Limitations of Using Mass Action Kinetics Method in Modeling Biochemical Systems: Illustration for a Second Order Reaction

It has been found that the decay in dimethylformamide and dimethylformamide-water mixtures of radical anions in five of the investigated 5-nitrofurans is governed by a second-order reaction. Only the decay of the radical anion generated from 5-nitro-2-furfural III may be described by an equation including parallel first- and second-order reactions; this behaviour is evidently caused by the relatively high stability of the corresponding dianion, this being an intermediate in the reaction path. The presence of a larger conjugated system in the substituent in position 2 results in a decrease of the unpaired electron density in the nitro group and, consequently, an increase in the stability of the corresponding radical anions.

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Kinetics of the reaction between hexamethylenediisocyanate and 1-pentanol

Collection of Czechoslovak Chemical Communications ◽

10.1135/cccc19833279 ◽

1983 ◽

Vol 48 (11) ◽

pp. 3279-3286

Author(s):

Slavko Hudeček ◽

Miloslav Bohdanecký ◽

Ivana Hudečková ◽

Pavel Špaček ◽

Pavel Čefelín

Keyword(s):

Liquid Chromatography ◽

Rate Constants ◽

Reversed Phase ◽

Order Reaction ◽

Second Order ◽

Second Order Reaction ◽

Reversed Phase Liquid Chromatography ◽

Consecutive Reactions ◽

Phase Liquid ◽

Kinetics Of

The reaction between hexamethylenediisocyanate and 1-pentanol in toluene was studied by means of reversed-phase liquid chromatography. By employing this method, it was possible to determine all components of the reaction mixture including both products, i.e. N-(6-isocyanate hexyl)pentylcarbamate and N,N'-bis(pentyloxycarbonyl)hexamethylenediamine. Relations for the calculation of kinetic constants were derived assuming a competitive consecutive second-order reaction. It was demonstrated that the reaction involved in this case is indeed a second-order reaction, and the rate constants of the first and second consecutive reactions were determined.

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Training an asymmetric signal perceptron through reinforcement in an artificial chemistry

Journal of The Royal Society Interface ◽

10.1098/rsif.2013.1100 ◽

2014 ◽

Vol 11 (93) ◽

pp. 20131100 ◽

Cited By ~ 14

Author(s):

Peter Banda ◽

Christof Teuscher ◽

Darko Stefanovic

Keyword(s):

State Of The Art ◽

Chemical Species ◽

Mass Action ◽

Mass Action Kinetics ◽

Dna Strand Displacement ◽

Autonomous Adaptation ◽

Biochemical Systems ◽

Dna Strand ◽

Logic Functions ◽

Application Specific

State-of-the-art biochemical systems for medical applications and chemical computing are application-specific and cannot be reprogrammed or trained once fabricated. The implementation of adaptive biochemical systems that would offer flexibility through programmability and autonomous adaptation faces major challenges because of the large number of required chemical species as well as the timing-sensitive feedback loops required for learning. In this paper, we begin addressing these challenges with a novel chemical perceptron that can solve all 14 linearly separable logic functions. The system performs asymmetric chemical arithmetic, learns through reinforcement and supports both Michaelis–Menten as well as mass-action kinetics. To enable cascading of the chemical perceptrons, we introduce thresholds that amplify the outputs. The simplicity of our model makes an actual wet implementation, in particular by DNA-strand displacement, possible.

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Internal-state nonequilibrium effects for a fast, second-order reaction

The Journal of Physical Chemistry ◽

10.1021/j100247a003 ◽

1985 ◽

Vol 89 (1) ◽

pp. 5-7 ◽

Cited By ~ 5

Author(s):

Carmay Lim ◽

Donald G. Truhlar

Keyword(s):

Internal State ◽

Order Reaction ◽

Second Order ◽

Second Order Reaction ◽

Nonequilibrium Effects

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Analytical resolution of a parallel second-order reaction mechanism

International Journal of Chemical Kinetics ◽

10.1002/kin.10126 ◽

2003 ◽

Vol 35 (6) ◽

pp. 246-251

Author(s):

A. E. Croce ◽

L. V. Mogni ◽

C. Vicente Irrazábal

Keyword(s):

Reaction Mechanism ◽

Order Reaction ◽

Second Order ◽

Second Order Reaction ◽

Analytical Resolution

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Ribonucleic acid–deoxyribonucleic acid hybridization as a second-order reaction

Biochemical Journal ◽

10.1042/bj1350573 ◽

1973 ◽

Vol 135 (3) ◽

pp. 573-576 ◽

Cited By ~ 14

Author(s):

Bryan D. Young ◽

John Paul

Keyword(s):

Dna Hybridization ◽

Ribonucleic Acid ◽

Deoxyribonucleic Acid ◽

Order Reaction ◽

Second Order ◽

Second Order Reaction ◽

Reaction Theory

Certain features of RNA–DNA hybridization can be accounted for in terms of second-order-reaction theory. These include the use of annealing kinetics to estimate RNA complexity and the occurrence of approximately linear double-reciprocal plots.

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