Two-dimensional codistribution spectroscopy to determine the sequential order of distributed presence of species

Novel insights into the relationship between the functional groups and photoactivity of biochar-derived dissolved organic matter

Due to the production of a large amount of biochar, highly photoactive biochar-derived dissolved organic matter (BDOM) from different sources is released into surface water. This study investigated the molecular composition of BDOM (sludge, bamboo and stalk BDOM) using Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) and used tetracycline (TC) as model pollutant to investigate the relationship between molecular composition and BDOM photoactivity, specifically focusing on reactive oxygen species (ROS) production. The results indicate that the fluorescence signal intensity of humic acid-like and aromatic proteins in the plant-derived BDOM are significantly higher than that derived from sewage sludge. FT-ICR MS results also showed that plant-derived BDOM contained more CHO molecular formula. Photodegradation experiments of TC mediated by various BDOM analogues demonstrated the photoactivity is highly correlated with the components and functional groups. The electrochemical experiments and density functional theory (DFT) calculations further verified that the aromatic moiety, sulfydryl group and amino group of BDOM affected the electronic supply and energy transfer. Higher electron and energy transfer favor the reaction of BDOM with the ground state oxygen to generate ROS, thus promoting photodegradation of TC. This study provides a new basis for better assessing the ecological risks of BDOM.

Applying fluorescence spectroscopy coupled with Gaussian band fitting to reveal dynamic variation process of humus fractions from riparian soils along an urbanized river

Humus, an important fraction of soil organic matter, play an environmental role on nutrients, organic and inorganic pollutants in riparian zones of urbanized rivers. In this study, dynamic variation process of humus fractions from riparian soils was revealed along Puhe River. Composite soil samples of four depths were collected from four land-uses, i.e., eco-conservation area (ECA), industrial area (INA), urban/town area (UTA), rural/agricultural area (RAA). Based on synchronous fluorescence spectra coupled with Gaussian band fitting, fulvic/humic acid predominantly contained tyrosine-like (TYLF), tryptophan-like (TRLF), microbial-like (MLF), fulvic-like (FLF) and humic-like (HLF) substances within each soil profile. TRLF, MLF and FLF (89.43-90.30 %) are the representative components in fulvic-acid, while MLF and HLF (52.81-59.97 %) in humic-acid. Phenolic, carboxylic and humified materials were present in both humus. According to 2-dimensitonal correlation spectroscopy and canonical correlation analysis, fulvic/humic acid within the ECA soil profile could be mainly derived from the degradations of terrestrial plant metabolites and residuals. Within the INA, fulvic-acid could be associated with treated/untreated wastewater, which entered the river and flew into the riparian during high flow period; whereas humic-acid could be relative to the terrestrials. Fulvic-acid had the same source as humic-acid in the UTA, which might be concerned with scattered domestic sewage and livestock wastewater, rather than the fluvial water. Furthermore, the source of fulvic/humic acid in the RAA was the crop metabolites and residuals, apart from the livestock wastewater. Noticeably, the variations of humus fractions in the ECA and RAA roughly occurred in 0-60 cm, while approximately in 20-80 cm in the INA and UTA. This proved that humus fractions in the former were referred to the plant/crop residuals, whereas humus fractions in the latter were those the terrestrials and fluvial water. This study could provide a key support for the construction and restoration of the urbanized riparian zone.

Two-Dimensional Clustering of Spectral Changes for the Interpretation of Raman Hyperspectra

