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At least 235 records · Page 13

Bridging the gap between molecules and materials in quantum chemistry with localized active spaces

The number of materials that “bridge the gap” between single molecules and extended solids, such as metal-organic frameworks and organic semiconductors, has been increasing. Consequently, there is a growing need for modeling approaches that effectively integrate the real-space molecular perspective employed by computational chemists and the reciprocal-space dispersive perspective employed by computational physicists. Here, we propose the localized active space (LAS) approach as a promising method to successfully bridge this gap. The LAS approach extends the active space concept from multiconfigurational methods such as complete active space self-consistent field theory to multiple molecular fragments via a product-form wave function ansatz. Here, we apply this method to solid state phenomena by treating each unit cell as a fragment with different sets of local quantum numbers (e.g., charge and excitation number). State interaction between these LAS states (LASSI) thus provides a comprehensive basis for the study of charge and energy transfer, meeting and surpassing the capabilities of single-reference fragmentation approaches such as constrained density functional theory (cDFT). Most centrally, we show how combining this LASSI approach with multiconfigurational pair-density functional theory (MC-PDFT) provides an elegant and efficient method to compute band structures that capture multiconfigurational character. We apply the LASSI band structure approach to the computation of band gaps in stretched hydrogen chain, polyacetylene, and bulk nickel oxide (NiO), finding good or excellent quantitative agreement with reference values in all cases. Additionally, we use the LAS basis in one-dimensional model systems to demonstrate its ability to treat difficult solid-state phenomena such as exciton transfer and excitation at p-n junctions.

method development↗

Fused-ring isomerism modulates molecular packing and device performance in non-halogenated organic solar cells

Subtle changes in molecular backbone geometry impact intermolecular interactions and performance of organic solar cells. Here, three isomeric small-molecule acceptors (NaO1, NaO2, and NaO3) are investigated to reveal how different fused-ring configurations control molecular packing, electronic coupling, and film formation. Structural and spectroscopic analyses show that the linearly fused NaO1 forms a compact three-dimensional packing network with large and balanced electronic couplings (>24 meV) across multiple directions, while the more curved analogues exhibit excessive crystallization and phase segregation. In-situ optical measurements demonstrate that NaO1 promotes fast and continuous structural evolution during film formation, resulting in smooth morphology and homogeneous phase distribution. These structural and dynamic advantages facilitate efficient charge generation and transport, accompanied by reduced non-radiative energy loss, ultimately achieving an efficiency of 20.07% for non-halogenated ternary devices. Our findings highlight how fused-ring isomerism decisively governs structure–packing–performance relationships in organic solar cells.

36 MATERIALS SCIENCE↗

Small-molecule modulation of β-arrestins

β-Arrestins are multifunctional regulators of G-protein-coupled receptor (GPCR) signalling and orchestrate diverse downstream signalling events and physiological responses across the GPCR superfamily. Although GPCR pharmacology has advanced to target orthosteric and allosteric sites, as well as G proteins and GPCR kinases, direct chemical tools to modulate β-arrestin activities have remained conspicuously absent. Here we report the identification of small-molecule inhibitors that selectively target β-arrestins and delineate their mechanism of action through integrated pharmacological, biochemical, biophysical and structural analyses. These inhibitors disrupt β-arrestin engagement with agonist-activated GPCRs, impairing desensitization, internalization and β-arrestin-dependent physiological functions while sparing G protein–receptor coupling. Cryo-electron microscopy, molecular dynamics simulations and structure-guided mutagenesis reveal that one modulator, Cmpd-5, engages a pocket within the central crest of β-arrestin1 formed by the middle, C and lariat loops, a critical receptor-binding interface, stabilizing a distinct conformation that is incompatible with full β-arrestin–receptor engagement. Together, these findings establish a mechanistic framework for β-arrestin modulation, reveal a novel allosteric site for structure-based drug design, and open new avenues for transducer-targeted, pathway-specific GPCR therapeutic agents.

