Absolute Spectrofluorometry

Laser-Induced Fluorescence (LIF) Spectroscopy of Trapped Molecular Ions in the Gas Phase

This review focuses on the laser-induced fluorescence (LIF) spectroscopy of trapped gas-phase molecular ions, a developing field of research. Following a brief description of the theory and experimental approaches employed in general for fluorescence spectroscopy, the review summarizes the current state-of-the-art intrinsic fluorescence measurement techniques employed for gas-phase ions. Whereas the LIF spectroscopy of condensed matter systems is a well-developed area of research, the instrumentation used for such studies is not directly applicable to gas-phase ions. However, some measurement schemes employed in condensed-phase experiments could be highly beneficial for gas-phase investigations. We have included a brief discussion on some of these techniques as well. Quadrupole ion traps are commonly used for spatial confinement of ions in the ion-trap-based LIF. One of the main challenges involved in such experiments is the poor signal-to-noise ratio (SNR) arising due to weak gas-phase fluorescence emission, high background noise, and small solid angle for the fluorescence collection optics. The experimental approaches based on the integrated high-finesse optical cavities employed for the condensed-phase measurements provide a better (typically an order of magnitude more) SNR in the detected fluorescence than the single-pass detection schemes. Another key to improving the SNR is to exploit the maximum solid angle of light collection by choosing high numerical aperture (NA) collection optics. A combination of these two approaches integrated with ion traps could transmogrify this field, allowing one to study even weak fluorescence emission from gas-phase molecular ions. The review concludes by discussing the scope of the advances in the LIF instrumentation for detailed spectral characterization of fluorophores of weak gas-phase fluorescence emission, considering fluorescein as one example.

Exploiting the distinctive properties of the bacterial and human MutS homolog sliding clamps on mismatched DNA

MutS homologs (MSHs) are highly conserved core components of DNA mismatch repair. Mismatch recognition provokes ATP-binding by MSH proteins that drives a conformational transition from a short-lived lesion-searching clamp to an extremely stable sliding clamp on the DNA. Here, we have expanded on previous bulk biochemical studies to examine the stability, lifetime, and kinetics of bacterial and human MSH sliding clamps on mismatched DNA using surface plasmon resonance and single-molecule analysis of fluorescently labeled proteins. We found that ATP-bound MSH complexes bound to blocked-end or very long mismatched DNAs were extremely stable over a range of ionic conditions. These observations underpinned the development of a high-throughput Förster resonance energy transfer system that specifically detects the formation of MSH sliding clamps on mismatched DNA. The Förster resonance energy transfer system is capable of distinguishing between HsMSH2-HsMSH3 and HsMSH2-HsMSH6 and appears suitable for chemical inhibitor screens. Taken together, our results provide additional insight into MSH sliding clamps as well as methods to distinguish their functions in mismatch repair.

Recalling the effect of fluorescence anisotropy on the measurement of quantum yields

We present a quantitative analysis of the deviations introduced by the anisotropy of the fluorescence on the measurement of the quantum yield of emission. Errors of up to 40% can be encountered depending on the characteristics of both sample and apparatus. Additionally, we have analyzed the effect of anisotropy on the study of fluorescence quenching in Stern-Volmer experiments, and on the reconstruction of time-resolved emission spectra. We conclude that the use of polarizers is recommended provided they are well characterized.

Odorant-binding protein from the stable fly (Stomoxys calcitrans) has a high-histidine N-terminal extension that binds transition metals

The role of odorant- and pheromone-binding proteins (OBPs) in olfactory function is not fully understood. We found an OBP sequence from the stable fly, Stomoxys calcitrans, ScalOBP60, that has a 25 amino acid N-terminal extension with a high content of histidine and acidic amino acids, suggesting a possible metal binding activity. A search of public databases revealed a large number of other fly OBPs with histidine-rich N-terminal extensions, as well as beetle, wasp and ant OBPs with histidine-rich C-terminal extensions. We recombinantly expressed ScalOBP60, as well as a truncated sequence which lacks the histidine-rich N-terminal region, tScalOBP60. Using fluorescence quenching and electrospray quadrupole time-of-flight mass spectrometry (ESI-QTOF), we detected two different types of metal-binding sites. Divalent copper, nickel and zinc bind to the N-terminal histidine-rich region, and divalent copper binds to an internal sequence position. Comparison of the ESI-QTOF spectra of ScalOBP60 and tScalOBP60 showed that the histidine-rich sequence is structurally disordered, but it becomes more ordered in the presence of divalent metal. When copper is bound to the internal site, binding of a hydrophobic ligand to ScalOBP60 is inhibited. The internal and N-terminal metal sites interact allosterically, possibly through a conformational equilibrium, suggesting a mechanism for metal regulation of ligand binding to ScalOBP60. Based on our studies of ScalOBP60, we propose several possible olfactory and non-olfactory functions for this OBP.

