Fiber-based stray light suppression in spectroscopy using periodic shadowing.

Stray light is a known strong interference in spectroscopic measurements. Photons from high-intensity signals that are scattered inside the spectrometer, or photons that enter the detector through unintended ways, will be added to the spectrum as an interference signal. A general experimental solution to this problem is presented here by introducing a customized fiber for signal collection. The fiber-mount to the spectrometer consists of a periodically arranged fiber array that, combined with lock-in analysis of the data, is capable of suppressing stray light for improved spectroscopy. The method, which is referred to as fiber-based periodic shadowing, was applied to Raman spectroscopy in combustion. The fiber-based stray-light suppression method is implemented in an experimental setup with a high-power high-repetition-rate laser system used for Raman measurements in different room-temperature gas mixtures and a premixed flame. It is shown that the stray-light level is reduced by up to a factor of 80. Weak spectral lines can be distinguished, and therefore better molecular species identification, as well as concentration and temperature evaluation, were performed. The results show that the method is feasible and efficient in practical use and that it can be employed as a general tool for improving spectroscopic accuracy.

Improved temporal contrast of streak camera measurements with periodic shadowing.

Periodic shadowing, a concept used in spectroscopy for stray light reduction, has been implemented to improve the temporal contrast of streak camera imaging. The capabilities of this technique are first proven by imaging elastically scattered picosecond laser pulses and are further applied to fluorescence lifetime imaging, where more accurate descriptions of fluorescence decay curves were observed. This all-optical approach can be adapted to various streak camera imaging systems, resulting in a robust technique to minimize space-charge induced temporal dispersion in streak cameras while maintaining temporal coverage and spatial information.

Structural analysis of the anti-malaria active agent chloroquine under physiological conditions.

UV resonance Raman spectroscopy was applied for a selective enhancement of molecular vibrations of the important antimalarial chloroquine under physiological conditions. The resonance Raman spectra of chloroquine at pH values resembling the pH value of blood and the pH value of the acid food vacuole of plasmodium can unambiguously be distinguished via Raman resonantly enhanced mode at 721 cm(-1). These vibrations are assigned to -(CH2)n- rocking mode of the chloroquine side chain and are expected to be influenced by protonation of chloroquine. Furthermore, vibrations belonging to the quinoline ring (important for pi-pi-interactions to hemozoin) are resonantly enhanced and can be studied selectively. A convincing mode assignment was performed by means of DFT calculations. These calculations proved that the different protonation states of chloroquine remarkably influence various vibrational modes, the molecular geometry, and molecular orbitals. The presented results are of significant relevance for a Raman spectroscopical localization of chloroquine inside the acid food vacuole of plasmodium, the study of pi-pi-interactions of chloroquine to the biological target molecules hematin and hemozoin and the protonation state of chloroquine during this docking process. The protonation of the weak base chloroquine is considered to be crucial for an accumulation inside the acid food vacuole of plasmodium and an object for resistances against this drug.

Spectroscopic and computational studies on the coordination-driven self-assembly complexes (ZnL)2 and (NiL)2 [L= bis(2,4-dimethyldipyrrin-3-yl)methane].

FT-IR, FT-Raman and electronic absorption spectroscopies were utilized in conjunction with density functional theory (DFT) calculations to investigate the ground and excited states of self-assembled dinuclear dimeric helicates (ZnL)2 and (NiL)2 [L = bis(2,4-dimethyldipyrrin-3-yl)methane]. These studies afford a detailed description of the ground-state geometric and electronic structures of (ZnL)2 and (NiL)2 and provide a comparison with similar geometrical metal-porphyrins. The results demonstrate that enlarging the basis set used in the DFT calculations results in an obvious alteration of the calculated bond lengths but negligible alteration of the calculated bond angles. The predicted spectra are in good agreement with the experimental ones with the deviations generally less than 30 cm(-1). In comparison with vibrational spectra of metal-porphyrins, the breathing vibration of the pyrrole ring is shifted by over 100 cm(-1) toward higher wavenumber due to local conjugation of molecular geometry. Time-dependent density functional theory (TD-DFT) provides a good description of the excitation energy. Because of the break in symmetry, the absorption band (corresponding to the Q-band of porphyrin) of (ZnL)2 and (NiL)2 is no longer weak. Local conjugation makes the absorption wavelength of (NiL)2 and (ZnL)2 shift to the blue compared with those of NiP and ZnP.

