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At least 1,315 records · Page 73

Spatially Offset Femtosecond Stimulated Raman Spectroscopy: Observing Exciton Transport through a Vibrational Lens

To design better molecular electronic devices, we need a strong understanding of how charges or excitons propagate, as many efficiency losses arise during transport. Exciton transport has been difficult to study because excitons tend to be short-lived, have short diffusion lengths, and can easily recombine. Here, we debut spatially offset femtosecond stimulated Raman spectroscopy (SO-FSRS), a three-pulse ultrafast microscopy technique. By offsetting the photoexcitation beam, we can monitor Raman spectral changes as a function of both time and position. We used SO-FSRS on 6,13-bis(triisopropylsilylethynyl) pentacene, a well-studied organic semiconductor used in photovoltaics and field-effect transistors. Furthermore, we demonstrated that the fast exciton and free charge carrier transport axes are identical and observed that exciton transport is less anisotropic by a factor of ~3. SO-FSRS is the first technique that directly tracks molecular structural evolution during exciton transport, which can provide roadmaps for tailor-making molecules for specific electronic devices.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

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↗

Auger Recombination Lifetime Scaling for Type I and Quasi-Type II Core/Shell Quantum Dots

Having already achieved near-unity quantum yields, with promising properties for light-emitting diode, lasing, and charge separation applications, colloidal core/shell quantum dots have great technological potential. The shell thickness and band alignment of the shell and core materials are known to influence the efficiency of these devices. In many such applications, improving the efficiency requires a deep understanding of multiexcitonic states. In this paper, we elucidate the shell thickness and band alignment dependencies of the biexciton Auger recombination lifetime for quasi-type II CdSe/CdS and type I CdSe/ZnS core/shell quantum dots. We find that the biexciton Auger recombination lifetime increases with the total nanocrystal volume for quasi-type II CdSe/CdS core/shell quantum dots and is independent of the shell thickness for type I CdSe/ZnS core/shell quantum dots. To perform these calculations and compute Auger recombination lifetimes, we developed a low-scaling approach based on the stochastic resolution of identity. The numerical approach provided a framework for studying the scaling of the biexciton Auger recombination lifetimes in terms of the shell thickness dependencies of the exciton radii, Coulomb couplings, and density of final states in quasi-type II CdSe/CdS and type I CdSe/ZnS core/shell quantum dots.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Machine Learning Reveals the Critical Interactions for SARS-CoV-2 Spike Protein Binding to ACE2

SARS-CoV and SARS-CoV-2 bind to the human ACE2 receptor in practically identical conformations, although several residues of the receptor-binding domain (RBD) differ between them. Herein, we have used molecular dynamics (MD) simulations, machine learning (ML), and free-energy perturbation (FEP) calculations to elucidate the differences in binding by the two viruses. Although only subtle differences were observed from the initial MD simulations of the two RBD–ACE2 complexes, ML identified the individual residues with the most distinctive ACE2 interactions, many of which have been highlighted in previous experimental studies. FEP calculations quantified the corresponding differences in binding free energies to ACE2, and examination of MD trajectories provided structural explanations for these differences. Lastly, the energetics of emerging SARS-CoV-2 mutations were studied, showing that the affinity of the RBD for ACE2 is increased by N501Y and E484K mutations but is slightly decreased by K417N.

60 APPLIED LIFE SCIENCES↗

Distinct Chemistries Explain Decoupling of Slip and Wettability in Atomically Smooth Aqueous Interfaces

Despite essentially identical crystallography and equilibrium structuring of water, nanoscopic channels composed of hexagonal boron nitride and graphite exhibit an order-of-magnitude difference in fluid slip. We investigate this difference using molecular dynamics simulations, demonstrating that its origin is in the distinct chemistries of the two materials. In particular, the presence of polar bonds in hexagonal boron nitride, absent in graphite, leads to Coulombic interactions between the polar water molecules and the wall. We demonstrate that this interaction is manifested in a large typical lateral force experienced by a layer of oriented hydrogen atoms in the vicinity of the wall, leading to the enhanced friction in hexagonal boron nitride. The fluid adhesion to the wall is dominated by dispersive forces in both materials, leading to similar wettabilities. Finally, our results rationalize recent observations that the difference in frictional characteristics of graphite and hexagonal boron nitride cannot be explained on the basis of the minor differences in their wettabilities.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Engineering Band Gap and Photoconduction in Semiconducting Metal Organic Frameworks: Metal Node Effect

