A practical approach for estimating the escape ratio of near-infrared solar-induced chlorophyll fluorescence
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Zeng, Yelu (ORCID:0000000342671841)↗
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Competing Intermolecular and Molecule–Surface Interactions: Dipole–Dipole-Driven Patterns in Mixed Carborane Self-Assembled Monolayers
Carboranedithiol isomers adsorbing with opposite orientations of their dipoles on surfaces are self-assembled together to form mixed monolayers where both lateral dipole–dipole and lateral thiol–thiolate (S–H···S) interactions provide enhanced stability over single-component monolayers. Here, we demonstrate the first instance of the ability to map individual isomers in a mixed monolayer using the model system carboranedithiols on Au{111}. The addition of methyl groups to one isomer provides both an enhanced dipole moment and extra apparent height for differentiation via scanning tunneling microscopy (STM). Associated computational investigations rationalize favorable interactions of mixed pairs and the associated stability changes that arise from these interactions. Both STM images and Monte Carlo simulations yield similarly structured mixed monolayers, where approximately 10% of the molecules have reversed dipole moment orientations but no direct chemical attachment to the surface, leading to homogeneous monolayers with no apparent phase separation. Deprotonating the thiols by depositing the molecules under basic conditions eliminates the lateral S–H···S interactions while accentuating the dipole–dipole forces. The molecular system investigated is composed of isomeric molecules with opposite orientations of dipoles and identical surface packing, which enables the mapping of individual molecules within the mixed monolayers and enables analyses of the contributions of the relatively weak lateral interactions to the overall stability of the assemblies.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Systematic Improvement of Quantum Monte Carlo Calculations in Transition Metal Oxides: sCI-Driven Wavefunction Optimization for Reliable Band Gap Prediction
Accurate determination of the electronic properties of correlated oxides remains a significant challenge for computational theory. Traditional Hubbard-corrected density functional theory (DFT+U) frequently encounters limitations in precisely capturing electron correlation, particularly in predicting band gaps. We introduce a systematic methodology to enhance the accuracy of diffusion Monte Carlo (DMC) simulations for both ground and excited states, focusing on LiCoO 2 as a case study. By employing a selected configuration interaction (sCI) approach, we demonstrate the capability to optimize wavefunctions beyond the constraints of single-reference DFT+U trial wavefunctions. Here, we show that the sCI framework enables accurate prediction of band gaps in LiCoO 2 , closely aligning with experimental values and substantially improving traditional computational methods. The study uncovers a nuanced mixed state of t 2g and e g orbitals at the band edges that is not captured by conventional single-reference methods, further elucidating the limitations of PBE+U in describing d-d excitations. Our findings advocate for the adoption of beyond-DFT methodologies, such as sCI, to capture the essential physics of excited-state wavefunctions in strongly correlated materials. The improved accuracy in band gap predictions and the ability to generate more reliable trial wavefunctions for DMC calculations underscore the potential of this approach for broader applications in the study of correlated oxides. This work not only provides a pathway for more accurate simulations of electronic structures in complex materials but also suggests a framework for future investigations of the excited states of other challenging systems.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Negative Ion Photoelectron Spectroscopy Confirms the Prediction of the Relative Energies of the Low-Lying Electronic States of 2,7-Naphthoquinone
Cryogenic negative ion photoelectron (NIPE) spectra of the radical anion of 2,7-naphthoquinone (NQ•–) have been taken at 20 K, using 193, 240, 266, 300, and 355 nm lasers for electron detachment. The electron affinity of the NQ diradical is determined from the first resolved peak in the NIPE spectrum to be 2.880 ± 0.010 eV. CASPT2/aug-cc-pVDZ calculations predict with reasonable accuracy the positions of the 0–0 bands in the three lowest electronic states of NQ. In addition, the Franck–Condon factors calculated from the CASPT2/aug-cc-pVDZ optimized geometries, vibrational frequencies, and normal modes successfully simulate the vibrational structures in these bands. The NIPE spectrum of NQ•– confirms that, as predicted, 3B2 is the ground state, and the 1B2 and 1A1 states are, respectively, 12.7 and 16.4 kcal/mol higher in energy than the triplet ground state. The experimental value of ?EST = 12.7 kcal/mol in NQ and the finding that 1B2 is the lower energy of the two singlet states confirm the results of the previous calculations on NQ. These calculations predicted an increase in ?EST on the substitution of both methylene groups in 2,7-naphthoquinodimethane (NQDM) by oxygens in NQ, thus providing a dramatic contrast to the decrease of 17.5 kcal/mol in ?EST found for substitution of one methylene group by one oxygen on going from trimethylenemethane (TMM) to oxyallyl (OXA).
