Temperature Dependence in the Terahertz Spectrum of Nicotinamide: Anharmonicity and Hydrogen-Bonded Network

Dehydration kinetics and mechanism of the stable isonicotinamide hydrate revealed by terahertz spectroscopy and DFT calculation

The dehydration behavior of pharmaceutical hydrates has a great influence on its physiochemical properties such as stability, dissolution rate and bioavailability. However, how the intermolecular interactions vary during dehydration process remains elusive. In this work, we employed terahertz time-domain spectroscopy (THz-TDS) to probe the low-frequency vibrations and the dehydration process of isonicotinamide hydrate I (INA-H I). Theoretical solid-state DFT calculation was conducted to reveal its mechanism. Vibrational modes which are responsible for the THz absorption peaks were decomposed for better understanding the characters of these low-frequency modes. The result suggests translational motion is the dominant component for water molecules in THz region. Evolution of the THz spectrum of INA-H I during dehydration provides direct evidence of the variations of crystal structure. Based on the THz measurements, a two-step kinetics mode including first-rate reaction and three-dimensional nuclei growth is proposed. And we nure that the low-frequency vibrations of water molecules are the origin of dehydration process of hydrate.

Van der Waals interactions regulating the hydration of 2-methacryloyloxyethyl phosphorylcholine, the constructing monomer of biocompatible polymers

Van der Waals (VDW) interactions provide fantastic properties for biological systems that function at room temperature. The VDW interaction, which primarily contributes to weak hydrogen bonding, is expected to play a key role in regulating hydrophobic hydration to express the biologically inert biocompatible function of polymerized MPCs (2-methacryloyloxyethyl phosphorylcholine). This report explores at the molecular level the biologically inert function of polymerized MPCs through an array of vibrational spectroscopic and computational characterization of MPC monomers, as temperature-dependent change of intramolecular weak hydrogen bonding. Synchrotron Fourier transform infrared microspectroscopy and terahertz time-domain spectroscopy were used to investigate temperature-dependent spectral changes in the low frequency vibrations of the MPC over the temperature range from cryogenic to room temperature, and the results were analysed by highly reliable well-established density functional theory (DFT) calculations. Complicated spectral features in the low frequency energy region and the uncertain conformations of the MPC in the amorphous powder state are clearly resolved under a polarizable continuum model and dispersion correction to pure DFT calculations.

Terahertz signal analysis and substance identification via Zernike moments

Terahertz (THz) spectra contain chemical information, along with noise and variable backgrounds. Measurement environmental changes and spectral signal differences caused by changes in the sample state can degrade the accuracy of the calibration models. This problem obviously hinders practical applications of THz spectroscopy. To tackle this problem, a three-dimensional spectrum was first self-constructed and converted into an intensity image. Zernike moments with inherently invariant properties were then used to describe the THz intensity image and extract the invariant features for further analysis. Considering the reconstruction error and computational cost, the highest order of Zernike moments and the most effective moments were selected and applied to multi-classifiers including support vector machines, naive Bayes, and regularized linear discriminant analysis. Experiments used a THz dataset collected from four chemical substances (melamine, tartaric acid, lactose, and glucose) at five thicknesses (1.0 mm, 1.5 mm, 2.0 mm, 2.5 mm, and 3.0 mm). The results confirmed the effectiveness of the proposed approach. The obtained results show that compare to traditional absorption spectrum features, Zernike moment features are less sensitive to spectral variations caused by changes in sample status. They have better feature representation ability with lower feature vector dimensions. This suggests that they can be integrated into the design of systems for THz spectral classification to increase the robustness and generalization capability of the classifier.

Study of temperature-dependent terahertz spectra of isonicotinamide in the form I using the quasi-harmonic approximation

Anharmonicity of molecular vibrational motions is closely associated with the thermal property of crystals. However, the origin of anharmonicity is still not fully understood. Low-frequency vibrations, which are usually defined in the terahertz (THz) range, show excellent sensitivity to anharmonicity. In this work, anharmonicity of isonicotinamide in the form I was investigated by using temperature-dependent terahertz time-domain spectroscopy and quasi-harmonic approximation (QHA) approach at PBE-D3 and PBE-MBD levels. Both DFT calculations suggest the variation of p-p stacking conformation dominates in the thermal expansion of unit cell. The frequency shifts of the modes in THz range obtained by QHA approach are found to be qualitatively consistent with the observation, demonstrating QHA approach is a useful tool for the interpretation of frequency shifts of modes induced by temperature.

