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The identification and quantification of caffeine is a common need in the food and pharmaceutical industries and lately also in the field of environmental science. For that purpose, Raman spectroscopy has been used as an analytical technique, but the interpretation of the spectra requires reliable and accurate computational protocols, especially as regards the Resonance Raman (RR) variant. Herein, caffeine solutions are sampled using Molecular Dynamics simulations. Upon quantification of the strength of the non-covalent intermolecular interactions such as hydrogen bonding between caffeine and water, UV-Vis, Raman, and RR spectra are computed. The results provide general insights into the hydrogen bonding role in mediating the Raman spectral signals of caffeine in aqueous solution. Also, by analyzing the dependence of RR enhancement on the absorption spectrum of caffeine, it is proposed that the sensitivity of the RR technique could be exploited at excitation wavelengths moderately far from 266 nm, yet achieving very low detection limits in the quantification caffeine content. [ABSTRACT FROM AUTHOR]

Due to the drastic required thermodynamical requirements, a photoelectrode material that can function as both a photocathode and a photoanode remains elusive. In this work, we demonstrate for the first time that, under simulated solar light and without co‐catalysts, donor‐acceptor conjugated acetylenic polymers (CAPs) exhibit both impressive oxygen evolution (OER) and hydrogen evolution (HER) photocurrents in alkaline and neutral medium, respectively. In particular, poly(2,4,6‐tris(4‐ethynylphenyl)‐1,3,5‐triazine) (pTET) provides a benchmark OER photocurrent density of ~200 μA cm−2 at 1.23 V vs. reversible hydrogen electrode (RHE) at pH 13 and a remarkable HER photocurrent density of ~190 μA cm−2 at 0.3 V vs. RHE at pH 6.8. By combining theoretical investigations and electrochemical‐operando Resonance Raman spectroscopy, we show that the OER proceeds with two different mechanisms, with the electron‐depleted triple bonds acting as single‐site OER in combination with the C4‐C5 atoms of the phenyl rings as dual sites. The HER, instead, occurs via an electron transfer from the tri‐acetylenic linkages to the triazine rings, which act as the HER active sites. This work represents a novel application of organic‐based materials and contributes to the development of high‐performance photoelectrochemical catalysts for the solar fuels' generation. [ABSTRACT FROM AUTHOR]

Time‐dependent density functional theory (TDDFT) was applied to gain insights into the electronic and vibrational spectroscopic properties of an important electron transport mediator, methyl viologen (MV2+). An organic dication, MV2+ has numerous applications in electrochemistry that include energy conversion and storage, environmental remediation, and chemical sensing and electrosynthesis. MV2+ is easily reduced by a single electron transfer to form a radical cation species (MV•+), which has an intense UV–visible absorption near 600 nm. The redox properties of the MV2+/MV•+ couple and light‐sensitivity of MV•+ have made the system appealing for photo‐electrochemical energy conversion (e.g., solar hydrogen generation from water) and the study of photo‐induced charge transfer processes through electronic absorption and resonance Raman spectroscopic measurements. The reported work applies leading TDDFT approaches to investigate the electronic and vibrational spectroscopic properties of MV2+ and MV•+. Using a conventional hybrid exchange functional (B3‐LYP) and a long‐range corrected hybrid exchange functional (ωB97X‐D3), including with a conductor‐like polarizable continuum model to account for solvation, the electronic absorption and resonance Raman spectra predicted are in good agreement with experiment. Also analyzed are the charge transfer character and natural transition orbitals derived from the TDDFT vertical excitations calculated. The findings and models developed further the understanding of the electronic properties of viologens and related organic redox mediators important in renewable energy applications and serve as a reference for guiding the interpretation of electronic absorption and Raman spectra of the ions. [ABSTRACT FROM AUTHOR]

Establishing the fundamental chemical principles that govern molecular electronic quantum decoherence has remained an outstanding challenge. Fundamental questions such as how solvent and intramolecular vibrations or chemical functionalization contribute to the decoherence remain unanswered and are beyond the reach of state-of-the-art theoretical and experimental approaches. Here we address this challenge by developing a strategy to isolate electronic decoherence pathways for molecular chromophores immersed in condensed phase environments that enables elucidating how electronic quantum coherence is lost. For this, we first identify resonance Raman spectroscopy as a general experimental method to reconstruct molecular spectral densities with full chemical complexity at room temperature, in solvent, and for fluorescent and non-fluorescent molecules. We then show how to quantitatively capture the decoherence dynamics from the spectral density and identify decoherence pathways by decomposing the overall coherence loss into contributions due to individual molecular vibrations and solvent modes. We illustrate the utility of the strategy by analyzing the electronic decoherence pathways of the DNA base thymine in water. Its electronic coherences decay in -30 fs. The early-time decoherence is determined by intramolecular vibrations while the overall decay by solvent. Chemical substitution of thymine modulates the decoherence with hydrogen-bond interactions of the thymine ring with water leading to the fastest decoherence. Increasing temperature leads to faster decoherence as it enhances the importance of solvent contributions but leaves the earlytime decoherence dynamics intact. The developed strategy opens key opportunities to establish the connection between molecular structure and quantum decoherence as needed to develop chemical strategies to rationally modulate it. [ABSTRACT FROM AUTHOR]

The identification and quantification of caffeine is a common need in the food and pharmaceutical industries and lately also in the field of environmental science. For that purpose, Raman spectroscopy has been used as an analytical technique, but the interpretation of the spectra requires reliable and accurate computational protocols, especially as regards the Resonance Raman (RR) variant. Herein, caffeine solutions are sampled using Molecular Dynamics simulations. Upon quantification of the strength of the non-covalent intermolecular interactions such as hydrogen bonding between caffeine and water, UV-Vis, Raman, and RR spectra are computed. The results provide general insights into the hydrogen bonding role in mediating the Raman spectral signals of caffeine in aqueous solution. Also, by analyzing the dependence of RR enhancement on the absorption spectrum of caffeine, it is proposed that the sensitivity of the RR technique could be exploited at excitation wavelengths moderately far from 266 nm, yet achieving very low detection limits in the quantification caffeine content.

Metformin (MF) is one of the most important medicaments in the market. It has been extensively employed in the treatment of type-2 diabetes, but its analytical detection is rather complicated, requiring, for instance, high-performance chromatographic methods. Here, we report that metformin reacts with the pentacyanidoferrate(II) complex, generating a deep red product in the presence of sodium percarbonate, Na2CO3·1.5H2O2. A colorimetric assay has been performed by measuring the absorption band at 520 nm, with a limit of detection (LOD) of 0.018 mmol/L. The reaction can also be probed by Raman spectroscopy, since the [FeIII(CN)5MF]3− complex, exhibits a strong resonance effect which enhances the vibrational peaks of the iron(III)-guanidine chromophore. The Raman spectral features are associated with the Fe(III)-NC-bonds and the metal-to-ligand charge-transfer transition, as confirmed by DFT calculations.