Complexation of 1,3-dihetaryl-5-phenyl-2-pyrazoline Derivatives with Polyvalent Metal Ions: Quantum Chemical Modeling and Experimental Investigation

1,3,5-Triaryl-2-pyrazoline derivatives with a pyridine ring in position 1 and 2-benzimidazolyl or 2-benzothiazolyl bicycles in position 3 were synthesized. Spectral properties in solvents of similar polarity, i.e. aprotic acetonitrile and in protic methanol, were studied, complexation with cadmium and mercury ions in acetonitrile was elucidated as well. Quantum-chemical modeling with application of the elements of Bader's atoms-in-molecules (AIM) theory of the title molecules conformational structure and 1:1 stoichiometry complexes formed with polyvalent metals of various nature (Mg, Zn, Cd, Pb, Hg, Ba) was conducted. The principal possibility of “nitrogen-sulfur” switching of the metal ions binding sites for the benzothiazole derivative was revealed, and makes possible to classify this compound as “smart ligand”.

Fluorescence Anisotropy Detection of Barrier Crossing and Ultrafast Conformational Dynamics in the S2 State of β-Carotene

Carotenoids are usually only weakly fluorescent despite being very strong absorbers in the mid-visible region because their first two excited singlet states, S₁ and S₂, have very short lifetimes. To probe the structural mechanisms that promote the nonradiative decay of the S₂ state to the S₁ state, we have carried out a series of fluorescence lineshape and anisotropy measurements with a prototype carotenoid, β-carotene, in four aprotic solvents. The anisotropy values observed in the fluorescence emission bands originating from the S₂ and S₁ states reveal that the large internal rotations of the emission transition dipole moment, as much as 50° relative to that of the absorption transition dipole moment, are initiated during ultrafast evolution on the S₂ state potential energy surface and persist upon nonradiative decay to the S₁ state. Electronic structure calculations of the orientation of the transition dipole moment account for the anisotropy results in terms of torsional and pyramidal distortions near the center of the isoprenoid backbone. The excitation wavelength dependence of the fluorescence anisotropy indicates that these out-of-plane conformational motions are initiated by passage over a low-activation energy barrier from the Franck-Condon S₂ structure. This conclusion is consistent with detection over the 80-200 K range of a broad, red-shifted fluorescence band from a dynamic intermediate evolving on a steep gradient of the S₂ state potential energy surface after crossing the activation barrier. The temperature dependence of the oscillator strength and anisotropy indicate that nonadiabatic passage from S₂ through a conical intersection seam to S₁ is promoted by the out-of-plane motions of the isoprenoid backbone with strong hindrance by solvent friction.

Absolute and Relative Methods for Fluorescence Quantum Yield Evaluation of Quantum Dots

Optical spectroscopy techniques are crucial for the evaluation and use of quantum dots (QDs) in life and materials science. In that context, the fluorescence quantum yield (Φ_f) is an essential parameter in the assessment of the luminescent features of QDs. The fluorescence quantum yield can be defined as the ratio of the number of emitted photons to the number of absorbed photons by a luminescent material. In this chapter, we describe absolute and relative methods to measure the fluorescence quantum yield of QDs in solution phase. The advantages and limitations of the techniques are reviewed.

Extinction spectra of suspensions of microspheres: determination of the spectral refractive index and particle size distribution with nanometer accuracy

A method is presented to infer simultaneously the wavelength-dependent real refractive index (RI) of the material of microspheres and their size distribution from extinction measurements of particle suspensions. To derive the averaged spectral optical extinction cross section of the microspheres from such ensemble measurements, we determined the particle concentration by flow cytometry to an accuracy of typically 2% and adjusted the particle concentration to ensure that perturbations due to multiple scattering are negligible. For analysis of the extinction spectra, we employ Mie theory, a series-expansion representation of the refractive index and nonlinear numerical optimization. In contrast to other approaches, our method offers the advantage to simultaneously determine size, size distribution, and spectral refractive index of ensembles of microparticles including uncertainty estimation.

Determination of the photoluminescence quantum yield of dilute dye solutions (IUPAC Technical Report)

Procedures for the determination of photoluminescence quantum yields with optical methods are addressed, and challenges associated with these measurements are discussed. Special emphasis is dedicated to relative measurements of fluorescent (i.e., short excited-state lifetime), transparent, dilute dye solutions in conventional cuvettes in a 0°/90° measurement geometry. Recommendations on the selection of suitable quantum yield standards are presented, and requirements for the documentation of photoluminescence quantum yields are derived.

1,4-bis-(3-hydroxy-4-oxo-4H-chromen-2-yl)-benzene (bis-flavonol): synthesis, spectral properties and principle possibility of the excited state double proton transfer reaction

Synthesis and systematic investigation of the spectral-luminescent properties of “bis-flavonol” {1,4-bis-(3-hydroxy-4-oxo-4H-chromen-2-yl)-benzene} were performed. Hypothetical possibility for the double excited-state proton transfer reaction in bis-flavonol is discussed based on both quantum-chemical modeling and experimental data. Consecutive S1*-state transfer of the two protons of the title molecule is shown to be energetically unfavorable, however, still preserving a possibility for the concerted double proton transfer in the excited dienol form.

