On the refractive index correction in luminescence spectroscopy

Locating and Visualizing Crystals for X-Ray Diffraction Experiments

Macromolecular crystallography has advanced from using macroscopic crystals, which might be >1 mm on a side, to crystals that are essentially invisible to the naked eye, or even under a standard laboratory microscope. As crystallography requires recognizing crystals when they are produced, and then placing them in an X-ray, electron, or neutron beam, this provides challenges, particularly in the case of advanced X-ray sources, where beams have very small cross sections and crystals may be vanishingly small. Methods for visualizing crystals are reviewed here, and examples of different types of cases are presented, including: standard crystals, crystals grown in mesophase, in situ crystallography, and crystals grown for X-ray Free Electron Laser or Micro Electron Diffraction experiments. As most techniques have limitations, it is desirable to have a range of complementary techniques available to identify and locate crystals. Ideally, a given technique should not cause sample damage, but sometimes it is necessary to use techniques where damage can only be minimized. For extreme circumstances, the act of probing location may be coincident with collecting X-ray diffraction data. Future challenges and directions are also discussed.

Measurement of Scattering and Absorption Cross Sections of Dyed Microspheres

Measurements of absorbance and fluorescence emission were carried out on aqueous suspensions of polystyrene (PS) microspheres with a diameter of 2.5 µm using a spectrophotometer with an integrating sphere detector. The apparatus and the principles of measurements were described in our earlier publications. Microspheres with and without green BODIPY(@) dye were measured. Placing the suspension inside an integrating sphere (IS) detector of the spectrophotometer yielded (after a correction for fluorescence emission) the absorbance (called A in the text) due to absorption by BODIPY(@) dye inside the microsphere. An estimate of the absorbance due to scattering alone was obtained by subtracting the corrected BODIPY(@) dye absorbance (A) from the measured absorbance of a suspension placed outside the IS detector (called A1 in the text). The absorption of the BODIPY(@) dye inside the microsphere was analyzed using an imaginary index of refraction parameterized with three Gaussian-Lorentz functions. The Kramer-Kronig relation was used to estimate the contribution of the BODIPY(@) dye to the real part of the microsphere index of refraction. The complex index of refraction, obtained from the analysis of A, was used to analyze the absorbance due to scattering ((A1 - A) in the text). In practice, the analysis of the scattering absorbance, A1-A, and the absorbance, A, was carried out in an iterative manner. It was assumed that A depended primarily on the imaginary part of the microsphere index of refraction with the other parameters playing a secondary role. Therefore A was first analyzed using values of the other parameters obtained from a fit to the absorbance due to scattering, A1-A, with the imaginary part neglected. The imaginary part obtained from the analysis of A was then used to reanalyze A1-A, and obtain better estimates of the other parameters. After a few iterations, consistent estimates were obtained of the scattering and absorption cross sections in the wavelength region 300 nm to 800 nm.

Measurement of Scattering and Absorption Cross Sections of Microspheres for Wavelengths between 240 nm and 800 nm

A commercial spectrometer with a 150 mm integrating sphere (IS) detector was used to estimate the scattering and absorption cross sections of monodisperse polystyrene microspheres suspended in water. Absorbance measurements were performed with the sample placed inside the IS detector. The styrene absorption was non zero for wavelengths less than 300 nm. Correction for fluorescence emission by styrene was carried out and the imaginary part of the index of refraction, ni, was obtained. Absorbance measurements with the sample placed outside the IS detector were sensitive to the loss of photons from the incident beam due to scattering. The absorbance data was fitted with Lorenz-Mie scattering cross section and a correction for the finite acceptance aperture of the spectrometer. The fit parameters were the diameter, the suspension concentration, and the real part of the index of refraction. The real part of the index was parameterized using an expansion in terms of powers of the inverse wavelength. The fits were excellent from 300 nm to 800 nm. By including the imaginary part obtained from the absorbance measurements below 300 nm, it was possible to obtain a good fit to the observed absorbance data over the region 240 nm to 800 nm. The value of ni at 266 nm was about 0.0060±0.0016 for microspheres with diameters of 1.5 μm, 2.0 μm, and 3.0 μm. The scattering cross section, absorption cross section, and the quantum yield at 266 nm of microsphere with a diameter of 2.0 μm was 5.65±0.01 μm(2), 1.54±0.03 μm(2), and 0.027±0.002 respectively. The styrene absorption reduces the scattering cross section by 20 % at 266 nm.

Measurement of Scattering Cross Section with a Spectrophotometer with an Integrating Sphere Detector

A commercial spectrometer with an integrating sphere (IS) detector was used to measure the scattering cross section of microspheres. Analysis of the measurement process showed that two measurements of the absorbance, one with the cuvette placed in the normal spectrometer position, and the second with the cuvette placed inside the IS, provided enough information to separate the contributions from scattering and molecular absorption. Measurements were carried out with microspheres with different diameters. The data was fitted with a model consisting of the difference of two terms. The first term was the Lorenz-Mie (L-M) cross section which modeled the total absorbance due to scattering. The second term was the integral of the L-M differential cross section over the detector acceptance angle. The second term estimated the amount of forward scattered light that entered the detector. A wavelength dependent index of refraction was used in the model. The agreement between the model and the data was good between 300 nm and 800 nm. The fits provided values for the microsphere diameter, the concentration, and the wavelength dependent index of refraction. For wavelengths less than 300 nm, the scattering cross section had significant spectral structure which was inversely related to the molecular absorption. This work addresses the measurement and interpretation of the scattering cross section for wavelengths between 300 nm and 800 nm.

Comparing coherent and spontaneous Raman scattering under biological imaging conditions

We compare imaging based on coherent and spontaneous Raman scattering (SpRS) under conditions relevant for biological imaging. Using a broadband laser source, we perform spectral domain imaging of polystyrene beads using coherent Stokes Raman scattering and SpRS and find comparable signal levels. Short interaction lengths, low molecule number, and low incident power all reduce the advantages available with coherent Raman methods. We present calculations to support our measurements.

Excitation transport and trapping in a synthetic chlorophyllide substituted hemoglobin: orientation of the chlorophyll S1 transition dipole

Excitation transport in synthetic zinc chlorophyllide substituted hemoglobin has been observed by pico -second time-resolved fluorescence depolarization experiments. In this hybrid molecular system, two zinc chlorophyllide molecules are substituted into the beta-chains of hemoglobin, while deoxy hemes remain in the alpha-chains. The rate of excitation transfer between the two chlorophyllides is analyzed in terms of the distance and orientation dependences predicted by the F orster dipole-dipole theory. In this analysis, the beta-beta interchromophore geometry is assumed to be that of the deoxyhemoglobin crystal structure. When combined with steady-state fluorescence depolarization data of the complementary hybrid containing zinc chlorophyllide in the alpha-chains, these experiments provide the necessary information to determine the orientation of the S1 transition dipole moment in the zinc chlorophyllide molecule. We also find that the fluorescence lifetime of the zinc chlorophyllide is 1.42 ns when the heme is in the deoxy state but 3.75 ns when the heme is ligated to carbon monoxide. This is explained by irreversible excitation transfer from the S1 state of the zinc chlorophyllide to the lower energy excited states present in deoxy heme.