scholarly journals Kinetic Analysis for Macrocyclizations Involving Anionic Template at the Transition State

2012 ◽  
Vol 2012 ◽  
pp. 1-14 ◽  
Author(s):  
Vicente Martí-Centelles ◽  
M. Isabel Burguete ◽  
Santiago V. Luis
Keyword(s):  
Differential Equation ◽  
Reaction Mechanism ◽  
Kinetic Model ◽  
Transition State ◽  
Kinetic Analysis ◽  
Kinetic Models ◽  
Comprehensive Analysis ◽  
Anionic Template

Several kinetic models for the macrocyclization of aC2pseudopeptide with a dihalide through aSN2reaction have been developed. These models not only focus on the kinetic analysis of the main macrocyclization reaction, but also consider the competitive oligomerization/polymerization processes yielding undesired oligomeric/polymeric byproducts. The effect of anions has also been included in the kinetic models, as they can act as catalytic templates in the transition state reducing and stabilizing the transition state. The corresponding differential equation systems for each kinetic model can be solved numerically. Through a comprehensive analysis of these results, it is possible to obtain a better understanding of the different parameters that are involved in the macrocyclization reaction mechanism and to develop strategies for the optimization of the desired processes.

Reactions of an Aluminium(I) Reagent with 1,2-, 1,3- and 1,5-Dienes: Dearomatisation, Reversibility, and a Pericyclic Mechanism

2019 ◽  
Author(s):  
Clare Bakewell ◽  
Martí Garçon ◽  
Richard Y Kong ◽  
Louisa O'Hare ◽  
Andrew J. P. White ◽  
...  
Keyword(s):  
Reaction Mechanism ◽  
Dft Calculations ◽  
Transition State ◽  
Reaction Pathways ◽  
Aromatic Rings ◽  
Aromatic Character ◽  
Pericyclic Reaction

The reactions of an aluminium(I) reagent with a series of 1,2-, 1,3- and 1,5-dienes are reported. In the case of 1,3-dienes the reaction occurs by a pericyclic reaction mechanism, specifically a cheletropic cycloaddition, to form aluminocyclopentene containing products. This mechanism has been interrogated by stereochemical experiments and DFT calculations. The stereochemical experiments show that the (4+1) cycloaddition follows a suprafacial topology, while calculations support a concerted albeit asynchronous pathway in which the transition state demonstrates aromatic character. Remarkably, the substrate scope of the (4+1) cycloaddition includes dienes that are either in part, or entirely, contained within aromatic rings. In these cases, reactions occur with dearomatisation of the substrate and can be reversible. In the case of 1,2- or 1,5-dienes complementary reactivity is observed; the orthogonal nature of the C=C π-bonds (1,2-diene) and the homoconjugated system (1,5-diene) both disfavour a (4+1) cycloaddition. Rather, reaction pathways are determined by an initial (2+1) cycloaddition to form an aluminocyclopropane intermediate which can in turn undergo insertion of a further C=C π-bond leading to complex organometallic products that incorporate fused hydrocarbon rings.

A New Adsorption Rate Equation in Batch Systems

2018 ◽  
Author(s):  
yongson hong ◽  
Kye-Ryong Sin ◽  
Jong-Su Pak ◽  
Chol-Min Pak
Keyword(s):  
Experimental Data ◽  
Kinetic Analysis ◽  
Adsorption Kinetics ◽  
Rate Equation ◽  
Kinetic Models ◽  
Adsorption Kinetic ◽  
Adsorption Rate ◽  
Batch Systems ◽  
New View

<p><b>In this paper, the deficiencies and cause of previous adsorption kinetic models were revealed, new adsorption rate equation has been proposed and its validities were verified by kinetic analysis of various experimental data.</b> <b>This work is a new view on the adsorption kinetics rather than a comment on the previous adsorption papers.</b></p>

Reaction mechanism studies. 5. The mechanism of the diaxial → diequatorial rearrangement of β-chlorothioethers

1968 ◽  
Vol 46 (1) ◽  
pp. 9-13 ◽  
Author(s):  
J. F. King ◽  
K. Abikar
Keyword(s):  
Reaction Mechanism ◽  
Transition State ◽  
Nitro Group ◽  
Ion Pair ◽  
Concerted Mechanism

p-Methoxy- and p-nitro substituted analogues (1b and 1c) of the diaxial β-chlorothioether 2β-chloro-3α-(phenylthio)-5α-cholestane (1a), have been prepared and found to undergo the diaxial → diequatorial rearrangement. The rates of rearrangement of these compounds show the sequence p-methoxy > H > p-nitro. It is concluded that the transition state for the rearrangement is polarized in the sense of a sulfonium chloride (3). The rearrangement of 1a is 1600 times faster in butanol than in decalin (at 110°). There is thus no inherent insensitivity to solvent change in a rearrangement in which there may be a "four-atom arrangement" in the transition state, a conclusion relevant to previous work on the diaxial → diequatorial rearrangement of 1,2-dibromides (1). It was further found that the nitro group slowed the rearrangement (at 110°) more in butanol than in decalin, an observation regarded as consistent with, but not requiring, the incursion of a merged ion-pair, cyclic concerted mechanism.

