A modified mean normalization method to reduce the effect of peak overlap in two-dimensional correlation spectroscopy

Innovative FO-SPR Label-free Strategy for Detecting Anti-RBD Antibodies in COVID-19 Patient Serum and Whole Blood

The ongoing COVID-19 pandemic has emphasized the urgent need for rapid, accurate, and large-scale diagnostic tools. Next to this, the significance of serological tests (i.e., detection of SARS-CoV-2 antibodies) also became apparent for studying patients' immune status and past viral infection. In this work, we present a novel approach for not only measuring antibody levels but also profiling of binding kinetics of the complete polyclonal antibody response against the receptor binding domain (RBD) of SARS-CoV-2 spike protein, an aspect not possible to achieve with traditional serological tests. This fiber optic surface plasmon resonance (FO-SPR)-based label-free method was successfully accomplished in COVID-19 patient serum and, for the first time, directly in undiluted whole blood, omitting the need for any sample preparation. Notably, this bioassay (1) was on par with FO-SPR sandwich bioassays (traditionally regarded as more sensitive) in distinguishing COVID-19 from control samples, irrespective of the type of sample matrix, and (2) had a significantly shorter time-to-result of only 30 min compared to >1 or 4 h for the FO-SPR sandwich bioassay and the conventional ELISA, respectively. Finally, the label-free approach revealed that no direct correlation was present between antibody levels and their kinetic profiling in different COVID-19 patients, as another evidence to support previous hypothesis that antibody-binding kinetics against the antigen in patient blood might play a role in the COVID-19 severity. Taking all this into account, the presented work positions the FO-SPR technology at the forefront of other COVID-19 serological tests, with a huge potential toward other applications in need for quantification and kinetic profiling of antibodies.

Probing Protein Secondary Structure Influence on Active Centers with Hetero Two-Dimensional Correlation (Resonance) Raman Spectroscopy: A Demonstration on Cytochrome C

The functionality of active centers in proteins is governed by the secondary and higher structure of proteins which often lead to structures in the active center that are different from the structures found in protein-free models of the active center. To elucidate this structure-function relationship, it is therefore necessary to investigate both the protein structure and the local structure of the active center. In this work, we investigate the application of hetero (resonance) Raman two-dimensional correlation spectroscopy (2D-COS) to this problem. By employing a combination of near-infrared-Fourier transform-Raman- and vis-resonance Raman spectroscopy, we could show that this combination of techniques is able to directly probe the structure-function relationship of proteins. We were able to correlate the transition of the heme center in cytochrome c from low to high spin with changes in the secondary structure with the above mentioned two spectroscopic in situ techniques and without sample preparation. Thereby, we were able to reveal that the combination of a spectroscopic method to selectively observe the active center with a technique that monitors the whole system offers a promising toolkit to investigate the structure-function relationship of proteins with photoactive centers in general.

Influence of Hydration on the Structure and Interactions of Ethaline Deep-Eutectic Solvent: A Spectroscopic and Computational Study

Deep-eutectic solvents (DESs) are regarded as alternative green solvents to ionic liquids. In this work we report the structural properties and hydrogen bonding (H-bonding) interactions of an aqueous DES system. The used DES, ethaline (ETH), is composed of choline chloride and ethylene glycol (EG) in 1 : 2 molar ratio. The investigations were carried out by FTIR spectroscopy combined with quantum chemical calculations. Excess spectroscopy and two-dimensional correlation spectroscopy (2D-COS) were used to explore the data in detail. The results showed that, upon mixing, ETH transforms to EG dimers and trimers and D₂ O clusters transform to various ETH-D₂ O complexes. Theoretical calculations show that water molecules insert between the anion and cation of ETH, break the strong doubly ionic Cl^-… H-O_Ch+ H-bond, share charges of the ions and form H-bond with them, thus modulate the interaction properties of ETH. This study deepens our molecular-level understanding of the system and would shed light on its applications.

