Thesis (M.Sc.)--York University, 2005. Graduate Programme in Physics and Astronomy. / Typescript. Includes bibliographical references (leaves 48-50). Also available on the Internet. MODE OF ACCESS via web browser by entering the following URL: http://gateway.proquest.com/openurl?url%5Fver=Z39.88-2004&res%5Fdat=xri:pqdiss &rft_val_fmt=info:ofi/fmt:kev:mtx:dissertation&rft_dat=xri:pqdiss:MR11883

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This thesis focuses on the ultrafast isomerization reaction of retinal in both rhodopsin and bacteriorhodopsin, examples of sensory and energy transduction proteins that exploit the same photoactive chromophore for two very different functions. In bacteriorhodopsin, retinal isomerizes from an all-trans to 13-cis conformation as the primary event in light- driven proton pumping. In the visual pigment rhodopsin, the retinal chromophore isomerizes from an 11-cis to all-trans geometry as the primary step leading to our sense of vision. This diversity of function for nominally identical systems raises the question as to just how optimized are these proteins to arrive at such drastically different functions? Previous work has employed transient absorption spectroscopy to probe retinal protein photochemistry, but many of the relevant electronic and nuclear dynamics of isomerization are masked by inhomogeneous broadening effects and strong spectral overlap between reactant and photoproduct states. This work exploits the unique properties of two-dimensional photon echo spectroscopy to deconvolve inhomogeneous broadening and spectral overlap effects and fully reveal the dynamics that direct retinal isomerization in proteins. In bacteriorhodopsin, vibrational coupling to the reaction coordinate results in a surface crossing event prior to the conventional conical intersection associated with isomerization to the J intermediate. In rhodopsin, however, a similarly early vibrationally-mediated barrier crossing event is observed, resulting in spectral signals consistent with the known photoproduct state appearing an order of magnitude faster than determined from conventional transient absorption measurements. The competing overlapping spectral signals that obscured the initial dynamics when probed with transient absorption spectroscopy are now clearly resolved with two-dimensional photon echo spectroscopy. These experiments illustrate the critical role of the protein in directing the outcome of retinal photochemistry. The protein controls the reaction pathway through steric interactions between the binding pocket and the retinal chromophore, the result of which directly sets the isomerization coordinate and indirectly controls the vibrational coupling to the reaction coordinate based on the local retinal structure. The new insight from this work is the extraordinary degree of selective vibrational coupling involved in directing the isomerization reaction in retinal proteins.

This thesis focuses on the ultrafast isomerization reaction of retinal in both rhodopsin and bacteriorhodopsin, examples of sensory and energy transduction proteins that exploit the same photoactive chromophore for two very different functions. In bacteriorhodopsin, retinal isomerizes from an all-trans to 13-cis conformation as the primary event in light- driven proton pumping. In the visual pigment rhodopsin, the retinal chromophore isomerizes from an 11-cis to all-trans geometry as the primary step leading to our sense of vision. This diversity of function for nominally identical systems raises the question as to just how optimized are these proteins to arrive at such drastically different functions? Previous work has employed transient absorption spectroscopy to probe retinal protein photochemistry, but many of the relevant electronic and nuclear dynamics of isomerization are masked by inhomogeneous broadening effects and strong spectral overlap between reactant and photoproduct states. This work exploits the unique properties of two-dimensional photon echo spectroscopy to deconvolve inhomogeneous broadening and spectral overlap effects and fully reveal the dynamics that direct retinal isomerization in proteins. In bacteriorhodopsin, vibrational coupling to the reaction coordinate results in a surface crossing event prior to the conventional conical intersection associated with isomerization to the J intermediate. In rhodopsin, however, a similarly early vibrationally-mediated barrier crossing event is observed, resulting in spectral signals consistent with the known photoproduct state appearing an order of magnitude faster than determined from conventional transient absorption measurements. The competing overlapping spectral signals that obscured the initial dynamics when probed with transient absorption spectroscopy are now clearly resolved with two-dimensional photon echo spectroscopy. These experiments illustrate the critical role of the protein in directing the outcome of retinal photochemistry. The protein controls the reaction pathway through steric interactions between the binding pocket and the retinal chromophore, the result of which directly sets the isomerization coordinate and indirectly controls the vibrational coupling to the reaction coordinate based on the local retinal structure. The new insight from this work is the extraordinary degree of selective vibrational coupling involved in directing the isomerization reaction in retinal proteins.

Thesis (Ph. D.)--University of Chicago, Dept. of Chemistry. / Includes bibliographical references. Also available on the Internet.

