Intermolecular Vibrations in Hydrophobic Amino Acid Crystals: Experiments and Calculations

Abstract

Intermolecular vibrations of amino acid crystals occur in the THz, or far-infrared, region of the electromagnetic spectrum. We have measured the THz and Raman spectra of DL-leucine as well as two polymorphs of DL-valine, the spectroscopic properties of which have not previously been compared. Theoretical modeling of intermolecular vibrations in hydrophobic amino acids is challenging because the van der Waals interactions between molecules are not accounted for in standard density functional theory. Therefore, to calculate the vibrational modes, we used a recently developed approach that includes these nonlocal electron correlation forces. We discuss methods for comparing results from different theoretical models using metrics other than calculated vibrational frequency and intensity, and we also report a new approach enabling concise comparison of vibrational modes that involve complicated mixtures of inter- and intramolecular displacements.

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 …”

“…[41][42][43][44] Frequency calculations have been reported in a broad spectrum of systems, including explosives, 45 hydrocarbons, 23,39,46 pharmaceuticals, [47][48][49][50] and biomolecules. 40,43,44,[51][52][53][54][55][56][57][58] Given the impact of THz spectroscopy and ab initio DFT simulations, we have systematically investigated the basic structure of molecular phonon modes. 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.…”

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.…”

“…Percentage contribution of translational, librational and intramolecular motions to the first 50 frequency modes of l-Asp and l-Asn are provided in Figure S1 in Supplementary Materials. In order to gain an insight to the direction toward which the molecule predominately translates and rotates and which kind of stretching and torsion that are involved in a vibrational mode, Schmuttenmaer and his coworkers [21] proposed an effective and intuitive method to quantify those vibrational characters of molecules. They distributed one vibrational mode into a large number of vibrations including three translational axes, three librational axes and a given number of bond angles and dihedral angles.…”

“…Other researchers [14,20,18] developed this method by considering the contribution from molecular rotation. Recently, in order to gain deeper insights into collective atomic motions of compound, a more sophisticated but very intuitive analysis method called "vibrational character ID strips" was proposed by Schmuttenmaer and coworkers [21]. In this method, one strip represents one vibrational mode.…”