Alkyne-Tagged Raman Probes for Local Environmental Sensing by Hydrogen-Deuterium Exchange

On-Chip Capture, Raman-Silent Polymer Labeling, and Digital Mapping Analysis of Escherichia coli O157:H7 in Beverages All-in-One

Escherichia coli O157:H7 is one of the most susceptible foodborne pathogens, easily causing food poisoning and other health risks. It is of great significance to establish a quantitative method with higher sensitivity and less time consumption for foodborne pathogens analysis. The Raman-silent signal has a good performance for avoiding interference from the food matrix so as to achieve accurate signal differentiation. In this work, we presented a preparation-mapping all-in-one method for digital mapping analysis. We prepared a functionalized Raman-silent polymer label of Escherichia coli O157:H7, which was captured on a porous 4-mercaptophenylboric acid@Ag foam chip. To improve accuracy and widen the detection range, a digital mapping quantitative strategy was employed in data extraction and processing. By transfer mapping information into digitized statistical results, the limitation of obtaining reproducible intensity values just by randomly selected spots on the substrate can be addressed. With a wide linear range of 1.0 × 101-1.0 × 105 CFU mL-1 and a limit of detection of 4.4 CFU mL-1, this all-in-one method had good sensitivity performance. Also, this method achieved good precision and selectivity in a series of experiments and was successfully applied to the analysis of beverage samples.

Biomedical applications, perspectives and tag design concepts in the cell - silent Raman window

Spectroscopic studies increasingly employ Raman tags exhibiting a signal in the cell - silent region of the Raman spectrum (1800-2800 cm-1), where bands arising from biological molecules are inherently absent. Raman tags bearing functional groups which contain a triple bond, such as alkyne and nitrile or a carbon-deuterium bond, have a distinct vibrational frequency in this region. Due to the lack of spectral background and cell-associated bands in the specific area, the implementation of those tags can help overcome the inherently poor signal-to-noise ratio and presence of overlapping Raman bands in measurements of biological samples. The cell - silent Raman tags allow for bioorthogonal imaging of biomolecules with improved chemical contrast and they have found application in analyte detection and monitoring, biomarker profiling and live cell imaging. This review focuses on the potential of the cell - silent Raman region, reporting on the tags employed for biomedical applications using variants of Raman spectroscopy.

Transient stimulated Raman scattering spectroscopy and imaging

Stimulated Raman scattering (SRS) has been developed as an essential quantitative contrast for chemical imaging in recent years. However, while spectral lines near the natural linewidth limit can be routinely achieved by state-of-the-art spontaneous Raman microscopes, spectral broadening is inevitable for current mainstream SRS imaging methods. This is because those SRS signals are all measured in the frequency domain. There is a compromise between sensitivity and spectral resolution: as the nonlinear process benefits from pulsed excitations, the fundamental time-energy uncertainty limits the spectral resolution. Besides, the spectral range and acquisition speed are mutually restricted. Here we report transient stimulated Raman scattering (T-SRS), an alternative time-domain strategy that bypasses all these fundamental conjugations. T-SRS is achieved by quantum coherence manipulation: we encode the vibrational oscillations in the stimulated Raman loss (SRL) signal by femtosecond pulse-pair sequence excited vibrational wave packet interference. The Raman spectrum was then achieved by Fourier transform of the time-domain SRL signal. Since all Raman modes are impulsively and simultaneously excited, T-SRS features the natural-linewidth-limit spectral line shapes, laser-bandwidth-determined spectral range, and improved sensitivity. With ~150-fs laser pulses, we boost the sensitivity of typical Raman modes to the sub-mM level. With all-plane-mirror high-speed time-delay scanning, we further demonstrated hyperspectral SRS imaging of live-cell metabolism and high-density multiplexed imaging with the natural-linewidth-limit spectral resolution. T-SRS shall find valuable applications for advanced Raman imaging.

