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Effect of Substituents on the O-O Bond Rupture of Different Organic Peroxides in Toluene Solution  [PDF]
G. N. Eyler,A. I. Ca?izo,C. M. Mateo,E. E. Alvarez,R. K. Nesprías
Molecules , 2000, DOI: 10.3390/50300360
Abstract: The thermal decomposition reaction of cyclic organic peroxides was studied in toluene solution in a wide temperature range. The kinetic data show an important substituent effect on the unimolecular homolysis of the O-O bond of these molecules.
Theoretical kinetic study of thermal unimolecular decomposition of cyclic alkyl radicals  [PDF]
Baptiste Sirjean,Pierre-Alexandre Glaude,M. F. Ruiz-Lopez,René Fournet
Physics , 2009,
Abstract: While many studies have been reported on the reactions of aliphatic hydrocarbons, the chemistry of cyclic hydrocarbons has not been explored extensively. In the present work, a theoretical study of the gas-phase unimolecular decomposition of cyclic alkyl radicals was performed by means of quantum chemical calculations at the CBS-QB3 level of theory. Energy barrier and high-pressure limit rate constants were calculated systematically. Thermochemical data were obtained from isodesmic reactions and the contribution of hindered rotors was taken into account. Classical transition state ...
Unifying thermodynamic and kinetic descriptions of single-molecule processes: RNA unfolding under tension  [PDF]
J. M. Rubi,D. Bedeaux,S. Kjelstrup
Physics , 2007, DOI: 10.1021/jp073413w
Abstract: We use mesoscopic non-equilibrium thermodynamics theory to describe RNA unfolding under tension. The theory introduces reaction coordinates, characterizing a continuum of states for each bond in the molecule. The unfolding considered is so slow that one can assume local equilibrium in the space of the reaction coordinates. In the quasi-stationary limit of high sequential barriers, our theory yields the master equation of a recently proposed sequential-step model. Non-linear switching kinetics is found between open and closed states. Our theory unifies the thermodynamic and kinetic descriptions and offers a systematic procedure to characterize the dynamics of the unfolding process
A theoretical view on unimolecular rectification  [PDF]
R Stadler,V Geskin,J Cornil
Physics , 2008,
Abstract: The concept of single molecule rectifiers proposed in a theoretical work by Aviram and Ratner in 1974 was the starting point of the now vibrant field of molecular electronics. In the meantime, a built-in asymmetry in the conductance of molecular junctions has been reported at the experimental level. In this contribution, we present a theoretical comparison of three different types of unimolecular rectifiers: i) systems where the donor- and acceptor-part of the molecules are taken from charge-transfer salt components; ii) zwitterionic systems; and iii) Tour wires with nitro substituents. We conduct an analysis of the rectification mechanism in these three different types of asymmetric molecules on the basis of parameterized quantum-chemical models as well as with a full non-equilibrium Greens function / density functional theory (NEGF-DFT) treatment of the current/voltage characteristics of the respective metal/molecule/metal junctions. We put a particular emphasis on the prediction of rectification ratios (RR), which are crucial for the assessment of the technological usefulness of single molecule junctions as diodes. We also compare our results with values reported in the literature for other types of molecular rectification, where the essential asymmetry is not induced by the structure of the molecule alone but either by a difference in the electronic coupling of the molecule to the two electrodes or by attaching alkyl chains of different lengths to the central molecular moiety.
Equilibrium and kinetic studies of the stannate(IV)-polyol reaction
Jolocam Mbabazi, John Wasswa, Muhammad Ntale
Bulletin of the Chemical Society of Ethiopia , 2010,
Abstract: The stability constants of 1:1 stannate(IV)-polyol complexes in aqueous media have been determined using a conductimetric technique. The constants are fairly large, and lie in the range 5.3-123.0 for the ten ligands investigated. These values were subsequently used in conjunction with kinetic data to postulate a mechanism involving the species Sn(OH)5- as intermediate in the formation of the chelates. The stannate(IV)-polyol reaction, though taking place at higher pH values, is acid-catalysed and follows first-order kinetics in the oxyanion, but at large ligand-oxyanion mole ratios the reaction exhibits zero-order rate dependence on the polyol. These features taken together are consistent with a unimolecular nucleophilic substitution on the oxyanion. KEY WORDS: Hexahydroxystannate(IV), Polyol, Stability constants, Conductimetric method, Mechanism Bull. Chem. Soc. Ethiop. 2010, 24(3), 447-456.
Equilibrium and kinetic studies of the stannate(IV)-polyol reaction
Jolocam Mbabazi,John Wasswa,Muhammad Ntale
Bulletin of the Chemical Society of Ethiopia , 2010,
Abstract: The stability constants of 1:1 stannate(IV)-polyol complexes in aqueous media have been determined using a conductimetric technique. The constants are fairly large, and lie in the range 5.3-123.0 for the ten ligands investigated. These values were subsequently used in conjunction with kinetic data to postulate a mechanism involving the species Sn(OH)5- as intermediate in the formation of the chelates. The stannate(IV)-polyol reaction, though taking place at higher pH values, is acid-catalysed and follows first-order kinetics in the oxyanion, but at large ligand-oxyanion mole ratios the reaction exhibits zero-order rate dependence on the polyol. These features taken together are consistent with a unimolecular nucleophilic substitution on the oxyanion.
