Intramolecular Vibrations in Low-Frequency Normal Modes of Amino Acids: l-Alanine in the Neat Solid State

Abstract

This paper presents a theoretical analysis of the low-frequency phonons of L-alanine by using the solid-state density functional theory at the Γ point. We are particularly interested in the intramolecular vibrations accessing low-frequency phonons via harmonic coupling with intermolecular vibrations. A new mode-analysis method is introduced to quantify the vibrational characteristics of such intramolecular vibrations. We find that the torsional motions of COO(-) are involved in low-frequency phonons, although COO(-) is conventionally assumed to undergo localized torsion. We also find the broad distributions of intramolecular vibrations relevant to important functional groups of amino acids, e.g., the COO(-) and NH3(+) torsions, in the low-frequency phonons. The latter finding is illustrated by the concept of frequency distribution of vibrations. These findings may lead to immediate implications in other amino acid systems.

Mixing of intermolecular and intramolecular vibrations in optical phonon modes: terahertz spectroscopy and solid‐state density functional theory

“…Functionals that take account of dispersion forces have particularly allowed normal mode simulations with unprecedented accuracy . Frequency calculations have been reported in a broad spectrum of systems, including explosives, hydrocarbons, pharmaceuticals, and biomolecules …”

“…We are primarily concerned with the extent to which conventional knowledge of molecular phonon modes is valid and applicable and if there are any new properties. This work reviews our progress on the quantitative characterization of optical phonon modes in C 60 , anthracene, adenine, α ‐glycine, and l ‐alanine crystals . Structural information for these systems is provided in Table .…”

“…A firm correlation is thus established between the internal modes of the gas and solid phases, where the gas‐phase modes provide a good basis for the solid phase. In the second situation, molecules undergo dramatic conformational changes in the condensation process (e.g., amino acids); thus, the molecule site group in the solid phase is no longer a subgroup of the point group of the gas‐phase molecule. Because the correlation between the gas‐phase and solid‐phase internal modes is lost, the gas‐phase internal modes are no longer suitable for the solid phase; a particular approach was therefore developed for constructing the intended solid‐phase internal‐mode basis.…”

The effect of the flexibility of hydrogen bonding network on low-frequency motions of amino acids. Evidence from Terahertz spectroscopy and DFT calculations

“…The term "intramolecular vibrations" is used to refer to such kind of motions. Although in theory intermolecular vibrations require much less energy than intramolecular vibrations, it has been revealed by many work that the inter-and intramolecular vibrations are never separable [12,18,19,21]. Especially in low-frequency mode region, to a great extent, they couple with each other.…”

“…However, modeling small molecules like amino acids is a good start towards revealing complex motions of large molecules. Many studies [9,10,11,12,13,12,14,15,16,17,18,19] based on DFT method have been devoted to understand the low-frequency vibrations of small molecules in solid state.…”