Two-step kinetic model of the self-assembly mechanism for diphenylalanine micro/nanotube formation.

Peptide nanostructures compose a new class of materials that have gained attention due to their interesting properties. Among them, nanotubes of diphenylalanine (FF) and its analogues have been one of the most studied structures in the last few years. Their importance originates from the need to better understand the formation of ß-amyloid fibrils which are associated with Alzheimer's disease. In this work, the FF self-assembly process was probed using time-resolved Raman microscopy. The changes in the Raman spectra are followed over time after injecting water into a FF-film until micro/nanotubes (MNTs) are formed. Specific features of the Raman spectra clearly suggest that FF-molecules after water injection form an intermediate species before forming FF-MNTs. The broad Raman bands observed for the intermediate species suggest the presence of very heterogeneous structures based on FF. The FF-MNTs appear almost instantaneously (detected via the rise of the typical Raman bands of FF-MNTs at 761, 1249 and 1426 cm-1) after the intermediate structures are formed. This delayed formation of FF-MNTs supports a nucleation process. The formation via nucleation of FF-MNTs is further corroborated by a simulation of the Raman spectra based on a 2-step kinetic model and the respective vibrational Raman modes are identified using Density Functional Theory vibrational calculations. Our results indicate that the driving force for the FF-MNT patterning process is the electric dipole re-orientation originating from the FF dipeptide unit connectivity over time.

Relaxation dynamics of deeply supercooled confined water in L,L-diphenylalanine micro/nanotubes.

The temperature dependence (10-290 K) of the low-frequency (20-150 cm(-1)) Raman-active phonon modes of deeply supercooled confined water in L,L-diphenylalanine micro/nanotubes was analyzed. The isolated dynamics of a specific geometry of a water cluster (pentamer) in a supercooled confined regime was studied in detail. A fragile-to-strong transition at 204 K was observed and related to the crossing of the Widom line. Analysis of peptide vibrational modes coupled to water hydrogen bonds indicated that hydrogen bond fluctuations play an irrelevant role in this system. Our results are in agreement with the second critical point of water existence hypothesis.

Unusual specific heat of almost dry L-cysteine and L-cystine amino acids.

A detailed quantitative analysis of the specific heat in the 0.5- to 200-K temperature range for almost dry L-cysteine and its dimer, L-cystine, amino acids is presented. We report the occurrence of a sharp first-order transition at ∼76 K for L-cysteine associated with the thiol group ordering which was successfully modeled with the two-dimensional Ising model. We demonstrated that quantum rotors, two-level systems (TLS), Einstein oscillators, and acoustic phonons (the Debye model) are essential ingredients to correctly describe the overall experimental data. Our analysis pointed out the absence of the TLS contribution to the low temperature specific heat of L-cysteine. This result was similar to that found in other noncrystalline amorphous materials, e.g., amorphous silicon, low density amorphous water, and ultrastable glasses. L-cystine presented an unusual nonlinear acoustic dispersion relation ω(q)=vq0.95 and a Maxwell-Boltzmann-type distribution of tunneling barriers. The presence of Einstein oscillators with ΘE∼70 K was common in both systems and adequately modeled the boson peak contributions.

Boson peak as a probe of quantum effects in a glassy state of biomolecules: the case of L-cysteine.

Some physical properties of hydrated biomolecules, e.g., the occurrence of a boson peak, have been recognized to resemble those of glassy states. The present work shows that quantum fluctuations play a fundamental role in describing the glassy state of biomolecules, particularly at lower hydration levels. There is a linear relationship between the quantumness and the slope of the temperature dependence of the boson peak frequency, which is used to classify the extent of quantum contributions to the glassy state of glasses in general. Lastly, we demonstrate that the boson peak two-band spectral structure that is observed in some cases can be directly linked to the anisotropy of the elastic properties of the material. The amino acid L-cysteine is studied in detail. The findings are compared with previously reported data for other macromolecules.