The reduction of SO2 to fixed forms of sulfur can address the growing concerns regarding its detrimental effect on health and the environment as well as enable its valorization into valuable chemicals. The naturally occurring heme enzyme sulfite reductase (SiR) is known to reduce SO2 to H2S and is an integral part of the global sulfur cycle. However, its action has not yet been mimicked in artificial systems outside of the protein matrix even after several decades of structural elucidation of the enzyme. While the coordination of SO2 to transition metals is documented, its reduction using molecular catalysts has remained elusive. Herein reduction of SO2 by iron(II) tetraphenylporphyrin is demonstrated. A combination of spectroscopic data backed up by theoretical calculations indicate that FeIITPP reduces SO2 by 2e−/2H+ to form an intermediate [FeIII−SO]+ species, also proposed for SiR, which releases SO. The SO obtained from the chemical reduction of SO2 could be evidenced in the form of a cheletropic adduct of butadiene resulting in an organic sulfoxide. [ABSTRACT FROM AUTHOR]

Glioma is one of the most refractory types of brain tumor. Accurate tumor boundary identification and complete resection of the tumor are essential for glioma removal during brain surgery. We present a method based on visible resonance Raman (VRR) spectroscopy to identify glioma margins and grades. A set of diagnostic spectral biomarkers features are presented based on tissue composition changes revealed by VRR. The Raman spectra include molecular vibrational fingerprints of carotenoids, tryptophan, amide I/II/III, proteins, and lipids. These basic in situ spectral biomarkers are used to identify the tissue from the interface between brain cancer and normal tissue and to evaluate glioma grades. The VRR spectra are also analyzed using principal component analysis for dimension reduction and feature detection and support vector machine for classification. The cross-validated sensitivity, specificity, and accuracy are found to be 100%, 96.3%, and 99.6% to distinguish glioma tissues from normal brain tissues, respectively. The area under the receiver operating characteristic curve for the classification is about 1.0. The accuracies to distinguish normal, low grade (grades I and II), and high grade (grades III and IV) gliomas are found to be 96.3%, 53.7%, and 84.1% for the three groups, respectively, along with a total accuracy of 75.1%. A set of criteria for differentiating normal human brain tissues from normal control tissues is proposed and used to identify brain cancer margins, yielding a diagnostic sensitivity of 100% and specificity of 71%. Our study demonstrates the potential of VRR as a label-free optical molecular histopathology method used for in situ boundary line judgment for brain surgery in the margins.

Coproporphyrin ferrochelatases (CpfCs) are enzymes catalyzing the penultimate step in the coproporphyrin‐dependent (CPD) heme biosynthesis pathway, which is mainly utilized by monoderm bacteria. Ferrochelatases insert ferrous iron into a porphyrin macrocycle and have been studied for many decades, nevertheless many mechanistic questions remain unanswered to date. Especially CpfCs, which are found in the CPD pathway, are currently in the spotlight of research. This pathway was identified in 2015 and revealed that the correct substrate for these ferrochelatases is coproporphyrin III (cpIII) instead of protoporphyrin IX, as believed prior the discovery of the CPD pathway. The chemistry of cpIII, which has four propionates, differs significantly from protoporphyrin IX, which features two propionate and two vinyl groups. These findings let us to thoroughly describe the physiological cpIII‐ferrochelatase complex in solution and in the crystal phase. Here, we present the first crystallographic structure of the CpfC from the representative monoderm pathogen Listeria monocytogenes bound to its physiological substrate, cpIII, together with the in‐solution data obtained by resonance Raman and UV–vis spectroscopy, for wild‐type ferrochelatase and variants, analyzing propionate interactions. The results allow us to evaluate the porphyrin distortion and provide an in‐depth characterization of the catalytically‐relevant binding mode of cpIII prior to iron insertion. Our findings are discussed in the light of the observed structural restraints and necessities for this porphyrin‐enzyme complex to catalyze the iron insertion process. Knowledge about this initial situation is essential for understanding the preconditions for iron insertion in CpfCs and builds the basis for future studies. PDB Code(s): 8AT8 and 8AW7; [ABSTRACT FROM AUTHOR]

Heme-based sensor proteins are used by organisms to control signaling and physiological effects in response to their gaseous environment. Globin-coupled sensors (GCS) are oxygen-sensing proteins that are widely distributed in bacteria. These proteins consist of a heme globin domain linked by a middle domain to various output domains, including diguanylate cyclase domains, which are responsible for synthesizing c -di-GMP, a bacterial second messenger crucial for regulating biofilm formation. To understand the roles of heme pocket residues in controlling activity of the diguanylate cyclase domain, variants of the Pectobacterium carotovorum GCS (Pcc GCS) were characterized by enzyme kinetics and resonance Raman (rR) spectroscopy. Results of these studies have identified roles for hydrogen bonding and heme edge residues in modulating heme pocket conformation and flexibility. Better understanding of the ligand-dependent GCS signaling mechanism and the residues involved may allow for future development of methods to control O 2 -dependent c -di-GMP production. Investigation of heme pocket residues in the PccGCS heme active site and the inverse correlation plot for CO adducts of wild-type Pcc GCS (Globin Coupled Sensors from Pectobacterium carotovorum), Pcc Globin (the isolated globin domain from Pectobacterium carotovorum), and their variants. [Display omitted] • Globin coupled sensor (GCS) proteins play a vital role in signaling through the second messenger c -di-GMP. • Enzyme kinetics and rR spectroscopy are used to study the structure and functional relationship of the Pcc GCS protein. • The kinetic study shows that the distal hydrogen-bonding residues (Y57 and S82) are essential for modulating O 2 binding. • rR spectroscopy reveals detailed structural changes in the heme active site of key GCS variants (Y57F, S82A and V122Y). [ABSTRACT FROM AUTHOR]

Cytochrome c oxidase (CcO) reduces O 2 , pumps protons in the mitochondrial respiratory chain, and is essential for oxygen consumption in the cell. The coiled-coil-helix-coiled-coil-helix domain-containing 2 (CHCHD2; also known as mitochondrial nuclear retrograde regulator 1 [MNRR1], Parkinson's disease 22 [PARK22] and aging-associated gene 10 protein [AAG10]) is a protein that binds to CcO from the intermembrane space and positively regulates the activity of CcO. Despite the importance of CHCHD2 in mitochondrial function, the mechanism of action of CHCHD2 and structural information regarding its binding to CcO remain unknown. Here, we utilized visible resonance Raman spectroscopy to investigate the structural changes around the hemes in CcO in the reduced and CO-bound states upon CHCHD2 binding. We found that CHCHD2 has a significant impact on the structure of CcO in the reduced state. Mapping of the heme peripheries that result in Raman spectral changes in the structure of CcO highlighted helices IX and X near the hemes as sites where CHCHD2 takes action. Part of helix IX is exposed in the intermembrane space, whereas helix X, located between both hemes, may play a key role in proton uptake to a proton-loading site in the reduced state for proton pumping. Taken together, our results suggested that CHCHD2 binds near helix IX and induces a structural change in helix X, accelerating proton uptake. Coiled-coil-helix-coiled-coil-helix domain-containing 2 (CHCHD2) is located in the mitochondrial intermembrane space and functions to activate cytochrome c oxidase (CcO). Resonance Raman spectroscopic analyses demonstrated that helices IX and X near the hemes are the sites of CHCHD2 influence. CHCHD2 could accelerate proton uptake in the H-pathway by modulating a water cavity next to helix X. [Display omitted] • Resonance Raman spectroscopy probes structural changes in CcO upon CHCHD2 binding. • CHCHD2 influences the structure of reduced CcO greater than CO-bound CcO. • Movements of helices IX and X are suggested to occur in reduced CcO by CHCHD2. • CHCHD2 could accelerate the proton uptake process prior to O 2 binding to CcO. [ABSTRACT FROM AUTHOR]

