Imaging 3D molecular orientation by orthogonal-pair polarization IR microscopy

Effects of Polarizer-Analyzer Configurations for FTIR Spectroscopy: Implications for Multiple Polarization Algorithms

Polarized Fourier transform infrared (p-FTIR) spectroscopy is a widely used technique for determining orientational information in thin organic materials. Conventionally, a single polarizer is placed in the path of the incident light (termed the polarizer). Occasionally, a second polarizer is also placed after the sample (referred to as the analyzer). However, this polarizer-analyzer configuration has the potential to induce polarization-dependent variances in the final spectra beyond those that are expected, i.e., the squared-cosine relationship of absorptance with respect to polarization angle is no longer accurate. These variances are due to changes in the polarization state of the transmitted light induced by the sample and have yet to be explored in the context of p-FTIR. Consequently, this study employs both theoretical and experimental approaches to identify the effects of including a second polarizer in p-FTIR analyses of anisotropic organic samples. For thin samples, the most significant spectral variance arising from only birefringence is observed on the shoulders of the dichroic peaks. By adopting a crossed polarizer configuration, it is shown that there is potential to identify anisotropy of samples that are generally considered too thick for p-FTIR analysis by exploiting this feature. Furthermore, the squared-cosine relationship of absorptance with respect to the polarization angle is also shown to be inapplicable when a second parallel-oriented polarizer is included. Accordingly, a function that accounts for the second polarizer is proposed for multiple polarization techniques.

Scattering correction for samples with cylindrical domains measured with polarized infrared spectroscopy

Scattering artifacts are one of the most common effects distorting transmission spectra in Fourier-Transform Infrared spectroscopy. Their increased impact, strongly diminishing the quantitative and qualitative power of IR spectroscopy, is especially observed for structures with a size comparable to the radiation wavelength. To tackle this problem, a wide range of preprocessing techniques based on the Extended Multiplicative Scattering Correction method was developed, using physical properties to remove scattering presence in the spectra. However, until recently those algorithms were mostly focused on spherically shaped samples, for example, cells. Here, an algorithm for samples with cylindrical domains is described, with additional implementation of a linearly polarized light case, which is crucial for the growing field of polarized IR imaging and spectroscopy. An open-source code with GPU based implementation is provided, with a calculation time of several seconds per spectrum. Optimizations done to improve the throughput of this algorithm allow the application of this method into the standard preprocessing pipeline of small datasets.

Linearly Polarized Infrared Spectroscopy for the Analysis of Biological Materials

The analysis of biological samples with polarized infrared spectroscopy (p-IR) has long been a widely practiced method for the determination of sample orientation and structural properties. In contrast to earlier works, which employed this method to investigate the fundamental chemistry of biological systems, recent interests are moving toward "real-world" applications for the evaluation and diagnosis of pathological states. This focal point review provides an up-to-date synopsis of the knowledge of biological materials garnered through linearly p-IR on biomolecules, cells, and tissues. An overview of the theory with special consideration to biological samples is provided. Different modalities which can be employed along with their capabilities and limitations are outlined. Furthermore, an in-depth discussion of factors regarding sample preparation, sample properties, and instrumentation, which can affect p-IR analysis is provided. Additionally, attention is drawn to the potential impacts of analysis of biological samples with inherently polarized light sources, such as synchrotron light and quantum cascade lasers. The vast applications of p-IR for the determination of the structure and orientation of biological samples are given. In conclusion, with considerations to emerging instrumentation, findings by other techniques, and the shift of focus toward clinical applications, we speculate on the future directions of this methodology.

3D Orientation Imaging of Polymer Chains with Polarization-Controlled Coherent Raman Microscopy

Despite the ubiquity of three-dimensional (3D) anisotropic materials, their 3D molecular alignment cannot be measured using conventional two-dimensional (2D) polarization imaging. Here, we present images of the 3D angles of molecular orientations with submicrometer spatial resolution acquired through polarization-controlled coherent anti-Stokes Raman scattering microscopy. The hyperspectral Raman data of a polyethylene (PE) film were converted into images, showing the polymer chains' 3D angles and order parameters. The 3D orientation images of PE chains in ring-banded spherulites show that the azimuthal angles of the chains are perpendicular to the crystal growth direction, while the out-of-plane angles display limited-range oscillations synchronous with ring banding. The prevailing crystal growth model of fully twisting lamellae is inconsistent with the observed restricted oscillations of the out-of-plane direction, which are unobservable through conventional 2D projected imaging. This high-resolution, label-free, quantitative imaging of 3D molecular orientation can become a standard measurement tool for the microscopic structures of complex synthetic and biological materials.

Super-Resolved 3D Mapping of Molecular Orientation Using Vibrational Techniques

When a sample has an anisotropic structure, it is possible to obtain additional information controlling the polarization of incident light. With their straightforward instrumentation approaches, infrared (IR) and Raman spectroscopies are widely popular in this area. Single-band-based determination of molecular in-plane orientation, typically used in materials science, is here extended by the concurrent use of two vibration bands, revealing the orientational ordering in three dimension. The concurrent analysis was applied to IR spectromicroscopic data to obtain orientation angles of a model polycaprolactone spherulite sample. The applicability of this method spans from high-resolution, diffraction-limited Fourier transform infrared (FT-IR) and Raman imaging to super-resolved optical photothermal infrared (O-PTIR) imaging. Due to the nontomographic experimental approach, no image distortion is visible and nanometer scale orientation domains can be observed. Three-dimensional (3D) bond orientation maps enable in-depth characterization and consequently precise control of the sample’s physicochemical properties and functions.