Temperature-Dependent Low-Frequency Vibrations of Thiamine Crystal Containing Hydrated Ions

An investigation on 3-hydroxybenzaldehyde for exploring terahertz low-frequency vibration modes with quasi-harmonic approximation method

3-Hydroxybenzaldehyde (3-HBA) was investigated in the range of 0.6-2.8 THz by terahertz time-domain spectroscopy (THz-TDS) and solid-state density functional theory (ss-DFT) with first-principles calculation. Four distinct peaks were found respectively, and among them, the intensity disparity between experiment and simulation spectra at 2.04 THz was recognized as the biggest inconsistency. Considering thermal behavior can be responsible for this, quasi-harmonic approximation (QHA) method was introduced to mimic the unit cell volume expansion. According to vibrational modes analysis, it was ascertained that the biggest vibrational modes discrepancy was also located at 2.04 THz. Molecules in 0% and 4% unit cell expansion exhibit an opposite rotational direction in a-b plane compared with 2% unit cell expansion. Noncovalent intermolecular interactions were investigated with independent gradient model (IGM), and the result indicates that hydrogen bonding is the dominating noncovalent interaction of 3-HBA. While calculating systematic potential energy to the displaced bonds stretching involving hydrogen atoms, it was found the anomalous potential energy variation to the bond stretching provides a possible explanation for the rotation direction divergence, that is, the rotation direction divergence can be related to some hydrogen atoms seeking lower overall potential energy around their equilibrium positions during bond stretching in response to the variational intermolecular van der Waals force. This research combined THz-TDS with the quasi-harmonic approximation method, elucidating the principle of vibrational characteristics in different volumes, which is beneficial to the investigation of the terahertz low-frequency vibration to thermal behavior as a reference in biochemistry and other fields.

Van der Waals interactions regulating the hydration of 2-methacryloyloxyethyl phosphorylcholine, the constructing monomer of biocompatible polymers

Van der Waals (VDW) interactions provide fantastic properties for biological systems that function at room temperature. The VDW interaction, which primarily contributes to weak hydrogen bonding, is expected to play a key role in regulating hydrophobic hydration to express the biologically inert biocompatible function of polymerized MPCs (2-methacryloyloxyethyl phosphorylcholine). This report explores at the molecular level the biologically inert function of polymerized MPCs through an array of vibrational spectroscopic and computational characterization of MPC monomers, as temperature-dependent change of intramolecular weak hydrogen bonding. Synchrotron Fourier transform infrared microspectroscopy and terahertz time-domain spectroscopy were used to investigate temperature-dependent spectral changes in the low frequency vibrations of the MPC over the temperature range from cryogenic to room temperature, and the results were analysed by highly reliable well-established density functional theory (DFT) calculations. Complicated spectral features in the low frequency energy region and the uncertain conformations of the MPC in the amorphous powder state are clearly resolved under a polarizable continuum model and dispersion correction to pure DFT calculations.

Terahertz spectroscopy for interpreting the formation and hierarchical structures of silk fibroin oligopeptides

Determining the configuration and conformation of peptides is crucial for interpreting their structure-property relationships. In this work, we present nondestructive terahertz time-domain spectroscopy combined with density functional theory (DFT) and potential energy distribution (PED) analysis to identify the hierarchical structures of oligopeptides. The characteristic THz spectra of silk fibroin oligopeptides have been measured. Supported by DFT and PED analysis, the intrinsic differences among the dipeptides were identified by the collective vibrational modes of "R" groups and terminal groups linked by molecular chains of amido bonds or benzene rings. For tetrapeptides and hexapeptides, a few weak resonances and intensity differences were distinguished by the vibration mode of the molecular collective network formed by the interaction of amide planes and intramolecular hydrogen bond interactions. According to the THz absorption analyses of amide planes and intramolecular interactions within the molecular chains of silk fibroin oligopeptide isomer pairs, the formation and hierarchical structures were successfully interpreted using THz spectroscopy. This investigation develops a better understanding of the peptide formation mechanism, which further provides guidance in interpreting the formation of silk.