Bacteria use the second messenger cyclic dimeric guanosine monophosphate (c -di-GMP) to control biofilm formation and other key phenotypes in response to environmental signals. Changes in oxygen levels can alter c -di-GMP signaling through a family of proteins termed globin coupled sensors (GCS) that contain diguanylate cyclase domains. Previous studies have found that GCS diguanylate cyclase activity is controlled by ligand binding to the heme within the globin domain, with oxygen binding resulting in the greatest increase in catalytic activity. Herein, we present evidence that heme-edge residues control O 2 -dependent signaling in Pcc GCS, a GCS protein from Pectobacterium carotovorum , by modulating heme distortion. Using enzyme kinetics, resonance Raman spectroscopy, small angle X-ray scattering, and multi-wavelength analytical ultracentrifugation, we have developed an integrated model of the full-length Pcc GCS tetramer and have identified conformational changes associated with ligand binding, heme conformation, and cyclase activity. Taken together, these studies provide new insights into the mechanism by which O 2 binding modulates activity of diguanylate cyclase-containing GCS proteins. A heme edge tryptophan and arginine that hydrogen bonds to the heme propionate modulate O 2 binding, heme conformation, activity of the diguanylate cyclase domain, and globin coupled sensor conformation. A heme edge tryptophan and arginine that hydrogen bonds to the heme propionate modulate O 2 binding, heme conformation, activity of the diguanylate cyclase domain, and globin coupled sensor conformation. [Display omitted] • Heme edge residue modulates O 2 -dependent activation of a diguanylate cyclase-containing globin coupled sensor. • Hydrogen bonding to heme propionate is required for sensing heme ligation state and maintaining heme conformation. • Tetrameric globin coupled sensor forms a compact structure that exhibits conformational changes upon O 2 binding. [ABSTRACT FROM AUTHOR]

Organometallic molecules offer some of the most promising scaffolds for interaction with G‐quadruplex nucleic acids. We report the efficient synthesis of a family of organoplatinum(II) complexes, featuring a 2‐([2,2′‐bipyridin]‐6‐yl)phenyl tridentate (N∧N∧C) ligand, that incorporates peripheral side‐chains aiming at enhancing and diversifying its interaction capabilities. These include a di‐isopropyl carbamoyl amide, a morpholine ethylenamide, two enantiomeric proline imides and an oxazole. The binding affinities of the Pt‐complexes were evaluated via UV‐vis and fluorescence titrations, against 5 topologically‐distinct DNA structures, including c‐myc G‐quadruplex, two telomeric (22AG) G‐quadruplexes, a duplex (ds26) and a single‐stranded (polyT) DNA. All compounds exhibited binding selectivity in favour of c‐myc, with association constants (Ka) in the range of 2–5×105 M−1, lower affinity for both folds of 22AG and for ds26 and negligible affinity for polyT. Remarkable emission enhancements (up to 200‐fold) upon addition of excess DNA were demonstrated by a subset of the compounds with c‐myc, providing a basis for optical selectivity, since optical response to all other tested DNAs was low. A c‐myc DNA‐melting experiment showed significant stabilizing abilities for all compounds, with the most potent binder, the morpholine‐Pt‐complex, exhibiting a ΔTm>30 °C, at 1 : 5 DNA‐to‐ligand molar ratio. The same study implied contributions of the diverse side‐chains to helix stabilization. To gain direct evidence of the nature of the interactions, mixtures of c‐myc with the four most promising compounds were studied via UV Resonance Raman (UVRR) spectroscopy, which revealed end‐stacking binding mode, combined with interactions of side‐chains with loop nucleobase residues. Docking simulations were conducted to provide insights into the binding modes for the same four Pt‐compounds, suggesting that the binding preference for two alternative orientations of the c‐myc G‐quadruplex thymine 'cap' ('open' vs. 'closed'), as well as the relative contributions to affinity from end‐stacking and H‐bonding, are highly dependent on the nature of the interacting Pt‐complex side‐chain. [ABSTRACT FROM AUTHOR]

[Display omitted] 9-cyanopyronin is a promising scaffold that exploits resonance Raman enhancement to enable sensitive, highly multiplexed biological imaging. Here, we developed cyano-Hydrol Green (CN-HG) derivatives as resonance Raman scaffolds to expand the color palette of 9-cyanopyronins. CN-HG derivatives exhibit sufficiently long wavelength absorption to produce strong resonance Raman enhancement for near-infrared (NIR) excitation, and their nitrile peaks are shifted to a lower frequency than those of 9-cyanopyronins. The fluorescence of CN-HG derivatives is strongly quenched due to the lack of the 10th atom, unlike pyronin derivatives, and this enabled us to detect spontaneous Raman spectra with high signal-to-noise ratios. CN-HG derivatives are powerful candidates for high performance vibrational imaging. [ABSTRACT FROM AUTHOR]

The actinobacterial coproheme decarboxylase from Corynebacterium diphtheriae catalyzes the final reaction to generate heme b via the "coproporphyrin‐dependent" heme biosynthesis pathway in the presence of hydrogen peroxide. The enzyme has a high reactivity toward H2O2 used for the catalytic reaction and in the presence of an excess of H2O2 new species are generated. Resonance Raman data, together with electronic absorption spectroscopy and mass spectrometry, indicate that an excess of hydrogen peroxide for both the substrate (coproheme) and product (heme b) complexes of this enzyme causes a porphyrin hydroxylation of ring C or D, which is compatible with the formation of an iron chlorin‐type heme d species. A similar effect has been previously observed for other heme‐containing proteins, but this is the first time that a similar mechanism is reported for a coproheme enzyme. The hydroxylation determines a symmetry lowering of the porphyrin macrocycle, which causes the activation of A2g modes upon Soret excitation with a significant change in their polarization ratios, the enhancement and splitting into two components of many Eu bands, and an intensity decrease of the non‐totally symmetric modes B1g, which become polarized. This latter effect is clearly observed for the isolated ν10 mode upon either Soret or Q‐band excitations. The distal His118 is shown to be an absolute requirement for the conversion to heme d. This residue also plays an important role in the oxidative decarboxylation, because it acts as a base for deprotonation and subsequent heterolytic cleavage of hydrogen peroxide. [ABSTRACT FROM AUTHOR]

