Combining theory and experiment for X-ray absorption spectroscopy and resonant X-ray scattering characterization of polymers

An improved understanding of fundamental chemistry, electronic structure, morphology, and dynamics in polymers and soft materials requires advanced characterization techniques that are amenable to in situ and operando studies. Soft X-ray methods are especially useful in their ability to non-destructively provide information on specific materials or chemical moieties. Analysis of these experiments, which can be very dependent on X-ray energy and polarization, can quickly become complex. Complementary modeling and predictive capabilities are required to properly probe these critical features. Here, we present relevant background on this emerging suite of techniques. We focus on how the combination of theory and experiment has been applied and can be further developed to drive our understanding of how these methods probe relevant chemistry, structure, and dynamics in soft materials

From Mendel’s discovery on pea to today’s plant genetics and breeding

In 2015, we celebrated the 150th anniversary of the presentation of the seminal work of Gregor Johann Mendel. While Darwin’s theory of evolution was based on differential survival and differential reproductive success, Mendel’s theory of heredity relies on equality and stability throughout all stages of the life cycle. Darwin’s concepts were continuous variation and “soft” heredity; Mendel espoused discontinuous variation and “hard” heredity. Thus, the combination of Mendelian genetics with Darwin’s theory of natural selection was the process that resulted in the modern synthesis of evolutionary biology. Although biology, genetics, and genomics have been revolutionized in recent years, modern genetics will forever rely on simple principles founded on pea breeding using seven single gene characters. Purposeful use of mutants to study gene function is one of the essential tools of modern genetics. Today, over 100 plant species genomes have been sequenced. Mapping populations and their use in segregation of molecular markers and marker–trait association to map and isolate genes, were developed on the basis of Mendel's work. Genome-wide or genomic selection is a recent approach for the development of improved breeding lines. The analysis of complex traits has been enhanced by high-throughput phenotyping and developments in statistical and modeling methods for the analysis of phenotypic data. Introgression of novel alleles from landraces and wild relatives widens genetic diversity and improves traits; transgenic methodologies allow for the introduction of novel genes from diverse sources, and gene editing approaches offer possibilities to manipulate gene in a precise manner

Competing Effects of Fluorination on the Orientation of Aromatic and Aliphatic Phosphonic Acid Monolayers on Indium Tin Oxide

Transparent conductive oxides such as indium tin oxide (ITO) are common substrates for optoelectronic devices, including organic light-emitting diodes and organic solar cells. Tailoring the interface between the oxide and the active layer by adjusting the work function or wettability of the oxide can improve the performance of these devices in both emissive and photovoltaic applications. The use of carefully designed surface modifiers that form self-assembled monolayers (SAMs) can allow the tuning of the surface of one oxide material to optimize its properties for use with a variety of different organic semiconductors or for different applications. Fluorinated phosphonic-acid-based SAMs can affect the interface dipole and the work function of a metal oxide. Fluorination may also affect the molecular packing and the orientation of the SAM once bound to the surface. We utilize angle-dependent near-edge X-ray absorption fine structure (NEXAFS) spectroscopy to determine the molecular orientations of octylphosphonic acid, phenylphosphonic acid, and fluorinated derivatives on ITO and correlate the molecular orientations derived from these studies with predictions from density functional theory (DFT). We account quantitatively for the effect of surface roughness on the measured orientations. We observe that fluorination of the octylphosphonic acid SAM results in a more upright orientation, an effect we attribute to intermolecular forces and increased steric bulk. In contrast, fluorination of the phenylphosphonic acid SAM leads to a less upright orientation that we associate with changes in binding mode

Electron-Transfer Processes in Zinc Phthalocyanine–Phosphonic Acid Monolayers on ITO: Characterization of Orientation and Charge-Transfer Kinetics by Waveguide Spectroelectrochemistry

Using a monolayer of zinc phthalocyanine (ZnPcPA) tethered to indium tin oxide (ITO) as a model for the donor/transparent conducting oxide (TCO) interface in organic photovoltaics (OPVs), we demonstrate the relationship between molecular orientation and charge-transfer rates using spectroscopic, electrochemical, and spectroelectrochemical methods. Both monomeric and aggregated forms of the phthalocyanine (Pc) are observed in ZnPcPA monolayers. Potential-modulated attenuated total reflectance (PM-ATR) measurements show that the monomeric subpopulation undergoes oxidation/reduction with <i>k</i>_s,app = 2 × 10² s^–1, independent of Pc orientation. For the aggregated ZnPcPA, faster orientation-dependent charge-transfer rates are observed. For in-plane-oriented Pc aggregates, <i>k</i>_s,app = 2 × 10³ s^–1, whereas for upright Pc aggregates, <i>k</i>_s,app = 7 × 10² s^–1. The rates for the aggregates are comparable to those required for redox-active interlayer films at the hole-collection contact in organic solar cells

Orientation of Phenylphosphonic Acid Self-Assembled Monolayers on a Transparent Conductive Oxide: A Combined NEXAFS, PM-IRRAS, and DFT Study

Self-assembled monolayers (SAMs) of dipolar phosphonic acids can tailor the interface between organic semiconductors and transparent conductive oxides. When used in optoelectronic devices such as organic light emitting diodes and solar cells, these SAMs can increase current density and photovoltaic performance. The molecular ordering and conformation adopted by the SAMs determine properties such as work function and wettability at these critical interfaces. We combine angle-dependent near-edge X-ray absorption fine structure (NEXAFS) spectroscopy and polarization modulation infrared reflection absorption spectroscopy (PM-IRRAS) to determine the molecular orientations of a model phenylphosphonic acid on indium zinc oxide, and correlate the resulting values with density functional theory (DFT). We find that the SAMs are surprisingly well-oriented, with the phenyl ring adopting a well-defined tilt angle of 12–16° from the surface normal. We find quantitative agreement between the two experimental techniques and density functional theory calculations. These results not only provide a detailed picture of the molecular structure of a technologically important class of SAMs, but also resolve a long-standing ambiguity regarding the vibrational-mode assignments for phosphonic acids on oxide surfaces, thus improving the utility of PM-IRRAS for future studies