We report a systematic study on the correlation of the metal nodes in M-THQ conducting MOFs (M = Fe, Ni, Cu and Zn; THQ = tetra-hydroxybenzoquinone) with their structure, photophysical property, and photoconductivity. We found that structural preference in these MOFs is controlled by metal node identity where Cu prefers a square planar coordination which leads to a 2D Kagome type structure. Fe, Ni and Zn prefer an octahedral sphere which leads to a 3D structure. Fe-THQ has the smallest band gap and highest photoconduction as well as a long-lived ligand to metal charge transfer state due to the mixed valence state revealed by time resolved optical and X-ray absorption and tera hertz spectroscopy. Furthermore, these results demonstrate the importance of the metal node in tuning the photophysical and photocatalytic properties of MOFs.

14 SOLAR ENERGY↗

Polarizability Plays a Decisive Role in Modulating Association between Molecular Cations and Anions

Electrostatic interactions involving proteins depend on not only the ionic charges involved but also their chemical identities. Here we examine the origins of incompletely understood differences in the strength of association of different pairs of monovalent molecular ions that are relevant to protein–protein and protein–ligand interactions. Cationic analogues of the basic amino acid side chains are simulated, along with oxyanionic analogues of cation-exchange ligands and acidic amino acids. Experimentally observed association trends with respect to the cations, but not anions, are captured by a nonpolarizable model. An effective continuum correction to account for electronic polarizability can capture both trends better but at the expense of fidelity to the underlying free energy landscape for ion-pair association. Finally, a polarizable model proves decisive in capturing experimentally suggested trends with respect to both cations and anions; critically, the free energy landscape for ion-pair association is itself altered, thus altering configurational sampling.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Emulating Quantum Entangled Biphoton Spectroscopy Using Classical Light Pulses

We show that for a class of quantum light spectroscopy (QLS) experiments using n = 0, 1, 2, ··· classical light pulses and an entangled photon pair (a biphoton state) where one photon acts as a reference without interacting with the matter sample, identical signals can be obtained by replacing the biphotons with classical-like coherent states of light, where these are defined explicitly in terms of the parameters of the biphoton states. An input-output formulation of quantum nonlinear spectroscopy is used to prove this equivalence. We demonstrate the equivalence numerically by comparing a classical pump–quantum probe experiment with the corresponding classical pump–classical probe experiment. This analysis shows that understanding the equivalence between entangled biphoton probes and carefully designed classical-like coherent state probes leads to quantum-inspired classical experiments that yield equivalent signals and provides insights for the future design of QLS experiments that could provide a true quantum advantage.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Sonochemical Synthesis and Ion Transport Properties of Surfactant-Stabilized Carbon Nanotube Porins

Carbon nanotube porins (CNTPs), short segments of carbon nanotubes stabilized by a lipid coating, are a promising example of artificial membrane channels that mimic a number of key behaviors of biological ion channels. While the lipid-assisted synthesis of CNTPs may facilitate their subsequent incorporation into lipid bilayers, it limits the applicability of these pores in other self-assembled membrane materials and also precludes the use of large scale purified CNT feedstocks. In this report we demonstrate that CNTPs can be synthesized by sonochemical cutting of long CNT feedstocks in the presence of different surfactants, producing CNTS with transport properties identical to those obtained by the lipid-assisted procedure. Our results open up a large variety of synthetic routes for CNTP production.

