Encounter Pair Research Articles

The kinetics of protein-protein recognition

We examine a simple kinetic model for association that incorporates the basic features of protein-protein recognition within the rigid body approximation, that is, when no large conformation change occurs. Association starts with random collision at the rate k(coll) predicted by the Einstein-Smoluchowski equation. This creates an encounter pair that can evolve into a stable complex if and only if the two molecules are correctly oriented and positioned, which has a probability p(r). In the absence of long-range interactions, the bimolecular rate of association is p(r) k(coll). Long-range electrostatic interactions affect both k(coll) and p(r). The collision rate is multiplied by q(t), a factor larger than 1 when the molecules carry net charges of opposite sign as coulombic attraction makes collisions more frequent, and less than 1 in the opposite case. The probability p(r) is multiplied by a factor q(r) that represents the steering effect of electric dipoles, which preorient the molecules before they collide. The model is applied to experimental data obtained by Schreiber and Fersht (Nat. Struct. Biol. 3:427-431, 1996) on the kinetics of barnase-barstar association. When long-range electrostatic interactions are fully screened or mutated away, q(t)q(r) approximately 1, and the observed rate of productive collision is p(r) k(coll) approximately 10(5) M(-1) x s(-1). Under these conditions, p(r) approximately 1.5 x 10(-5) is determined by geometric constraints corresponding to a loss of rotational freedom. Its value is compatible with computer docking simulations and implies a rotational entropy loss deltaS(rot) approximately 22 e.u. in the transition state. At low ionic strength, long-range electrostatic interactions accelerate barnase-barstar association by a factor q(t)q(r) of up to 10(5) as favorable charge-charge and charge-dipole interactions work together to make it much faster than free diffusion would allow.

Salt and Specific Cation Effects in the Quenching of Triplet State Tetrakis(μ-pyrophosphite-P,P‘)diplatinate(II) by Acidopentacyanocobaltate(III) Anions

In the presence of moderate to high concentrations of electrolytes, the emission of *(Pt 2(pop)4) 4- (where pop ) I-pyrophosphite-P,P') is quenched by the complexes (Co(CN)5X) 3- (where X ) N3 - ,I - ,B r - ,C l - , but not CN - ). The salt effects on the emission decay lifetime quenching rate constants between these anionic species have been studied in the presence of MCl, MCl2 ,o r R nNH4-nCl (where M, M', and R represent alkali, alkaline earth metals, and alkyl respectively, n ) 0-3) and Kn X( X )Cl - ,B r - ,N O 3 - ,S O 4 2 - , (Co(CN)6) 3- , n ) 1-3). At 0.5 M cation concentration, second-order quenching rate constants, kq, are in the nearly diffusion- controlled range, 10 7 -10 9 L mol -1 s -1 , and kq decreases by an order of magnitude across the series of quenchers (Co(CN)5I) 3- > (Co(CN)5N3) 3- > (Co(CN)5Br) 3- > (Co(CN)5Cl) 3- . On the basis of a detailed study of (Co(CN)5I) 3- , the quenching efficiency increases with background electrolyte concentration and the measured rate constants are in good agreement with predictions based on the Debye-Smoluchowski and Debye-Eigen equations for diffusion-controlled formation and dissociation in ionic solution of an encounter pair, together with a rate constant of 1.2 10 9 s -1 for the quenching step. However, the analysis provides further evidence for the Olson-Simonson effect; that is, in the presence of multivalent electrolyte ions, the salt effects are determined by the counterion concentration, here the cation, rather than by the ionic strength. Specific cation effects are observed such that the quenching rate constants increase in the following sequences: Li + < Na + < K + < Cs + ;M g 2 + <Ca 2+ < Sr 2+ < Ba 2+ ;N H 4 + <MeNH3 + < Me2NH2 + < Me3NH + ;E t 3NH + < Et2NH2 + < EtNH3 + ; n-PrNH3 + < EtNH3 + < MeNH3 + . For the alkali or alkaline-earth cations the large effects seen require participation of the cation in the transition state for the quenching step; the alkylammonium cations are also effective in this role, but the small differences in their efficiencies can be rationalized in terms of their effects on water structure.

