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At least 217 records · Page 12

Refining T c Prediction in Hydrides via Symbolic‐Regression‐Enhanced Electron‐Localization‐Function‐Based Descriptors

Hydrogen‐based materials are able to possess extremely high superconducting critical temperatures, T c s , due to hydrogen's low atomic mass and strong electron–phonon interaction. Recently, a descriptor based on the Electron Localization Function (ELF) has enabled the rapid estimation of the T c of hydrogen‐containing compounds from electronic networking properties, but its applicability has been limited by the small size and homogeneity of the training dataset used. Herein, the model is re‐examined, compiling a publicly available combined dataset of 244 binary and ternary hydride superconductors. The analysis shows that though ELF‐based networking remains a valuable descriptor, its predictive power declines with increasing compositional complexity. However, by introducing the molecularity index, defined as the highest value of the ELF at which two hydrogen atoms connect, and applying symbolic regression, the accuracy of the predictions can be substantially enhanced. These results establish a more robust framework for assessing superconductivity in hydride materials, facilitating accelerated screening of novel candidates through integration with crystal structure prediction methods or high‐throughput searches.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Route to high-$T_c$ superconductivity via CH 4 -intercalated H 3 S hydride perovskites

While exploring potential superconductors in the C-S-H ternary system using first-principles crystal structure prediction methods, we uncovered a class of hydride perovskites based on the intercalation of methane into an H 3 S framework. These intriguing H 3 S–CH 4 structures emerge as metastable at ~100 GPa. Further, electron-phonon coupling calculations indicate that phases with CSH 7 stoichiometry are potential superconductors with $T_c$ values ranging from 100 K to 190 K at megabar pressures. The results are expected to guide the experimental search for new high-$T_c$ superconductors, including those stable at lower pressures than previously documented superconducting hydrides such as H 3 S and LaH 10 .

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Structural, Vibrational, and Electronic Properties of 1D-TlInTe 2 under High Pressure: A Combined Experimental and Theoretical Study

Analogous to 2D layered transition-metal dichalcogenides, the TlSe family of quasi-one dimensional chain materials with the Zintl-type structure exhibits novel phenomena under high pressure. In the present work, we have systematically investigated the high-pressure behavior of TlInTe 2 using Raman spectroscopy, synchrotron X-ray diffraction (XRD), and transport measurements, in combination with first principles crystal structure prediction (CSP) based on evolutionary approach. We found that TlInTe2 undergoes a pressure-induced semiconductor-to-semimetal transition at 4 GPa, followed by a superconducting transition at 5.7 GPa (with T c = 3.8 K). An unusual giant phonon mode (A g ) softening appears at ~10–12 GPa as a result of the interaction of optical phonons with the conduction electrons. The high-pressure XRD and Raman spectroscopy studies reveal that there is no structural phase transitions observed up to the maximum pressure achieved (33.5 GPa), which is in agreement with our CSP calculations. In addition, our calculations predict two high-pressure phases above 35 GPa following the phase transition sequence as I4/mcm (B37) → Pbcm → Pm$\bar{3}$m (B2). Electronic structure calculations suggest Lifshitz (L1 & L2-type) transitions near the superconducting transition pressure. Furthermore, our findings on TlInTe 2 open up a new avenue to study unexplored high-pressure novel phenomena in TlSe family induced by Lifshitz transition (electronic driven), giant phonon softening, and electron–phonon coupling.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Geometry-complete perceptron networks for 3D molecular graphs

Abstract Motivation The field of geometric deep learning has recently had a profound impact on several scientific domains such as protein structure prediction and design, leading to methodological advancements within and outside of the realm of traditional machine learning. Within this spirit, in this work, we introduce GCPNet, a new chirality-aware SE(3)-equivariant graph neural network designed for representation learning of 3D biomolecular graphs. We show that GCPNet, unlike previous representation learning methods for 3D biomolecules, is widely applicable to a variety of invariant or equivariant node-level, edge-level, and graph-level tasks on biomolecular structures while being able to (1) learn important chiral properties of 3D molecules and (2) detect external force fields. Results Across four distinct molecular-geometric tasks, we demonstrate that GCPNet’s predictions (1) for protein–ligand binding affinity achieve a statistically significant correlation of 0.608, more than 5%, greater than current state-of-the-art methods; (2) for protein structure ranking achieve statistically significant target-local and dataset-global correlations of 0.616 and 0.871, respectively; (3) for Newtownian many-body systems modeling achieve a task-averaged mean squared error less than 0.01, more than 15% better than current methods; and (4) for molecular chirality recognition achieve a state-of-the-art prediction accuracy of 98.7%, better than any other machine learning method to date. Availability and implementation The source code, data, and instructions to train new models or reproduce our results are freely available at https://github.com/BioinfoMachineLearning/GCPNet.