77 NANOSCIENCE AND NANOTECHNOLOGY↗

A Perspective into Operando Methods for Probing Catalytic Interfaces

Rational design of electrocatalysts for (photo)electrochemical (PEC) processes like hydrogen and oxygen evolution and CO2 reduction reactions is aided by the recent improvements in capabilities of operando measurements, where morphology, composition, and/or function are probed during active catalysis. Through operando microscopy and spectroscopy, structure, catalytic microenvironment, oxidation state, adsorbates, and products can be measured to gain a better understanding of catalyst behavior and suggest possible improvements. Visualizing evolving catalyst morphologies, surface compositions, and electrochemical behavior also helps address many fundamental research questions for a better understanding of catalytic mechanisms. Correlating morphology with chemical identity or functional behavior using a variety of innovative microscopy methods is particularly promising for guiding development of next generation catalysts, and there are also many recent examples of using AI and robotics tools to innovate and speed development. In this Perspective, advances made over the past few years in operando imaging of catalysts relevant to solar fuels will be explored, followed by an outlook on technological developments in instrumentation, sample design, and computational power that may be applied to this field.

Catalysts↗

High-Performance Semiempirical Excited-State Molecular Dynamics Powered by Graphics Processing Units

Here, this Letter introduces excited-state molecular dynamics in PYSEQM, a GPU-accelerated semiempirical quantum chemistry engine implemented in PyTorch. The new module enables Born–Oppenheimer molecular dynamics (BOMD) using configuration-interaction singles and random phase approximation for excited states, allowing long trajectories and large statistical ensembles to be simulated efficiently on a single GPU. We also implement an extended Lagrangian excited-state BOMD (XL-ESMD) scheme that propagates auxiliary electronic variables, enabling relaxed ground and excited-state convergence thresholds without compromising energy conservation. The excited-state BOMD implementation scales smoothly from small chromophores to a nearly 900-atom dendrimer (taking 6.5 s per MD step). PYSEQM also supports batched execution, allowing many geometries or trajectories to be evaluated in a single GPU launch, substantially increasing throughput and making ensemble-based protocols routine. As a demonstration, we compute absorption, emission, and infrared spectra from trajectories propagated on the ground and first excited states. The XL-ESMD scheme yields identical spectra at significantly lower computational cost, establishing the role of extended Lagrangian based dynamics for efficient excited-state BOMD simulations. Beyond raw performance, PYSEQM’s PyTorch foundation provides automatic differentiation for forces, efficient GPU batching, and seamless interfacing with machine learning models. These capabilities position PYSEQM as a practical platform for machine learning-augmented excited-state dynamics and lay the foundation for future data-driven nonadiabatic excited-state dynamics modeling of ultrafast spectroscopic probes.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Prediction and Experimental Verification of Electrolyte Solvation Structure from an OMol25-Trained Interatomic Potential

A molecular-level understanding of electrolyte solvation structure and ion–ion correlations is critical to developing next-generation battery chemistries. Atomistic simulation capabilities with sufficient accuracy, speed, and transferability to deliver reliable structural insights while avoiding arduous system-specific reparameterization are thus highly desirable. Machine learning interatomic potentials (MLIPs) trained on large, chemically diverse data sets are revolutionizing computational chemistry, enabling molecular dynamics simulations of battery electrolytes with near-DFT accuracy over 10,000× faster than DFT. While previous MLIP training data sets with suitable elemental coverage for electrolytes have been based on inorganic materials, the Open Molecules 2025 (OMol25) data set provides large-scale molecular DFT MLIP training data with broad elemental coverage and specifically samples tens of millions of electrolyte configurations. Here, we integrate computational modeling with experimental validation to systematically assess the ability of large-scale MLIPs pretrained on materials data or on OMol25 to accurately resolve nanoscale structural organization and ion-solvation characteristics in Na-ion battery electrolytes across diverse physicochemical conditions and compositional regimes. We find that the OMol25-trained Universal Model of Atoms (UMA-OMol) predicts experimentally measured densities and X-ray structure factors in substantially better agreement compared to state-of-the-art models trained only on inorganic materials data. Using UMA-OMol, we further analyze systematic trends in solvation structure as a function of cation identity, anion chemistry, salt concentration, and solvent topology. We observe that increasing system temperature amplifies the heterogeneity within the solvation environment, perturbing cation–solvent interactions and promoting the formation of contact ion pairs (CIPs). Moreover, subtle variations in the solvent topology of glyme-based electrolytes cause pronounced changes in ion correlations and solvation structure. The experimental agreement and microscopic insights shown here position OMol25-trained MLIPs as a practical route to predictive, high-throughput electrolyte simulations beyond the limits of classical force fields and direct DFT molecular dynamics, serving as a powerful tool for accelerating the design of next-generation Na-ion battery electrolytes and beyond.

