Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

The discovery of the hydrogen bond from p-Nitrothiophenol by Raman spectroscopy: Guideline for the thioalcohol molecule recognition tool.

ABSTRACT: Inter- and intra- molecular hydrogen bonding plays important role in determining molecular structure, physical and chemical properties, which may be easily ignored for molecules with a non-typical hydrogen bonding structure. We demonstrated in this paper that the hydrogen bonding is responsible for the different Raman spectra in solid and solution states of p-Nitrothiophenol (PNTP). The consistence of the theoretical calculation and experiment reveals that the intermolecular hydrogen bonding yields an octatomic ring structure (8) of PNTP in the solid state, confirmed by the characteristic S-H---O stretching vibration mode at 2550?cm^-1; when it comes to the solution state, the breakage of hydrogen bond of S-H---O induced the S-H stretching vibration at 2590?cm^-1. Our findings may provide a simple and fast method for identifying the intermolecular hydrogen bonding.

SUBMITTER: Ling Y

PROVIDER: S-EPMC5034243 | biostudies-literature | 2016 Sep

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

The discovery of the hydrogen bond from p-Nitrothiophenol by Raman spectroscopy: Guideline for the thioalcohol molecule recognition tool.

Ling Yun Y Xie Wen Chang WC Liu Guo Kun GK Yan Run Wen RW Wu De Yin Y Tang Jing J

Scientific reports 20160923

Inter- and intra- molecular hydrogen bonding plays important role in determining molecular structure, physical and chemical properties, which may be easily ignored for molecules with a non-typical hydrogen bonding structure. We demonstrated in this paper that the hydrogen bonding is responsible for the different Raman spectra in solid and solution states of p-Nitrothiophenol (PNTP). The consistence of the theoretical calculation and experiment reveals that the intermolecular hydrogen bonding yie ...[more]

PMID: 27659311

Similar Datasets

Point-of-Care Determination of Acetaminophen Levels with Multi-Hydrogen Bond Manipulated Single-Molecule Recognition (eMuHSiR).

Project description:This work aims to face the challenge of monitoring small molecule drugs accurately and rapidly for point-of-care (POC) diagnosis in current clinical settings. Overdose of acetaminophen (AP), a commonly used over the counter (OTC) analgesic drug, has been determined to be a major cause of acute liver failure in the US and the UK. However, there is no rapid and accurate detection method available for this drug in the emergency room. The present study examined an AP sensing strategy that relies on a previously unexplored strong interaction between AP and the arginine (Arg) molecule. It was found that as many as 4 hydrogen bonds can be formed between one Arg molecule and one AP molecule. By taking advantages of this structural selectivity and high tenability of hydrogen bonds, Arg, immobilized on a graphene surface via electrostatic interactions, was utilized to structurally capture AP. Interestingly, bonded AP still remained the perfect electrochemical activities. The extent of Arg-AP bonds was quantified using a newly designed electrochemical (EC) sensor. To verify the feasibility of this novel assay, based on multihydrogen bond manipulated single-molecule recognition (eMuHSiR), both pharmaceutical and serum sample were examined. In commercial tablet measurement, no significant difference was seen between the results of eMuHSiR and other standard methods. For measuring AP concentration in the mice blood, the substances in serum, such as sugars and fats, would not bring any interference to the eMuHSiR in a wide concentration range. This eMuHSiR method opens the way for future development of small molecule detection for the POC testing.

| S-EPMC6556375 | biostudies-literature

Direct observation of single-molecule hydrogen-bond dynamics with single-bond resolution.

Project description:The hydrogen bond represents a fundamental interaction widely existing in nature, which plays a key role in chemical, physical and biochemical processes. However, hydrogen bond dynamics at the molecular level are extremely difficult to directly investigate. Here, in this work we address direct electrical measurements of hydrogen bond dynamics at the single-molecule and single-event level on the basis of the platform of molecular nanocircuits, where a quadrupolar hydrogen bonding system is covalently incorporated into graphene point contacts to build stable supramolecule-assembled single-molecule junctions. The dynamics of individual hydrogen bonds in different solvents at different temperatures are studied in combination with density functional theory. Both experimental and theoretical results consistently show a multimodal distribution, stemming from the stochastic rearrangement of the hydrogen bond structure mainly through intermolecular proton transfer and lactam-lactim tautomerism. This work demonstrates an approach of probing hydrogen bond dynamics with single-bond resolution, making an important contribution to broad fields beyond supramolecular chemistry.

| S-EPMC5825177 | biostudies-literature

Surface Enhanced Raman Spectroscopy for Single Molecule Protein Detection.