Two-dimensional correlation spectroscopy (2D-COS) is a technique that permits the examination of synchronous and asynchronous changes present in hyperspectral data. It produces two-dimensional correlation coefficient maps that represent the mutually correlated changes occurring at all Raman wavenumbers during an implemented perturbation. To focus our analysis on clusters of wavenumbers that tend to change together, we apply a k-means clustering to the wavenumber profiles in the perturbation domain decomposition of the two-dimensional correlation coefficient map. These profiles (or trends) reflect peak intensity changes as a function of the perturbation. We then plot the co-occurrences of cluster members two-dimensionally in a manner analogous to a two-dimensional correlation coefficient map. Because wavenumber profiles are clustered based on their similarity, two-dimensional cluster member spectra reveal which Raman peaks change in a similar manner, rather than how much they are correlated. Furthermore, clustering produces a discrete partitioning of the wavenumbers, thus a two-dimensional cluster member spectrum exhibits a discrete presentation of related Raman peaks as opposed to the more continuous representations in a two-dimensional correlation coefficient map. We demonstrate first the basic principles of the technique with the aid of synthetic data. We then apply it to Raman spectra obtained from a polystyrene perchlorate model system followed by Raman spectra from mammalian cells fixed with different percentages of methanol. Both data sets were designed to produce differential changes in sample components. In both cases, all the peaks pertaining to a given component should then change in a similar manner. We observed that component-based profile clustering did occur for polystyrene and perchlorate in the model system and lipids, nucleic acids, and proteins in the mammalian cell example. This confirmed that the method can translate to "real world" samples. We contrast these results with two-dimensional correlation spectroscopy results. To supplement interpretation, we present the cluster-segmented mean spectrum of the hyperspectral data. Overall, this technique is expected to be a valuable adjunct to two-dimensional correlation spectroscopy to further facilitate hyperspectral data interpretation and analysis.

Effects of NCO/OH Ratios on Bio-Based Polyurethane Film Properties Made from Acacia mangium Liquefied Wood

The compatibility between isocyanate and polyol plays an important role in determining a polyurethane product's performance. This study aims to evaluate the effect of varying the ratios between polymeric methylene diphenyl diisocyanate (pMDI) and Acacia mangium liquefied wood polyol on the polyurethane film properties. A. mangium wood sawdust was liquefied in polyethylene glycol/glycerol co-solvent with H₂SO₄ as a catalyst at 150 °C for 150 min. The A. mangium liquefied wood was mixed with pMDI with difference NCO/OH ratios to produce film through the casting method. The effects of the NCO/OH ratios on the molecular structure of the PU film were examined. The formation of urethane, which was located at 1730 cm^-1, was confirmed via FTIR spectroscopy. The TGA and DMA results indicated that high NCO/OH ratios increased the degradation temperature and glass transition from 275 °C to 286 °C and 50 °C to 84 °C, respectively. The prolonged heat appeared to boost the crosslinking density of the A. mangium polyurethane films, which finally resulted in a low sol fraction. From the 2D-COS analysis, the hydrogen-bonded carbonyl (1710 cm^-1) had the most significant intensity changes with the increasing NCO/OH ratios. The occurrence of the peak after 1730 cm^-1 revealed that there was substantial formation of urethane hydrogen bonding between the hard (PMDI) and soft (polyol) segments as the NCO/OH ratios increased, which gave higher rigidity to the film.

Investigation of the Influence of Stress on Label-Free Bacterial Surface-Enhanced Raman Spectra

Label-free surface-enhanced Raman spectroscopy (SERS) has been proposed as a promising bacterial detection technique. However, the quality of the collected bacterial spectra can be affected by the time between sample acquisition and the SERS measurement. This study evaluated how storage stress stimuli influence the label-free SERS spectra of Pseudomonas syringae samples stored in phosphate buffered saline. The results indicate that when faced with nutrient limitations and changes in osmatic pressure, samples at room temperature (25 °C) exhibit more significant spectral changes than those stored at cold temperature (4 °C). At higher temperatures, bacterial communities secrete extracellular biomolecules that induce programmed cell death and result in increases in the supernatant SERS signals. Surviving cells consume cellular components to support their metabolism, thus leading to measurable declines in cell SERS intensity. Two-dimensional correlation spectroscopy analysis suggests that cellular component signatures decline sequentially in the following order: proteins, nucleic acids, and lipids. Extracellular nucleic acids, proteins, and carbohydrates are secreted in turn. After subtracting the SERS changes resulting from storage, we evaluated bacterial response to viral infection. P. syringae SERS profile changes enable accurate bacteriophage Phi6 quantification over the range of 10⁴-10¹⁰ PFU/mL. The results indicate that storage conditions impact bacterial label-free SERS signals and that such influences need to be accounted for and if possible avoided when detecting bacteria or evaluating bacterial response to stress stimuli.

