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DOE OSTI2025

Pressure-Induced Stacking of Rhodamine 6G Molecules

Extended conjugation of molecular π systems are of great significance for solar cells and organic light-emitting diodes as these can serve as new light absorbing and emitting chromophores. This research demonstrates the potential of using pressure and solvent environment to create larger assemblies of molecular π-conjugated systems. Here, we selected rhodamine 6G (Rh6G) to study the pressure-induced stacking of molecules in three different solvents: methanol (MeOH), isopropanol (IPA), and 16:3:1 mixture of methanol: ethanol: water (MEW). Absorption, emission, and fluorescence lifetime were studied at pressures up to 11.38 GPa. We found that pressure-induced stacking mechanisms can present solvent dependence: high pressures tend to create emissive Haggregates in MeOH and MEW, but excimers in IPA. This work guides and demonstrates routes to stacking of organic molecules using high pressures and provides fundamental insights into the formation of extended conjugation π systems.

Johnson, Kade [Univ. of Texas at San Antonio, TX (↗

DOE OSTI2025

Linear and Nonlinear X-ray Spectra of Chiral Molecules: X-ray Circular Dichroism, Sum- and Difference-Frequency Generation of Fenchone and Cysteine

Recent advancements in X-ray light sources enable element-sensitive nonlinear spectroscopies for probing molecular chirality. We simulate X-ray absorption spectroscopy, X-ray circular dichroism (XCD), and nonlinear optical/X-ray SFG and DFG (OX SFG/DFG) signals for two prototypical chiral molecules, fenchone and cysteine. Furthermore, our multireference simulations reproduce experimental data and reveal how novel X-ray spectroscopies exploit the site- and element-sensitivity of X-rays to uncover molecular asymmetry. The XCD spectra show strong asymmetries at chiral centers, while distant atoms contribute weaker signals. The OX SFG/DFG signals, under fixed resonant optical excitation, strongly depend on the core and valence excitations. This allows us to introduce two-dimensional (2D) chirality-sensitive valence-core spectroscopy, which provides insight into the overlap between valence orbitals and local molecular asymmetry. Finally, our estimates using realistic laser and X-ray pulse parameters demonstrate that such nonlinear experiments are feasible at XFELs, offering a promising tool for investigating chiral molecules.

Circular dichroism spectroscopy↗

DOE OSTI2025

Single-Atom Doping at the Molecule–Metal Interface: How Rh Affects Surface Explosion Kinetics

Controlling chemical reactions at interfaces is central to many fields, including atmospheric, environmental, and biological chemistry as well as catalysis and corrosion. We performed a fundamental study of how catalytically active Rh atoms placed at and above a molecule-metal interface influence the surface reaction kinetics of tartaric acid (TA) decomposition. Specifically, TA decomposition on Cu(100) exhibits autocatalytic decomposition kinetics involving a slow initiation step followed by fast decomposition of the molecular layer. These so-called “surface explosions” are extremely sensitive to initial conditions, making it fundamentally interesting to study how the placement of reactive atoms affects the reaction rate. Temperature-programmed reaction (TPR) experiments reveal that Rh atoms embedded in the Cu(100) surface beneath TA (TA/Rh/Cu) or atop the TA layer (Rh/TA/Cu) reduce the decomposition temperature and modify the reaction rate constants. Isothermal TPR analysis reveals that Rh enhances both the initiation rate constant, k i , and the explosion rate constant, k e , facilitating explosive decomposition at lower temperatures. This result provides evidence that both the initiation and explosion steps occur at the metal-molecule interface and are accelerated by the presence of Rh at this interface. This study illustrates how small amounts of reactive elements may be used to control nonlinear kinetic processes at interfaces.

desorption↗

DOE OSTI2025

An Integral Activity-Based Protein Profiling Method for Higher Throughput Determination of Protein Target Sensitivity to Small Molecules

