Structural and IR and Raman spectral analysis of cyclo(His-Phe) dipeptide

Çeli̇k, Sefa; Özel, Ayşen E.; Kecel, Serda; Akyüz, Sevim

doi:10.1016/j.vibspec.2012.01.014

Cited by 25 publications

(8 citation statements)

References 36 publications

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“…Density functional theory (DFT) calculation has been applied to reproduce experimental Raman spectra and perform vibrational mode assignment, which provides a powerful tool to investigate Raman spectra at the molecular level . Raman spectra of two similar chemicals, 2‐chlorotoluene and 2‐bromotoluene, have been investigated with both experimental method and DFT calculation.…”

Section: Introductionmentioning

confidence: 99%

pH‐sensing nanostar probe using surface‐enhanced Raman scattering (SERS): theoretical and experimental studies

Yang

Yuan

Fales

et al. 2013

J Raman Spectroscopy

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Local pH environment has been considered to be a potential biomarker for tumor diagnosis because solid tumors contain highly acidic environments. A pH‐sensing nanoprobe based on surface‐enhanced Raman scattering (SERS) using nanostars under near‐infrared excitation has been developed for potential biomedical applications. To theoretically investigate the effect of protonation state on SERS spectra of p‐mercaptobenzoic acid (pMBA), we used the density functional theory (DFT) with the B3LYP functional to calculate Raman vibrational spectra of pMBA‐Au/Ag complex in both protonated and deprotonated states. Vibrational spectral bands were assigned with DFT calculation and used to investigate SERS spectral changes observed from experiment when varying pH value between five and nine. The SERS peak position of pMBA at ~1580 cm−1 was identified to be a novel pH‐sensing index, which has small but noticeable downshift with pH increase. This phenomenon is confirmed and well‐explained with theoretical simulation. The study demonstrates that SERS is a sensitive tool to monitor minor structural changes due to local pH environment, and DFT calculations can be used to investigate Raman spectra changes associated with minor differences in molecular structure. Copyright © 2013 John Wiley & Sons, Ltd.

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Section: Introductionmentioning

confidence: 99%

pH‐sensing nanostar probe using surface‐enhanced Raman scattering (SERS): theoretical and experimental studies

Yang

Yuan

Fales

et al. 2013

J Raman Spectroscopy

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“…Cyclic dipeptides provide excellent models for theoretical studies as well as the development of new pharmaceutical compounds because of their simplicity and limited conformational freedom. In recent years, there has been a growing awareness to understand the specific function of each peptide and their structure . DKPs have long been disregarded, however, more recently, they have received an increasing amount of attention in drug discovery .…”

Section: Discussionmentioning

confidence: 99%

Cyclo(d-Tyr-d-Phe): a new antibacterial, anticancer, and antioxidant cyclic dipeptide fromBacillussp. N strain associated with a rhabditid entomopathogenic nematode

et al. 2013

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A new microbial cyclic dipeptide (diketopiperazine), cyclo(D-Tyr-D-Phe) was isolated for the first time from the ethyl acetate extract of fermented modified nutrient broth of Bacillus sp. N strain associated with rhabditid Entomopathogenic nematode. Antibacterial activity of the compound was determined by minimum inhibitory concentration and agar disc diffusion method against medically important bacteria and the compound recorded significant antibacterial against test bacteria. Highest activity was recorded against Staphylococcus epidermis (1 µg/ml) followed by Proteus mirabilis (2 µg/ml). The activity of cyclo(D-Tyr-D-Phe) against S. epidermis is better than chloramphenicol, the standard antibiotics. Cyclo(D-Tyr-D-Phe) recorded significant antitumor activity against A549 cells (IC50 value: 10 μM) and this compound recorded no cytotoxicity against factor signaling normal fibroblast cells up to 100 μM. Cyclo(D-Tyr-D-Phe) induced significant morphological changes and DNA fragmentation associated with apoptosis in A549 cells. Acridine orange/ethidium bromide stained cells indicated apoptosis induction by cyclo(D-Tyr-D-Phe). Flow cytometry analysis showed that the cyclo(D-Tyr-D-Phe) did not induce cell cycle arrest. Effector molecule of apoptosis such as caspase-3 was found activated in treated cells, suggesting apoptosis as the main mode of cell death. Antioxidant activity was evaluated by free radical scavenging and reducing power activity, and the compound recorded significant antioxidant activity. The free radical scavenging activity of cyclo(D-Tyr-D-Phe) is almost equal to that of butylated hydroxyanisole, the standard antioxidant agent. We also compared the biological activity of natural cyclo(D-Tyr-D-Phe) with synthetic cyclo(D-Tyr-D-Phe) and cyclo(L-Tyr-L-Phe). Natural and synthetic cyclo(D-Tyr-D-Phe) recorded similar pattern of activity. Although synthetic cyclo(L-Tyr-L-Phe) recorded lower activity. But in the case of reducing power activity, synthetic cyclo(L-Tyr-L-Phe) recorded significant activity than natural and synthetic cyclo(D-Tyr-D-Phe). The results of the present study reveals that cyclo(D-Tyr-D-Phe) is more bioactive than cyclo(L-Tyr-L-Phe). To the best of our knowledge, this is the first time that cyclo(D-Tyr-D-Phe) has been isolated from microbial natural source and also the antibacterial, anticancer, and antioxidant activity of cyclo(D-Tyr-D-Phe) is also reported for the first time.

