Examination of l-Glutamic Acid Polymorphs by Solid-State Density Functional Theory and Terahertz Spectroscopy

Insights into the terahertz response of L-glutamic acid and its receptor

L-Glutamic acid (L-Glu) is a basic unit of proteins and also serves as an important neurotransmitter in the central nervous system. Its structural properties are critical for biological functions and selective receptor recognition. Although this molecule has been extensively studied, the low frequency vibrational behavior that is closely related to conformational changes and the intermolecular interactions between L-Glu and its receptors are still unclear. In this study, we acquired the fingerprint spectrum of L-Glu by using air plasma terahertz (THz) time-domain spectroscopy in the 0.5-18 THz range. The low frequency vibrational characteristics of L-Glu were investigated through density functional theory (DFT) calculations. The THz responses of the ligand binding domain of the NMDAR-L-Glu complex were studied by the ONIOM method, with a focus on discussing the normal modes and interactions of ligand L-Glu and water molecules. The results illustrate that THz spectroscopy exhibits a sensitive response to the influence of L-Glu on the structure of the NMDAR. The water molecules in proteins have various strong vibration modes in the THz band, showing specificity, diversity and complexity of vibrational behavior. There is potential for influencing and regulating the structural stability of the NMDAR-L-Glu complex through water molecules.

Investigating the function and design of molecular materials through terahertz vibrational spectroscopy

Terahertz spectroscopy has proved to be an essential tool for the study of condensed phase materials. Terahertz spectroscopy probes the low-frequency vibrational dynamics of atoms and molecules, usually in the condensed phase. These nuclear dynamics, which typically involve displacements of entire molecules, have been linked to bulk phenomena ranging from phase transformations to semiconducting efficiency. The terahertz region of the electromagnetic spectrum has historically been referred to as the 'terahertz gap', but this is a misnomer, as there exist a multitude of methods for accessing terahertz frequencies, and now there are cost-effective instruments that have made terahertz studies much more user-friendly. This Review highlights some of the most exciting applications of terahertz vibrational spectroscopy so far, and provides an in-depth overview of the methods of this technique and its utility to the study of the chemical sciences.

Terahertz Spectroscopy Study of the Stereoisomers of Threonine

The terahertz (THz) band contains a wealth of information about vibration and rotational energy levels, most of the vibration modes between amino acid molecules are in the THz band, so it reflects many unique absorption characteristics in the THz band. The use of terahertz time-domain spectroscopy can not only effectively identify different kinds of amino acids but also distinguish various isomers of the same amino acid due to the varied vibration modes. The absorption spectra of four stereoisomers of threonine were investigated by terahertz time-domain spectroscopy (THz-TDS) and Fourier transform infrared spectroscopy. The results show that the isomers show similarity in the infrared band, while manifest evidently the similarity between enantiomers L-threonine and D-threonine, and between L-allo-threonine and D-allo-threonine, and the difference between diastereoisomer L-threonine/D-threonine and L-allo-threonine/D-allo-threonine in the terahertz band. In order to fully understand the origin of the terahertz absorption characteristics of isomer molecules, simulation calculations were carried out in combination with density functional theory to connect the vibrational modes and molecular structures, Furthermore, the unit cell configurations of L-thr and L-allo-thr and the differences between various low-frequency vibrational modes are analyzed from the perspective of hydrogen bond configuration. By further extracting terahertz optical parameters such as refractive index and imaginary part of the dielectric constant of threonine isomers, the results show that the refractive index spectrum and dielectric loss spectrum can clearly show the response characteristics of the orientation polarization of dipole inside threonine isomers in terahertz band.

The Relevance of Crystal Forms in the Pharmaceutical Field: Sword of Damocles or Innovation Tools?

