Houng-Wei Wang

Localized Gaussian type orbital-periodic boundary condition-density functional theory study of infinite-length single-walled carbon nanotubes with various tubular diameters.

The detailed geometrical structures of zigzag and armchair type single-walled carbon nanotubes (SWCNTs) with infinite tubular length were investigated using localized Gaussian type orbital-periodic boundary condition-density functional theory (LGTO-PBC-DFT) method. The structures of (n, 0) zigzag SWCNTs were optimized for n = 5-21, (n, n) armchair SWCNTs for n = 3-12. For comparison, the optimized geometry of a two-dimensional graphite sheet was also calculated. It was found that the optimized structures of the SWCNTs showed two C-C bond lengths that decrease with an increase in the tubular diameter. More specifically, the two bond lengths converged with those found in the two-dimensional graphite sheet. We also found a degeneracy in the highest occupied crystal orbitals if identical bond lengths were employed for the zigzag SWCNTs and the two-dimensional graphite sheet. This implies that the two different bond lengths found in the zigzag SWCNTs and the two-dimensional graphite sheet are probably due to the Jahn-Teller effect. The armchair SWCNTs show two slightly different bond lengths if the diameter is less than 12 A; otherwise they are almost identical, approaching the longer bond length of the two-dimensional graphite sheet. This can be due to the fact that the armchair SWCNTs do not have degeneracy in occupied crystal orbitals for identical C-C bond lengths. The crossing point of the conducting and valence bands of each armchair SWCNT were also calculated and show a diameter dependence in which the deviation from 2pi/3a decreases as diameter increases.

Atomistic nucleation sites of Pt nanoparticles on N-doped carbon nanotubes

The atomistic nucleation sites of Pt nanoparticles (Pt NPs) on N-doped carbon nanotubes (N-CNTs) were investigated using C and N K-edge and Pt L3-edge X-ray absorption near-edge structure (XANES)/extended X-ray absorption fine structure (EXAFS) spectroscopy. Transmission electron microscopy and XANES/EXAFS results revealed that the self-organized Pt NPs on N-CNTs are uniformly distributed because of the relatively high binding energies of the adsorbed Pt atoms at the imperfect sites. During the atomistic nucleation process of Pt NPs on N-CNTs, stable Pt-C and Pt-N bonds are presumably formed, and charge transfer occurs at the surface/interface of the N-CNTs. The findings in this study were consistent with density functional theory calculations performed using cluster models for the undoped, substitutional-N-doped and pyridine-like-N-doped CNTs.

Analysis of vibrational spectra of solid-state adenine and adenosine in the terahertz region

The low-frequency vibrations of crystalline adenine and adenosine were studied by 5 K terahertz (THz) spectroscopy and solid-state density functional theory (DFT) based on a harmonic model. The accuracy of the calculations was assessed from aspects of frequencies and isotope shifts. The anharmonicity of the potential surface was discussed by observing the thermal shift of the sequence bands. An analytical method was proposed for quantifying the contributions of the intermolecular and intramolecular motions to the normal modes. Adenine exhibited weak coupling between the intermolecular and intramolecular vibrations. The adenine and ribose moieties of adenosine, which are linked through a glycosidic bond, showed intense relative vibrations strongly coupled with the intermolecular vibrations. This finding reveals that adenosine has high flexibility, which arises from the glycosidic bond. An experimental method was further proposed to identify the intermolecular or intramolecular modes.

Terahertz spectroscopy and solid-state density functional theory calculation of anthracene: effect of dispersion force on the vibrational modes.

The phonon modes of molecular crystals in the terahertz frequency region often feature delicately coupled inter- and intra-molecular vibrations. Recent advances in density functional theory such as DFT-D(*) have enabled accurate frequency calculation. However, the nature of normal modes has not been quantitatively discussed against experimental criteria such as isotope shift (IS) and correlation field splitting (CFS). Here, we report an analytical mode-decoupling method that allows for the decomposition of a normal mode of interest into intermolecular translation, libration, and intramolecular vibrational motions. We show an application of this method using the crystalline anthracene system as an example. The relationship between the experimentally obtained IS and the IS obtained by PBE-D(*) simulation indicates that two distinctive regions exist. Region I is associated with a pure intermolecular translation, whereas region II features coupled intramolecular vibrations that are further coupled by a weak intermolecular translation. We find that the PBE-D(*) data show excellent agreement with the experimental data in terms of IS and CFS in region II; however, PBE-D(*) produces significant deviations in IS in region I where strong coupling between inter- and intra-molecular vibrations contributes to normal modes. The result of this analysis is expected to facilitate future improvement of DFT-D(*).

