Results for “MOLECULAR INTERACTION” — Page 6

DOE OSTI2024

Dynamic embedding of effective harmonic normal mode vibrations in all-atomistic energy gap fluctuations: Case study of light harvesting 2 complex

Environmental effects in excitation energy transfer have mostly been modeled by baths of harmonic oscillators, but to what extent such modeling provides a reliable description of actual interactions between molecular systems and environments remains an open issue. Here, we address this issue by investigating fluctuations in the excitation energies of the light harvesting 2 complex using a realistic all-atomistic simulation of the potential energy surface. Our analyses reveal that molecular motions exhibit significant anharmonic features, even for underdamped intramolecular vibrations. In particular, we find that the anharmonicity contributes to the broadening of spectral densities and substantial overlaps between neighboring peaks, which complicates the meaning of mode frequencies constituting a bath model. Thus, we develop a strategy to construct a minimally underdamped harmonic bath that has a clear connection to all-atomistic dynamics by utilizing actual normal modes of molecules but optimizing their frequencies such that the resulting bath model can best reproduce the all-atomistic simulation results. By subtracting the underdamped contribution from the entire fluctuations, we also show that identifying a residual spectral density representing all other contributions with overdamped behavior is possible. We find that this can be fitted well with a well-established analytic form of a spectral density function or, alternatively, modeled as explicit time dependent fluctuations with muti-exponential or power law type correlation functions. We provide an assessment and the implications of these possibilities. The approach presented here can also serve as a general strategy to construct a simplified bath model that can effectively represent the underlying all-atomistic bath dynamics.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2024

Investigations of atomic and molecular processes of NBI-heated discharges in the MAST Upgrade Super-X divertor with implications for reactors

This experimental study presents an in-depth investigation of the performance of the MAST-U Super-X divertor during NBI-heated operation (up to 2.5 MW) focussing on volumetric ion sources and sinks as well as power losses during detachment. The particle balance and power loss analysis revealed the crucial role of Molecular Activated Recombination and Dissociation (MAR and MAD) ion sinks in divertor particle and power balance, which remain pronounced in the change from ohmic to higher power (NBI heated) L-mode conditions. The importance of MAR and MAD remains with double the absorbed NBI heating. MAD results in significant power dissipation (up to ${\sim} 20\%$ of $P_\textrm{SOL}$), mostly in the cold ($T_e \lt 5$ eV) detached region. Theoretical and experimental evidence is found for the potential contribution of $D^-$ to MAR and MAD, which warrants further study. These results suggest that MAR and MAD can be relevant in higher power conditions than the ohmic conditions studied previously. Post-processing reactor-scale simulations suggests that MAR and MAD can play a significant role in divertor physics and synthetic diagnostic signals of reactor-scale devices, which are currently underestimated in exhaust simulations. This raises implications for the accuracy of reactor-scale divertor simulations of particularly tightly baffled (alternative) divertor configurations.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2025

Programmable exploration of magnetic states in Lieb-kagome interpolated lattices

We investigate a hybrid modeling framework in which a quantum annealer is used to simulate magnetic interactions in molecular qubit lattices inspired by experimentally realizable systems. Using phthalocyanine assemblies as a structurally constrained prototype, we model a continuous deformation from a Lieb to a kagome lattice, revealing frustration-driven disorder and magnetic field-induced reordering in the spin structure. Here, the goal is to show how a quantum annealer can operate as a physically instantiated, programmable platform to emulate experimentally relevant lattice deformations and produce observables in a manner analogous to an experimental measurement, enabling the characterization of magnetic arrangements beyond the reach of current molecular architectures. This surrogate modeling approach offers a pathway to explore and iteratively design tunable magnetic states in synthetic materials. The synthetic design, structural characterization, and quantum simulation framework established here defines a modular and scalable paradigm for probing the limits of engineered matter across chemistry, condensed matter, and quantum information science.