Kahsai, Alem W. [Duke University, Durham, NC (Unit↗

Accuracy of XAS theory for unraveling structural changes of adsorbates: CO on Ni(100)

Studying surface reactions using ultrafast optical pump and X-ray probe experiments relies on accurate calculations of X-ray spectra of adsorbates for correct identification of the spectral signatures and their dynamical evolution. We show that experimental XAS can be well reproduced for the different binding sites in a static prototype system CO/Ni(100) at a standard DFT (GGA) level of theory, using a plane-wave basis and pseudopotentials. This validates its utility in analyzing ultrafast X-ray probe experiments. The accuracy of computed relative core level binding energies is about 0.2 eV, representing a lower limit for which spectral features can be resolved with this method. We also show that the commonly used Z +1 approximation gives very good core binding energy shifts overall. However, we find a discrepancy for CO adsorbed in the hollow site, which we assign to the significantly stronger hybridization in hollow bonding than in on-top.

74 ATOMIC AND MOLECULAR PHYSICS↗

Erratum: “Breaking covalent bonds in the context of the many-body expansion (MBE). I. The purported ‘first row anomaly’ in XH n (X = C, Si, Ge, Sn; n = 1–4)” [J. Chem. Phys. 156, 244303 (2022)]

We have noted typographical errors in TABLE V of J. Chem. Phys. 156, 244303 (2022). Specifically, the values of the angles φ HχH for the XH 2 species in both the ( 3 B 1 ) and ( 1 A 1 ) states were incorrectly reported as half of the correct values. Additionally, the values of the same angles for the XH 3 and XH 4 species were reported correctly.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

PigmentHunter: A point-and-click application for automated chlorophyll-protein simulations

Chlorophyll proteins (CPs) are the workhorses of biological photosynthesis, working together to absorb solar energy, transfer it to chemically active reaction centers, and control the charge-separation process that drives its storage as chemical energy. Yet predicting CP optical and electronic properties remains a serious challenge, driven by the computational difficulty of treating large, electronically coupled molecular pigments embedded in a dynamically structured protein environment. To address this challenge, we introduce here an analysis tool called PigmentHunter, which automates the process of preparing CP structures for molecular dynamics (MD), running short MD simulations on the nanoHUB.org science gateway, and then using electrostatic and steric analysis routines to predict optical absorption, fluorescence, and circular dichroism spectra within a Frenkel exciton model. Inter-pigment couplings are evaluated using point-dipole or transition-charge coupling models, while site energies can be estimated using both electrostatic and ring-deformation approaches. The package is built in a Jupyter Notebook environment, with a point-and-click interface that can be used either to manually prepare individual structures or to batch-process many structures at once. Here, we illustrate PigmentHunter’s capabilities with example simulations on spectral line shapes in the light harvesting 2 complex, site energies in the Fenna–Matthews–Olson protein, and ring deformation in photosystems I and II.

14 SOLAR ENERGY↗

Rotational coherence dominates early-time dynamics and produces long-time revivals in the S 2 state of azulene

Here, the ultrafast dynamics of azulene have been debated for decades, with reported picosecond decay constants variously attributed to intramolecular vibrational redistribution (IVR), internal conversion, or rotational dephasing. Using polarization- and femtosecond time-resolved resonance-enhanced multiphoton ionization spectroscopy with a nanosecond delay window, we disentangle this long-standing inconsistency and show that the early 2–5 ps decay component arises entirely from the rotational dephasing of an excited-state wavepacket. Identical time constants extracted from the decay of the parallel signal and the rise of the perpendicular signal across multiple vibronic origins provide an unambiguous rotational anisotropy signature, eliminating the need for IVR-based interpretations. Extending the measurement window to 1.3 ns reveals well-structured J-type and C-type rotational coherence revivals in S 2 azulene on top of the well-documented fluorescence decay, demonstrating that both the short- and long-time dynamics contain information about the coherent rotational dynamics. These results show that azulene, and by extension polycyclic aromatic hydrocarbons, can sustain structured rotational coherence deep into the nanosecond regime, positioning PAHs as model systems for quantum-coherent wavepacket dynamics and providing a framework for probing coherence, decoherence, and rotational control in electronically rich molecular systems.

