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All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Synthesis and Post-Processing of Chemically Homogeneous Nanothreads from 2,5-Furandicarboxylic Acid

Compared with conventional, solution-phase approaches, solid-state reaction methods can provide unique access to novel synthetic targets. Nanothreads—one-dimensional diamondoid polymers formed through the compression of small molecules—represent a new class of materials produced via solid-state reactions, however, the formation of chemically homogeneous products with targeted functionalization represents a persistent challenge. Through careful consideration of molecular precursor stacking geometry and functionalization, we report here the scalable synthesis of chemically homogeneous, functionalized nanothreads through the solid-state polymerization of 2,5-furandicarboxylic acid. The resulting product possesses high-density, pendant carboxyl functionalization along both sides of the backbone, enabling new opportunities for the post-synthetic processing and chemical modification of nanothread materials applicable to a broad range of potential applications.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Correlation of Broad Absorption Band with Small Singlet‐Triplet Energy Gap in Organic Photovoltaics

Abstract Organic photovoltaics (OPV) are one of the most effective ways to harvest renewable solar energy, with the power conversion efficiency (PCE) of the devices soaring above 19 % when processed with halogenated solvents. The superior photocurrent of OPV over other emerging photovoltaics offers more opportunities to further improve the efficiency. Tailoring the absorption band of photoactive materials is an effective way to further enhance OPV photocurrent. However, the field has mostly been focusing on improving the near‐infrared region photo‐response, with the absorption shoulders in short‐wavelength region (SWR) usually being neglected. Herein, by developing a series of non‐fullerene acceptors (NFAs) with varied side‐group conjugations, we observe an enhanced SWR absorption band with increased side‐group conjugation length. The underpinning factors of how molecular structures and geometries improve SWR absorption are clearly elucidated through theoretical modelling and crystallography. Moreover, a clear relationship between the enhanced SWR absorption and reduced singlet‐triplet energy gap is established, both of which are favorable for the OPV performance and can be tailored by rational structure design of NFAs. Finally, the rationally designed NFA, BO‐TTBr, affords a decent PCE of 18.5 % when processed with a non‐halogenated green solvent.

Chemistry↗
DOE OSTI2020

ELSI — An open infrastructure for electronic structure solvers

Routine applications of electronic structure theory to molecules and periodic systems need to compute the electron density from given Hamiltonian and, in case of non-orthogonal basis sets, overlap matrices. System sizes can range from few to thousands or, in some examples, millions of atoms. Different discretization schemes (basis sets) and different system geometries (finite non-periodic vs. infinite periodic boundary conditions) yield matrices with different structures. The ELectronic Structure Infrastructure (ELSI) project provides an open-source software interface to facilitate the implementation and optimal use of high-performance solver libraries covering cubic scaling eigensolvers, linear scaling density-matrix-based algorithms, and other reduced scaling methods in between. In this paper, we present recent improvements and developments inside ELSI, mainly covering (1) new solvers connected to the interface, (2) matrix layout and communication adapted for parallel calculations of periodic and/or spin-polarized systems, (3) routines for density matrix extrapolation in geometry optimization and molecular dynamics calculations, and (4) general utilities such as parallel matrix I/O and JSON output. The ELSI interface has been integrated into four electronic structure code projects (DFTB+, DGDFT, FHI-aims, SIESTA), allowing us to rigorously benchmark the performance of the solvers on an equal footing. Based on results of a systematic set of large-scale benchmarks performed with Kohn–Sham density-functional theory and density-functional tight-binding theory, we identify factors that strongly affect the efficiency of the solvers, and propose a decision layer that assists with the solver selection process. As a result, we describe a reverse communication interface encoding matrix-free iterative solver strategies that are amenable, e.g., for use with planewave basis sets.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2024

Ferromagnetic Exchange and Slow Magnetic Relaxation in Cobalt Bis(1,2-dithiolene)-Bridged Dilanthanide Complexes