77 NANOSCIENCE AND NANOTECHNOLOGY↗

DOE OSTI2025

Molecular mechanisms of mycorrhizal‐decomposer interactions and impacts on terrestrial biogeochemistry (Final Technical Report)

Soil microorganisms make nutrients available for plants and control a large portion of greenhouse gas emissions from terrestrial ecosystems by respiring CO 2 to the atmosphere, yet our understanding of how they do this is not clear enough to predict the rate of carbon (C) and nutrient flow through soils and the ecosystems they support. A common and abundant type of soil microorganism that associates with the roots of live plants, known as ectomycorrhizal fungi (EMF), is often able to control the amount of nutrients and C that are released from soil (e.g., as CO 2 respired to the atmosphere) during decomposition by microorganisms.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2025

Deep potential molecular dynamics simulations of low-temperature plasma-surface interactions

Machine learning approaches to potential generation for molecular dynamics (MD) simulations of low-temperature plasma-surface interactions could greatly extend the range of chemical systems that can be modeled. Empirical potentials are difficult to generalize to complex combinations of multiple elements with interactions that might include covalent, ionic, and metallic bonds. This work demonstrates that a specific machine learning approach, Deep Potential Molecular Dynamics (DeepMD), can generate potentials that provide a good model of plasma etching in the Si-Cl-Ar system. Comparisons are made between MD results using DeepMD models and empirical potentials, as well as experimental measurements. Pure Si properties predicted by the DeepMD model are in reasonable agreement with experimental results. Simulations of Si bombardment by Ar + ions demonstrate the ability of the DeepMD method to predict sputtering yields as well as the depth of the amorphous-crystalline interface. Etch yields as a function of flux ratio and ion energy for simultaneous Cl 2 and Ar + impacts are in good agreement with previous simulation results and experiment. Predictions of etch yields and etch products during plasma-assisted atomic layer etching of Si-Cl 2 -Ar are shown to be in good agreement with MD predictions using empirical potentials and with experiment. Finally, good agreement was also seen with measurements for the spontaneous etching of Si by Cl atoms at 300 K. Further, the demonstration that DeepMD can reproduce results from MD simulations using empirical potentials is a necessary condition to future efforts to extend the method to a much wider range of systems for which empirical potentials may be difficult or impossible to obtain.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2025

Enhancing Thermal Transport in Polymeric Composites Via Engineered Noncovalent Filler–Polymer Interactions

Understanding thermal transport mechanisms in polymeric composites allows us to expand the boundaries of thermal conductivity in them, either increasing it for more efficient heat dissipation or decreasing it for better thermal insulation. But, these mechanisms are not fully understood. Systematic experimental investigations remain limited. Practical strategies to tune the interfacial thermal resistance (ITR) between fillers and polymers and the thermal conductivity of composites remain elusive. Here, we studied the thermal transport in representative polymer composites, using polyethylene (PE) or polyaniline (PANI) as matrices and graphite as fillers. PANI, with aromatic rings in its backbone, interacts with graphite through strong noncovalent π–π stacking interactions, whereas PE lacks such interactions. We can then quantify how π–π stacking interactions between graphite and polymers enhance thermal transport in composites. PE/graphite and PANI/graphite composites with the same 1.5% filler volume fractions show a ∼22.82% and ∼34.85% enhancement in thermal conductivity compared to pure polymers, respectively. Calculated ITRs in PE/graphite and PANI/graphite are ~6 x 10 -8 m 2 KW -1 and ~1 x 10 -8 m 2 KW -1 , respectively, highlighting how π–π stacking interactions reduce ITR. Molecular dynamics (MD) simulations suggest that π–π stacking interactions between PANI chains and graphite surfaces enhance alignment of PANI's aromatic rings with graphite surfaces. This allows more carbon atoms from PANI chains to interact with graphite surfaces at a shorter distance compared to PE chains. Finally, our work indicates that tuning the π–π stacking interactions between polymers and fillers is an effective approach to reduce the ITR and enhance the thermal conductivity of composites.

