Probing DNA structural heterogeneity by identifying conformational subensembles of a bicovalently bound cyanine dye.

DNA is a re-configurable, biological information-storage unit, and much remains to be learned about its heterogeneous structural dynamics. For example, while it is known that molecular dyes templated onto DNA exhibit increased photostability, the mechanism by which the structural dynamics of DNA affect the dye photophysics remains unknown. Here, we use femtosecond, two-dimensional electronic spectroscopy measurements of a cyanine dye, Cy5, to probe local conformations in samples of single-stranded DNA (ssDNA-Cy5), double-stranded DNA (dsDNA-Cy5), and Holliday junction DNA (HJ-DNA-Cy5).

Tunable Electronic Structure via DNA-Templated Heteroaggregates of Two Distinct Cyanine Dyes.

Molecular excitons are useful for applications in light harvesting, organic optoelectronics, and nanoscale computing. Electronic energy transfer (EET) is a process central to the function of devices based on molecular excitons. Achieving EET with a high quantum efficiency is a common obstacle to excitonic devices, often owing to the lack of donor and acceptor molecules that exhibit favorable spectral overlap.

Improving Rare-Earth Mineral Separation with Insights from Molecular Recognition: Functionalized Hydroxamic Acid Adsorption onto Bastnäsite and Calcite.

Enhancing the separation of rare-earth elements (REEs) from gangue materials in mined ores requires an understanding of the fundamental interactions driving the adsorption of collector ligands onto mineral interfaces. In this work, we examine five functionalized hydroxamic acid ligands as potential collectors for the REE-containing bastnäsite mineral in froth flotation using density functional theory calculations and a suite of surface-sensitive analytical spectroscopies. These include vibrational sum frequency generation, attenuated total reflectance Fourier transform infrared, Raman, and X-ray photoelectron spectroscopies.

Tuning between Quenching and Energy Transfer in DNA-Templated Heterodimer Aggregates.

Molecular excitons, which propagate spatially via electronic energy transfer, are central to numerous applications including light harvesting, organic optoelectronics, and nanoscale computing; they may also benefit applications such as photothermal therapy and photoacoustic imaging through the local generation of heat via rapid excited-state quenching. Here we show how to tune between energy transfer and quenching for heterodimers of the same pair of cyanine dyes by altering their spatial configuration on a DNA template. We assemble "transverse" and "adjacent" heterodimers of Cy5 and Cy5.

Ion Pairing and Molecular Orientation at Liquid/Liquid Interfaces: Self-Assembly and Function.

Molecular orientation plays a pivotal role in defining the functionality and chemistry of interfaces, yet accurate measurements probing this important feature are few, due, in part, to technical and analytical limitations in extracting information from molecular monolayers. For example, buried liquid/liquid interfaces, where a complex and poorly understood balance of inter- and intramolecular interactions impart structural constraints that facilitate the formation of supramolecular assemblies capable of new functions, are difficult to probe experimentally. Here, we use vibrational sum-frequency generation spectroscopy, numerical polarization analysis, and atomistic molecular dynamics simulations to probe molecular orientations at buried oil/aqueous interfaces decorated with amphiphilic oligomers.

Correction: Interfacial acidity on the strontium titanate surface: a scaling paradigm and the role of the hydrogen bond.

Correction for 'Interfacial acidity on the strontium titanate surface: a scaling paradigm and the role of the hydrogen bond' by Robert C. Chapleski, Jr. , , 2021, , 23478-23485, DOI: 10.

Interfacial acidity on the strontium titanate surface: a scaling paradigm and the role of the hydrogen bond.

A fundamental understanding of acidity at an interface, as mediated by structure and molecule-surface interactions, is essential to elucidate the mechanisms of a range of chemical transformations. While the strength of an acid in homogeneous gas and solution phases is conceptually well understood, acid-base chemistry at heterogeneous interfaces is notoriously more complicated. Using density functional theory and nonlinear vibrational spectroscopy, we present a method to determine the interfacial Brønsted-Lowry acidity of aliphatic alcohols adsorbed on the (100) surface of the model perovskite, strontium titanate.

Additive manufacturing of strong silica sand structures enabled by polyethyleneimine binder.