Applying synchronous fluorescence spectra with Gaussian band fitting and two-dimensional correlation to characterize structural composition of DOM from soils in an aquatic-terrestrial ecotone

Dissolved organic matter (DOM), the primary participant of carbon and nitrogen cycle, has a great impact on the behavior and fate of organic pollutants and heavy metals in eutrophic lakes. The dynamic spectral properties of DOM fractions were revealed in an aquatic-terrestrial ecotone under the different types of land use. Composite soil samples of different depths (0-20, 20-40 and 40-60 cm) were collected from four different land uses along a disturbed-impact gradient in Taihu Lake, China, i.e., grassland (GRL), forest land (FOL), paddy field (PAF), and vegetable field (VEF). DOM mainly consisted of tyrosine-like material (TYLF), tryptophan-like material (TRLF), microbial humic-like material (MHLF), fulvic-like material (FLF) and humic-like material (HLF) within all soil profiles, where TRLF was the dominant component (61.30 %) using synchronous fluorescence spectroscopy (SFS) combined with principal component analysis and Gaussian band fitting. Based on two-dimensional correlation spectroscopy with SFS and Fourier transform infrared, the variation order of DOM fractions was FLF → MHLF → HLF → TRLF → TYLF within the GRL soil profile, and MHLF exhibited an oppositive change with aliphatic OH and amide I in protein. The order of DOM fractions was MHLF → FLF → HLF → TYLF → TRLF within the FOL soil profile, and the change trend of MHLF remained oppositive with aliphatic OH and CO in ester. The order of DOM within the PAF soil profile fractions was TRLF → MHLF → HLF → TYLF → FLF, and changing trends of TYLF were oppositive to aliphatic OH, CH bending vibration, CH bending vibration and CO in ester. The order of DOM fractions was HLF → TYLF → TRLF → FLF → MHLF within the VEF soil profile, where the changing trend TYLF remained oppositive to aliphatic OH, CH deformations in lignin and aliphatic group and amide I in protein. This study may provide important support for alleviating lake water eutrophication or pollution.

Continuing progress in the field of two-dimensional correlation spectroscopy (2D-COS), part II. Recent noteworthy developments

This comprehensive survey review compiles noteworthy developments and new concepts of two-dimensional correlation spectroscopy (2D-COS) for the last two years. It covers review articles, books, proceedings, and numerous research papers published on 2D-COS, as well as patent and publication trends. 2D-COS continues to evolve and grow with new significant developments and versatile applications in diverse scientific fields. The healthy, vigorous, and diverse progress of 2D-COS studies in many fields strongly confirms that it is well accepted as a powerful analytical technique to provide an in-depth understanding of systems of interest.

Continuing progress in the field of two-dimensional correlation spectroscopy (2D-COS), part I. Yesterday and today

This comprehensive survey review, as the first of three parts, compiles past developments and early concepts of two-dimensional correlation spectroscopy (2D-COS) and subsequent evolution, as well as its early applications in various fields for the last 35 years. It covers past review articles, books, proceedings, and numerous research papers published on 2D-COS. 2D-COS continues to evolve and grow with new significant developments and versatile applications in diverse scientific fields. The healthy, vigorous, and diverse progress of 2D-COS studies in many fields confirms that it is well accepted as a powerful analytical technique to provide the in-depth understanding of systems of interest.