Development of a universal method for vibrational analysis of the terminal alkyne C≡C stretch

The terminal alkyne C≡C stretch has a large Raman scattering cross section in the "silent" region for biomolecules. This has led to many Raman tag and probe studies using this moiety to study biomolecular systems. A computational investigation of these systems is vital to aid in the interpretation of these results. In this work, we develop a method for computing terminal alkyne vibrational frequencies and isotropic transition polarizabilities that can easily and accurately be applied to any terminal alkyne molecule. We apply the discrete variable representation method to a localized version of the C≡C stretch normal mode. The errors of (1) vibrational localization to the terminal alkyne moiety, (2) anharmonic normal mode isolation, and (3) discretization of the Born-Oppenheimer potential energy surface are quantified and found to be generally small and cancel each other. This results in a method with low error compared to other anharmonic vibrational methods like second-order vibrational perturbation theory and to experiments. Several density functionals are tested using the method, and TPSS-D3, an inexpensive nonempirical density functional with dispersion corrections, is found to perform surprisingly well. Diffuse basis functions are found to be important for the accuracy of computed frequencies. Finally, the computation of vibrational properties like isotropic transition polarizabilities and the universality of the localized normal mode for terminal alkynes are demonstrated.

Triple-Bond Vibrations: Emerging Applications in Energy and Biological Sciences

Triple bonds, such as that formed between two carbon atoms (i.e., C≡C) or that formed between one carbon atom and one nitrogen atom (i.e., C≡N), afford unique chemical bonding and hence vibrational characteristics. As such, they are not only frequently used to construct molecules with tailored chemical and/or physical properties but also employed as vibrational probes to provide site-specific chemical and/or physical information at the molecular level. Herein, we offer our perspective on the emerging applications of various triple-bond vibrations in energy and biological sciences with a focus on C≡C and C≡N triple bonds.

Ratiometric analysis of reversible thia-Michael reactions using nitrile-tagged molecules by Raman microscopy

Ratiometric Raman analysis of reversible thia-Michael reactions was achieved using α-cyanoacrylic acid (αCNA) derivatives. Among αCNAs, the smallest derivative, ThioRas (molecular weight: 167 g mol-1), and its glutathione adduct were simultaneously detected in various subcellular locations using Raman microscopy.

"Photochemical Surgery" of 1D Metal-Organic Frameworks with a Site-Selective Solubilization/Crystallization Strategy

One-dimensional (1D) hybrid MOFs are attractive if they consist of different MOF blocks with interconnected channels. However, the precision synthesis of such 1D multiblock MOFs with the desired block lengths and sequences remains a formidable challenge. Herein we propose the "photochemical surgery" method, which combines top-down and bottom-up approaches to enable the site-selective solubilization (removal)/crystallization (reconstruction) of 1D MOFs. We employed photoreactive MOFs, which were prepared by complexing either Cd2+ or Zn2+ with a mixture containing a photochromic bispyridyl ligand (PyDTEopen or PyDTZEopen) and an isophthalate (5-nitroisophthalate (nip2-) or 5-bromoisophthalate (bip2-)). These MOFs were obtained as high-aspect-ratio, needlelike, colorless crystals that bore 1D channels oriented parallel to the long needle axis. When photoreactive DTECdMOFNO2 ([Cd(nip)(PyDTEopen)(H2O)]n), for example, was immobilized at both ends with a metal alloy on a glass substrate and exposed to UV light through a photomask for 60 min in N,N-dimethylformamide/methanol (DMF/MeOH), the unmasked part was removed via solubilization to produce a 50 μm gap. The resulting specimen was immersed for 24 h at 25 °C in DMF/MeOH containing the necessary components for the construction of DTZECdMOFNO2 ([Cd(nip)(PyDTZEopen)(H2O)]n). Eventually, the gap was filled with DTZECdMOFNO2 to produce a triblock hybrid MOF (DTECdMOFNO2-DTZECdMOFNO2-DTECdMOFNO2). The result of a guest diffusion experiment confirmed that the newly formed DTZECdMOFNO2 block shared its 1D channels with the host DTECdMOFNO2 blocks. "Photochemical surgery" can be applied to synthesize 1D hybrid MOFs bearing unconventional sequences and morphologies, e.g., honeycomb- and inverted-honeycomb-patterned hybrids.