Activity-based protein profiling (ABPP) is a chemoproteomic technique that uses small molecule probes to label active enzymes selectively and covalently in complex proteomes. Competitive ABPP, which involves treatment of the active proteome with an analyte of interest, is especially powerful for profiling how small molecules impact specific protein activities. Advances in higher throughput workflows have made it possible to generate extensive competitive ABPP data across diverse biological samples, making this approach highly appealing for characterizing shared and unique proteins affected by perturbations such as drug or chemical exposures. To use the competitive ABPP approach effectively to understand potential adverse effects of chemicals of concern (CoC), a wide range of concentrations may be needed, particularly for chemicals that lack potency or toxicity data. In this work, we present an integral competitive ABPP method that enables target sensitivity determination for different organophosphate (OP) pesticides as model toxicants. Using previously developed OP-ABPs, we optimized conditions for tandem mass tag (TMT) multiplexing of ABPP samples and compared conventional competitive ABPP involving samples at discrete paraoxon concentrations to pooled samples across that same concentration range. We then expanded our approach to compare protein target sensitivities toward two additional OP pesticides, chlorpyrifos oxon and malaoxon. The results showed that differences in integral intensities for the pooled competition sample can be used to evaluate the relative sensitivity of specific proteins without increasing the overall number of samples. For 8 CoC concentrations of interest, this strategy reduced the number of TMT plexes and the corresponding number of LC–MS/MS analyses 3-fold. In conclusion, we envision the integral ABPP (IABPP) method will provide a means to screen diverse chemicals more rapidly to identify both high and low sensitivity protein targets.

activity-based probes↗

DOE OSTI2025

Motion of Molecules in Supramolecular Scaffolds Enhances Bone Regeneration

The regeneration of human tissues is a great scientific challenge and a critical factor to achieve a long healthspan and prevent disabilities due to injury or disease. Materials chemistry can contribute to this goal with the development of bioactive supramolecular systems that can signal cells for regeneration. Recent work in our laboratory using in vivo models of spinal cord injury and cartilage regeneration has demonstrated that the motion of bioactive molecules in supramolecular scaffolds enhances receptor signaling. We report here on a novel molecular strategy to control supramolecular motion in filamentous assemblies using bone regeneration as a functional target. The supramolecular assemblies are composed of monomers that arrange, by design, with either parallel or antiparallel β-sheets, and some of them contain a terminal peptide sequence that binds BMP-2. We found that parallel β-sheet supramolecular assemblies promote greater osteogenic differentiation of progenitor cells in vitro relative to antiparallel assemblies, as well as superior quality of newly regenerated bone in a rat model of spinal fusion. Furthermore, these assemblies drastically reduce the dangerous supraphysiological dose of BMP-2 used clinically for spinal fusion. Here, we attribute the enhanced bioactivity to the weaker nature of hydrogen bonds in parallel relative to antiparallel β-sheet assemblies, which in turn allows greater supramolecular motion and cell signaling of the growth factor-binding molecules.

Anatomy↗

DOE OSTI2025

Hyperfine-to-rotational energy transfer in ultracold atom–molecule collisions of Rb and KRb

Energy transfer between different mechanical degrees of freedom in atom–molecule collisions has been studied and largely understood. However, systems involving spins remain less explored. Here, in this study, we directly observed energy transfer from atomic hyperfine to molecular rotation in the 87 Rb ($| {F}_{a},{M}_{{F}_{a}}\rangle =| 2,2\rangle$) + 40 K 87 Rb (X 1 Σ + , rotational state N = 0) ⟶ Rb ($| 1,1\rangle$) + KRb ( N = 0, 1, 2) collision with state-to-state precision. We also performed quantum scattering calculations that rigorously included the coupling between spin and rotational degrees of freedom at short range under the assumption of rigid-rotor KRb monomers moving along a single potential energy surface. The calculated product rotational state distribution deviates from the observations even after extensive tuning of the atom–molecule potential energy surface. In addition, our ab initio calculations indicate that spin–rotation coupling is enhanced close to a conical intersection that is energetically accessible at short range. This, together with the deviation, suggests that vibrational degrees of freedom and conical intersections play an important part in the coupling. Our observations confirm that spin is coupled to mechanical rotation at short range and establish a benchmark for future theoretical studies.

chemical physics↗

DOE OSTI2026

Attosecond response of molecules to impulsive ionization

When matter interacts with energetic radiation it can undergo sudden, or impulsive, ionization. This process can drive chemical change and occurs widely in space and planetary atmospheres, yet its comprehensive description challenges our current theoretical and computational capabilities as it requires advanced treatment of electron correlation and nonadiabatic dynamics beyond the Born–Oppenheimer approximation. Here, in this study, we measure the response of the para-aminophenol molecule to sudden ionization. Using attosecond X-ray absorption spectroscopy, we resolve the ultrafast dynamics of the ionized molecule with atomic precision. A subfemtosecond decay corresponds to states undergoing non-radiative decay, whereas few-femtosecond oscillatory signatures are associated with electronic wavepacket motion in stable cation states that later couple to nuclear motion. We compare our measurement with state-of-the-art computational modelling, qualitatively reproducing the observed response across multiple timescales. These results provide a benchmark for computational models of sudden ionization and ultrafast charge motion in matter.