This review is aimed to provide to an “educated but non-expert” readership and an overview of the scientific, commercial, and ethical importance of investigating the crystalline forms (polymorphs, hydrates, and co-crystals) of active pharmaceutical ingredients (API). The existence of multiple crystal forms of an API is relevant not only for the selection of the best solid material to carry through the various stages of drug development, including the choice of dosage and of excipients suitable for drug development and marketing, but also in terms of intellectual property protection and/or extension. This is because the physico-chemical properties, such as solubility, dissolution rate, thermal stability, processability, etc., of the solid API may depend, sometimes dramatically, on the crystal form, with important implications on the drug’s ultimate efficacy. This review will recount how the scientific community and the pharmaceutical industry learned from the catastrophic consequences of the appearance of new, more stable, and unsuspected crystal forms. The relevant aspects of hydrates, the most common pharmaceutical solid solvates, and of co-crystals, the association of two or more solid components in the same crystalline materials, will also be discussed. Examples will be provided of how to tackle multiple crystal forms with screening protocols and theoretical approaches, and ultimately how to turn into discovery and innovation the purposed preparation of new crystalline forms of an API.

Terahertz spectroscopy of temperature-induced transformation between glutamic acid, pyroglutamic acid and racemic pyroglutamic acid

Under heating conditions, L-Glutamic acid (L-Glu) can be dehydrated to form L-pyroglutamic acid (L-PGA), and L-PGA can racemize to form DL-PGA. Here, we characterized this transformation at different temperatures and times by terahertz time domain spectroscopy (THz-TDS). By Powder X-ray diffraction (PXRD), the validity of THz spectroscopy is verified. The results prove that the reaction rate of dehydration and racemization is significantly affected by temperature. The THz spectra divided the reactions into three stages. At 150-155 °C, the reaction changes drastically. Furthermore, we found that the absorption intensity at 0.97 and 1.55 THz has a good dependence on the reaction temperature and time, showing a non-linear relationship (R² > 0.98). Our findings suggest that the chemical transformation and reaction rate can be sensitively probed by terahertz spectroscopy, which provides a potential method for the quantitative analysis of reaction products.

Selected Applications of Terahertz Pulses in Medicine and Industry

This article contains a brief summary of areas where terahertz technology is making an impact in research and industrial applications. We cover some of its uses in the pharmaceutical setting, where both imaging and spectroscopy play important roles. Medical applications are also being pursued in many research laboratories, primarily for imaging purposes and following on from the first results just over 20 years ago. The three-dimensional imaging capability of pulsed terahertz allows for the observation of tumours below the surface of tissue, such as basal cell carcinoma of skin. The recent use of the technology in studies of cultural heritage has shown to increase our understanding of the past. The power of terahertz is exemplified by the discussion on its importance in different industries, such as semiconductor circuit manufacturing and automotive assembly.

Examination of proline, hydroxyproline and pyroglutamic acid with different polar groups by terahertz spectroscopy

Hydroxyproline (HYP) and pyroglutamic acid (PGA), as amino acid derivatives, are highly similar in structure to proline (Pro). However, their low-frequency vibrations show significant differences in the range of 0.25-2.6 THz. Therefore, this study investigated the reasons for the differences combined with terahertz time domain spectroscopy (THz-TDS) and density functional theory (DFT). The results show that HYP and PGA have stronger absorption of terahertz waves due to the existence of polar substituents. Furthermore, the absorption peaks of HYP and PGA are significant red shifted and blue shifted, respectively. We believe that this is caused by the change in the strength of intermolecular hydrogen bonds. Our findings demonstrate that dipole and hydrogen bond effects play a significant role in low-frequency vibrations.

Selective desolvation in two-step nucleation mechanism steers crystal structure formation

The two-step nucleation (TSN) theory and crystal structure prediction (CSP) techniques are two disjointed yet popular methods to predict nucleation rate and crystal structure, respectively. The TSN theory is a well-established mechanism to describe the nucleation of a wide range of crystalline materials in different solvents. However, it has never been expanded to predict the crystal structure or polymorphism. On the contrary, the existing CSP techniques only empirically account for the solvent effects. As a result, the TSN theory and CSP techniques continue to evolve as separate methods to predict two essential attributes of nucleation - rate and structure. Here we bridge this gap and show for the first time how a crystal structure is formed within the framework of TSN theory. A sequential desolvation mechanism is proposed in TSN, where the first step involves partial desolvation to form dense clusters followed by selective desolvation of functional groups directing the formation of crystal structure. We investigate the effect of the specific interaction on the degree of solvation around different functional groups of glutamic acid molecules using molecular simulations. The simulated energy landscape and activation barriers at increasing supersaturations suggest sequential and selective desolvation. We validate computationally and experimentally that the crystal structure formation and polymorph selection are due to a previously unrecognized consequence of supersaturation-driven asymmetric desolvation of molecules.