Binder Jet Additive Manufacturing (BJAM) is a versatile AM technique that can form parts from a variety of powdered materials including metals, ceramics, and polymers. BJAM utilizes inkjet printing to selectively bind these powder particles together to form complex geometries. Adoption of BJAM has been limited due to its inability to form strong green parts using conventional binders.

Ion Pairing Mediates Molecular Organization Across Liquid/Liquid Interfaces.

Liquid/liquid interfaces play a central role in scientific fields ranging from nanomaterial synthesis and soft matter electronics to nuclear waste remediation and chemical separations. This diversity of functions arises from an interface's ability to respond to changing conditions in its neighboring bulk phases. Understanding what drives this interfacial flexibility can provide novel avenues for designing new functional interfaces.

Mapping the Interfacial Chemistry and Structure of Partially Fluorinated Bottlebrush Polymers and Their Linear Analogues.

Polymer interfaces are key to a range of applications including membranes for chemical separations, hydrophobic coatings, and passivating layers for antifouling. While important, challenges remain in probing the interfacial monolayer where the molecular ordering and orientation can change depending on the chemical makeup or processing conditions. In this work, we leverage surface specific vibrational sum frequency generation (SFG) and the associated dependence on molecular symmetry to elucidate the ordering and orientations of key functional groups for poly(2,2,2-trifluoroethyl methacrylate) bottlebrush polymers and their linear polymer analogues.

A Molecular-Scale Approach to Rare-Earth Beneficiation: Thinking Small to Avoid Large Losses.

Separating rare-earth-element-rich minerals from unwanted gangue in mined ores relies on selective binding of collector molecules at the interface to facilitate froth flotation. Salicylhydroxamic acid (SHA) exhibits enhanced selectivity for bastnäsite over calcite in microflotation experiments. Through a multifaceted approach, leveraging density functional theory calculations, and advanced spectroscopic methods, we provide molecular-level mechanistic insight to this selectivity.

Hydrogen-Bond-Driven Chemical Separations: Elucidating the Interfacial Steps of Self-Assembly in Solvent Extraction.

Chemical separations, particularly liquid extractions, are pervasive in academic and industrial laboratories, yet a mechanistic understanding of the events governing their function are obscured by interfacial phenomena that are notoriously difficult to measure. In this work, we investigate the fundamental steps of ligand self-assembly as driven by changes in the interfacial H-bonding network using vibrational sum frequency generation. Our results show how the bulk pH modulates the interfacial structure of extractants at the buried oil/aqueous interface via the formation of unique H-bonding networks that order and bridge ligands to produce self-assembled aggregates.

Molecular Recognition at Mineral Interfaces: Implications for the Beneficiation of Rare Earth Ores.

Ce-bastnäsite is the single largest mineral source for light rare-earth elements. In view of the growing industrial importance of rare-earth minerals, it is critical to develop more efficient methods for separating the valuable rare-earth-containing minerals from the surrounding gangue. In this work, we employ a combination of periodic density functional theory (DFT) and molecular mechanics (MM) calculations together with the molecular design program HostDesigner to identify bis-phosphinate ligands that preferentially bind to the (100) Ce-bastnäsite surface rather than the (104) calcite surface.

Insight into the Mechanisms Driving the Self-Assembly of Functional Interfaces: Moving from Lipids to Charged Amphiphilic Oligomers.

Polymer-stabilized liquid/liquid interfaces are an important and growing class of bioinspired materials that combine the structural and functional capabilities of advanced synthetic materials with naturally evolved biophysical systems. These platforms have the potential to serve as selective membranes for chemical separations and molecular sequencers and to even mimic neuromorphic computing elements. Despite the diversity in function, basic insight into the assembly of well-defined amphiphilic polymers to form functional structures remains elusive, which hinders the continued development of these technologies.

A new approach to vibrational sum frequency generation spectroscopy using near infrared pulse shaping.