atoms↗

DOE OSTI2025

Interactions of Polar and Nonpolar Groups of Alcohols in Zeolite Pores

Understanding the quantitative interactions among zeolite pore walls, Bro̷nsted acid sites, and molecules with both polar and nonpolar regions is essential for scoping out the potential of zeolites as sorbents and catalysts. Purely siliceous zeolites (MFI and Beta in the present study) are hydrophobic, whereas those containing aluminum are considered hydrophilic, preferentially adsorbing organic molecules even in aqueous environments. To characterize these interactions, we use primary alcohols of increasing molecular weight, quantifying their specific interactions in the confined pore space of the alkyl (CH x ) and OH groups. Three types of interactions were identified: (i) alkyl CH x groups interacting with the zeolite pore walls (approximately 10 kJ mol −1 per carbon), (ii) alcohol OH groups interacting with the pore walls (30−35 kJ mol −1 ), and (iii) alcohol OH groups interacting with Bro̷nsted acid sites (37 kJ mol −1 ). All three interactions were well mirrored by computational simulations. The contribution of the alkyl CH x groups was inferred from the incremental increase in sorption enthalpy with increasing molecular weight; the interaction strength of the OH groups was determined by extrapolating the global adsorption enthalpy of the alcohols to a hypothetical OH group without an alkyl group. This value was identical to the adsorption enthalpy of water. The experiments demonstrated that only water has an adsorption enthalpy on zeolite pore walls lower than its condensation enthalpy (30−35 kJ mol −1 vs 45 kJ mol −1 ), limiting the concentration of water that can be adsorbed.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2025

Examining astrophysical gas cloud collapse using an optical depth-scaled, x-ray-irradiated, carbon-foam sphere

When stellar radiation interacts with a molecular cloud, the cloud's fate depends on the strength of the incident radiation and the radiation's mean-free-path within the cloud [F. Bertoldi, Astrophys. J. 346, 735–755 (1989)]. Under the right conditions, the radiation compresses the cloud and a star formation may occur. Where and when the stellar formation occurs in the cloud's collapse are open questions. Direct observation of the complete star–cloud lifecycle is nearly impossible due to the immense timescales and distances over which the interaction occurs. Laboratory astrophysics offers a way to investigate such a system by scaling the important astrophysical parameters to the laboratory. This work describes laboratory experiments to study the radiation-driven implosion of clouds, using x rays from a laser-irradiated, thin, gold foil as a surrogate star and a carbon-foam sphere as a surrogate cloud. An optically thick system, theoretically corresponding to a star-forming regime, was selected by choice of the foam density. Gold foil and sphere motions were imaged by x-ray radiography. Radiographic images show the formation of an interface between rarefied gold and carbon plasmas, a shock moving into the sphere, and a blunting of the initial sphere's shape. Measurements show that the shock moved linearly around 64 μm/ns into the sphere, and the gold–carbon interface formed by 2 ns at the sphere edge remained stationary. The deformation of the sphere was driven by the incident radiation and not by mechanical pressures applied by gold plasma. The blunting of the sphere was likely due to the geometric reduction of flux near the sphere's poles. Higher x-ray flux near the sphere's equator caused high compression and a faster shock, which flattened the sphere. We will discuss the results and implications of our observations.

VanDervort, R. W. [University of Michigan 1 , Ann ↗

DOE OSTI2025

Reversible Physical Gelation of Thermotropic Liquid Crystals Driven by Nanoplate Self-Assembly

