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Joel Gilmore

Publications and source records attributed to Joel Gilmore.

8 recordsLinked to original sources

Quantum Transition State Theory for proton transfer reactions in enzymes

We consider the role of quantum effects in the transfer of hyrogen-like species in enzyme-catalysed reactions. This study is stimulated by claims that the observed magnitude and temperature dependence of kinetic isotope effects imply that quantum tunneling below the energy barrier associated with the transition state significantly enhances the reaction rate in many enzymes. We use a path integral approach which provides a general framework to understand tunneling in a quantum system which interacts with an environment at non-zero temperature. Here the quantum system is the active site of the enzyme and the environment is the surrounding protein and water. Tunneling well below the barrier only occurs for temperatures less than a temperature $T_0$ which is determined by the curvature of potential energy surface near the top of the barrier. We argue that for most enzymes this temperature is less than room temperature. For physically reasonable parameters quantum transition state theory gives a quantitative description of the temperature dependence and magnitude of kinetic isotope effects for two classes of enzymes which have been claimed to exhibit signatures of quantum tunneling. The only quantum effects are those associated with the transition state, both reflection at the barrier top and tunneling just below the barrier. We establish that the friction due to the environment is weak and only slightly modifies the reaction rate. Furthermore, at room temperature and for typical energy barriers environmental degrees of freedom with frequencies much less than 1000 cm$^{-1}$ do not have a significant effect on quantum corrections to the reaction rate.

quant-ph

Quantum dynamics of electronic excitations in biomolecular chromophores: role of the protein environment and solvent

We consider continuum dielectric models as minimal models to understand the effect of a surrounding globular protein and solvent on the quantum dynamics of electronic excitations in a biological chromophore. We derive expressions for the frequency dependent spectral density which describes the coupling of the electronic levels in the chromophore to its environment. The magnitude and frequency dependence of the spectral density determines whether or not the quantum dynamics is coherent or incoherent, and thus whether on not one can observe quantum interference effects such as Rabi oscillations. We find the contributions to the spectral density from each component of the chromophore environment: the bulk solvent, protein, and water bound to the protein. The relative importance of each component to the quantum dynamics of the chromophore is determined by the dynamics' time scale. Our results provide a natural explanation and model for the different time scales observed in the spectral density extracted from the solvation dynamics probed by ultra-fast laser spectroscopy techniques such as the dynamic Stokes shift and three pulse photon echo spectroscopy. Our results are used to define under what conditions the dynamics of the excited chromophore is dominated by the surrounding protein and when it is dominated by dielectric fluctuations in the solvent. We show that even when the chromophore is shielded from the solvent by the protein ultra-fast solvation can be dominated by the solvent. We suggest that the ultra-fast solvation recently seen in some biological chromophores should not necessarily be assigned to ultra-fast protein dynamics. Spectral densities estimated from our continuum models and extracted from experiment suggest that most quantum dynamics of electronic excitations is incoherent.

quant-ph

Quantitative scattering of melanin solutions

The optical scattering coefficient of a dilute, well solubilised eumelanin solution has been accurately measured as a function of incident wavelength, and found to contribute less than 6% of the total optical attenuation between 210 and 325nm. At longer wavelengths (325nm to 800nm) the scattering was less than the minimum sensitivity of our instrument. This indicates that UV and visible optical density spectra can be interpreted as true absorption with a high degree of confidence. The scattering coefficient vs wavelength was found to be consistent with Rayleigh Theory for a particle radius of 38+-1nm.

physics.bio-ph

A Quantum Yield Map for Synthetic Eumelanin

The quantum yield of synthetic eumelanin is known to be extremely low and it has recently been reported to be dependent on excitation wavelength. In this paper, we present quantum yield as a function of excitation wavelength between 250 and 500 nm, showing it to be a factor of 4 higher at 250 nm than at 500 nm. In addition, we present a definitive map of the steady-state fluorescence as a function of excitation and emission wavelengths, and significantly, a three-dimensional map of the specific quantum yield: the fraction of photons absorbed at each wavelength that are subsequently radiated at each emission wavelength. This map contains clear features, which we attribute to certain structural models, and shows that radiative emission and specific quantum yield are negligible at emission wavelengths outside the range of 585 and 385 nm (2.2 and 3.2 eV), regardless of excitation wavelength. This information is important in the context of understanding melanin biofunctionality, and the quantum molecular biophysics therein.

physics.chem-ph

Quantitative Fluorescence Excitation Spectra for Synthetic Eumelanin

Previously reported excitation spectra for eumelanin are sparse and inconsistent. Moreover, these studies have failed to account for probe beam attenuation and emission reabsorption within the samples, making them qualitative at best. We report for the first time quantitative excitation spectra for synthetic eumelanin, acquired for a range of solution concentrations and emission wavelengths. Our data indicate that probe beam attenuation and emission reabsorption significantly affect the spectra even in low-concentration eumelanin solutions and that previously published data do not reflect the true excitation profile. We apply a correction procedure (previously applied to emission spectra) to account for these effects. Application of this procedure reconstructs the expected relationship of signal intensity with concentration, and the normalised spectra show a similarity in form to the absorption profiles. These spectra reveal valuable information regarding the photophysics and photochemistry of eumelanin. Most notably, an excitation peak at 365 nm (3.40 eV), whose position is independent of emission wavelength, is possibly attributable to a DHICA component singly linked to a polymeric structure.

cond-mat.soft

Spin-boson models for quantum decoherence of electronic excitations of biomolecules and quantum dots in a solvent

We give a theoretical treatment of the interaction of electronic excitations (excitons) in biomolecules and quantum dots with the surrounding polar solvent. Significant quantum decoherence occurs due to the interaction of the electric dipole moment of the solute with the fluctuating electric dipole moments of the individual molecules in the solvent. We introduce spin boson models which could be used to describe the effects of decoherence on the quantum dynamics of biomolecules which undergo light-induced conformational change and on biomolecules or quantum dots which are coupled by Forster resonant energy transfer.

cond-mat.soft

Criteria for quantum coherent transfer of excitons between chromophores in a polar solvent

We show that the quantum decoherence of Forster resonant energy transfer between two optically active molecules can be described by a spin-boson model. This allows us to give quantitative criteria, in terms of experimentally measurable system parameters, that are necessary for coherent Bloch oscillations of excitons between the chromophores. Experimental tests of our results should be possible with Flourescent Resonant Energy Transfer (FRET) spectroscopy. Although we focus on the case of protein-pigment complexes our results are also relevant to quantum dots and organic molecules in a dielectric medium.

quant-ph

Quantitative photoluminescence of broad band absorbing melanins: A procedure to correct for inner filter and re-absorption effects

We report methods for correcting the photoluminescence emission and excitation spectra of highly absorbing samples for re-absorption and inner filter effects. We derive the general form of the correction, and investigate various methods for determining the parameters. Additionally, the correction methods are tested with highly absorbing fluorescein and melanin (broadband absorption) solutions; the expected linear relationships between absorption and emission are recovered upon application of the correction, indicating that the methods are valid. These procedures allow accurate quantitative analysis of the emission of low quantum yield samples (such as melanin) at concentrations where absorption is significant.

physics.bio-ph