Broadband terahertz signatures and vibrations of dopamine

Dopamine (DA) is an essential neurotransmitter and hormone of the nervous system, its structural and conformational properties play critical roles in biological functions and signal transmission processes. Although this neuroactive molecule has been studied extensively, the low-frequency vibration features that are closely related to the conformation and molecular interactions in the terahertz (THz) band still remain unclear. In this study, a broadband THz time-domain spectroscopy (THz-TDS) system in the frequency band of 0.5-18 THz was used to characterize the unique THz fingerprint of DA. In addition, density functional theory (DFT) calculations were performed to analyze the vibrational properties of DA. The results suggest that each THz resonant absorption peak of DA corresponds to specific vibrational modes, and the collective vibration also exists in the broadband THz range. Moreover, the interactions between the DA ligand and the D2 and D3 receptors were investigated by docking, and the simulated THz spectra were obtained. The results indicate the dominant role of hydrogen bonding interactions and the specificity of molecular conformation. This work may help to understand the resonance coupling between THz electromagnetic waves and neurotransmitters.

Temperature-Dependent Low-Frequency Vibrations of Thiamine Crystal Containing Hydrated Ions

Low-frequency vibrations of crystalline molecules are very sensitive to the local environment in which the molecules, for example, hydrated ions captured in crystals, find themselves. We present low-temperature X-ray crystallographic measurements on the harvested thiamine crystal containing hydrated ions and its temperature-dependent terahertz spectra and synchrotron infrared microspectra. It is found from the X-ray structure that the hydrated ions and hydration water are in a similar environment to liquid, although those are captured in crystals. The vibrationally resolved THz spectra of two states in the present organic crystals containing hydrated ions are well explained by the difference in the hydrogen-bonded pattern. Peak assignments were performed based on highly accurate first-principles calculations incorporating relativistic effects and dispersion corrections. The temperature dependences are observed for the vibrations around the chloride ions and hydration water due to the loose binding of chloride ions, the bond elongation with increasing temperature, and the cleavage of weak hydrogen bonds.

Characteristic terahertz absorption spectra of paramylon and paramylon-ester compounds

Paramylon is a long-chain polysaccharide, composed of glucose units connected via β-(1,3) glycosidic bonds, that spontaneously forms a three-strand helical bundle. Paramylon-esters can be made by partially or fully replacing saccharide chain hydroxide groups with carboxylic functional groups, such as stearoyl (CH₃(CH₂)₁₆CO) and palmitoyl (CH₃(CH₂)₂₄CO). The paramylon-ester with carboxylic acids has superior characteristics, including high thermal resistance, stability and transparency under visible light, which are necessary for thermoplastic applications. In this study, the absorption coefficient α(ν) and absorbance spectra of paramylons and paramylon-esters were measured in the 0.3-8.0 THz range and compared with the corresponding spectra of glucose and cellulose. Paramylon and paramylon-ester molecules were found to exhibit unique, so-called fingerprint, α(ν)peaks at 4.0, 6.0 and 8.0 THz, and 2.5 and 5.0 THz, respectively. We speculate that the spectral features observed are owing to intermolecular interaction modes of the weakly coupled polysaccharide chains. The paramylons with different molecular weights show very similar absorption features in the low-frequency side, both in spectral shapes and intensities, indicating that absorption is independent of molecular size. The paramylon-esters with varying degrees of substitution (DS) are similar spectral shapes but different intensities. A linear correlation between α(ν) peak intensity and the DS of paramylon-esters was established with the R² value above 0.99. This behavior can be used for the detection and identification of novel paramylon-ester molecules.

Terahertz spectroscopic characterizations and DFT calculations of carbamazepine cocrystals with nicotinamide, saccharin and fumaric acid

Carbamazepine cocrystals with nicotinamide, saccharin and fumaric acid were synthesized and characterized by time-domain terahertz spectroscopy. Lattice vibrations of cocrystals with their individual constituents were investigated by means of the dispersion-corrected density functional theory with and without cell parameter constraints. The simulated THz spectra successfully reproduce the features of all the crystals in their experimental spectra. A better agreement between experimental and theoretical THz spectra is achieved when the cell parameter constraints are applied in geometry optimization. Some intensive modes of neat carbamazepine and cocrystals were discussed in terms of the motions of hydrogen bonds. The effect of lattice vibration on these cocrystallizations was further examined to gain insights into the thermodynamics. It is found that lattice vibration is favorable for all these cocrystal formations.

