High-Resolution Terahertz Spectroscopy of Crystalline Trialanine: Extreme Sensitivity to β-Sheet Structure and Cocrystallized Water

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.

Compact, tunable polarization transforming reflector for quasi-optical devices used in terahertz science

We describe the design, fabrication, and characterization of a compact polarization transforming reflector (PTR). The device can be easily tuned over a broad frequency range, has very little insertion losses, and can easily be integrated into quasi-optical systems that are based on a half-cube design. By varying the distance between the wire grid and a flat mirror, the polarization state of an arbitrary polarized Gaussian incident beam can be set to an output Gaussian beam in either linear or circular polarization. In addition, by varying the orientation of the wire grid, the PTR can be used as a universal polarizer, a property that has not been discussed or demonstrated in the literature. The ability to control the electric field polarization at Terahertz (THz) frequencies is essential for many applications, such as THz spectroscopy and high-field electron paramagnetic resonance spectroscopy.

Triglycine (GGG) Adopts a Polyproline II (pPII) Conformation in Its Hydrated Crystal Form: Revealing the Role of Water in Peptide Crystallization

Polyproline II (pPII) is a left-handed 31-helix conformation, which has been observed to be the most abundant secondary structure in unfolded peptides and proteins compared to α-helix and β-sheet. Although pPII has been reported as the most stable conformation for several unfolded short chain peptides in aqueous solution, it is rarely observed in their solid state. Here, we show for the first time a glycine homopeptide (gly-gly-gly) adopting the pPII conformation in its crystalline dihydrate structure. The single crystal X-ray structure with molecular dynamic simulation suggests that a network of water and the charged carboxylate group is critical in stabilizing the pPII conformation in solid state, offering an insight into the structures of unfolded regions of proteins and the role of water in peptide crystallization.

HR-Si prism coupled tightly confined spoof surface plasmon polaritons mode for terahertz sensing

We report a high-resistivity silicon (HR-Si) prism coupled terahertz (THz) spoof surface plasmon polaritons (SSPPs) on flat subwavelength metasurface. Using a high refractive index prism as an external coupler, a more tightly confined SSPPs mode can be excited in a smaller resonant cavity, leading to strong light-matter interaction. Besides, theoretical analysis and experimental results have both indicated that the SSPPs resonance response to the filling patterns of analyte in the resonant cavity are quite different. In particular, we have found that the interaction between analyte and SSPPs wave can be maximized when the analyte filled with the whole resonant cavity and a higher sensitivity for THz sensing can be obtained. A high sensitivity varied from 0.31 THz/RIU to 0.85 THz/RIU is predicted. Furthermore, these SSPPs modes exhibit high Q-factor, and characteristic spectra of water caused by surface plasmon resonance (SPR) are observed, which is significant in promoting the THz-SPR sensing of polar liquids or aqueous analytes with THz metasurfaces.

Co-Crystal Formation of Antibiotic Nitrofurantoin Drug and Melamine Co-Former Based on a Vibrational Spectroscopic Study

The co-crystallization of active pharmaceutical ingredients (APIs) has received increasing attention due to the modulation of the relative physicochemical properties of APIs such as low solubility, weak permeability and relatively inferior oral bioavailability. Crystal engineering plays a decisive role in the systematic design and synthesis of co-crystals by means of exerting control on the inter-molecular interactions. The characterization and detection of such co-crystal formations plays an essential role in the field of pharmaceutical research and development. In this work, nitrofurantoin (NF), melamine (MELA) and their hydrated co-crystal form were characterized and analyzed by using terahertz time-domain spectroscopy (THz-TDS) and Raman vibrational spectroscopy. According to the experimental THz spectra, the hydrated co-crystal form has characteristic absorption peaks at 0.67, 1.05, 1.50 and 1.73 THz, while the THz spectra for the two raw parent materials (NF and MELA) are quite different within this spectral region. Similar observations were made from the experimental Raman vibrational spectra results. Density functional theory (DFT) calculation was performed to help determine the major vibrational modes of the hydrated co-crystal between nitrofurantoin and melamine, as well as identify the structural changes due to inter- and/or intra-molecular hydrogen bonding motifs between NF and MELA. The results of the theoretical frequency calculations corroborate the THz and Raman experimental spectra. The characteristic bands of the NF⁻MELA-hydrated co-crystal between nitrofurantoin and melamine were also determined based on the DFT simulated calculation. The reported results in this work provide us with a wealth of structural information and a unique vibrational spectroscopic method for characterizing the composition of specific co-crystals and inter-molecular hydrogen bonding interactions upon pharmaceutical co-crystallization.

