Vibrational and structural properties of L-Alanyl-L-Phenylalanine dipeptide by Raman spectroscopy, infrared and DFT calculations

Silva, C.B.; Filho, J.G. da Silva; Pinheiro, G.S.; Teixeira, Alexandre Magno Rodrigues; Freire, Paulo

doi:10.1016/j.vibspec.2018.08.001

Cited by 21 publications

(8 citation statements)

References 62 publications

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“…A prominent vibration at 1712 (model) and 1717 cm –1 (experiment) was attributed to the CO stretch of the Orn amide I. The proposed band assignments of GS in Table are also in general agreement with the GS literature and those which have been made from DFT calculations on dipeptides and other compounds such as methylacetamide and polycyclic aromatic hydrocarbons. , …”

Section: Resultssupporting

confidence: 81%

Temperature-Induced Effects on the Structure of Gramicidin S

et al. 2023

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We report on the structure of Gramicidin S (GS) in a model membrane mimetic environment represented by the amphipathic solvent 1-octanol using one-dimensional (1D) and two-dimensional (2D) IR spectroscopy. To explore potential structural changes of GS, we also performed a series of spectroscopic measurements at differing temperatures. By analyzing the amide I band and using 2D-IR spectral changes, results could be associated to the disruption of aggregates/oligomers, as well as structural and conformational changes happening in the concentrated solution of GS. The ability of 2D-IR to enable differentiation in melting transitions of oligomerized GS structures is attributed to the sensitivity of the technique to vibrational coupling. Two melting transition temperatures were identified; at T m1 in the range 41−47 °C where the GS aggregates/oligomers disassemble and at T m2 = 57 ± 2 °C where there is significant change involving GS β-sheet-type hydrogen bonds, whereby it is proposed that there is loss of interpeptide hydrogen bonds and we are left with mainly intrapeptide β-sheet and β-turn hydrogen bonds of the smaller oligomers. Further analysis with quantum mechanical/molecular mechanics (QM/MM) simulations and second derivative results highlighted the participation of active GS side chains. Ultimately, this work contributes toward understanding the GS structure and the formulation of GS analogues with improved bioactivity.

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Section: Resultssupporting

confidence: 81%

Temperature-Induced Effects on the Structure of Gramicidin S

et al. 2023

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“…Figure 2 compares infrared absorption spectra of bulk MOPHE and MOPHE-D 5 compounds dispersed in the KBr tablet. Assignments of the main infrared bands based on our calculations and previous publications [30][31][32][33][34][35][36][37][38][39] are given in Table 1. Figure 2 compares infrared absorption spectra of bulk MOPHE and MOPHE-D5 compounds dispersed in the KBr tablet.…”

Section: Assignments Of Mophe Infrared Absorption Bandsmentioning

confidence: 99%

Reflection Absorption Infrared Spectroscopy Characterization of SAM Formation from 8-Mercapto-N-(phenethyl)octanamide Thiols with Phe Ring and Amide Groups

et al. 2020

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Multifunctional amide-containing self-assembled monolayers (SAMs) provide prospects for the construction of interfaces with required physicochemical properties and distinctive stability. In this study, we report the synthesis of amide-containing thiols with terminal phenylalanine (Phe) ring functionality (HS(CH2)7CONH(CH2)2C6H5) and the characterization of the formation of SAMs from these thiols on gold by reflection absorption infrared spectroscopy (RAIRS). For reliable assignments of vibrational bands, ring deuterated analogs were synthesized and studied as well. Adsorption time induced changes in Amide-II band frequency and relative intensity of Amide-II/Amide-I bands revealed two-state sigmoidal form dependence with a transition inflection points at 2.2 ± 0.5 and 4.7 ± 0.5 min, respectively. The transition from initial (disordered) to final (hydrogen-bonded, ordered) structure resulted in increased Amide-II frequency from 1548 to 1557 cm−1, which is diagnostic for a strongly hydrogen-bonded amide network in trans conformation. However, the lateral interactions between the alkyl chains were found to be somewhat reduced when compared with well-ordered alkane thiol monolayers.

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“…We remark the fact that these experimental bands are insensitive to the thermal treatment and can therefore be safely assigned to the side [phenyl–CH 2 ]– group, practically unaffected by cyclization. Once assigned the precise fingerprint of [phenyl–CH 2 ], we can analyze a few specific differences between the l -PheAla and r -PheAla spectra (Table (2.2)), referring the interested reader to the SI for a complete assignment of the Raman spectra. ,− In l -PheAla, the broad and weak band at ≈1680 cm –1 is compatible with the band computed at 1686 cm –1 in the l -zwi configuration, assigned to the CO stretching of the CO–NH group, also involving the NH 3 + group that, interacting with CO through a H-bond, may cause an overestimation of the vibrational frequency in this model system. On the other hand, the weak feature at 1650 cm –1 in r -PheAla is compatible with the band calculated at 1687 cm –1 in the c -neu configuration and assigned to the symmetric stretching of the two CO bonds.…”

Section: Discussionmentioning

confidence: 86%

Insights into the Thermally Activated Cyclization Mechanism in a Linear Phenylalanine-Alanine Dipeptide

et al. 2022

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Dipeptides, the prototype peptides, exist in both linear ( l -) and cyclo ( c -) structures. Since the first mass spectrometry experiments, it has been observed that some l -structures may turn into the cyclo ones, likely via a temperature-induced process. In this work, combining several different experimental techniques (mass spectrometry, infrared and Raman spectroscopy, and thermogravimetric analysis) with tight-binding and ab initio simulations, we provide evidence that, in the case of l -phenylalanyl- l -alanine, an irreversible cyclization mechanism, catalyzed by water and driven by temperature, occurs in the condensed phase. This process can be considered as a very efficient strategy to improve dipeptide stability by turning the comparatively fragile linear structure into the robust and more stable cyclic one. This mechanism may have played a role in prebiotic chemistry and can be further exploited in the preparation of nanomaterials and drugs.

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Vibrational and structural properties of L-Alanyl-L-Phenylalanine dipeptide by Raman spectroscopy, infrared and DFT calculations

Cited by 21 publications

References 62 publications

Temperature-Induced Effects on the Structure of Gramicidin S

Temperature-Induced Effects on the Structure of Gramicidin S

Reflection Absorption Infrared Spectroscopy Characterization of SAM Formation from 8-Mercapto-N-(phenethyl)octanamide Thiols with Phe Ring and Amide Groups

Insights into the Thermally Activated Cyclization Mechanism in a Linear Phenylalanine-Alanine Dipeptide

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