Surface-enhanced Resonance Raman Spectra Research Articles

Effects of magnetite on nitrate-dependent anaerobic oxidation of methane in an anaerobic membrane biofilm reactor: Metatranscriptomic analysis and mechanism prediction

Magnetite has been widely reported to accelerate methane production in anaerobic digestion. However, the effects of magnetite on the process of methane consumption, specifically nitrate-dependent anaerobic oxidation of methane (AOM), and its underlying mechanisms remain poorly understood. In this study, the addition of magnetite significantly improved the removal of nitrate in an anaerobic membrane biofilm reactor (AnMBfR) (25.2 ± 2.5 mg NO3−-N/L/d) compared to that in an AnMBfR without magnetite (8.7 ± 4.2 mg NO3−-N/L/d). Metatranscriptomic analysis showed that genes encoding type IV pilus assembly proteins were highly expressed in nitrate/nitrite-reducing bacteria in the biofilms of the two AnMBfRs. Specifically, the transcript abundance of these genes was observed to be higher in the presence of magnetite (gene expression levels, log2FPKM = 13.08) compared to the absence of magnetite (12.04). Biofilms with magnetite exhibited a linear increase in electron transfer resistance with increasing temperature, and the decrease in pH significantly increased their conductivity, indicating a metallic-like conductivity. Contrarily, an increase in temperature or decrease in pH did not influence the resistance or conductivity of biofilms without magnetite. Some of these cytochrome c (CYC)-like proteins were electrically active in the electrochemical Fourier transform infrared spectra and were closely associated with the outer-membrane multi-heme c-type cytochromes (OMCs). The intensities of the OMC-like bands in the surface-enhanced resonance Raman spectra with biofilms in the presence of magnetite were higher than those without magnetite. This study suggests that magnetite promotes the nitrate-dependent AOM process because of the formation of methanotrophic consortia based on direct interspecies electron transfer (DIET).

Simultaneous Sensing of H2 O, D2 O and HOD through Peroxo Vibrations.

Detection of HOD simultaneously in the presence of a mixture of H2 O and D2 O is still an experimental challenge. Till date, there is no literature report of simultaneous detection of H2 O, D2 O and HOD based on vibrational spectra. Herein we report simultaneous quantitative detection of H2 O, D2 O and HOD in the same reaction mixture with the help of bridged polynuclear peroxo complex in absence and presence of Au nanoparticles on the basis of a peroxide vibrational mode in resonance Raman and surface enhanced resonance Raman spectrum. We synthesize bridged polynuclear peroxo complex in different solvent mixture of H2 O and D2 O. Due to the formation of different nature of hydrogen bonding between peroxide and solvent molecules (H2 O, D2 O and HOD), vibrational frequency of peroxo bond is significantly affected. Mixtures of different H2 O and D2 O concentrations produce different HOD concentrations and that lead to different intensities of peaks positioned at 897, 823 and 867 cm-1 indicating H2 O, D2 O and HOD, respectively. The lowest detection limits (LODs) were 0.028 mole fraction of D2 O in H2 O and 0.046 mole faction of H2 O in D2 O. In addition, for the first time the results revealed that the cis-peroxide forms two hydrogen bonds with solvent molecules.