Physically gelled soft materials, driven by the self-assembly of low-molecular-mass gelators (LMGs), have emerged as a platform for designing advanced gels that exhibit reversible gelation and property tunability. Liquid crystal (LC) gels are of great interest due to their supramolecular orderings as gel hosts and their enhanced electro-optical properties. In this study, we demonstrate the physical gelation of a nematic LC driven by nanoplate self-assembly, expanding the concept of gelators from small molecules to nanoparticles. These nanoplates are functionalized with promesogenic ligands and form a fibrillar network in LCs with face-to-face interplate stacking, resembling LMGs. The critical gelation volume fraction in the tilt test is only 0.14 v %, comparable to values reported for LMGs. Rheological analyses confirm viscoelastic properties characteristic of gelation. In situ small-angle X-ray scattering (SAXS) characterizes the formation of nanoplate networks in the LC with decreasing temperature, wherein LC mesogens become trapped in pores. Molecular dynamics (MD) simulations reveal that the interaction between ligand-coated nanoplates and LC-forming mesogens induces a multidomain LC structure, increasing friction between LC domains and stabilizing the gel. This study establishes direct relationships among molecular interactions, nanostructures, and mechanical properties in physically gelled LCs. In conclusion, the findings inspire the future gelator design of both LMGs and nanoplates, with potential applicability in bioscaffold engineering and liquid crystalline nanocomposites.

36 MATERIALS SCIENCE↗

DOE OSTI2024

Deep-Learning Interatomic Potential Connects Molecular Structural Ordering to the Macroscale Properties of Polyacrylonitrile

Polyacrylonitrile (PAN) is an important commercial polymer, bearing atactic stereochemistry resulting from nonselective radical polymerization. As such, an accurate, fundamental understanding of governing interactions among PAN molecular units is indispensable for advancing the design principles of final products at reduced processability costs. While ab initio molecular dynamics (AIMD) simulations can provide the necessary accuracy for treating key interactions in polar polymers, such as dipole–dipole interactions and hydrogen bonding, and analyzing their influence on the molecular orientation, their implementation is limited to small molecules only. Herein, we show that the neural network interatomic potentials (NNIPs) that are trained on the small-scale AIMD data (acquired for oligomers) can be efficiently employed to examine the structures and properties at large scales (polymers). NNIP provides critical insight into intra- and interchain hydrogen-bonding and dipolar correlations and accurately predicts the amorphous bulk PAN structure validated by modeling the experimental X-ray structure factor. Furthermore, the NNIP-predicted PAN properties, such as density and elastic modulus, are in good agreement with their experimental values. Overall, the trend in the elastic modulus is found to correlate strongly with the PAN structural orientations encoded in the Hermans orientation factor. In conclusion, this study enables the ability to predict the structure–property relations for PAN and analogues with sustainable ab initio accuracy across scales.

36 MATERIALS SCIENCE↗

DOE OSTI2025

Data from "Deep Potential Molecular Dynamics Simulations of Low-Temperature Plasma-Surface Interactions"

Data and input files related to the paper "Deep Potential Molecular Dynamics Simulations of Low-Temperature Plasma-Surface Interactions" (https://doi.org/10.1116/6.0004027). This includes the final DP model used in all simulations, training data set, example input files to run DeepMD (with LAMMPS), and data tables summarizing the results obtained from the simulations.

machine learning models↗

DOE OSTI2025

Nature of molybdenum carbide surfaces for catalytic hydrogen dissociation using machine-learned potentials: an ensemble-averaged perspective

Molybdenum carbides with an electronic structure similar to noble metals have gained attention as a promising low-cost catalyst for biomass valorization and the hydrogen evolution reaction. However, our fundamental understanding of the catalyst surface and how different phases of these catalysts behave at varying reaction conditions is limited to ground state density functional theory calculations as ab initio molecular dynamics (AIMD) is computationally prohibitive at relevant length and time scales. Here, in this work, we train a multi-atomic cluster expansion (MACE) machine-learned interatomic potentials (MLIP) to study hydrogen dissociation and dynamics over Mo, δ-MoC, α-Mo 2 C, and β-Mo 2 C surfaces at varying temperatures and hydrogen partial pressures. Our simulations identify unique and different molecular and atomic hydrogen adsorption sites on different surfaces that do not depend on the temperature. At low hydrogen pressures, the surface coverage is monolayer, which transitions to two-layer adsorption at higher pressures. We find that atomic hydrogen diffusion and recombinations are preferred over molybdenum atom hollow sites, while the diffusion over carbon-terminated facets was negligible, signifying particularly strong C–H interactions. In contrast, molecular hydrogen adsorption occurs mostly atop Mo or the bridging sites. At a comparable hydrogen loading, β-Mo 2 C (001) is the most active surface for hydrogen dissociation reaction. This work provides insights into the dynamic nature of the hydrogen dissociation chemistry and the diversity of hydrogen adsorption sites on molybdenum carbides.