The effect of the flexibility of hydrogen bonding network on low-frequency motions of amino acids. Evidence from Terahertz spectroscopy and DFT calculations

Low-frequency modes of L-Asp and L-Asn were studied in the range from 0.1 to 3.0THz using time-domain Terahertz spectroscopy and density functional theory calculation. The results show that PBE-D2 shows more success than BLYP-D2 in prediction of THz absorption spectra. To compare their low-frequency modes, we adopted "vibrational character ID strips" proposed by Schmuttenmaer and coworkers [Journal of Physical Chemistry B, 117, 10444(2013)]. We found that the most intense THz absorption peaks of two compounds both involve severe distortion of their hydrogen bonding networks. Due to less rigid hydrogen bonding network in L-Asp, the side chain (carboxyl group) of L-Asp exhibits larger motions than that (carboxamide group) of L-Asn in low-frequency modes.

Characterization of peptides self-assembly by low frequency Raman spectroscopy

Low Frequency Vibrational (LFV) modes of peptides and proteins are attributed to the lattice vibrations and are dependent on their structural organization and self-assembly. Studies taken in order to assign specific absorption bands in the low frequency range to self-assembly behavior of peptides and proteins have been challenging. Here we used a single stage Low Frequency Raman (LF-Raman) spectrometer to study a series of diastereomeric analogue peptides to investigate the effect of peptides self-assembly on the LF-Raman modes. The structural variation of the diastereomeric analogues resulted in distinct self-assembly groups, as confirmed by transmission electron microscopy (TEM) and dynamic light scattering (DLS) data. Using LF-Raman spectroscopy, we consistently observed discrete peaks for each of the self-assembly groups. The correlation between the spectral features and structural morphologies was further supported by principal component analysis (PCA). The LFV modes provide further information on the degrees of freedom of the entire peptide within the higher order organization, reflecting the different arrangement of its hydrogen bonding and hydrophobic interactions. Thus, our approach provides a simple and robust complementary method to structural characterization of peptides assemblies.

Characterization of structural changes in peptide assemblies by low frequency Raman spectroscopy.

Terahertz spectra of l-phenylalanine and its monohydrate

The low-frequency vibrational property of l-phenylalanine (l-Phe) and l-phenylalanine monohydrate (l-Phe·H₂O) has been investigated by terahertz time-domain spectroscopy (THz-TDS) at room and low temperature ranging from 0.5 to 4.5THz. Distinctive THz absorption spectra of the two compounds were observed. Density functional theory (DFT) calculations based on the crystal structures have been performed to simulate the vibrational modes of l-Phe and l-Phe·H₂O and the results agree well with the experimental observations. The study indicates that the characterized features of l-Phe mainly originate from the collective vibration of molecules. And the characterized features of l-Phe·H₂O mainly come from hydrogen bond interactions between l-Phe and water molecules. l-Phe and l-Phe·H₂O were also verified by differential scanning calorimetry and thermogravimetry (DSC-TG) and powder X-ray diffraction (PXRD) examinations.

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.

Structural analysis of bioinspired nano materials with synchrotron far IR spectroscopy

Synchrotron far-infrared spectroscopy was used in conjunction with density functional theory vibrational analysis to ascertain the core structure of self-assembled fibrous superstructures formed by unnatural β³-tripeptides.

Optical measurements of long-range protein vibrations

Protein biological function depends on structural flexibility and change. From cellular communication through membrane ion channels to oxygen uptake and delivery by haemoglobin, structural changes are critical. It has been suggested that vibrations that extend through the protein play a crucial role in controlling these structural changes. While nature may utilize such long-range vibrations for optimization of biological processes, bench-top characterization of these extended structural motions for engineered biochemistry has been elusive. Here we show the first optical observation of long-range protein vibrational modes. This is achieved by orientation-sensitive terahertz near-field microscopy measurements of chicken egg white lysozyme single crystals. Underdamped modes are found to exist for frequencies >10 cm(-1). The existence of these persisting motions indicates that damping and intermode coupling are weaker than previously assumed. The methodology developed permits protein engineering based on dynamical network optimization.

Revealing the interactions between pentagon–octagon–pentagon defect graphene and organic donor/acceptor molecules: a theoretical study

The cyano group interacts strongly with 5–8–5 defect graphene, changes the bands near the Fermi level and enhances the infrared light absorption.