Vibrational Spectro-Electrochemistry of Heme Proteins

Heme proteins perform a plethora of distinct cellular functions, including e.g. electron transport (ET), energy conversion, detoxification, catalysis, signaling, and gene regulation, and as such inspire a myriad of biotechnological applications. We use resonance Raman (RR) and Surface enhanced RR (SERR) spectroscopies to probe the architecture of the heme pocket in diverse heme proteins and enzymes, which is essential for the understanding of their physiological properties as well as for the evaluation of their potential for development of the 3rd generation bioelectronic devices (1,2). Moreover, plasmonic metal that gives origin to the surface enhancement of the Raman signal of the molecules found in its close proximity can serve as an electrode, thus driving electrochemical processes. In the case of heme proteins attached to plasmonic Ag electrodes, SERR spectra selectively show vibrational bands originating from the heme moiety only, which are sensitive to spin, coordination and redox state and of the heme iron. These properties that govern the catalytic performance of heme enzymes can be monitored in potential dependent manner by SERR spectro-electrochemistry.We have demonstrated that SERR spectro-electrochemistry possesses unique capacity of to i) disentangle ET processes in multi hemic proteins, such as 28 heme containing nitrite reductase, which represent a challenge for all other experimental approaches and ii) detect subtle immobilization induced structural changes in enzymes of biotechnological interest, which e.g. in the case of cytochrome P450 may prevent their successful applications (1-4). Here we show that SERRS monitoring of electrocatalytic processes by immobilized heme peroxidases, can provide information on catalytically relevant species in situ. Several members of a recently discovered family of heme dye-decolorizing peroxidases (DyPs) that possess remarkable catalytic properties in solution and high biotechnological potential, have been immobilized on biocompatible Ag electrodes. Their structural and electrocatalytic properties studied by RR, SERR spectro-electrochemistry and electrochemistry (2). The immobilized DyP from Pseudomonas putida (PpDyP), in particular, shows native structure and outstanding analytical and catalytic parameters, and hence an exceptional potential for development of 3rd generation biosensors for H2O2 detection. In terms of sensitivity, the bioelectrodes carrying immobilized PpDyP outperform HRP based counterparts reported in the literature (2,4). The biosensor based on a PpDyP variant that harbors mutations at the second shell of the heme cavity reveals further improved storage. Our work highlights the importance of integrated, multidisciplinary approach to simultaneously evaluate the structure and catalytic properties of the enzymes, which ensures faster identification and optimization of the promising candidates for biotechnological applications.

A Resonance Raman Marker Band Characterizes the Slow and Fast Form of Cytochrome c Oxidase.

Cytochrome c oxidase (CcO) in its as-isolated form is known to exist in a slow and fast form, which differ drastically in their ability to bind oxygen and other ligands. While preparation methods have been established that yield either the fast or the slow form of the protein, the underlying structural differences have not been identified yet. Here, we have performed surface enhanced resonance Raman (SERR) spectroscopy of CcO immobilized on electrodes in both forms. SERR spectra obtained in resonance with the heme a3 metal-to-ligand charge transfer (MLCT) transition at 650 nm displayed a sharp vibrational band at 748 or 750 cm-1 when the protein was in its slow or fast form, respectively. DFT calculations identified the band as a mode of the His-419 ligand that is sensitive to the oxygen ligand and the protonation state of Tyr-288 within the binuclear complex. Potential-dependent SERR spectroscopy showed a redox-induced change of this band around 525 mV versus Ag/AgCl exclusively for the fast form, which coincides with the redox potential of the Tyr-O/Tyr-O- transition. Our data points to a peroxide ligand in the resting state of CcO for both forms. The observed frequencies and redox sensitivities of the Raman marker band suggest that a radical Tyr-288 is present in the fast form and a protonated Tyr-288 in the slow form.

Characterisation of the Cyanate Inhibited State of Cytochrome c Oxidase

Heme-copper oxygen reductases are terminal respiratory enzymes, catalyzing the reduction of dioxygen to water and the translocation of protons across the membrane. Oxygen consumption is inhibited by various substances. Here we tested the relatively unknown inhibition of cytochrome c oxidase (CcO) with isocyanate. In contrast to other more common inhibitors like cyanide, inhibition with cyanate was accompanied with the rise of a metal to ligand charge transfer (MLCT) band around 638 nm. Increasing the cyanate concentration furthermore caused selective reduction of heme a. The presence of the CT band allowed for the first time to directly monitor the nature of the ligand via surface-enhanced resonance Raman (SERR) spectroscopy. Analysis of isotope sensitive SERR spectra in comparison with Density Functional Theory (DFT) calculations identified not only the cyanate monomer as an inhibiting ligand but suggested also presence of an uretdion ligand formed upon dimerization of two cyanate ions. It is therefore proposed that under high cyanate concentrations the catalytic site of CcO promotes cyanate dimerization. The two excess electrons that are supplied from the uretdion ligand lead to the observed physiologically inverse electron transfer from heme a3 to heme a.

Intramolecular and Metal-to-Molecule Charge Transfer Electronic Resonances in the Surface-Enhanced Raman Scattering of 1,4-Bis((E)-2-(pyridin-4-yl)vinyl)naphthalene.

