Intrinsic Spectroscopic Properties Research Articles

Estimating the Acid-Base Properties and Electrical Charge of Organic Matter Using Spectrophotometry.

Spectrophotometric acid-base titration is a simple and powerful technique to evaluate the properties of proton binding sites of natural organic matter (NOM) at environmentally relevant concentrations. However, it is challenging to quantify the chemical charges (Q) carried by NOM at these concentrations. Based on a previous work, which relates the variation of Q with the specific UV-vis differential absorbance (ΔAλ,pH) at a given wavelength (λ) and pH of a dissolved NOM sample, the present work proposes a method to investigate any NOM sample. It determines specific features in the absorbance spectra attributed to proton-inert chromophores (A0,λ) and to the deprotonation processes of carboxylic (A1,λ) and phenolic groups (A2,λ). It enables to select sample-specific wavelength (λmid), where both these functional groups significantly contribute to the variation of absorbance with pH. The linear regression analysis of Aλmid,pH vs Q for various NOM reference samples evidenced that the sample-specific slope (SNOM) and intercept (INOM) were related to the intrinsic spectroscopic properties of the sample (A0,λmid, A1,λmid, and A2,λmid). This approach can thus be used to approximate the Q values of the NOM samples at environmentally relevant concentrations: a pre-requisite for predicting the fate and behavior of metal ions in natural systems.

Technologies for Direct Detection of Covalent Protein-Drug Adducts.

In the past two decades, drug candidates with a covalent binding mode have gained the interest of medicinal chemists, as several covalent anticancer drugs have successfully reached the clinic. As a covalent binding mode changes the relevant parameters to rank inhibitor potency and investigate structure-activity relationship (SAR), it is important to gather experimental evidence on the existence of a covalent protein-drug adduct. In this work, we review established methods and technologies for the direct detection of a covalent protein-drug adduct, illustrated with examples from (recent) drug development endeavors. These technologies include subjecting covalent drug candidates to mass spectrometric (MS) analysis, protein crystallography, or monitoring intrinsic spectroscopic properties of the ligand upon covalent adduct formation. Alternatively, chemical modification of the covalent ligand is required to detect covalent adducts by NMR analysis or activity-based protein profiling (ABPP). Some techniques are more informative than others and can also elucidate the modified amino acid residue or bond layout. We will discuss the compatibility of these techniques with reversible covalent binding modes and the possibilities to evaluate reversibility or obtain kinetic parameters. Finally, we expand upon current challenges and future applications. Overall, these analytical techniques present an integral part of covalent drug development in this exciting new era of drug discovery.

Cryogenic fluorescence spectroscopy of oxazine ions isolated in vacuo.

Recent developments in fluorescence spectroscopy have made it possible to measure both absorption and dispersed fluorescence spectra of isolated molecular ions at liquid-nitrogen temperatures. Absorption is here obtained from fluorescence-excitation experiments and does not rely on ion dissociation. One large advantage of reduced temperature compared to room-temperature spectroscopy is that spectra are narrow, and they provide information on vibronic features that can better be assigned from theoretical simulations. We report on the intrinsic spectroscopic properties of oxazine dyes cooled to about 100 K. They include six cations (crystal violet, darrow red, oxazine-1, oxazine-4, oxazine-170 and nile blue) and one anion (resorufin). Experiments were done with a home-built setup (LUNA2) where ions are stored, mass-selected, cooled, and photoexcited in a cylindrical ion trap. We find that the Stokes shifts are small (14-50 cm-1), which is ascribed to rigid geometries, that is, there are only small geometrical changes between the electronic ground and excited states. However, both the absorption and the emission spectra of darrow-red cations are broader than those of the other ionic dyes, which is likely associated with a less symmetric electronic structure and more non-zero Franck-Condon factors for the vibrational progressions. In the case of resorufin, the smallest ion under study, vibrational features are assigned based on calculated spectra.