Analysis of delayed luminescence from some quenchers of Tb(DPA)3−3 emission: proof for an energy transfer quenching mechanism

The long-lived luminescence from Tb(DPA)3−3 (DPA=pyridine-2,6-dicarboxylate dianion) can be quenched by Rhodamine 6G, Rhodamine B, some urobilin derivatives and Ru(phen)2+3 (phen=1,10-phenanthroline). Using time-resolved emission spectroscopy we have studied these reactions. The observation of delayed luminescence from the quenchers constitutes direct evidence that electronic energy transfer is involved in the quenching process. Quantitative analysis of the delayed fluorescence and of the lanthanide emission, in conjunction with measurement of the luminescence quantum yield of Tb(DPA)3−3 (φ=0.7±0.15), shows that the production of the electronically excited quencher state in the quenching process occurs with nearly unit efficiency for all the quenchers studied. Additional experimental evidence is provided for the view that energy transfer takes place in encounter pairs where donor and acceptor are in close contact.

Ground- and Excited-State Electron Donor−Acceptor (EDA) Complexes from (Dibenzoylmethanato)boron Difluoride and Substituted Benzenes: Their Relation to the Reaction Mechanism

The ground-state EDA complex of (dibenzoylmethanato)boron difluoride (DBMBF2) with substituted benzenes (SB) was studied by absorption spectroscopy to determine the equilibrium constant and enthalpy of the molecular association process in acetonitrile and cyclohexane. Excitation of the EDA complexes showed the corresponding exciplex fluorescence due to excitation of DBMBF2 in the presence of SB. Integration of these data with the previously published kinetics and thermodynamics of the exciplex formation and decay showed that both types of excitations converged on the exciplex energy well and that the former excitation goes through the Franck−Condon state, *(A-D+)v, which is different in molecular distance and electron and energy distributions. In acetonitrile, the discrepancy of fluorescence intensities from two excitations is taken as proof for electron transfer at the encounter pair on the energy surface to generate radical ions. This also implies that excitation of EDA complexes in acetonitrile forms the corresponding exciplexes directly (without the intermediacy of the encounter pair), which undergo solvolysis to give free ions. A mechanism is proposed to represent the observed photochemistry and photophysics.

Mechanistic Studies on the Dual Reaction Pathways of Singlet Excited Dibenzoyl(methanato)boron Difluoride (DBMBF2): Reactions of the Excimer and Exciplexes

The mechanism of the interaction of singlet excited dibenzoyl(methanato)boron difluoride (*DBMBF2 = *A) with olefins and substituted benzenes (SB) was investigated by the determination of effective quenching distances (Reff) from fluorescence monitors in acetonitrile as analyzed by the Smoluchowski−Collins−Kimball equation and by solvent effects on the dichotomy of the formation of cycloadducts and [4 + 2] dimers from 1,3-cyclohexadiene (CHD) and 1,3-cyclooctadiene (1,3-COD). The correlation of Reff with directly demonstrates that the reactants have to get closer to affect electron transfer from these substrates as the driving force become more positive and coalesce on exciplexes. Both photophysical and photochemical probes converge on the partition of encounter pairs to the SSRIP (the ket pathway which leads to radical ion reactions and nonfluorescent) and exciplexes (the kex pathway which leads to cycloadducts and fluorescent species); the former pathway was promoted by low redox energies of donor−accep...

Spin catalysis of the radical recombination reaction

Rate constant of the recombination of alkyl radicals with nitroxide biradicals in dioxane and ethyl benzene exceed rate constants with ‘parent’ mono radicals by 10%–50%. The difference in reactivity is attributed to spin catalysis of the recombination reaction which occurs in the encounter pair of an alkyl radical with one of the biradical termini by the second spin-carrying terminus.

Quenching-resolved emission anisotropy: a steady state fluorescence method to study protein dynamics