Electrochemical surface-enhanced Raman scattering (SERS) of the cruciform system 1,4-bis((E)-2-(pyridin-4-yl)vinyl)naphthalene (bpyvn) was recorded on nanostructured silver surfaces at different electrode potentials by using excitation laser lines of 785 and 514.5 nm. SERS relative intensities were analyzed on the basis of the resonance Raman vibronic theory with the help of DFT calculations. The comparison between the experimental and the computed resonance Raman spectra calculated for the first five electronic states of the Ag2-bpyvn surface complex model points out that the selective enhancement of the SERS band recorded at about 1600 cm−1, under 785 nm excitation, is due to a resonant Raman process involving a photoexcited metal-to-molecule charge transfer state of the complex, while the enhancement of the 1570 cm−1 band using 514.5 nm excitation is due to an intramolecular π→π* electronic transition localized in the naphthalenyl framework, resulting in a case of surface-enhanced resonance Raman spectrum (SERRS). Thus, the enhancement of the SERS bands of bpyvn is controlled by a general chemical enhancement mechanism in which different resonance processes of the overall electronic structure of the metal-molecule system are involved.

Charge-transfer surface-enhanced resonance Raman spectra of benzene-like derivative compounds under the effect of an external electric field.

Since the discovery of surface-enhanced resonance Raman scattering (SERS), elucidating the charge-transfer (CT) mechanism has been a challenging and controversial process. Different theoretical models have been proposed to explain the effect of applied electrode potential on SERS-CT, but achieving a high-quality conserved trend of experimental observations and explaining the nature of the selective enhancement of the signals is not a trivial task and the results and conclusions are still in dispute. We investigated recently the performance of time-dependent excited-state gradient approximation under the effects of a uniform finite electric field in a simulation of the experimental spectra of pyridine on an Ag electrode. The singular patterns of the experimental spectra for symmetric and non-symmetric benzene-like derivative compounds and the consistent trends of enhancements of their signals under various electrode potentials motivated us to extend our simulation studies to 4-methylpyridine, pyrazine and pyrimidine molecules on silver metal clusters. For these molecules, selective enhancement and de-enhancement of totally symmetric (υ6a, υ9a and υ8a) and non-totally symmetric (υ6b and υ8b) modes upon changing the field were obtained and matched well with experimental observations. The selective enhancement of each signal in a zero field was explained by means of excited-state vector gradients and excited-state charge density difference for the S0→ SCT transition. On-field calculations showed slight perturbations of the geometries and electronic structures of the molecules. These on-field calculations also directly affected the magnitude of specific excited-state vector gradients and dimensionless displacements, and moreover the patterns of the spectra. The results of this investigation provided insight into the nature of the selective enhancements of signals and may help researchers propose the selection rules of SERS-CT.

Comparative assessment of density functional methods for evaluating essential parameters to simulate SERS spectra within the excited state energy gradient approximation

The prospect of challenges in reproducing and interpretation of resonance Raman properties of molecules interacting with metal clusters has prompted the present research initiative. Resonance Raman spectra based on the time-dependent gradient approximation are examined in the framework of density functional theory using different methods for representing the exchange-correlation functional. In this work the performance of different XC functionals in the prediction of ground state properties, excitation state energies, and gradients are compared and discussed. Resonance Raman properties based on time-dependent gradient approximation for the strongly low-lying charge transfer states are calculated and compared for different methods. We draw the following conclusions: (1) for calculating the binding energy and ground state geometry, dispersion-corrected functionals give the best performance in comparison to ab initio calculations, (2) GGA and meta GGA functionals give good accuracy in calculating vibrational frequencies, (3) excited state energies determined by hybrid and range-separated hybrid functionals are in good agreement with EOM-CCSD calculations, and (4) in calculating resonance Raman properties GGA functionals give good and reasonable performance in comparison to the experiment; however, calculating the excited state gradient by using the hybrid functional on the hessian of GGA improves the results of the hybrid functional significantly. Finally, we conclude that the agreement of charge-transfer surface enhanced resonance Raman spectra with experiment is improved significantly by using the excited state gradient approximation.