Two different time-resolved spectroscopic techniques are discussed theoretically and demonstrated experimentally in dilute gases. The first technique involves extending the advantages of Stark-effect based time-resolved spectroscopy to non-polar molecules. This involves the development of a stable, TEM₀₀ mode, cw, CO₂ laser capable of switching rapidly and controllably between two frequencies. Design problems and output characteristics are discussed. The frequency switchable laser is applied to the CO₂ 10.6 μm P(16) coincidence with the non-polar molecule SF₆. The population relaxation time, T₁, is measured using two-pulse delayed nutation. The decay of induced dipoles is studied using the phenomenon of photon echoes. It is found that the echoes decay in a manner characteristic of dephasing dominated by velocity-changing collisions. A fit of the data to a model for such decays gives values of γ(ab) ≡ 1/T₂ (the non-velocity-changing contribution to the dipole decay rate), Γ(VC) (the total probability of a velocity-changing collision per unit time), and Δu which is related to the mean velocity change of SF₆ upon a velocity changing collision. A comparison with the published results of the similar Stark experiments on C¹³ H₃F are made. The second technique involves the development of an alternative to the pulsed excitation typically used in time-resolved T₁ studies. This involves inversion of a portion of the velocity distribution by adiabatic rapid passage (ARP) techniques. The center of this portion is then probed in the manner of previous delayed nutation experiments. The system preparation is shown theoretically to be different and simpler than the pulse case. In addition, ARP preparation gives a larger signal than two-pulse delayed nutation experiments. ARP experiments on N¹⁴H₃ and N¹⁵H₃ are described and compared to two-pulse delayed notation experiments. The single exponential decay best fits to the data from the two methods are found to be in agreement. We would expect the N¹⁵H₃ results to be very similar to the N¹⁴H₃ results, though reduced rotational resonance effects in its upper state should give it an overall slower decay. It is indeed found that the decay appears to be a simple exponential as did the N¹⁴H₃ data over the time range studied. The pressure dependent single exponential decay rate for N¹⁵H₃ is however roughly 45% larger than the rate for N¹⁴H₃ in the pressure range from 0.5 to 9 mTorr.

Coherent transient effects are the optical analogs of the many transient phenomena seen in pulsed nuclear magnetic resonance experiments on spin systems. For example, photon-echo and optical nutation are the respective optical equivalents of spin echo and transient nutation of nuclear magnetic resonance. In Stark-switching and frequency-switching techniques the laser field and the molecules are brought into resonance in a sequence of pulses, the rest of the time they remain well off-resonance. So far it has been assumed that the off-resonance field does not have any measureable influence on the experimental results and is utilized to implement a very efficient detection scheme. This work discusses how the off-resonance field affects the coherent transient effects. It is shown here how this field, by inducing changes in the index of refraction as small as 10⁻⁶ produces easily observable effects in photon echo and delayed optical nutation.

Thesis (Ph. D.)--University of Washington, 2000. / Vita. Includes bibliographical references (leaves 142-145).

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Nous avons mis en place un dispositif permettant l’acquisition d'échos de photons stimulés infrarouges à l’échelle femtoseconde. Le but est d'examiner la dynamique vibrationnelle aux temps courts de métaux carbonyles (W(CO)₆ and Fe(CO)₅) piégés en matrice cryogénique (4-50 K). Cet environnement solide, issu de la condensation d'un mélange gazeux contenant une impureté et un gaz inerte (N₂, CH₄, Ar, etc.), est propice à l’étude de systèmes dans leur état fondamental. L’excitation d’une vibration moléculaire s’atténue toujours temporellement, ce qui correspond dans le domaine spectral à un élargissement des raies d’absorption. L’étude de la dynamique vibrationnelle vise à examiner les causes physiques à l’origine de cet élargissement spectral. Typiquement, elles sont de trois sortes : phénomènes intramoléculaires, interactions entre molécules piégées et interactions entre la molécule piégée et l’environnement. Les échos de photons permettent de distinguer les contributions homogènes et inhomogènes de l’élargissement spectral et de caractériser les processus de déphasage, de relaxation des populations et de diffusion spectrale. Parmi les résultats obtenus, nous avons mis en évidence l'influence des phonons spécifiques aux matrices moléculaires (ex : libration de N₂ et rotation de CH₄ ) sur le déphasage vibrationnel ainsi que l’influence de la transition de phase du méthane solide à 20 K sur la dynamique vibrationnelle. Nous avons également montré que la dynamique vibrationnelle était dépendante du site cristallographique dans lequel est piégée la molécule. Enfin, en excitant plusieurs modes de vibration simultanément, nous avons pu examiner les couplages intramoléculaires. / We built an experimental set-up in order to generate infrared stimulated photon echoes at the femtosecond timescale. The purpose is to examine the short time vibrational dynamics of metal carbonyls (W(CO)₆ and Fe(CO)₅) trapped in cryogenic matrices (4-50 K). This environment, resulting from the condensation of a gas mixture containing the impurity and an inert gas (N₂, CH₄, Ar, etc.), is well suited to study systems in their ground state. An excited molecular vibration is always damped in the time domain. It corresponds in the frequency domain to a broadening of the absorption line. The study of the vibrational dynamics aims at examining the physical causes of this spectral broadening. Typically, there are three kinds of causes: intramolecular phenomena, interactions between trapped molecules and interactions between the impurity and the environment. Photon echoes allow distinguishing between the homogeneous and the inhomogeneous contributions of the spectral broadening and characterizing dephasing process, population relaxation and spectral diffusion. Among the obtained results, we highlighted the influence of phonons that are specific to molecular matrices (ex: N₂ libration and CH₄ rotation) on the vibrational dephasing. Moreover, we observed the influence of the phase transition of solid methane at 20 K on the vibrational dynamics. We also showed that the vibrational dynamics depends on the site in which the molecule is trapped. Finally, when exciting several vibrational modes, we are also able to study intramolecular couplings.