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DOE OSTI2020

Chemical and structural investigation of the paroxetine-human serotonin transporter complex

Antidepressants target the serotonin transporter (SERT) by inhibiting serotonin reuptake. Structural and biochemical studies aiming to understand binding of small-molecules to conformationally dynamic transporters like SERT often require thermostabilizing mutations and antibodies to stabilize a specific conformation, leading to questions about relationships of these structures to the bonafide conformation and inhibitor binding poses of wild-type transporter. To address these concerns, we determined the structures of ΔN72/ΔC13 and ts2-inactive SERT bound to paroxetine analogues using single-particle cryo-EM and x-ray crystallography, respectively. We synthesized enantiopure analogues of paroxetine containing either bromine or iodine instead of fluorine. We exploited the anomalous scattering of bromine and iodine to define the pose of these inhibitors and investigated inhibitor binding to Asn177 mutants of ts2-active SERT. These studies provide mutually consistent insights into how paroxetine and its analogues bind to the central substrate-binding site of SERT, stabilize the outward-open conformation, and inhibit serotonin transport.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2025

Subsurface hydrogen, curvature, and strain: lessons from electro-reduction of benzaldehyde on nano-structured Pd catalysts

The unique ability of palladium (Pd) to absorb hydrogen and form a bulk hydride is vital for chemical transformations that involve hydrogenation reactions. Nano-structured Pd catalysts offer a promise of tuning these reaction rates by exploiting variations of reactant binding energies depending on the surface structure and morphological constraints that result in inhomogeneous strain. However, the interplay between the nano-structure of Pd and the ability of Pd to adsorb (and absorb) hydrogen as well as other reactive species needs to be better understood for a rational understanding of competitive chemical transformations at Pd surfaces. We consider the effects of the surface corrugation, strain, and subsurface Pd hydride on the reduction of benzaldehyde to benzyl alcohol in two qualitatively different samples – Pd nanoparticles and Pd gels formed by quasi-one-dimensional chains of these nanoparticles. Our electrochemical measurements and computational modelling suggest that surface concave sites, inherent to Pd gels, facilitate hydrogen transfer to the Pd subsurface region, thus weakening benzaldehyde binding to the surface. This effect is further modulated by the strain, depending on the local coordination environment on the corrugated surface. Furthermore, these findings demonstrate how structurally complex samples in the form of gels provide degrees of freedom for controlling the behavior of metal catalysts that are not available in isolated nanoparticles, which paves the way for new approaches in the design of catalytic materials and synthesis of metal hydrides.

Padavala, Sri Krishna Murthy [University of Minnes↗

DOE OSTI2023

Two excited-state datasets for quantum chemical UV-vis spectra of organic molecules

Abstract We present two open-source datasets that provide time-dependent density-functional tight-binding (TD-DFTB) electronic excitation spectra of organic molecules. These datasets represent predictions of UV-vis absorption spectra performed on optimized geometries of the molecules in their electronic ground state. The GDB-9-Ex dataset contains a subset of 96,766 organic molecules from the original open-source GDB-9 dataset. The ORNL_AISD-Ex dataset consists of 10,502,904 organic molecules that contain between 5 and 71 non-hydrogen atoms. The data reveals the close correlation between the magnitude of the gaps between the highest occupied molecular orbital (HOMO) and the lowest unoccupied molecular orbital (LUMO), and the excitation energy of the lowest singlet excited state energies quantitatively. The chemical variability of the large number of molecules was examined with a topological fingerprint estimation based on extended-connectivity fingerprints (ECFPs) followed by uniform manifold approximation and projection (UMAP) for dimension reduction. Both datasets were generated using the DFTB+ software on the “Andes” cluster of the Oak Ridge Leadership Computing Facility (OLCF).