Comment on "Sensitive marker bands for the detection of spin states of heme in surface-enhanced resonance Raman scattering spectra of metmyoglobin" by Y. Kitahama, M. Egashira, T. Suzuki, I. Tanabe and Y. Ozaki.

We contrast recently reported surface-enhanced resonance Raman spectra (SERRS) of myoglobin on silver nanoparticles with established knowledge about this complex. We conclude that the detected bands are not related to the spin states of the protein cofactor, being rather originated by a heme coordination change induced by the metal surface.

2nd coordination sphere controlled electron transfer of iron hangman complexes on electrodes probed by surface enhanced vibrational spectroscopy.

Iron hangman complexes exhibit improved catalytic properties regarding O2 and H2O2 reduction, which are attributed to the presence of a proton donating group in defined vicinity of the catalytic metal centre. Surface enhanced resonance Raman (SERR) and IR (SEIRA) spectro-electrochemistry has been applied concomitantly for the first time to analyse such iron hangman porphyrin complexes attached to electrodes in aqueous solution. While the SERR spectra yield information about the redox state of the central iron, the SEIRA spectra show protonation and deprotonation events of the 2nd coordination sphere. To investigate the influence of a proton active hanging group on the heterogeneous electron transfer between the iron porphyrin and the electrode, two hangman complexes with either an acid or ester functional group were compared. Using time resolved SERR spectroscopy the electron transfer rates of both complexes were determined. Complexes with an acid group showed a slow electron transfer rate at neutral pH that increased significantly at pH 4, while complexes with an ester group exhibited a much faster, but pH independent rate. SEIRA measurements were able to determine directly for the first time a pKa value of 3.4 of a carboxylic hanging group in the immobilized state that shifted to 5.2 in D2O buffer solution. The kinetic data showed an increase of the heterogeneous electron transfer rate with the protonation degree of the acid groups. From these results, we propose a PCET which is strongly modulated by the protonation state of the acid hanging group via hydrogen bond interactions.

Design of a peptide linker group to increase the surface enhanced Raman spectroscopy signal intensity of a rhodamine-nanoparticle system

The surface enhanced resonance Raman spectra of three modified carboxy-x-rhodamine dyes were recorded using Au nanoparticles and an excitation laser operating at 670 nm. The dyes were modified with a linker group designed both to increase the surface enhanced Raman spectroscopy signal and to couple the dye to the Au nanoparticles surface. The maximum signal intensity was recorded for a Cys-Gly linker with Cys thiol group acting as the coupling point to the Au surface and Gly-NH2 group used to attach the carboxy-x-rhodamine dye. This gave a signal intensity in the 1503 cm−1 Raman peak that was more than 20 times greater than for the unmodified dye. The Au nanoparticles used had a diameter of 49.8 ± 1.2 nm and were synthesised by the citrate reduction method.

Characterization of the Electron Transfer of a Ferrocene Redox Probe and a Histidine-Tagged Hemoprotein Specifically Bound to a Nitrilotriacetic-Terminated Self-Assembled Monolayer

We report the selective, controlled binding of a model redox probe, 1,1'-bis(N-imidazolylmethyl)ferrocene (Fc-Im2), and a small redox hemoprotein, histidine-tagged recombinant human neuroglobin (hNb), at the surface of metal electrodes (gold and SER-active silver) modified by a self-assembled monolayer (SAM) of a nitrilotriacetic (NTA)-terminated thiol. The resulting SAMs were characterized by cyclic voltammetry and surface-enhanced resonance Raman (SERR) spectroscopy coupled to electrochemistry. Once specifically bounded to the Ni(II)-NTA-modified gold electrode, nearly ideal cyclic voltammetric behavior with relatively fast electron-transfer (ET) communication through the SAM was determined for the Fc-Im2 redox probe. However, no direct electron transfer could be evidenced for the hNb redox protein under the same conditions. This outcome was different from the result obtained during SERR experiments coupled to electrochemistry in which a direct electrochemical conversion of hNb immobilized on a Ni(II)-NTA-modified SER-active Ag electrode was observed. The SERR spectra of the immobilized hNb was the same as the resonance Raman spectra of the protein in homogeneous solution, allowing us to conclude that the native structure of hNb was retained upon immobilization and that the direct ET was not the result of some partial or complete protein denaturation. The long-range ET rate constant (kET) through the SAM was determined by time-resolved SERR spectroscopy. A value of kET=0.12 s(-1) was obtained, which is within the predicted range of a fully nonadiabatic ET through a SAM thickness of approximately 26 A and close to the values previously determined for analogous small redox proteins at similar long-range ET distances. A SERR spectroelectrochemical titration of the immobilized hNb was also carried out, showing both an apparent standard potential (E0') negatively shifted by 100 mV compared with hNb in solution and a gentle slope in the titration curve. These results suggest a range of chemical environments in the surroundings of the redox protein and a variety of interactions with the NTA-terminated SAM. The influence of protein immobilization on E0' is discussed together with the long-range ET rate constant and molecular orientation of the surface-immobilized hNb.