59 BASIC BIOLOGICAL SCIENCES↗

Structural Insights into Mechanisms Underlying Mitochondrial and Bacterial Cytochrome c Synthases

Mitochondrial holocytochrome c synthase (HCCS) is an essential protein in assembling cytochrome c (cyt c) of the electron transport system. HCCS binds heme and covalently attaches the two vinyls of heme to two cysteine thiols of the cyt c CXXCH motif. Human HCCS recognizes both cyt c and cytochrome c1 of complex III (cytochrome bc1). HCCS is mutated in some human diseases and it has been investigated recombinantly by mutational, biochemical, and reconstitution studies in the past decade. Here, we employ structural prediction programs (e.g., AlphaFold 3) on HCCS and its two substrates, heme and cytochrome c. The results, when combined with spectroscopic and functional analyses of HCCS and variants, provide insights into the structural basis for heme binding, apocyt c binding, covalent attachment, and release of the holocyt c product. Results from in vitro reconstitution of purified human HCCS using cyt c and cyt c1 peptides as acceptors are consistent with the structural modeling of substrate binding. Reconstitution of HCCS and cyt c1 provides an approach to studying cyt c1 assembly, which has been refractile to recombinant in vivo reconstitution (unlike HCCS and cyt c). We propose a structural basis for release of the holocyt c product from HCCS based on in vitro studies and on cryoEM structures of the bacterial cyt c synthase (CcsBA) active site. We analyze the kinetoplastid mitochondrial synthase (KCCS), and hypothesize a molecular evolutionary path from mitochondrial endosymbiosis to the current HCCS.

Biochemistry & Molecular Biology↗

Crystal structure of an atypical cobalamin riboswitch reveals RNA structural adaptability as basis for promiscuous ligand binding

Cobalamin riboswitches encompass a structurally diverse group of cis-acting, gene regulatory elements found mostly in bacterial messenger RNA and are classified into subtypes based on secondary and tertiary characteristics. An unusual variant of the cobalamin riboswitch with predicted structural features was identified in Bacillus subtilis over a decade ago, but its structure and mechanisms of cobalamin selectivity and translational control have remained unsolved. We present the crystal structure of the aptamer domain of this atypical cobalamin riboswitch and a model for the complete riboswitch, including its expression platform domain. We demonstrate that this riboswitch binds to multiple cobalamin derivatives and correlate its promiscuous behavior to its structure and unique arrangement of peripheral elements. Comparative structural analyses between conventional cobalamin riboswitches and the B. subtilis cobalamin riboswitch reveal that the likely basis for this promiscuous ligand binding is intrinsic structural adaptability encoded in the RNA structure. It suggests that cobalamin selectivity might ultimately be viewed as existing on a spectrum of affinity for each derivative rather than as belonging to distinct types based on ligand specificities. Our work provides an interesting and notable example of functional coupling of ligand-sensing and adaptive folding by a structured RNA molecule.

