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This paper presents the green synthesis of silver nanoparticles (AgNPs) using orange (Citrus sinensis) peel extract. The effects of different factors such as silver ion concentration, reaction time, temperature, pH, and extract quantity on the AgNPs synthesis were studied, enabling us to determine optimum synthesis conditions. We characterized the AgNPs with different techniques: UV–Visible Spectroscopy, Field Emission Scanning Electron Microscopy (FESEM), FTIR, and XRD. The AgNPs showed yellowish brown to golden brown colors and a surface plasmon resonance (SPR) absorption band around a wavelength of 420 nm. FESEM images showed polydisperse AgNPs having an average size of about 55 nm. The XRD profile of the synthesized nanoparticles showed peaks that are characteristic of silver while the FTIR spectrum highlighted the functional groups associated with reducing silver ions and stabilizing the AgNPs. With the selected optimum conditions, the AgNPs were formed in less than 1 min. This is the fastest reaction time so far reported and is significantly shorter than in earlier reports. The AgNPs colloid solution was applied as nanosensor in the visual colorimetric detection of mercury(II) ions in water. The golden brown AgNPs colloid solution turned colorless and the characteristic SPR absorption band disappeared when mercury(II) ions were added to the solution. While the AgNPs show good sensitivity and selectivity for the colorimetric detection of mercury(II) ions with a detection limit of 1.24 × 10−6 mol/L (0.25 ppm), we also demonstrated the suitability of the method for detecting mercury(II) ions in drinking water.

The fluorescence signal levels produced by smart probes (SPs) largely depend on the type of fluorophore label used and the quenching efficiency of the quencher. However, there has been little emphasis on the effects of terminal location of the fluorophore and the modifications used to attach the fluorophore to the oligonucleotide chain. To this end, we have conducted a comparative study of the fluorescent signaling characteristics of six SPs consisting of three fluorophores: 6-FAM, ATTO488 and TAMRA, each of which was attached to either the 3′ end or the 5′ end of the oligonucleotide probe to make two SPs each. In each case, the fluorophore was paired with guanosine quenchers and we determined the fluorescence signaling characteristic of each SP by hybridizing it with the complementary target and measuring the fluorescence signal produced. Our results showed that the melting temperatures (Tm’s) of each two SPs consisting of the same fluorophore were different before hybridization with targets but were similar once hybridized. We also found that each two SPs made of the same fluorophore gave different fluorescence signal levels. Our data also revealed a subtle correlation between Tm differences and fluorescence intensity differences for each pair of SPs consisting of the same fluorophore. We interpret the observed differences in Tm’s and fluorescence signals in terms of possible structural differences in the linker moieties used for coupling the fluorophores to the 3′ and 5′ ends as well as possible differences in the efficiency of coupling the fluorophore during the probe synthesis.

Zinc plays a key role in many physiological processes and has implications for the environment. Consequently, detection of chelatable zinc ion (Zn2+ ) has attracted widespread interest from the research community. Lanthanide-based luminescent probes offer particular advantages, such as high water solubility, long luminescence lifetimes and a large Stokes' shift, over common organic dye-based fluorescent sensors. Here, we report the synthesis of terbium and europium complex-based probes, Tb-1 and Eu-1, for sensitive and selective detection of Zn2+ in water. These probes featured the incorporation of bis(2-pyridylmethyl)]amine (DPA) receptor for Zn2+ chelation and the 1,4,7-tris(carboxymethyl)-1,4,7,10-tetraazacyclododecane (DO3A) ring to chelate lanthanide (Ln3+ ). Tb-1 and Eu-1 displayed high selectivity for Zn2+ ions over a wide range of competing ions, with limits of detection of 0.50 ± 0.1 μM and 1.5 ± 0.01 μM, respectively. Density functional theory simulations were in good agreement with experimental observations, displaying high Zn2+ selectivity compared with most competing ions. In the competing ions experiments, the luminescence response of Tb-1 and Eu-1 was moderately quenched by some ions such as Cu2+ , this was linked to the comparable binding abilities of these ions for the receptor of the probe.