A Spectroscopic View on Cosmic PAH Emission

ConspectusPolycyclic aromatic hydrocarbon molecules (PAHs) are ubiquitously present at high abundances in the Universe. They are detected through their infrared (IR) fluorescence UV pumped by nearby massive stars. Hence, their infrared emission is used to determine the star formation rate in galaxies, one of the key indicators for understanding the evolution of galaxies. Together with fullerenes, PAHs are the largest molecules found in space. They significantly partake in a variety of physical and chemical processes in space, influencing star and planet formation as well as galaxy evolution.Since the IR features from PAHs originate from chemical bonds involving only nearest neighbor atoms, they have only a weak dependence on the size and structure of the molecule, and it is therefore not possible to identify the individual PAH molecules that make up the cosmic PAH family. This strongly hampers the interpretation of their astronomical fingerprints. Despite the lack of identification, constraints can be set on the characteristics of the cosmic PAH family thanks to a joint effort of astronomers, physicists, and chemists.This Account presents the spectroscopic properties of the cosmic PAH emission as well as the intrinsic spectroscopic properties of PAHs and astronomical modeling of the PAH evolution required for the interpretation of the cosmic PAH characteristics. We discuss the observed spectral signatures tracing PAH properties such as charge, size, and structure and highlight the related challenges. We discuss the recent success of anharmonic calculations of PAH infrared absorption and emission spectra and outline the path forward. Finally, we illustrate the importance of models on PAH processing for the interpretation of the astronomical data in terms of the charge balance and PAH destruction.Throughout this Account, we emphasize that huge progress is on the horizon on the astronomical front. Indeed, the world is eagerly awaiting the launch of the James Webb Space Telescope (JWST). With its incredible improvement in spatial resolution, combined with its complete spectral coverage of the PAH infrared emission bands at medium spectral resolution and superb sensitivity, the JWST will revolutionize PAH research. Previous observations could only present spectra averaged over regions with vastly different properties, thus greatly confusing their interpretation. The amazing spatial resolution of JWST will disentangle these different regions. This will allow us to quantify precisely how PAHs are modified by the physical conditions of their host environment and thus trace how PAHs evolve across space. However, this will only be achieved when the necessary (and still missing) fundamental properties of PAHs, outlined in this Account, are known. We strongly encourage you to join this effort.

Spectroscopic and Photophysical Investigation of Model Dipyrroles Common to Bilins: Exploring Natural Design for Steering Torsion to Divergent Functions.

Biliproteins are a unique class of photosynthetic proteins in their diverse, and at times, divergent biophysical function. The two contexts of photosynthetic light harvesting and photoreception demonstrate characteristically opposite criteria for success, with light harvesting demanding structurally-rigid chromophores which minimize excitation quenching, and photoreception requiring structural flexibility to enable conformational isomerization. The functional plasticity borne out in these two biological contexts is a consequence of the structural plasticity of the pigments utilized by biliproteins―linear tetrapyrroles, or bilins. In this work, the intrinsic flexibility of the bilin framework is investigated in a bottom-up fashion by reducing the active nuclear degrees of freedom through model dipyrrole subunits of the bilin core and terminus free of external protein interactions. Steady-state spectroscopy was carried out on the dipyrrole (DPY) and dipyrrinone (DPN) subunits free in solution to characterize their intrinsic spectroscopic properties including absorption strengths and nonradiative activity. Transient absorption (TA) spectroscopy was utilized to determine the mechanism and kinetics of nonradiative decay of the dipyrrole subunits, revealing dynamics dominated by rapid internal conversion with some Z→E isomerization observable in DPY. Computational analysis of the ground state conformational landscapes indicates enhanced complexity in the asymmetric terminal subunit, and the prediction was confirmed by heterogeneity of species and kinetics observed in TA. Taken together, the large oscillator strengths (f ∼ 0.6) of the dipyrrolic derivatives and chemically-efficient spectral tunability seen through the ∼100 nm difference in absorption spectra, validate Nature's "selection" of multi-pyrrole pigments for light capture applications. However, the rapid deactivation of the excited state via their natural torsional activity when free in solution would limit their effective biological function. Comparison with phytochrome and phycocyanin 645 crystal structures reveals binding motifs within the in vivo bilin environment that help to facilitate or inhibit specific inter-pyrrole twisting vital for protein operation.