59 BASIC BIOLOGICAL SCIENCES↗

Borg extrachromosomal elements of methane-oxidizing archaea have conserved and expressed genetic repertoires

Borgs are huge extrachromosomal elements (ECE) of anaerobic methane-consuming “Candidatus Methanoperedens” archaea. Here, we used nanopore sequencing to validate published complete genomes curated from short reads and to reconstruct new genomes. 13 complete and four near-complete linear genomes share 40 genes that define a largely syntenous genome backbone. We use these conserved genes to identify new Borgs from peatland soil and to delineate Borg phylogeny, revealing two major clades. Remarkably, Borg genes encoding nanowire-like electron-transferring cytochromes and cell surface proteins are more highly expressed than those of host Methanoperedens, indicating that Borgs augment the Methanoperedens activity in situ. We reconstructed the first complete 4.00 Mbp genome for a Methanoperedens that is inferred to be a Borg host and predicted its methylation motifs, which differ from pervasive TC and CC methylation motifs of the Borgs. Thus, methylation may enable Methanoperedens to distinguish their genomes from those of Borgs. Very high Borg to Methanoperedens ratios and structural predictions suggest that Borgs may be capable of encapsulation. The findings clearly define Borgs as a distinct class of ECE with shared genomic signatures, establish their diversification from a common ancestor with genetic inheritance, and raise the possibility of periodic existence outside of host cells.

59 BASIC BIOLOGICAL SCIENCES↗

Simulated structure and thermodynamics of decagonal Al-Co-Cu quasicrystals

Atomic structures of Al-Co-Cu decagonal quasicrystals (dQCs) are investigated using empirical oscillating pair potentials (EOPP) in molecular dynamic (MD) simulations that we enhance by Monte Carlo (MC) swapping of chemical species and replica exchange. Predicted structures exhibit planar decagonal tiling patterns and are periodic along the perpendicular direction. We then recalculate the energies of promising structures using first-principles density functional theory (DFT), along with energies of competing phases. We find that our τ -inflated sequence of QC approximants (QCAs) are energetically unstable at low temperature by at least 3 meV/atom. Extending our study to finite temperatures by calculating harmonic vibrational entropy, as well as anharmonic contributions that include chemical species swaps and tile flips, our results suggest that the quasicrystal phase is entropically stabilized at temperatures in the range 600-800 K and above. It decomposes into ordinary (though complex) crystal phases at low temperatures, including a partially disordered B2-type phase. We discuss the influence of density and composition on QC phase stability; we compare the structural differences between Co-rich and Cu-rich quasicrystals; and we analyze the role of entropy in stabilizing the quasicrystal, concluding with a discussion of the possible existence of “high entropy” quasicrystals. Published by the American Physical Society 2024

Huang, Yang (ORCID:0009000045917347)↗

Improved accuracy and transferability of molecular-orbital-based machine learning: Organics, transition-metal complexes, non-covalent interactions, and transition states

We report molecular-orbital-based machine learning (MOB-ML) provides a general framework for the prediction of accurate correlation energies at the cost of obtaining molecular orbitals. The application of Nesbet’s theorem makes it possible to recast a typical extrapolation task, training on correlation energies for small molecules and predicting correlation energies for large molecules, into an interpolation task based on the properties of orbital pairs. We demonstrate the importance of preserving physical constraints, including invariance conditions and size consistency, when generating the input for the machine learning model. Numerical improvements are demonstrated for different datasets covering total and relative energies for thermally accessible organic and transition-metal containing molecules, non-covalent interactions, and transition-state energies. MOB-ML requires training data from only 1% of the QM7b-T dataset (i.e., only 70 organic molecules with seven and fewer heavy atoms) to predict the total energy of the remaining 99% of this dataset with sub-kcal/mol accuracy. This MOB-ML model is significantly more accurate than other methods when transferred to a dataset comprising of 13 heavy atom molecules, exhibiting no loss of accuracy on a size intensive (i.e., per-electron) basis. It is shown that MOB-ML also works well for extrapolating to transition-state structures, predicting the barrier region for malonaldehyde intramolecular proton-transfer to within 0.35 kcal/mol when only trained on reactant/product-like structures. Finally, the use of the Gaussian process variance enables an active learning strategy for extending the MOB-ML model to new regions of chemical space with minimal effort. We demonstrate this active learning strategy by extending a QM7b-T model to describe non-covalent interactions in the protein backbone–backbone interaction dataset to an accuracy of 0.28 kcal/mol.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Disorderly Conduct of Benzamide IV: Crystallographic and Computational Analysis of High Entropy Polymorphs of Small Molecules