This mini-review, mainly based on our resonance Raman studies on the structural origin of cooperative O2 binding in human adult hemoglobin (HbA), aims to answering why HbA is a tetramer consisting of two α and two β subunits. Here, we focus on the Fe-His bond, the sole coordination bond connecting heme to a globin. The Fe-His stretching frequencies reflect the O2 affinity and also the magnitude of strain imposed through globin by inter-subunit interactions, which is the origin of cooperativity. Cooperativity was first explained by Monod, Wyman, and Changeux, referred to as the MWC theory, but later explained by the two tertiary states (TTS) theory. Here, we related the higher-order structures of globin observed mainly by vibrational spectroscopy to the MWC theory. It became clear from the recent spectroscopic studies, X-ray crystallographic analysis, and mutagenesis experiments that the Fe-His bonds exhibit different roles between the α and β subunits. The absence of the Fe-His bond in the α subunit in some mutant and artificial Hbs inhibits T to R quaternary structural change upon O2 binding. However, its absence from the β subunit in mutant and artificial Hbs simply enhances the O2 affinity of the α subunit. Accordingly, the inter-subunit interactions between α and β subunits are nonsymmetric but substantial for HbA to perform cooperative O2 binding. [ABSTRACT FROM AUTHOR]

Coproporpyhrin III is the substrate of coproporphyrin ferrochelatases (CpfCs). These enzymes catalyse the insertion of ferrous iron into the porphyrin ring. This is the penultimate step within the coproporphyrin‐dependent haeme biosynthesis pathway. This pathway was discovered in 2015 and is mainly utilised by monoderm bacteria. Prior to this discovery, monoderm bacteria were believed to utilise the protoporphyrin‐dependent pathway, analogously to diderm bacteria, where the substrate for the respective ferrochelatase is protoporphyrin IX, which has two propionate groups at positions 6 and 7 and two vinyl groups at positions 2 and 4. In this work, we describe for the first time the interactions of the four‐propionate substrate, coproporphyrin III, and the four‐propionate product, iron coproporphyrin III (coproheme), with the CpfC from Listeria monocytogenes and pin down differences with respect to the protoporphyrin IX and haeme b complexes in the wild‐type (WT) enzyme. We further created seven LmCpfC variants aiming at altering substrate and product coordination. The WT enzyme and all the variants were comparatively studied by spectroscopic, thermodynamic and kinetic means to investigate in detail the H‐bonding interactions, which govern complex stability and substrate specificity. We identified a tyrosine residue (Y124 in LmCpfC), coordinating the propionate at position 2, which is conserved in monoderm CpfCs, to be highly important for binding and stabilisation. Importantly, we also describe a tyrosine‐serine‐threonine triad, which coordinates the propionate at position 4. The study of the triad variants indicates structural differences between the coproporphyrin III and the coproheme complexes. Enzyme: EC 4.99.1.9 [ABSTRACT FROM AUTHOR]

Mycobacterium tuberculosis DosS is critical for the induction of M. tuberculosis dormancy genes in response to nitric oxide (NO), carbon monoxide (CO), or hypoxia. These environmental stimuli, which are sensed by the DosS heme group, result in autophosphorylation of a DosS His residue, followed by phosphotransfer to an Asp residue of the response regulator DosR. To clarify the mechanism of gaseous ligand recognition and signaling, we investigated the hydrogen-bonding interactions of the iron-bound CO and NO ligands by site-directed mutagenesis of Glu-87 and His-89. Autophosphorylation assays and molecular dynamics simulations suggest that Glu-87 has an important role in ligand recognition, whereas His-89 is essential for signal transduction to the kinase domain, a process for which Arg-204 is important. Mutation of Glu-87 to Ala or Gly rendered the protein constitutively active as a kinase, but with lower autophosphorylation activity than the wild-type in the Fe(II) and the Fe(II)-CO states, whereas the E87D mutant had little kinase activity except for the Fe(II)-NO complex. The H89R mutant exhibited attenuated autophosphorylation activity, although the H89A and R204A mutants were inactive as kinases, emphasizing the importance of these residues in communication to the kinase core. Resonance Raman spectroscopy of the wild-type and H89A mutant indicates the mutation does not alter the heme coordination number, spin state, or porphyrin deformation state, but it suggests that interdomain interactions are disrupted by the mutation. Overall, these results confirm the importance of the distal hydrogen-bonding network in ligand recognition and communication to the kinase domain and reveal the sensitivity of the system to subtle differences in the binding of gaseous ligands.

Prominent resonance Raman and photoluminescence spectroscopic differences between AA' and AB stacked bilayer molybdenum disulfide (MoS2) grown by chemical vapor deposition are reported. Bilayer MoS2 islands consisting of the two stacking orders were obtained under identical growth conditions. Resonance Raman and photoluminescence spectra of AA' and AB stacked bilayer MoS2 were obtained on Au nanopyramid surfaces under strong plasmon resonance. Both resonance Raman and photoluminescence spectra show distinct features indicating clear differences in interlayer interaction between these two phases. The implication of these findings on device applications based on spin and valley degrees of freedom will be discussed.

Ultraviolet resonance Raman (UVRR) scattering is a highly sensitive and selective vibrational spectroscopic technique with a broad range of applications from polyaromatic hydrocarbons (PAHs) to biomolecular systems (peptides/proteins and nucleic acids) and catalysts. The interpretation of experimental UVRR spectra is not as straightforward as in purely vibrational Raman scattering (Placzek approximation) due to the involvement of higher lying electronic states and vibronic coupling. This necessitates the comparison with theoretical UVRR spectra computed by electronic structure calculations. Anthracene is an ideal model system for such a comparison between experiment and theory because it is rigid, symmetric, and of moderate size. By taking into account Herzberg–Teller contributions including Duschinsky effects, bulk solvent effects, and anharmonic contributions, a good qualitative agreement close to the resonance condition is achieved. The present study shows that within the framework of time‐dependent density functional theory (TD‐DFT), a general and robust approach for the analysis and interpretation of resonance Raman spectra of medium‐ to large‐size molecules is available. [ABSTRACT FROM AUTHOR]

Ultraviolet resonance Raman (UVRR) spectroscopy is a powerful vibrational spectroscopic technique for the label-free monitoring of molecular recognition of peptides or proteins with supramolecular ligands such as guanidiniocarbonyl pyrroles (GCPs). The use of UV laser excitation enables Raman binding studies of this class of supramolecular ligands at submillimolar concentrations in aqueous solution and provides a selective signal enhancement of the carboxylate binding site (CBS). A current limitation for the extension of this promising UVRR approach from peptides to proteins as binding partners for GCPs is the UV-excited autofluorescence from aromatic amino acids observed for laser excitation wavelengths >260 nm. These excitation wavelengths are in the electronic resonance with the GCP for achieving both a signal enhancement and the selectivity for monitoring the CBS, but the resulting UVRR spectrum overlaps with the UV-excited autofluorescence from the aromatic binding partners. This necessitates the use of a laser excitation

