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  1. Free, publicly-accessible full text available November 27, 2024
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  3. The prediction of stable crystal structures is an important part of designing solid-state crystalline materials with desired properties. Recent advances in structural feature representations and generative neural networks promise the ability to efficiently create new stable structures to use for inverse design and to search for materials with tailored functionalities. 
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    Free, publicly-accessible full text available July 3, 2024
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  5. The incorporation of noncanonical amino acids (ncAAs) into fluorescent proteins is promising for red-shifting their fluorescence and benefiting tissue imaging with deep penetration and low phototoxicity. However, ncAA-based red fluorescent proteins (RFPs) have been rare. The 3-aminotyrosine modified superfolder green fluorescent protein (aY-sfGFP) represents a recent advance, yet the molecular mechanism for its red-shifted fluorescence remains elusive while its dim fluorescence hinders applications. Herein, we implement femtosecond stimulated Raman spectroscopy to obtain structural fingerprints in the electronic ground state and reveal that aY-sfGFP possesses a GFP-like instead of RFP-like chromophore. Red color of aY-sfGFP intrinsically arises from a unique “double-donor” chromophore structure that raises ground-state energy and enhances charge transfer, notably differing from the conventional conjugation mechanism. We further developed two aY-sfGFP mutants (E222H and T203H) with significantly improved (∼12-fold higher) brightness by rationally restraining the chromophore's nonradiative decay through electronic and steric effects, aided by solvatochromic and fluorogenic studies of the model chromophore in solution. This study thus provides functional mechanisms and generalizable insights into ncAA-RFPs with an efficient route for engineering redder and brighter fluorescent proteins. 
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    Free, publicly-accessible full text available June 15, 2024
  6. Abstract Antrophyum is one of the largest genera of vittarioid ferns (Pteridaceae) and is most diverse in tropical Asia and the Pacific Islands, but also occurs in temperate Asia, Australia, tropical Africa and the Malagasy region. The only monographic study of Antrophyum was published more than a century ago and a modern assessment of its diversity is lacking. Here, we reconstructed a comprehensively sampled and robustly supported phylogeny for the genus based on four chloroplast markers using Bayesian inference, maximum likelihood and maximum parsimony analyses. We then explored the evolution of the genus from the perspectives of morphology, systematics and historical biogeography. We investigated nine critical morphological characters using a morphometric approach and reconstructed their evolution on the phylogeny. We describe four new species and provide new insight into species delimitation. We currently recognize 34 species for the genus and provide a key to identify them. The results of biogeographical analysis suggest that the distribution of extant species is largely shaped by both ancient and recent dispersal events. 
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    Free, publicly-accessible full text available August 1, 2024
  7. The versatile functions of fluorescent proteins (FPs) as fluorescence biomarkers depend on their intrinsic chromophores interacting with the protein environment. Besides X-ray crystallography, vibrational spectroscopy represents a highly valuable tool for characterizing the chromophore structure and revealing the roles of chromophore–environment interactions. In this work, we aim to benchmark the ground-state vibrational signatures of a series of FPs with emission colors spanning from green, yellow, orange, to red, as well as the solvated model chromophores for some of these FPs, using wavelength-tunable femtosecond stimulated Raman spectroscopy (FSRS) in conjunction with quantum calculations. We systematically analyzed and discussed four factors underlying the vibrational properties of FP chromophores: sidechain structure, conjugation structure, chromophore conformation, and the protein environment. A prominent bond-stretching mode characteristic of the quinoidal resonance structure is found to be conserved in most FPs and model chromophores investigated, which can be used as a vibrational marker to interpret chromophore–environment interactions and structural effects on the electronic properties of the chromophore. The fundamental insights gained for these light-sensing units (e.g., protein active sites) substantiate the unique and powerful capability of wavelength-tunable FSRS in delineating FP chromophore properties with high sensitivity and resolution in solution and protein matrices. The comprehensive characterization for various FPs across a colorful palette could also serve as a solid foundation for future spectroscopic studies and the rational engineering of FPs with diverse and improved functions. 