Driver, Taran [SLAC National Accelerator Laborator↗

DOE OSTI2024

Raman enhancement induced by exciton hybridization in molecules and 2D materials

Abstract Surface-enhanced Raman spectroscopy (SERS) is a powerful technique for trace-level fingerprinting. Recently, layered two-dimensional (2D) materials have gained significant interest as SERS substrates for providing stable, uniform, and reproducible Raman enhancement with the potential for trace-level detection. Yet, the development of effective 2D SERS substrates is still hindered by the lack of fundamental understanding of the coupling mechanism between target molecules and substrates. Here, we report a systematic excitation-dependent Raman spectroscopy investigation on the coupling between 2D materials such as SnS 2 , MoS 2 , WSe 2 , and graphene and small organic molecules like rhodamine 6G (Rh 6G). Strong coupling between SnS 2 and Rh 6G is found due to their degenerate excitons through Raman excitation profiles (REP), leading to the enhancement of Rh 6G vibrational modes that are observable down to 10 −13 M. Our study shows that exciton coupling in the substrate-adsorbate complex plays a vital role in the Raman enhancement effect, opening a new route for designing SERS substrates for high sensitivity.

Materials Science↗

DOE OSTI2024

Analysis of bonding motifs in unusual molecules II: infinitene

The bonding structures of infinitene, the Chemical and Engineering News 2021 Molecule of the Year, is studied by means of oriented quasi-atomic orbitals (QUAOs) to assess the degree of aromaticity within the molecule.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2024

Influence of shape on crystal structure and optical properties of heterocyclic conjugated molecules

Organic optoelectronics are increasingly important due to their tunablilty, flexibility, and solution processability. Tuning optical properties of these materials as solids relies on the balance of weak non-covalent interactions that dictate crystal structure, but are difficult to predict. Our research aims to improve our understanding of how electrostatic interactions can direct and facilitate intramolecular interactions that dictate emergent properties of crystalline materials. This paper focuses on exploring how multi-fused thiophene ring systems that are popular in modern organic optoelectronic materials impact intramolecular interactions, while also investigating the role of molecular shape. In these examples, the shape of heterocyclic systems correlate with the crystal structures: while the bent heterocyclics show no discrete and discernable intramolecular interactions, those with bent shapes interact cofacially with one of the electron poor ArF pendants by twisting the arylene ethynylene backbone. Two of the control molecules, which bear non-fluorinated benzyl ester substituents, show intramolecular edge-face interactions, and several of these molecules show clear polymorphic behavior. Furthermore, these findings further our understanding of how discrete interactions can be altered not only by electrostatics, but also by shape, allowing for increasingly nuanced control over the crystal structures and optical properties of optoelectronic materials.

Guzmán, Elisa↗

DOE OSTI2025

Experimental determination of the magnetic anisotropy in five-coordinated Co( II ) field-induced single molecule magnets

Magnetic anisotropy of the central metal atom is a crucial property of single molecule magnets (SMMs). Small structural changes can alter the magnetic properties, and accurate experimental methods to investigate magnetic anisotropy are therefore critical. Here, we investigate two five-coordinated Co( II ) SMMs, [CoCl 2 Cltpy] (1) and [CoBr 2 Cltpy] (2) (Cltpy = 4′-chloro-2,2′:6′,2′′-terpyridine), through multiple techniques. Ab initio theoretical calculations performed on the two compounds show that both possess axial magnetic anisotropy with the magnetic easy axis pointing towards one of the terminal halogen atoms. Theoretical calculations on SMMs are typically done on isolated molecular species, and to validate this approximation the magnetic anisotropy was further studied through experimental techniques. EPR measurements confirm an axial anisotropy of 1, and magnetic measurements provide experimental Zero-Field Splitting (ZFS) parameters, showing that the values from theoretical calculations are slightly overestimated. The X-ray electron density determined from 20 K single-crystal synchrotron X-ray diffraction data provides estimated d-orbital populations also suggesting axial magnetic anisotropy in both systems, and furthermore suggesting a more pronounced axiality in 1 compared to 2. This is in good agreement with the results obtained from both magnetic measurements and theoretical calculations. The magnetic anisotropy of 1 is quantified experimentally through polarized powder neutron diffraction via the site susceptibility method, confirming an axial magnetic anisotropy of the compound. A slight deviation in the easy axis direction is observed between experimental and theoretical results. This, together with the overestimation of the ZFS parameters from theoretical calculations, shows that experimental investigation of the magnetic anisotropy of SMMs is of high relevance. Magnetic anisotropy of the central metal atom is a crucial property of single molecule magnets (SMMs).