The construction of multinuclear lanthanide-based molecules with significant magnetic exchange interactions represents a key challenge in the realization of single-molecule magnets with high operating temperatures. Here, we report the synthesis and magnetic characterization of two series of heterobimetallic compounds, (Cp* 2 Ln) 2 (μ-Co(pdt) 2 ) (Ln = Y 3+ , Gd 3+ , Dy 3+ ; pdt 2– = 1,2-diphenylethylenedithiolate) and [K(18-crown-6)][(Cp* 2 Ln) 2 (μ-Co(pdt) 2 )] (Ln = Y 3+ , Gd 3+ ), featuring two lanthanide centers bridged by a cobalt bis(1,2-dithiolene) complex. Dc magnetic susceptibility data collected for the Gd congeners indicate significant Gd–Co ferromagnetic exchange interactions with fits affording J = +11.5 and +7.33 cm –1 , respectively. Magnetization decay and ac magnetic susceptibility measurements carried out on the single-molecule magnet (Cp* 2 Dy) 2 (μ-Co(pdt) 2 ) reveal full suppression of quantum tunneling and open-loop hysteresis persisting up to 3.5 K. These results, along with those of high-field EPR spectroscopy, suggest that transition metalloligands can enforce strong exchange interactions with adjacent lanthanide centers while maintaining a geometry that preserves molecular anisotropy. Furthermore, the magnetic properties of [K(18-crown-6)][(Cp* 2 Gd) 2 (μ-Co(pdt) 2 )] show that increasing the spin of the ground state of the bridging complex may be a viable alternative to increasing J in obtaining well-isolated, strongly coupled magnetic ground states.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Accurate Hellmann–Feynman forces from density functional calculations with augmented Gaussian basis sets

The Hellmann–Feynman (HF) theorem provides a way to compute forces directly from the electron density, enabling efficient force calculations for large systems through machine learning (ML) models for the electron density. The main issue holding back the general acceptance of the HF approach for atom-centered basis sets is the well-known Pulay force which, if naively discarded, typically constitutes an error upward of 10 eV/Å in forces. In this work, we demonstrate that if a suitably augmented Gaussian basis set is used for density functional calculations, the Pulay force can be suppressed, and HF forces can be computed as accurately as analytical forces with state-of-the-art basis sets, allowing geometry optimization and molecular dynamics to be reliably performed with HF forces. Our results pave a clear path forward for the accurate and efficient simulation of large systems using ML densities and the HF theorem.

Pathak, Shivesh (ORCID:0000000172798195)↗
DOE OSTI2020

Exotic Photonic Molecules via Lennard-Jones-like Potentials

Ultracold systems offer an unprecedented level of control of interactions between atoms. An important challenge is to achieve a similar level of control of the interactions between photons. Towards this goal, we propose a realization of a novel Lennard-Jones-like potential between photons coupled to the Rydberg states via electromagnetically induced transparency (EIT). This potential is achieved by tuning Rydberg states to a Förster resonance with other Rydberg states. In this work, we consider few-body problems in 1D and 2D geometries and show the existence of self-bound clusters (“molecules”) of photons. We demonstrate that for a few-body problem, the multibody interactions have a significant impact on the geometry of the molecular ground state. This leads to phenomena without counterparts in conventional systems: For example, three photons in two dimensions preferentially arrange themselves in a line configuration rather than in an equilateral-triangle configuration. Our result opens a new avenue for studies of many-body phenomena with strongly interacting photons.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2020

