Application of a transparent window vibrational probe (azido probe) to the structural dynamics of model dipeptides and amyloid β-peptide

Cai, Kezhou; Liu, Jia; Liu, Yanan; Feng, Chen; Yan, Guiyang; Lin, Huiqiu

doi:10.1016/j.saa.2019.117681

Cited by 3 publications

(7 citation statements)

References 115 publications

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“…As it is far away from Mode 38, it does not form FR with Mode 38 but coupling is visible. The same is true for Over (25), which is more than 50 cm −1 to the right of Mode 38. The band to the left of Mode 38 includes two combination bands, Comb (18,30) and Comb (17,30).…”

Section: -Azidotoleune In Nndmamentioning

confidence: 53%

“…The azide asymmetric stretch blue shifts in THF calculations. Like in NNDMA, Comb (15,30) and Over (25) are very far (Δω′ > 100 and >65 cm −1 , respectively) away energetically from mode 38, and Comb (18,30) and Comb- (17,30) are positioned close. Table S7 shows TFR values for possible modes that can resonantly couple with the azide asymmetric stretch for 4-azidotoluene in a THF solvent.…”

Section: Solvent Effects Onmentioning

confidence: 84%

“…Here, again, Comb (18,30) has a TFR value >1 because Comb- (18,30) is strongly coupled to the azide asymmetric stretch. Although both Comb (15,30) and Over (25) are far away in frequency from the fundamental vibration mode 38, they show TFR values ∼0.55 and ∼0.45, respectively. Therefore, both Comb (15,30) and Over (25) are weakly coupled to the azide asymmetric stretch.…”

Section: Solvent Effects Onmentioning

confidence: 95%

“…Moreover, Comb (17,30) has a lower than 30 km mol −1 intensity. The overtone mode, Over (25), is very far away in frequency from Mode 38 and has an intensity of ∼10 km mol −1 . All other vibrational modes have an intensity of less than 10 km mol −1 .…”

Section: -Azidotoleune In Nndmamentioning

confidence: 98%

“…The intensity of Comb (17,30) in THF varies for different basis sets as it did in NNDMA. Over (25) has an intensity of ∼10 km mol −1 , and all other vibrational modes within the transparent window have lower intensity than 10 km mol −1 . These observations verify that changing the solvents does not influence the identity of FRs, but the intensity of each vibrational transition in all calculations is lower with THF.…”

Section: Solvent Effects Onmentioning

confidence: 99%

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Effects of the Intramolecular Group and Solvent on Vibrational Coupling Modes and Strengths of Fermi Resonances in Aryl Azides: A DFT Study of 4-Azidotoluene and 4-Azido-N-phenylmaleimide

Perera,

Aikawa,

Shaner

et al. 2023

J. Phys. Chem. A

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The high transition dipole strength of the azide asymmetric stretch makes aryl azides good candidates as vibrational probes (VPs). However, aryl azides have complex absorption profiles due to Fermi resonances (FRs). Understanding the origin and the vibrational modes involved in FRs of aryl azides is critically important toward developing them as VPs for studies of protein structures and structural changes in response to their surroundings. As such, we studied vibrational couplings in 4-azidotoluene and 4-azido-N-phenylmaleimide in two solvents, N,N-dimethylacetamide and tetrahydrofuran, to explore the origin and the effects of intramolecular group and solvent on the FRs of aryl azides using density functional theory (DFT) calculations with the B3LYP functional and seven basis sets, 6-31G(d,p), 6-31+G(d,p), 6-31++G(d,p), 6-311G(d,p), 6-311+G(d,p), 6-311++G(d,p), and 6-311++G(df,pd). Two combination bands consisting of the azide symmetric stretch and another mode form strong FRs with the azide asymmetric stretch for both molecules. The FR profile was altered by replacing the methyl group with maleimide. Solvents change the relative peak position and intensity more significantly for 4-azido-N-phenylmaleimide, which makes it a more sensitive VP. Furthermore, the DFT results indicate that a comparison among the results from different basis sets can be used as a means to predict more reliable vibrational spectra.

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