Spectroscopic and time-dependent density functional investigation of the role of structure on the acid-base effects of citrinin detection

A time-dependent density functional theory (TD-DFT) study was carried out on tautomers of the mycotoxin citrinin in the neutral, anionic, and cationic forms to gain insight into the role of chemical structure on detection. Steady-state fluorescence studies of citrinin in micellar aqueous solutions produced unusual results for ionic surfactants and the neutral Triton X-100 enhanced fluorescence emission. Ground-state and time-dependent density functional studies were carried out on five tautomers of citrinin using the B3LYP density functional and the 6-311+G(2df,2p) basis set. The investigation revealed that deprotonation is a major factor governing the shifts in fluorescence excitation and emission maxima. Moreover, the position of the lowest unoccupied molecular orbitals is removed from the fluorophore moiety of citrinin in the dianionic state which is consistent with the diminished fluorescence of the toxin in basic solutions. The ionic characteristics of certain chemosensors can influence the structure and intrinsic spectroscopic properties of citrinin.

High Susceptibility of Histidine to Charge Solvation Revealed by Cold Ion Spectroscopy.

Histidine remained the last aromatic amino acid for which the intrinsic spectroscopic properties and structures were obscure. We measured the UV and IR spectra of protonated histidine, isolated in the gas phase, using photofragmentation cold ion spectroscopy. Unexpectedly, the UV absorption appears strongly redshifted relative to that of the cation in aqueous solutions. In investigating this phenomenon, we solved the geometries of all abundant conformers using IR conformer-selective spectroscopy and ab initio quantum chemical calculations. In all of the structures, the proton resides on the imidazole ring. The measured UV spectra of protonated methylimidazole, histamine and histidine, together with calculations of the electronic spectra for the latter, suggest that, in comparison with other aromatic amino acids, such location of proton makes UV absorption of histidine highly sensitive to the local environment of its side chain.

ChemInform Abstract: Zn(II) and Cu(II) Complexes Containing Bioactive O,O‐Chelated Ligands: Homoleptic and Heteroleptic Metal‐Based Biomolecules

AbstractReview: 127 refs.

On the dual phosphorescence of xanthone and chromone in glassy hydrocarbon hosts.

Trace quantities of hydrogen-bonding impurities in otherwise highly purified and dried glassy hydrocarbon matrices at 77K can modify the relative triplet state energy levels, and hence the photophysical properties of two aromatic ketones, xanthone and chromone, to the extent that the intrinsic spectroscopic properties are obscured. The intrinsic spectroscopic properties of each are revealed in multicrystalline n-alkane Shpol'skii matrices, and also can be observed in rigorously purified and dried hydrocarbon glasses at 77K. The extreme sensitivity to stoichiometric, and even substoichiometric quantities of hydrogen-bonding impurities arises from the near-degeneracy of the two lowest-lying triplet states, and the sensitive nature of the n→π* blueshift phenomena to specific hydrogen-bonding interactions.

Zn(ii) and Cu(ii) complexes containing bioactive O,O-chelated ligands: Homoleptic and heteroleptic metal-based biomolecules.

Historically, many useful drugs have been developed from natural sources and their mechanisms of action deeply investigated for therapeutic applications. Recently, the interaction between pharmacologically active biomolecules and transition metal ions has opened the way to the construction of new drugs, where the unique properties of metal complexes are combined with the specific mechanisms of action of the coordinated bioligands of natural extraction. In this context, this perspective summarizes some recent research studies devoted to the development of new metal-based drugs containing Zn(ii) or Cu(ii) metal ions. Both metals have a strong tendency to form highly stable complexes with N,N- and O,O-donor ligands bound through chelation, giving rise, particularly when the bound organic molecules are drug candidates of natural extraction, to drug delivery systems, new biologically active complexes and potential diagnostic agents due to their intrinsic spectroscopic properties.