Direct electrochemical responses of cytochrome c on a gold electrode modified by thiol-containing monolayer of Schiff base (SB) or its metal complexes (M-SB, M = Fe, Mn, Cr) have been investigated to determine the role of the monolayer in promoting heterogeneous electron transfer. The monolayer of the SB prepared in situ by the sequential association of L-cysteine followed by conjugation with salicylaldehyde on a freshly cleaned gold electrode formed a stable thin film of cytochrome c. The thin films of cytochrome c on SB or M-SB modified electrode showed quasi-reversible cyclic voltammetric signals, and the observed midpoint potential agreed with that reported earlier. The surface coverage (Γ) of the active cytochrome c in the thin film was found to vary with the nature of the metal ion in M-SB, and the value of Γ increased in the order: SB < Mn-SB < Cr-SB < Fe-SB in the monolayer, suggesting that the metal ion coordination may be important for the stability of the monolayer of M-SB and the formation of the thin film of the protein. The electron transfer rates ( k s ) were found to be faster with the SB or M-SB monolayers compared to many other small promoters reported earlier. The k s values were however almost independent of the metal binding to the SB, indicating that the electron transfer across the monolayer of the SB complex may not be the rate determining step for the heterogeneous electron transfer from the gold electrode to cytochrome c. The monolayers of Schiff base (SB) and its metal complexes self-assembled through thiol linkages to the gold electrode was shown to efficiently promote direct electrochemistry of cytochrome c immobilized as thin films on the promoter at the electrode surface. [ABSTRACT FROM AUTHOR]

Resonance Raman spectra and excitation profiles have been measured and semiquantitatively modeled for core/shell quantum dots consisting of 2.7 nm diameter zincblende CdSe cores and thin (0.5 nm) or thick (1.6 nm) CdS shells. The Raman spectra show previously reported trends of increased peak frequency for both the CdSe and the CdS longitudinal optical (LO) phonons with increasing shell thickness. We also find a strong dependence of the peak CdS frequency on excitation energy and a large discrepancy between the experimental frequency of the CdSe + CdS combination band and the sum of the corresponding fundamental frequencies. This suggests that the dominant transitions at high excitation energies are localized on either the CdSe core or the CdS shell and thereby cannot enhance combination band transitions between core and shell. The CdS to CdSe Raman intensity ratios at high excitation energies further support this picture. The electron-phonon coupling for the CdSe LO phonon in the lowest excitonic transition is slightly weaker in the core/shell structures than in pure CdSe quantum dots, contrary to expectations for the Fröhlich coupling mechanism. Possible explanations for this discrepancy are discussed.

[Display omitted] • Ferrochelatases insert ferrous iron in porphyrins in the heme biosynthesis pathway. • The porphyrin proximal ligand is not conserved in the active site of ferrochelatases. • Proximal mutations alter the H-bonds between the porphyrin and the protein. • Effects on the activity are induced by the polarity of the mutated proximal ligand. • The weak coordination by the proximal ligand is essential for substrate and product. Ferrochelatases catalyze the insertion of ferrous iron into the porphyrin during the heme b biosynthesis pathway, which is fundamental for both prokaryotes and eukaryotes. Interestingly, in the active site of ferrochelatases, the proximal ligand coordinating the porphyrin iron of the product is not conserved, and its catalytic role is still unclear. Here we compare the L. monocytogenes bacterial coproporphyrin ferrochelatase native enzyme together with selected variants, where the proximal Tyr residue was replaced by a His (i.e. the most common ligand in heme proteins), a Met or a Phe (as in human and actinobacterial ferrochelatases, respectively), in their Fe(III), Fe(II) and Fe(II)–CO adduct forms. The study of the active site structure and the activity of the proteins in solution has been performed by UV–vis electronic absorption and resonance Raman spectroscopies, biochemical characterization, and classical MD simulations. All the mutations alter the H-bond interactions between the iron porphyrin propionate groups and the protein, and induce effects on the activity, depending on the polarity of the proximal ligand. The overall results confirm that the weak or non-existing coordination of the porphyrin iron by the proximal residue is essential for the binding of the substrate and the release of the final product. [ABSTRACT FROM AUTHOR]

Resonance Raman spectra and absolute differential Raman cross-sections have been measured for CdSe nanocrystals in both the wurtzite and zincblende crystal forms at four excitation wavelengths from 457.9 to 514.5 nm. The frequency and bandshape of the longitudinal optical (LO) phonon fundamental is essentially identical for both crystal forms at each excitation wavelength. The LO phonon overtone to fundamental intensity ratio appears to be slightly higher for the wurtzite form, which may suggest slightly stronger exciton-phonon coupling from the Fröhlich mechanism in the wurtzite form. The LO fundamental Raman cross-sections are very similar for both crystal forms at each excitation wavelength. © 2012 Elsevier B.V. All rights reserved.

Resonance Raman spectra and absolute differential Raman cross-sections have been measured for CdSe nanocrystals in both the wurtzite and zincblende crystal forms at four excitation wavelengths from 457.9 to 514.5 nm. The frequency and bandshape of the longitudinal optical (LO) phonon fundamental is essentially identical for both crystal forms at each excitation wavelength. The LO phonon overtone to fundamental intensity ratio appears to be slightly higher for the wurtzite form, which may suggest slightly stronger exciton-phonon coupling from the Fröhlich mechanism in the wurtzite form. The LO fundamental Raman cross-sections are very similar for both crystal forms at each excitation wavelength. © 2012 Elsevier B.V. All rights reserved.

We unravel the potentialities of resonance Raman spectroscopy to detect ibuprofen in diluted aqueous solutions. In particular, we exploit a fully polarizable quantum mechanics/molecular mechanics (QM/MM) methodology based on fluctuating charges coupled to molecular dynamics (MD) in order to take into account the dynamical aspects of the solvation phenomenon. Our findings, which are discussed in light of a natural bond orbital (NBO) analysis, reveal that a selective enhancement of the Raman signal due to the normal mode associated with the C–C stretching in the ring, νC=C, can be achieved by properly tuning the incident wavelength, thus facilitating the recognition of ibuprofen in water samples.

