Trp-cage is a synthetic 20-residue miniprotein which folds rapidly and spontaneously to a well-defined globular structure more typical of larger proteins. Due to its small size and fast folding, it is an ideal model system for experimental and theoretical investigations of protein folding mechanisms. However, Trp-cage's exact folding mechanism is still a matter of debate. Here we investigate Trp-cage's relaxation dynamics in the amide I' spectral region (1530-1700 cm(-1)) using time-resolved infrared spectroscopy. Residue-specific information was obtained by incorporating an isotopic label ((13)C═(18)O) into the amide carbonyl group of residue Gly11, thereby spectrally isolating an individual 310-helical residue. The folding-unfolding equilibrium is perturbed using a nanosecond temperature-jump (T-jump), and the subsequent re-equilibration is probed by observing the time-dependent vibrational response in the amide I' region. We observe bimodal relaxation kinetics with time constants of 100 ± 10 and 770 ± 40 ns at 322 K, suggesting that the folding involves an intermediate state, the character of which can be determined from the time- and frequency-resolved data. We find that the relaxation dynamics close to the melting temperature involve fast fluctuations in the polyproline II region, whereas the slower process can be attributed to conformational rearrangements due to the global (un)folding transition of the protein. Combined analysis of our T-jump data and molecular dynamics simulations indicates that the formation of a well-defined α-helix precedes the rapid formation of the hydrophobic cage structure, implying a native-like folding intermediate, that mainly differs from the folded conformation in the orientation of the C-terminal polyproline II helix relative to the N-terminal part of the backbone. We find that the main free-energy barrier is positioned between the folding intermediate and the unfolded state ensemble, and that it involves the formation of the α-helix, the 310-helix, and the Asp9-Arg16 salt bridge. Our results suggest that at low temperature (T ≪ Tm) a folding path via formation of α-helical contacts followed by hydrophobic clustering becomes more important.

We study experimentally time-resolved emission of CdSe quantum dots in an environment with a controlled local density of states (LDOS). The decay rate is measured versus frequency and as a function of distance to a mirror. We observe a linear relation between the decay rate and the LDOS, allowing us to determine the size-dependent quantum efficiency and oscillator strength. We find that the quantum efficiency decreases with increasing emission energy mostly due to an increase in nonradiative decay. For the first time, we manage to obtain the oscillator strength of the important class of CdSe quantum dots. The oscillator strength varies weakly with frequency in agreement with behavior of quantum dots in the strong confinement limit. Surprisingly, the measured absolute values are a factor of 5 below theoretically calculated values. Our results are relevant for applications of CdSe quantum dots in spontaneous emission control and cavity quantum electrodynamics. * URL: www.photonicbandgaps.com arXiv:0808.3191v1 [physics.optics]

Disclaimer/Complaints regulationsIf you believe that digital publication of certain material infringes any of your rights or (privacy) interests, please let the Library know, stating your reasons. In case of a legitimate complaint, the Library will make the material inaccessible and/or remove it from the website. Please Ask the Library: http://uba.uva.nl/en/contact, or a letter to: Library of the University of Amsterdam, Secretariat, Singel 425, 1012 WP Amsterdam, The Netherlands. You will be contacted as soon as possible. Abstract. The photo-fading of crystal violet (CV), one of the earliest synthetic dyes and an ink component, is examined both in solution and on paper. Aqueous solutions of CV were exposed to UV light (365nm) and samples were taken at constant time intervals and analysed with a High Performance Liquid Chromatography-Photo Diode Array (HPLC-PDA) and Liquid Chromatography-Mass Spectroscopy (LC-MS). Demethylation products were positively identified. Also, deamination probably occurred. The oxidation at the central carbon likely generates Michler's ketone (MK) or its derivatives, but still needs confirmation. To study CV on paper, Whatman paper was immersed in CV and exposed to UV light. Before and after different irradiation periods, reflectance spectra were recorded with Fibre Optic Reflectance Spectrophotometry (FORS). A decrease in CV concentration and a change in aggregation type for CV molecules upon irradiation was observed. Colorimetric L*a*b* values before and during irradiation were also measured. Also, CV was extracted from paper before and after different irradiation periods and analysed with HPLC-PDA. Photo-fading of CV on paper produced the same products as in solution, at least within the first 100 hours of irradiation. Finally, a photo-fading of CV in the presence of MK on Whatman paper was performed. It was demonstrated that MK both accelerates CV degradation and is consumed during the reaction. The degradation pathway identified in this work is suitable for explaining the photo/fading of other dyes belonging to the triarylmethane group.

Control over spontaneous emission of quantum dots is important for many applications, especially as light sources in photonic materials and nanostructures [1][2][3]. Colloidal CdSe quantum dots have recently generated enormous interest because of the tunability of their emission energy with particle diameter over the entire visible range. The strength of the interaction of a quantum dot with the light field is determined by the oscillator strength, making the oscillator strength a crucial parameter for successful inhibition and enhancement of spontaneous emission.Here we present measurements of the oscillator strength and quantum efficiency of ensembles of colloidal CdSe quantum dots as a function of emission energy or equivalently quantum dot size. It is the first time the oscillator strength is determined from emission, giving highly accurate values that can be used to test theories.A transmission electron micrograph is shown in Fig. 1, where an average diameter of 4.1 nm is found. The total decay rate is measured as a function of normalised LDOS for different sizes of quantum dots in our ensemble. A linear relation between total decay rate and LDOS is found, as expected from Fermi's golden rule [4]. The total decay rate consists of radiative and nonradiative decay rate. Since the nonradiative rate is independent of LDOS while the radiative rate increases linearly, the measured total decay rate can be separated in radiative and nonradiative components. We find that the total decay rate increases with emission energy in agreement with Van Driel et al.[5]. This increase is mostly due to an increase in nonradiative decay rate. The radiative decay rate found in our experiments is hardly dependent on emission energy.From the radiative decay rate the oscillator strength is obtained, see Fig. 2. The oscillator strength is nearly independent on emission energy suggesting that the quantum dots are in the strong confinement regime. The expected trend in the strong confinement regime [6] is shown in Fig. 2 with the line and results of tight binding calculations [7] are also plotted. Qualitatively the same trend can be seen. However the absolute value of the oscillator strength of around 0.7 found experimentally surprisingly is a factor of 6 lower than expected from theory. We will discuss consequences for spontaneous emission control and cavity quantum electrodynamics. References[1] T. splitting with a single quantum dot in a photonic crystal nanocavity", Nature 432, 200 (2004) [2] J.