We report a new assay system for the detection of miR-21 in cancer cells. The new assay works at room temperature and it does not involve enzymatic amplification. It consists a hairpin smart probe, designed to specifically recognize miR-21 target sequence. We tested the performance and sequence recognition capability of the smart probe to confirm desired specifications. We used the smart probe for the sequence-specific recognition of synthetic miR-21 oligonucleotides as well as mismatch sequences and we found that the probe recognizes the target sequence-specifically, while discriminating against mismatched sequences. We determined the limit of detection and limit of quantitation for the miR-21 oligonucleotides to be 1.72 nM and 5.78 nM, respectively, while the sensitivity is 6.90 × 10

A series of known Pb(II) metal–organic frameworks (MOFs) have been synthesized from the reaction of PbX2 (X = Cl, NO3 and OAc) with bpy (where bpy = 4,4-bipyridine) using three synthetic methods, namely solvothermal, mechanochemical and liquid-assisted grinding (LAG). The synthesized compounds were characterized with powder X-ray diffraction (PXRD) patterns and matched with calculated X-ray diffraction patterns of reported crystal structures of Pb(II)-based MOFs. Interestingly, most of the compounds can be easily prepared by solvent-free methods either mechanochemically or by LAG methods. Finally, the successfully synthesized MOFs were subjected to photoluminescence study. Solid-state photoluminescence of the selected MOFs has been studied by suspending the MOFs particles in various solvents. Although they are not soluble in the solvents used, the MOFs show a fair amount of solvent-dependent emission quenching that roughly correlate with solvent polarity. With further exploration and investigations, the observed solvatochromic emission behavior of these compounds may find importance in solvent sensing applications.

A sensitive hairpin smart probe (SP) has been developed and tested for its sequence-specificity and sensitivity for detecting microRNAs (miRNAs). The loop sequence of this SP is perfectly complementary to microRNA-21 (miR-21) sequence. This miRNA regulates certain biological processes and has been implicated in certain forms of cancer. The stem of the new SP consists of a fluorophore on one end and multiple guanine bases on the opposing end are used as quenchers. The fluorescence of the SP is significantly quenched by the guanine bases at room temperature and in the absence of the miR-21 target. The presence of miR-21 switches on the fluorescence due to spontaneous hybridization of the SP with this target, which also forces the stem hybrid of the SP apart. This new SP successfully discriminated between the perfect miR-21 target and two closely similar single-base mismatch sequences. When the SP was incubated with the miR-21 at 37 ℃, the hybridization kinetics increased seven times, compared to room temperature hybridization. Overall, this new SP shows good detection sensitivity and gives a limit of detection and limit of quantitation of 14.0 nM and 46.7 nM, respectively. This detection platform represents a simple, fast, mix-and-read homogeneous assay for sequence-specific detection of miR-21, and it can be adapted for other related diagnostic applications.

Here, ketones bearing two bulky substituents, named bulky-bulky ketones, were successfully reduced to their corresponding optically-enriched alcohols using various mutants of Thermoanaerobacter pseudoethanolicus secondary alcohol dehydrogenase (TeSADH). Substituted 2-tetralones in particular were reduced to 2-tetralols with high conversion and high enantioselectivity. The pharmacological importance of substituted 2-tetralols as key drug-building blocks makes our biocatalytic reduction method a highly essential tool. We showed that changing the position of the substituent on the aromatic ring of 2-tetralones impacted their binding affinity and the reaction maximum catalytic rate. Docking studies with several TeSADH mutants explained how the position of the substituent on the tetralone influences the binding orientation of substituted 2-tetralones and their reaction stereoselectivity.

A one-dimensional hydrogen-bonded triple-stranded ladder coordination polymer [Cd(bpe)1.5(NO3)2(H2O)] (1) (where bpe = trans-1,2-bis(4-pyridyl)ethylene) containing three parallel C═C double bonds was synthesized. This compound undergoes photochemical [2 + 2] cycloaddition and produces rctt-tetrakis(4-pyridyl)cyclobutane (rctt-tpcb) in up to 67% yield via Single-Crystal-to-Single-Crystal (SCSC) transformation. Triple-stranded ladder-like structures have never before displayed such a kind of SCSC transformation. Furthermore, photoirradiation of ground 1 produces rctt-tpcb in up to 100% yield in the solid state. On the basis of the alignment of three C═C olefinic bonds of bpe ligands in parallel, only two out of the three aligned bpe are expected to undergo [2 + 2] photodimerization. However, the quantitative yield from the solid-state photochemical [2 + 2] cycloaddition reaction has been achieved via grinding of crystals of 1 to a powder. The effects of grinding on photoreactivity of 1 were thoroughly studied using 1H NMR spectroscopy, thermogravimetric analysis (TGA), and Raman spectroscopy. These studies indicate that the molecular movements of the hydrogen-bonded ladders are reinforced due to the loss of coordinated water molecules and the further crystal repacking via bond-breaking/forming of the hydrogen-bonded assemblies during mechanical grinding. The 100% photodimerization of ground 1 shows that the grinding accelerates internal molecular motions of ladder structures within the crystals lattice. The solid-state photoluminescence of 1, before and after UV irradiation, was investigated at room temperature, both indicative of interesting luminescent properties.