Zhan, Jie [University of Georgia, Athens, GA (Unit↗

A chemical dynamics study on the gas-phase formation of triplet and singlet C 5 H 2 carbenes

Significance Carbenes represent key reactive intermediates in molecular mass growth processes leading to carbonaceous nanostructures in the interstellar medium and in combustion systems. However, due to their short lifetimes and tendency for dimerization, carbenes represent one of the foremost obscured classes of reactive intermediates, with the preparation of carbenes in the gas phase remaining largely elusive. By merging molecular beams with electronic structure and quasi-classical trajectory calculations and exploiting triplet pentadiynylidene (HCCCCCH) and singlet ethynylcyclopropenylidene (c-C 5 H 2 ) carbene as benchmarks, we present a versatile protocol to unravel the dynamics leading to exotic carbenes under single-collision conditions. These elementary mechanisms are of significance to our understanding of the fundamental processes leading to unsaturated organic transients in extreme, hydrocarbon-rich environments.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Isotopic and vibrational-level dependence of H 2 dissociation by electron impact

The low-energy electron-impact dissociation of molecular hydrogen has been a source of disagreement between various calculations and measurements for decades. Excitation of the ground state of H 2 into the dissociative b 3 $Σ$$$^{+}_{u}$ state is now well understood, with the most recent measurements being in excellent agreement with the molecular convergent close-coupling (MCCC) calculations of both integral and differential cross sections [Zawadzki et al., Phys. Rev. A 98, 062704 (2018)]. However, in the absence of similar measurements for vibrationally excited or isotopically substituted H 2 , cross sections for dissociation of these species must be determined by theory alone. We have identified large discrepancies between MCCC calculations and the recommended R-matrix cross sections for dissociation of vibrationally excited H 2 , D 2 , T 2 , HD, HT, and DT [Trevisan et al., Plasma Phys. Contr. Fusion 44 1263 (2002); Plasma Phys. Contr. Fusion 44, 2217 (2002)], with disagreement in both the isotope effect and dependence on initial vibrational level. Furthermore, we investigate the source of the discrepancies, and discuss the consequences for plasma models, which have incorporated the previously recommended data.

74 ATOMIC AND MOLECULAR PHYSICS↗

Imaging the Progression of Radiolytic Damage in Molecular Crystals with Scanning Nanobeam Electron Diffraction

Almost every electron microscopy experiment is fundamentally limited by radiation damage. Nevertheless, little is known about the onset and progression of radiolysis in beam-sensitive materials. Here we apply ambient-temperature scanning nanobeam electron diffraction to record simultaneous dual-space movies of organic and organometallic nanocrystals at sequential stages of beam-induced radiolytic decay. We show that the underlying mosaic of coherently diffracting domains undergoes internal rearrangement as a function of accumulating electron fluence, causing the intensities of some associated Bragg reflections to fade nonmonotonically. Furthermore, we demonstrate that repeated irradiation at a single probe position leads to the isotropic propagation of delocalized radiolytic damage well beyond the direct footprint of the incident beam. We refer to these expanding tides of amorphization as “impact craters.”

59 BASIC BIOLOGICAL SCIENCES↗

Promising approaches for the assembly of the catalytically active, recombinant Desulfomicrobium baculatum hydrogenase with substitutions at the active site

