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At least 127 records · Page 7

Excited states in variational Monte Carlo using a penalty method

Here, in this article, the authors present a technique using variational Monte Carlo to solve for excited states of electronic systems. This technique is based on enforcing orthogonality to lower energy states, which results in a simple variational principle for the excited states. Energy optimization is then used to solve for the excited states. This technique is applied to the well-characterized benzene molecule, in which ~10 000 parameters are optimized for the first 12 excited states. Agreement within ~0.2 eV is obtained with higher scaling coupled cluster methods; small disagreements with experiment are likely due to vibrational effects.

36 MATERIALS SCIENCE↗

BiGEST

Natural products have provided a rich reservoir of beneficial compounds in public health including antibiotics, therapeutics, and immunosuppressants. These natural products are synthesized by enzymes encoded by Biosynthetic Gene Clusters (BGCs), clusters of co-localized biosynthetic genes. Computational detection of BGCs has become a crucial step in natural product discovery. While this process has been facilitated in bacterial and fungal organisms thanks to the currently available tools (e.g., antiSMASH), a large spectrum of eukaryotic organisms have been neglected by these existing tools due to the scarcity and incompleteness of genome annotation resources. Here, we introduce Biosynthetic Gene cluster Extensive Search Tool (BiGEST) to provide an extensive annotation-free search for BGCs in diverse eukaryotic organisms. As a result, BiGEST uncovers eukaryotic BGCs that could be undetected by other BGC detection tools.

Adriani, Lisa↗

Data from: A high-quality genome assembly of the tetraploid Teucrium chamaedrys unveils a recent whole genome duplication and a large biosynthetic gene cluster for diterpenoid metabolism

Teucrium is well known for making clerodane-type diterpenoids that are produced from the backbone kolavanyl diphosphate. In order to begin to elucidate some of the complex biosynthetic pathways of these medicinal compounds, we identified and functionally characterized several kolavanyl diphosphate synthases from T. chamaedrys . Along the way, we discovered the genome of this species to be one of the largest genomes published from the Lamiaceae family, to which it belongs. This tetraploid, 3 Gbp genome is especially rich in diterpene synthase genes, with 74 putative sequences identified.

biosynthetic gene cluster (BGC)↗

Triple Excitations in Green’s Function Coupled Cluster Solver for Studies of Strongly Correlated Systems in the Framework of Self-Energy Embedding Theory

Embedding theories became important approaches used for accurate calculations of both molecules and solids. In these theories, a small chosen subset of orbitals is treated with an accurate method, called an impurity solver, capable of describing higher correlation effects. Ideally, such a chosen fragment should contain multiple orbitals responsible for the chemical and physical behavior of the compound. Handling a large number of chosen orbitals presents a very significant challenge for the current generation of solvers used in the physics and chemistry community. Here, we develop a Green’s function coupled cluster singles doubles and triples (GFCCSDT) solver that can be used for a quantitative description in both molecules and solids. This solver allows us to treat orbital spaces that are inaccessible to other accurate solvers. At the same time, GFCCSDT maintains high accuracy of the resulting self-energy. Moreover, in conjunction with the GFCCSD solver, it allows us to test the systematic convergence of computational studies. Developing the CC family of solvers paves the road to fully systematic Green’s function embedding calculations in solids. In this paper, we focus on the investigation of GFCCSDT self-energies for a strongly correlated problem of SrMnO 3 solid. Subsequently, we apply this solver to solid MnO showing that an approximate variant of GFCCSDT is capable of yielding a high accuracy orbital resolved spectral function.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Phase Discovery and Selected Synthesis of Subvalent Niobium Tellurides Using a Polytelluride Flux Strategy

Transition metal subchalcogenides involve electron-rich metals and can facilitate an in-depth understanding of the relationships among quantum properties such as superconductivity, charge density wave, and topological band structures. However, effective experimental routes toward synthesizing transition metal subchalcogenides are still lacking, hindering the development of new quantum materials. Herein, we propose a eutectic polytelluride flux strategy as an excellent solution to address phase discovery and crystal growth in transition metal subtelluride systems. We report new phases easily and selectively synthesized using a eutectic “K 3 Te 4 ” polytelluride flux upon adjusting the ratio of Nb metal to flux in the starting materials (K/Nb/Te = 3:x:4). Using a high Nb content in the solvent (x = 2 and 1), crystals of KNb 3 Te 3 O 0.38 and K 0.9 Nb 3 Te 4 are obtained. Both subtellurides exhibit diverse Nb clusters, including face-sharing and edge-sharing Nb 6 octahedral columns and zig-zag Nb chains. Reducing the Nb content to x = 0.33 leads to the formation of a layered compound, K 1.06 NbTe 2 . This compound comprises a NbTe 6 trigonal prism with K intercalated between the layers. Single crystals of known binary Nb tellurides can also be grown using another eutectic flux “KTe 3 . 2 ”, and the obtained NbTe 2 exhibits a new polymorphism with extra trimerization along the b-axis in the Nb–Nb bonded double zig-zag cluster. Finally, precise control over the structural dimensionality and oxidation state, combined with the facile crystal growth process, makes our synthetic strategy an efficient route to explore quantum materials in transition metal subchalcogenides.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Prediction of structure and cation ordering in an ordered normal-inverse double spinel