Augmented Two-Dimensional Correlation Spectroscopy for the Joint Analysis of Correlated Changes in Spectroscopic and Disparate Sources

Here, we present an augmented form of two-dimensional correlation spectroscopy, that integrates in a single format data from spectroscopic and multiple non-spectroscopic sources for analysis. The integration is affected by augmenting every spectrum in a hyperspectral data set with relevant non-spectroscopic data to permit two-dimensional correlation analysis^(2D-COS) of the ensemble of augmented spectra. A k-means clustering is then applied to the results of the perturbation domain decomposition to determine which Raman peaks cluster with any of the non-spectroscopic data. We introduce and explain the method with the aid of synthetic spectra and synthetic non-spectroscopic data. We then demonstrate this approach with data using Raman spectra from human embryonic stem cell aggregates undergoing directed differentiation toward pancreatic endocrine cells and parallel bioassays of hormone mRNA expression and C-peptide levels in spent medium. These pancreatic endocrine cells generally contain insulin or glucagon. Insulin has disulfide bonds that produce Raman scattering near 513 cm^-1, but no tryptophan. For insulin-positive cells, we found that the application of multisource correlation analysis revealed a high correlation between insulin mRNA and Raman scattering in the disulfide region. In contrast, glucagon has no disulfide bonds but does contain tryptophan. For glucagon-positive cells, we also observed a high correlation between glucagon mRNA and tryptophan Raman scattering (∼757 cm^-1). We conclude with a discussion of methods to enhance spectral resolution and its effects on the performance of multisource correlation analysis.

Spectroscopic investigation of the interaction between extracellular polymeric substances and tetracycline during sorption onto anaerobic ammonium-oxidising sludge

In this study, the interaction between extracellular polymeric substances (EPS) and tetracycline during sorption onto anaerobic ammonium-oxidising (anammox) sludge was investigated. The results showed that EPS significantly enhanced the adsorption efficiency of tetracycline by sludge, and the adsorption data were better fitted with the pseudo-second-order kinetics model. Further, the concentration of proteins in the EPS decreased from 12.31 ± 0.42 to 6.82 ± 0.46 mg/gVSS for various tetracycline dosages (0-20 mg/L), whereas the concentration of polysaccharides did not change. Multiple spectroscopic methods were used to analyze the interaction between EPS and tetracycline. A three-dimensional excitation-emission matrix revealed that the fluorescence intensity of protein-like substances obviously decreased with the increasing addition of tetracycline. According to synchronous fluorescence spectra analysis, static quenching was the major quenching process and there was one type of binding site in the protein-like substances. Additionally, two-dimensional correlation spectroscopy showed that tryptophan-like aromatic protein was more susceptible to tetracycline binding than tyrosine-like aromatic protein. Moreover, the main functional groups involved in complexation of tetracycline and EPS were C-O, C-C and C-N (stretching vibration) and the pyrrole ring of the tryptophan side chain. This study provides useful information on the interaction between EPS and tetracycline and demonstrates the role of EPS in protecting microorganism from tetracycline in the anammox process.

Alzheimer's disease-related amyloid β peptide causes structural disordering of lipids and changes the electric properties of a floating bilayer lipid membrane

Neurodegeneration in Alzheimer's disease is associated with disruption of the neuronal cell membrane by the amyloid β (Aβ) peptide. However, the disruption mechanism and the resulting changes in membrane properties remain to be elucidated. To address this issue, herein the interaction of amyloid β monomers (AβMs) and amyloid β oligomers (AβOs) with a floating bilayer lipid membrane (fBLM) was studied using electrochemical and IR spectroscopy techniques. IR measurements showed that both Aβ forms interacted similarly with the hydrophobic membrane core (lipid acyl chains), causing conformational and orientational changes of the lipid acyl chains, thus decreasing acyl chain mobility and altering the lipid packing unit cell. In the presence of AβOs, these changes were more significant than those in the presence of AβMs. However, respective interactions of AβMs and AβOs with the membrane hydrophilic exterior (lipid heads) were quite different. AβMs dehydrated lipid heads without affecting their orientation while AβOs changed the orientation of lipid heads keeping their hydration level intact. Electrochemical measurements showed that only AβOs porated the fBLM, thus significantly changing the fBLM electrical properties. The present results provide new molecular-level insight into the mechanism of membrane destruction by AβOs and changes in the membrane properties.