Background: Hydrogenases (H2ases) are metalloenzymes capable of the reversible conversion of protons and electrons to molecular hydrogen. Exploiting the unique enzymatic activity of H2ases can lead to advancements in the process of biohydrogen evolution and green energy production. Results: Here we created of a functional, optimized operon for rapid and robust production of recombinant [NiFe] Desulfomicrobium baculatum hydrogenase (Dmb H2ase). The conversion of the [NiFeSe] Dmb H2ase to [NiFe] type was performed on genetic level by site-directed mutagenesis. The native dmb operon includes two structural H2ase genes, coding for large and small subunits, and an additional gene, encoding a specific maturase (protease) that is essential for the proper maturation of the enzyme. Dmb, like all H2ases, needs intricate bio-production machinery to incorporate its crucial inorganic ligands and cofactors. Strictly anaerobic, sulfate reducer D. baculatum bacteria are distinct, in terms of their biology, from E. coli. Thus, we introduced a series of alterations within the native dmb genes. As a result, more than 100 elements, further compiled into 32 operon variants, were constructed. The initial requirement for a specific maturase was omitted by the artificial truncation of the large Dmb subunit. The assembly of the produced H2ase subunit variants was investigated both, in vitro and in vivo. This approach resulted in 4 recombinant [NiFe] Dmb enzyme variants, capable of H 2 evolution. The aim of this study was to overcome the gene expression, protein biosynthesis, maturation and ligand loading bottlenecks for the easy, fast, and cost-effective delivery of recombinant [NiFe] H2ase, using a commonly available E. coli strains. Conclusion: The optimized genetic constructs together with the developed growth and purification procedures appear to be a promising platform for further studies toward fully-active and O 2 tolerant, recombinant [NiFeSe] Dmb H2ase, resembling the native Dmb enzyme. It could likely be achieved by selective cysteine to selenocysteine substitution within the active site of the [NiFe] Dmb variant.

59 BASIC BIOLOGICAL SCIENCES↗

Octave-spanning mid-infrared femtosecond OPA in a ZnGeP 2 pumped by a 2.4 μm Cr:ZnSe chirped-pulse amplifier

We report on the highly efficient, octave-spanning mid-infrared (mid-IR) optical parametric amplification (OPA) in a ZnGeP 2 (ZGP) crystal, pumped by a 1 kHz, 2.4 μm, 250 fs Cr:ZnSe chirped-pulse amplifier. The full spectral coverage of 3−10 μm with the amplified signal and idler beams is demonstrated. The signal beam in the range of ∼3 − 5 μm is produced by either white light generation (WLG) in YAG or optical parametric generation (OPG) in ZGP using the common 2.4 μm pump laser. We demonstrate the pump to signal and idler combined conversion efficiency of 23% and the pulse energy of up to 130 μJ with ∼2 μJ OPG seeding, while we obtain the efficiency of 10% and the pulse energy of 55 μJ with ∼0.2 μJ WLG seeding. The OPA output energy is limited by the available pump pulse energy (0.55 mJ at ZGP crystal) and therefore further energy scaling is feasible with multi-stage OPA and higher pump pulse energy. The autocorrelation measurements based on random quasi-phase matching show that the signal pulse durations are ∼318 fs and ∼330 fs with WLG and OPG seeding, respectively. In addition, we show the spectrally filtered 30 μJ OPA output at 4.15 μm suitable for seeding a Fe:ZnSe amplifier. Our ultrabroadband femtosecond mid-IR source is attractive for various applications, such as strong-field interactions, dielectric laser electron acceleration, molecular spectroscopy, and medical surgery.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Table-Top High Photon Energy Sources for Chemical Dynamics Investigations

Time-resolved spectroscopies using high-energy photons in the vacuum ultraviolet (VUV) to the X-ray region of the electromagnetic spectrum, have proven to be powerful probes of chemical dynamics. These high-energy photons can access valence and core orbitals of molecules and materials, providing key information on molecular and electronic structure and their time evolution. This report details the development of table-top sources of extreme ultraviolet (XUV) and VUV pulses at Sandia National Laboratories for use in studies of gas phase chemical dynamics. Femtosecond duration XUV pulses are produced using laser-driven high harmonic generation and their detected range span ~40-140 eV photon energies. These pulses are used in conjunction with ultraviolet pulses in a pump-probe scheme to study excited state dynamics of gas phase molecules. VUV pulses at 7.75 eV are generated using a four-wave-mixing scheme driven by 800 nm and 266 nm pulses in an argon-filled hollow-core fiber.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Scalable Heterogeneous Execution of a Coupled-Cluster Model with Perturbative Triples