A fluorescent smart probe (SP) was used to detect a mixed-base ribonucleic acids sequence. While the SP presents excellent sensitivity for the target, it gives subtle discrimination between the perfect target sequence and several mismatch sequences. Its sequence-specificity for the target was greatly enhanced by using nucleic acid blockers (NABs), which are unlabeled, non-fluorescent hairpin oligonucleotides that are perfectly complementary to those mismatch sequences. This approach is simple, feasible at room temperature, requires no amplification enzymes, and it is suitable for applications requiring routine nucleic acids sequence detection and quantification methods such as genetic testing and biomedical diagnostics.

This study examined the fluorescence emission properties of bulk 4-Cyano-4′-pentylbiphenyl (5CB) and 4-Cyano-4′-hexylbiphenyl (6CB) and their variation with temperature. The temperature-dependent fluorescence emission spectra of these two thermotropic liquid crystals (LCs) were measured between 4 and 80 °C and the changes in fluorescence intensities and wavelengths were monitored. The fluorescence spectra of both liquid crystals are characterized by emissions of two structurally different excimers centred around 380–386 nm and 412 nm. The results show that the specific changes in intensity and wavelength differ between the two LCs and suggest presence of two different molecular conformers as the temperature changes. During nematic-isotropic phase transition, the fluorescence spectra show significant intensity increase, which can be exploited for sensitive analytical applications. The crystalline-nematic phase transition of 5CB was found to be 22 °C and the nematic-isotropic liquid transition occurred at 35.5 °C. On the other hand, the crystalline-nematic phase transition of 6CB occurred at 16 °C, while its nematic-isotropic phase transition was observed at 29 °C. The dramatic temperature-dependent phase changes observed in the bulk LCs were completely absent in a solution of 6CB. The observed temperature-dependent spectral evolutions are discussed in the context of possible excimer conformations that exist in different mesophases of the two liquid crystals as well as change in the angle between the two benzene rings, which can contribute to excimer behaviour during phase transitions.

A new macro-Raman system equipped with a motorized translational sample stage and low-frequency shift capabilities was developed for bulk composition and homogeneity analysis of multi-component pharmaceutical powders. Different sampling methods including single spot and scanning measurement were compared. It was found that increasing sample volumes significantly improved the precision of quantitative composition analysis, especially for poorly mixed powders. The multi-pass cavity of the macro-Raman system increased effective sample volumes by 20 times from the sample volume defined by the collection optics, i.e., from 0.02μL to about 0.4μL. A stochastic model simulating the random sampling process of polydisperse microparticles was used to predict the sampling errors for a specific sample volume. Comparison of fluticasone propionate mass fractions of the commercial products Flixotide® 250 and Seretide® 500 simulated for different sampling volumes with experimentally measured compositions verified that the effective sample volume of a single point macro-Raman measurement in the multi-pass cavity of this instrument was between 0.3μL and 0.5μL. The macro-Raman system was also successfully used for blend uniformity analysis. It was concluded that demixing occurred in the binary mixture of l-leucine and d-mannitol from the observation that the sampling errors indicated by the standard deviations of measured leucine mass fractions increased during mixing, and the standard deviation values were all larger than the theoretical lower limit determined by the simulation. Since sample volume was shown to have a significant impact on measured homogeneity characteristics, it was concluded that powder homogeneity analysis results, i.e., the mean of individual test results and absolute and relative standard deviations, must be presented together with the effective sample volumes of the applied testing techniques for any measurement of powder homogeneity to be fully meaningful.

