussia Dr.
Abstract Cyclostreptin (CS) is a recently discovered natural product with cytotoxic activity caused by microtubule stabilization. It is the only known microtubule-stabilizing agent (MSA) that covalently binds to tubulin. It also exhibits the fast-binding kinetics seen for other MSAs. Through careful peptide digestion and mass spectrometry analysis, Buey et al. found that two amino acids are labeled by CS: Asn228, near the known taxane-binding site, and Thr220, in the type I microtubule pore. This led Buey et al. to propose Thr220 resides at the site previously predicted to be a way station or low-affinity site. By using molecular dynamics simulations and structural considerations of the microtubule pore and tubulin dimer, we conclude that postulation of a low-affinity site is unnecessary to explain the available experimental data. An alternative explanation views the microtubule pore as a structural entity that presents a substantial kinetic barrier to ligand passage to the known taxane-binding site,an entry point to the microtubule lumen that becomes completely blocked if cyclostreptin is bound at Thr220. Simulations of the free dimer also suggest a common mechanism of microtubule stabilization for taxane site MSAs through their conformational effect on the M-loop. Such an effect explains the low tubulin polymerization caused by cyclostreptin in vitro despite its covalent attachment. [source]

Metal-Mediated Formation of Carbon,Halogen Bonds

Arkadi Vigalok Prof. Dr.
Abstract Organic halides represent basic starting materials for numerous metal-catalyzed organic transformations. Generally, the carbon,halogen is broken in the first step, that is, an oxidative addition reaction, of the catalytic cycle. On the other hand, very little is known about the reverse reaction, carbon,halogen reductive elimination from a transition-metal center. In this Concept article, we describe the examples of C(sp3)halide and C(sp2)halide reductive-elimination reactions which demonstrate that this type of reactivity can be quite common in organometallic chemistry. Although the thermodynamic driving force for the formation of carbon,halogen bonds is relatively small, the kinetic barrier for these reactions can also be low. Thus, Chalide reductive elimination can compete favorably with the more established organic transformations, such as CC reductive elimination. [source]

Solution NMR evidence for a cis Tyr-Ala peptide group in the structure of [Pro93Ala] bovine pancreatic ribonuclease A

Ying Xiong
Abstract Proline peptide group isomerization can result in kinetic barriers in protein folding. In particular, the cis proline peptide conformation at Tyr92-Pro93 of bovine pancreatic ribonuclease A (RNase A) has been proposed to be crucial for chain folding initiation. Mutation of this proline-93 to alanine results in an RNase A molecule, P93A, that exhibits unfolding/refolding kinetics consistent with a cis Tyr92-Ala93 peptide group conformation in the folded structure (Dodge RW, Scheraga HA, 1996, Biochemistry 35:1548,1559). Here, we describe the analysis of backbone proton resonance assignments for P93 A together with nuclear Overhauser effect data that provide spectroscopic evidence for a type VI ,-bend conformation with a cis Tyr92-Ala93 peptide group in the folded structure. This is in contrast to the reported X-ray crystal structure of [Pro93Gly]-RNase A (Schultz LW, Hargraves SR, Klink TA, Raines RT, 1998, Protein Sci 7:1620,1625), in which Tyr92-Gly93 forms a type-II ,-bend with a trans peptide group conformation. While a glycine residue at position 93 accommodates a type-II bend (with a positive value of 93), RNase A molecules with either proline or alanine residues at this position appear to require a cis peptide group with a type-VI ,-bend for proper folding. These results support the view that a cis Pro93 conformation is crucial for proper folding of wild-type RNase A. [source]