The CCSD(T) coupled-cluster model with perturbative triples is considered a gold standard for computational modeling of the correlated behavior of electrons in molecular systems. A fundamental constraint is the relatively small global-memory capacity in GPUs compared to the main-memory capacity on host nodes, necessitating relatively smaller tile sizes for high-dimensional tensor contractions in NWChem's GPU-accelerated implementation of the CCSD(T) method. A coordinated redesign is described to address this limitation and associated data movement overheads, including a novel fused GPU kernel for a set of tensor contractions, along with inter-node communication optimization and data caching. The new implementation of GPU-accelerated CCSD(T) improves overall performance by 3.4x. Finally, we discuss the trade-offs in using this fused algorithm on current and future supercomputing platforms.

Kim, Jinsung↗

Seeing structural evolution of organic molecular nano-crystallites using 4D scanning confocal electron diffraction (4D-SCED)

Abstract Direct observation of organic molecular nanocrystals and their evolution using electron microscopy is extremely challenging, due to their radiation sensitivity and complex structure. Here, we introduce 4D-scanning confocal electron diffraction (4D-SCED), which enables direct in situ observation of bulk heterojunction (BHJ) thin films. 4D-SCED combines confocal electron optic setup with a pixelated detector to record focused spot-like diffraction patterns with high angular resolution, using an order of magnitude lower dose than previous methods. We apply it to study an active layer in organic solar cells, namely DRCN5T:PC 71 BM BHJ thin films. Structural details of DRCN5T nano-crystallites oriented both in- and out-of-plane are imaged at ~5 nm resolution and dose budget of ~5 e − /Å 2 . We use in situ annealing to observe the growth of the donor crystals, evolution of the crystal orientation, and progressive enrichment of PC 71 BM at interfaces. This highly dose-efficient method opens more possibilities for studying beam sensitive soft materials.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Structural Gating Enhances Long-Distance Light-Driven Interfacial Electron Transfer

Structural gating provides a molecular means to transfer electrons preferentially in one desired vectorial direction, a behavior needed for applications in artificial photosynthesis. At the interfaces utilized herein, visible-light absorption by a transition metal complex opens a “structural gate” by planarization of otherwise rotating phenyl rings in p-phenylene ethynylene (PE) bridge units. Planarization provides a conjugated pathway for electron flow toward a conductive oxide surface. Interfacial electron transfer to the oxide restores rotation and closes the gate to the unwanted recombination reaction. This structural gating results in nearly quantitative long-distance (>20 Å) interfacial electron transfer that occurs ~1000 times faster than transfer in the opposite direction. A comparative kinetic study of these complexes with those that contain ionic bridge units, without gating function, as a function of the applied potential and hence –ΔG° provided a physical basis for the structural gating. A small distance-dependent reorganization energy with weak electronic coupling underlies the success of this gate that enables efficient long-distance electron transfer and slow recombination.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Unraveling the mechanism of tip-enhanced molecular energy transfer

Electronic Energy Transfer (EET) between chromophores is fundamental in many natural light-harvesting complexes, serving as a critical step for solar energy funneling in photosynthetic plants and bacteria. The complicated role of the environment in mediating this process in natural architectures has been addressed by recent scanning tunneling microscope experiments involving EET between two molecules supported on a solid substrate. These measurements demonstrated that EET in such conditions has peculiar features, such as a steep dependence on the donor-acceptor distance, reminiscent of a short-range mechanism more than of a Förster-like process. By using state of the art hybrid ab initio/electromagnetic modeling, here we provide a comprehensive theoretical analysis of tip-enhanced EET. In particular, we show that this process can be understood as a complex interplay of electromagnetic-based molecular plasmonic processes, whose result may effectively mimic short range effects. Therefore, the established identification of an exponential decay with Dexter-like effects does not hold for tip-enhanced EET, and accurate electromagnetic modeling is needed to identify the EET mechanism.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