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

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

Advances in terahertz (THz) spectroscopy and solid‐state density functional theory (DFT) have enabled a better understanding of low‐frequency molecular phonon modes in the region that includes intermolecular interactions. Normal modes in this region, in particular, may have contributions under the harmonic approximation from both intermolecular and intramolecular nuclear motions. A newly developed mode analysis allows us to characterize molecular optical phonon modes in terms of intermolecular and intramolecular vibrational mixing for the C60 , anthracene, adenine, α‐glycine, and l‐alanine crystals. Through systematic investigation, two forms of the vibrational mixing have been identified. One is strong mixing within similar characteristic frequency regions, while the other is weak mixing of distinct characteristic frequency regions separated by a large gap. The former is predictable from classical mechanics and appears in molecular systems having structural flexibility. The latter is nonclassical and has been illustrated in amino acids. This finding provides new insights into the nature of molecular optical phonon modes and related physical and/or chemical processes such as energy transfer between internal and external modes with large energy separation. WIREs Comput Mol Sci 2016, 6:386–409. doi: 10.1002/wcms.1256

Characteristics of Low-Frequency Molecular Phonon Modes Studied by THz Spectroscopy and Solid-State ab Initio Theory: Polymorphs I and III of Diflunisal

THz absorption spectra of two polymorphs of diflunisal, form I and form III, exhibit distinct features due to the influence of packing conformations on the frequency distributions and IR activities of gamma point phonon modes within the 100 cm(-1) region. In order to understand the origins of these THz modes, we perform a detailed mode analysis. The result shows that although the spectral features are different, these low-frequency phonon modes of the two molecular polymorphs have similar vibrational characteristics in terms of harmonic couplings of intermolecular and intramolecular vibrations.

Application of THz vibrational spectroscopy to molecular characterization and the theoretical fundamentals: an illustration using saccharide molecules

This work illustrates several theoretical fundamentals for the application of THz vibrational spectroscopy to molecular characterization in the solid state using two different types of saccharide systems as examples. Four subjects have been specifically addressed: (1) the qualitative differences in the molecular vibrational signatures monitored by THz and mid-IR vibrational spectroscopy; (2) the selection rules for THz vibrational spectroscopy as applied to crystalline and amorphous systems; (3) a normal mode simulation, using α-l-xylose as an example; and (4) a rigorous mode analysis to quantify the percentage contributions of the intermolecular and intramolecular vibrations to the normal mode of interest.

Low-frequency vibration study of amino acids using terahertz spectroscopy and solid-state density functional theory

Understanding the low-frequency normal modes of amino acids, the building blocks of proteins, is crucial to reveal the vibration-function relationship in the macromolecular system. Recent advances in terahertz spectroscopy (THz) and solid-state density functional theory (DFT) have ensured an accurate description of low-frequency modes of amino acids. New knowledge people have learnt so far is that the inter- and intra-molecular vibrations are strongly mixed with each other in the THz region through the vibrational coordinate mixing. Rich information is believed embedded in this phenomenon. We introduce a generalized mode-analysis method that allows for the accurate decomposition of a normal mode of interest into the three intermolecular translations, three principal librations and various intrinsic intramolecular vibrations. This mode-analysis method will be demonstrated in the crystalline C60 systems and then applied to shed light on the nature of low-frequency phonons of glycine, diglycine and triglycine. This method helps reveal new intramolecular vibrational modes on the first hand, and more importantly, illuminate a new phenomenon of the frequency distribution of intramolecular vibrations (FDIV). FDIV describes the possible broad distributions of important intramolecular vibrations in the low-frequency normal modes. The FDIV concept may indicate an additional mechanism for the intramolecular vibrations to become thermally active and participate in various biological functions.