Evaluation of coupling terms between intra- and intermolecular vibrations in coarse-grained normal-mode analysis: does a stronger acid make a stiffer hydrogen bond?

Using theory of harmonic normal-mode vibration analysis, we developed a procedure for evaluating the anisotropic stiffness of intermolecular forces. Our scheme for coarse-graining of molecular motions is modified so as to account for intramolecular vibrations in addition to relative translational/rotational displacement. We applied this new analytical scheme to four carboxylic acid dimers, for which coupling between intra- and intermolecular vibrations is crucial for determining the apparent stiffness of the intermolecular double hydrogen bond. The apparent stiffness constant was analyzed on the basis of a conjunct spring model, which defines contributions from true intermolecular stiffness and molecular internal stiffness. Consequently, the true intermolecular stiffness was in the range of 43-48 N m(-1) for all carboxylic acids studied, regardless of the molecules' acidity. We concluded that the difference in the apparent stiffness can be attributed to differences in the internal stiffness of the respective molecules.

Applying terahertz technology for nondestructive detection of crack initiation in a film-coated layer on a swelling tablet

Here, we describe a nondestructive approach using terahertz wave to detect crack initiation in a film-coated layer on a drug tablet. During scale-up and scale-down of the film coating process, differences in film density and gaps between the film-coated layer and the uncoated tablet were generated due to differences in film coating process parameters, such as the tablet-filling rate in the coating machine, spray pressure, and gas-liquid ratio etc. Tablets using the PEO/PEG formulation were employed as uncoated tablets. We found that heat and humidity caused tablets to swell, thereby breaking the film-coated layer. Using our novel approach with terahertz wave nondestructively detect film surface density (FSD) and interface density differences (IDDs) between the film-coated layer and an uncoated tablet. We also found that a reduced FSD and IDD between the film-coated layer and uncoated tablet increased the risk of crack initiation in the film-coated layer, thereby enabling us to nondestructively predict initiation of cracks in the film-coated layer. Using this method, crack initiation can be nondestructively assessed in swelling tablets after the film coating process without conducting accelerated stability tests, and film coating process parameters during scale-up and scale-down studies can be appropriately established.

Noncovalent interactions between modified cytosine and guanine DNA base pair mimics investigated by terahertz spectroscopy and solid-state density functional theory

Modified cytosine and guanine nucleobases cocrystallize in a hydrogen bonding configuration similar to that observed in native DNA. The noncovalent interactions binding these base pairs in the crystalline solid were investigated using terahertz (THz) spectroscopy and solid-state density functional theory (DFT). While stronger hydrogen bonding interactions are responsible for the general molecular orientations in the crystalline state, it is the weaker dipole-dipole and dispersion forces that determine the overall packing arrangement. The inclusion of dispersion interactions in the DFT calculations was found to be necessary to accurately simulate the unit cell structure and THz vibrational spectrum. Using properly modeled intermolecular potentials, the lattice vibrational motions of the cytosine and guanine derivatives were calculated. The vibrational characters of the modes exhibited by the DNA base pair mimic in the THz region were primarily rotational motions and are indicative of the energies and the nature of vibrations that would likely be observed between similar base pairs in DNA molecules.

DEVELOPMENT OF COMPUTATIONAL METHODOLOGIES FOR THE PREDICTION AND ANALYSIS OF SOLID-STATE TERAHERTZ SPECTRA

The analytical applications of terahertz (THz) spectroscopy for the characterization of molecular solids have been limited by the lack of information concerning the assignment of observed spectral features to specific internal (intramolecular) and external (intermolecular) atomic motions. Computational methodologies addressing the assignment of spectral data are the enabling technology for moving THz spectroscopy to the forefront of available detection methods for both imaging and spectroscopic applications. Solid-state density functional theory (DFT) studies have been performed on the high explosives cyclotetramethylenetetranitramine (HMX) and pentaerythritol tetranitrate (PETN) in order to address the dependencies of the predictions of solid-state vibrations in the terahertz (3 to 120 cm−1) region on the choice of basis set and integration grid size, building on previous work that examined this dependency on the choice of density functional. DFT THz simulations reveal that both the choice of basis set and grid size have important influences on the reproduction of spectral features. The sensitivity to basis set choice is most pronounced in the calculation of vibrational intensities, where it is found that THz absorption intensities are most accurately reproduced when derived from basis set-sensitive Mulliken atomic charges as opposed to basis set-insensitive atomic charges generated by the Hirshfeld partitioning method.