Abstract Spinels represent an important class of technologically relevant materials, used in diverse applications ranging from dielectrics, sensors and energy materials. While solid solutions combining two “single spinels” have been explored in a number of past studies, no ordered “double” spinels have been reported. Based on our first principles computations, here we predict the existence of such a double spinel compound MgAlGaO 4 , formed by an equimolar mixing of MgAl 2 O 4 normal and MgGa 2 O 4 inverse spinels. After studying the details of its atomic and electronic structure, we use a cluster expansion based effective Hamiltonian approach with Monte Carlo simulations to study the thermodynamic behavior and cation distribution as a function of temperature. Our simulations provide strong evidence for short-ranged cation order in the double spinel structure, even at significantly elevated temperatures. Finally, an attempt was made to synthesize the predicted double spinel compound. Energy Dispersive X-ray Spectrometry and X-ray diffraction Rietveld refinements were performed to characterize the single-phase chemical composition and local configurational environments, which showed a favorable agreement with the theoretical predictions. These findings suggest that a much larger number of compounds can potentially be realized within this chemical space, opening new avenues for the design of spinel-structured materials with tailored functionality.

36 MATERIALS SCIENCE↗

Crystalline phase transitions and water-soluble complexes of copper(Ⅰ) 2-hydroxyethanethiolate

We report the coordination polymer copper(I) 2-hydroxyethanethiolate, (CuSCH 2 CH 2 OH) n , though insoluble in all common solvents, dissolved readily in basic aqueous solutions of the thiolate anion (HOCH 2 CH 2 S – ) of 2-mercaptoethanol to form a single species: the tetranuclear cluster [Cu 4 (μ-SCH 2 CH 2 OH) 6 ] 2– . From this solution were grown X-ray quality single crystals of copper(I) 2-hydroxyethanethiolate. This compound underwent a hitherto unknown crystal phase transition at ca. 6 °C, from point group P2 1 2 1 2 1 to Pna2 1 , with noticeable changes in the geometry of the Cu-S layer and in the orientation of the alkylthiolate side chains. When the bulky base tetrabutylammonium hydroxide was employed in the aqueous thiolate solution used to dissolve (CuSCH 2 CH 2 OH) n , the water-soluble polynuclear copper(I) complex bis(tetrabutylammonium) hexakis(μ-2-hydroxyethanethiolato) tetracuprate(I), [(C 4 H 9 ) 4 N] 2 [Cu 4 (μ-SCH 2 CH 2 OH) 6 ], could be isolated as X-ray quality crystals. Structural characterization of this complex revealed a tetrahedral arrangement of copper(I) centers with thiolates bridging the edges of the tetrahedra. On standing, this complex degraded to a larger polynuclear Cu(I) sulfide cluster.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Neptunyl and Uranyl Peroxide Chemistry in Molten Salts, Uranyl Structures from Nature, and Thermodynamic Studies Extending into the Transuranium Elements (Final Report)

This project was initially funded in 2007 and the current technical report is for 2019-2022. The specific objectives of this project (2019-2022) were: (1) Synthesis of actinide peroxide compounds in molten salt eutectics, (2) Studies of new uranyl minerals with fascinating structures and compositions, (3) Drop-solution calorimetric studies of actinide compounds extending into the transuranium elements, with an emphasis on the uranyl-sulfate system, (4) Continuation of studies of uranyl vanadate clusters synthesized using ionic liquids, (5) The training of Ph.D. graduate students in actinide chemistry, and to introduce undergraduate students to actinide research through providing research assistantships and supervision. The report lists 67 archival journal papers describing the work, of which 23 were since 2019. Highlights of the work are summarized for the period 2019-2022.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

Zero-Valent Iron Permeable Reactive Barrier to Remediate Volatile Organic Compounds in Groundwater - 20209