Fluorescence techniques can be used to obtain information about biological objects in a non-destructive manner. One of these techniques is fluorescence quenching which involves a decrease in the fluorescence emission of a biological object by externally added quenchers. Quencher molecules produce two kinds of quenching: static and dynamic. Static quenching occurs due to encounter pair formation between quencher and fluorophore molecules, while dynamic quenching requires bimolecular collisions. Unless one of the mechanisms can be neglected, steady state quenching experiments cannot provide information on the contributions of the two processes. However, time-resolved experiments are sensitive only to the dynamic process, and thus provide selective information about the relative motion of the quencher and fluorophore. Since the two quenching events are controlled by different physicochemical parameters, it is necessary to resolve them. In this paper, we describe a steady state method to resolve the static and dynamic quenching constants (rather than time-resolved techniques). Our method is based on the simultaneous determination of the fluorescence intensity and emission anisotropy data and can be regarded as the further development of quenching-resolved emission anisotropy (QREA). Since the steady state anisotropy and fluorescence lifetime are inversely related, by determining the steady state fluorescence anisotrophy, changes in the fluorescence lifetime (and hence the dynamic quenching process) can be monitored (if other parameters influencing the anisotropy remain constant). We present a theoretical description of the method, computer simulations testing its accuracy and results of model experiments with pyridoxamine-phosphate-labelled lysozyme and acrylamide. By changing the external viscosity, we obtained data on the theoretical inverse relationship between the dynamic quenching constant and viscosity. The application conditions are also discussed.

Femtosecond optical spectroscopy in liquids: Applications to the study ofreaction dynamics

The elucidation of detailed mechanisms of ultrafast events that occur inreactions has been made possible by recent advances in spectroscopy techniquesthat use ultrashort laser pulse generation. Ultrashort laser pulses (100femtoseconds duration, 1 fs = 10 −15 s) allow to initiate selectivephotochemical processes (single charge transfer for instance) and to obtainunique informations on the dynamics of primary steps of radical reactionsinvolving ultrafast electron or proton transfer: transient electronicrelaxation, formation of solvation cage, encounter pair formation, ion-moleculereaction. Recent investigations on the femtochemistry of neat liquid water andionic aqueous solutions are reviewed and discussed.

Fractal approach to the kinetics of an encounter pair between asymmetric reagents

In this paper the fractal approach of diffusion-controlled reactions is extended to asymmetric reactivity. The results show a strong influence of the scaling behaviour of reactive trajectories on the probability that particles recollide after a no-reactive collision, and on the probability that this recollision may be reactive. This influence is smaller when rotational motion is assumed. For very large values of the rotational velocity the probability that a recollision may be reactive reaches a constant value, which only depends on geometrical considerations.

Comparison of the enantioselective quenching of the luminescence of dysprosium(III) and terbium(III) tris complexes of 2,6-pyridinedicarboxylate by resolved ruthenium(1,10-phenanthroline)32+

Comparison is made between the enantioselective excited-state quenching of optically active tris-terdentate D 3 complexes of Tb(III) and Dy(III) with 2,6-pyridinedicarboxylate by resolved Ru(1,10-phenanthroline) 3 2+ . It is found that the enantioselective quenching of the two species display almost identical dependence on temperature and solvent composition. The quenching is discussed within the contexts of a simple model involving encounter pair formation, reorientation, and energy transfer. From the results given, it is concluded that the enantioselectivity in the quenching does not depend significantly upon the nature of the chiral electronic states of the donor lanthanide ions but rather has its origin in stereochemical structural aspects of the encounter pair formed between the oppositely charged chiral complexes

Solvent effects on the reactivity of solvated electrons with ammonium and nitrate ions in 1-butanol–water solvents

Values of the rate constants, k2 (106 m3 mol−1 s−1), of solvated electrons,[Formula: see text] with several related salts, in pure water and pure 1-butanol solvents at 298 K are, respectively, as follows: LiNO3, 9.2, 0.19; NH4NO3, 10, 8.3; NH4ClO4, 1.5 × 10−3, 12 in 20 mol% water; LiClO4, 1.0 × 10−4, &lt; 1.0 × 10−4. The value of [Formula: see text] in water solvent is 48 times larger than that in 1-butanol solvent, whereas [Formula: see text] in water is 10−4 times smaller than the value in 1-butanol. This enormous reversal of solvent effects on [Formula: see text] reaction rates is the first observed for ionic reactants. The solvent participates chemically in the [Formula: see text] reaction, and the overall rate constant increases with increasing viscosity and dielectric relaxation time. This unusual behavior is attributed to a greatly increased probability of reaction of an encounter pair with increasing duration of the encounter. Effective reaction radii κRr for [Formula: see text] and [Formula: see text] were estimated with the aid of measured electrical conductances of the salt solutions in all the solvents. Values of κRr are (2–7) × 10−10 m, except for NH4,s+ in 100 and 99 mol% water, which are 2.6 and 2.7 × 10−14 m, respectively. The effective radii of the ions for mutual diffusion increase with increasing butanol content of the solvent, from ~50 pm in water to ~150 pm in 1-butanol, due to the increasing average size of the molecules that solvate the ions.