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2025

Extending quantum-mechanical benchmark accuracy to biological ligand-pocket interactions

Predicting the binding affinity of ligands to protein pockets is key in the drug design pipeline. The flexibility of ligand-pocket motifs arises from a range of attractive and repulsive electronic interactions during binding. Accurately accounting for all interactions requires robust quantum-mechanical (QM) benchmarks, which are scarce for ligand-pocket systems. Additionally, disagreement between “gold standard” Coupled Cluster (CC) and Quantum Monte Carlo (QMC) methods casts doubt on many benchmarks for larger non-covalent systems. We introduce the “QUantum Interacting Dimer” (QUID) benchmark framework containing 170 non-covalent (non-)equilibrium systems modeling chemically and structurally diverse ligand-pocket motifs. Symmetry-adapted perturbation theory shows that QUID broadly covers non-covalent binding motifs and energetic contributions. Robust binding energies are obtained using complementary CC and QMC methods, achieving agreement of 0.5 kcal/mol. The benchmark data analysis reveals that several dispersion-inclusive density functional approximations provide accurate energy predictions, though their atomic van der Waals forces differ in magnitude and orientation. Contrarily, semiempirical methods and empirical force fields require improvements in capturing non-covalent interactions (NCIs) for out-of-equilibrium geometries. The wide span of NCIs, highly accurate interaction energies, and analysis of molecular properties take QUID beyond the “gold standard” for QM benchmarks of ligand-protein systems.

Puleva, Mirela [University of Luxembourg, Luxembou↗

DOE OSTI2021

Size and Stoichiometry Effects on the Reactivity of MoCy Nanoparticles Towards Ethylene

Molybdenum carbides are promising catalysts alternative to Pt-group metals for the hydrogenation of unsaturated hydrocarbons. Nanostructuring has been shown to be an efficient way to boost the catalytic activity of these materials with MoCy nanoparticles (NPs) exhibiting a good performance when encapsulated inside zeolites or dispersed on inert supports such as carbon or gold. In this work, we focus on a systematic DFT study of the interaction of MoCy NPs with ethylene (C 2 H 4 ), as a general and simple approach for examining binding and activation of C≡C bonds. Models for 14 NPs, with a Mo/C ratio in the 0.67 to 2.00 range, have been built following a cascade procedure. Several chemical descriptors, including the adsorption energy, structural NPs distortion, C≡C deformation, and C 2 H 4 attachment energy have been analyzed along with a meticulous geometric and electronic characterization of bare NPs and C2H4 binding. The present results show that 1:1 stoichiometric Mo 6 C 6 , Mo 12 C 12 , and Mo 24 C 24 , and the non-stochiometric Mo 4 C 6 , Mo 8 C 12 (MetCar), and Mo 14 C 13 (Nanocube) are excellent systems for the binding and activation of ethylene, exhibiting a much bigger reactivity than a bulk δ-MoC(001) surface with a similar Mo:C ratio. In addition, C 2 H 4 binding on the NPs with a Mo/C < 1.08 is advantageous since, apart from a rather large adsorption energy, implies low energy values for NPs deformation (from 0.00 to 0.31 eV), C≡C distortion (from 0.30 to 0.52 eV), and C 2 H 4 attachment (from -2.12 to -2.58 eV). These theoretical results point to the ideal MoCy size and composition for C 2 H 4 binding, providing a background for further experimental studies aimed at the preparation of MoCy NPs as hydrogenation catalysts.

36 MATERIALS SCIENCE↗

DOE OSTI2022

The Importance of Avoided Crossings in Understanding High Valley Degeneracy in Half‐Heusler Thermoelectric Semiconductors

Abstract Half‐Heusler (hH) compounds are promising candidates for inexpensive, low‐toxicity thermoelectric materials. It is well known that engineering electronic bands with high valley degeneracy is an effective approach for enhancing the performance of thermoelectric materials, and there are several routes for achieving high valley degeneracy in hH systems. For instance, there are multiple locations in the first Brillouin zone where the valence band maximum can be found (at the Γ‐, L‐, or W‐point), and there are two competing low‐lying conduction bands at the X‐point, where the conduction band minimum is located. By converging the multiple valence band and conduction band extrema, the valley degeneracy, and hence, performance of these materials can be improved. Here, group theoretical and tight‐binding approaches, in addition to first‐principles density functional theory calculations, are used to study the chemical origins of various band extrema in both the n‐type and p‐type compounds, with particular focus on ZrNiSn and NbFeSb. Specifically, the importance of avoided crossings is explained. The results of this work can be used to better understand and develop design strategies for engineering better performing hH thermoelectrics.