08 HYDROGEN↗

DOE OSTI2026

Investigating PVC polymer–plasticizer interactions with atomistic MD simulations and potential of mean force calculations

For this work, atomistic molecular dynamics (MD) simulations coupled with potential of mean force (PMF) calculations were employed to investigate the interactions between PVC polymer chains containing 6–20 repeating units and various plasticizers, with the goal of identifying potential replacements for the toxic plasticizer di(2-ethylhexyl)phthalate (DEHP) used in blood bags. The selected plasticizers belong to various chemical families, such as orthophthalates, citrates, adipates, and the terephthalate DEHT. Both the polymer and the plasticizers lack ionizable groups, and their interactions are primarily governed by van der Waals and electrostatic forces. A model correlating PMF profiles with interaction forces was developed and validated across polyvinyl chloride (PVC) polymers of different lengths and all investigated plasticizers. This model provides insight into how structural variations in plasticizers influence their respective PMF values. The study ranks the investigated plasticizers based on binding affinity, identifying TOTM (tris(2-ethylhexyl) trimellitate, TEHTM), BTHC (butyryl trihexyl citrate, Citroflex B-6), ATHC (acetyl trihexyl citrate, Citroflex A-6, CA-6), and DEHT (bis(2-ethylhexyl)terephthalate, DOTP/DEHTP) as promising alternatives for further investigation. This comprehensive study encompasses PVC polymers of four different lengths and 14 plasticizers, with all data averaged over 30 independent simulations. The approach provides a deeper understanding of molecular interactions, enabling the tailoring of polymer–plasticizer systems for diverse applications, including extractables and leachables, with relevance spanning materials science to biomedical engineering, and also serves as a basis for developing coarse-grained simulation protocols. Overall, this study provides valuable insights for designing safer and more efficient plasticizer substitutes and is well supported by other studies.