Electric-Field-Driven Molecular Recognition Reactions of Guanine with 1,2-Dipalmitoyl-sn-glycero-3-cytidine Monolayers Deposited on Gold Electrodes

Monolayers of 1,2-dipalmitoyl-sn-glycero-3-cytidine were incubated with guanine in a 0.1 M NaF electrolyte at the surface of a Langmuir trough and transferred to gold (111) electrodes using the Langmuir-Schaefer technique. Chronocoulometry and photon polarization modulation infrared reflection absorption spectroscopy were employed to investigate the influence of the static electric field on the orientation and conformation of the cytidine nucleolipid molecules on the metal surface in the presence of guanine and to monitor the molecular recognition of guanine with the cytosine moiety. When the monolayer is exposed to guanine solutions, the cytosine moiety binds to the guanine residue in either a Watson-Crick complex at positively charged electrode surfaces or a noncomplexed state at negative surface charges. The positive electrostatic field causes the cytosine moiety and the cytosine-guanine complex to adopt a nearly parallel orientation with respect to the plane of the monolayer with a measured tilt angle of ∼10°. The parallel orientation is stabilized by the interactions between the permanent dipole of the cytosine moiety or the Watson-Crick complex and the static electric field. At negative charge densities, the tilt of the cytosine moiety increases by ∼15-20°, destabilizing the complex. Our results demonstrate that the static electric field has an influence on the molecular recognition reactions between nucleoside base pairs at the metal-solution interface and can be controlled by altering the surface charge at the metal.

Characterizing Properties and Environmental Behaviors of Dissolved Organic Matter Using Two-Dimensional Correlation Spectroscopic Analysis

Dissolved organic matter (DOM) exists ubiquitously in environments and plays critical roles in pollutant mitigation, transformation, and organic geochemical cycling. Understanding its properties and environmental behaviors is critically important to develop water treatment processes and environmental remediation strategies. Generalized two-dimensional correlation spectroscopy (2DCOS), which has numerous advantages, including enhancing spectral resolution and discerning specific order of structural change under an external perturbation, could be used as a powerful tool to interpret a wide range of spectroscopic signatures relating to DOM. A suite of spectroscopic signatures, such as UV-vis, fluorescence, infrared, and Raman spectra that can be analyzed by 2DCOS, is able to provide additional structural information hiding behind the conventional one-dimensional spectra. In this article, the most recent advances in 2DCOS applications for analyzing DOM-related environmental processes are reviewed, and the state-of-the-art novel spectroscopic techniques in 2DCOS are highlighted. Furthermore, the main limitations and requirements of current approaches for exploring DOM-related environmental processes and how these limitations and drawbacks can be addressed are explored. Finally, suggestions and new approaches are proposed to significantly advance the development of 2DCOS in analyzing the properties and behaviors of DOM in natural and engineered environments.

Two-dimensional correlation and codistribution spectroscopy (2DCOS and 2DCDS) analyses of time-dependent ATR IR spectra of d-glucose anomers undergoing mutarotation process in water

Two cyclic diastereoisomeric structures, known as α- and β-anomers of d-glucose with different configurations around C1 with OH groups in axial or equitroial positions, undergo the mutarotation conversion to each other in water. Two-dimensional correlation and codistribution spectroscopy (2DCOS and 2DCDS) analyses were applied to the time-dependent ATR IR spectra of aqueous solutions of α- and β-d-glucose undergoing such mutarotation conversion. 2DCOS analysis reveals that the increase and decrease in the IR intensities after the dissolution of α- or β-d-glucose are not fully synchronized, suggesting the mutarotation of d-glucose in water is not a simple binary conversion process but a multi-step reaction involving an intermediate species with a finite and observable concentration level and lifetime. 2DCDS analysis of the time-dependent ATR IR spectra clearly demonstrated the presence of intermediate species contributing to the band positions overlapped close to bands for α- and β-d-glucose. The fact that band positions identified for the intermediate species for α- to β-d-glucose conversion are the same for the reverse reaction suggests that they arise from the same species, most likely the open-ring structure produced by the hydrolysis.

