Surface enhanced Raman spectroscopy and quantum chemical studies on glycine single crystal

Parameswari, A.; Premkumar, S.; Premkumar, R.; Benial, A. Milton Franklin

doi:10.1016/j.molstruc.2016.03.025

Cited by 23 publications

(11 citation statements)

References 47 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…2 b, also confirms that the initial powder and the samples processed by HPT under 1 and 6 GPa have similar spectra. A comparison between these spectra and the reported wavenumbers in the literature 29 , 30 confirms that the three samples contain pure α-glycine. Taken altogether, Fig.…”

Section: Resultssupporting

confidence: 74%

Glycine amino acid transformation under impacts by small solar system bodies, simulated via high-pressure torsion method

Edalati

Taniguchi

Floriano

et al. 2022

Sci Rep

View full text Add to dashboard Cite

Impacts by small solar system bodies (meteoroids, asteroids, comets and transitional objects) are characterized by a combination of energy dynamics and chemical modification on both terrestrial and small solar system bodies. In this context, the discovery of glycine amino acid in meteorites and comets has led to a hypothesis that impacts by astronomical bodies could contribute to delivery and polymerization of amino acids in the early Earth to generate proteins as essential molecules for life. Besides the possibility of abiotic polymerization of glycine, its decomposition by impacts could generate reactive groups to form other essential organic biomolecules. In this study, the high-pressure torsion (HPT) method, as a new platform for simulation of impacts by small solar system bodies, was applied to glycine. In comparison with high-pressure shock experiments, the HPT method simultaneously introduces high pressure and deformation strain. It was found that glycine was not polymerized in the experimental condition assayed, but partially decomposed to ethanol under pressures of 1 and 6 GPa and shear strains of < 120 m/m. The detection of ethanol implies the inherent availability of remaining nitrogen-containing groups, which can incorporate to the formation of other organic molecules at the impact site. In addition, this finding highlights a possibility of the origin of ethanol previously detected in comets.

show abstract

Section: Resultssupporting

confidence: 74%

Glycine amino acid transformation under impacts by small solar system bodies, simulated via high-pressure torsion method

Edalati

Taniguchi

Floriano

et al. 2022

Sci Rep

View full text Add to dashboard Cite

show abstract

“…The amide I vibration has been found to be heavily dependent on the formation of intramolecular hydrogen bonds in proteins, and hydrogen bonds, in turn, are integral in the stabilization of various protein secondary structures [ 1 , 2 , 3 , 4 , 5 , 6 , 7 , 8 , 9 ]. As a result, vibrational spectroscopy combined with density functional theory (DFT) computations is commonly employed to investigate the molecular geometries, dynamics, and secondary structures of short peptide chains [ 9 , 10 , 11 , 12 , 13 , 14 , 15 , 16 , 17 , 18 , 19 , 20 , 21 , 22 , 23 , 24 , 25 , 26 , 27 , 28 , 29 , 30 , 31 , 32 , 33 , 34 , 35 , 36 , 37 , 38 , 39 , 40 , 41 , 42 , 43 ]. Navarette and coworkers reported the Raman and IR vibrational spectra for l -glutamic acid [ 44 ], l -aspartic acid (D) [ 35 ], and the glutamic acid (EE) and aspartic acid (DD) dipeptides [ 35 ] in their seminal works and found that these molecules are zwitterio...…”

Section: Introductionmentioning

confidence: 99%

Tracking the Amide I and αCOO− Terminal ν(C=O) Raman Bands in a Family of l-Glutamic Acid-Containing Peptide Fragments: A Raman and DFT Study

et al. 2021

View full text Add to dashboard Cite

The E-hook of β-tubulin plays instrumental roles in cytoskeletal regulation and function. The last six C-terminal residues of the βII isotype, a peptide of amino acid sequence EGEDEA, extend from the microtubule surface and have eluded characterization with classic X-ray crystallographic techniques. The band position of the characteristic amide I vibration of small peptide fragments is heavily dependent on the length of the peptide chain, the extent of intramolecular hydrogen bonding, and the overall polarity of the fragment. The dependence of the E residue’s amide I ν(C=O) and the αCOO− terminal ν(C=O) bands on the neighboring side chain, the length of the peptide fragment, and the extent of intramolecular hydrogen bonding in the structure are investigated here via the EGEDEA peptide. The hexapeptide is broken down into fragments increasing in size from dipeptides to hexapeptides, including EG, ED, EA, EGE, EDE, DEA, EGED, EDEA, EGEDE, GEDEA, and, finally, EGEDEA, which are investigated with experimental Raman spectroscopy and density functional theory (DFT) computations to model the zwitterionic crystalline solids (in vacuo). The molecular geometries and Boltzmann sum of the simulated Raman spectra for a set of energetic minima corresponding to each peptide fragment are computed with full geometry optimizations and corresponding harmonic vibrational frequency computations at the B3LYP/6-311++G(2df,2pd) level of theory. In absence of the crystal structure, geometry sampling is performed to approximate solid phase behavior. Natural bond order (NBO) analyses are performed on each energetic minimum to quantify the magnitude of the intramolecular hydrogen bonds. The extent of the intramolecular charge transfer is dependent on the overall polarity of the fragment considered, with larger and more polar fragments exhibiting the greatest extent of intramolecular charge transfer. A steady blue shift arises when considering the amide I band position moving linearly from ED to EDE to EDEA to GEDEA and, finally, to EGEDEA. However, little variation is observed in the αCOO− ν(C=O) band position in this family of fragments.