A large amount of research within organic biosensors is dominated by organic electrochemical transistors (OECTs) that use conducting polymers such as poly(3,4‐ethylene dioxythiophene) doped with poly(styrenesulfonate) (PEDOT:PSS). Despite the recent advances in OECT‐based biosensors, the sensing is solely reliant on the amperometric detection of the bioanalytes. This is typically accompanied by large undesirable parasitic electrical signals from the electroactive components in the electrolyte. Herein, we present the use of in situ resonance Raman spectroscopy to probe subtle molecular structural changes of PEDOT:PSS associated with its doping level. We demonstrate how such doping level changes of PEDOT:PSS can be used, for the first time, on operational OECTs for sensitive and selective metabolite sensing while simultaneously performing amperometric detection of the analyte. We test the sensitivity by molecularly sensing a lowest glucose concentration of 0.02 mM in phosphate‐buffered saline solution. By changing the electrolyte to cell culture media, the selectivity of in situ resonance Raman spectroscopy is emphasized as it remains unaffected by other electroactive components in the electrolyte. The application of this molecular structural probe highlights the importance of developing biosensing probes that benefit from high sensitivity of the material's structural and electrical properties while being complimentary with the electronic methods of detection. [ABSTRACT FROM AUTHOR]

Abstract: Pentacyanidoferrate(II) complexes of aromatic N-heterocycles, such as 4-cyanopyridine, exhibit characteristic colors and strong metallochromism associated with the donor-acceptor interactions of the metal ions with the cyanide ligands. In the presence of transition metal ions insoluble polymeric complexes are formed, displaying bright yellow, red, brown and green colors with zinc(II), nickel(II), copper(II) and iron(III) ions, respectively. Such metallochromic response is better observed on filter paper, allowing applications in analytical spot tests. The effects can be explored visually and probed by means of modern instrumental facilities, including spectrophotometric and resonance Raman techniques. In this way, by using the cyanopyridinepentacyanidoferrates, the Prussian Blue test for ferric ions can be extended to the entire row of transition metal elements, providing a new and modern insight of such classical Feigl’s spot tests.

Channelrhodopsins (ChRs) belong to the unique class of light-gated ion channels. The structure of channelrhodopsin-2 from Chlamydomonas reinhardtii (CrChR2) has been resolved, but the mechanistic link between light-induced isomerization of the chromophore retinal and channel gating remains elusive. Replacements of residues C128 and D156 (DC gate) resulted in drastic effects in channel closure. T127 is localized close to the retinal Schiff base and links the DC gate to the Schiff base. The homologous residue in bacteriorhodopsin (T89) has been shown to be crucial for the visible absorption maximum and dark–light adaptation, suggesting an interaction with the retinylidene chromophore, but the replacement had little effect on photocycle kinetics and proton pumping activity. Here, we show that the T127A and T127S variants of CrChR2 leave the visible absorption maximum unaffected. We inferred from hybrid quantum mechanics/molecular mechanics (QM/MM) calculations and resonance Raman spectroscopy that the hydroxylic side chain of T127 is hydrogen-bonded to E123 and the latter is hydrogen-bonded to the retinal Schiff base. The C=N–H vibration of the Schiff base in the T127A variant was 1674 cm−1, the highest among all rhodopsins reported to date. We also found heterogeneity in the Schiff base ground state vibrational properties due to different rotamer conformations of E123. The photoreaction of T127A is characterized by a long-lived P2380 state during which the Schiff base is deprotonated. The conservative replacement of T127S hardly affected the photocycle kinetics. Thus, we inferred that the hydroxyl group at position 127 is part of the proton transfer pathway from D156 to the Schiff base during rise of the P3530 intermediate. This finding provides molecular reasons for the evolutionary conservation of the chemically homologous residues threonine, serine, and cysteine at this position in all channelrhodopsins known so far. [ABSTRACT FROM AUTHOR]

Featured Application: Reliable and rapid analysis of free fatty acid (FFA) in olive oil is possible from the relative intensity ratio of characteristic vibrational modes observed by Raman spectroscopy. Free fatty acid (FFA) is one of the most critical parameters for evaluating the quality of olive oil. In this paper, we present a simple and rapid Raman spectroscopy method for analyzing free fatty acid in olive oil. First, FFA degradation of carotenoids in olive oil is confirmed by analyzing the relative intensity of characteristic vibrational modes and introducing an intensity decrease factor. Second, it is demonstrated that the relative intensity ratio of the two characteristic vibrational modes at 1525 cm−1 and 1655 cm−1 presents a good and rapid analysis of FFA content in olive oil; the relative intensity ratio decreases linearly with FFA content. In addition, resonance Raman scattering of carotenoid is discussed, showing that a green laser should be utilized to study FFA in olive oil. [ABSTRACT FROM AUTHOR]

Phenothiazine (PTZ) derivatives represent an important class of molecules, being studied in a number of fields of chemical and pharmaceutical research. The interesting chemical and biological properties of PTZs are considered to be related to their relative stable radical cations, whose formation and reactivity have been extensively studied. In this work, the radical cation of phenothiazine (PTZ+) was generated by the reaction with the mordenite solid acid, an environment in which this species is stabilized. The most intense electronic transition of PTZ+ is located at 516 nm. In order to characterize the electronic and molecular structure of this radical species, a resonance Raman and theoretical calculations of the structure, PTZ+ vibrational frequencies and electronic spectrum were calculated employing DFT B3LYP/6-31G(d,p) and TDDFT methods. In the ground state, PTZ+ is planar, in contrast to the folded structure of neutral PTZ. The strong Raman band at 476 cm−1 was assigned to a CSC bending mode. The reason for its preferential enhancement was investigated using TDDFT, in order to obtain the molecular orbitals involved in the electronic transition at 516 nm. The TDDFT calculations show that this transition is from SOMO-1 and SOMO-2, both double occupied molecular orbitals, localized at the aromatic rings and goes toward SOMO (single occupied molecular orbital). This SOMO has contributions of sulphur and nitrogen atomic orbitals, but with predominance of sulphur atomic orbitals, which are absent in SOMO-1 and SOMO-2. The predominance of sulphur atomic orbitals in the SOMO explains the preferential resonance Raman enhancement of a CSC vibrational mode. Image 1 • Phenothiazine cation radical (PTZ+) can be formed and stabilized in mordenite zeolite. • PTZ + gives resonance Raman spectra by excitation at the 516 nm electronic transition. • New ab initio calculations brought some changes in the vibrational assignment. • The most intensified vibrational mode is the C S C angular deformation. • The electronic excited state D 1 is planar and D 2 /D 3 have folded geometry. [ABSTRACT FROM AUTHOR]

Glioma is one of the most refractory types of brain tumor. Accurate tumor boundary identification and complete resection of the tumor are essential for glioma removal during brain surgery. We present a method based on visible resonance Raman (VRR) spectroscopy to identify glioma margins and grades. A set of diagnostic spectral biomarkers features are presented based on tissue composition changes revealed by VRR. The Raman spectra include molecular vibrational fingerprints of carotenoids, tryptophan, amide I/II/III, proteins, and lipids. These basic in situ spectral biomarkers are used to identify the tissue from the interface between brain cancer and normal tissue and to evaluate glioma grades. The VRR spectra are also analyzed using principal component analysis for dimension reduction and feature detection and support vector machine for classification. The cross-validated sensitivity, specificity, and accuracy are found to be 100%, 96.3%, and 99.6% to distinguish glioma tissues from normal brain tissues, respectively. The area under the receiver operating characteristic curve for the classification is about 1.0. The accuracies to distinguish normal, low grade (grades I and II), and high grade (grades III and IV) gliomas are found to be 96.3%, 53.7%, and 84.1% for the three groups, respectively, along with a total accuracy of 75.1%. A set of criteria for differentiating normal human brain tissues from normal control tissues is proposed and used to identify brain cancer margins, yielding a diagnostic sensitivity of 100% and specificity of 71%. Our study demonstrates the potential of VRR as a label-free optical molecular histopathology method used for in situ boundary line judgment for brain surgery in the margins. [ABSTRACT FROM AUTHOR]