Hydrogen-Bonded Organic Frameworks: A Rising Class of Porous Molecular Materials

Hydrogen-bonded organic frameworks (HOFs) are a class of porous molecular materials that rely on the assembly of organic building blocks by means of hydrogen-bonding interactions to form two-dimensional (2D) and three-dimensional (3D) crystalline networks. The reversible nature of the hydrogen-bond formation endows HOFs with the attributes of solution processability and simple regeneration. High-quality single crystals of HOFs can be grown easily for unambiguous superstructure determination by single-crystal X-ray diffraction, which is crucial for the elucidation of superstructure–property relationships. During the past decade, considerable progress has been achieved in realizing stable HOFs with permanent porosities by focusing on the design of molecular building blocks in order to introduce rigidity, auxiliary [π···π] interactions, and interpenetration of their frameworks to sustain the extended networks. The applications of HOFs are far-reaching, spanning catalysis, energy, and biomedical products as well as the storage and separation of fine chemicals. In this paper, we, first of all, provide an overview of the chronological development of HOFs, starting from the seminal work by Marsh and Duchamp in 1969 on the crystal superstructure of the hydrogen-bonded networks of trimesic acid. We identify the development of novel hydrogen-bonding motifs such as diaminotriazine (DTA), the introduction of the concept of molecular tectonics, and the establishment of permanent porosity in HOFs as being some of the milestones, which incentivized the current burgeoning research endeavors on developing HOFs as multifunctional materials. This Account is focused primarily on surveying the strategies for constructing porous 3D HOFs based on organic building blocks with peripheral carboxyl groups. These strategies are presented in the following categories: (1) the polycatenation of 2D networks by trigonal building blocks to form global 3D frameworks, (2) the utilization of building blocks with 3D geometries—tetrahedral and trigonal prismatic—that are predisposed to form 3D networks, and (3) the docking by shape-fitting of geometrically labile building blocks. We emphasize how the molecular geometry of the building blocks plays an important role in modulating the superstructures of extended frameworks so as to address specific applications. Recognizing that the in silico design of HOFs is the ultimate goal of researchers in this field, we also discuss the recent advances in superstructure prediction that lead to the formation of porous supramolecular crystals and assess the complications in implementing computational methods for HOFs with complex superstructures. We hope this Account will inspire the development of new supramolecular designs and creative approaches to crystal engineering that aid and abet the assembly of multifunctional HOFs with customizable properties.

36 MATERIALS SCIENCE↗
DOE OSTI2026

Atomic-Scale Imaging Reveals Polar-π Interactions in Two-Dimensional Molecular Superlattices

Controlling coassembly of synthetic oligomers into binary superlattices at the atomic level is challenging. Here, we report a strategy for programming polar-π interactions in oligomeric peptoids, a class of sequence-defined peptidomimetics, facilitating the formation of homogeneous two-dimensional (2D) superlattices. N-2-phenylethyl and N-(2-perfluorophenyl)ethyl side chains, similar in size, but with contrasting electrostatic characteristics, were introduced at defined sequence positions to generate favorable dipolar aromatic interactions. The resulting nanosheets exhibit different crystal motifs depending on the side chain interactions: systems containing only one type of aromatic side chain form a parallel V-shaped motif driven by π-π interactions, whereas a combination of both types of aromatic side chains, either within one backbone or through the coassembly of two distinct peptoids, adopt an antiparallel V-shaped superlattice with higher thermal stability, driven by polar-π interactions. Cryogenic transmission electron microscopy directly resolved the packing arrangement of perfluorophenyl and phenyl rings in individual nanosheet superlattices, confirming that intermolecular polar-π interaction dominates the superlattice motifs and increases lattice stability. Molecular dynamics simulations and density functional theory calculations further substantiate the energetic favorability of polar-π interactions over π-π interactions, rationalizing the formation of homogeneous superlattices with enhanced thermal stability. Our discoveries establish a design principle for binary coassembly using sequence-defined oligomers, which enables control over unit cell geometry, lattice stability, and molecular registration through aromatic side chain polarization and sequence control. This ability to program atomic-scale binary superlattices opens new avenues for designing functional 2D soft materials.

Lee, Yen Jea [Lawrence Berkeley National Laborator↗
DOE OSTI2024

Lattice Symmetry-Guided Charge Transport in 2D Supramolecular Polymers Promotes Triplet Formation

Singlet-to-triplet intersystem crossing (ISC) in organic molecules is intimately connected with their geometries: by modifying the molecular shape, symmetry selection rules pertaining to spin-orbit coupling can be partially relieved, leading to extra matrix elements for increased ISC. As an analog to this molecular design concept, the study finds that the lattice symmetry of supramolecular polymers also defines their triplet formation efficiencies. A supramolecular polymer self-assembled from weakly interacting molecules is considered. Its 2D oblique unit cell effectively renders it as a coplanar array of 1D molecular columns weakly bound to each other. Using momentum-resolved photoluminescence imaging in combination with Monte Carlo simulations, the study found that photogenerated charge carriers in the supramolecular polymer predominantly recombine as spin-uncorrelated carrier pairs through inter-column charge transfer states. This lattice-defined recombination pathway leads to a substantial triplet formation efficiency (≈60%) in the supramolecular polymer. These findings suggest that lattice symmetry of micro-/macroscopic structures relying on intermolecular interactions can be strategized for controlled triplet formation.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Morphological Transitions of a Photoswitchable Aramid Amphiphile Nanostructure