The US DOE-SRS, the US EPA, and the South Carolina Department of Health and Environmental Control determined it was appropriate to perform a non-time critical removal action at the P-Area Groundwater Operable Unit at the SRS to reduce the mass and downgradient transport of trichloroethylene in the P-Area groundwater plume. Contaminated groundwater discharges to a nearby stream, Steel Creek, within the SRS boundaries, resulting in trichloroethylene concentrations above the maximum contaminant level. Impact to surface water is limited in areal extent and supported by recently collected characterization data. The P-Area Groundwater Operable Unit encompasses the groundwater beneath an industrial area within SRS, P Area, where the P-Reactor once operated. The boundaries of the P-Area Groundwater Operable Unit extend northwest to Steel Creek, northeast toward PAR Pond, and southeast to Meyers Branch. Groundwater in the Upper Three Runs Aquifer of the P-Area Groundwater Operable Unit has been impacted by reactor and facility operations between 1954 and 1991, including tritium and volatile organic compounds. The P-Area surface units contributing to groundwater contamination were remediated as part of the P-Area Operable Unit in 2011. The P-Reactor closure is one of the first of its kind in the DOE Complex and is one of only a few full-sized production reactors in the US to undergo completion of final closure activities. The nature and extent of groundwater contamination was determined using a variety of investigative approaches such as groundwater monitoring wells, direct-push technology, and surface water samples. Groundwater contamination associated with trichloroethylene is primarily exhibited in a narrow plume that extends from the source area at P-Reactor and west to Steel Creek. Maximum contaminant level exceedances in groundwater occur over an area of ∼6.9 hectares for trichloroethylene with concentrations as high as 7.7 milligrams per liter. To the west of the P-Area facility area, the trichloroethylene groundwater plume is controlled by a buried geologic feature, assumed to be an old stream bed, that further narrows the groundwater plume in what has been designated as the 'neck area.' This narrowing of the groundwater plume provides an ideal location for a treatment barrier. The non-time critical removal action alternative chosen is to install a zero-valent iron permeable reactive barrier within the neck area of the trichloroethylene groundwater plume, perpendicular to groundwater flow direction. This technology will provide a treatment barrier that will reduce trichloroethylene groundwater concentrations by 90% and has an anticipated useful life of at least 25 years. A pre-design investigation was performed in the neck area to confirm site lithology, hydrogeology, geochemistry, and extent of trichloroethylene contamination prior to a final design. A treatability study, conducted as part of the pre-design investigation, indicated that the subsurface and groundwater in the PArea Groundwater Operable Unit is compatible with the zero-valent iron and will not lead to excessive buildup from mineralization/precipitation or biofouling. Probabilistic modeling was conducted using field and laboratory data to determine the expected performance of the zero-valent iron permeable reactive barrier. The model simulations indicated that a 3.81-centimeter thick barrier would provide greater than 90% reduction of trichloroethylene groundwater concentration. The final design of the zero-valent iron permeable reactive barrier is a barrier that will extend 80.5 linear meters in a 'zigzag' orientation to best transect the trichloroethylene plume and account for varying groundwater flow. The barrier will be installed from 13.7 meters below ground surface to 41.1 meters below ground surface for 65.8 linear meters and from 13.7 meters below ground surface to 36.6 meters below ground surface for 14.6 linear meters, the base of which is 'keyed' into a low permeability zone. The barrier is designed to a thickness of 10.2 centimeters, which was determined to reduce the trichloroethylene groundwater concentrations by greater than 90% with a safety factor of 2.67. A total of approximately 689 metric tons of zero-valent iron will be injected through 22 injection wells spaced 3.66 meters apart, using guar to suspend the zero-valent iron. Zero-valent iron permeable reactive barrier construction will be monitored through 23 installed resistivity receivers offset 7.32 meters from the zerovalent iron permeable reactive barrier. The zero-valent iron will be energized with a low-voltage 100 Hertz signal during injection and will be monitored using the resistivity receivers to ensure complete coalescence of the zero-valent iron permeable reactive barrier. The zero-valent iron was sized to have a hydraulic conductivity greater than the natural subsurface, thus promoting groundwater flow through the barrier. As contaminated groundwater contacts the zero-valent iron, volatile organic compounds, including trichloroethylene, are immediately degraded to harmless compounds such as ethylene. The performance of the zero-valent iron permeable reactive barrier will be monitored using three upgradient monitoring well clusters, six downgradient monitoring well clusters, and four in-wall monitoring wells. The in-wall monitoring wells will indicate immediate reduction of trichloroethylene mass in the groundwater and allow analyses of the zero-valent iron permeable reactive barrier health. (authors)