Magnetic field effects on excited-state oxygen-organic molecule interactions

The effects of an applied magnetic field (<22 KG) on (1) the lifetime of singlet oxygen ( 1 Δ g O 2 ) and (2) the quenching of triplet chrysene by ground-state oxygen ( 3 Σ g - O 2 ) were examined in liquid solvents and solid organic polymers. Each process involves a «spin-forbidden» transition between states of an oxygen-organic molecule (M) encounter pair. Under certain conditions, the 1 Δ g O 2 and 3 chrysene deactivation rates decreased with an increase in the magnetic field strength

Laser flash photolysis investigations of diffusion-controlled reactions in supercritical fluids

Laser flash photolysis has been used to investigate the triplet-triplet annihilation (TTA) process of benzophenone (Ph[sub 2]C=O) and the self-termination reaction of benzyl radical (PhCH[sub 2]) in supercritical CO[sub 2] and ethane. Kinetic measurements were performed at various pressures above the critical pressure along two isotherms, one close to the critical temperature of the solutions (35[degrees]C) and one further removed (50[degrees]C). The second-order rate constants obtained indicate that each reaction occurs at the diffusion limit when spin statistical factors are considered. No evidence of enhanced cage effects due to supercritical solvent clustering about diffusive encounter pairs or enhanced solute/solute interactions were observed in these experiments. Additionally, the photocleavage of dibenzyl ketone and the rate constants for decarbonylation of phenylacetyl radical (PhCH[sub 2]CO) have been examined under the above conditions and do not show any anomalous behavior or cage effects. 37 refs., 8 figs.

Pulse radiolysis studies of ion-electron recombination in gaseous argon

Using pulse radiolysis techniques, rates of recombination of Ar2+ ions with electrons in bulk argon were measured over a wide pressure range (150 to 1065 torr) at bulk gas temperatures of 295, 335, and 375 K. No pressure dependence for the total recombination rate constant was observed at any temperature studied. This observation is consistent with the model, whereby the encounter pair is stabilized by electron energy loss while in the Coulomb field of the cation. The presence of a Ramsauer minimum in the electron/argon atom momentum-transfer cross section versus energy profile means that, at low energies, energy loss is very slow. The neutral-assisted three-body recombination mechanism in argon does not significantly enhance the total rate of recombination above the two-body rate.

Quenching of singlet oxygen in solid organic polymers

The quenching of singlet molecular oxygen ( 1 Δ g O 2 ) by DABCO, triphenylamine and nickel(II) bis[diisopropyl dithiophosphate] (N) in solid polystyrene and poly(methyl methacrylate) was studied and compared with the results obtained in liquid analogs of the polymers. It is found that the bimolecular quenching rate constants for N and DABCO are smaller in the solid media. The N and DABCO data are consistent with a quenching process in the solids that is principally controlled by solute diffusion to form the 1 Δ g O 2 -Q encounter pair.

Erratum: Solvent structure effects on solvated electron reactions in mixed solvents: Negative ions in 1-propanol–water and 2-propanol–water

In models of the kinetics of chemical reactions in solution the solvent is commonly assumed to be a uniform continuum. An example is the Smoluchowski–Debye–Stokes–Einstein equation for the rate constant k2 of a bimolecular reaction between charged or polar species: k2 = κRTfrr/1.5ηrd where κ = probability that a reactant encounter pair will react, R = gas constant, T = temperature, f = Coulombic interaction factor, rr = effective radius for reaction, η = solvent viscosity, and rd = effective radius for mutual diffusion. The equation is useful in evaluating effects of bulk-fluid properties on reaction rates. Residual effects are attributed to more specific solvent behaviour. Rate constants and activation energies E2 of reactions of solvated electrons with and ions vary with the composition of 1-propanol–water and 2-propanol–water mixed solvents. Plots of k2η/fT against solvent composition are nonlinear and change with solvent pair and with reactant pair. Measured molar conductivities Λ0(Li+, ) and Λ0(2Li+,...