ChemInform Abstract: The Importance of Various Anchoring Groups Attached on Porphyrins as Potential Dyes for DSSC Applications

AbstractReview: 124 refs.

Interaction of the antibiotic norfloxacin with ionic micelles: pH-dependent binding.

The interaction of the antimicrobial drug norfloxacin (NFX) with anionic sodium dodecyl sulfate (SDS) and cationic cetyltrimethylammonium bromide (CTAB) micelles was studied using the intrinsic spectroscopic properties of NFX to obtain association constants and molecular modifications. Nonionic Tween(®) 20 micelles were also investigated, but the spectroscopic properties of NFX did not detect interactions with these micelles, and quenching by iodide suggested a weak association constant around 47M(-1). For SDS and CTAB, UV-Vis absorption spectroscopy, steady-state and time-resolved fluorometry were monitored as a function of surfactant concentration ranging from the premicellar to micellar region. It was found that cationic (pH 4.0) and zwitterionic NFX (pH 7.4) associate with SDS micelles, with binding constants equal to 5.4×10(3) and 1.7×10(3) M(-1), respectively. Premicellar interaction slightly decreases the critical micelle concentration of SDS. Association of anionic NFX (pH 10.6) is very weak. The fluorescence spectrum and lifetime showed that SDS-associated NFX is cationic and that the heterocycle penetrates the interfacial environment of decreased polarity. Cationic CTAB micelles do not bind cationic NFX, and the association constant with zwitterionic NFX is two orders of magnitude lower than that of SDS micelles. From a pharmacological point of view, it is important that at neutral pH, NFX presented a two orders of magnitude higher affinity for anionic than for cationic sites, and did not interact significantly with nonionic or zwitterionic micelle interfaces.

Concurrent quantification of tryptophan and its major metabolites

An imbalance in tryptophan (TRP) metabolites is associated with several neurological and inflammatory disorders. Therefore, analytical methods allowing for simultaneous quantification of TRP and its major metabolites would be highly desirable, and may be valuable as potential biomarkers. We have developed a HPLC method for concurrent quantitative determination of tryptophan, serotonin, 5-hydroxyindoleacetic acid, kynurenine, and kynurenic acid in tissue and fluids. The method utilizes the intrinsic spectroscopic properties of TRP and its metabolites that enable UV absorbance and fluorescence detection by HPLC, without additional labeling. The origin of the peaks related to analytes of interest was confirmed by UV–Vis spectral patterns using a PDA detector and mass spectrometry. The developed methods were validated in rabbit fetal brain and amniotic fluid at gestational day 29. Results are in excellent agreement with those reported in the literature for the same regions. This method allows for rapid quantification of tryptophan and four of its major metabolites concurrently. A change in the relative ratios of these metabolites can provide important insights in predicting the presence and progression of neuroinflammation in disorders such as cerebral palsy, autism, multiple sclerosis, Alzheimer disease, and schizophrenia.

Evaluation of intrinsic spectroscopic properties of chromophore assemblies by shielding with cyclohexyl base pairs within a DNA duplex

Here, we investigated spectroscopic behaviors of tetramethylrhodamine (TMR) homo- and hetero-dimers within DNA duplex. In order to shield the chromophores from natural base pairs, we used cyclohexyl base pairs as ‘insulators’; these pairs were inserted between the chromophores and nucleobases. When a single TMR moiety was sandwiched between cyclohexyl base pairs, the emission intensity increased by fivefold relative to a TMR between natural base pairs, because electron transfer from nucleobases was suppressed. Next, we inserted two TMRs between the cyclohexyl base pairs and found that they facilitated H-dimer formation of TMR; a distinct hypsochromic shift was induced only when cyclohexyl base pairs were inserted. We further examined quenching behavior of a TMR paired with a quencher dye between cyclohexyl base pairs. Interestingly, fluorescence from TMR was quenched by nitro methyl red more efficiently in the presence of cyclohexyl base pairs than in their absence. This suggests that neighboring natural base pairs disturbed electron or hole transfer between the fluorophore and the quencher. The cyclohexyl base pairs shielded the chromophore pair from the natural base pairs and allowed intrinsic electron transfer.