Slavensky, Hannah H. [Aarhus Univ. (Denmark)] (ORC↗

DOE OSTI2024

Tracking ultrafast non-adiabatic dissociation dynamics of the deuterated water dication molecule

Here, we applied reaction microscopy to elucidate fast non-adiabatic dissociation dynamics of deuterated water molecules after direct photo-double ionization at 61 eV with synchrotron radiation. For the very rare D + + O + + D breakup channel, the particle momenta, angular, and energy distributions of electrons and ions, measured in coincidence, reveal distinct electronic dication states and their dissociation pathways via spin–orbit coupling and charge transfer at crossings and seams on the potential energy surfaces. Notably, we could distinguish between direct and fast sequential dissociation scenarios. For the latter case, our measurements reveal the geometry and orientation of the deuterated water molecule with respect to the polarization vector that leads to this rare 3-body molecular breakup channel. Aided by multi-reference configuration-interaction calculations, the dissociation dynamics could be traced on the relevant potential energy surfaces and particularly their crossings and seams. This approach also unraveled the ultrafast time scales governing these processes.

74 ATOMIC AND MOLECULAR PHYSICS↗

DOE OSTI2024

A molecular ground electronic state with an occupied 5g spinor—The superheavy (E125)F molecule

Fully relativistic calculations, primarily at the 4-component coupled-cluster singles and doubles with perturbative triples [CCSD(T)] level of theory with the Dirac–Coulomb (DC) Hamiltonian, have been carried out for the superheavy (E125)F molecule using large Gaussian basis sets. The electronic ground state is determined to have an [Og]8s 2 5g 1 6f 3 configuration on E125 with an Ω = 6 ground state and an 8p electron largely donated to F. A Mulliken population analysis indicates that the ground state is mainly ionic with a partial charge of +0.79 on E125 and a single sigma bond involving the F 2p and E125 8p spinors. The occupied g spinor is not involved in the bonding. With the largest basis set used in this work, the (0 K) dissociation energy was calculated at the DC-CCSD(T) level of theory to be 7.02 eV. Analogous calculations were also carried out for the E125 atom, both the neutral and its cation. The lowest energy electron configuration of E125 + , [Og]$8s$$^{2}_{1/2}$$5g$$^{1}_{7/2}$$6f$$^{3}_{5/2}$ with a J = 6 ground state, was found to be similar to that in (E125)F, while the neutral E125 atom has an [Og]$8s$$^{2}_{1/2}$$5g$$^{1}_{7/2}$$6f$$^{2}_{5/2}$$7d$$^{1}_{3/2}$$8p$$^{1}_{1/2}$ ground state electron configuration with a J = 17/2 ground state. The ionization energy (IE) of E125 is reported for the first time and is calculated to be 4.70 eV at the DC-CCSD(T) level of theory. Non-relativistic calculations were also carried out on the E125 atom and the (E125)F molecule. Here, the non-relativistic ground state of the E125 atom was calculated to have a 5g 5 ground state with an IE of just 3.4 eV. The net effect of relativity on (E125)F is to stabilize its bonding.

38 RADIATION CHEMISTRY, RADIOCHEMISTRY, AND NUCLEA↗

DOE OSTI2025

Combining MicroED and native mass spectrometry for structural discovery of enzyme–small molecule complexes