Self-assembly of small amphiphilic molecules in water can lead to nanostructures of varying geometries with pristine internal molecular organization. Here we introduce a photoswitchable aramid amphiphile (AA), designed to exhibit extensive hydrogen bonding and robust mechanical properties upon self-assembly, while containing a vinylnitrile group for photoinduced cis-trans isomerization. We demonstrate spontaneous self-assembly of the vinylnitrile-containing AA in water to form nanoribbons. Upon UV irradiation, trans-to-cis isomerizations occur concomitantly with a morphological transition from nanoribbons to nanotubes. The nanotube structure persists in water for over six months, stabilized by strong and collective intermolecular interactions. We demonstrate that the nanoribbon-to-nanotube transition is reversible upon heating and that switching between states can be achieved repeatedly. Finally, we use electron microscopy to capture the transition and propose mechanisms for nanoribbon-to-nanotube rearrangement and vice versa. This stability and switchability of photoresponsive AA nanostructures make them viable for a range of future applications.

77 NANOSCIENCE AND NANOTECHNOLOGY↗
DOE OSTI2025

Multi-Dimensional Spectroscopy with Intense Entangled Beams: Entanglement-Enabled Phase Matching in a Collinear Beam Geometry

The experimental realization of quantum molecular spectroscopy with entangled photons remains challenging owing to the low signal-to-noise ratio resulting from the use of low-flux entangled photons. High-flux entangled photons via intense entangled beams can be used to improve the signal-to-noise ratio, but the presence of unentangled photons contaminates the quantum signal stemming from entangled photons. Here, we demonstrate how intense entangled beams can be used in multi-dimensional spectroscopy while retaining the advantage of photon entanglement. Our approach is broadly applicable to odd-ordered nonlinear spectroscopies, and it generates purely quantum spectroscopic signals. The proposed approach allows the recording of desired phase-matched signals even in a collinear beam geometry, which lifts the requirement of complicated beam geometry setups for phase matching in multi-dimensional spectroscopies.

Absorption spectroscopy↗
DOE OSTI2020

Suppressing Molecular Charging, Nanochemistry, and Optical Rectification in the Tip-Enhanced Raman Geometry

Classical vs quantum plasmons are operative in tapping vs contact mode tip-enhanced Raman scattering (TERS) and lead to distinct observables. Under otherwise identical experimental conditions, we illustrate the concept through tapping and contact mode TERS mapping of chemically functionalized silver nanocubes. Whereas molecular charging, chemical transformations, and optical rectification are prominent observables in contact mode TERS, the same effects are suppressed using tapping mode feedback. In effect, this work demonstrates that nanoscale physical and chemical processes can be accessed/suppressed on-demand in the TERS geometry. Further, the advantages of tapping mode TERS are otherwise highlighted with the latter in mind.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

Building molecular model series from heterogeneous CryoEM structures using Gaussian mixture models and deep neural networks

Cryogenic electron microscopy (CryoEM) produces structures of macromolecules at near-atomic resolution. However, building molecular models with good stereochemical geometry from those structures can be challenging and time-consuming, especially when many structures are obtained from datasets with conformational heterogeneity. Here we present a model refinement protocol that automatically generates series of molecular models from CryoEM datasets, which describe the dynamics of the macromolecular system and have near-perfect geometry scores. This method makes it easier to interpret the movement of the protein complex from heterogeneity analysis and to compare the structural dynamics observed from CryoEM data with results from other experimental and simulation techniques.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Imaging a light-induced molecular elimination reaction with an X-ray free-electron laser

Tracking the motion of individual atoms during chemical reactions represents a severe experimental challenge, especially if several competing reaction pathways exist or if the reaction is governed by the correlated motion of more than two molecular constituents. Here we demonstrate how ultrashort X-ray pulses combined with coincident ion imaging can be used to trace molecular iodine elimination from laser-irradiated diiodomethane (CH 2 I 2 ), a reaction channel of fundamental importance but small relative yield that involves the breaking of two molecular bonds and the formation of a new one. We map bending vibrations of the bound molecule, disentangle different dissociation pathways, image the correlated motion of the iodine atoms and the methylene group leading to molecular iodine ejection, and trace the vibrational motion of the formed product. Our results provide a quantitative mechanistic picture behind previously suggested reaction mechanisms and prove that a variety of geometries are involved in the molecular bond formation.