Brod, Madison K.↗

DOE OSTI2026

Ferromagnetic Insulator to Metal Transition in Noncentrosymmetric Graphene Nanoribbons

Engineering sublattice imbalance within the unit cell of bottom-up synthesized graphene nanoribbons (GNRs) represents a versatile tool for realizing custom-tailored quantum nanomaterials. The interaction between low-energy zero-modes (ZMs) not only contributes to frontier bands but can form the basis for magnetically ordered phases. Here, we present the bottom-up synthesis of a noncentrosymmetric GNR that places all ZMs on the majority sublattice sites. Scanning tunneling microscopy and spectroscopy reveal that strong electron–electron correlations, leading to the Stoner magnetic instability, drive the system into a ferromagnetically ordered insulating ground state featuring a sizable band gap of E g ∼1.2 eV. At higher temperatures, a chemical transformation induces an insulator-to-metal transition that quenches the ferromagnetic order. Tight-binding (TB), density functional theory, and GW calculations corroborate our experimental observations. Furthermore, this work showcases how control over molecular symmetry, sublattice polarization, and ZM hybridization in bottom-up synthesized nanographenes can open a path to the exploration of many-body physics in rationally designed quantum materials.

Band structure↗

DOE OSTI2020

Mechanochemical synthesis of pillar[5]quinone derived multi-microporous organic polymers for radioactive organic iodide capture and storage

The incorporation of supramolecular macrocycles into porous organic polymers may endow the material with enhanced uptake of specific guests through host–guest interactions. Here we report a solvent and catalyst-free mechanochemical synthesis of pillar[5]quinone (P5Q) derived multi-microporous organic polymers with hydrophenazine linkages (MHP-P5Q), which show a unique 3-step N 2 adsorption isotherm. In comparison with analogous microporous hydrophenazine-linked organic polymers (MHPs) obtained using simple twofold benzoquinones, MHP-P5Q is demonstrated to have a superior performance in radioactive iodomethane (CH 3 I) capture and storage. Mechanistic studies show that the rigid pillar[5]arene cavity has additional binding sites though host–guest interactions as well as the halogen bond (-I···N = C-) and chemical adsorption in the multi-microporous MHP-P5Q mainly account for the rapid and high-capacity adsorption and long-term storage of CH 3 I.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2024

An artificial intelligence accelerated virtual screening platform for drug discovery

Abstract Structure-based virtual screening is a key tool in early drug discovery, with growing interest in the screening of multi-billion chemical compound libraries. However, the success of virtual screening crucially depends on the accuracy of the binding pose and binding affinity predicted by computational docking. Here we develop a highly accurate structure-based virtual screen method, RosettaVS, for predicting docking poses and binding affinities. Our approach outperforms other state-of-the-art methods on a wide range of benchmarks, partially due to our ability to model receptor flexibility. We incorporate this into a new open-source artificial intelligence accelerated virtual screening platform for drug discovery. Using this platform, we screen multi-billion compound libraries against two unrelated targets, a ubiquitin ligase target KLHDC2 and the human voltage-gated sodium channel Na V 1.7. For both targets, we discover hit compounds, including seven hits (14% hit rate) to KLHDC2 and four hits (44% hit rate) to Na V 1.7, all with single digit micromolar binding affinities. Screening in both cases is completed in less than seven days. Finally, a high resolution X-ray crystallographic structure validates the predicted docking pose for the KLHDC2 ligand complex, demonstrating the effectiveness of our method in lead discovery.