We have developed a multipurpose vibrational sum frequency generation (vSFG) spectrometer that is uniquely capable of probing a broad range of chemical species, each requiring different experimental conditions, without optical realignment. Here, we take advantage of arbitrary near infrared (NIR) waveform generation using a 4f-pulse shaper equipped with a 2D spatial light modulator (SLM) to tailor upconversion pulses to meet sample dependent experimental requirements. This report details the experimental layout, details of the SLM calibration and implementation, and the intrinsic benefits/limitations of this new approach to vSFG spectroscopy.

Flexible approach to vibrational sum-frequency generation using shaped near-infrared light.

We describe a new approach that expands the utility of vibrational sum-frequency generation (vSFG) spectroscopy using shaped near-infrared (NIR) laser pulses. We demonstrate that arbitrary pulse shapes can be specified to match experimental requirements without the need for changes to the optical alignment. In this way, narrowband NIR pulses as long as 5.

Dynamic Sparse Sampling for Confocal Raman Microscopy.

The total number of data points required for image generation in Raman microscopy was greatly reduced using sparse sampling strategies, in which the preceding set of measurements informed the next most information-rich sampling location. Using this approach, chemical images of pharmaceutical materials were obtained with >99% accuracy from 15.8% sampling, representing an ∼6-fold reduction in measurement time relative to full field of view rastering with comparable image quality.

Second Harmonic Generation Guided Raman Spectroscopy for Sensitive Detection of Polymorph Transitions.

Second harmonic generation (SHG) was integrated with Raman spectroscopy for the analysis of pharmaceutical materials. Particulate formulations of clopidogrel bisulfate were prepared in two crystal forms (Form I and Form II). Image analysis approaches enable automated identification of particles by bright field imaging, followed by classification by SHG.

Synchrotron X-Ray Diffraction Dynamic Sampling for Protein Crystal Centering.

A supervised learning approach for dynamic sampling (SLADS) was developed to reduce X-ray exposure prior to data collection in protein structure determination. Implementation of this algorithm allowed reduction of the X-ray dose to the central core of the crystal by up to 20-fold compared to current raster scanning approaches. This dose reduction corresponds directly to a reduction on X-ray damage to the protein crystals prior to data collection for structure determination.

Dynamic X-ray diffraction sampling for protein crystal positioning.

A sparse supervised learning approach for dynamic sampling (SLADS) is described for dose reduction in diffraction-based protein crystal positioning. Crystal centering is typically a prerequisite for macromolecular diffraction at synchrotron facilities, with X-ray diffraction mapping growing in popularity as a mechanism for localization. In X-ray raster scanning, diffraction is used to identify the crystal positions based on the detection of Bragg-like peaks in the scattering patterns; however, this additional X-ray exposure may result in detectable damage to the crystal prior to data collection.

Powders Analysis by Second Harmonic Generation Microscopy.

A microscopy approach is developed for quantifying second harmonic generation (SHG) activity of powders that largely decouples linear and nonlinear optical interactions. Decoupling the linear and nonlinear optical effects provides a means to independently evaluate and optimize the role of each in crystal engineering efforts and facilitates direct comparisons between experimental and computational predictions of lattice hyperpolarizabilities. In this respect, the microscopy-based approach nicely complements well-established Kurtz-Perry ( J.

Exciton coupling model for the emergence of second harmonic generation from assemblies of centrosymmetric molecules.

A simple model is presented for interpreting the presence of substantial second harmonic generation (SHG) activity from assemblies of centrosymmetric molecular building blocks. Using butadiene as a computationally tractable centrosymmetric model system, time-dependent Hartree-Fock calculations of the nonlinear polarizability of butadiene dimer were well-described through exciton coupling arguments based on the electronic structure of the monomer and the relative orientation between the monomers within the dimer. Experimental studies of the centrosymmetric molecule 2,6-di-tert-butylanthraquinone suggest the formation of a combination of SHG-active and SHG-inactive crystal forms.

Kinetic trapping of metastable amino acid polymorphs.

Second harmonic generation (SHG) microscopy measurements indicate that inkjet-printed racemic solutions of amino acids can produce nanocrystals trapped in metastable polymorph forms upon rapid solvent evaporation. Polymorphism impacts the composition, distribution, and physico-kinetic properties of organic solids, with energetic arguments favoring the most stable polymorph. In this study, unfavored noncentrosymmetric crystal forms were observed by SHG microscopy.