Surface-Enhanced Raman Spectroscopy of Carbon Nanotubes in Aqueous Solution

Carbon nanotubes (CNTs) exhibit intrinsic spectroscopic properties and are potential Raman and NIR florescence probes for bioimaging. However, the weak Raman intensity greatly obstructs such applications. Surface-enhanced Raman scattering (SERS) has shown to be an effective way to increase the Raman signal. SERS has been widely studied for solid samples. However, solid state is distinctly different from the environment in biosystems. Herein, we studied the SERS of Au- nanoparticle-decorated CNTs in aqueous solution, which offers a similar environment to biosystems. We found that the func- tionalization of CNTs with -SH groups can improve the attachment of Au nanoparticles on tube surfaces thus benefit the SERS effect. The particle size is another important issue for SERS. Particles of 50 nm show much stronger enhancement than those of 12 nm. The Raman intensity of CNTs increases with the increase of the concentration of Au nanoparticles. Hexame- thylene diamine molecules can act as the bi-linkers between Au nanoparticles, compressing the interparticle distance. This was proved by the red-shift of the band at ca. 540 nm and the appearance of a broad band around 700 nm in the absorption spectra of Au nanoparticles. Therefore the addition of hexamethylene diamine can further increase the Raman signal of CNTs by the strong coupling of the surface plasma from the Au nanoparticles with very small interparticle distances. Two kinds of commonly used small molecule Raman probes p-aminothiophenol and Rhodamine B both show remarkably enhanced Raman intensity when added to the aqueous dispersion of Au/CNT hybrids. This shows that these Raman probe molecules can ab- sorb onto the Au/CNT hybrids and their Raman spectra are able to be greatly enhanced by Au nanoparticles decorated on CNTs. Because various Raman bands from either CNTs or Raman probe molecules can be used for Raman imaging, this kind of Raman probe molecule/Au/CNT tri-component hybrid systems may be used as a potential nanostructured platform for multiplexed Raman imaging based on SERS effect. Keywords carbon nanotubes; gold nanoparticles; surface enhanced Raman scattering (SERS); Raman spectroscopy for aqueous solution

On the Intrinsic Photophysics of Fluorescein

Not so bright: Ion trap mass spectrometry is used in conjunction with optical excitation and detection to study the intrinsic spectroscopic properties of the fluorescein cation, monoanion, and dianion in the gas phase. The dianion, which is a fluorescence quantum yield standard in solution, does not fluoresce significantly in the absence of solvent (see picture) because electron detachment is the favored deactivation pathway in the gas phase.

Conjugation of Fluorescent Proteins with DNA Oligonucleotides

This work describes the synthesis of covalent ssDNA conjugates of six fluorescent proteins, ECFP, EGFP, E(2)GFP, mDsRed, Dronpa, and mCherry, which were cloned with an accessible C-terminal cystein residue to enable site-selective coupling using a heterobispecific cross-linker. The resulting conjugates revealed similar fluorescence emission intensity to the unconjugated proteins, and the functionality of the tethered oligonucleotide was proven by specific Watson-Crick base pairing to cDNA-modified gold nanoparticles. Fluorescence spectroscopy analysis indicated that the fluorescence of the FP is quenched by the gold particle, and the extent of quenching varied with the intrinsic spectroscopic properties of FP as well as with the configuration of surface attachment. Since this study demonstrates that biological fluorophores can be selectively incorporated into and optically coupled with nanoparticle-based devices, applications in DNA-based nanofabrication can be foreseen.