Model-based analysis of coupled equilibrium-kinetic processes: indirect kinetic studies of thermodynamic parameters using the dynamic data

The Analyst ◽  
2015 ◽  
Vol 140 (9) ◽  
pp. 3121-3135
Author(s):  
Fereshteh Emami ◽  
Marcel Maeder ◽  
Hamid Abdollahi
Keyword(s):  
Kinetic Model ◽  
Thermodynamic Parameters ◽  
Kinetic Models ◽  
Kinetic Studies ◽  
Dynamic Data ◽  
Model Based ◽  
Kinetic Processes ◽  
Model Based Analysis

Schematic of intertwined equilibrium-kinetic model at time = 0,1,2…T when both equilibrium and kinetic models are solved explicitly.

scholarly journals Stochastic Kinetic Analysis of Developmental Pathway Bifurcation in Phage λ-Infected Escherichia coli Cells

Genetics ◽  
1998 ◽  
Vol 149 (4) ◽  
pp. 1633-1648 ◽  
Author(s):  
Adam Arkin ◽  
John Ross ◽  
Harley H McAdams
Keyword(s):  
Gene Expression ◽  
Kinetic Model ◽  
Kinetic Analysis ◽  
Molecular Level ◽  
Host Responses ◽  
Statistical Thermodynamic ◽  
Regulatory Systems ◽  
Regulatory Circuit ◽  
Phenotype Selection ◽  
Decision Circuit

Abstract Fluctuations in rates of gene expression can produce highly erratic time patterns of protein production in individual cells and wide diversity in instantaneous protein concentrations across cell populations. When two independently produced regulatory proteins acting at low cellular concentrations competitively control a switch point in a pathway, stochastic variations in their concentrations can produce probabilistic pathway selection, so that an initially homogeneous cell population partitions into distinct phenotypic subpopulations. Many pathogenic organisms, for example, use this mechanism to randomly switch surface features to evade host responses. This coupling between molecular-level fluctuations and macroscopic phenotype selection is analyzed using the phage λ lysis-lysogeny decision circuit as a model system. The fraction of infected cells selecting the lysogenic pathway at different phage:cell ratios, predicted using a molecular-level stochastic kinetic model of the genetic regulatory circuit, is consistent with experimental observations. The kinetic model of the decision circuit uses the stochastic formulation of chemical kinetics, stochastic mechanisms of gene expression, and a statistical-thermodynamic model of promoter regulation. Conventional deterministic kinetics cannot be used to predict statistics of regulatory systems that produce probabilistic outcomes. Rather, a stochastic kinetic analysis must be used to predict statistics of regulatory outcomes for such stochastically regulated systems.

scholarly journals Kinetic Analysis of the Effect of Poliovirus Receptor on Viral Uncoating: the Receptor as a Catalyst

2001 ◽  
Vol 75 (11) ◽  
pp. 4984-4989 ◽  
Author(s):  
Simon K. Tsang ◽  
Brian M. McDermott ◽  
Vincent R. Racaniello ◽  
James M. Hogle
Keyword(s):  
Activation Energy ◽  
Transition State ◽  
Kinetic Analysis ◽  
Transition State Theory ◽  
State Theory ◽  
Viral Receptor ◽  
Poliovirus Receptor ◽  
Entropic Stabilization ◽  
Entropic Effects

ABSTRACT We examined the role of soluble poliovirus receptor on the transition of native poliovirus (160S or N particle) to an infectious intermediate (135S or A particle). The viral receptor behaves as a classic transition state theory catalyst, facilitating the N-to-A conversion by lowering the activation energy for the process by 50 kcal/mol. In contrast to earlier studies which demonstrated that capsid-binding drugs inhibit thermally mediated N-to-A conversion through entropic stabilization alone, capsid-binding drugs are shown to inhibit receptor-mediated N-to-A conversion through a combination of enthalpic and entropic effects.

scholarly journals Reaction of a satirically hindered iron(III) porphyrin with peroxyacetic acid: Degradation kinetics

2005 ◽  
Vol 70 (8-9) ◽  
pp. 1105-1111 ◽  
Author(s):  
P. Prakash ◽  
Mary Francisca
Keyword(s):  
Reaction Mechanism ◽  
Spectroscopic Study ◽  
Kinetic Analysis ◽  
Peracetic Acid ◽  
Degradation Kinetics ◽  
Oxidative Degradation ◽  
Peroxyacetic Acid ◽  
Porphyrin Ligand ◽  
Uv Visible ◽  
Reversible Formation

A kinetic analysis of the reaction between peracetic acid (AcOOH), and tetrakis (pentafluorophenyl) - 21H, 23H-porphine iron(III) chloride Fe(F20TPP)Cl, in acetonitrile showed that the peracetic acid oxidatively destroys Fe(F20TPP)Cl. This is in contrast to an assumption that the oxidative degradation of metalloporphyrins can be prevented by the introduction of electron-withdrawing substituents into the phenyl groups of the porphyrin ligand. A UV-visible spectroscopic study showed a degree of macro cycle destruction of the tetrapyrrole conjucation of the metalloporphyrin. The degradation takes place via oxoperferryl species. The first step of the reaction mechanism is the reversible formation of an adduct ?X? (k1/k-1) between Fe(F20TPP)Cl and peracetic acid, followed by an irreversible step (k2) for the formation of oxoperferryl species.

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