MLIPs↗

Introducing Molecular Hypernetworks for Discovery in Multidimensional Metabolomics Data

Orthogonal separations of data from high-resolution mass spectrometry can provide insight into sample composition and address challenges of complete annotation of molecules in untargeted metabolomics. “Molecular networks” (MNs), as used in the Global Natural Products Social Molecular Networking platform, are a prominent strategy for exploring and visualizing molecular relationships and improving annotation. MNs are mathematical graphs showing the relationships between measured multidimensional data features. MNs also show promise for using network science algorithms to automatically identify targets for annotation candidates and to dereplicate features associated with a single molecular identity. Here, this paper introduces “molecular hypernetworks” (MHNs) as more complex MN models able to natively represent multiway relationships among observations. Compared to MNs, MHNs can more parsimoniously represent the inherent complexity present among groups of observations, initially supporting improved exploratory data analysis and visualization. MHNs also promise to increase confidence in annotation propagation, for both human and analytical processing. We first illustrate MHNs with simple examples, and build them from liquid chromatography- and ion mobility spectrometry-separated MS data. We then describe a method to construct MHNs directly from existing MNs as their “clique reconstructions”, demonstrating their utility by comparing examples of previously published graph-based MNs to their respective MHNs.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

IsoForma: An R Package for Quantifying and Visualizing Positional Isomers in Top-Down LC-MS/MS Data

Proteoforms, the different forms of a protein with sequence variations including post-translational modifications (PTMs), execute vital functions in biological systems such as cell signaling and epigenetic regulation. Precisely defining the stoichiometry of PTMs has been challenging because, in the widely used bottom-up proteomics methods, the detection occurs at the peptide level and thus the link between peptides and their specific modification site is lost, resulting in proteoform ambiguity. Advances in top-down mass spectrometry (MS) technology have permitted the direct characterization of intact proteoforms and their exact number of modification sites, allowing for the relative quantification of positional isomers (PI). Proteins with positional isomers refers to proteoforms with identical total mass and set of modifications but varying PTM site combinations. The relative abundance of PI can be estimated by matching proteoform-specific fragment ions to top-down tandem MS (MS2) data to localize and quantify modifications. However, current approaches heavily rely on manual annotation. Here, we present IsoForma, an open-source R package for relative quantification of PI within a single tool. We benchmarked IsoForma’s performance against two existing workflows and highlight the similarity of the results and improvements in speed. Overall, IsoForma provides a streamlined process, reduces the time of conducting isoform-based analyses, and offers an essential framework for developing customized proteoform analysis workflows. Finally, the software is open source and available at https://github.com/EMSL-Computing/isoforma-lib.

59 BASIC BIOLOGICAL SCIENCES↗

Confocal Raman Microscopy Investigation of Phospholipid Monolayers Deposited on Nitrile-Modified Surfaces in Porous Silica Particles

Phospholipid bilayers deposited on a variety of surfaces offer models for investigation of the lipid membrane structure and supports for biocompatible sensors. Hybrid-supported phospholipid bilayers (HSLBs) are stable membrane models for these investigations, typically prepared by self-assembly of a lipid monolayer over an n-alkane-modified surface. HSLBs have been prepared on n-alkyl chain-modified silica and used for lipophilicity-based chromatographic separations. The structure of these hybrid bilayers differs from vesicle membranes where the lipid head group spacing is greater due to interdigitation of the lipid acyl chains with the underlying n-alkyl chains bound to the silica surface. This interdigitated structure exhibits a broader melting transition at a higher temperature due to strong interactions between the lipid acyl chains and the immobile n-alkyl chains bound to silica. In the present work, we seek to reduce the interactions between a lipid monolayer and its supporting substrate by self-assembly of 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) on porous silica functionalized with nitrile-terminated surface ligands. The frequency of Raman scattering of the surface -C≡N stretching mode at the lipid–nitrile interface is consistent with an n-alkane-like environment and insensitive to lipid head group charge, indicating that the lipid acyl chains are in contact with the surface nitrile groups. The head group area of this lipid monolayer was determined from the within-particle phospholipid concentration and silica specific surface area and found to be 54 ± 2 Å 2 , equivalent to the head group area of a DMPC vesicle bilayer. The structure of these nitrile-supported phospholipid monolayers was characterized below and above their melting transition by confocal Raman microscopy and found to be nearly identical to DMPC vesicle bilayers. Their narrow gel-to-fluid-phase melting transition is equivalent to dispersed DMPC vesicles, indicating that the acyl chain structure on the nitrile support mimics the outer leaflet structure of a vesicle membrane.

