In condensed phases, a highly symmetric gas-phase molecule lowers its symmetry under perturbation of the solvent, which is vital to a variety of structural chemistry related processes. However, the dynamical aspects of solvent-mediated symmetry-breaking events remain largely unknown. Herein, direct evidence for two types of solvent-mediated symmetry-breaking events that coexist on the picosecond timescale in a highly symmetric anion, namely, hexacyanocobaltate, is presented: 1) an equilibrium symmetry-breaking event in which a solvent-bound species having lowered symmetry undergoes a population exchange reaction with the symmetry-retaining species; 2) a dynamic symmetry-breaking event that is composed of many dynamic population-exchange reactions under fluctuating solvent interactions. Ultrafast two-dimensional infrared spectroscopy is used to simultaneously observe and dynamically characterize these two events. This work opens a new window into molecular symmetry and structural dynamics under equilibrium and non-equilibrium conditions.

In this work, a non-natural amino acid, H-propargylglycine-OH (Pra), is chosen to examine the side-chain effect on the backbone conformation of small peptides. The conformations of two synthesized Pra-containing tripeptides, Ac-Pra-Pra-NH₂ (PPTP) and Ac-Pra-Ala-NH₂ (PATP), are examined by infrared (IR) spectroscopy in combination with molecular dynamics (MD) simulations and quantum chemical computations. By analyzing the joint distributions of backbone torsional angles, several significant conformations can be identified for the two tripeptides solvated in D₂O. At room temperature, 44 % of PPTP exists in the α-α conformation and 33 % of PATP exists in the α-polyproline-II conformation. Larger structural inhomogeneity is seen in both cases by MD simulations at elevated temperatures. Thus even a small side chain, such as the propargyl group can significantly alter the peptide backbone conformations. The results suggest that there is no overwhelming conformational propensity of the Pra residue in short peptides. IR spectra simulated in the amide-I region using two different methods, reasonably reproduce the experimental IR spectra and their temperature dependence.

Understanding the structure of amyloid-β (Aβ) aggregates is a key step towards elucidating the pathology of Alzheimer’s disease. In this work, three fragments of the Aβ_1–42 protein, Aβ_1–25 (DAEFRHDSGYEVHHQKLVFFAEDVG), Aβ_25–35 (GSNKGAIIGLM), and Aβ_33–42 (GLMVGGVVIA), were synthesized, and their aggregated structures were examined by linear infrared spectroscopy in the amide-I (mainly the CO stretching) region. The structures of the formed aggregates were found to be both sequence and pH dependent. The results suggest that instead of forming matured fibrils, as in the case of full-length Aβ_1–42, both Aβ_1–25 and Aβ_33–42 form a mixture of threadlike β-sheet fibril, soluble β-sheet oligomer, and random coil structures. The β-sheet conformations were found to be mainly antiparallel for the former and both parallel and antiparallel for the latter. However, the Aβ_25–35 fragment was found to form assembled fibrils containing predominantly parallel β-sheets. The conformation and morphology of the aggregates were also confirmed by circular dichroism measurements and transmission electron microscopy. Factors influencing the structures of the aggregates formed by the Aβ fragments were discussed.

Quantum chemical computations, molecular dynamics simulations, and linear and nonlinear infrared spectral simulations are carried out for four representative biomolecules: cellobiose, alanine tripeptide, L-α-glycerylphosphorylethanolamine, and the DNA base monomer guanine. Anharmonic transition frequencies and anharmonicities for the molecules in vacuum are evaluated. Instantaneous normal-mode analysis is performed and the vibrational frequency distribution correlations are examined for the molecules solvated in TIP3P water. Many local and regional motions of the biomolecules are predicted to be anharmonically coupled and their vibrational frequencies are predicted to be largely correlated. These coupled and correlated vibrational motions can be easily visualized by pairwise cross peaks in the femtosecond broadband two-dimensional infrared (2D IR) spectra, which are simulated using time-domain third-order nonlinear response functions. A network of distinctive spectral profiles of the 2D IR cross peaks, including peak orientations and positive and negative signal patterns, are shown to be intimately connected with the couplings and correlations. The results show that the vibrational couplings and correlations, driven by solvent interactions and also by intrinsic vibrational interactions, are vibrational mode dependent and thus chemical group dependent, and form the structural and dynamical basis of the anharmonic vibrators that are ubiquitous in biomolecules.