The excited‐state structural dynamics of benzaldehyde (BA) after population to the S3(πH‐1πL*) light‐absorbing state were studied using resonance Raman spectroscopy and complete active space self‐consistent field (CASSCF) calculations. The C‐band absorption cross section and the corresponding absolute resonance Raman cross sections in cyclohexane and methanol were simulated using the time‐dependent wave‐packets formalism, respectively. The results indicate that the major structural dynamics of BA and the homogeneous broadening of the absorption spectrum in cyclohexane are similar to those of BA in methanol or acetophenone (AP) in cyclohexane, whereas the inhomogeneous broadening of BA in cyclohexane is significantly different from that in methanol. It is proposed that the initial decay pathway of BA upon the C‐band absorption is mostly towards S3S2 and partly to S3,min. The roles of hydrogen bonding and polar–polar interaction in the spectral broadenings are discussed. [ABSTRACT FROM AUTHOR]

Although dimer radical ions of aromatic molecules in the liquid‐solution phase have been intensely studied, the understanding of charge‐localized dimers, in which the extra charge is localized in a single monomer unit instead of being shared between two monomer units, is still elusive. In this study, the formation of a charge‐localized dimer radical cation of 2‐ethyl‐9,10‐dimethoxyanthracene (DMA), (DMA)2.+ is investigated by transient absorption (TA) and time‐resolved resonance Raman (TR3) spectroscopic methods combined with a pulse radiolysis technique. Visible‐ and near‐IR TA signals in highly concentrated DMA solutions supported the formation of non‐covalent (DMA)2.+ by association of DMA and DMA.+. TR3 spectra obtained from 30 ns to 300 μs time delays showed that the major bands are quite similar to those of DMA except for small transient bands, even at 30 ns time delay, suggesting that the positive charge of non‐covalent (DMA)2.+ is localized in a single monomer unit. From DFT calculations for (DMA)2.+, our TR3 spectra showed the best agreement with the calculated Raman spectrum of charge‐localized edge‐to‐face T‐shaped (DMA)2.+, termed DT.+, although the charge‐delocalized asymmetric π‐stacked face‐to‐face (DMA)2.+, termed DF3.+, is the most stable structure of (DMA)2.+ according to the energetics from DFT calculations. The calculated potential energy curves for the association between DMA.+ and DMA showed that DT.+ is likely to be efficiently formed and contribute significantly to the TR3 spectra as a result of the permanent charge‐induced Coulombic interactions and a dynamic equilibrium between charge localized and delocalized structures. Charge‐induced dimer radical cations were generated by pulse radiolysis of 2‐ethyl‐9,10‐dimethoxyanthracene in solution. The formation of non‐covalent charge‐localized dimer radical cations was characterized by time‐resolved spectroscopic methods and DFT calculations. [ABSTRACT FROM AUTHOR]

The initial decay dynamics of 6AU in the S2 state was investigated by using resonance Raman spectroscopy, the time‐dependent wave‐packet theory in a Brownian oscillator model, and complete‐active space self‐consistent field (CASSCF) protocol. The vibrational spectra and the ultraviolet absorption bands were assigned on the basis of the Fourier transform (FT)‐Raman, FT‐infrared measurements, the density‐functional theory computations, and the normal mode analysis. The absorption cross section and the absolute resonance Raman cross sections were simulated simultaneously by using the time‐dependent wave‐packet theory in a Brownian oscillator model. The obtained normal mode displacements of the Franck–Condon active modes were then converted to the short‐time structural dynamics in easy‐to‐visualize internal coordinates. The roles of two pathways via the S2 → S1 internal conversion and the S2 → T3 intersystem crossing were evaluated through the comparison between the short‐time structural dynamics and the CASSCF/CASTP2 calculated structural changes between FC and S2S1 or between FC and S2T3. The results indicate that the structural dynamics in the Franck–Condon region of the S2 state is mostly toward the S2/S1 conical intersection, which supports the conclusion that the S2 → S1 internal conversion dominants the initial decay pathway of 6AU as revealed by the broadband fs TA spectroscopy, whereas the barrierless S2 → T3 intersystem‐crossing process is negligible owing to weak spin‐orbital coupling and unfavorable subsequent T3 → T2 → T1 decay. The reaction coordinates towards the planar S2(ππ*)/S1(nπ*) and severely distorted S2(ππ*)/S0 conical intersection points are proposed respectively, and the solvent effect on the initial decay mechanisms of 6AU, uracil, and thymine is clarified. The decay dynamics of 6‐azauracil was studied by using resonance Raman spectroscopy and complete‐active space self‐consistent field calculations. The initial wave‐packets of 6AU evolve predominantly towards S2S1 conical intersection but rather to S2T2 or S2T3 curve‐crossing. The significant short‐time structural dynamics along the CO stretch reaction coordinate for 6AU is an unambiguous evidence that the elimination of the S2 → S0 channel by more rigid C5N6 double bond initiates from the Franck–Condon region. [ABSTRACT FROM AUTHOR]

Improvements in the detection of biomarkers indicative of disease continue to be vital to human health. Toward this end, this paper presents (a) the development and characterization of a biomarker detection strategy based on the inherently stronger signals generated by surface‐enhanced resonance Raman scattering (SERRS), as opposed to surface‐enhanced Raman scattering (SERS); (b) the application of this approach to the detection of mannose‐capped lipoarabinomannan (ManLAM), an antigenic marker indicative of active tuberculosis infection; and (c) a comparison of readout for this SERRS platform to that of the more frequently used approach based on SERS. More specifically, the work detailed herein describes the design and testing of a SERRS immunoassay that incorporates a resonance Raman‐enhanced adlayer of cyanine 5 on a smooth gold capture surface and its application to biomarker detection when "turned on" by the tagging of captured ManLAM with gold nanoparticle labels. The results of these experiments demonstrated an improvement in the detection of ManLAM spiked into human serum in terms of limit of detection by 10× and analytical sensitivity of almost 40× when compared with SERS. Findings also indicate that these improvements arise primarily from the intrinsic increase in signal strength due to the resonance Raman effect and a small but measurable increase in nanoparticle label density. Potential routes to further improve the performance of this approach to immunoassay signal generation are briefly discussed. We apply turn‐on surface‐enhanced resonance Raman scattering (SERRS) as a novel detection strategy for a disease biomaker. This paper includes a detailed characterization of this novel sensor and a head‐to‐head performance comparison with a more conventional assay system. Ultimately we realized a 10× improvement in limit of detection and a ~40× improvement in analytical sensitivity. [ABSTRACT FROM AUTHOR]

