Kinetics of diffusion‐controlled reaction between chemically asymmetric molecules. II. Approximate steady‐state solution

Šolc, Karel; Stockmayer, W. H.

doi:10.1002/kin.550050503

Cited by 133 publications

(84 citation statements)

References 10 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Specific association rate constants at defined sites can be reduced significantly from the 108-109 M-' s-' expected for diffusion-controlled reactions by a variety of factors including restricted solid angle geometry (Solc & Stockmayer, 1973), conformational changes in which the substrate reacts with a minor conformer, association coupled with pre-organization or desolvation of the binding site (Julin & Kirsch, 1989;Cannon et al, 1996), or association with a minor prototropic form of the enzyme or ligand.…”

Section: Why Are Q Values So Small In Protein-protein Interactions?mentioning

confidence: 97%

Kinetic epitope mapping of the chicken lysozyme.HyHEL‐10 fab complex: Delineation of docking trajectories

1998

View full text Add to dashboard Cite

show abstract

Section: Why Are Q Values So Small In Protein-protein Interactions?mentioning

confidence: 97%

Kinetic epitope mapping of the chicken lysozyme.HyHEL‐10 fab complex: Delineation of docking trajectories

1998

View full text Add to dashboard Cite

show abstract

“…It has long been recognized that this assumption does not hold in many cases, and extensive theoretical approaches have been proposed to correct for the anisotropic reactivity of reactants (see, e.g., refs. [22][23][24][25][26]. In most of these models, the reactive sites are assumed to be on the surface of the molecules (22)(23)(24).…”

mentioning

confidence: 99%

“…[22][23][24][25][26]. In most of these models, the reactive sites are assumed to be on the surface of the molecules (22)(23)(24). In the present case O 2 is known to bind, from the encumbered side, to the cobalt center in the pocket formed by the four pickets (16).…”

mentioning

confidence: 99%

Molecular recognition of oxygen by protein mimics: Dynamics on the femtosecond to microsecond time scale

Zou

Baskin²,

Zewail³

2002

Proc. Natl. Acad. Sci. U.S.A.

View full text Add to dashboard Cite

Molecular recognition by biological macromolecules involves many elementary steps, usually convoluted by diffusion processes. Here we report studies of the dynamics, from the femtosecond to the microsecond time scale, of the different elementary processes involved in the bimolecular recognition of a protein mimic, cobalt picket-fence porphyrin, with varying oxygen concentration at controlled temperatures. Electron transfer, bond breakage, and thermal ''on'' (recombination) and ''off'' (dissociation) reactions are the different processes involved. The reaction on-rate is 30 to 60 times smaller than that calculated from standard Smoluchowski theory. Introducing a two-step recognition model, with reversibility being part of both steps, removes the discrepancy and provides consistency for the reported thermodynamics, kinetics, and dynamics. The transient intermediates are configurations defined by the contact between oxygen (diatomic) and the picket-fence porphyrin (macromolecule). This intermediate is critical in the description of the potential energy landscape but, as shown here, both enthalpic and entropic contributions to the free energy are important. In the recognition process, the net entropy decrease is ؊33 cal mol ؊1 K ؊1 ; ⌬H is ؊13.4 kcal mol ؊1 . U nderstanding the process of O 2 binding to hemoglobin and myoglobin is of importance in biological science because these molecules are responsible for the oxygen transportation and storage in mammalian cells. It has been shown by various kinetic studies that the binding process involves movement of oxygen through multiple energy barriers, facilitated by fluctuations in protein structure (1, 2). However, details regarding the origin of each barrier are difficult to determine because of the complex nature of the protein structure. Synthetic model porphyrins are used to mimic the structure and function of the proteins to obtain insights into the correlation between structure and function (3). Picket-fence porphyrin is one of these synthetic models (4). One side of the porphyrin plane is a cage formed by four pivalamido pickets. An attractive property of the picket fence is its high O 2 affinity at room temperature when there is a base attached to its unencumbered side, and the oxygen binding is reversible (4).Recently, our laboratory reported femtosecond dynamics of cobalt picket-fence porphyrin in benzene (5). From the transient absorption responses, the excited oxygenated picket-fence porphyrin was found to undergo energy relaxation within the porphyrin ring and porphyrin-to-metal electron transfer on the femtosecond scale, followed by reverse electron transfer and release of O 2 within 2 ps. No substantial recombination of O 2 to porphyrin occurred on a time scale up to 20 ns after the excitation, indicating the insignificance of geminate recombination. Because of the limitation of the maximum delay time available with the femtosecond system, the recombination process on longer time scales could not be observed.Here we report our detailed study, using transie...