36 MATERIALS SCIENCE↗

Solution Chemistry to Control Boron-Containing Monolayers on Silicon: Reactions of Boric Acid and 4-Fluorophenylboronic Acid with H- and Cl-terminated Si(100)

In this work, the reactions of boric acid and 4-fluorophenylboronic acid with H- and Cl-terminated Si(100) surfaces in solution were investigated. X-ray photoelectron spectroscopy (XPS) studies reveal that both molecules react preferentially with Cl–Si(100) and not with H–Si(100) at identical conditions. On Cl–Si(100), the reactions introduce boron onto the surface, forming a Si–O–B structure. The quantification of boron surface coverage demonstrates that the 4-fluorophenylboronic acid leads to ~2.8 times higher boron coverage compared to that of boric acid on Cl–Si(100). Consistent with these observations, density functional theory studies show that the reaction of boric acid and 4-fluorophenylboronic acid is more favorable with the Cl- versus H-terminated surface and that on Cl–Si(100) the reaction with 4-fluorophenylboronic acid is ~55.3 kJ/mol more thermodynamically favorable than the reaction with boric acid. The computational studies were also used to demonstrate the propensity of the overall approach to form high-coverage monolayers on these surfaces, with implications for selective-area boron-based monolayer doping.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Antivesiculation and Complete Unbinding of Tail-Tethered Lipids

Here, we report the effect of tail-tethering on vesiculation and complete unbinding of bilayered membranes. Amphiphilic molecules of a bolalipid, resembling the tail-tethered molecular structure of archaeal lipids, with two identical zwitterionic phosphatidylcholine headgroups self-assemble into a large flat lamellar membrane, in contrast to the multilamellar vesicles (MLVs) observed in its counterpart, monopolar nontethered zwitterionic lipids. The antivesiculation is confirmed by small-angle X-ray scattering (SAXS) and cryogenic transmission electron microscopy (cyro-TEM). With the net charge of zero and higher bending rigidity of the membrane (confirmed by neutron spin echo (NSE) spectroscopy), the current membrane theory would predict that membranes should stack with each other (aka “bind”) due to dominant van der Waals attraction, while the outcome of the nonstacking (“unbinding”) membrane suggests that the theory needs to include entropic contribution for the nonvesicular structures. This report pioneers an understanding of how the tail-tethering of amphiphiles affects the structure, enabling better control over the final nanoscale morphology.

36 MATERIALS SCIENCE↗

Subnanometer Thick Native sp 2 Carbon on Oxidized Diamond Surfaces

Oxygen-terminated diamond has a wide breadth of applications, which include stabilizing near-surface color centers, semiconductor devices, and biological sensors. Despite the vast literature on characterizing functionalization groups on diamond, the chemical composition of the shallowest portion of the surface (<1 nm) is challenging to probe with conventional techniques like XPS and FTIR. In this work, we demonstrate the use of angleresolved XPS to probe the first ten nanometers of both oxygen and hydrogen terminated (100) single-crystalline diamond grown via chemical vapor deposition (CVD). With the use of consistent peakfitting methods, the peak identities and relative peak binding energies were identified for sp 2 carbon, ether, hydroxyl, carbonyl, and C−H groups for both of these diamond surface terminations. For the oxygen-terminated sample, we also quantified the thickness of the sp 2 carbon layer situated on top of the bulk sp 3 diamond bonded carbon to be 0.3 ± 0.1 nm, based on the analysis of the Auger electron spectra and D-parameter calculations. These results indicate that the majority of the oxygen is bonded to the sp 2 carbon layer on the diamond, and not directly to the sp 3 diamond bonded carbon.

Carbon↗