Dissociative attachment of an electron to a molecule: kinetic theory  [PDF]
A. Rossani,A. M. Scarfone
Physics , 2005, DOI: 10.1140/epjb/e2006-00111-4
Abstract: Test particles interact with a medium by means of a bimolecular reversible chemical reaction. Two species are assumed to be much more numerous so that they are distributed according fixed distributions: Maxwellians and Dirac's deltas. Equilibrium and its stability are investigated in the first case. For the second case, a system is constructed, in view of an approximate solution.
On the relationships between kinetic schemes and two-state single molecule trajectories  [PDF]
Ophir Flomenbom,J. Klafter
Quantitative Biology , 2007, DOI: 10.1063/1.1979489
Abstract: Trajectories of a signal that fluctuates between two states which originate from single molecule activities have become ubiquitous. Common examples are trajectories of ionic flux through individual membrane-channels, and of photon counts collected from diffusion, activity, and conformational changes of biopolymers. By analyzing the trajectory, one wishes to deduce the underlying mechanism, which is usually described by a multi-substate kinetic scheme. In previous works, we divided kinetic schemes that generate two-state trajectories into two types: reducible schemes and irreducible schemes. We showed that all the information in trajectories generated from reducible schemes is contained in the waiting time probability density functions (PDFs) of the two states. It follows that reducible schemes with the same waiting time PDFs are not distinguishable. In this work, we further characterize the topologies of kinetic schemes, now of irreducible schemes, and further study two-state trajectories from the two types of scheme. We suggest various methods for extracting information about the underlying kinetic scheme from the trajectory (e. g., calculate the binned successive waiting times PDF and analyze the ordered waiting times trajectory), and point out the advantages and disadvantages of each. We show that the binned successive waiting times PDF is not only more robust than other functions when analyzing finite trajectories, but contains, in most cases, more information about the underlying kinetic scheme than other functions in the limit of infinitely long trajectories. For some cases however, analyzing the ordered waiting times trajectory may supply unique information about the underlying kinetic scheme.
Fabrication of Unimolecular Double-stranded DNA Microarrays on Solid Surfaces for Probing DNA-Protein/Drug Interactions  [PDF]
Jinke Wang,Tongxiang Li,Yunfei Bai,Yi Zhu,Zuhong Lu
Molecules , 2003, DOI: 10.3390/80100153
Abstract: We present a novel method for fabricating unimole cular double-stranded DNA microarrays on solid surfaces, which were used to probe sequence-specific DNA/protein interactions. For manufacturing the unimolecular double-stranded DNA microarrays, two kinds of special single-stranded oligonucleotides, constant oligonucleotide and target oligonucleotide, were chemically synthesized. The constant oligonucleotides with internal aminated dT were used to capture and immobilize the target oligonucleotides onto the solid surface, and also to provide a primer for later enzymatic extension reactions, while target oligonucleotides took the role of harbouring DNA-binding sites of DNA-binding proteins. The variant target oligonucleotides were annealed and ligated with the constant oligonucleotides to form the new unimolecular oligonucleotides for microspotting. The prepared unimolecular oligonucleotides were microspotted on aldehyde-derivatized glass slides to make partial-dsDNA microarrays. Finally, the partial-dsDNA microarrays were converted into a unimolecular complete-dsDNA microarray by a DNA polymerase extension reaction. The efficiency and accuracy of the polymerase synthesis were demonstrated by the fluorescent-labeled dUTP incorporation in the enzymatic extension reaction and the restriction endonuclease digestion of the fabricated unimolecular complete-dsDNA microarray. The accessibility and specificity of the sequence-specific DNA-binding proteins binding to the immobilized unimolecular dsDNA probes were demonstrated by the binding of Cy3 labeled NF-?B (p50·p50) to the unimolecular dsDNA microarray. This unimolecular dsDNA microarray provides a general technique for high-throughput DNA-protein or DNA-drugs interactions.
Mapping the Kinetic Barriers of a Large RNA Molecule's Folding Landscape  [PDF]
J?rg C. Schlatterer, Joshua S. Martin, Alain Laederach, Michael Brenowitz
PLOS ONE , 2014, DOI: 10.1371/journal.pone.0085041
Abstract: The folding of linear polymers into discrete three-dimensional structures is often required for biological function. The formation of long-lived intermediates is a hallmark of the folding of large RNA molecules due to the ruggedness of their energy landscapes. The precise thermodynamic nature of the barriers (whether enthalpic or entropic) that leads to intermediate formation is still poorly characterized in large structured RNA molecules. A classic approach to analyzing kinetic barriers are temperature dependent studies analyzed with Eyring's transition state theory. We applied Eyring's theory to time-resolved hydroxyl radical (?OH) footprinting kinetics progress curves collected at eight temperature from 21.5°C to 51°C to characterize the thermodynamic nature of folding intermediate formation for the Mg2+-mediated folding of the Tetrahymena thermophila group I ribozyme. A common kinetic model configuration describes this RNA folding reaction over the entire temperature range studied consisting of primary (fast) transitions to misfolded intermediates followed by much slower secondary transitions, consistent with previous studies. Eyring analysis reveals that the primary transitions are moderate in magnitude and primarily enthalpic in nature. In contrast, the secondary transitions are daunting in magnitude and entropic in nature. The entropic character of the secondary transitions is consistent with structural rearrangement of the intermediate species to the final folded form. This segregation of kinetic control reveals distinctly different molecular mechanisms during the two stages of RNA folding and documents the importance of entropic barriers to defining rugged RNA folding landscapes.
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