Benzamide, a simple derivative of benzoic acid and a common intermediate of pharmaceutical compounds, was reported to form two polymorphs in 1832, but the single crystal structure of the more stable form was not solved until 1959. Nearly 50 years later, the second form was characterized by powder diffraction, followed shortly thereafter by characterization of a third form, a polytype of the most thermodynamically stable Form I. These two new forms, Forms II and III, are metastable. Herein, we describe a fourth polymorph, Form IV, discovered by melt crystallization concurrently with its crystallization under confinement at small length scales (<10 nm), where it is stable indefinitely. Form III exists under confinement in larger pores, and melting point data for different pore sizes corroborate the existence of Form IV below 10 nm. Form IV is highly disordered, precluding indexing of powder diffraction data other than hk0 reflections. Nonetheless, a combination of powder X-ray diffraction and computational crystal structure prediction reveals that Form IV contains a 2D motif resembling that of Form II, but with longrange order in the third dimension masked by ubiquitous stacking faults. This approach relies on distilling a large number of candidate structures to a few possible disorder models based on benzamide tetrads that organize in 2D parquet-like tiles, with organization along the third dimension, that can be modeled with various stacking fault configurations having distinct intermolecular interactions and translations in the dimension orthogonal to the tiling planes. These observations reveal a bewildering crystallographic complexity for such a simple molecule. Nonetheless, the approach described herein demonstrates that challenging structures that may be abandoned prematurely because of poor crystallinity, twinning, or disorder can be solved.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Genomic and transcriptomic characterization of carbohydrate-active enzymes in the anaerobic fungus Neocallimastix cameroonii var. constans

Anaerobic gut fungi effectively degrade lignocellulose in the guts of large herbivores, but there remain a limited number of isolated, publicly available, and sequenced strains that impede our understanding of the role of anaerobic fungi within microbial communities. We isolated and characterized a new fungal isolate, Neocallimastix cameroonii var. constans, providing a transcriptomic and genomic understanding of its ability to degrade diverse carbohydrates. This anaerobic fungal strain was stably cultivated for multiple years in vitro among members of an initial enrichment microbial community derived from goat feces, and it demonstrated the ability to pair with other microbial members, namely, archaeal methanogens to produce methane from lignocellulose. Genomic analysis revealed a higher number of predicted carbohydrate-active enzymes encoded in the N. cameroonii var. constans genome compared to most other sequenced anaerobic fungi. The carbohydrate-active enzyme profile for this isolate contained 660 glycoside hydrolases, 160 carbohydrate esterases, 194 glycosyltransferases, and 85 polysaccharide lyases. Differential gene expression analysis showed the upregulation of thousands of genes (including predicted carbohydrate-active enzymes) when N. cameroonii var. constans was grown on lignocellulose (reed canary grass) compared to less complex substrates, such as cellulose (filter paper), cellobiose, and glucose. AlphaFold was used to predict functions of transcriptionally active yet poorly annotated genes, revealing feruloyl esterases that likely play an important role in lignocellulose degradation by anaerobic fungi. The combination of this strain's genomic and transcriptomic characterization, omics-informed structural prediction, and robustness in microbial co-culture make it a well-suited platform to conduct future investigations into bioprocessing and enzyme discovery.

CAZymes↗

The First Neptunium Dioxide Neutron Diffraction Experiment at HFIR

Here we present the first neutron diffraction experiment of a 50 mg sample of neptunium(IV) dioxide (NpO 2 ) powder at the High Flux Isotope Reactor (HFIR) using the wide-angle neutron diffractometer (WAND 2 ) HB-2C. We also provide a brief literature survey to pinpoint gaps in the crystal, electronic, and magnetic structure of NpO 2 to determine the optimum experiment to be pursued in the next HFIR user proposal cycle. Characterizing actinide materials with neutron diffraction, inelastic scattering, neutron imaging, polarized neutron studies, and small-angle neutron scattering techniques will increase our understanding of 5f electron behavior and elucidate atomic and magnetic structural properties. This strategy will help fill gaps in the literature and provide theoretical physicists with the data needed to build physical and chemical models to guide and validate computational methods. These methods may be used for predicting structural and chemical features of actinide-based materials. This proof-of-principle effort begins to uncover how to advance actinide science and technology at Oak Ridge National Laboratory (ORNL) using neutron capabilities. This effort has already sparked collaborative discussions between researchers outside the Radioisotope Science and Technology Division, including theoretical physicists from the Nuclear Nonproliferation Division and beamline scientists in the Neutron Scattering Division. We intend to continue pursuing neutron experiments and develop a scientific strategy focused on studying transuranium elements (e.g., Np, Pu, Am, and Cm) using the advanced neutron capabilities at ORNL.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