The Emerging Role of Raman Spectroscopy as an Omics Approach for Metabolic Profiling and Biomarker Detection toward Precision Medicine

Omics technologies have rapidly evolved with the unprecedented potential to shape precision medicine. Novel omics approaches are imperative toallow rapid and accurate data collection and integration with clinical information and enable a new era of healthcare. In this comprehensive review, we highlight the utility of Raman spectroscopy (RS) as an emerging omics technology for clinically relevant applications using clinically significant samples and models. We discuss the use of RS both as a label-free approach for probing the intrinsic metabolites of biological materials, and as a labeled approach where signal from Raman reporters conjugated to nanoparticles (NPs) serve as an indirect measure for tracking protein biomarkers in vivo and for high throughout proteomics. We summarize the use of machine learning algorithms for processing RS data to allow accurate detection and evaluation of treatment response specifically focusing on cancer, cardiac, gastrointestinal, and neurodegenerative diseases. We also highlight the integration of RS with established omics approaches for holistic diagnostic information. Further, we elaborate on metal-free NPs that leverage the biological Raman-silent region overcoming the challenges of traditional metal NPs. We conclude the review with an outlook on future directions that will ultimately allow the adaptation of RS as a clinical approach and revolutionize precision medicine.

Deuterium- and Alkyne-Based Bioorthogonal Raman Probes for In Situ Quantitative Metabolic Imaging of Lipids within Plants

Plants can rapidly respond to different stresses by activating multiple signaling and defense pathways. The ability to directly visualize and quantify these pathways in real time using bioorthogonal probes would have practical applications, including characterizing plant responses to both abiotic and biotic stress. Fluorescence-based labels are widely used for tagging of small biomolecules but are relatively bulky and with potential effects on their endogenous localization and metabolism. This work describes the use of deuterium- and alkyne-derived fatty acid Raman probes to visualize and track the real-time response of plants to abiotic stress within the roots. Relative quantification of the respective signals could be used to track their localization and overall real-time responses in their fatty acid pools due to drought and heat stress without labor-intensive isolation procedures. Their overall usability and low toxicity suggest that Raman probes have great untapped potential in the field of plant bioengineering.

Enhancing Alkyne-Based Raman Tags with a Sulfur Linker

Alkyne-based Raman tags have proven their utility for biological imaging. Although the alkynyl stretching mode is a relatively strong Raman scatterer, the detection sensitivity of alkyne-tagged compounds is ultimately limited by the magnitude of the probe's Raman response. In order to improve the performance of alkyne-based Raman probes, we have designed several tags that benefit from π-π conjugation as well as from additional n-π conjugation with a sulfur linker. We show that the sulfur linker provides additional enhancement and line width narrowing, offering a simple yet effective strategy for improving alkyne-based Raman tags. We validate the utility of various sulfur-linked alkyne tags for cellular imaging through stimulated Raman scattering microscopy.

Frequency Changes in Terminal Alkynes Provide Strong, Sensitive, and Solvatochromic Raman Probes of Biochemical Environments

The C≡C stretching frequencies of terminal alkynes appear in the "clear" window of vibrational spectra, so they are attractive and increasingly popular as site-specific probes in complicated biological systems like proteins, cells, and tissues. In this work, we collected infrared (IR) absorption and Raman scattering spectra of model compounds, artificial amino acids, and model proteins that contain terminal alkyne groups, and we used our results to draw conclusions about the signal strength and sensitivity to the local environment of both aliphatic and aromatic terminal alkyne C≡C stretching bands. While the IR bands of alkynyl model compounds displayed surprisingly broad solvatochromism, their absorptions were weak enough that alkynes can be ruled out as effective IR probes. The same solvatochromism was observed in model compounds' Raman spectra, and comparisons to published empirical solvent scales (including a linear regression against four meta-aggregated solvent parameters) suggested that the alkyne C≡C stretching frequency mainly reports on local electronic interactions (i.e., short-range electron donor-acceptor interactions) with solvent molecules and neighboring functional groups. The strong solvatochromism observed here for alkyne stretching bands introduces an important consideration for Raman imaging studies based on these signals. Raman signals for alkynes (especially those that are π-conjugated) can be exceptionally strong and should permit alkynyl Raman signals to function as probes at very low concentrations, as compared to other widely used vibrational probe groups like azides and nitriles. We incorporated homopropargyl glycine into a transmembrane helical peptide via peptide synthesis, and we installed p-ethynylphenylalanine into the interior of the Escherichia coli fatty acid acyl carrier protein using a genetic code expansion technique. The Raman spectra from each of these test systems indicate that alkynyl C≡C bands can act as effective and unique probes of their local biomolecular environments. We provide guidance for the best possible future uses of alkynes as solvatochromic Raman probes, and while empirical explanations of the alkyne solvatochromism are offered, open questions about its physical basis are enunciated.

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.