Yang, Zheng↗
Entropy-Driven Porous Liquids Allowing Gas Solubility in Solvent-Filled Imine-Based Porous Organic Cages
Porous liquids offer a promising platform for gas separation by combining fluid processability with intrinsic molecular porosity. Traditional Type II porous liquids are formed by dissolving porous molecular cages in size-excluded solvents, limiting solvent options and practical applications. In this work, we introduce a novel method of creating Type II porous liquids using common small solvents, where intrinsic porosity is achieved at elevated pressures due to the selective displacement of solvent molecules by gas molecules within the cage structures. Using molecular simulations, we investigate the behavior of CO 2 in solutions of the imine-based porous organic cage CC13 dissolved in small molecular solvents such as chloroform and 1,2-dimethoxyethane (DME). Grand canonical Monte Carlo simulations of solid-state CC13 reveal that selectivity reversal, where smaller CO 2 molecules displace larger solvent molecules inside the cage, is achievable at sufficiently high pressures. Temperature quench molecular dynamics simulations confirm that while CO 2 displacement within chloroform-filled cages is limited, DME enables entropy-driven cage CO 2 occupancy at pressures as low as ∼23 bar, setting up the foundation of an alternative way of forming Type II porous liquids.
adsorption↗
Computational Study of Indium Oxide Photoelectrodes
Using a combination of first-principles molecular dynamics simulations and electronic structure calculations, we characterize the atomistic structure and vibrational properties of a photocatalytic surface of In 2 O 3 , a promising photoelectrode for the production of hydrogen peroxide. We then investigate the surface in contact with water and show that the electronic states of In 2 O 3 are appropriately positioned in energy to facilitate the two-electron water oxidation reaction (WOR) over the competing four-electron oxygen evolution reaction. In conclusion, we further propose that the use of strained thin films interfaced with water is beneficial in decreasing the optical gap of In 2 O 3 and thus in utilizing a wider portion of the solar spectrum for the WOR.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Symmetry-Breaking and Self-Sorting in Block Copolymer-Based Multicomponent Nanocomposites
Co-assembly of inorganic nanoparticles (NPs) and nanostructured polymer matrix represents an intricate interplay of enthalpic or entropic forces. Particle size largely affects the phase behavior of the nanocomposite. Theoretical studies indicate that new morphologies would emerge when the particles become comparable to the soft matrix's size, but this has rarely been supported experimentally. By designing a multicomponent blend composed of NPs, block copolymer-based supramolecules, and small molecules, a 3-D ordered lattice beyond the native BCP's morphology was recently reported when the particle is larger than the microdomain of BCP. The blend can accommodate various formulation variables. In this work, when the particle size equals the microdomain size, a symmetry-broken phase appears in a narrow range of particle sizes and compositions, which we named the "train track" structure. In this phase, the NPs aligned into a 3-D hexagonal lattice and packed asymmetrically along the c axis, making the projection of the ac and the bc plane resemble train tracks. Computational studies show that the broken symmetry reduces the polymer chain deformation and stabilizes the metastable hexagonally perforated lamellar morphology. Given the mobility of the multicomponent blend, the system shows a self-sorting behavior: segregating into two macroscopic phases with different nanostructures based on only a few nanometers NP size differences. Smaller NPs form "train track" morphology, while larger NPs form a "simple hexagon" structure, where the NPs take a symmetric hexagonal arrangement. Detailed structural evolution and simulation studies confirm the systematic-wide cooperativity across different components, indicating the strong self-regulation of the multicomponent system.