Science & Technology - Other Topics↗

DOE OSTI2024

Twentieth Exotic Beam Summer School (EBSS2023)

The study of unstable nuclei with unusual ratios of protons to neutrons is one of the frontiers of science. Investigating these rare isotopes is critical for understanding the synthesis of the chemical elements in stellar explosions as well as the fundamental nature of the nuclear forces that bind atomic nuclei together. Scientific progress in this field is driven by the development of exotic beams in present and next-generation rare-isotope beam facilities including the Facility for Rare Isotope Beams (FRIB). Nuclear physics is a broad discipline, influencing our knowledge on subjects as diverse as weakly-bound nuclei, many-body quantum theory, the super heavy elements, and the inner structure of neutron stars. Applications based on nuclear science and technologies include medical diagnostics and therapies, materials science, and national security. The major goal achieved in this project was to hold Exotic Beam Summer School 2023 (EBSS2023), the twentieth installment of EBSS series, July 9-15, 2023 at the Facility for Rare Isotope Beams on the campus of Michigan State University to educate and train the next generation of scientists that will drive research with rare-isotope beams. FRIB became operational in 2022 and is now providing beams of exotic nuclei that will ramp up to unmatched intensities, exceeding what is available today by orders of magnitude. Beams available at FRIB are facilitating a wide variety of studies in nuclear structure, astrophysics, fundamental symmetries and societal applications. There is a large community of scientists interested in working with rare isotope beams; for example, the FRIB User Organization currently has over 1,700 members. In order to maximize the scientific output of FRIB, there must be a workforce continuously trained in both the physics of exotic beams and in the practical techniques of carrying out an experiment. This summer school series is designed to specifically address this need - to ensure that new generations of scientists from a broad range of institutions and backgrounds is trained, motivated, and equipped to push the field forward to new and important breakthroughs.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

NASA NTRS1996

Electronic Characterization of Defects in Narrow Gap Semiconductors-Comparison of Electronic Energy Levels and Formation Energies in Mercury Cadmium Telluride, Mercury Zinc Telluride, and Mercury Zinc Selenide

We have used a Green's function technique to calculate the energy levels and formation energy of deep defects in the narrow gap semiconductors mercury cadmium telluride (MCT), mercury zinc telluride (MZT) and mercury zinc selenide (MZS). The formation energy is calculated from the difference between the total energy with an impurity cluster and the total energy for the perfect crystal. Substitutional (including antisite), interstitial (self and foreign), and vacancy deep defects are considered. Relaxation effects are calculated (with molecular dynamics). By use of a pseudopotential, we generalize the ideal vacancy model so as to be able to consider relaxation for vacancies. Different charge states are considered and the charged state energy shift (as computed by a modified Haldane-Anderson model) can be twice that due to relaxation. Different charged states for vacancies were not calculated to have much effect on the formation energy. For all cases we find deep defects in the energy gap only for cation site s-like orbitals or anion site p-like orbitals, and for the substitutional case only the latter are appreciably effected by relaxation. For most cases for MCT, MZT, MZS, we consider x (the concentration of Cd or Zn) in the range appropriate for a band gap of 0.1 eV. For defect energy levels, the absolute accuracy of our results is limited, but the precision is good, and hence chemical trends are accurately predicted. For the same reason, defect formation energies are more accurately predicted than energy level position. We attempt, in Appendix B, to calculate vacancy formation energies using relatively simple chemical bonding ideas due to Harrison. However, these results are only marginally accurate for estimating vacancy binding energies. Appendix C lists all written reports and publications produced for the grant. We include abstracts and a complete paper that summarizes our work which is not yet available.