Probing the local structure and dynamics of nucleotides using vibrationally enhanced alkynyl stretching

Monitoring the site-specific local structure and dynamics of polynucleotides and DNA is important for understanding their biological functions. However, structurally characterizing these biomolecules with high time resolution has been known to be experimentally challenging. In this work, several 5-silylethynyl-2'-deoxynucleosides and 5-substituted phenylethynyl-2'-deoxynucleosides on the basis of deoxycytidine (dC) and deoxythymidine (dT) were synthesized, in which the alkynyl group shows intensified CC stretching vibration with infrared transition dipole moment magnitude close to that of typical CO stretching, and exhibits structural sensitivities in both vibrational frequency and spectral width. In particular, 5-trimethylsilylethynyl-2'-dC (^TMSEdC, molecule 1a) was examined in detail using femtosecond nonlinear IR spectroscopy. The solvent dependent CC stretching frequency of 1a can be reasonably interpreted mainly as the hydrogen-bonding effect between the solvent and cytosine base ring structure. Transient 2D IR and pump-probe IR measurements of 1a carried out comparatively in two aprotic solvents (DMSO and THF) and one protic solvent (MeOH) further reveal solvent dependent ultrafast vibrational properties, including diagonal anharmonicity, spectral diffusion, vibrational relaxation and anisotropy dynamics. These observed sensitivities are rooted in an extended π-conjugation of the base ring structure in which the CC group is actively involved. Our results show that the intensified CC stretching vibration can potentially provide a site-specific IR probe for monitoring the equilibrium and ultrafast structural dynamics of polynucleotides.

Raman Spectroscopy for Chemical Biology Research

In chemical biology research, various fluorescent probes have been developed and used to visualize target proteins or molecules in living cells and tissues, yet there are limitations to this technology, such as the limited number of colors that can be detected simultaneously. Recently, Raman spectroscopy has been applied in chemical biology to overcome such limitations. Raman spectroscopy detects the molecular vibrations reflecting the structures and chemical conditions of molecules in a sample and was originally used to directly visualize the chemical responses of endogenous molecules. However, our initial research to develop "Raman tags" opens a new avenue for the application of Raman spectroscopy in chemical biology. In this Perspective, we first introduce the label-free Raman imaging of biomolecules, illustrating the biological applications of Raman spectroscopy. Next, we highlight the application of Raman imaging of small molecules using Raman tags for chemical biology research. Finally, we discuss the development and potential of Raman probes, which represent the next-generation probes in chemical biology.

Iridium-catalyzed α-selective deuteration of alcohols

The development of chemoselective C(sp3)-H deuteration is of particular interest in synthetic chemistry. We herein report the α-selective, iridium(iii)-bipyridonate-catalyzed hydrogen(H)/deuterium(D) isotope exchange of alcohols using deuterium oxide (D2O) as the primary deuterium source. This method enables the direct, chemoselective deuteration of primary and secondary alcohols under basic or neutral conditions without being affected by coordinative functional groups such as imidazole and tetrazole. Successful substrates for deuterium labelling include the pharmaceuticals losartan potassium, rapidosept, guaifenesin, and diprophylline. The deuterated losartan potassium shows higher stability towards the metabolism by CYP2C9 than the protiated analogue. Kinetic and DFT studies indicate that the direct deuteration proceeds through dehydrogenation of alcohol to the carbonyl intermediate, conversion of [IrIII-H] to [IrIII-D] with D2O, and deuteration of the carbonyl intermediate to give the α-deuterated product.

Bringing Vibrational Imaging to Chemical Biology with Molecular Probes

As an emerging optical imaging modality, stimulated Raman scattering (SRS) microscopy provides invaluable opportunities for chemical biology studies using its rich chemical information. Through rapid progress over the past decade, the development of Raman probes harnessing the chemical biology toolbox has proven to play a key role in advancing SRS microscopy and expanding biological applications. In this perspective, we first discuss the development of biorthogonal SRS imaging using small tagging of triple bonds or isotopes and highlight their unique advantages for metabolic pathway analysis and microbiology investigations. Potential opportunities for chemical biology studies integrating small tagging with SRS imaging are also proposed. We next summarize the current designs of highly sensitive and super-multiplexed SRS probes, as well as provide future directions and considerations for next-generation functional probe design. These rationally designed SRS probes are envisioned to bridge the gap between SRS microscopy and chemical biology research and should benefit their mutual development.