show abstract

“…Since the classical theory is only strictly applicable to spherical molecules of uniform surface reactivity, a number of refinements to the basic theory have been proposed. The theory has been extended to n~olecules with orientation constraints due to limited accessibility of their active sites (5)(6)(7)(8)(9). Even moderate steric requirements (5-7) can produce drastic reductions in the diffusion controlled rate constants.…”

mentioning

confidence: 99%

Simultaneous diffusion and chemical activation control of the kinetics of the binding of carbon monoxide to ferroprotoporphyrin IX in glycerol–water mixtures of high viscosity

Hasinoff¹

1977

Can. J. Chem.

View full text Add to dashboard Cite

BRIAN B . HASINOFF. Can. J. Chem. 55,3955 (1977).The kinetics of the reaction of ferroprotoporphyrin IX with CO have been studied in mixed glycerol-water solvents of high viscosity in order that the simultaneous influence of chemical activation and diffusion control of the reaction might be observed. Analyses of curved Arrhenius plots indicated that in the low temperature high viscosity limits the reaction is largely diffusion controlled. The deviation of the second order diffusion rate constants, from that predicted by simple theory for reaction between uniformly reactive spheres of equal radii, is a factor of 0.3 to 0.9, depending upon the solvent composition. A couple of other models for diffusion controlled reaction, ascribing these deviations to changes of steric requirements, were also examined. BRIAN B . HASINOFF. Can. J. Chem. 55,3955 (1977) On a etudie la cinetique de la reaction de la ferroprotoporphyrine IX avec le CO dans des solvants mixtes de g l y c e r o l~a u de grande viscosite de f a~o n a pouvoir observer simultankment l'influence de l'aclivation chimique et du contrale de la diffusion sur la reaction. L'analyse des courbes d'Arrhenius indique qu'aux limites de basse temperature et de haute viscosite la reaction est grandement contralee par la diffusion. La dkviation des constantes de vitesse de diffusion du deuxieme ordre par rapport a celles qui sont prtdites par la theorie simple de la reaction entre des spheres reactives uniformes qui ont un rayon &gal est d'un facteur de 0.3 a 0.9 dkpendant de la composition du solvant. Une couple d'autres modeles pour une reaction contralee par la diffusion et attribuant ces deviations a des changements dans les facteurs steriques ont aussi kt6 examines.[Traduit par le journal]In a previous study (1) the reaction of ferroprotoporphyriil IX (heme) with carbon monoxide was studied by laser flash photolysis as a function of temperature and pressure in 100% glycerol and 80% vv/ ethylene glycol -water. A comparison of the activation enthalpies and activation volumes with the viscosity activation parameters indicated that in 100% glycerol the kinetics are almost totally controlled by diffusion. From a consideration of AV* (I), obtained in 80% vv/ ethylene glycol -water, a dissociative mechanism was indicated.This study extends the range of viscosities studied by using mixtures of glycerol and water, such that both chemical activation and diffusion control contribute to the kinetics. It is of interest to measure the kinetics in this region as a test of the applicability of the theory of diffusion controlled reactions. Glycerol-water solvent mixtures exhibit a wide range of viscosities (2) with large temperature coefficients so that the Can. J. Chem. Downloaded from www.nrcresearchpress.com by 52.36.4.81 on 05/10/18For personal use only.

show abstract

Kinetics of diffusion‐controlled reaction between chemically asymmetric molecules. II. Approximate steady‐state solution

Cited by 133 publications

References 10 publications

Kinetic epitope mapping of the chicken lysozyme.HyHEL‐10 fab complex: Delineation of docking trajectories

Kinetic epitope mapping of the chicken lysozyme.HyHEL‐10 fab complex: Delineation of docking trajectories

Molecular recognition of oxygen by protein mimics: Dynamics on the femtosecond to microsecond time scale

Simultaneous diffusion and chemical activation control of the kinetics of the binding of carbon monoxide to ferroprotoporphyrin IX in glycerol–water mixtures of high viscosity

Contact Info

Product

Resources

About