Patterson, James D.↗

NASA NTRS1998

Substrate Effects on Electronic Properties of Atomic Chains

Atomic chains, precise structures of adatoms created on an atomically regulated surface, are candidates for constituent elements in future electronics. It was predicted that Si chains were metallic and Mg chains were semiconducting, and a doping method was also discussed. The substrate was assumed to work as a non-interacting template holding the adatoms. However, this scheme requires a low-temperature environment so that the adatoms will not displace from their ideal positions due to unwanted thermal agitation. For better structural stability, we may seek a scheme to allow the adatoms to form chemical bonding with the substrate atoms and secure their positions. The chemical bonding has two major effects on the chain electronic properties. First, only the remaining s and p orbitals in an adatom not used for the chemical bonding can decide chain band structures, rather than the full set of orbitals previously assumed. Second, because of a possible HOMO energy difference between adatom and substrate atom, semiconducting chains are unintentionally doped. These effects are studied with a self-consistent tight-binding method with universal parameters. With one adatom per unit cell, adatom chains are semiconducting: (1) if adatoms are of group III and form one chemical bond per adatom, or (2) if adatoms are of group IV and form two chemical bonds. 'Me previous result [I I of realizing semiconducting chains by group II adatoms without chemical bonds is consistent with this picture. When the HOMO energy in an adatom is shallower than that in a substrate atom, the entire chain is positively polarized, unintentionally achieving p-type doping. When deeper, the chain is negatively charged, achieving n-type doping.

Yamada, Toshishige↗

DOE OSTI2021

Solid-Binding Proteins: Bridging Synthesis, Assembly, and Function in Hybrid and Hierarchical Materials Fabrication

There is considerable interest in the development of hybrid organic–inorganic materials because of the potential for harvesting the unique capabilities that each system has to offer. Proteins are an especially attractive organic component owing to the high amount of chemical information encoded in their amino acid sequence, their amenability to molecular and computational (re)design, and the many structures and functions they specify. Genetic installation of solid-binding peptides (SBPs) within protein frameworks affords control over the position and orientation of adhesive and morphogenetic segments, and a path toward predictive synthesis and assembly of functional materials and devices, all while harnessing the built-in properties of the host scaffold. Furthermore, we review the current understanding of the mechanisms through which SBPs bind to technologically relevant interfaces, with an emphasis on the variables that influence the process, and highlight the last decade of progress in the use of solid-binding proteins for hybrid and hierarchical materials synthesis.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2023

Enhancing the accuracy of density functional tight binding models through ChIMES many-body interaction potentials

Semi-empirical quantum models such as Density Functional Tight Binding (DFTB) are attractive methods for obtaining quantum simulation data at longer time and length scales than possible with standard approaches. However, application of these models can require lengthy effort due to the lack of a systematic approach for their development. In this work, we discuss the use of the Chebyshev Interaction Model for Efficient Simulation (ChIMES) to create rapidly parameterized DFTB models, which exhibit strong transferability due to the inclusion of many-body interactions that might otherwise be inaccurate. We apply our modeling approach to silicon polymorphs and review previous work on titanium hydride. We also review the creation of a general purpose DFTB/ChIMES model for organic molecules and compounds that approaches hybrid functional and coupled cluster accuracy with two orders of magnitude fewer parameters than similar neural network approaches. In all cases, DFTB/ChIMES yields similar accuracy to the underlying quantum method with orders of magnitude improvement in computational cost. In conclusion, our developments provide a way to create computationally efficient and highly accurate simulations over varying extreme thermodynamic conditions, where physical and chemical properties can be difficult to interrogate directly, and there is historically a significant reliance on theoretical approaches for interpretation and validation of experimental results.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2025

Unraveling Bacterial Adaptation Strategies in the Microbiome Shaped by the Chemical Environment of the Plant Rhizosphere

The rhizosphere is a dynamic environment where rhizodeposits that include primary and secondary metabolites and mucilage serve as nutrient sources for soil microorganisms, attracting them toward plant roots. However, understanding how these microbes specifically respond to plant root chemical signals has been hindered by the challenges of disentangling physical and chemical interactions between the microbes and plant roots. To address this, we implemented an innovative filter-based experimental setup on plant roots that creates a physical barrier while facilitating the exchange of chemical signals. The proteomic analysis of 10 Populus root-associated bacterial strains grown in the presence or absence of a plant in either individual or mixed community conditions provided detailed insights into the functional responses of these strains to the root chemical environment. Additionally, this approach allowed us to discern the impact of root exudates on overall community dynamics. In particular, metaproteomic analyses revealed that each of these 10 microbial members responds uniquely to the presence of the plant, with Bacillus and Pantoea exhibiting the most dramatic favorable impact. Proteomic examination revealed the details of metabolism fine-tuning, including processes such as chemotaxis and ATP-binding cassette transporter proteins. This study demonstrates the application of a filter-based experimental setup to study microbial responses to plant chemicals and sheds light on adaptation strategies employed by various bacterial strains for survival in the rhizosphere.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2021

