Abstract
To reduce the intense terahertz (THz) wave absorption of water and increase the signal-to-noise ratio, the THz spectroscopy detection of biomolecules usually operates using the nanofluidic channel technologies in practice. The effects of confinement due to the existence of nanofluidic channels on the conformation and dynamics of biomolecules are well known. However, studies of confinement effects on the THz spectra of biomolecules are still not clear. In this work, extensive all-atom molecular dynamics simulations are performed to investigate the THz spectra of the glycine oligopeptide solutions in free and confined environments. THz spectra of the oligopeptide solutions confined in carbon nanotubes (CNTs) with different radii are calculated and compared. Results indicate that with the increase of the degree of confinement (the reverse of the radius of CNT), the THz absorption coefficient decreases monotonically. By analyzing the diffusion coefficient and dielectric relaxation dynamics, the hydrogen bond life, and the vibration density of the state of the water molecules in free solution and in CNTs, we conclude that the confinement effects on the THz spectra of biomolecule solutions are mainly to slow down the dynamics of water molecules and hence to reduce the THz absorption of the whole solution in confined environments.
Highlights
Terahertz (THz) wave is one of the electromagnetic radiations lying between the millimeter and far-infrared waves with a frequency range from 0.1 to 10 THz [1]
We present all-atom molecular dynamics (MD) simulations to investigate the confinement effects on the THz spectrum of a glycine oligopeptide solution confined in carbon nanotubes (CNTs) with different radii
Biomolecules [41,42] in confined environments. These results indicate the CNT implements confinement effects on the Gly23 oligopeptide and water molecules
Summary
Terahertz (THz) wave is one of the electromagnetic radiations lying between the millimeter and far-infrared waves with a frequency range from 0.1 to 10 THz [1]. Polymers 2019, 11, 385 besides the intrinsic structural properties of the biomolecule, the THz spectrum is more related to the interaction between the biomolecule itself and its surrounding water molecules Due to these features, THz spectroscopy detection of biomolecules in aqueous solution is full of challenges. To overcome the strong absorption of water and improve the detection sensitivity, micro/nano-channels are widely utilized for THz spectroscopy measurements of biomolecular solutions. Brown et al [9,10] measured the THz spectrum of RNA molecules in solution using a 600-nm-wide and 500-nm-deep SiO2 nanochannel array and found the signal-to-noise ratio was greatly promoted and the spectral resolution improved to 10 GHz. Xia et al [11] anticipated the potential applications of nanochannel biochips applied in THz spectroscopy detection in their review article.
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