"train track" morphology↗
Thermophilic Chassis-Enabled High-Throughput Selection of a Thermostable Fluorogenic Reporter
Thermostable proteins show increased shelf life and performance at elevated temperatures and under harsh conditions, resulting in lower costs for various industrial and biotechnological applications. However, due to a limited understanding of the relationship between stability and function, protein stabilization remains primarily a trial-and-error approach. Therefore, building a combinatorial library of mutations predicted to improve stability, followed by experimental testing, represents a markedly improved methodology. However, the lack of high-throughput approaches to screen even a moderately sized library presents a major bottleneck in the field. Here, in this study, we use a thermophile, Parageobacillus thermoglucosidasius (Ptherm) to rapidly screen combinatorial libraries consisting of rationally designed thermostabilizing mutations (∼10 3 –10 4 ) of a mesophilic fluorescent reporter, Y-FAST. On a Petri dish, microbial growth at an elevated temperature and exposure to fluorogen yielded several colonies of Ptherm that showed distinct fluorescence at 55 and 68 °C in our two sequentially generated libraries using Rosetta and ProteinMPNN, respectively. The Y-FAST variants isolated from fluorescent colonies were brighter than Y-FAST and showed higher resistance to thermal and chemical denaturation. AlphaFold-predicted structures and MD simulations revealed stability-enhancing salt bridges and hydrogen bond networks in the isolated FAST variants. The moderately thermostable FAST (tsFAST) and hyperstable FAST (hsFAST) were then demonstrated as translation reporters for protein expression and folding at elevated temperatures, such as 55 and 68 °C. Our approach of combinatorial library generation and high-throughput screening in a thermophilic chassis could, in principle, be extended to other proteins fused to these translation reporters. Furthermore, the hsFAST protein is small─half the size of the green fluorescent protein─and does not require oxygen for maturation, making it ideal for engineering extremophilic anaerobes for biosensing and bioconversion.
59 BASIC BIOLOGICAL SCIENCES↗
UV-Photochemistry of the Disulfide Bond: Evolution of Early Photoproducts from Picosecond X-ray Absorption Spectroscopy at the Sulfur K-Edge
We have investigated dimethyl disulfide as the basic moiety for understanding the photochemistry of disulfide bonds, which are central to a broad range of biochemical processes. Picosecond time-resolved X-ray absorption spectroscopy at the sulfur K-edge provides unique element-specific insight into the photochemistry of the disulfide bond initiated by 267 nm femtosecond pulses. We observe a broad but distinct transient induced absorption spectrum which recovers on at least two time scales in the nanosecond range. We then employed RASSCF electronic structure calculations to simulate the sulfur-1s transitions of multiple possible chemical species, and identified the methylthiyl and methylperthiyl radicals as the primary reaction products. In addition, we identify disulfur and the CH 2 S thione as the secondary reaction products of the perthiyl radical that are most likely to explain the observed spectral and kinetic signatures of our experiment. Our study underscores the importance of elemental specificity and the potential of time-resolved X-ray spectroscopy to identify short-lived reaction products in complex reaction schemes that underlie the rich photochemistry of disulfide systems.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Pore‐Scale Modeling of Reactive Transport with Coupled Mineral Dissolution and Precipitation
Abstract We present a new pore‐scale model for multicomponent advective‐diffusive transport with coupled mineral dissolution and precipitation. Both dissolution and precipitation are captured simultaneously by introducing a phase transformation vector field representing the direction and magnitude of the overall phase change. An effective viscosity model is adopted in simulating fluid flow during mineral dissolution‐precipitation that can accurately capture the velocity field without introducing any empirical parameters. The proposed approach is validated against analytical solutions and interface tracking simulations in simplified structures. After validation, the proposed approach is employed in modeling realistic rocks where mineral dissolution and precipitation are dominant at different locations. We have identified three regimes for mineral dissolution‐precipitation coupling: (a) compact dissolution‐precipitation where dissolution is dominant near the inlet and precipitation is dominant near the outlet, (b) wormhole dissolution with clustered precipitation where dissolution generates wormholes in the main flow paths and precipitation clogs the secondary flow paths, and (c) dissolution dominant where all solid grains are gradually dissolved. In the three regimes, the proposed approach provides reliable porosity‐permeability relationships that cannot be described well by traditional macroscale models. We find that the permeability can increase while the overall porosity decreases when the main flow paths are expanded by dissolution and adjacent pore spaces are clogged by precipitation.
