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1. Using transition density models to interpret experimental optical spectra of exciton-coupled cyanine (iCy3)2 dimer probes of local DNA conformations at or near functional protein binding sites

   https://doi.org/10.1093/nar/gkad1163  

   Heussman, Dylan; Enkhbaatar, Lulu; Sorour, Mohammed I.; Kistler, Kurt A.; von Hippel, Peter H.; Matsika, Spiridoula; Marcus, Andrew H. (December 2023, Nucleic Acids Research)

   Abstract Exciton-coupled chromophore dimers are an emerging class of optical probes for studies of site-specific biomolecular interactions. Applying accurate theoretical models for the electrostatic coupling of a molecular dimer probe is a key step for simulating its optical properties and analyzing spectroscopic data. In this work, we compare experimental absorbance and circular dichroism (CD) spectra of ‘internally-labeled’ (iCy3)2 dimer probes inserted site-specifically into DNA fork constructs to theoretical calculations of the structure and geometry of these exciton-coupled dimers. We compare transition density models of varying levels of approximation to determine conformational parameters of the (iCy3)2 dimer-labeled DNA fork constructs. By applying an atomistically detailed transition charge (TQ) model, we can distinguish between dimer conformations in which the stacking and tilt angles between planar iCy3 monomers are varied. A major strength of this approach is that the local conformations of the (iCy3)2 dimer probes that we determined can be used to infer information about the structures of the DNA framework immediately surrounding the probes at various positions within the constructs, both deep in the duplex DNA sequences and at sites at or near the DNA fork junctions where protein complexes bind to discharge their biological functions. 

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2. Synthesis of redox-active fluorinated 5-hydroxytryptophans as molecular reporters for biological electron transfer

   https://doi.org/10.1039/d1cc00187f  

   Ohler, Amanda; Long, Hanna; Ohgo, Kei; Tyson, Kristin; Murray, David; Davis, Amanda; Whittington, Chris; Hvastkovs, Eli G.; Duffy, Liam; Haddy, Alice; et al (January 2021, Chemical Communications)

   null (Ed.)

   Fluorinated 5-hydroxytryptophans (F n -5HOWs) were synthesized in gram scale quantities and incorporated into a β-hairpin peptide and the protein azurin. The redox-active F n -5HOWs exhibit unique radical spectroscopic signatures that expand the function of 5HOW as probes for biological electron transfer. 

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3. Electrostatic modulation of multiple binding events between loquacious-PD and double-stranded RNA

   https://doi.org/10.1039/D4CP02151G  

   Moonitz, Sasha A; Do, Nhat T; Noriega, Rodrigo (July 2024, Physical Chemistry Chemical Physics)

   Electrostatics can alter the RNA-binding properties of proteins that display structure selectivity without sequence specificity. Loquacious-PD relies on this broad scope response to mediate the interaction of endonucleases with double stranded RNAs. Multimodal spectroscopic probes with in situ perturbations reveal an efficient and stable binding mechanism that disfavors high protein density complexes and is sensitive to local electrostatics. 

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4. Molecular factors determining brightness in fluorescence-encoded infrared vibrational spectroscopy

   https://doi.org/10.1063/5.0190231  

   Guha, Abhirup; Whaley-Mayda, Lukas; Lee, Seung Yeon; Tokmakoff, Andrei (March 2024, The Journal of Chemical Physics)

   Fluorescence-encoded infrared (FEIR) spectroscopy is a recently developed technique for solution-phase vibrational spectroscopy with detection sensitivity at the single-molecule level. While its spectroscopic information content and important criteria for its practical experimental optimization have been identified, a general understanding of the electronic and nuclear properties required for highly sensitive detection, i.e., what makes a molecule a “good FEIR chromophore,” is lacking. This work explores the molecular factors that determine FEIR vibrational activity and assesses computational approaches for its prediction. We employ density functional theory (DFT) and its time-dependent version (TD-DFT) to compute vibrational and electronic transition dipole moments, their relative orientation, and the Franck–Condon factors involved in FEIR activity. We apply these methods to compute the FEIR activities of normal modes of chromophores from the coumarin family and compare these predictions with experimental FEIR cross sections. We discuss the extent to which we can use computational models to predict the FEIR activity of individual vibrations in a candidate molecule. The results discussed in this work provide the groundwork for computational strategies for choosing FEIR vibrational probes or informing the structure of designer chromophores for single-molecule spectroscopic applications. 

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5. A microscopic perspective on moiré materials

   https://doi.org/10.1038/s41578-024-00682-1  

   Nuckolls, Kevin P; Yazdani, Ali (May 2024, Nature Reviews Materials)

   Contemporary quantum materials research is guided by themes of topology and electronic correlations. A confluence of these two themes is engineered in moiré materials, an emerging class of highly tunable, strongly correlated 2D materials designed by the rotational or lattice misalignment of atomically thin crystals. In moiré materials, dominant Coulomb interactions among electrons give rise to collective electronic phases, often with robust topological properties. Identifying the mechanisms responsible for these exotic phases is fundamental to our understanding of strongly interacting quantum systems and to our ability to engineer new material properties for potential future technological applications. In this Review, we highlight the contributions of local spectroscopic, thermodynamic and electromagnetic probes to the budding field of moiré materials research. These techniques have not only identified many of the underlying mechanisms of the correlated insulators, generalized Wigner crystals, unconventional superconductors, moiré ferroelectrics and topological orbital ferromagnets found in moiré materials, but have also uncovered fragile quantum phases that have evaded spatially averaged global probes. Furthermore, we highlight recently developed local probe techniques, including local charge sensing and quantum interference probes, that have uncovered new physical observables in moiré materials. 

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