Atomic and molecular interactions with photons↗
DOE OSTI2025

Imaging transient molecular configurations in UV-excited diiodomethane

Femtosecond structural dynamics of diiodomethane (CH 2 I 2 ) triggered by ultraviolet (UV) photoabsorption at 290 and 330 nm are studied using time-resolved coincident Coulomb explosion imaging driven by a near-infrared probe pulse. Here, we map the dominant single-photon process, the cleavage of the carbon–iodine bond producing rotationally excited CH 2 I radical, identify the contributions of the three-body (CH 2 + I + I) dissociation and molecular iodine formation channels, which are primarily driven by the absorption of more than one UV photon, and demonstrate the existence of a weak reaction pathway involving the formation of short-lived transient species resembling iso-CH 2 I 2 -like geometries with a slightly shorter I–I separation compared to the ground-state CH 2 I 2 . These transient molecular configurations, which can be separated from the other channels by applying a set of conditions on the correlated momenta of three ionic fragments, are formed within ∼100 fs after the initial photoexcitation and decay within the next 100 fs.

Atomic and molecular processes↗
DOE OSTI2025

Optimizing microfluidic flow cell geometry for in situ resonant soft X-ray characterization of molecular nanostructures

Liquid-phase resonant soft X-ray scattering (LP-RSoXS) is an emerging label-free technique to probe chemically resolved nanostructures of molecular or hybrid materials in liquid environments. Still, quantitative analysis is hindered by the pressure-induced deformation of thin silicon nitride (SiN) membranes used as windows in microfluidic flow cells, which attenuates the signal in nonlinear ways, making experimental optimization difficult. Here, in this work, we directly characterize this deformation under experimental conditions for a variety of cell configurations. We use this to develop a predictive model that combines transmission effects of SiN bowing, incident X-ray beam profiles, and material-dependent resonant scattering cross sections to simulate the effective scattering intensity at the detector across the carbon K-edge. Maps of the total signal across the flow cell window reveal that increasing the window width and polymer concentration shifts the anisotropic intensity distributions from the center toward the edges of the window. It was determined that an optimal SiN thickness of 50 nm, with a window aperture of 104 μm, maximizes the total signal for typical solute concentrations and energies across the carbon K-edge. Our results overturn the assumption that corner regions dominate the scattering signal, offering explicit design guidelines for maximizing LP-RSoXS signals and significantly advancing the quantitative application of this technique to the characterization of molecular and hybrid nanostructured materials in liquids.

Grabner, Devin [Washington State Univ., Pullman, W↗
DOE OSTI2021

CTRAMER: An open-source software package for correlating interfacial charge transfer rate constants with donor/acceptor geometries in organic photovoltaic materials

In this paper, we present CTRAMER (Charge-Transfer RAtes from Molecular dynamics, Electronic structure, and Rate theory)—an opensource software package for calculating interfacial charge-transfer (CT) rate constants in organic photovoltaic (OPV) materials based on ab initio calculations and molecular dynamics simulations. The software is based on identifying representative donor/acceptor geometries within interfacial structures obtained from molecular dynamics simulation of donor/acceptor blends and calculating the corresponding Fermi’s golden rule CT rate constants within the framework of the linearized-semiclassical approximation. While the methods used are well established, the integration of these state-of-the-art tools originating from different disciplines to study photoinduced CT processes with explicit treatment of the environment, in our opinion, makes this package unique and innovative. The software also provides tools for investigating other observables of interest. After outlining the features and implementation details, the usage and performance of the software are demonstrated with results from an example OPV system.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