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

Low-Frequency Vibrational Spectra of 4-Fluorophenol Studied by THz Spectroscopy and Solid-State Density Functional Theory

Hydrogen bonds serve as important intermolecular interactions organizing the spatial arrangement of molecular crystals. Determining the hydrogen-bond orientations remains a challenging task. In the previous XRD study, the authors assumed a single crystal structure of 4-fluorophenol in which molecules form hexamer-ring clusters via anticlockwise hydrogen bonding. However, the existence of the other structure, which adopts clockwise hydrogen bonding, remains uncertain and warrants further exploration. We unveil distinctive fingerprint information associated with both structures by using high-resolution terahertz spectroscopy. The distinct structures result in different intramolecular geometries of 4-fluorophenol regarding the O-H bond configurations, which are manifested by a noticeable peak splitting in the 20-200 cm-1 frequency range. This result illustrates the sensitivity of THz spectroscopy to hydrogen-bond conformational polymorphism. Our findings represent a significant advancement in utilizing high-resolution THz spectroscopy to resolve hydrogen-bond orientations in molecular crystals with possible broad applicability across diverse hydrogen-bonded organic and inorganic framework materials.

Harmonic and anharmonic studies on THz spectra of two vanillin polymorphs

Polymorphism commonly exists in organic molecular crystals. The fingerprint features in low-frequency vibrational range are important information reflecting different intermolecular interactions of polymorphs. Interpreting these features is very helpful to understand vibrational property of polymorphs and reveal the thermodynamic stability. In this work, the low-frequency vibrations of form I and II of vanillin are investigated using terahertz time-domain spectroscopy. Static DFT calculation and ab initio molecular dynamics (AIMD) are employed to interpret their low-frequency vibrations of both forms in harmonic and anharmonic ways, respectively. Their low-frequency vibration characteristics in harmonic calculations are discussed, and anharmonic mode couplings between OH bond stretch and the stretching and bending motion of hydrogen bonds are uncovered. Moreover, the thermodynamic energies including electronic potential energy and vibrational/kinetic energy arising from nuclear motions are calculated. The result reveals that the stability order of the two forms is mainly dependent on their electric potential energy difference.

Study of low-frequency spectroscopic characteristics of γ-aminobutyric acid with THz and low-wavenumber Raman spectroscopy

γ-aminobutyric (GABA) is the most important inhibitory neurotransmitier in vertebrate central nervous systems. The content level of GABA is related to the different degree of malignancy gliomas. Thus, it can be considered a promising glioma biomarker. In this paper, the spectroscopic properties of GABA have been characterized by combining the THz spectroscopy with low-wavenumber Raman spectroscopy. The experimental results showed that, GABA exhibited three absorption peaks and three refractive index peaks in the range of 0.6-2.1 THz. The limit of detection can reach up to 0.428 % based on the absorption coefficient at the peak of 2.04 THz. Moreover, the low-wavenumber Raman spectrum of GABA showed seven characteristic peaks at 41.0, 50.8, 58.8, 77.2, 98.8, 115.6, 141.2 cm-1 in 0-150 cm-1 region. Moreover, the THz and low-wavenumber theoretical spectra of GABA were simulated with solid-state density function theory, respectively. The calculated results were in good agreement with the experimental observations. On the basis of calculated result, the vibrational motions of each THz and Raman characteristic modes were quantitatively decomposed by analytical mode-decoupling method, where the contribution percentages of external translation, external librations and intramolecular vibration of each vibration modes were analyzed Furthermore, the low-frequency characteristics of GABA was analyzed by combining the THz and low-wavenumber Raman spectroscopy. It is beneficial for the structural information analysis and quantitative identification of biomarker GABA in early stage diagnosis of glioma.

Identification and low-frequency vibrational analysis of three free anthraquinones via terahertz spectroscopy

In this study, terahertz time-domain spectroscopy (THz-TDS) was used to obtain the terahertz absorption spectra of three free anthraquinones (Chrysophanol, Emodin, Physcion) in the frequency range of 0.2-4.3 THz. The results show that terahertz spectroscopy is an effective detecting such compounds. Meanwhile, the theoretical spectrum using density functional theory calculations agrees well with the experimental spectrum. A modal decoupling method was used to identify each low-frequency vibrational mode and determine the average contribution of different atoms and groups. Modal decoupling provides a better understanding of molecules' mixed vibrational modes and enables quantifying the atoms' vibrational contributions. Results show that the substituent group facilitates the transition between the fundamental vibrational modes; subsequently, the substituent group shifts the vibrational centre of gravity of the three molecules and affects the vibrational contribution of hydrogen bonds. Furthermore, insignificant Emodin absorption is related to the nearly symmetrical structure formed by the substituents. The feasibility of terahertz analysis of differential molecular structures has also been confirmed.