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“…23,28 Examples exist in the literature where DFT dimer simulations have been shown to do reasonably well at reproducing infrared spectra where there exist strong intermolecular attractions between adjacent molecules. 42,43 An inspection of the DFT results in Figure 2d−f demonstrates that the ODH dimer simulations in Figure 2e,f do a better job of reproducing the SEIRA/ATR-FTIR spectra of ODH than the infrared simulation extracted from one ODH molecule in Figure 2d. This is most apparent when comparing bands in the OH bend region between 1100 and 1250 cm −1 .…”

Section: ■ Experimental Sectionmentioning

confidence: 99%

“…Table 2 has vibrational frequencies in the fingerprint region from Figure 4. In columns 1 and 2 are band frequencies for SEIRA spectra of 5 and 400 μL exposures of a 50 ppm solution of PDH/CH 2 Cl 2 , column 3 has the band frequencies for the ATR/FTIR of PDH powder, column 4 has band frequencies from gas-phase hydroquinone obtained from the literature, 42 column 5 has band frequencies from the infrared DFT simulation of one PDH, column 6 has band frequencies from the infrared DFT simulation of the PDH dimer in Figure 1a, and column 7 has the corresponding mode assignments.…”

Section: ■ Experimental Sectionmentioning

confidence: 99%

Surface-Enhanced Infrared Absorption and Density Functional Theory Study of Dihydroxybenzene Isomer Adsorption on Silver Nanostructures

et al. 2013

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A combination of surface-enhanced infrared absorption (SEIRA) and density functional theory (DFT) was used to study the adsorption of the dihydroxybenzene (DH) isomers on silver nanostructures (SNSs). No evidence was observed for the oxidation of any of the DH isomers during adsorption on SNSs. It was found that the SNSs weakened intermolecular hydrogen bonding in thin DH layers adsorbed on SNSs versus the bulk powders with the effect being more pronounced for para-dihydroxybenzene (PDH) than ortho-dihydroxybenzene (ODH) and meta-dihydroxybenzene (MDH). DFT simulations of the infrared spectra of ODH and MDH dimers were good reproductions of the SEIRA spectra and infrared spectra of ODH/MDH powder, but DFT dimer infrared simulations were less effective at modeling the PDH results due to the large variations of hydrogen bonding between PDH films formed on SNSs versus PDH powder. Hydrogen-bonding effects were observed between acetone and both PDH and ODH in thin layers adsorbed on SNSs, and C−H•••O hydrogen bonding was also seen between n-heptane and PDH and ODH in adsorption experiments on SNSs. These hydrogen-bonding effects were not detected between MDH and either acetone or n-heptane due to differences in resonance effects between MDH versus ODH and PDH.

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Structural and IR and Raman spectral analysis of cyclo(His-Phe) dipeptide

Cited by 25 publications

References 36 publications

pH‐sensing nanostar probe using surface‐enhanced Raman scattering (SERS): theoretical and experimental studies

pH‐sensing nanostar probe using surface‐enhanced Raman scattering (SERS): theoretical and experimental studies

Cyclo(d-Tyr-d-Phe): a new antibacterial, anticancer, and antioxidant cyclic dipeptide fromBacillussp. N strain associated with a rhabditid entomopathogenic nematode

Surface-Enhanced Infrared Absorption and Density Functional Theory Study of Dihydroxybenzene Isomer Adsorption on Silver Nanostructures

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