Structural Properties and Hydrogen-Bonding Interactions in Binary Mixtures Containing a Deep-Eutectic Solvent and Acetonitrile

Deep-eutectic solvents (DESs) are a new class of green solvents. Here, we report the hydrogen bonding and structural properties of the archetypal DES ethaline, a mixture of choline chloride (ChCl) and ethylene glycol (EG) of a 1:2 molar ratio, and its pseudo-binary mixtures with acetonitrile. The investigations were carried out employing Fourier-transform infrared (FTIR) spectroscopy combined with quantum chemical calculations. Excess and two-dimensional (2D)-correlation spectroscopies were used to identify favorable species in the solutions and to explore the heterogeneity. The results show that the mixing process is the transformation from ethaline and CH₃CN dimer to the complexes of ethaline-1CH₃CN and ethaline-2CH₃CN, together with the increased percentages of the EG dimer, EG trimer, and CH₃CN monomer with respect to their total amounts in the mixtures. Theoretical calculations show that, for ChCl, the positive charge is located at the methyl groups and methylenes, rendering their ability to form hydrogen bonds. Adding CH₃CN to ethaline can hardly break apart the doubly ionic hydrogen bonds between Ch⁺ and Cl^-. The cosolvent molecules mainly surround the core structure of ethaline, forming noncovalent hydrogen bonds with hydroxyl groups of EG/Ch⁺ but not Cl^-. These in-depth studies on the properties of ethaline and CH₃CN/CD₃CN mixed solvents may shed light on exploring their applications.

Coherent Anti-Stokes-Stokes Raman Cross-Correlation Spectroscopy: Asymmetric Frequency Shifts in Hydrogen-Bonded Pyridine-Water Complexes

Hydrogen bonding is a vital molecular interaction for bio-molecular systems, yet deep understanding of its ways of creating various complexes requires extensive empirical testing. A hybrid femtosecond/picosecond coherent Raman spectroscopic technique is applied to study pyridine-water complexes. Both the coherent Stokes and anti-Stokes Raman spectra are recorded simultaneously as the concentration of water in pyridine varied. A 3 ps and 10 cm^-1 narrowband probe pulse enables us to observe well-resolved Raman spectra. The hydrogen bonding between pyridine and water forms the complexes that have altered vibrational frequencies. These red and blue shifts were observed to be uneven. This asymmetry was result of the generated background nonlinear optical processes of pyridine-water complexes. This asymmetry tends to disappear as probe pulse further delayed attaining background-free coherent Raman spectra. For better visualization, spectral analyses both traditional two-dimensional correlation spectroscopy and recent second-order correlation functions defined in frequency domain are employed. Recognized as a label-free and background-free technique, the coherent Raman spectroscopy, complemented with a known high-resolution spectroscopic correlation analysis, has potential in studying the hydrogen-bonded pyridine-water complexes. These complexes are of great biological importance both due to the ubiquitous nature of hydrogen bonds and due to the close resemblance to chemical bases in macro-biomolecules.

Two-dimensional correlation spectroscopic studies on coordination between organic ligands and Ni2+ ions

³A_2g→³T_1g(P) transition band of Ni²⁺ is used to probe the coordination of Ni²⁺. Two-dimensional asynchronous spectra (2DCOS) are generated using the Double Asynchronous Orthogonal Sample Design (DAOSD), Asynchronous Spectrum with Auxiliary Peaks (ASAP) and Two-Trace Two-Dimensional (2T2D) approaches. Cross peaks relevant to the ³A_2g→³T_1g(P) transition band of Ni²⁺ are utilized to probe coordination between Ni²⁺ and various ligands. We studied the spectral behavior of the ³A_2g→³T_1g(P) transition band when Ni²⁺ is coordinated with ethylenediaminetetraacetic acid disodium salt (EDTA). The pattern of cross peaks in 2D asynchronous spectrum demonstrates that coordination brings about significant blue shift of the band. In addition, the absorptivity of the band increases remarkably. The interaction between Ni²⁺ and galactitol is also investigated. Although no clearly observable change is found on the ³A_2g→³T_1g(P) transition band when galactitol is introduced, the appearance of cross peak in 2D asynchronous spectrum demonstrates that coordination indeed occurs between Ni²⁺ and galactitol. Furthermore, the pattern of cross peak indicates that peak position, bandwidth and absorptivity of the ³A_2g→³T_1g(P) transition band of Ni(galactitol)_x²⁺ is considerably different from those of Ni(H₂O)₆²⁺. Thus, 2DCOS is helpful to reveal subtle spectral variation, which might be helpful in shedding light on the physical-chemical nature of coordination.