58 GEOSCIENCES↗
Enhancing selectivity of cation exchange with anion receptors
Here, we introduce a new supramolecular strategy where an anion receptor modifies the selectivity ligands for cations. This is demonstrated by combining the classic anion receptor calix[4]pyrrole (C4P) and a phenolic ligand, which leads to remarkable enhancement in selectivity for Cs + over Na + . Crystal structures and molecular simulations confirmed the persistent formation of ion-pair C4P–Cs + –phenolate complexes, while the smaller Na + ion cannot efficiently interact.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
The O K -2 V spectrum of CO: the influence of the second core-hole
Using synchrotron radiation in the tender X-ray regime, a photoelectron spectrum showing the formation of single site double-core-hole pre-edge states, involving the K shell of the O atom in CO, has been recorded by means of high-resolution electron spectroscopy. The experimentally observed structures have been simulated, interpreted and assigned, employing state-of-the-art ab initio quantum chemical calculations, on the basis of a theoretical model, accounting for their so-called direct or conjugate character. Features appearing above the double ionization threshold have been reproduced by taking into account the strong mixing between multi-excited and continuum states. The shift of the σ* resonance below the double ionization threshold, in combination with the non-negligible contributions of multi-excited configurations in the final states reached, gives rise to a series of avoided crossings between the different potential energy curves.
74 ATOMIC AND MOLECULAR PHYSICS↗
Ab initio molecular dynamics on quantum computers
Ab initio molecular dynamics (AIMD) is a valuable technique for studying molecules and materials at finite temperatures where the nuclei evolve on potential energy surfaces obtained from accurate electronic structure calculations. In this work, we present an approach to running AIMD simulations on noisy intermediate-scale quantum (NISQ)-era quantum computers. The electronic energies are calculated on a quantum computer using the variational quantum eigensolver (VQE) method. Algorithms for computation of analytical gradients entirely on a quantum computer require quantum fault-tolerant hardware, which is beyond NISQ-era. Therefore, we compute the energy gradients numerically using finite differences, the Hellmann-Feynman theorem, and a correlated sampling technique. This method only requires additional classical calculations of electron integrals for each degree of freedom without any additional computations on a quantum computer beyond the initial VQE run. As a proof of concept, AIMD simulations are demonstrated for the H-2 molecule on IBM quantum devices. In addition, we demonstrate the validity of the method for larger molecules using full configuration interaction wave functions. As quantum hardware and noise mitigation techniques continue to improve, the method can be utilized for studying larger molecular systems.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Solvation governs cation transference in glyme-based lithium battery electrolytes
The efficacy of electrochemical systems is governed by the cation transference number, which represents the fraction of current carried by the working ion. Energy is wasted when field-induced motion also drives anions and solvent molecules, decreasing the transference number to near-zero. We present a systematic study of cation transference in a series of electrolytes: tetraglyme (TG), octaglyme (OG), and poly(ethylene oxide) (PEO) mixed with lithium bis(trifluoromethanesulfonyl)imide. In all three electrolytes, starting from the dilute salt concentration limit, the experimentally measured cation transference number decreases with increasing concentration, reaching a minimum between -0.1 and -0.2, before rising back to positive values. Explicit measurements of field-induced species' velocities by electrophoretic nuclear magnetic resonance indicate that negative cation transference numbers in TG and OG electrolytes are dictated by solvation interactions with minimal contribution from anion-cation interactions. Simulation-based solvation structures indicate that OG serves as a bridge between TG and PEO. Multi-charge positive clusters, which are negligible in TG, become increasingly important at higher chain lengths (OG and PEO). As migrating cations drag their solvation shells, this solvation-induced motion is amplified in glyme electrolytes because of covalent interactions between solvating glyme molecules and free glyme molecules.