A goldilocks computational protocol for inhibitor discovery targeting DNA damage responses including replication-repair functions

While many researchers can design knockdown and knockout methodologies to remove a gene product, this is mainly untrue for new chemical inhibitor designs that empower multifunctional DNA Damage Response (DDR) networks. Here, we present a robust Goldilocks (GL) computational discovery protocol to efficiently innovate inhibitor tools and preclinical drug candidates for cellular and structural biologists without requiring extensive virtual screen (VS) and chemical synthesis expertise. By computationally targeting DDR replication and repair proteins, we exemplify the identification of DDR target sites and compounds to probe cancer biology. Our GL pipeline integrates experimental and predicted structures to efficiently discover leads, allowing early-structure and early-testing (ESET) experiments by many laboratories. By employing an efficient VS protocol to examine protein-protein interfaces (PPIs) and allosteric interactions, we identify ligand binding sites beyond active sites, leveraging in silico advances for molecular docking and modeling to screen PPIs and multiple targets. A diverse 3,174 compound ESET library combines Diamond Light Source DSI-poised, Protein Data Bank fragments, and FDA-approved drugs to span relevant chemotypes and facilitate downstream hit evaluation efficiency for academic laboratories. Two VS per library and multiple ranked ligand binding poses enable target testing for several DDR targets. This GL library and protocol can thus strategically probe multiple DDR network targets and identify readily available compounds for early structural and activity testing to overcome bottlenecks that can limit timely breakthrough drug discoveries. By testing accessible compounds to dissect multi-functional DDRs and suggesting inhibitor mechanisms from initial docking, the GL approach may enable more groups to help accelerate discovery, suggest new sites and compounds for challenging targets including emerging biothreats and advance cancer biology for future precision medicine clinical trials.

59 BASIC BIOLOGICAL SCIENCES↗

Exploring the Structural, Dynamic, and Functional Properties of Metal–Organic Frameworks through Molecular Modeling

This review spotlights the role of atomic-level modeling in research on metal-organic frameworks (MOFs), especially the key methodologies of density functional theory (DFT), Monte Carlo (MC) simulations, and molecular dynamics (MD) simulations. The discussion focuses on how periodic and cluster-based DFT calculations can provide novel insights into MOF properties, with a focus on predicting structural transformations, understanding thermodynamic properties and catalysis, and providing information or properties that are fed into classical simulations such as force field parameters or partial charges. Classical simulation methods, highlighting force field selection, databases of MOFs for high-throughput screening, and the synergistic nature of MC and MD simulations, are described. By predicting equilibrium thermodynamic and dynamic properties, these methods offer a wide perspective on MOF behavior and mechanisms. Additionally, the incorporation of machine learning (ML) techniques into quantum and classical simulations is discussed. These methods can enhance accuracy, expedite simulation setup, reduce computational costs, as well as predict key parameters, optimize geometries, and estimate MOF stability. By charting the growth and promise of computational research in the MOF field, the aim is to provide insights and recommendations to facilitate the incorporation of computational modeling more broadly into MOF research.