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

Cluster-Spin-Glass Magnetic Behavior and Morphology in the Coordination Polymer Alloys Fe y Co 1– y BTT

We report the synthesis of a series of pseudo-1D coordination polymer (CP) materials with the formula Fe y Co 1–y BTT (BTT = 1,3,5-benzenetrithiolate). These materials were structurally characterized by PXRD Rietveld, EXAFS, and PDF analyses, revealing that the CP superstructure enables a continuous and isomorphous alloy between the two homometallic compounds. Lower Fe loadings exhibit emergent spin glass magnetic behavior, such as memory effects and composition-dependent spin glass response time constants ranging from 6.9 × 10 –9 s to 1.8 × 10 –6 s. These data are consistent with the formation of spin clusters within the lattice. The magnetic behavior in these materials was modeled via replica exchange Monte Carlo simulation, which provides a good match for the experimentally measured spin glassing and magnetic phase transitions. Furthermore, these findings underscore how the rigid superstructure of CP and MOF scaffolds can enable the systematic tuning of physical properties, such as the spin glass behavior described here.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Resolving the Atomic Structure of Sequential Infiltration Synthesis Derived Inorganic Clusters

Sequential infiltration synthesis (SIS) is a route to the precision deposition of inorganic solids in analogy to atomic layer deposition but occurs within (vs upon) a soft material template. SIS has enabled exquisite nanoscale morphological complexity in various oxides through selective nucleation in block copolymers templates. However, the earliest stages of SIS growth remain unresolved, including the atomic structure of nuclei and the evolution of local coordination environments, before and after polymer template removal. We employed In K-edge extended X-ray absorption fine structure and atomic pair distribution function analysis of high-energy X-ray scattering to unravel (1) the structural evolution of InO x H y clusters inside a poly(methyl methacrylate) (PMMA) host matrix and (2) the formation of porous In 2 O 3 solids (obtained after annealing) as a function of SIS cycle number. Early SIS cycles result in InO x H y cluster growth with high aspect ratio, followed by the formation of a three-dimensional network with additional SIS cycles. That the atomic structures of the InO x H y clusters can be modeled as multinuclear clusters with bonding patterns related to those in In 2 O 3 and In(OH) 3 crystal structures suggests that SIS may be an efficient route to 3D arrays of discrete-atom-number clusters. As a result, annealing the mixed inorganic/polymer films in air removes the PMMA template and consolidates the as-grown clusters into cubic In 2 O 3 nanocrystals with structural details that also depend on SIS cycle number.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

The behavior of methane–water mixtures under elevated pressures from simulations using many-body potentials

Non-polarizable empirical potentials have been proven to be incapable of capturing the mixing of methane–water mixtures at elevated pressures. Although density functional theory-based ab initio simulations may circumvent this discrepancy, they are limited in terms of the relevant time and length scales associated with mixing phenomena. Here, we show that the many-body MB-nrg potential, designed to reproduce methane–water interactions with coupled cluster accuracy, successfully captures this phenomenon up to 3 GPa and 500 K with varying methane concentrations. Two-phase simulations and long time scales that are required to fully capture the mixing, affordable due to the speed and accuracy of the MBX software, are assessed. Constructing the methane–water equation of state across the phase diagram shows that the stable mixtures are denser than the sum of their parts at a given pressure and temperature. As a result, we find that many-body polarization plays a central role, enhancing the induced dipole moments of methane by 0.20 D during mixing under pressure. Overall, the mixed system adopts a denser state, which involves a significant enthalpic driving force as elucidated by a systematic many-body energy decomposition analysis.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Structure based virtual screening identifies small molecule effectors for the sialoglycan binding protein Hsa

Infective endocarditis (IE) is a cardiovascular disease often caused by bacteria of the viridans group of streptococci, which includes Streptococcus gordonii and Streptococcus sanguinis. Previous research has found that serine-rich repeat (SRR) proteins on the S. gordonii bacterial surface play a critical role in pathogenesis by facilitating bacterial attachment to sialylated glycans displayed on human platelets. Despite their important role in disease progression, there are currently no anti-adhesive drugs available on the market. Here, we performed structure-based virtual screening using an ensemble docking approach followed by consensus scoring to identify novel small molecule effectors against the sialoglycan binding domain of the SRR adhesin protein Hsa from the S. gordonii strain DL1. The screening successfully predicted nine compounds which were able to displace the native ligand (sialyl-T antigen) in an in vitro assay and bind competitively to Hsa. Furthermore, hierarchical clustering based on the MACCS fingerprints showed that eight of these small molecules do not share a common scaffold with the native ligand. This study indicates that SRR family of adhesin proteins can be inhibited by diverse small molecules and thus prevent the interaction of the protein with the sialoglycans. This opens new avenues for discovering potential drugs against IE.