A study was conducted to demonstrate ultraviolet resonance Raman (UVRR) investigations of peptide and protein structure and dynamics. The tuning of the excitation wavelengths allowed the probing of different chromophoric segments of a macromolecule. Another advantage of deep UV Raman measurements was that there was no interference from molecular relaxed fluorescence, as those chromophores that had their first transition below 260 nm were highly flexible and possessed small fluorescence quantum yields. UVRR was also used in pump-probe measurements to give kinetic information on fast biological processes. It was a powerful technique for studying static protein structure and for studying protein dynamics, such as in protein folding. The rapid development of UVRR was aided by the latest advancements in lasers, optics, and detectors.

UV resonance Raman spectroscopy (UVRR) is a powerful method that has the requisite selectivity and sensitivity to incisively monitor biomolecular structure and dynamics in solution. In this perspective, we highlight applications of UVRR for studying peptide and protein structure and the dynamics of protein and peptide folding. UVRR spectral monitors of protein secondary structure, such as the Amide III(3) band and the C(α)-H band frequencies and intensities can be used to determine Ramachandran Ψ angle distributions for peptide bonds. These incisive, quantitative glimpses into conformation can be combined with kinetic T-jump methodologies to monitor the dynamics of biomolecular conformational transitions. The resulting UVRR structural insight is impressive in that it allows differentiation of, for example, different α-helix-like states that enable differentiating π- and 3(10)- states from pure α-helices. These approaches can be used to determine the Gibbs free energy landscape of individual peptide bonds along the most important protein (un)folding coordinate. Future work will find spectral monitors that probe peptide bond activation barriers that control protein (un)folding mechanisms. In addition, UVRR studies of sidechain vibrations will probe the role of side chains in determining protein secondary, tertiary and quaternary structures.

Current techniques being used for sunscreen analysis are incapable of direct determination of the active ingredients in sunscreen formulations. Therefore, the development of methodologies for rapid in situ analysis of sunscreens is desirable. This paper describes the application of ultraviolet resonance Raman spectroscopy (UVRRS) to the direct in situ analysis of sunscreen formulations. High-quality UV resonance Raman spectra were obtained for five sunscreen active ingredients (AIs), mixtures of the AIs and real sunscreen formulation samples. The spectra from the sunscreen formulations gave distinct spectral signatures indicative of the sunscreen AIs in each sample, with essentially no interference from the complex sunscreen matrix. Also, despite the fact that many of the AIs are fluorescent, no fluorescence interferences in the resonance Raman spectra were observed. Excitation wavelength-dependent studies throughout the 244–275 nm region demonstrate that the best discrimination of the AIs was achieved at an excitation wavelength of 244 nm. Thus, by tuning the excitation wavelength within the absorption bands of the AIs, complete identification of these analytes can be achieved in situ without any sample pretreatment or separation. The limit of detection found for a common AI in situ with this technique is 0.23% (w/w), the limit of quantitation is 0.78% (w/w), while the dynamic range is between 0.8% and 50% (w/w). The technique is fast, robust, lacks any major interference, and can be adapted for routine online quality control.

International audience; Raman and photoacoustic (PA) infrared spectra of fluorene and four derivatives (2,3-benzofluorene, 2-methylfluorene, 2-ethylfluorene and 1,8-dimethylfluorene) were recorded and analyzed in this investigation. Mid-and far-infrared PA spectra were examined from about 2000 to 100 cm −1. The Raman spectra spanned the same wavenumber range. Observed bands in both PA and Raman spectra were compared with DFT (harmonic) and variational (anharmonic) calculations, and with published spectra. The DFT calculations provided single-molecule frequencies, whereas the variational method yielded results for both monomeric and dimeric species. Many previously unknown bands, including numerous features due to combination and overtone transitions, were identified and assigned in this work.