36 MATERIALS SCIENCE↗

Structure and Antigenicity of the Porcine Astrovirus 4 Capsid Spike

Porcine astrovirus 4 (PoAstV4) has been recently associated with respiratory disease in pigs. In order to understand the scope of PoAstV4 infections and to support the development of a vaccine to combat PoAstV4 disease in pigs, we designed and produced a recombinant PoAstV4 capsid spike protein for use as an antigen in serological assays and for potential future use as a vaccine antigen. Structural prediction of the full-length PoAstV4 capsid protein guided the design of the recombinant PoAstV4 capsid spike domain expression plasmid. The recombinant PoAstV4 capsid spike was expressed in Escherichia coli, purified by affinity and size-exclusion chromatography, and its crystal structure was determined at 1.85 Å resolution, enabling structural comparisons to other animal and human astrovirus capsid spike structures. The recombinant PoAstV4 capsid spike protein was also used as an antigen for the successful development of a serological assay to detect PoAstV4 antibodies, demonstrating that the recombinant PoAstV4 capsid spike retains antigenic epitopes found on the native PoAstV4 capsid. These studies lay a foundation for seroprevalence studies and the development of a PoAstV4 vaccine for swine.

Virology↗

Semiconductor Nanostructures by Scientific Design (Final Technical Report)

We developed and used quantum simulation techniques to predict structural, electronic, optical and thermal properties affecting the scientific design of semiconductor nanostructures. We focused on the study of surfaces and interfaces at the nanoscale, in particular embedding and solvation of semiconductor nanoparticles, and provided a microscopic description of nanostructured materials in realistic environments, directly comparable with experimental conditions. We addressed three major problems: (i) the design of realistic structural models of integrated nanostructures, e.g. quantum dots embedded in solid matrices and nanostructures immersed in fluids; (ii) the development of efficient and accurate calculations to describe the excited state properties of nanostructures, beyond standard Density Functional Theory, so as to understand and predict electronic properties involved in renewable energy applications, for example solar conversion devices. In particular we developed and used methods based on a many body perturbation theory. (iii) the development of calculations of heat transport properties of nanostructured materials, for thermoelectric applications, including predictive calculations of thermal and electrical conductivity and of Seebeck coefficients. Specifically, we developed and used methods based on the Boltzmann transport equation and molecular dynamics.

77 NANOSCIENCE AND NANOTECHNOLOGY↗

The Li–F–H ternary system at high pressures

Evolutionary crystal structure prediction searches have been employed to explore the ternary Li-F-H system at 300 GPa. Metastable phases were uncovered within the static lattice approximation, with LiF 3 H 2 , LiF 2 H, Li 3 F 4 H, LiF 4 H 4 , Li 2 F 3 H and LiF 3 H lying within 50 meV/atom of the 0 K convex hull. All of these phases contain H n F¯ n+1 (n = 1; 2) anions, and Li + cations. Other structural motifs such as LiF slabs, $H$ $^{+}_{3}$ molecules and F δ- ions are present in some of the low enthalpy Li-F-H structures. The bonding within the H n F¯ n+1 molecules, which may be bent or linear, symmetric or asymmetric, is analyzed. The five phases closest to the hull are insulators, while LiF 3 H is metallic and predicted to have a vanishingly small superconducting critical temperature. Li 3 F 4 H is predicted to be stable at zero pressure. Furthermore, this study lays the foundation for future investigations of the role of temperature and anharmonicity on the stability and properties of compounds and alloys in the Li-F-H ternary system.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Structural diversity and clustering of bacterial flagellar outer domains

Supercoiled flagellar filaments function as mechanical propellers within the bacterial flagellum complex, playing a crucial role in motility. Flagellin, the building block of the filament, features a conserved inner D0/D1 core domain across different bacterial species. In contrast, approximately half of the flagellins possess additional, highly divergent outer domain(s), suggesting varied functional potential. In this study, we report atomic structures of flagellar filaments from three distinct bacterial species: Cupriavidus gilardii , Stenotrophomonas maltophilia , and Geovibrio thiophilus . Our findings reveal that the flagella from the facultative anaerobic G. thiophilus possesses a significantly more negatively charged surface, potentially enabling adhesion to positively charged minerals. Furthermore, we analyze all AlphaFold predicted structures for annotated bacterial flagellins, categorizing the flagellin outer domains into 682 structural clusters. This classification provides insights into the prevalence and experimental verification of these outer domains. Remarkably, two of the flagellar structures reported herein belong to a distinct cluster, indicating additional opportunities on the study of the functional diversity of flagellar outer domains. Our findings underscore the complexity of bacterial flagellins and open up possibilities for future studies into their varied roles beyond motility.

Science & Technology - Other Topics↗