Secondary structure of the third extracellular loop responsible for ligand selectivity of a mammalian gonadotropin-releasing hormone receptor.

The extracellular loop 3 (ECL3) of the mammalian gonadotropin-releasing hormone receptor (GnRH-R) contains an acidic amino acid (Glu(301) in the mouse GnRH-R) that confers agonist selectivity for Arg(8) in mammalian GnRH. It is proposed that a specific conformation of ECL3 is necessary to orientate the carboxyl side chain of the acidic residue for interaction with Arg(8) of GnRH, which is supported by decreased affinity for Arg(8) GnRH but not Gln(8) GnRH when an adjacent Pro is mutated to Ala. To probe the structural contribution of the loop domain to the proposed presentation of the carboxyl side chain, we synthesized a model peptide (CGPEMLNRVSEPGC) representing residues 293-302 of mouse ECL3, where Cys and Gly residues are added symmetrically at the N and C termini, respectively, allowing the introduction of a disulfide bridge to simulate the distances at which the ECL3 is tethered to the transmembrane domains 6 and 7 of the receptor. The ability of the ECL3 peptide to bind GnRH with low affinity was demonstrated by its inhibition of GnRH stimulation of inositol phosphate production in cells expressing the GnRH-R. The CD bands of the ECL3 peptides exhibited a superposition of predominantly unordered structure and partial contributions from beta-sheet structure. Likewise, the analysis of the amide I and amide III bands from micro-Raman and FT Raman experiments revealed mainly unordered conformations of the cyclic and of the linear peptide. NMR data demonstrated the presence of a beta-hairpin among an ensemble of largely disordered structures in the cyclic peptide. The location of the turn linking the two strands of the hairpin was assigned to the three central residues L(296), N(297), and R(298). A small population of structured species among an ensemble of predominantly random coil conformation suggests that the unliganded receptor represents a variety of structural conformers, some of which have the potential to make contacts with the ligand. We propose a mechanism of receptor activation whereby binding of the agonist to the inactive receptor state induces and stabilizes a particular structural state of the loop domain, leading to further conformational rearrangements across the transmembrane domain and signal propagating interaction with G proteins. Interaction of the Glu(301) of the receptor with Arg(8) of GnRH induces a folded configuration of the ligand. Our proposal thus suggests that conformational changes of both ligand and receptor result from this interaction.

Cytotoxic activity of Gd(III)- and Dy(III)-complexes.

The complexes of gadolinium(III) and dysprosium(III) were synthesized by reaction of the respective inorganic salts with 3,5-pyrazoledicarboxylic acid in amounts equal to metal to ligand molar ratio of 1 : 2. The structures of the final complexes were determined by means of spectral and elemental analyses. To help further the binding mode elucidation in the new Gd(III)- and Dy(III)-complexes of H(3)pdc, detailed vibrational analysis was performed on the basis of comparison of experimental vibrational spectra of the ligand and its Ln(III)-complexes using data theoretically predicted by us earlier, as well as data from the literature about related compounds. Significant differences in the IR and Raman spectra of the complexes were observed as compared to the spectra of the ligand. The ligand and the complexes were tested for their cytotoxic activities on the chronic myeloid leukemia-derived K-562, overexpressing the BCR-ABL fusion protein and the non-Hodgkin lymphoma-derived DOHH-2, characterized by a re-expression of the anti-apoptotic protein bcl-2 cell lines. The results obtained indicate that the tested compounds exerted a considerable cytotoxic activity upon the evaluated cell lines in a concentration-dependent manner, which enabled the construction of dose-response curves and the calculation of the corresponding IC(50) values. The inorganic salts exerted a very weak cytotoxic effect on these cells. This is in contrast to the lanthanide complexes, which exhibited potent cytotoxic activity, even more than the activity of cisplatin towards K-562 and DOHH-2 cell lines.

Experimental observation of different-order components of a vibrational wave packet in a bulk dielectric using high-order Raman scattering.

We use high-order Raman scattering in a bulk dielectric to characterize coherent dynamics with precision typical for gas phase experiments. The experimental pump-probe approach allows for the simultaneous observation and separation in space and time of the individual contributions of different-order Raman processes to a coherent wave packet without relying on phase-matching conditions and within the same experimental geometry. We propose a novel technique to discriminate between stimulated excitation of vibronic levels in the impulsive and intermediate excitation regimes, futhermore allowing us to distinguish between different pathways contributing to the same fifth-order Raman processes.