Electron Transfer Kinetics of Cytochrome c Probed by Time-Resolved Surface-Enhanced Resonance Raman Spectroscopy

An improved setup including a measuring cell was designed for time-resolved surface-enhanced resonance Raman (SERR) spectroscopy. The cell is based on a rotating disk electrode (RDE) made from electrochemically roughened Ag. Cytochrome c (cc) adsorbed on a monolayer of mercaptoethanol is investigated with respect to heterogeneous electron transfer. Cyclic voltammograms and potential-dependent static SERR spectra indicate cc to be electroactive on the Ag electrode. The standard redox potential was found to be 234 mV. Time-resolved SERR spectra were then measured triggered by periodic potential pulses changing the protein between the oxidized and reduced state at a frequency of 10 Hz. Monoexponential functions obtained from the intensity of the band at 1361 cm-1 plotted versus time yielded the rate constants of heterogeneous electron transfer to be k(ox) = 46 +/- 7 s(-1) and k(red) = 84 +/- 20 s(-1). These relatively low rates are in line with the orientation of cc on the mercaptoethanol-modified Ag electrode. In this case the heme cleft pointed away from the surface thus hampering electron transfer.

Resonance Raman and Surface-Enhanced Resonance Raman Spectra of LH2 Antenna Complex from Rhodobacter sphaeroides and Ectothiorhodospira sp. Excited in the Qx and Qy Transitions †

Resonance Raman and Surface-Enhanced Resonance Raman Spectra of LH2 Antenna Complex from Rhodobacter sphaeroides and Ectothiorhodospira sp. Excited in the Qx and Qy Transitions †

Classification of single-molecule surface-enhanced resonance Raman spectra of Rhodamine 6G from isolated Ag colloidal particles by principal component analysis

Surface enhanced resonance Raman (SERR) spectra of Rhodamine 6G are measured from single isolated Ag particles and analyzed by using a chemometrics technique, principal component analysis (PCA). The Ag particles are incubated with various amounts of R6G yielding the ratio of Ag particles to R6G molecules from 1:1 to 1:1000. Acquired SERR spectra are considered due to a single or very few R6G molecules. PCA is used to determine the number of chemically distinguishable species that contribute to the measured SERR spectra. A simple clustering tool, score bi-plot, is then inspected on grouping of the SERR spectra. The spectra are found to be largely similar except for the variability in the intensity and position of the bands that is believed to be correlated with the lifetime of the strong enhancement at specific places on an Ag surface. The spectra from four different Ag particles carrying more than 1000 R6G molecules are, however, unambiguously separated. Different aspects of the applied data analysis method and physicochemical perspective of the results are discussed.

Immunoassay utilizing biochemistry reaction product via surface-enhanced Raman scattering in near field

We propose here a kind of applications of surface-enhanced Raman scatterin (SERS) to immunology. It is a new enzyme immunoassay based on SERS. In the propose system, antibody immobilized on a solid substrate reacts with antigen, which binds with another antibody labeled with peroxidase. If this immunocomplex is subjected to reaction with o-phenylenediamine and hydrogenperoxide, azoaniline is generated. This azo compound is adsorbed on a silver colloid and only the azo compound gives a strong surface-enhanced resonance Raman (SERRS) spectrum. A linear relationship was observed between the peak intensity of the N=N stretching band and the concentration of antigen, revealing that one can determin the concentration of antigen by the SERRS measurement of the reaction product. The detectic limit of this SERS enzyme immunoassay method was found to be about 10-15 mol/L.