Vibrational two-dimensional correlation spectroscopy (2DCOS) study of proteins

A tutorial is provided for the generalized two-dimensional correlation spectroscopy (2DCOS), which is applicable to the vibrational spectroscopic study of proteins and related systems. In 2DCOS, similarity or dissimilarity among variations of spectroscopic intensities, which are induced by applying an external perturbation to the sample, is examined by constructing correlation spectra defined by two independent spectral variable axes. By spreading congested or overlapped peaks along the second dimension, apparent spectral resolution is enhanced and interpretation of complex spectra becomes simplified. A set of simple rules for the intensities and signs of correlation peaks is used to extract insightful information. Simulated IR spectra for a model protein are used to demonstrate the specific utility of 2DCOS. Additional tools useful in the 2DCOS analysis of proteins, such as data segmentation assisted with moving-window analysis, 2D codistribution analysis, Pareto scaling, and null-space projection are also discussed.

Schiff Base Proton Acceptor Assists Photoisomerization of Retinal Chromophores in Bacteriorhodopsin

In this study, we investigated the ultrafast dynamics of bacteriorhodopsins (BRs) from Haloquadratum walsbyi (HwBR) and Haloarcula marismortui (HmBRI and HmBRII). First, the ultrafast dynamics were studied for three HwBR samples: wild-type, D93N mutation, and D104N mutation. The residues of the D93 and D104 mutants correspond to the control by the Schiff base proton acceptor and donor of the proton translocation subchannels. Measurements indicated that the negative charge from the Schiff base proton acceptor residue D93 interacts with the ultrafast and substantial change of the electrostatic potential associated with chromophore isomerization. By contrast, the Schiff base proton donor assists the restructuring of the chromophore cavity hydrogen-bond network during the thermalization of the vibrational hot state. Second, the ultrafast dynamics of the wild-types of HwBR, HmBRI, and HmBRII were compared. Measurements demonstrated that the hydrogen-bond network in the extracellular region in HwBR and HmBRII slows the photoisomerization of retinal chromophores, and the negatively charged helices on the cytoplasmic side of HwBR and HmBRII accelerate the thermalization of the vibrational hot state of retinal chromophores. The similarity of the correlation spectra of the wild-type HmBRI and D104N mutant of HwBR indicates that inactivation of the Schiff base proton donor induces a positive charge on the helices of the cytoplasmic side.

Characterization of a Self-Assembled Monolayer of 1-Thio-β-D-Glucose with Electrochemical Surface Enhanced Raman Spectroscopy Using a Nanoparticle Modified Gold Electrode

Preparation of a nanoparticle modified gold substrate designed for characterization of hydrophilic self-assembled monolayers (SAMs) of 1-thio-β-D-glucose (TG) with electrochemical surface-enhanced Raman spectroscopy (EC-SERS) is presented. Citrate stabilized gold nanoparticles were deposited on a polycrystalline gold electrode and subjected to an electrochemical desorption procedure to completely remove all traces of adsorbed citrate. Complete desorption of citrate was confirmed by recording cyclic voltammetry curves and SERS spectra. The citrate-free nanoparticle modified gold electrode was then incubated in a 1 mg mL(-1) aqueous solution of TG for 16 h prior to being characterized by EC-SERS. The SERS spectra confirmed that at potentials more negative than -0.10 V vs SCE thioglucose forms a monolayer in which the majority of the molecules preserve their lactol ring structure and only a small fraction of molecules appear to be oxidized. At potentials more positive than -0.10 V, the oxidation of TG molecules becomes prominent, and at potentials more positive than 0.20 V vs SCE, the monolayer of TG consists chiefly of oxidized product. The SERS spectra collected in the double layer region suggest the SAM of TG is well hydrated and hence can be used for hydrophilic modifications of a gold surface.