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At least 289 records · Page 16

Navigating Transition-Metal Chemical Space: Artificial Intelligence for First-Principles Design

Conspectus The variability of chemical bonding in open-shell transition-metal complexes not only motivates their study as functional materials and catalysts but also challenges conventional computational modeling tools. Here, tailoring ligand chemistry can alter preferred spin or oxidation states as well as electronic structure properties and reactivity, creating vast regions of chemical space to explore when designing new materials atom by atom. Although first-principles density functional theory (DFT) remains the workhorse of computational chemistry in mechanism deduction and property prediction, it is of limited use here. DFT is both far too computationally costly for widespread exploration of transition-metal chemical space and also prone to inaccuracies that limit its predictive performance for localized d electrons in transition-metal complexes. These challenges starkly contrast with the well-trodden regions of small-organic-molecule chemical space, where the analytical forms of molecular mechanics force fields and semiempirical theories have for decades accelerated the discovery of new molecules, accurate DFT functional performance has been demonstrated, and gold-standard methods from correlated wavefunction theory can predict experimental results to chemical accuracy. The combined promise of transition-metal chemical space exploration and lack of established tools has mandated a distinct approach. In this Account, we outline the path we charted in exploration of transition-metal chemical space starting from the first machine learning (ML) models (i.e., artificial neural network and kernel ridge regression) and representations for the prediction of open-shell transition-metal complex properties. The distinct importance of the immediate coordination environment of the metal center as well as the lack of low-level methods to accurately predict structural properties in this coordination environment first motivated and then benefited from these ML models and representations. Once developed, the recipe for prediction of geometric, spin state, and redox potential properties was straightforwardly extended to a diverse range of other properties, including in catalysis, computational “feasibility”, and the gas separation properties of periodic metal–organic frameworks. Interpretation of selected features most important for model prediction revealed new ways to encapsulate design rules and confirmed that models were robustly mapping essential structure–property relationships. Encountering the special challenge of ensuring that good model performance could generalize to new discovery targets motivated investigation of how to best carry out model uncertainty quantification. Distance-based approaches, whether in model latent space or in carefully engineered feature space, provided intuitive measures of the domain of applicability. With all of these pieces together, ML can be harnessed as an engine to tackle the large-scale exploration of transition-metal chemical space needed to satisfy multiple objectives using efficient global optimization methods. In practical terms, bringing these artificial intelligence tools to bear on the problems of transition-metal chemical space exploration has resulted in ML-model assessments of large, multimillion compound spaces in minutes and validated new design leads in weeks instead of decades.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Spatial separation of triplet excitons drives endothermic singlet fission

Molecules that undergo singlet fission, converting singlet excitons into pairs of triplet excitons, have potential as photovoltaic materials. The possible advantages of endothermic singlet fission (enhanced use of photon energy and larger triplet energies for coupling with common absorbers) motivated us to assess the role of exciton delocalization in the activation of this process. Here we report the synthesis of a series of linear perylene oligomers that undergo endothermic singlet fission and have endothermicities in the range 5-10 kBT at room temperature in solution. We study these compounds using transient spectroscopy and modelling to unravel the singlet and triplet dynamics. We show that the minimal number of coupled chromophores needed to undergo endothermic singlet fission is three, which provides sufficient statistical space for triplet excitons to separate and avoid annihilation - and a subsequent fast return to the singlet state. Our data additionally suggest that torsional motion of chromophores about the molecular axis following triplet-pair separation contributes to the increase in entropy, thus lengthening the triplet lifetime in longer oligomers.

14 SOLAR ENERGY↗

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↗

13C-labeling reveals how membrane lipid components contribute to triacylglycerol accumulation in Chlamydomonas

Abstract Lipid metabolism in microalgae has attracted much interest due to potential utilization of lipids as feedstocks for biofuels, nutraceuticals, and other high-value compounds. Chlamydomonas reinhardtii is a model organism for characterizing the synthesis of the neutral lipid triacylglycerol (TAG), from which biodiesel is made. While much of TAG accumulation under N-deprivation is the result of de novo fatty acid (FA) synthesis, recent work has revealed that approximately one-third of FAs, especially polyunsaturated FAs (PUFAs), come from preexisting membrane lipids. Here, we used 13C-isotopic labeling and mass spectrometry to analyze the turnover of glycerol backbones, headgroups, FAs, whole molecules, and molecular fragments of individual lipids. About one-third of the glyceryl backbones in TAG are derived from preexisting membrane lipids, as are approximately one-third of FAs. The different moieties of the major galactolipids turn over synchronously, while the FAs of diacylglyceryltrimethylhomoserine (DGTS), the most abundant extraplastidial lipid, turn over independently of the rest of the molecule. The major plastidic lipid monogalactosyldiacylglycerol (MGDG), whose predominant species is 18:3α/16:4, was previously shown to be a major source of PUFAs for TAG synthesis. This study reveals that MGDG turns over as whole molecules, the 18:3α/16:4 species is present in both DAG and TAG, and the positional distribution of these PUFAs is identical in MGDG, DAG, and TAG. We conclude that headgroup removal with subsequent acylation is the mechanism by which the major MGDG species is converted to TAG during N-deprivation. This has noteworthy implications for engineering the composition of microalgal TAG for food, fuel, and other applications.