The employment of contrast agents in photoacoustic imaging has gained significant attention within the past few years for their biomedical applications. In this study, the use of silica-coated superparamagnetic iron oxide (Fe 3 O 4 ) nanoparticles (SPION) was investigated as a contrast agent in biomedical photoacoustic imaging. SPIONs have been widely used as Food-and-Drug-Administration (FDA)-approved contrast agents for magnetic resonance imaging (MRI) and are known to have an excellent safety profile. Using our frequency-domain photoacoustic correlation technique (“the photoacoustic radar") with modulated laser excitation, we examined the effects of nanoparticle size, concentration and biological medium (e.g. serum, sheep blood) on its photoacoustic response in turbid media (intralipid solution). Maximum detection depth and minimum measurable SPION concentration were determined experimentally. The detection was performed using a single element transducer. The nanoparticle-induced optical contrast ex vivo in dense muscular tissues (avian pectus) was evaluated using a phased array photoacoustic probe and the strong potential of silicacoated SPION as a possible photoacoustic contrast agent was demonstrated. This study opens the way for future clinical applications of nanoparticle-enhanced photoacoustic imaging in cancer therapy.

Thymine is one of the pyrimidine nucleobases found in DNA. Upon absorption of UV light, thymine forms a number of photoproducts, including the cyclobutyl photodimer, the pyrimidine pyrimidinone [6-4] photoproduct and the photohydrate. Here, we use UV resonance Raman spectroscopy to measure the initial excited-state structural dynamics of the N(1)-substituted thymine derivatives N(1)-methylthymine, thymidine, and thymidine 5'-monophosphate in an effort to understand the role of the N1 substituent in determining the excited-state structural dynamics and the subsequent photochemistry. The UV resonance Raman spectrum of thymidine and thymidine 5'-monophosphate are similar to that of thymine, suggesting that large masses at N(1) effectively isolate the vibrations of the nucleobase. However, the UV resonance Raman spectrum of N(1)-methylthymine is significantly different, suggesting that the methyl group couples into the thymine ring vibrations. The resulting resonance Raman intensities and absorption spectra are self-consistently simulated with a time-dependent expression to quantitatively extract the initial excited-state slopes, homogeneous and inhomogeneous linewidths, and electronic parameters. These results are discussed in the context of the known photochemistry of thymine and its derivatives.

Molecular beacons (MBs) are sensitive probes for many DNA sequence-specific applications, such as DNA damage detection, but suffer from technical and cost limitations. We have designed smart probes with self-quenching properties as an alternative to molecular beacons to monitor sequence-specific UV-induced photodamage of oligonucleotides. These probes have similar stem-loop structural characteristics as molecular beacons, but quenching is achieved instead via photoinduced intramolecular electron transfer by neighboring guanosine residues. Our results indicate that the probes are sensitive enough to detect nanomolar target concentrations and are specific enough to discriminate single-base damage. When the probes were used to monitor UV-induced photodamage in oligonucleotide sequences that differ by a single-base mismatch, the photodamage time constant was higher for the perfectly complementary target sequences than for the mismatch sequences, indicating that these probes are specific for each target sequence. In addition, time constants obtained for oligonucleotide target sequences with both stem and loop base mismatches are lower than those with only loop mismatches, suggesting that these sequences are also specifically distinguished by the smart probes. These probes thus constitute robust, sensitive, specific, and cheaper alternatives to MBs for sequence-specific DNA damage detection.

Cytosine is a nucleobase found in both DNA and RNA, while uracil is found only in RNA. Uracil has abstractable protons at N3 and N1. Cytosine has only one abstractable proton at N1 but can also accept a proton at N3. The pKa values of these protons are well-known, but the effect of the change in protonation on the rest of the molecule is not well understood and is very important in base stacking, base pairing, and protein−nucleic acid interactions. In this paper, UV resonance Raman (UVRR) spectroscopy is used to probe the structures of both cytosine and uracil at varying pH to determine the structural changes that take place. The results show that cytosine has increased electronic delocalization when moving to either basic or acidic environments, whereas uracil shows no significant change in acidic environment but increases its electronic delocalization in basic environment.

Nucleic acids are the very essence of life, containing the genetic potential of all organisms. However, the sheer size of nucleic acids makes them susceptible to a variety of environmental insults. Of these, ultraviolet-induced damage to nucleic acids has received extensive attention due to its role in disease. The primary step in ultraviolet-induced damage is the absorption of light and the subsequent electronic and structural dynamics on the excited-state potential energy surface. In this chapter, we will review the use of Raman and resonance Raman spectroscopy as a means of obtaining excited-state structural dynamics. Specifically, the application of Raman and resonance Raman spectroscopy to determine the excited-state structural dynamics of nucleic acids and their components will be discussed