show abstract

“…The molecular structure of glycine could be analyzed by the vibrational frequencies of the functional groups NH 3 + , COO – , and CH 2 . As shown in Figure b, the Raman spectra of the glycine powder had 11 peaks331.84, 481.64, 567.94, 658.10, 863.71, 1018.31, 1106.91, 1302.64, 1387.06, 1630.75, and 2942.64 cm –1 , which are represented by CCN bending vibrations, COO – rocking vibrations, COO – wagging vibrations, COO – bending vibrations, C–C stretching vibrations, C–N stretching vibrations, NH 3 + rocking vibrations, CH 2 wagging vibrations, (COO – ) symmetric stretching or CH 2 bending vibrations, NH 3 + bending vibrations, and CH 2 stretching vibrations, respectively. , The intensity of all peaks in the glycine powder spectra was higher than that in the glycine solution. Some peaks representing CCN, COO – , and NH 3 + vibrations were not observable in the glycine solution spectrum, indicating that the glycine solution (200 mg/mL) had a low Raman signal.…”

Section: Resultsmentioning

confidence: 99%

“…In the glycine solution, the revealed peaks of the ν(C–C) and ν(CH 2 ) vibrations, respectively, shifted from 863.71 to 875.74 cm –1 and from 2942.64 to 2961.52 cm –1 due to the glycine interacting with the H 2 O molecules and forming a hydrogen bond. This blue shift phenomenon occurred because of the increased vibrational frequency of the molecule. − …”

Section: Resultsmentioning

confidence: 99%

Magnetic Carbon Nanofibers Prepared with Ni and Ni/Graphitic Carbon Nanoparticle Catalysts for Glycine Detection Using Surface-Enhanced Raman Spectroscopy

Prasiwi

Saraswati

Anwar

et al. 2021

ACS Appl. Nano Mater.

View full text Add to dashboard Cite

The combination of a noble metal with a carbon nanomaterial for surface-enhanced Raman scattering (SERS) has been commonly explored using metal-outside surface decoration to achieve a dominant electromagnetic enhancement mechanism. The use of a non-noble metal encapsulated inside carbon nanofibers (CNFs) for SERS is an interesting field of research because its heterogeneous structure possibly amplifies charge transfer, which induces the chemical enhancement mechanismbased SERS phenomena. This study investigated the use of magnetic CNFs in SERS for detecting small amino acid glycine as an analyte model. The magnetic CNFs were successfully synthesized via chemical vapor deposition (CVD) using Ni and carbon-wrapped Ni nanoparticles (Ni/C) as catalysts. The Ni/C catalyst was prepared via submerged arc discharge in a medium of ethanol/H 2 O. The CVD process was performed at different temperatures with Ar/C 2 H 2 gases, beginning with a synthesis temperature of 600 °C. The morphological analysis of the CVD product showed that the products had a typical structure of CNF-encapsulated Ni nanoparticles. However, Ni and Ni/C catalysts grew CNFs in different features. Ni/C-CNFs had a homogeneous diameter size and more crystalline graphitic carbon layers than Ni-CNFs. All produced CNFs possessed magnetic properties that correlated well with the Ni amount and its crystallization. The Raman intensity of glycine with the SERS substrate of dispersed CNFs grown using both catalysts was significantly higher than the normal Raman signal. The enhancement factor (EF) using the Ni/C-CNF substrate was higher (∼6 × 10 3 ) than that of the Ni-CNF substrate. The increase in the CVD temperature during CNF preparation led to increased Raman intensity and EF value. The crystalline graphitic structure in CNFs consisting of π-bonds and intra-and inter-layer overlapping p-orbital possessed accumulated electron transfer, which remarkably yielded SERS enhancement. The present work opens potential future research avenues to use these magnetic CNFs as SERS substrate with a considerable EF in biosensor applications.

show abstract

Surface enhanced Raman spectroscopy and quantum chemical studies on glycine single crystal

Cited by 23 publications

References 47 publications

Glycine amino acid transformation under impacts by small solar system bodies, simulated via high-pressure torsion method

Glycine amino acid transformation under impacts by small solar system bodies, simulated via high-pressure torsion method

Tracking the Amide I and αCOO− Terminal ν(C=O) Raman Bands in a Family of l-Glutamic Acid-Containing Peptide Fragments: A Raman and DFT Study

Magnetic Carbon Nanofibers Prepared with Ni and Ni/Graphitic Carbon Nanoparticle Catalysts for Glycine Detection Using Surface-Enhanced Raman Spectroscopy

Contact Info

Product

Resources

About