Interexcited State Photophysics I: Benchmarking Density Functionals for Computing Nonadiabatic Couplings and Internal Conversion Rate Constants

We present the first benchmarking study of nonadiabatic matrix coupling elements (NACMEs) calculated using different density functionals. Using the S₁ → S₀ transition in perylene solvated in toluene as a case study, we calculate the photophysical properties and corresponding rate constants for a variety of density functionals from each rung of Jacob's ladder. The singlet photoluminescence quantum yield (sPLQY) is taken as a measure of accuracy, measured experimentally here as 0.955. Important quantum chemical parameters such as geometries, absorption, emission, and adiabatic energies, NACMEs, Hessians, and transition dipole moments were calculated for each density functional basis set combination (data set) using density functional theory based multireference configuration interaction (DFT/MRCI) and compared to experiment where possible. We were able to derive simple relations between the TDDFT and DFT/MRCI photophysical properties; with semiempirical damping factors of ∼0.843 ± 0.017 and ∼0.954 ± 0.064 for TDDFT transition dipole moments and energies to DFT/MRCI level approximations, respectively. NACMEs were dominated by out-of-plane derivative components belonging to the center-most ring atoms with weaker contributions from perturbations along the transverse and longitudinal axes. Calculated theoretical spectra compared well to both experiment and literature, with fluorescence lifetimes between 7.1 and 12.5 ns, agreeing within a factor of 2 with experiment. Internal conversion (IC) rates were then calculated and were found to vary wildly between 10⁶-10¹⁶ s^-1 compared with an experimental rate of the order 10⁷ s^-1. Following further testing by mixing data sets, we found a strong dependence on the method used to obtain the Hessian. The 5 characterized data sets ranked in order of most promising are PBE0/def2-TZVP, ωB97XD/def2-TZVP, HCTH407/TZVP, PBE/TZVP, and PBE/def2-TZVP.

Optimizing a coarse-grained space for approximate normal-mode vibrations of molecular heterodimers

We applied the method of coarse-graining the intermolecular vibrations to molecular heterodimers assembled by double hydrogen bonding. This method is based on principal component analysis, by which the original atomic displacement vectors are projected onto a lower-dimensional space spanned by a basis set of translations, librations, and intramolecular vibrations of the constituent molecules. Compared with homodimers, the following points are particularly noted: (1) alignment of the constituent molecules in a non-symmetric atomic arrangement of the whole system and (2) the scheme of reordering the bases to construct an optimal coarse-grained space. We tested three schemes for reordering the intramolecular vibration vectors to determine that the best one is equivalent to size reduction based on the singular value decomposition. The coarse-graining analysis affords three parameters, Φ_intra, Φ_inter, and Φ_app, which are relevant to the mechanical nature of the molecular assembly. The Φ_intra values account for the internal stiffness of molecules, while the Φ_inter values are true stiffness constants of the intermolecular force and show a good correlation with the association energies of the dimers. The Φ_app values are the apparent intermolecular stiffness smaller than Φ_inter, as a result of compensation for neglecting intramolecular vibrations. All these values are consistent with each other under the coupled oscillator model, showing that the present coarse-graining analysis is valid for heterodimers as well as homodimers.

Ultra-broadband terahertz fingerprint spectrum of melatonin with vibrational mode analysis

Melatonin (MLT), as a neurotransmitter and an endogenous neurohormone, plays an important role in physiological functions through interactions with specific receptors. The conformations of MLT are closely related to its biological activities and functions. However, the internal relationship between the structure and interaction of MLT and its allosteric transition remains unclear. In this work, we obtain the broadband fingerprint terahertz (THz) spectrum of MLT in the range of 0.5-18 THz using the air-plasma terahertz time-domain spectroscopy (THz-TDS) system. DFT calculations are employed to analyze the vibration characteristics of MLT. The result shows that the low-frequency vibrations mainly come from the strong coupling between inter- and intramolecular vibrations, and the contribution of intramolecular vibrations gradually dominates with increasing frequency. Meanwhile, the local vibrations of the different functional groups distribute widely in the THz low-frequency band, relating to the diversity of conformational changes in the molecule. The intermolecular hydrogen bonds (HBs) have distinct resonant responses and play critical roles in the THz low-frequency vibrations. The study reveals the complex characteristics of the resonant coupling of MLT with THz electromagnetic waves. The results will help to understand the conformational preferences of MLT in neural signal transmission processes.

Terahertz Fingerprints of Short-Range Correlations of Disordered Atoms in Diflunisal

This work proposes a terahertz (THz) spectroscopy approach to the investigation of one of the outstanding problems in crystallography-the structure analysis of a crystal with disorder. Form I of diflunisal, in which the two ortho sites on one phenyl ring of diflunisal show occupational disorder, was used for an illustration. THz radiation interacts with the collective vibrations of correlated disorder, thus providing a promising tool to examine the symmetry of short-range correlations of disordered atoms. Through a thorough examination of the selection rule of THz vibrations in which the disordered atoms are involved to different extents, we deduced that only four short-range correlation possibilities of disorder exist and all of them display unambiguous fingerprint peaks in the 50-170 cm^-1 frequency region. We finally proposed an alternating packing model in which the correlation lengths of disorder are on the nanometer scale.