2-(benzimidazol-2-yl)-3-hydroxychromone derivatives: spectroscopic properties and a possibile alternative intramolecular proton phototransfer

Three 2-(benzimidazol-2-yl)-3-hydroxychromone derivatives were synthesized. Their spectroscopic and fluorescent properties, due to excited state intramolecular proton transfer (ESIPT) from OH to carbonyl, were studied. Theoretical possibility of an alternative intramolecular H-bonding and experimental evidence for such behavior are discussed.

Qualification of a fluorescence spectrometer for measuring true fluorescence spectra

New analytical methods using fluorescence detection are becoming increasingly quantitative and require easy-to-use material standards for fluorometer qualification and method validation. NIST is responding to this need by developing and producing such standards. Reported here is the first step in this process, which is to qualify a research-grade fluorescence spectrometer for measuring true fluorescence spectra of reference material candidates. "True" spectra are defined here as those with fluorescence intensity, either relative or absolute as required, and wavelength both being reported with high accuracy and known precision, after wavelength has been calibrated and corrections for excitation intensity and detection system response have been applied. The uncertainties determined in relative and absolute intensity-corrected fluorescence spectra using both calibrated source (CS)- and calibrated detector (CD)-based methods were compared. The CS-based method gave uncertainties, typically about +/-5% for relative spectral correction, that were about half that of the CD-based method for determining both relative and absolute spectral correction factors. Absolute spectral correction factors can be determined using either method without knowing the optical geometry of the instrument. The absolute spectral correction factors were found to have much larger uncertainties than the corresponding relative correction factors with uncertainties for the CS-based method of +/-10% to +/-15% being typical and +/-20% or more not being uncommon, particularly for excitation and emission wavelengths below 400 nm. Uncertainties arising from detection system nonlinearity and instrument polarization ratios were also explored.

Role of Monovalent Counterions in the Ultrafast Dynamics of DNA

This paper examines the contribution of counterion motion to the electric-field dynamics in the interior of DNA. The electric field is measured by a coumarin fluorophore that is synthetically incorporated into an oligonucleotide, where it replaces a native base pair. The DNA is a 17-base-pair oligomer with no A- or G-tracts. Time-resolved Stokes-shift measurements on the coumarin are made from 40 ps to 40 ns with each of the alkali ions and or one of several tetraalkylammonium ions as the DNA counterion. With the possible exception of rubidium, there are no indications of site-specific binding of the counterions. For sodium and other ions with a smaller hydrodynamic radius, the dynamics are identical and are fit to a power law. For larger ions, there is a progressive increase in the rate of shifting after 1 ns. This effect correlates with the hydrodynamic radius of the counterion. The lack of change in the spectral shape of the emission shows that neither the broadly distributed power-law relaxation nor the extra nanosecond dynamics are due to heterogeneity in the relaxation rates of different helices.

Determination of absolute chemiluminescence quantum yields for reactions of bis-(pentachlorophenyl) oxalate, hydrogen peroxide and fluorescent compounds

Absolute chemiluminescence quantum yields (phi CL) for reactions of bis-(pentachlorophenyl) oxalate (PCPO), hydrogen peroxide (H2O2) and 9:10 diphenyl anthracene (DPA) have been determined. A fully corrected chemiluminescence monitoring spectrometer was calibrated for spectral sensitivity using the chemiluminescence of the bis-(pentachlorophenyl) oxalate system as a liquid light source, the total photon output of which had previously been determined by chemical actinometry. At high (PCPO)/(H2O2) ratios phi CL was found to be independent of PCPO and H2O2 concentrations.

A method for measuring membrane microviscosity using pyrene excimer formation. Application to human erythrocyte ghosts

In order to determine the microviscosity of human erythrocyte membrane suspensions, a method has been developed which is based on pyrene excimer formation. First, measurements of partitioning of pyrene into membranes, in conjunction with known values for the volume of the lipid compartment of erythrocyte ghosts are used to determine the concentration of pyrene in the membrane lipid. Secondly, reported measurements of the diffusion constants of aromatic hydrocarbons similar in structure to pyrene, are used to derive an empirical equation relating solvent viscosity and the diffusion constant of pyrene. Then, measurements of pyrene excimer formation in a series of solvents ranging up to several poise in viscosity are used to determine that the interaction diameter of the excimer formation reaction is 3 +/- 1 A. Finally all these data are brought together in order to conclude that the viscosity of the lipid in the human erythrocyte ghost is 8.0, 4.0 and 1.6 P at 10, 25 and 40 degrees C, respectively.

Quantum counter photodetectors: a new design

A new design for quantum counter cells is described that uses total internal reflection to minimize depth-of-penetration and polarization effects. This new cell is compared to a standard 1-cm thick quantum counter cylindrical cell. Solutions of 5 g/liter of rhodamine B chloride in ethylene glycol were used in both cells. The fluorescence emission from the cell was found to be significantly less polarized and also less dependent on excitation wavelength.