Analysis of Flavonoid Compounds by Terahertz Spectroscopy Combined with Chemometrics

Flavonoids are a large class of polyphenols widely distributed in plants in the free form or as glycosides, and they have antioxidation, antibacterial, antitumor growth, and other pharmacological effects. As an important active component of traditional Chinese medicine, they have high medicinal value and development prospects. In this work, the biomolecular properties of 10 common flavonoids, including baicalein, baicalin, apigenin, quercetin, naringenin, hesperetin, daidzein, genistein, puerarin, and gastrodin, are studied by terahertz time-domain spectroscopy (THz-TDS) in the range of 0.2-2.5 THz. The results reveal that these flavonoids have different characteristic absorption peaks in the terahertz band. Moreover, the terahertz absorption characteristics of samples in the temperature range of 78-320 K are studied. The results show that the characteristic absorption peaks gradually increase with the decrease in temperature, and the frequency position of the absorption peak has a slight blue shift. Furthermore, qualitative identification and quantitative analysis of flavonoids are carried out by terahertz spectra combined with chemometrics. Specifically, a series of mixtures of three flavonoids with similar molecular structures under various concentrations are analyzed. The partial least-squares regression (PLSR) model and the artificial neural network (ANN) model are applied to quantitatively analyze the ternary mixture. The results confirm that the ANN model obtains the best predicted value, with the root-mean-square errors in the prediction set (RMSEP) of 1.27% for daidzein. In summary, the biomolecular properties of flavonoids are studied by the THz-TDS technique, and a rapid, effective, and nondestructive method for qualitative identification and quantitative analysis of flavonoids is provided. The results demonstrate that this method has potential application value in the detection of Chinese herbal medicine and has better referential significance for the study of other biomolecules, especially for isomers or similar molecular structures.

Vibrational spectra of pyrazinamide and isoniazid studied by terahertz spectroscopy and density functional theory

Pyrazinamide and isoniazid, as two first-line anti-tuberculosis drugs, are investigated by terahertz time-domain spectroscopy (THz-TDS). Both pyrazinamide and isoniazid have three absorption peaks, at 0.50, 0.71, 1.42 THz and 1.16, 1.46, 1.56 THz, respectively, which can be used as the basis for qualitative identification of these two drugs. In order to gain insight into the origin of the characteristic absorption peaks, density functional theory (DFT) based on single molecular, dimer, and crystalline structures of pyrazinamide and isoniazid are performed. The purpose of the calculation based on the single molecular structure is to understand the intramolecular interaction, while those based on the dimer and crystalline structures are to investigate the intermolecular interactions in PNZ and INZ. Comparing the theoretical results of the dimer and crystalline based structures reveals that the crystalline structure leads to vibrational spectra that are closer to the experimental values in terms of the number of absorption peaks and the positions of the absorption peaks. Vibrational mode assignments can be summarized as that the characteristic absorption peaks of pyrazinamide mainly come from intermolecular interaction, and the characteristic absorption peaks of isoniazid originate from both the intramolecular and intermolecular interactions. Our experimental and theoretical results indicate that the combination of THz-TDS with DFT is an effective approach for identification of molecules with pharmaceutical significance.

Assessment of the VDW interaction converting DMAPS from the thermal-motion form to the hydrogen-bonded form

Assessment of van der Waals (VDW) interactions is fundamental to all of the central quest of structure that regulates the biological function. VDW interactions contributing to intramolecular weak hydrogen bonding are regarded as an important force to regulate the thermal stimuli-sensitive function of sulfobetaine methacrylate, DMAPS. We present here the conversion from the thermal-motion form at room temperature to the weak-hydrogen-bonded form against thermal motion as a terahertz spectral change with a definite isosbestic point from an absorption peak of one form to the other. Vibrational absorptions are used as a probe for assessing VDW interactions in conjunction with highly reliable and well-established density functional theory (DFT) calculations for analysis. Complicated spectral features and uncertain conformations of DMAPS in the amorphous state are clearly resolved under the polarizable continuum model and the dispersion correction for the pure DFT calculations.

Intermolecular hydrogen bond stretching vibrations observed in terahertz spectra of crystalline vitamins

Intermolecular hydrogen bond stretching vibrations in the crystal of vitamins has several specific properties in the THz spectrum.

Monitoring cis-to-trans isomerization of azobenzene using terahertz time-domain spectroscopy

We present terahertz time-domain spectroscopy (THz-TDS) to explore the conformational dynamics of thermally induced and photoinduced isomerization of azobenzene.