New lanthanum (III) complex--synthesis, characterization, and cytotoxic activity.

The complex of lanthanum (III) was synthesized reacting the respective inorganic salt with 5-aminoorotic acid in amounts equal to the metal:ligand molar ratio of 1:3. The complex was prepared by adding an aqueous solution of lanthanum (III) nitrate to an aqueous solution of the ligand, subsequently raising the pH of the mixture gradually to approx. 5.0 through addition of a dilute solution of sodium hydroxide. The structure of the final complex was determined by means of spectral data (IR, Raman,( 1)H-NMR) and elemental analysis. Significant differences in the IR spectrum of the complex were observed as compared to the spectrum of the ligand. A comparative analysis of the Raman spectrum of the complex with that of the free 5-aminoorotic acid allowed a straightforward assignment of the vibrations of the ligand groups involved in coordination. The ligand and the complex were tested for the cytotoxic activities on the chronic myeloid leukemia derived K-562, overexpressing the BCR-ABL fusion protein and the non-Hodgkin lymphoma derived DOHH-2, characterized by a re-expression of the anti-apoptotic protein bcl-2 cell lines. The results obtained indicate that the tested compounds exerted a considerable cytotoxic activity upon the evaluated cell lines in a concentration-dependent matter, which enabled the construction of dose-response curves and the calculation of the corresponding IC(50 )values. The inorganic salt exerted a very weak cytotoxic effect on these cells, which is in contrast to the lanthanum (III) complex.

In vivo localization and identification of the antiplasmodial alkaloid dioncophylline A in the tropical liana Triphyophyllum peltatum by a combination of fluorescence, near infrared Fourier transform Raman microscopy, and density functional theory calculations.

Near infrared Fourier transform (NIR FT) micro Raman spectroscopy in combination with density functional theory (DFT) calculations has been applied for an in vivo localization of the antiplasmodial naphthylisoquinoline alkaloid dioncophylline A (1) in the tropical liana Triphyophyllum peltatum. Fluorescence microscopy images suggest finding this active agent in 10 mum big inclusions located in the cortex of the stem or the beginning of the leaves. By means of spatially resolved FT Raman micro spectroscopy, we could detect dioncophylline A (1) in these inclusions. FT Raman spectroscopy is an extremely selective tool capable of differentiating between various structurally similar naphthylisoquinoline alkaloids. With the help of DFT calculations, we succeeded in assigning the differences found in the FT Raman spectra of the various naphthylisoquinolines to nuC=C vibrations of the naphthyl ring. The presented results are of relevance for the investigation and extraction of new antimalarial active agents.

The excited-state chemistry of protochlorophyllide a: a time-resolved fluorescence study.

The excited-state processes of protochlorophyllide a, the precursor of chlorophyll a in chlorophyll biosynthesis, are studied using picosecond time-resolved fluorescence spectroscopy. Following excitation into the Soret band, two distinct fluorescence components, with emission maxima at 640 and 647 nm, are observed. The 640 nm emitting component appears within the time resolution of the experiment and then decays with a time constant of 27 ps. In contrast, the 647 nm emitting component is built up with a 3.5 ps rise time and undergoes a subsequent decay with a time constant of 3.5 ns. The 3.5 ps rise kinetics are attributed to relaxations in the electronically excited state preceding the nanosecond fluorescence, which is ascribed to emission out of the thermally equilibrated S(1) state. The 27 ps fluorescence, which appears within the experimental response of the streak camera, is suggested to originate from a second minimum on the excited-state potential-energy surface. The population of the secondary excited state is suggested to reflect a very fast motion out of the Franck-Condon region along a reaction coordinate different from the one connecting the Franck-Condon region with the S(1) potential-energy minimum. The 27 ps-component is an emissive intermediate on the reactive excited-state pathway, as its decay yields the intermediate photoproduct, which has been identified previously (J. Phys. Chem. B 2006, 110, 4399-4406). No emission of the photoproduct is observed. The results of the time-resolved fluorescence study allow a detailed spectral characterization of the emission of the excited states in protochlorophyllide a, and the refinement of the kinetic model deduced from ultrafast absorption measurements.

Ultrafast excited-state excitation dynamics in a quasi-two-dimensional light-harvesting antenna based on ruthenium(II) and palladium(II) chromophores.