The resonance Raman (rR) spectra of the oxidized type 1 copper active site (Cu T1) in Thermus thermophilus HB27 laccase (Tth -lac) has been determined in the 20 to 80 °C temperature range using 633-nm excitation. The positions and relative intensities of rR peaks are virtually independent of temperature, indicating that Cu T1 ligation is robust over the investigated range. The intensity-weighted average of Tth -lac Cu-S Cys vibrations (< ν (Cu-S Cys)>) = 423 cm−1) is higher than those of most cupredoxins but is comparable to those of other multicopper oxidases (MCOs). < ν (Cu-S Cys)> values for Tth -lac and several Cu T1 centers in cupredoxins and MCOs do not correlate well with Cu-S Cys bond lengths but do exhibit systematic trends with redox thermodynamic properties. F. Ann Walker was a great scholar and dear friend. While at Columbia in the early 1960s, I (HBG) followed her graduate work at Brown on the effects of axial ligands on vanadyl ion EPR spectra. Dick Carlin, her thesis adviser, invited me to serve as external member of her thesis committee. I joined, made my way to Providence, met her just before the exam, and greatly admired (enjoyed!) her thoughtful responses to questions from physical chemists about metal-oxo electronic structures. Our friendship grew stronger over the years, enhanced by lively discussions of heme protein chemistry in San Francisco, Pasadena, Tucson, and at Gordon Research Conferences. Ann was a superstar in biological inorganic chemistry. She will be sorely missed but not forgotten. The resonance Raman spectrum of the blue copper active site in Thermus thermophilus HB27 laccase exhibits features attributable to Cu-S Cys vibrations. The invariance of this spectrum in the 20–80 °C temperature range indicates that the coordination environment remains intact. [Display omitted] • The resonance Raman spectrum of the type 1 copper site in Thermus thermophilus HB27 laccase is temperature independent. • The type 1 copper coordination environment in Thermus thermophilus HB27 laccase is robust between 20 and 80 °C. • Average Cu-S(Cysteine) vibrational frequencies in type 1 copper active sites correlate with redox thermodynamic properties. [ABSTRACT FROM AUTHOR]

The soil chromophyte alga Xanthonema (X.) debile contains only non-carbonyl carotenoids and Chl-a. X. debile has an antenna system denoted Xanthophyte light-harvesting complex (XLH) that contains the carotenoids diadinoxanthin, heteroxanthin, and vaucheriaxanthin. The XLH pigment stoichiometry was calculated by chromatographic techniques and the pigment-binding structure studied by resonance Raman spectroscopy. The pigment ratio obtained by HPLC was found to be close to 8:1:2:1 Chl-a:heteroxanthin:diadinoxanthin:vaucheriaxanthin. The resonance Raman spectra suggest the presence of 8-10 Chl-a, all of which are 5-coordinated to the central Mg, with 1-3 Chl-a possessing a macrocycle distorted from the relaxed conformation. The three populations of carotenoids are in the all-trans configuration. Vaucheriaxanthin absorbs around 500-530 nm, diadinoxanthin at 494 nm and heteroxanthin at 487 nm at 4.5 K. The effective conjugation length of heteroxanthin and diadinoxanthin has been determined as 9.4 in both cases; the environment polarizability of the heteroxanthin and diadinoxanthin binding pockets is 0.270 and 0.305, respectively. [ABSTRACT FROM AUTHOR]

Abstract Cationic manganese(III) ortho N -substituted pyridylporphyrins (MnP) act as efficient antioxidants catalyzing superoxide dismutation and accelerating peroxynitrite reduction. Importantly, MnP can reach mitochondria offering protection against reactive species in different animal models of disease. Although an LC-MS/MS-based method for MnP quantitation and subcellular distribution has been reported, a direct method capable of evaluating both the uptake and the redox state of MnP in living cells has not yet been developed. In the present work we applied resonance Raman (RR) spectroscopy to analyze the intracellular accumulation of two potent MnP-based lipophilic SOD mimics, MnTnBuOE-2-PyP5+ and MnTnHex-2-PyP5+ within endothelial cells. RR experiments with isolated mitochondria revealed that the reduction of Mn(III)P was affected by inhibitors of the electron transport chain, supporting the action of MnP as efficient redox active compounds in mitochondria. Indeed, RR spectra confirmed that MnP added in the Mn(III) state can be incorporated into the cells, readily reduced by intracellular components to the Mn(II) state and oxidized by peroxynitrite. To assess the combined impact of reactivity and bioavailability, we studied the kinetics of Mn(III)TnBuOE-2-PyP5+ with peroxynitrite and evaluated the cytoprotective capacity of MnP by exposing the endothelial cells to nitro-oxidative stress induced by peroxynitrite. We observed a preservation of normal mitochondrial function, attenuation of cell damage and prevention of apoptotic cell death. These data introduce a novel application of RR spectroscopy for the direct detection of MnP and their redox states inside living cells, and helps to rationalize their antioxidant capacity in biological systems. Graphical abstract fx1 Highlights • Raman Resonance was utilized to reveal the redox state of Mn-porphyrins (MnP) in cells. • Mn(III)P are readily reduced intracellularly to the Mn(II) state. • Intramitochondrial oxidation of a peroxynitrite-sensitive probe is inhibited by MnP. • The cytotoxicity of peroxynitrite is neutralized by MnP via a catalytic redox cycle. [ABSTRACT FROM AUTHOR]

The Raman ν1 band corresponding to the polarization of various length carotenoid (Car) and polyene molecules was theoretically analysed using the density functional theory (DFT) approach. The polarization and other properties of Car and polyene monomers were estimated by using global scalar properties. The results demonstrate a linear dependence between the frequency of the so-called ν1 Raman band corresponding to the C=C stretching modes, and the global hardness (and global softness) for all molecules of different conjugation lengths. Linear correlations between all global scalar properties and the conjugation length were for polyene structures only. From these calculations an additional relationship was also identified: upon s-cis-isomerisation the effective conjugation length and global softness increased for polyenes, while the effective conjugation length and global softness decreased for carotenoids containing β-rings at their ends. According to the electrophilicity index study, charge transfer processes (CT) should be favourable in longer carotenoid and polyene structures. A linear dependence of electronegativity was found for polyene and particular Cars subgroups. The electrophilicity index was very sensitive to special groups bonded to the polyene chain of Cars. Finally, the conjugation length of the Cars did not have a linear dependence on the electronegativity, chemical potential and electrophilicity index, but almost a linear dependence was seen on the global hardness while the polyene models had a linear dependence in all cases. [ABSTRACT FROM AUTHOR]