Spectroscopic Analyses of the Biofuels-Critical Phytochemical Coniferyl Alcohol and Its Enzyme-Catalyzed Oxidation Products

Lignin composition (monolignol types of coniferyl, sinapyl or p-coumaryl alcohol) is causally related to biomass recalcitrance. We describe multiwavelength (220, 228, 240, 250, 260, 290, 295, 300, 310 or 320 nm) absorption spectroscopy of coniferyl alcohol and its laccase- or peroxidase-catalyzed products during real time kinetic, pseudo-kinetic and endpoint analyses, in optical turn on or turn off modes, under acidic or basic conditions. Reactions in microwell plates and 100 μL volumes demonstrated assay miniaturization and high throughput screening capabilities. Bathochromic and hypsochromic shifts along with hyperchromicity or hypochromicity accompanied enzymatic oxidations by laccase or peroxidase. The limits of detection and quantitation of coniferyl alcohol averaged 2.4 and 7.1 μM respectively, with linear trend lines over 3 to 4 orders of magnitude. Coniferyl alcohol oxidation was evident within 10 minutes or with 0.01 μg/mL laccase and 2 minutes or 0.001 μg/mL peroxidase. Detection limit improved to 1.0 μM coniferyl alcohol with Km of 978.7 ± 150.7 μM when examined at 260 nm following 30 minutes oxidation with 1.0 μg/mL laccase. Our assays utilized the intrinsic spectroscopic properties of coniferyl alcohol or its oxidation products for enabling detection, without requiring chemical synthesis or modification of the substrate or product(s). These studies facilitate lignin compositional analyses and augment pretreatment strategies for reducing biomass recalcitrance.

Direct glucose determination in blood using a reagentless optical biosensor

This paper demonstrates that glucose determination in blood can be done directly (without sample pretreatment) using a reagentless reversible biosensor based on the intrinsic spectroscopic properties of peroxidase (HRP). The biosensor, prepared by HRP and glucose oxidase entrapment in a polyacrylamide gel matrix, works in continuous mode, presents a linear response range from 1.5×10−6 up to 5.5×10−5M and can be used for at least 750 measurements; in the best conditions (0.1M pH 6 phosphate buffer, HRP and GOx amounts in the polymersation mixture for the sensor film preparation 0.0165 and 0.0010g, respectively) the minimum samples rate is 30h−1. For glucose determination, blood is simply diluted in water (until haemolysis is completed) and fed into the sensor without a cleaning step between samples; the blood absorption is corrected in a simple way by working at a proper reference wavelength. The biosensor signals have been mathematically modeled in order to facilitate the design of sensors based on the same idea for other biochemical compounds.

Structural Characterization of an Equilibrium Unfolding Intermediate in Cytochrome c

Although the denaturant-induced unfolding transition of cytochrome c was initially thought to be a cooperative process, recent spectroscopic studies have shown deviations from two-state behavior consistent with accumulation of an equilibrium intermediate. However, little is known about the structural and thermodynamic properties of this state, and whether it is stabilized by the presence of non-native heme ligands. We monitored the reversible denaturant-induced unfolding equilibrium of oxidized horse cytochrome c using various spectroscopic probes, including fluorescence, near and far-UV CD, heme absorbance bands in the Soret, visible and near-IR regions of the spectrum, as well as 2D NMR. Global fitting techniques were used for a quantitative interpretation of the results in terms of a three-state model, which enabled us to determine the intrinsic spectroscopic properties of the intermediate. A well-populated intermediate was observed in equilibrium experiments at pH 5 using either guanidine-HCl or urea as a denaturant, both for wild-type cytochrome c as well as an H33N mutant chosen to prevent formation of non-native His-heme ligation. For a more detailed structural characterization of the intermediate, we used 2D 1H-15N correlation spectroscopy to follow the changes in peak intensity for individual backbone amide groups. The equilibrium state observed in our optical and NMR studies contains many native-like structural features, including a well-structured alpha-helical sub-domain, a short Trp59-heme distance and solvent-shielded heme environment, but lacks the native Met80 sulfur-iron linkage and shows major perturbations in side-chain packing and other tertiary interactions. These structural properties are reminiscent of the A-state of cytochrome c, a compact denatured form found under acidic high-salt conditions, as well as a kinetic intermediate populated at a late stage of folding. The denaturant-induced intermediate also resembles alkaline forms of cytochrome c with altered heme ligation, suggesting that disruption of the native methionine ligand favors accumulation of structurally analogous states both in the presence and absence of non-native ligands.