Indices to evaluate the reliability of coarse-grained representations of mixed inter/intramolecular vibrations

We propose some methods for quantifying the reliability of coarse-grained representations of displacement vectors of normal mode vibrations. In the framework of our basic theory, the original displacement vectors are projected onto a lower-dimensional (i.e., a coarse-grained) space. Four types of functions denoted fidelity indices were introduced as measures of the similarity of the original to the restored displacement vectors. These indices were applied to several hydrogen-bonded homodimers, and the behavior of each index was examined. We found that a coarse-grained representation with high reliability resulted in the accurate restoration of properties such as eigenfrequency, modal mass, and modal stiffness.

A terahertz study of taurine: Dispersion correction and mode couplings

The low-frequency characteristics of polycrystalline taurine were studied experimentally by terahertz (THz) absorption spectroscopy and theoretically by ab initio density-functional simulations. Full optimizations with semi-empirical dispersion correction were performed in spectral computations and vibrational mode assignments. For comparison, partial optimizations with pure density functional theory were conducted in parallel. Results indicate that adding long-range dispersion correction to the standard DFT better reproduces the measured THz spectra than the popular partial optimizations. The main origins of the observed absorption features were also identified. Moreover, a coupled-oscillators model was proposed to explain the experimental observation of the unusual spectralblue-shift with the increase of temperature. Such coupled-oscillators model not only provides insights into the temperature dynamics of non-bonded interactions but also offers an opportunity to better understand the physical mechanisms behind the unusual THz spectral behaviors in taurine. Particularly, the simulation approach and novel coupled-oscillators model presented in this work are applicable to analyze the THz spectra of other molecular systems.

Terahertz spectroscopy of 2,4,6-trinitrotoluene molecular solids from first principles

We present a computational analysis of the terahertz spectra of the monoclinic and the orthorhombic polymorphs of 2,4,6-trinitrotoluene. Very good agreement with experimental data is found when using density functional theory that includes Tkatchenko–Scheffler pair-wise dispersion interactions. Furthermore, we show that for these polymorphs the theoretical results are only weakly affected by many-body dispersion contributions. The absence of dispersion interactions, however, causes sizable shifts in vibrational frequencies and directly affects the spatial character of the vibrational modes. Mode assignment allows for a distinction between the contributions of the monoclinic and orthorhombic polymorphs and shows that modes in the range from 0 to ca. 3.3 THz comprise both inter- and intramolecular vibrations, with the former dominating below ca. 1.5 THz. We also find that intramolecular contributions primarily involve the nitro and methyl groups. Finally, we present a prediction for the terahertz spectrum of 1,3,5-trinitrobenzene, showing that a modest chemical change leads to a markedly different terahertz spectrum.

Elucidation of Chiral Symmetry Breaking in a Racemic Polymer System with Terahertz Vibrational Spectroscopy and Crystal Orbital Density Functional Theory

The conservation of chiral symmetry has been used as a fundamental rule to determine polymer packing conformations in racemic systems. We have illustrated, through the interplay of polarization terahertz (THz) spectroscopy and solid-state density functional theory, that the chiral symmetry is not conserved in a poly(lactic acid) stereocomplex (scPLA) system. Poly(l-lactic acid) (PLLA) displays a weaker violation of the 3₁ screw symmetry than poly(d-lactic acid) (PDLA) and possesses a stronger intramolecular vibrational energy, on average, in the low-frequency gamma-point phonon modes than does PDLA. Polarization THz spectroscopy adds a new dimension to polymer crystallography through which new phenomena are expected to be revealed.

Modeling Polymorphic Molecular Crystals with Electronic Structure Theory

Interest in molecular crystals has grown thanks to their relevance to pharmaceuticals, organic semiconductor materials, foods, and many other applications. Electronic structure methods have become an increasingly important tool for modeling molecular crystals and polymorphism. This article reviews electronic structure techniques used to model molecular crystals, including periodic density functional theory, periodic second-order Møller-Plesset perturbation theory, fragment-based electronic structure methods, and diffusion Monte Carlo. It also discusses the use of these models for predicting a variety of crystal properties that are relevant to the study of polymorphism, including lattice energies, structures, crystal structure prediction, polymorphism, phase diagrams, vibrational spectroscopies, and nuclear magnetic resonance spectroscopy. Finally, tools for analyzing crystal structures and intermolecular interactions are briefly discussed.

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.

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.

Terahertz time-domain and low-frequency Raman spectroscopy of organic materials

With the ongoing proliferation of terahertz time-domain instrumentation from semiconductor physics into applied spectroscopy over the past decade, measurements at terahertz frequencies (1 THz ≡ 10(12) Hz ≡ 33 cm(-1)) have attracted a sustained growing interest, in particular the investigation of hydrogen-bonding interactions in organic materials. More recently, the availability of Raman spectrometers that are readily able to measure in the equivalent spectral region very close to the elastic scattering background has also grown significantly. This development has led to renewed efforts in performing spectroscopy at the interface between dielectric relaxation phenomena and vibrational spectroscopy. In this review, we briefly outline the underlying technology, the physical phenomena governing the light-matter interaction at terahertz frequencies, recent examples of spectroscopic studies, and the current state of the art in assigning spectral features to vibrational modes based on computational techniques.