Elucidation of Agonist and Antagonist Dynamic Binding Patterns in ER-α by Integration of Molecular Docking, Molecular Dynamics Simulations and Quantum Mechanical Calculations

Estrogen receptor alpha (ERα) is a ligand-dependent transcriptional factor in the nuclear receptor superfamily. Many structures of ERα bound with agonists and antagonists have been determined. However, the dynamic binding patterns of agonists and antagonists in the binding site of ERα remains unclear. Therefore, we performed molecular docking, molecular dynamics (MD) simulations, and quantum mechanical calculations to elucidate agonist and antagonist dynamic binding patterns in ERα. 17β-estradiol (E2) and 4-hydroxytamoxifen (OHT) were docked in the ligand binding pockets of the agonist and antagonist bound ERα. The best complex conformations from molecular docking were subjected to 100 nanosecond MD simulations. Hierarchical clustering was conducted to group the structures in the trajectory from MD simulations. The representative structure from each cluster was selected to calculate the binding interaction energy value for elucidation of the dynamic binding patterns of agonists and antagonists in the binding site of ERα. The binding interaction energy analysis revealed that OHT binds ERα more tightly in the antagonist conformer, while E2 prefers the agonist conformer. The results may help identify ERα antagonists as drug candidates and facilitate risk assessment of chemicals through ER-mediated responses.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2025

Molecular-Scale Insights into the Heterogeneous Interactions between an m -Terphenyl Isocyanide Ligand and Noble Metal Nanoparticles

The structural and chemical properties of metal nanoparticles are often dictated by their interactions with molecular ligand shells. These interactions are highly material-specific and can vary significantly even among elements within the same group or materials with similar crystal structure. In this study, we surveyed the heterogeneous interactions between an m-terphenyl isocyanide ligand and Au and Ag nanoparticles (NPs) at the single-molecule limit. Specifically, we found that the ligation behavior with this molecule differs significantly between that of Au and AgNPs. Surface-enhanced Raman spectroscopy measurements revealed unique enhancement factors for two molecular vibrational modes between two metal surfaces, indicating different ligand binding geometries. Molecular-level characterization using scanning tunneling microscopy allowed us to directly visualize these variations between Ag and Au surfaces, which we assign as two distinct binding mechanisms. This molecular-scale visualization provides clear insights into the different ligand–metal interactions as well as the chemical behavior and spectroscopic characteristics of isocyanide-functionalized NPs.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

NASA NTRS2002

Fc-receptor-mediated phagocytosis is regulated by mechanical properties of the target

Phagocytosis is an actin-based process used by macrophages to clear particles greater than 0.5 microm in diameter. In addition to its role in immunological responses, phagocytosis is also necessary for tissue remodeling and repair. To prevent catastrophic autoimmune reactions, phagocytosis must be tightly regulated. It is commonly assumed that the recognition/selection of phagocytic targets is based solely upon receptor-ligand binding. Here we report an important new criterion, that mechanical parameters of the target can dramatically affect the efficiency of phagocytosis. When presented with particles of identical chemical properties but different rigidity, macrophages showed a strong preference to engulf rigid objects. Furthermore, phagocytosis of soft particles can be stimulated with the microinjection of constitutively active Rac1 but not RhoA, and with lysophosphatidic acid, an agent known to activate the small GTP-binding proteins of the Rho family. These data suggest a Rac1-dependent mechanosensory mechanism for phagocytosis, which probably plays an important role in a number of physiological and pathological processes from embryonic development to autoimmune diseases.

NASA Program Fundamental Space Biology↗