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.

New Insights into the Crystallographic Disorder in the Polymorphic Forms of Aspirin from Low-Frequency Vibrational Analysis

Terahertz time-domain spectroscopy (THz-TDS) is applied to two polymorphs of acetylsalicylic acid (aspirin), and the experimental spectra are compared to lattice dynamical calculations using high accuracy density functional theory. The calculations confirm that forms I and II have very close energetic and thermodynamic properties and also that they show similar spectral features in the far-infrared region, reflecting the high degree of similarity in their crystal structures. Unique vibrational modes are identified for each polymorph which allow them to be distinguished using THz-TDS measurements. The observation of spectral features attributable to both polymorphic forms in a single sample, however, provides further evidence to support the hypothesis that crystalline aspirin typically comprises intergrown domains of forms I and II. Differences observed in the baseline of the measured THz-TDS spectra indicate a greater degree of structural disorder in the samples of form II. Calculated Gibbs free-energy curves show a turning point at 75 K, inferring that form II is expected to be more stable than form I above this temperature as a result of its greater vibrational entropy. The calculations do not account for any differences in configurational entropy that may arise from expected structural defects. Further computational work on these structures, such as ab initio molecular dynamics, would be very useful to further explore this perspective. Here, aspirin is a model system to show how the additional insight from the low-frequency vibrational information complements the structural data and allows for quantitative thermodynamic information of pharmaceutical polymorphs to be extracted. The methodology is directly applicable to other polymorphic systems.

On-the-spot quenching for effective implementation of cooling crystallization in a continuous-flow microfluidic device

Illustrated is a microfludic cooling crystallization device that can effectively screen polymorphs, growth rates, and morphology of crystalline materials.

The necessity of periodic boundary conditions for the accurate calculation of crystalline terahertz spectra

Terahertz vibrational spectroscopy has emerged as a powerful spectroscopic technique, providing valuable information regarding long-range interactions - and associated collective dynamics - occurring in solids. However, the terahertz sciences are relatively nascent, and there have been significant advances over the last several decades that have profoundly influenced the interpretation and assignment of experimental terahertz spectra. Specifically, because there do not exist any functional group or material-specific terahertz transitions, it is not possible to interpret experimental spectra without additional analysis, specifically, computational simulations. Over the years simulations utilizing periodic boundary conditions have proven to be most successful for reproducing experimental terahertz dynamics, due to the ability of the calculations to accurately take long-range forces into account. On the other hand, there are numerous reports in the literature that utilize gas phase cluster geometries, to varying levels of apparent success. This perspective will provide a concise introduction into the terahertz sciences, specifically terahertz spectroscopy, followed by an evaluation of gas phase and periodic simulations for the assignment of crystalline terahertz spectra, highlighting potential pitfalls and good practice for future endeavors.

Thermal neutron cross sections of amino acids from average contributions of functional groups

The experimental thermal neutron cross sections of the 20 proteinogenic amino acids have been measured over the incident-neutron energy range spanning from 1 meV to 10 keV and data have been interpreted using the multi-phonon expansion based on first-principles calculations. The scattering cross section, dominated by the incoherent inelastic contribution from the hydrogen atoms, can be rationalised in terms of the average contributions of different functional groups, thus neglecting their correlation. These results can be used for modelling the total neutron cross sections of complex organic systems like proteins, muscles, or human tissues from a limited number of starting input functions. This simplification is of crucial importance for fine-tuning of transport simulations used in medical applications, including boron neutron capture therapy as well as secondary neutrons-emission induced during proton therapy. Moreover, the parametrized neutron cross sections allow a better treatment of neutron scattering experiments, providing detailed sample self-attenuation corrections for a variety of biological and soft-matter systems.