A detailed study on the excited-state-excitation migration taking place within the tetranuclear complex [{(tbbpy)(2)Ru(tmbi)}(2){Pd(allyl)}(2)](PF(6))(2) (tbbpy = 4,4'-di-tert-butyl-2,2'-bipyridine and tmbi = 5,6,5',6'-tetramethyl-2,2'-bibenzimidazolate) is presented. The charge transfer is initiated by the photoexcitation into the lowest metal-to-ligand charge-transfer (MLCT) band of one of the peripheral ruthenium(II) chromophores and terminates on the central structurally complex Pd(2) (II)(allyl)(2) subunit. Thus, the system under investigation can be thought of as a functional model for the photosynthesis reaction center in plants. The kinetic steps involved in the overall process are inferred from femtosecond time-resolved transient-grating kinetics recorded at spectral positions within the regions of ground-state bleach and transient absorption. The kinetics features a complex non-exponential time behavior and can be fitted to a bi-exponential rise (tau(1)> or =200 fs, tau(2) approximately 1.5 ps) and a mono- or bi-exponential decay, depending on the experimental situation. The data leads to the formulation of a model for the intramolecular excitation-hopping ascribing intersystem crossing and subsequent cooling as the two fastest observed processes. Following these initial steps, charge transfer from the ruthenium to the central complex Pd(2)(allyl)(2) moiety is observed with a characteristic time constant of 50 ps. A 220-ps component that is observed in the ground-state recovery only is attributed to excitation equilibration between the two identical Pd(allyl) chromophores.

Raman, surface enhanced Raman spectroscopy, and DFT calculations: a powerful approach for the identification and characterization of 5-fluorouracil anticarcinogenic drug species.

The normal Raman and SERS spectra of 5-fluorouracil (5-FU) in water solution and attached to a biological artificial model (a silver colloid) at different pH values were recorded and discussed. The DFT calculation results helped us to establish for the first time the most stable resonance structure for each of the tautomeric forms (i.e., two enol and two enolate forms) and to interpret the Raman and SERS spectra. At alkaline pH, both deprotonated forms of 5-FU were found to be present in solution and to adsorb on the Ag surface in a perpendicular orientation or an orientation not significantly tilted from the surface normal. The N3-deprotonated form seems to be the dominant tautomer in the adsorbed state, more probably attached through the O7 atom. At acid pH values, the N3-deprotonated form was again found to be the mainly chemisorbed species adopting a similar orientation. The combination of these two approaches (i.e., the theoretical and experimental one) proved to be a viable candidate for inclusion in a rapid, sensitive biological method of detecting and studying such essential anticarcinogenic species or biological threats in different conditions.

DFT/TDDFT studies of the geometry, electronic structure and spectra of (12S)-1,4,7,10-tetraazadicyclo[10,3,0]-pentadecane-3,11-dione and its derivatives.

The FT-Raman and UV-visible spectra of (12S)-1,4,7,10-tetraazadicyclo[10,3,0]-pentadecane-3,11-dione and its derivatives were obtained and discussed. The harmonic vibrational wavenumbers and the corresponding Raman scattering activities in their electronic ground-states were calculated at the DFT-B3LYP/6-31G(d) level of theory. The calculated wavenumbers were then scaled and compared with the experimental values. The 7-(2,4-dinitrophenyl)-(12S)-1,4,7,10-tetrazadicyclo[10,3,0]-pentadecane-3,11-dione derivative has mainly an amide (II) character, while the others have an amide (I) character. Moreover, the different substituents do not cause a significant shift of the vibrational mode of the macrocyclic plane. The electronic vertical excitation energy and the oscillator strength were determined with the help of TDDFT calculations and by employing pure (BLYP) and hybrid (B3LYP, B3P86, and mPW1PW91) functionals together with the 6-31G(d) basis set. The BLYP functional reproduces the UV-vis absorption spectra better than the B3LYP, B3P86, or mPW1PW91 hybrid functionals. A dimolecular model, which considers hydrogen-bonded structures, proved that strong inter- and intramolecular hydrogen bonds are present in these compounds. Due to the transannular effect, the UV-vis absorption spectrum of macrocyclic dioxotetraamines is completely different from that of single amide compounds.

Visible and UV coherent Raman spectroscopy of dipicolinic acid.

