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Noam Agmon

Publications and source records attributed to Noam Agmon.

12 recordsLinked to original sources
PubMed2006

Deactivation mechanism of the green fluorescent chromophore.

We report time-resolved fluorescence data for the anion of p-hydroxybenzylidene dimethylimidazolinone (p-HBDI), a model chromophore of the green fluorescence protein, in viscous glycerol-water mixtures over a range of temperatures, T. The markedly nonexponential decay of the excited electronic state is interpreted with the aid of an inhomogeneous model possessing a Gaussian coordinate-dependent sink term. A nonlinear least-squares fitting routine enables us to achieve quantitative fits by adjusting a single activation parameter, which is found to depend linearly on 1/T. We derive an analytic expression for the absolute quantum yield, which is compared with the integrated steady-state fluorescence spectra. The microscopic origins of the model are discussed in terms of two-dimensional dynamics, coupling the phenyl-ring rotation to a swinging mode that brings this flexible molecule to the proximity of a conical intersection on its multidimensional potential energy surface.

Fluorescence↗
PubMed2005

Transition in the temperature-dependence of GFP fluorescence: from proton wires to proton exit.

In green fluorescent protein, photo-excitation leads to excited-state proton transfer from its chromophore, leaving behind a strongly fluorescing anion, while the proton is commonly thought to migrate internally to Glu-222. X-ray data show that the protein contains more extended hydrogen-bonded networks that can support proton migration (i.e., proton wires). Here we study the temperature-dependence of the transient fluorescence from both the acid and anionic forms up to 15 ns. At low temperatures, we find that the (lifetime-corrected) fluorescence of the acidic form decays asymptotically as t(-1/2), following quantitatively the solution of a one-dimensional diffusion equation for reversible geminate recombination with quenching. This indicates proton migration along the internal proton wires. A small degree of geminate proton quenching is attributed to the formation of the zwitterion by proton migration on a side-branch of the proton wire. Above 230 K, the fluorescence kinetics undergo a transition, exhibiting an asymptotic t(-3/2) decay, and the quenching effect disappears. We interpret these findings as evidence for a conformational change enabling the rotation of Thr-203, which eventually allows the proton to escape to the exterior solution.

Animals↗
PubMed2005

Diffusion-influenced excited-state reversible transfer reactions, A* + Bright harpoon over left harpoonC* + D, with two different lifetimes: theories and simulations.

We report accurate Brownian simulation results for the kinetics of the pseudo-first-order diffusion-influenced excited-state reversible transfer reaction A(*) + Bright harpoon over left harpoonC(*) + D with two different lifetimes using two different propagation algorithms. The results are used to test approximate solutions for this many-particle problem. Available theories fail when one of the two reactions or (decay) rate constants is large. To remedy this situation, we develop two uniform approximations, which are based on introducing a generalized Smoluchowski term into the relaxation-time approximation. The best of these is the extended unified theory of reversible target reactions, which reduces correctly in all limits and exhibits superior agreement with simulations.

Journal Article↗
PubMed2005

A hierarchy of functionally important relaxations within myoglobin based on solvent effects, mutations and kinetic model.

Geminate CO rebinding in myoglobin is studied for two viscous solvents, trehalose and sol-gel (bathed in 100% glycerol) at several temperatures. Mutations in key distal hemepocket residues are used to eliminate or enhance specific relaxation modes. The time-resolved data are analyzed with a modified Agmon-Hopfield model which is capable of providing excellent fits in cases where a single relaxation mode is dominant. Using this approach, we determine the relaxation rate constants of specific functionally important modes, obtaining also their Arrhenius activation energies. We find a hierarchy of distal pocket modes controlling the rebinding kinetics. The "heme access mode" (HAM) is responsible for the major slow-down in rebinding. It is a solvent-coupled cooperative mode which restricts ligand return from the xenon cavities. Bulky side-chains, like those His64 and Trp29 (in the L29W mutant), operate like overdamped pendulums which move over and block the binding site. They may be either unslaved (His64) or moderately slaved (Trp29) to the solvent. Small side-chain relaxations, most notably of leucines, are revealed in some mutants (V68L, V68A). They are conjectured to facilitate inter-cavity ligand motion. When all relaxations are arrested (H64L in trehalose), we observe pure inhomogeneous kinetics with no temperature dependence, suggesting that proximal relaxation is not a factor on the investigated timescale.

Binding Sites↗
PubMed2005

Proton pathways in green fluorescence protein.

Proton pathways in green fluorescent protein (GFP) are more extended than previously reported. In the x-ray data of wild-type GFP, a two-step exit pathway exists from the active site to the protein surface, controlled by a threonine switch. A proton entry pathway begins at a glutamate-lysine cluster around Glu-5, and extends all the way to the buried Glu-222 near the active site. This structural evidence suggests that GFP may function as a portable light-driven proton-pump, with proton emitted in the excited state through the switchable exit pathway, and replenished from Glu-222 and the Glu-5 entry pathway in the ground state.