Single cell spectroscopy: noninvasive measures of small-scale structure and function

The advancement of spectroscopy methods attained through increases in sensitivity, and often with the coupling of complementary techniques, has enabled real-time structure and function measurements of single cells. The purpose of this review is to illustrate, in light of advances, the strengths and the weaknesses of these methods. Included also is an assessment of the impact of the experimental setup and conditions of each method on cellular function and integrity. A particular emphasis is placed on noninvasive and nondestructive techniques for achieving single cell detection, including nuclear magnetic resonance, in addition to physical, optical, and vibrational methods.

Spectral insight into intensity variations in phase-transition processes using two-dimensional correlation analysis

Two-dimensional correlation spectroscopy (2D-COS) is widely used in studies of phase-transition processes to provide valuable order information that is useful in investigating these mechanisms. During phase-transition processes, the spectral intensity always changes in an "S"- or "anti-S"-shaped curve. Sample selection of the large and complicated dataset for 2D correlation analysis may impact the resulting sequence and should be given serious consideration. Additionally, the relationship between the sequential order obtained from 2D-COS and the parameters of the intensity change, namely, the transition point and the change rate, is still poorly defined. This article makes an attempt to resolve these problems based on the analysis of simulated spectra by assuming that the band intensity changes in a sigmoid manner without a step delay. It is concluded that the sample range around a transition point with a drastic intensity change defined by asynchronous perturbation-correlation moving-window (PCMW2D) analysis is a reasonable choice, and in this region a band that changes earlier as determined by 2D-COS most likely has an earlier phase-transition point. Also, from the results of segmental analysis, it is proposed that 2D-COS can distinguish the sequence of two bands using only rate difference; however, the rate difference and the form of the intensity change should be considered comprehensively. The insights from the simulated results are applied to analyze the temperature-dependent infrared (IR) spectra of poly[di(butyl)vinyl terephthalate] (PDBVT). The phase-transition mechanism of PDBVT can be clearly found using a suitable sample selection method.

Natural Logarithm Derivative Method: a novel and easy methodology for finding maximums in overlapping experimental peaks

The method of the First Derivative usually fails to detect overlapped peaks, especially when they appear as shoulders of the main one. Furthermore, the determination of the position of the maximum with this method is based on a single point, and it is highly dependent of the noise level of the experimental data. In this work, we propose an easy method to accurately estimate peak positions, based on a linearization of Gaussian curves. The method, which we called Natural Logarithm Derivative Method (NLDM), is also able to detect to a certain extent overlapping peaks, even when appearing as shoulders. Several factors such as the Lorentzian influence in the peak shape, the experimental error in the numerical calculations, or the minimum separation between peaks in order to be properly resolved are studied. The method is assayed with real samples, demonstrating the possibility of finding overlapping peaks in dyes, and in mixtures of dyes.

An insight into sequential order in two-dimensional correlation spectroscopy

Determination of the sequential order of events is a very important feature of generalized two-dimensional correlation spectroscopy (2D-COS). Recently, queries have been put forward on the actual effectiveness of this method when changes are non-periodic, particularly in the presence of local sequential order. Consequently, it brings an urgent necessity to understand the true connotation of the sequential order parameter derived from 2D-COS analysis. This article presents an attempt to address these questions based on the analysis of simulated spectra by assuming the band intensity changes in a logarithmic, exponential, hyperbolic, or polynomial manner. It is concluded that for two events changing monotonically and without local sequential orders, one event occurring prior to the other as determined using 2D-COS means in most cases that the former has both a shorter half-time and a greater half-intensity. As a rule of thumb, intensity versus the perturbation factor should be plotted before performing the 2D-COS analysis to determine the sequential order of the involved events. In the presence of obvious local sequential order, 2D-COS analysis is unnecessary. Otherwise, sequential order can be determined quite reliably based on 2D-COS analysis.