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    Free, publicly-accessible full text available August 1, 2024
  8. Electron-hole bound pairs, or excitons, are common excitations in semiconductors. They can spontaneously form and condense into a new insulating ground state—the so-called excitonic insulator—when the energy of electron-hole Coulomb attraction exceeds the band gap. In the presence of electron-phonon coupling, a periodic lattice distortion often concomitantly occurs. However, a similar structural transition can also be induced by electron-phonon coupling itself, therefore hindering the clean identification of bulk excitonic insulators (e.g., which instability is the driving force of the phase transition). Using high-resolution synchrotron x-ray diffraction and angle-resolved photoemission spectroscopy, we identify key electron-phonon coupling effects in a leading excitonic insulator candidate Ta 2 NiSe 5 . These include an extensive unidirectional lattice fluctuation and an electronic pseudogap in the normal state, as well as a negative electronic compressibility in the charge-doped broken-symmetry state. In combination with first principles and model calculations, we use the normal state electronic spectra to quantitatively determine the electron-phonon interaction vertex g and interband Coulomb interaction V in the minimal lattice model, the solution to which captures the experimental observations. Moreover, we show how the Coulomb and electron-phonon coupling effects can be unambiguously separated based on the solution to quantified microscopic models. Finally, we discuss how the strong lattice fluctuations enabled by low dimensionality relate to the unique electron-phonon interaction effects beyond the textbook Born-Oppenheimer approximation. 
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    Free, publicly-accessible full text available October 1, 2024
  9. Metal oxide thermal reduction, enabled by microwave-induced plasma, was used to synthesize high entropy borides (HEBs). This approach capitalized on the ability of a microwave (MW) plasma source to efficiently transfer thermal energy to drive chemical reactions in an argon-rich plasma. A predominantly single-phase hexagonal AlB2-type structural characteristic of HEBs was obtained by boro/carbothermal reduction as well as by borothermal reduction. We compare the microstructural, mechanical, and oxidation resistance properties using the two different thermal reduction approaches (i.e., with and without carbon as a reducing agent). The plasma-annealed HEB (Hf0.2, Zr0.2, Ti0.2, Ta0.2, Mo0.2)B2 made via boro/carbothermal reduction resulted in a higher measured hardness (38 ± 4 GPa) compared to the same HEB made via borothermal reduction (28 ± 3 GPa). These hardness values were consistent with the theoretical value of ~33 GPa obtained by first-principles simulations using special quasi-random structures. Sample cross-sections were evaluated to examine the effects of the plasma on structural, compositional, and mechanical homogeneity throughout the HEB thickness. MW-plasma-produced HEBs synthesized with carbon exhibit a reduced porosity, higher density, and higher average hardness when compared to HEBs made without carbon. 
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    Free, publicly-accessible full text available June 1, 2024
  10. Proton transfer processes of organic molecules are key to charge transport and photoprotection in biological systems. Among them, excited-state intramolecular proton transfer (ESIPT) reactions are characterized by quick and efficient charge transfer within a molecule, resulting in ultrafast proton motions. The ESIPT-facilitated interconversion between two tautomers (PS and PA) comprising the tree fungal pigment Draconin Red in solution was investigated using a combination of targeted femtosecond transient absorption (fs-TA) and excited-state femtosecond stimulated Raman spectroscopy (ES-FSRS) measurements. Transient intensity (population and polarizability) and frequency (structural and cooling) dynamics of –COH rocking and –C=C, –C=O stretching modes following directed stimulation of each tautomer elucidate the excitation-dependent relaxation pathways, particularly the bidirectional ESIPT progression out of the Franck–Condon region to the lower-lying excited state, of the intrinsically heterogeneous chromophore in dichloromethane solvent. A characteristic overall excited-state PS-to-PA transition on the picosecond timescale leads to a unique “W”-shaped excited-state Raman intensity pattern due to dynamic resonance enhancement with the Raman pump–probe pulse pair. The ability to utilize quantum mechanics calculations in conjunction with steady-state electronic absorption and emission spectra to induce disparate excited-state populations in an inhomogeneous mixture of similar tautomers has broad implications for the modeling of potential energy surfaces and delineation of reaction mechanisms in naturally occurring chromophores. Such fundamental insights afforded by in-depth analysis of ultrafast spectroscopic datasets are also beneficial for future development of sustainable materials and optoelectronics. 
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    Free, publicly-accessible full text available April 1, 2024