Shet, Sai Athmeeya G. [Sri Sathya Sai Institute of↗

DOE OSTI2024

National User Resource for Biological Accelerator Mass Spectrometry

The National User Resource for Biological Accelerator Mass Spectrometry (User Resource) will provide isotopic analysis (primarily radiocarbon or 14C) by accelerator mass spectrometry (AMS) for NIH- funded researchers across the United States and will be the only User Resource of its type in the United States. The User Resource will provide measurement capability and expertise to a research community that requires highly sensitive, quantitative isotope analyses. Since commissioning a new accelerator mass spectrometer in June 2014, we have measured over 4000 samples a year for collaborators and service users. The User Resource will enable us to continue to meet these research needs, as well as provide for new users whose research programs would benefit from AMS as a measurement tool. The User Resource’s forte will be ultra-high sensitivity quantitation of radiocarbon and selected other radioisotopes for research studies where isotopes are required. Radioisotope labeling studies have been and will continue to be an important tool for addressing many complex biomedical science problems. AMS is a specialized and unique type of mass spectrometry that provides absolute quantitation of radiocarbon and other relevant radioisotopes with extreme sensitivity, having limits of detection in real samples on the order of a few attomol/mg of sample at measurement precisions of ~3%. It is the only instrumental method capable of quantifying radioisotope-labeled agents routinely in real-world samples with such precision and sensitivity. The sensitivity of AMS allows for the quantification of radiolabeled metabolites in extremely complex matrices of cells and organisms at very low concentrations and in small samples. AMS allows studies to be conducted without perturbing metabolism leading to more relevant quantification of metabolic rates and pathways. In addition, it enables quantification of pharmacokinetic and metabolic properties of toxicants at environmentally relevant concentrations in model systems as well as the ability to quantify pharmacokinetics and other molecular endpoints directly in humans. Such quantitative assessments can 1) improve risk assessment for toxicants, 2) address safety and efficacy considerations for therapeutic entities, 3) deepen understanding of xenobiotic and intermediary metabolism, 4) help understand the interactions between critical molecular pathways, and 5) improve efforts to model and predict various metabolic and biological states. These capabilities have been applied in a number of areas including research in carcinogenesis, toxicology, nutrition, pharmacology/drug development and basic biological science. As a NIGMS National Resource the National User Resource for Biological Accelerator Mass Spectrometry will help NIH funded scientists achieve a deeper understanding of the etiology of human health concerns by (1) enabling the quantification of pharmacokinetics and other molecular endpoints directly in humans; (2) offering the ability to conduct quantitative studies using biologics such as proteins or lipids, and thereby reducing the amount of radioisotope usage in biomedical labs; and (3) enabling more relevant studies of metabolic pathways in health and disease through the use of much lower, more biologically-relevant, concentrations of metabolic substrates in cells and intact organisms. Such studies support NIGMS’s basic biomedical research areas that contribute to the understanding of fundamental cellular and physiological principles and enable research supported by the Biophysics, Biomedical Technology, and Computational Biosciences (BBCB); Genetics and Molecular, Cellular, and Developmental Biology (GMCDB); Pharmacology, Physiology, Biological Chemistry (PPBC) and Training, Workforce Development, and Diversity (TWD) Divisions.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

DOE OSTI2025

National User Resource for Biological Accelerator Mass Spectrometry (Final Report)

The National User Resource for Biological Accelerator Mass Spectrometry (User Resource) will provide isotopic analysis (primarily radiocarbon or 14C) by accelerator mass spectrometry (AMS) for NIH- funded researchers across the United States and will be the only User Resource of its type in the United States. The User Resource will provide measurement capability and expertise to a research community that requires highly sensitive, quantitative isotope analyses. Since commissioning a new accelerator mass spectrometer in June 2014, we have measured over 4000 samples a year for collaborators and service users. The User Resource will enable us to continue to meet these research needs, as well as provide for new users whose research programs would benefit from AMS as a measurement tool. The User Resource’s forte will be ultra-high sensitivity quantitation of radiocarbon and selected other radioisotopes for research studies where isotopes are required. Radioisotope labeling studies have been and will continue to be an important tool for addressing many complex biomedical science problems. AMS is a specialized and unique type of mass spectrometry that provides absolute quantitation of radiocarbon and other relevant radioisotopes with extreme sensitivity, having limits of detection in real samples on the order of a few attomol/mg of sample at measurement precisions of ~3%. It is the only instrumental method capable of quantifying radioisotope-labeled agents routinely in real-world samples with such precision and sensitivity. The sensitivity of AMS allows for the quantification of radiolabeled metabolites in extremely complex matrices of cells and organisms at very low concentrations and in small samples. AMS allows studies to be conducted without perturbing metabolism leading to more relevant quantification of metabolic rates and pathways. In addition, it enables quantification of pharmacokinetic and metabolic properties of toxicants at environmentally relevant concentrations in model systems as well as the ability to quantify pharmacokinetics and other molecular endpoints directly in humans. Such quantitative assessments can 1) improve risk assessment for toxicants, 2) address safety and efficacy considerations for therapeutic entities, 3) deepen understanding of xenobiotic and intermediary metabolism, 4) help understand the interactions between critical molecular pathways, and 5) improve efforts to model and predict various metabolic and biological states. These capabilities have been applied in a number of areas including research in carcinogenesis, toxicology, nutrition, pharmacology/drug development and basic biological science. As a NIGMS National Resource the National User Resource for Biological Accelerator Mass Spectrometry will help NIH funded scientists achieve a deeper understanding of the etiology of human health concerns by (1) enabling the quantification of pharmacokinetics and other molecular endpoints directly in humans; (2) offering the ability to conduct quantitative studies using biologics such as proteins or lipids, and thereby reducing the amount of radioisotope usage in biomedical labs; and (3) enabling more relevant studies of metabolic pathways in health and disease through the use of much lower, more biologically-relevant, concentrations of metabolic substrates in cells and intact organisms. Such studies support NIGMS’s basic biomedical research areas that contribute to the understanding of fundamental cellular and physiological principles and enable research supported by the Biophysics, Biomedical Technology, and Computational Biosciences (BBCB); Genetics and Molecular, Cellular, and Developmental Biology (GMCDB); Pharmacology, Physiology, Biological Chemistry (PPBC) and Training, Workforce Development, and Diversity (TWD) Divisions. Over the next five years, our goals are to: 1. Improve the efficiency of operation for AMS measurements through installation of new interfaces to our AMS systems, technical modifications to improve gas accepting ion source efficiency and upgrading our data analysis software for improved ease of use and data reporting. 2. Increase the accessibility and visibility of ultra-sensitive 14C measurements for the biomedical research community by training of new investigators and expanding our national user base. 3. Provide high throughput, ultra-sensitive 14C analysis for the NIGMS and NIH user community.