60 APPLIED LIFE SCIENCES↗

Toward DMRG-tailored coupled cluster method in the 4c-relativistic domain

There are three essential problems in computational relativistic chemistry: Electrons moving at relativistic speeds, close lying states, and dynamical correlation. Currently available quantum-chemical methods are capable of solving systems with one or two of these issues. However, there is a significant class of molecules in which all the three effects are present. These are the heavier transition metal compounds, lanthanides, and actinides with open d or f shells. For such systems, sufficiently accurate numerical methods are not available, which hinders the application of theoretical chemistry in this field. In this paper, we combine two numerical methods in order to address this challenging class of molecules. These are the relativistic versions of coupled cluster methods and the density matrix renormalization group (DMRG) method. To the best of our knowledge, this is the first relativistic implementation of the coupled cluster method externally corrected by DMRG. The method brings a significant reduction of computational costs as we demonstrate on the system of TlH, AsH, and SbH.

Brandejs, Jan (ORCID:0000000221073095)↗

A Microporous Metal–Organic Framework Incorporating Both Primary and Secondary Building Units for Splitting Alkane Isomers

We demonstrate the assembly of a mononuclear metal center, a hexanuclear cluster, and a V-shaped, trapezoidal tetracarboxylate linker into a microporous MOF featuring an unprecedented 3-nodal (4,4,8)-c lyu topology. Here, the compound, HIAM-302, represents the first example that incorporates both primary building unit (PBU) and hexanuclear secondary building unit (SBU) in one structure, which should be attributed to the desymmetrized geometry of the organic linker. HIAM-302 possesses optimal pore dimensions and can separate mono-branched and di-branched alkanes through selective molecular sieving, which is of significant value in petrochemical industry.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Exploring a New Regime of Molecular Orbital Physics in 4⁢d Cluster Magnets with Resonant Inelastic X-Ray Scattering

Molecular orbital systems with clusters of heavy transition metal (TM) ions are one of the most important classes of model materials for studying the interplay between local physics and effects of itinerancy. Despite a large number of candidates identified in the family of 4⁢d TM materials, an understanding of their physics from competing microscopic energy scales is still missing. Here, we bridge this gap by reporting the first resonant inelastic x-ray scattering (RIXS) measurement on a well-known series of Ru cluster magnets with a 6⁢H-perovskite structure Ba 3 ⁢M⁢Ru 2 ⁢O 9 (M 3+ = In 3+ , Y 3+ , La 3+ ) comprised of Ru dimers. In addition to providing a microscopic explanation for their anomalous magnetic properties, our RIXS measurements combined with theoretical modeling uncover a new regime of molecular orbital physics where the combined effect of large hopping and small spin-orbit coupling results in highly fragile electronic states in the Ru-dimer compounds directly manifested as an abrupt change in the RIXS spectrum accompanying a tiny change in the local structure tuned by the M-site ion. This unique combination of energy scales found only in the 4⁢d but not the 5⁢d cluster magnets highlights the value of these materials as a new platform for studying quantum phase transition involving molecular orbitals.

36 MATERIALS SCIENCE↗

Accurate and efficient parameterization of an atomic cluster expansion (ACE) potential for ammonia under extreme conditions

We present a machine learning interatomic potential for ammonia designed to capture its complex multiphase behavior, including both molecular and superionic phases. The potential is based on the atomic cluster expansion (ACE) formulation and has been parameterized to facilitate high-fidelity molecular dynamics simulations of ammonia under extreme conditions, for pressures up to 100 GPa and for temperatures above 500 K and up to 6000 K. A diverse range of configurations was generated through high-quality ab initio molecular dynamics simulations, covering insulating and superionic ice phases, liquid ammonia, molecular nitrogen (N 2 ) and hydrogen (H 2 ), and metastable compounds that form upon dissociation, including $NH^{+}_{4}$, $H^{+}_{3}$, N 2 H 4 , and N 3 H. We demonstrate that the ammonia ACE potential accurately reproduces experimental and density functional theory predicted isotherms and Hugoniots. Crucially, the potential is able to capture the intricate phase behavior of ammonia, including the transition from insulating molecular fluid to the superionic phase. This work provides a robust interatomic potential that can be used for large-scale, accurate simulations of ammonia under extreme thermodynamic conditions, offering a powerful tool for investigating its behavior in various phases and applications.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