Diagnosis of Glioma Molecular Markers by Terahertz Technologies

This review considers glioma molecular markers in brain tissues and body fluids, shows the pathways of their formation, and describes traditional methods of analysis. The most important optical properties of glioma markers in the terahertz (THz) frequency range are also presented. New metamaterial-based technologies for molecular marker detection at THz frequencies are discussed. A variety of machine learning methods, which allow the marker detection sensitivity and differentiation of healthy and tumor tissues to be improved with the aid of THz tools, are considered. The actual results on the application of THz techniques in the intraoperative diagnosis of brain gliomas are shown. THz technologies’ potential in molecular marker detection and defining the boundaries of the glioma’s tissue is discussed.

Terahertz fingerprint characterization of 2,4-dichlorophenoxyacetic acid and its enhanced detection in food matrices combined with spectral baseline correction

Rapid and accurate detection of pesticide residues in food matrices are of great significance to food safety. This study aimed to characterize the fingerprint peaks of 2,4-dichlorophenoxyacetic acid (2,4-D) and to enhance its detection accuracy in food matrices by using terahertz (THz) time-domain spectroscopy. Density functional theory was used to simulate molecular dynamics of 2,4-D peaks (1.35, 1.60, 2.37 and 3.00 THz). Four baseline correction methods, including asymmetric least squares smoothing (AsLS), adaptive iteratively reweighted penalized least squares (AirPLS), background correction (Backcor), baseline estimation and denoising with sparsity (BEADS) were compared and used to eliminate spectral baselines of Zizania latifolia (ZIZLA), rice and maize containing 2,4-D residues, from 0.1 to 4 THz. Based on the peak information of 1.35 THz, the detection limit and accuracy of 2,4-D residues in these food matrices were significantly improved after THz spectral baseline correction, providing a new feasibility for food safety and agricultural applications.

Terahertz-spectroscopy for non-destructive determination of crystallinity of L-tartaric acid in smartFilms® and tablets made from paper

Newly developed active pharmaceutical ingredients (API) often experience low solubility in aqueous media and thus possess poor oral bioavailability. The SmartFilm®-technology is a novel approach to overcome poor solubility. The technique uses commercial paper in which API can be loaded in amorphous state, thus increasing dissolution rate dc/dt and solubility c_s when compared to bulk material. However, the preservation of the amorphous state is a prerequisite for an efficient use of the smartFilm-technology and thus the crystalline state needs to be inspected during storage. Preferably, this should be done non-destructively. Traditional techniques, such as x-ray diffraction (XRD) or differential scanning calorimetry (DSC), do not allow for non-destructive crystallinity investigations, whereas Terahertz (THz) spectroscopy is a non-destructive technique, that is sensitive to the crystalline state of many molecular crystals. Therefore, the potential of THz-spectroscopy for crystallinity state inspection of API in smartFilms and tablets made from smartFilms was investigated in this study. The THz results obtained were compared to results obtained from XRD and DSC measurements. Whereas DSC measurements failed to reliably detect crystalline API in the smartFilms, XRD and THz-spectroscopy showed similar results and revealed that it was possible to prepare smartFilms loaded with >23% (w/w) amorphous API. Results indicate the great potential of THz spectroscopy for the non-destructive determination of the crystalline state of APIs in smartFilms and/or tablets made from paper.

Periodic DFT Calculations-Review of Applications in the Pharmaceutical Sciences

In the introduction to this review the complex chemistry of solid-state pharmaceutical compounds is summarized. It is also explained why the density functional theory (DFT) periodic calculations became recently so popular in studying the solid APIs (active pharmaceutical ingredients). Further, the most popular programs enabling DFT periodic calculations are presented and compared. Subsequently, on the large number of examples, the applications of such calculations in pharmaceutical sciences are discussed. The mentioned topics include, among others, validation of the experimentally obtained crystal structures and crystal structure prediction, insight into crystallization and solvation processes, development of new polymorph synthesis ways, and formulation techniques as well as application of the periodic DFT calculations in the drug analysis.