Im, Julia↗
Nonlinear Alfvén instability simulation and EP transport for ITER reversed shear (steady-state) and monotonic q-profile regimes *
The nonlinear evolution and dynamics of energetic particle (EP) driven instabilities in both steady-state (reversed shear q-profile) and monotonic q-profile regimes of ITER are examined using the global gyro-Landau closure model FAR3d. Both neutral beam and alpha components are included, leading to synergistic effects between the two populations. In order to maintain computational feasibility, the present nonlinear simulation includes all toroidal mode numbers ranging from n = 0 to 15. It cannot be excluded that n’s above this range could introduce larger linear growth rates; however, as indicated from the results, the n = 0 to 15 range is sufficient to provide a strong linear drive and significant nonlinear transport effects. While the toroidal mode numbers n = 6,13 dominate the linear instability growth phase, nonlinear energy transfers in the saturated phase reverse this trend, leading to the dominance of lower n’s in the saturated phase of the simulation. Zonal flow structure generation and EP density flattening are further consequences of the nonlinear phase. The density profile flattening is caused by collectively driven EP radial transport fluxes, which have non-local characteristics. Instantaneous alpha particle transport fluxes are significant (Γ α ~ 2 x 10 20 m –2 s –1 ) for the reversed shear regime and lower (Γ α ~ 1.1 x 10 20 m –2 s –1 ) for the monotonic q-profile case.
AE↗
High-pressure structural behavior of silicon telluride Si2Te3 nanoplates
The high-pressure behavior of silicon telluride (Si2Te3), a two-dimensional (2D) layered material, was investigated using synchrotron x-ray powder diffraction in a diamond anvil cell to 11.5GPa coupled with first-principles theory. Si2Te3 undergoes a phase transition at <1GPa from a trigonal to a hexagonal crystal structure. At higher pressures (>8.5GPa), x-ray diffraction showed the appearance of new peaks possibly coincident with a new phase transition, though we suspect Si2Te3 retains a hexagonal structure. Density functional theory calculations of the band structure reveal metallization above 9.1GPa consistent with previous measurements of the Raman spectra and disappearance of color and transparency at pressure. The theoretical Raman spectra reproduce the prominent features of the experiment, though a deeper analysis suggests that the orientation of Si dimers dramatically influences the vibrational response. Given the complex structure of Si2Te3, simulation of the resulting high-pressure phase is complicated by disordered vacancies and the initial orientations of Si–Si dimers in the crushed layered phase.
Li, Bohan↗
In situ analysis of the structural transformation of glassy carbon under compression at room temperature
Room temperature compression of graphitic materials leads to interesting superhard sp 3 rich phases which are sometimes transparent. In the case of graphite itself, the sp 3 rich phase is proposed to be monoclinic M-carbon; however, for disordered materials such as glassy carbon the nature of the transformation is unknown. We compress glassy carbon at room temperature in a diamond anvil cell, examine the structure in situ using x-ray diffraction, and interpret the findings with molecular dynamics modeling. Experiment and modeling both predict a two-stage transformation. First, the isotropic glassy carbon undergoes a reversible transformation to an oriented compressed graphitic structure. This is followed by a phase transformation at ~35 GPa to an unstable, disordered sp 3 rich structure that reverts on decompression to an oriented graphitic structure. Analysis of the simulated sp 3 rich material formed at high pressure reveals a noncrystalline structure with two different sp 3 bond lengths.
75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
Metamagnetism of few-layer topological antiferromagnets
MnBi 2 Te 4 (MBT) materials are a promising class of antiferromagnetic topological insulators whose films provide access to novel and technologically important topological phases, including quantum anomalous Hall states and axion insulators. MBT device behavior is expected to be sensitive to the various collinear and noncollinear magnetic phases that are accessible in applied magnetic fields. Here, we use classical Monte Carlo simulations and electronic structure models to calculate the ground state magnetic phase diagram as well as topological and optical properties for few-layer films with up to six septuple layers. Using magnetic interaction parameters appropriate for MBT, we find that it is possible to prepare a variety of different magnetic stacking sequences, some of which have sufficient symmetry to disallow nonreciprocal optical response and Hall transport coefficients. Other stacking arrangements do yield large Faraday and Kerr signals, even when the ground state Chern number vanishes.
36 MATERIALS SCIENCE↗