We use time-resolved coherent Raman spectroscopy to obtain molecule-specific signals from dipicolinic acid (DPA), which is a marker molecule for bacterial spores. We use femtosecond laser pulses in both visible and UV spectral regions and compare experimental results with theoretical predictions. By exciting vibrational coherence on more than one mode simultaneously, we observe a quantum beat signal that can be used to extract the parameters of molecular motion in DPA. The signal is enhanced when an UV probe pulse is used, because its frequency is near-resonant to the first excited electronic state of the molecule. The capability for unambiguous identification of DPA molecules will lead to a technique for real-time detection of spores.

Quantitative analysis of serum and serum ultrafiltrate by means of Raman spectroscopy.

The fast and reliable determination of concentrations of blood, plasma or serum constituents is a major requirement in clinical chemistry. We explored Raman spectroscopy as a reagent-free tool for predicting the concentrations of different parameters in serum and serum ultrafiltrate. In an investigation using samples from 247 blood donors (which we believe to be the largest study on Raman spectroscopy of serum so far) the concentrations of glucose, triglycerides, urea, total protein, cholesterol, high density lipoprotein, low density lipoprotein and uric acid were determined with an accuracy within the clinically interesting range. After training a multivariate algorithm for data analysis, using 148 samples, concentrations were predicted blindly for the remaining 99 serum samples based solely on the Raman spectra. Relative errors of prediction around 12% were obtained. Moreover, to the best of our knowledge, differentiation between HDL and LDL cholesterol as well as the quantification of uric acid was for the first time successfully accomplished for serum-based Raman spectroscopy. Finally, we showed that ultrafiltration can efficiently reduce fluorescent light background to improve prediction accuracy such that the relative coefficient of variation was reduced for glucose and urea in ultrafiltrate by more than a factor of 2 when compared to serum.

Femtosecond time-resolved spectroscopy of elementary molecular dynamics.

Femtosecond time-resolved coherent anti-Stokes Raman spectroscopy (CARS) is applied in order to prepare and monitor laser-induced vibrational coherences (wave packets) of different samples mainly in its electronic ground state but also in excited states. The time evolution of these wave packets gives information on the dynamics of molecular vibrations. In a first example the femtosecond (fs) CARS transients of iodine are investigated. By changing the relative delay between the applied laser pulses of this non-degenerated four-wave mixing technique, both the wavepacket motion on the electronically excited and the ground states can be detected as oscillations in the coherent anti-Stokes signal. Second we report on selective excitation of the vibrational modes in the electronic ground state of polymers of diacetylene by means of a femtosecond time-resolved CARS scheme. This selectivity is achieved by varying the phase shape (chirp) and the relative delay between the exciting laser pulses.

Population dynamics in vibrational modes during non-Born-Oppenheimer processes: CARS spectroscopy used as a mode-selective filter.

The coupling of specific nuclear and electronic degrees of freedom of a molecular system during non-radiative electronic transitions plays a central role in photochemistry and photobiology. This breakdown of the Born-Oppenheimer approximation during processes such as internal conversion determines the mechanism and product distribution of photochemical reactions and is responsible for the high efficiency of photobiological processes. In order to explore this phenomena in beta-carotene, a molecule that plays a primary role as an auxiliary light-harvesting pigment in photosynthesis, a spectroscopic method was employed that allows for the individual vibrational modes to be monitored selectively within the dynamics of an internal conversion process. This spectroscopic technique employs an initial pump laser to excite the molecule into an excited electronic state and resolves the subsequent relaxation process by interrogating the system with a time-delayed, coherent anti-Stokes Raman process (CARS), which acts as a mode-selective filter for observing the population flow within specific vibrational modes with a time resolution in the femtosecond regime.

The excited-state dynamics of phycocyanobilin in dependence on the excitation wavelength.

The primary light-induced processes of phycocyanobilin were studied by means of transient-grating spectroscopy, whereby the excitation wavelength was varied over the spectral region of the ground-state absorption. On the basis of the results obtained, both the rate of the photoreaction in phycocyanobilin and the ratio of the decay of different excited-state species via two decay channels depend on the excitation wavelength. Furthermore, the formation of the photoreaction product is also dependent on the pump color. These data support a recently established model for the primary photoprocesses in phycocyanobilin. In addition, phycocyanobilin protonated at the basic pyrrolenine-type nitrogen atom was included in the transient absorption study. The decay behavior was found to be almost unchanged when compared with the unprotonated form, and this suggests that protonation of the tetrapyrrole ring structure has no effect on the overall photochemistry.