With the goal of accelerating the discovery of small molecule–protein complexes, we leverage fast, low-dose, event-based electron counting microcrystal electron diffraction (MicroED) data collection and native mass spectrometry. This approach, which we term electron diffraction with native mass spectrometry (ED-MS), allows assignment of protein target structures bound to ligands with data obtained from crystal slurries soaked with mixtures of known inhibitors and crude biosynthetic reactions. This extends to libraries of printed ligands dispensed directly onto TEM grids for later soaking with microcrystal slurries, and complexes with noncovalent ligands. ED-MS resolves structures of the natural product, epoxide-based cysteine protease inhibitor E-64, and its biosynthetic analogs bound to the model cysteine protease, papain. It further identifies papain binding to its preferred natural products, by showing that two analogs of E-64 outcompete others in binding to papain crystals, and by detecting papain bound to E-64 and an analog from crude biosynthetic reactions, without purification. ED-MS also resolves binding of the CTX-M-14 β-lactamase, a target of active drug development, to the non-β-lactam inhibitor, avibactam, alone or in a cocktail of unrelated compounds. These results illustrate the utility of ED-MS for natural product ligand discovery and for structure-based screening of small molecule binders to macromolecular targets, promising utility for drug discovery.

MicroED↗

DOE OSTI2025

Attosecond X-Ray Core-Level Chronoscopy of Aromatic Molecules

Attosecond photoemission or photoionization delays are a unique probe of the structure and the electronic dynamics of matter. However, the spectral congestion of valence photoelectron spectra sets fundamental limits to the complexity of systems that can be studied, and the delocalization of valence electron wave functions blurs the spatial origin of the photoelectron wave packet. Using attosecond x-ray pulses from LCLS, we demonstrate the key advantages of measuring core-level delays: The photoelectron spectra remain atomlike, the measurements become element specific, and the observed scattering dynamics originate from a pointlike source when multicenter interference effects are negligible. We exploit these unique features to reveal the effects of changing functional groups (C-H vs N) and symmetry on attosecond scattering dynamics by measuring and calculating the photoionization delays between N−1⁢𝑠 and C−1⁢𝑠 core shells of a series of aromatic azabenzene molecules. Remarkably, the delays increase with the number of nitrogen atoms in the molecule and reveal multiple resonances. We identify two previously unknown mechanisms regulating the associated attosecond dynamics, namely the enhanced confinement of the trapped wave function with the replacement of C-H groups by N atoms and the decrease of the coupling strength among the photoemitted partial waves with increasing symmetry. This study demonstrates the unique opportunities opened by measurements of core-level photoionization delays for unraveling attosecond electron dynamics in complex matter.

Ji, Jia-Bao [Eidgenoessische Technische Hochschule↗

DOE OSTI2026

Single-molecule infrared spectroscopy with scanning tunneling microscopy

Probing vibrations at the single-molecule level is essential for achieving bond-specific chemical control in realistic heterogeneous environments. Here, we introduce a new measurement scheme that integrates frequency-tunable infrared excitation with scanning tunneling microscopy to characterize vibration-mediated nuclear motions of single molecules. We first validated the technique by monitoring the infrared-induced rotation of the ethynyl radical and then applied it to mapping pyrrolidine’s conformational dynamics. The resulting broadband spectra captured fundamental vibrational modes together with rich overtone and combination bands inaccessible by conventional methods, which we confirmed with isotopic substitutions. Density functional theory calculations showed that delocalized modes coupled with pyrrolidine ring puckering drive the structural transition, revealing altered selection rules compared with traditional infrared spectroscopy. Here, this new experimental platform enables molecular vibrations and transformations to be probed with atomic precision.

Liang, Kangkai [University of California, San Dieg↗

DOE OSTI2024

Chiral catalysis of nuclear fusion in molecules

At low energies, nuclear fusion is strongly affected by electron screening of the Coulomb repulsion among the fusing nuclei. It may thus be possible to catalyze nuclear fusion in molecules (i.e., to fuse specific nuclei in situ) through quantum control of electron wave functions in intense laser fields. The circularly polarized (chiral) laser field can effectively squeeze the electron wave functions, greatly enhancing the screening in the spatial region relevant for the fusion process. Here, we estimate the corresponding fusion probabilities, and find that the proposed chiral catalysis of nuclear fusion in molecules may be observable, potentially with important practical applications.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2024

Charm meson and charm-meson molecule in an expanding hadron gas

We present our studies on the evolution of charm mesons after the kinetic freeze-out of the expanding hadron gas produced in a heavy-ion collision and the thermal correction to a loosely bound charm-meson molecule in a pion gas. The πD* → πD* reaction rates have t-channel singularities that give contributions inversely proportional to the thermal width of the D. The ratio of the D 0 and D + production rate can differ significantly from those predicted using the measured D* branching fractions. The thermal correction to a loosely bound charm-meson molecule in a pion gas comes primarily from the complex thermal energy shift of the charm-meson constituents.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