FEMTOSECOND SPECTROSCOPY OF SOLVATED ELECTRON IN AQUEOUS MEDIA

The elucidation of detailed mechanisms of ultrafast events that occur in molecular charge transfer or reaction dynamics has been made possible by recent advances in spec- troscopy techniques that use ultrashort laser pulse generation. Ultrashort laser pulses (100 femtoseconds duration, 1 fs = 10 s) allow to initiate selective photochemical processes (single charge transfer for instance) and to obtain unique informations on the dynamics of primary steps of radical reactions involving ultrafast electron or proton transfer: formation of the hydration cage around an electron, encounter pair formation, ion-molecule reaction. Recent investigations on the non-equilibrium states of electron in aqueous media are dis- cussed.

Solvent structure effects on solvated electron reactions in mixed solvents: positive ions in 1-propanol/water and 2-propanol/water

In models of the kinetics of chemical reactions in solution the solvent is commonly assumed to be a uniform continuum. An example is the Smoluchowski–Debye–Stokes–Einstein equation for the rate constant k2 of a bimolecular reaction between charged or polar species:[Formula: see text]where κ is the probability that a reactant encounter pair will react, R is the gas constant, T is the temperature, f is a factor that reflects the effect of electrostatic interaction between the reactants on their probability of attaining the closeness of approach rr at which reaction occurs, η is the solvent viscosity, and rd is the effective radius of the reactant entities for mutual diffusion. The equation is useful in evaluating effects of bulk fluid properties on reaction rates. Residual effects are attributed to more specific solvent behaviour.Rate constants k2, activation energies E2, and pre-exponential factors A2 of reactions of solvated electrons [Formula: see text] with [Formula: see text] [Formula: see text] and [Formula: see text] ions vary with the composition of 1-propanol/water and 2-propanol/water mixed solvents. Plots of k2η/fT against solvent composition are nonlinear and change with the solvent pair and with reactant pair. Measured molar conductivities [Formula: see text] [Formula: see text] [Formula: see text] and [Formula: see text] indicate that the values of rd for the mutual diffusion of the cations and anions have a minimum near 90 mol% water, and that the values in pure propanol-1 or −2 (150–190 pm) are larger than those in pure water solvent (26 pm for [Formula: see text] 70 pm for the metal ions). The liquid structure influences both the rate of diffusion and the probability of reaction of a reactant encounter pair. Key words: alcohol/water mixed solvents, positive ions, reaction kinetics, solvated electron, solvent effects.

Femtosecond spectroscopy of ultrafast reactions in aqueous media

The elucidation of detailed mechanisms of ultrafast events that occur in molecular charge transfer or reaction dynamics has been made possible by recent advances in spectroscopy techniques that use ultrashort laser pulse generation. Ultrashort laser pulses (100 femtoseconds duration, 1 fs=10-15 s) allow initiation of selective photochemical processes (photoejection of epithermal electrons), and obtaining of unique information on the dynamics of primary steps of radical reactions involving ultrafast electron or proton-transfer: formation of the hydration cage around an electron, encounter pair formation, ion-molecule reactions. Recent investigations on the non-equilibrium reaction processes in the universal protic solvent (water) are presented.

Solvent structure effects on solvated electron reactions in mixed solvents: Negative ions in 1-propanol–water and 2-propanol–water

In models of the kinetics of chemical reactions in solution the solvent is commonly assumed to be a uniform continuum. An example is the Smoluchowski–Debye–Stokes–Einstein equation for the rate constant k2 of a bimolecular reaction between charged or polar species: k2 = κRTfrr/1.5ηrd where κ = probability that a reactant encounter pair will react, R = gas constant, T = temperature, f = Coulombic interaction factor, rr = effective radius for reaction, η = solvent viscosity, and rd = effective radius for mutual diffusion. The equation is useful in evaluating effects of bulk-fluid properties on reaction rates. Residual effects are attributed to more specific solvent behaviour. Rate constants and activation energies E2 of reactions of solvated electrons [Formula: see text] with [Formula: see text] and [Formula: see text] ions vary with the composition of 1-propanol–water and 2-propanol–water mixed solvents. Plots of k2η/fT against solvent composition are nonlinear and change with solvent pair and with reactant pair. Measured molar conductivities Λ0(Li+, [Formula: see text]) and Λ0(2Li+, [Formula: see text]) indicate the solvent dependence of rd for the mutual diffusion of Li+ and [Formula: see text] or [Formula: see text]. The liquid structure influences both the rate of diffusion of the reactants and the probability of reaction of a reactant encounter pair.