Project description:A two-step process of protein detection at a single molecule level using SERS was developed as a proof-of-concept platform for medical diagnostics. First, a protein molecule was bound to a linker in the bulk solution and then this adduct was chemically reacted with the SERS substrate. Traut's Reagent (TR) was used to thiolate Bovine serum albumin (BSA) in solution followed by chemical cross linking to a gold surface through a sulfhydryl group. A Glycine-TR adduct was used as a control sample to identify the protein contribution to the SER spectra. Gold SERS substrates were manufactured by electrochemical deposition. Solutions at an ultralow concentration were used for attaching the TR adducts to the SERS substrate. Samples showed the typical behavior of a single molecule SERS including spectral fluctuations, blinking and Raman signal being generated from only selected points on the substrate. The fluctuating SER spectra were examined using Principle Component Analysis. This unsupervised statistics allowed for the selecting of spectral contribution from protein moiety indicating that the method was capable of detecting a single protein molecule. Thus we have demonstrated, that the developed two-step methodology has the potential as a new platform for medical diagnostics.

| S-EPMC6710251 | biostudies-literature

Surface-enhanced Raman spectroscopy for drug discovery: peptide-RNA binding.

Project description:The ever-growing demand for new drugs highlights the need to develop novel cost- and time-effective techniques for drug discovery. Surface-enhanced Raman spectroscopy (SERS) is an emerging ultrasensitive and label-free technique that allows for the efficient detection and characterization of molecular interactions. We have recently developed a SERS platform for detecting a single protein molecule linked to a gold substrate (Almehmadi et al. Scientific Reports 2019). In this study, we extended the approach to probe the binding of potential drugs to RNA targets. To demonstrate the proof of concept, two 16-amino acid residue peptides with close primary structures and different binding affinities to the RNA CUG repeat related to myotonic dystrophy were tested. Three-microliter solutions of the RNA repeat with these peptides at nanomolar concentrations were probed using the developed approach, and the binding of only one peptide was demonstrated. The SER spectra exhibited significant fluctuations along with a sudden strong enhancement as spectra were collected consecutively from individual spots. Principal component analysis (PCA) of the SER spectral datasets indicated that free RNA repeats could be differentiated from those complexed with a peptide with 100% accuracy. The developed SERS platform provides a novel opportunity for label-free screening of RNA-binding peptides for drug discovery. Schematic representation of the SERS platform for drug discovery developed in this study.

| S-EPMC9404289 | biostudies-literature

Crystal structure of new formamidinium triiodide jointly refined by single-crystal XRD, Raman scattering spectroscopy and DFT assessment of hydrogen-bond network features.

Project description:A novel triiodide phase of the formamidinium cation, CH5N2 +·I3 -, crystallizes in the triclinic space group P at a temperature of 110 K. The structure consists of two independent isolated triiodide ions located on inversion centers. The centrosymmetric character of I3 - was additionally confirmed by the observed pronounced peaks of symmetrical oscillations of I3 - at 115-116 cm-1 in Raman scattering spectra. An additional structural feature is that each terminal iodine atom is connected with three neighboring planar formamidinium cations by N-H⋯I hydrogen bonding with the N-H⋯I bond length varying from 2.81 to 3.08 Å, forming a deformed two-dimensional framework of hydrogen bonds. A Mulliken population analysis showed that the calculated charges of hydrogen atoms correlate well with hydrogen-bond lengths. The crystal studied was refined as a three-component twin with domain ratios of 0.631 (1):0.211 (1):0.158 (1).

| S-EPMC8382056 | biostudies-literature

Structural Recognition of Triple-Stranded DNA by Surface-Enhanced Raman Spectroscopy.

Project description:Direct, label-free analysis of nucleic acids via surface-enhanced Raman spectroscopy (SERS) has been continuously expanding its range of applications as an intriguing and powerful analytical tool for the structural characterization of diverse DNA structures. Still, interrogation of nucleic acid tertiary structures beyond the canonical double helix often remains challenging. In this work, we report for the first time the structural identification of DNA triplex structures. This class of nucleic acids has been attracting great interest because of their intriguing biological functions and pharmacological potential in gene therapy, and the ability for precisely engineering DNA-based functional nanomaterials. Herein, structural discrimination of the triplex structure against its duplex and tertiary strand counterparts is univocally revealed by recognizing key markers bands in the intrinsic SERS fingerprint. These vibrational features are informative of the base stacking, Hoogsteen hydrogen bonding and sugar-phosphate backbone reorganization associated with the triple helix formation. This work expands the applicability of direct SERS to nucleic acids analysis, with potential impact on fields such as sensing, biology and drug design.

| S-EPMC7912272 | biostudies-literature

Digital surface enhanced Raman spectroscopy for quantifiable single molecule detection in flow.