Surface-Enhanced Resonance Raman Spectroscopic Studies of the Cd(II) and Hg(II) Complexes of 1-(2-Pyridylazo)-2-naphthol Adsorbed on Silver Sol

The resonance Raman (RR) and surface-enhanced resonance Raman (SERRS) spectra of M(PAN)2 complexes (M = Cd and Hg, PAN- = 1-(2-pyridylazo)-2-naphtholate) are reported and assigned, and the nature of the adsorbed species are determined. Vibrational assignments are supported by ab initio calculations at the B3-LYP/LanL2DZ level. There is clear evidence for chemisorption of these complexes on the silver surface, which gives rise to substantial alteration of the Raman spectrum. Comparison of the variation of Raman intensities with excitation wavelength for the RR and SERRS spectra indicates that there is a modification of electronic structure upon adsorption. Alterations in the Raman spectrum upon adsorption were successfully interpreted by ab initio calculations of the interaction of M(PAN)2 complexes with surface silver atoms binding through the azo group α-nitrogen atoms.

Surface and resonance enhanced micro-Raman spectroscopy of xanthene dyes at the single-molecule level

Surface enhanced resonance Raman spectra of various rhodamine dyes, of pyronine G and thiopyronine adsorbed on isolated silver clusters were recorded at the single-molecule level with a high-resolution confocal laser microscope equipped with a spectrograph and a CCD-detector. The comparison of the spectra shows that the xanthene chromophore dominates the surface enhanced resonance Raman scattering spectra and wavelength selective excitation shows that resonance excitation contributes significantly to the spectral enhancement.

Surface-Enhanced Resonance Raman Spectroscopic and Electrochemical Study of Cytochrome c Bound on Electrodes through Coordination with Pyridinyl-Terminated Self-Assembled Monolayers

Cytochrome c (Cyt-c) is immobilized on Ag and Au electrodes coated with self-assembled monolayers (SAM), comprised of pyridine-terminated alkanethiols and a shorter chain diluent thiol. Surface-enhanced resonance Raman (SERR) spectroscopy of coated Ag electrodes reveals that the adsorbed Cyt-c forms a potential-dependent coordination equilibrium with a predominant five-coordinated high-spin (5cHS) state in the reduced form and six-coordinated low-spin (6cLS) state prevailing in the oxidized form. In the oxidized species, the native Met-80 ligand of the heme is replaced by a pyridinyl residue of the bifunctional thiols that according to earlier scanning tunneling microscopy form islands in the hydrophobic monolayer. The redox potentials derived from the SERR band intensities are estimated to be -0.24 and -0.18 V (vs AgCl) for the 6cLS and 5cHS states, respectively, and lie in the range of the midpoint potential determined for Cyt-c on coated Au electrodes by cyclic voltammetry (CV). Whereas in the latter case, a nearly ideal Nernstian behavior for a one-electron couple was observed, the SERR spectroscopic analysis yields about 0.4 for the number of transferred electrons for each spin state. This discrepancy is mainly attributed to a distribution of substates of the immobilized protein in both the 6cLS and 5cHS forms, as indicated by substantial band broadening in the SERR spectra. These substates may arise from different orientations and heme pocket structures and exhibit different redox properties. Whereas SERR spectroscopy probes all adsorbed Cyt-c species including those that are largely redox inactive, CV measurements reflect only the substates that are electrochemically active.

Linearly moving low-volume spectroelectrochemical cell for microliter-scale surface-enhanced resonance Raman spectroscopy of heme proteins.

Surface-enhanced resonance Raman spectra of cytochrome c on silver electrodes coated with self-assembled monolayers of mercaptopropionic acid were recorded at different potentials using 50 microL of a micromolar solution. For this purpose, a linearly moving, low-volume, small spectroelectrochemical cell was designed and used together with a Raman microprobe. The quality of the spectra obtained is good, and the spectra show essentially the same features reported by other authors using much larger volumes. The cell described in this paper is shown to be useful for studying the spectroelectrochemistry of photosensitive compounds such as heme proteins, which are available only in very small amounts (nanomoles to picomoles).