H-bond network in amino acid cocrystals with H2O or H2O2. The DFT study of serine-H2O and serine-H2O2

The structure, IR spectrum, and H-bond network in the serine-H(2)O and serine-H(2)O(2) crystals were studied using DFT computations with periodic boundary conditions. Two different basis sets were used: the all-electron Gaussian-type orbital basis set and the plane wave basis set. Computed frequencies of the IR-active vibrations of the titled crystals are quite different in the range of 10-100 cm(-1). Harmonic approximation fails to reproduce IR active bands in the 2500-2800 frequency region of serine-H(2)O and serine-H(2)O(2). The bands around 2500 and 2700 cm(-1) do exist in the anharmonic IR spectra and are caused by the first overtone of the OH bending vibrations of H(2)O and a combination vibration of the symmetric and asymmetric bendings of H(2)O(2). The quantum-topological analysis of the crystalline electron density enables us to describe quantitatively the H-bond network. It is much more complex in the title crystals than in a serine crystal. Appearance of water leads to an increase of the energy of the amino acid-amino acid interactions, up to ~50 kJ/mol. The energy of the amino acid-water H-bonds is ~30 kJ/mol. The H(2)O/H(2)O(2) substitution does not change the H-bond network; however, the energy of the amino acid-H(2)O(2) contacts increases up to 60 kJ/mol. This is caused by the fact that H(2)O(2) is a much better proton donor than H(2)O in the title crystals.

Evidence of protein collective motions on the picosecond timescale

We investigate the presence of structural collective motions on a picosecond timescale for the heme protein, cytochrome c, as a function of oxidation and hydration, using terahertz (THz) time domain spectroscopy and molecular dynamics simulations. The THz response dramatically increases with oxidation, with the largest increase for lowest hydrations, and highest frequencies. For both oxidation states the THz response rapidly increases with hydration saturating above ∼25% (g H(2)O/g protein). Quasiharmonic vibrational modes and dipole-dipole correlation functions were calculated from molecular dynamics trajectories. The collective mode density of states alone reproduces the measured hydration dependence, providing strong evidence of the existence of these motions. The large oxidation dependence is reproduced only by the dipole-dipole correlation function, indicating the contrast arises from diffusive motions consistent with structural changes occurring in the vicinity of buried internal water molecules. This source for the observed oxidation dependence is consistent with the lack of an oxidation dependence in nuclear resonant vibrational spectroscopy measurements.

Terahertz spectroscopic differentiation of microstructures in protein gels

We demonstrate that terahertz (THz) spectroscopy can be used to differentiate soft protein microstructures. Differentiation of soft microstructures in gels has to date been performed using optical imaging techniques (e.g. electron microscope), but a non-destructive differentiation tool is lacking. Particulate and fine-stranded (fibrillar) soft protein microstructures are of interest, particularly to medical researchers, because they form from naturally occurring proteins that are thought to be involved in several human diseases, such as Alzheimer's disease. In this study, globular beta-lactoglobulin structures with diameters of 2 microm, and fibrillar structures with diameters less than 0.03 microm are observed between 0.8 and 1.5 THz. Results show that the globular structures have a decline in THz transmission when compared to the fibrillar ones. The cause of this decline is possibly due to Rayleigh scattering from the globular microstructures.

THz investigations of condensed phase biomolecular systems

Terahertz (THz) spectroscopic investigations of crystalline dipeptide nanotubes are discussed in the frequency region from 0.6 (2 cm(-1)) to 3 THz (100 cm(-1)). The THz region provides access to collective modes of biomolecular systems and is therefore sensitive to the large scale motions important for understanding the impact of environmental stimuli in biomolecular systems. The focus of this chapter is on THz spectral changes observed in this region when crystals of alanyl isoleucine (AI) and isoleucyl alanine (IA) nanotubes are exposed to water. Of biological significance is the water permeability through hydrophobic pore regions as exemplified in the disparate behavior of these two dipeptide nanotubes. AI is known from X-ray studies and confirmed here to act reversibly to the exchange of water while IA does not accept water into its pore region. Both quantum chemical and classical calculations are performed to better understand the subtle balance that determines guest molecule absorption and conduction through these hydrophobic channels. Examination of the vibrational character of the THz modes with and without water suggests water mode coupling/decoupling with collective modes of the nanotube may play an important role in the permeability dynamics.