Calculating the Complex Permittivity of Powdered Crystalline Material at Infrared and Terahertz Frequencies

In this paper we calculate the complex permittivity of a crystalline material supported in a non-absorbing medium. To do this we have developed a software package, PDielec, which post processes solid state quantum mechanical and molecular mechanical calculations of the phonons and dielectric response of the crystalline material. Using an effective medium approximation, the package calculates the internal electric field arising from different particle morphologies and calculates the resulting shift in absorption frequency and intensity arising from the coupling between each phonon mode and the resultant internal field

Determining the THz and Infrared Spectral Properties of Single Crystals and Thin Crystalline Films from First Principles

We present recent developments to the software packaged PDielec that can be used to post-process solid-state DFT calculations to determine the THz spectra of single crystals and thin crystalline films, including effects of crystalline orientation, beam incidence angle and beam polarisation, allowing the full interpretation of complex THz spectra. We use the explosive Cyclotrimethylenetrinitramine (RDX) as a previously well studied example

Exploring the Stability and Disorder in the Polymorphs of L-Cysteine through Density Functional Theory and Vibrational Spectroscopy

Static and dynamic density functional calculations are reported for the four known polymorphs of l-cysteine. Static calculations are used to explore the relative free energies (within the harmonic approximation) of the polymorphs as a function of pressure. An important feature of the structural differences between the polymorphs is shown to be the dihedral angle of the C–C–S–H bond. It is shown that, by varying this angle, it is possible to move between hydrogen bonding motifs S–H···S and S–H···O in all four polymorphs. The energetics for dihedral angle rotation are explored, and the barriers for rotation between the hydrogen bonding motifs have been calculated for each polymorph. Two possible models for the experimental disorder observed in Form I at room temperature are explored using both static and dynamic methods; a domain disorder model, where the disorder is localized, and a dispersed disorder model, where the disorder is randomly distributed throughout the crystal. Molecular dynamics calculations show transitions between the two hydrogen bonding motifs occurring in the dispersed disorder model at 300 and 350 K. In addition, molecular dynamics calculations of Form IV also showed the onset of hydrogen bond disorder at 300 K. Calculations of the predicted infrared and terahertz absorption are performed for both the static and dynamic simulations, and the results are compared with experimental results to understand the influence of disorder on the observed spectra

PDielec: The calculation of infrared and terahertz absorption for powdered crystals

The Python package PDielec is described, which calculates the infrared absorption characteristics of a crystalline material supported in a non-absorbing medium. PDielec post processes solid-state quantum mechanical and molecular mechanical calculations of the phonons and dielectric response of the crystalline material. Using an effective medium method, the package calculates the internal electric field arising from different particle morphologies and calculates the resulting shift in absorption frequency and intensity arising from the coupling between a phonon and the internal field. The theory of the approach is described, followed by a description of the implementation within PDielec. Finally, a section providing several examples of its application is given

Estimation of Spectroscopic Uncertainty and Correlation in Terahertz Time Domain Spectroscopy

We present a method of calculating the measurement variance-covariance matrix of a spectroscopic sample’s complex refractive index from time-domain statistics in order to estimate uncertainty of a measurement. We compare this method to a numerical analysis and previously derived methodology, and show that our time-based estimate is both accurate and adaptable to complex extraction models

Multilayer Extraction of Complex Refractive Index in Broadband Transmission Terahertz Time-Domain Spectroscopy

In terahertz spectroscopy, multi-layered samples often need to be measured, for instance in a liquid flow cell, and this complicates the extraction of material parameters. We present a spectroscopic parameter extraction algorithm for multilayer samples that can also be used to extract the thickness of an unknown sample laye

Calculating the Complex Permittivity of Powdered Crystalline Materials

Solid-state density functional theory calculations including periodic boundary conditions have become well established for calculating the THz spectra of crystalline materials. Here we compare a range of DFT programs and calculation parameters including a number of van der Waals’ dispersive corrections in combination with our post-processing tool, PDielec, to calculate the complex permittivity of a range of powdered crystalline materials

Probing temperature- and solvent-dependent protein dynamics using terahertz time-domain spectroscopy

The effect of temperature on the terahertz-frequency-range material properties of lyophilized and single-crystal hen egg-white lysozyme has been measured using terahertz time-domain spectroscopy, with the results presented and discussed in the context of protein and solvent dynamical and glass transitions. Lyophilized hen egg-white lysozyme was measured over a temperature range from 4 to 290 K, and a change in the dynamical behaviour of the sample at around 100 K was observed through a change in the terahertz absorption spectrum. Additionally, the effect of cryoprotectants on the temperature-dependent absorption coefficient is studied, and it is demonstrated that terahertz time-domain spectroscopy is capable of resolving the true glass transition temperature of single-crystal hen egg-white lysozyme at 150 K, which is in agreement with literature values measured using differential scanning calorimetry

Multiscale correlative tomography: an investigation of creep cavitation in 316 stainless steel

Creep cavitation in an ex-service nuclear steam header Type 316 stainless steel sample is investigated through a multiscale tomography workflow spanning eight orders of magnitude, combining X-ray computed tomography (CT), plasma focused ion beam (FIB) scanning electron microscope (SEM) imaging and scanning transmission electron microscope (STEM) tomography. Guided by microscale X-ray CT, nanoscale X-ray CT is used to investigate the size and morphology of cavities at a triple point of grain boundaries. In order to understand the factors affecting the extent of cavitation, the orientation and crystallographic misorientation of each boundary is characterised using electron backscatter diffraction (EBSD). Additionally, in order to better understand boundary phase growth, the chemistry of a single boundary and its associated secondary phase precipitates is probed through STEM energy dispersive X-ray (EDX) tomography. The difference in cavitation of the three grain boundaries investigated suggests that the orientation of grain boundaries with respect to the direction of principal stress is important in the promotion of cavity formation

Accurate Parameter Extraction From Liquids Measured Using On-chip Terahertz Spectroscopy

We introduce a method for estimating the permittivity of liquid samples measured using integrated microfluidic/planar Goubau line terahertz waveguides, in which simulation results are incorporated with measurement data to enable accurate frequency-dependent analysis