Animals↗
PubMed2005

Elementary steps in excited-state proton transfer.

The absorption of a photon by a hydroxy-aromatic photoacid triggers a cascade of events contributing to the overall phenomenon of intermolecular excited-state proton transfer. The fundamental steps involved were studied over the last 20 years using a combination of theoretical and experimental techniques. They are surveyed in this sequel in sequential order, from fast to slow. The excitation triggers an intramolecular charge transfer to the ring system, which is more prominent for the anionic base than the acid. The charge redistribution, in turn, triggers changes in hydrogen-bond strengths that set the stage for the proton-transfer step itself. This step is strongly influenced by the solvent, resulting in unusual dependence of the dissociation rate coefficient on water content, temperature, and isotopic substitution. The photolyzed proton can diffuse in the aqueous solution in a mechanism that involves collective changes in hydrogen-bonding. On longer times, it may recombine adiabatically with the excited base or quench it. The theory for these diffusion-influenced geminate reactions has been developed, showing nice agreement with experiment. Finally, the effect of inert salts, bases, and acids on these reactions is analyzed.

Journal Article↗
PubMed2005

A bond-order analysis of the mechanism for hydrated proton mobility in liquid water.

Bond-order analysis is introduced to facilitate the study of cooperative many-molecule effects on proton mobility in liquid water, as simulated using the multistate empirical valence-bond methodology. We calculate the temperature dependence for proton mobility and the total effective bond orders in the first two solvation shells surrounding the H(5)O(2) (+) proton-transferring complex. We find that proton-hopping between adjacent water molecules proceeds via this intermediate, but couples to hydrogen-bond dynamics in larger water clusters than previously anticipated. A two-color classification of these hydrogen bonds leads to an extended mechanism for proton mobility.

Journal Article↗
PubMed2004

Exact solution of the excited-state geminate A*+B <==> C*+D reaction with two different lifetimes and quenching.

The authors obtain, in the Laplace transform space, the exact analytic solution for the Green function and survival probabilities for the excited-state diffusion-influenced reversible geminate reaction, A*+B <==> C*+D, with two different lifetimes and in the presence of an added quenching process. This extends a previous investigation by Popov and Agmon [J. Chem. Phys. 117, 5770 (2002)] of the ground-state reaction without quenching. The long-time asymptotic behavior of the survival probabilities is obtained in the time domain. It is found to be different from the equal-lifetime case. This paper also provides a useful short-time approximation for the kinetics.

Journal Article↗
PubMed2004

Influence of diffusion on the kinetics of excited-state association--dissociation reactions: comparison of theory and simulation.

Several recent theories of the kinetics of diffusion influenced excited-state association--dissociation reactions are tested against accurate Brownian dynamics simulation results for a wide range of parameters. The theories include the relaxation time approximation (RTA), multiparticle kernel decoupling approximations and the so-called kinetic theory. In the irreversible limit, none of these theories reduce to the Smoluchowski result. For the pseudo-first-order target problem, we show how the RTA can be modified so that the resulting formalism does reduce correctly in the irreversible limit. We call this the unified Smoluchowski approximation, because it unites modern theories of reversible reactions with Smoluchowski's theory of irreversible reactions.

Computer Simulation↗
PubMed2004

Coupling of protein relaxation to ligand binding and migration in myoglobin.

Protein relaxation, ligand binding, and ligand migration into a hydrophobic cavity in myoglobin are unified by a bounded diffusion model which produces an accurate fit to complex ligand rebinding data over eight decades in time and a 160 K temperature range, in qualitative agreement with time-resolved x-ray crystallography. Protein relaxation operates in a cyclic manner to move the ligand away from the binding site.

Animals↗
PubMed2002

Electronic determinants of photoacidity in cyanonaphthols.

We present semiempirical AM1 calculations for the ground and excited state of 2-naphthol and some of its cyano derivatives in the gas phase. Following photoexcitation, the Mulliken electron density on the oxygen diminishes slightly for the acid and more conspicuously for the anionic conjugated base. This agrees with the measured solvatochromic parameters for 2-naphthol. In both electronic states, we find a nice correlation with the measured pK values in water. The electronic charge distribution on the distal ring of the anion agrees with the experimental acidity order in both S(0) and S(1). Upon excitation, it increases predominantly in positions 3, 5, and 8. The ring system of the anion assumes an alternate quinoidal structure in the ground state of the anion, which becomes more symmetric in the relaxed excited state. This suggests that the enhanced aromatic character of a 4n electron system in the excited state allows for better delocalization of the oxygen charge within the ring.

Journal Article↗