47 OTHER INSTRUMENTATION↗

DOE OSTI2025

Single-Molecule Vibrational Characterization of Binding Geometry Effects on Isocyanide–Metal Interactions

Isocyanide−metal binding is governed by σ-donation and π-back-bonding, which affects the isocyanide stretching energy, a characteristic probe for ligand−metal interactions. While extensive correlations exist between structure and spectroscopy in molecular isocyanide−metal systems, interactions of isocyanide with crystalline metallic surfaces, where ligands often bind in various geometries, remain underexplored. Conventional vibrational spectroscopies such as infrared and Raman spectroscopies lack the molecular-scale resolution to distinguish this binding inhomogeneity. In contrast, inelastic electron tunneling spectroscopy with scanning tunneling microscopy (STM-IETS) directly visualizes ligand adsorption geometries and their vibrational signatures. Using STM-IETS, we investigate a metal-adsorbed m -terphenyl isocyanide ligand and find that the adsorption geometry on Cu(100) induces a significant shift in isocyanide stretching frequency, more prominent than replacing Cu(100) with Ag(111). Density functional theory confirms that this shift arises from atomic-scale variations in coordination environments. This study elucidates how precise binding influences the vibrational fingerprints of isocyanide ligands, an often-overlooked factor in understanding the isocyanide−metal interplay.

77 NANOSCIENCE AND NANOTECHNOLOGY↗

DOE OSTI2025

Structure of the human autophagy factor EPG5 and the molecular basis of its conserved mode of interaction with Atg8-family proteins

Not provided.

Cell Biology↗

DOE OSTI2025

Molecular basis for human respiratory syncytial virus transcriptional regulator NS1 interactions with MED25

The Mediator complex facilitates interactions between transcription factors and RNA polymerase II, a process that is required for host gene transcription, including in response to viral infections. Among the many subunits in the Mediator complex, the MED25 subunit has been shown to be a target for viral activators during infection. Here we provide the molecular basis for the interaction between human respiratory syncytial virus (hRSV) nonstructural 1 protein (NS1) and the activator interaction domain (ACID) of MED25. The X-ray crystal structure of the complex revealed that NS1 straddles and binds two faces of MED25 ACID. This interaction is distinct from previously known viral activators. Importantly, our data support the conformational flexibility of viral transcriptional regulators. Furthermore, ChIP-seq and RNA-seq analysis identified the ATF3 transcription factor and a role for NS1/Mediator/ATF3 interaction in host gene regulation in hRSV infections. Our findings provide a molecular basis for hRSV NS1-based regulation of host gene transcription and reveal how viruses exploit the conformational heterogeneity at fuzzy transcription activator interfaces.

60 APPLIED LIFE SCIENCES↗