Water-Mediated Electronic Structure of Oligopeptides Probed by Their UV Circular Dichroism, Absorption Spectra, and Time-Dependent DFT Calculations

Abstract

We investigate the UV absorption spectra of a series of cationic GxG (where x denotes a guest residue) peptides in aqueous solution and find that the spectra of a subset of peptides with x = A, L, I, K, N, and R (and, to a lesser extent, peptides with x = D and V) vary as a function of temperature. To explore whether or not this observation reflects conformational dependencies, we carry out time-dependent density functional calculations for the polyproline II (pPII) and β-strand conformations of a limited set of tripeptides (x = A, V, I, L, and R) in implicit and explicit water. We find that the calculated CD spectra for pPII can qualitatively account for the experimental spectra irrespective of the water model. The reproduction of the β-strand UV-CD spectra, however, requires the explicit consideration of water. Based on the calculated absorption spectra, we explain the observed temperature dependence of the experimental spectra as being caused by a reduced dispersion (larger spectral density) of the overlapping NV 2 band and the influence of water on electronic transitions in the β-strand conformation. Contrary to conventional wisdom, we find that both the NV 1 and NV 2 band are the envelopes of contributions from multiple transitions that involve more than just the HOMOs and LUMOs of the peptide groups. A natural transition orbital analysis reveals that some of the transitions with significant oscillator strength have a charge-transfer character. The overall manifold of transitions, in conjunction with their strengths and characters, depends on the peptide's backbone conformation, peptide hydration, and also on the side chain of the guest residue. It is particularly noteworthy that molecular orbitals of water contribute significantly to transitions in β-strand conformations. Our results reveal that peptide groups, side chains, and hydration shells must be considered as an entity for a physically valid characterization of UV absorbance and circular dichroism. File list (2) download file view on ChemRxiv UV_CD_Absorption paper_final.pdf (4.17 MiB) download file view on ChemRxiv SI_UV_CD_Absorption_paper.pdf (11.34 MiB)

A computational approach for modeling electronic circular dichroism of solvated chromophores

“…41 Finally, the calculations of the UV-electronic circular dichroism (UV-ECD) and UV-Photoabsorption spectra have been performed at the Time-Dependent DFT (TDDFT) level analyzing the lowest 70 and 100 excited-states for GAG + and (GVGVP) 2 , respectively. In order to allow an easy comparison with the experimental data, [28][29][30][31] the calculated spectra have been reported in terms of ε (photoabsorption) and Δε (ECD). The individual UV-ECD spectra relative to the most relevant conformations in presence of the explicit solvent are reported in Figures S3-S8.…”

Imidazolium based gemini amphiphiles derived from L-valine. Structural elements and surfactant properties

“…The position of this amide band is significantly red shifted in comparison with the average positions observed in amides, [71] including peptidic and pseudopeptidic structures. [36,72,73] This must be attributed to the influence of the solvent and the long aliphatic tails, as red shifts are usually reported for n-* transitions of amides when changing the solvent from polar to apolar. [71] The second band, less intense and with the fine structure partly observed, appears in the 255-280 nm region and is associated to the substituted benzene ring of the spacer.…”

Rearrangement of aniline(H2O)n (n = 0–12) clusters upon photoionization and their excited state properties: Density functional theory and time‐dependent density functional theory study

“…We chose these three functionals because hydrogen bonding interactions and excited state energies are found very close to the gold standard CC2 or CCSD(T) methods. 34,35 Very recently, Kumar et al reported that wB97XD/cc-pVTZ functional is essential for accurate prediction of chargetransfer excitations and hydrogen bonding interactions. 35 The low-lying 10 excited singlet states were calculated at wB97XD-optimized S 0 geometries for all the clusters and the excited state dipole moments were calculated at the same level of theory.…”

“…Besides, electronic structure calculations were carried out by time‐dependent density functional theory (TD‐DFT) methods employing M06‐2X, w B97XD, and CAM‐B3LYP functionals with cc‐pVTZ basis set. We chose these three functionals because hydrogen bonding interactions and excited state energies are found very close to the gold standard CC2 or CCSD(T) methods 34,35 . Very recently, Kumar et al reported that w B97XD/cc‐pVTZ functional is essential for accurate prediction of charge‐transfer excitations and hydrogen bonding interactions 35 .…”