Pressure-induced phase transitions in DL-glutamic acid monohydrate crystal

DL-glutamic acid monohydrate crystal was synthesized from an aqueous solution by slow evaporation technique. The crystal was submitted to high-pressure (1 atm-14.3 GPa) to investigate its vibrational behavior and the occurrence of phase transitions. We performed Raman spectroscopy as probe and through the analysis of the spectra we discovered three structural phase transitions. The first one occurs around 0.9 GPa. In this phase transition, glutamic acid molecules suffer modifications in their conformations while water molecules are less affected. The second phase transition at 4.8 GPa involves conformational changes related to CO₂^-, NH₃⁺ units and the water molecules, while the third one, between 10.9 and 12.4 GPa, involves motions of several parts of the glutamic acid as well as the water molecules. Considering the dynamic of high pressure, the second phase of DL-glutamic acid monohydrate crystal presented a better stability compared with the second phase of its polymorphs α and β L-glutamic acid. In addition, water molecules seem to play important role on this structural stability. All changes are reversible.

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.

Terahertz spectroscopy of enantiomeric and racemic pyroglutamic acid

The low-frequency vibrational properties of D-, L- and DL-pyroglutamic acid (PGA) have been investigated with the terahertz time-domain spectroscopy (THz-TDS) from 0.5 to 4.5 THz. The enantiomers (D- and L-PGA) present similar absorption spectra, while the spectrum of racemate (DL-PGA) is obviously different. The temperature-dependent THz spectra of different PGA were recorded in the range of 293-83 K. The spectral changes during the cooling process suggest that D- and L-PGA undergo a structural phase transition, and no phase change of DL-PGA was found. The results indicate that THz spectroscopy is highly sensitive to the crystal structure of molecules. The density functional theory (DFT) calculations based on the crystal structures were performed to simulate the sample's THz spectra. It was demonstrated that the characteristic resonant absorption peaks of the enantiomeric and racemic PGA in the low-frequency THz region originate from the different vibrations, which corresponding to the specific structures and intermolecular interactions. The conformational diversity and fluctuation may help to understand the properties of PGA in biochemistry and functional material.

Industrial Applications of Terahertz Sensing: State of Play

This paper is a survey of existing and upcoming industrial applications of terahertz technologies, comprising sections on polymers, paint and coatings, pharmaceuticals, electronics, petrochemicals, gas sensing, and paper and wood industries. Finally, an estimate of the market size and growth rates is given, as obtained from a comparison of market reports.

A comparative evaluation of the activities of thiol group and hydroxyl group in low-frequency vibrations using terahertz spectroscopy and DFT calculations

Low-frequency vibrations of biomolecules govern many biological processes like allostery of proteins, binding interaction and solvation. Revealing how involved are different groups of molecules in low-frequency vibrations is of significance to understand the behaviors of biomolecules. To compare the activities of hydroxyl group and thiol group in low-frequency vibrations, we conducted THz measurements and DFT calculations of l‑serine and l‑cysteine. We performed quantitative analyses on their low-frequency vibrations to study their difference. Statistical analyses on the vibrational modes in our studied range suggest the thiol group shows a higher level of activity in low-frequency vibrations than hydroxyl group.

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.

Methyl-rotation dynamics in metal–organic frameworks probed with terahertz spectroscopy

In ZIF-8 and its cobalt analogue ZIF-67, the imidazolate methyl-groups, which point directly into the void space, have been shown to freely rotate – even down to cryogenic temperatures.

Quantification of cation–anion interactions in crystalline monopotassium and monosodium glutamate salts

Specific anion–cation orbital interactions lead to the large structural and spectral differences observed in crystalline monosodium and monopotassium glutamates.

Concomitant polymorphism and the martensitic-like transformation of an organic crystal

Terahertz vibrational spectroscopy and solid-state density functional theory together reveal the true nature of a pseudo-continuous crystalline polymorphic phase transition.

Intermolecular anharmonicity in molecular crystals: interplay between experimental low-frequency dynamics and quantum quasi-harmonic simulations of solid purine

A combined experimental spectroscopic and theoretical quasi-harmonic investigation of intermolecular anharmonicity in crystalline purine.