Project description:Surface enhanced Raman scattering (SERS) provides a label free method of analyzing molecules from diverse and complex signals, potentially with single molecule sensitivity. The chemical specificity inherent in the SERS spectrum can identify molecules; however signal variability arising from the diversity of plasmonic environments can limit quantification, particularly at low concentrations. Here we show that digitizing, or counting SERS events, can decrease the limit of detection in flowing solutions enabling quantification of single molecules. By using multivariate curve resolution and establishing a score threshold, each individual spectrum can be classified as containing an event or not. This binary "yes/no" can then be quantified, and a linear region can be established. This method was shown to lower the limit of detection to the lowest physical limit, and lowered the limit of detection by an order of magnitude from the traditional, intensity based LOD calculations.

| S-EPMC11229883 | biostudies-literature

Serum Raman spectroscopy as a diagnostic tool in patients with Huntington's disease.

Project description:Huntington's disease (HD) is an autosomal dominant neurodegenerative disorder caused by an abnormal CAG expansion in exon 1 of the huntingtin (HTT) gene. Given its genetic basis it is possible to study patients both in the pre-manifest and manifest stages of the condition. While disease onset can be modelled using CAG repeat size, there are no easily accessible biomarkers that can objectively track disease progression. Here, we employed a holistic approach using spectral profiles generated using both surface-enhanced Raman spectroscopy (SERS) and Raman Spectroscopy (RS), on the serum of healthy participants and HD patients covering a wide spectrum of disease stages. We found that there was both genotype- and gender-specific segregation on using the full range in the fingerprint region with both SERS and RS. On a more detailed interrogation using specific spectral intervals, SERS revealed significant correlations with disease progression, in particular progression from pre-manifest through to advanced HD was associated with serum molecules related to protein misfolding and nucleotide catabolism. Thus, this study shows the potential of Raman spectroscopy-based techniques for stratification of patients and, of SERS, in particular, to track disease status through provision of 'spectral' biomarkers in HD, with clinical applications for other diseases and trials looking at disease modifying therapies.

| S-EPMC7067270 | biostudies-literature

Dissecting structure of prion amyloid fibrils by hydrogen-deuterium exchange ultraviolet Raman spectroscopy.

Project description:The molecular mechanisms underlying structural diversity of amyloid fibrils or prion strains formed within the same primary structure is considered to be one of the most enigmatic questions in prion biology. We report here on the direct characterization of amyloid structures using a novel spectroscopic technique, hydrogen-deuterium exchange ultraviolet Raman spectroscopy. This method enables us to assess the structural differences within highly ordered cross-β-cores of two amyloid states produced within the same amino acid sequence of full-length mammalian prion protein. We found that while both amyloid states consisted of β-structures, their cross-β-cores exhibited hydrogen bonding of different strengths. Moreover, Raman spectroscopy revealed that both amyloid states displayed equally narrow crystalline-like bands, suggesting uniform structures of cross-β-cores within each state. Taken together, these data suggest that highly polymorphous fibrils can display highly uniform structures of their cross-β-core and belong to the same prion strain.

| S-EPMC3490051 | biostudies-literature

On the Hydrogen Bond Strength and Vibrational Spectroscopy of Liquid Water.

Project description:In the present work, we introduce two new metrics i.e. hydrogen-bond strength and charge-transfer between the donor/acceptor water molecules as a measure of hydrogen-bond rearrangement dynamics. Further, we also employ a simple model based on energy flux through the donor-acceptor water pairs to quantify the extent of the local hydrogen-bond network reorganization. Most importantly, we report a linear relationship between the OH stretch frequency and the charge and energy transfer through donor-acceptor water pairs. We demonstrate that the vibrational frequency fluctuations, which are used to determine third-order non-linear spectroscopic observables like the short-time slope of three pulse photon echo, can be used as an analog of the fluctuations in the hydrogen-bond strength and charge-transfer. The timescales obtained from our hydrogen-bond strength correlation and charge-transfer correlation decay are in excellent agreement with the computed frequency-time correlation function, as well as with recent vibrational echo experiments.

| S-EPMC6237855 | biostudies-other

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data