Plant Sciences↗

Spin-flop-like transition as quantum critical point in Cs2⁢RuO4

We report thermodynamic, neutron diffraction, and inelastic neutron scattering measurements on Cs2⁢RuO4, a member of the celebrated family of frustrated magnets Cs2⁢𝑀⁢𝑋4 (𝑀 = Cu, Co, 𝑋 = Br, Cl). Unlike the previously studied members, it is based on 4⁢𝑑 transition metal ions with 𝑆=1. Mapping out the 𝐻−𝑇 magnetic phase diagram reveals an unusual continuous spin-flop-like phase transition associated with a quantum critical point within the antiferromagnetically ordered phase. A quantitative analysis of the complex magnetic excitation spectrum measured in zero field allows us to derive a model magnetic Hamiltonian for this compound. Its main feature is a frustration of magnetic anisotropy on a level that is much higher than in any of the previously studied species. This frustration naturally explains the peculiar phase transition observed.

Nabi, S [Laboratory for Solid State Physics, ETH Z↗

Quantal diffusion approach for multinucleon transfer processes in the 58,64 Ni + 208 Pb reactions: Toward the production of unknown neutron-rich nuclei

In recent years, substantial efforts have been made for the study of multinucleon transfer reactions at energies around the Coulomb barrier both experimentally and theoretically, aiming at the production of unknown neutron-rich heavy nuclei. It is crucial to provide reliable theoretical predictions based on microscopic theories with sufficient predictive power. Purpose: This article aims to clarify the applicability of the quantal diffusion approach based on the stochastic mean-field (SMF) theory for multinucleon transfer processes. Isotope production cross sections are evaluated for the reactions of 64 Ni + 208 Pb at E c.m. = 268 MeV and 58 Ni + 208 Pb at E c.m. = 270 MeV and are compared with available experimental data. Methods: Three-dimensional time-dependent Hartree-Fock (TDHF) calculations are carried out for a range of initial orbital angular momenta with Skyrme SLy4d functional. Quantal diffusion equations, derived based on the SMF theory, for variances and covariance of neutron and proton numbers of reaction products are solved, with microscopic drift and diffusion coefficients obtained from time evolution of occupied single-particle orbitals in TDHF. Secondary de-excitation processes, both particle evaporation and fission, are simulated by a statistical compound-nucleus de-excitation model, gemini++. Dynamics of a fast isospin equilibration process followed by a slow drift toward the mass symmetry are commonly observed, as expected. Various reaction outcomes are evaluated, including average mass and charge numbers of reaction products, total kinetic energy loss (TKEL), scattering angle, contact time, and production cross sections for primary and secondary products. By comparing with the experimental data, we find that SMF and TDHF quantitatively reproduce experimental data for few-nucleon-transfer channels around the average values. In contrast, for many-nucleon-transfer channels, we find that the SMF approach provides much better description of the experimentally measured isotopic distributions. The results underline the importance of beyond-mean-field effects, especially one-body (mean-field) fluctuations and correlations, in describing multinucleon transfer processes. Moreover, through a combined analysis of SMF with a statistical model, gemini++, we find a significant contribution of transfer-induced fission, which is consistent with the experimental observation. In some cases, the SMF approach overestimates the isotopic width, requiring further improvements of the theoretical description. Possible ways to improve the description are discussed. The SMF approach is designed to describe the quantum many-body problem according to an ensemble of mean-field trajectories, taking into account part of many-body correlations in the description. As it requires feasible computational costs comparable to the ordinary TDHF approach, together with further model improvements, it will be a promising tool in the search for optimal reaction conditions to produce yet-unknown neutron-rich heavy nuclei through the multinucleon transfer reaction.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Quantum Application Specifications and Benchmarks

This software describes computational tasks for quantum computers that are derived from LANL basic science research applications such as the modeling of materials, chemicals and compounds at atomic scales. The computations focus on quantum simulation tasks, such as quantum dynamics, thermal state preparation and ground state estimation. The primary function of the software is to develop estimates of the requirements for large-scale fault-tolerant quantum computers to solve these scientific computations. The secondary focus of the software are codes for assessing the limitations of conducting quantum computations on classical computers.

Coffrin, Carleton↗

PNNL-CompBio/ML_UVvisModels

Four (4) ML models that are trained on compounds with known experimental UV-Vis spectra.

McNaughton, Andrew [Pacific Northwest National Lab↗

Optimal production of Phanerochaete chrysosporium manganese peroxidases and Trametes sp. C30 laccase hybrid Lac131 in Aspergillus niger for lignin bioconversion

Background Incorporating the production of related ligninolytic enzymes into industrial filamentous fungus Aspergillus niger will enhance the bioconversion of lignocelluloses to various chemical products. Results In this study, transgenic expression of Phanerochaete chrysosporium manganese peroxidases (mnps) and Trametes sp. C30 laccase hybrid Lac131 (lac131) were examined and optimized in A. niger 11414 prtT∆ strain. Five mnps (mnp1, mnp2, mnp3, mnp4, and mnp5) and lac131 genes were expressed separately or in combination. The transgenic strain containing the entire mnp2 genomic coding sequence (gmnp2) exhibited the highest mnP activity among the five mnp over-expression strains in the modified minimal medium (mMM) with addition of 5 g/L bovine hemoglobin (bHg). We examined the effects of hemin and bHg on mnP production in the gmnp2 strain cultures and found that at least 1 g/L bHg was required, while hemin was not. Culture conditions for mnP production were further optimized for the gmnp2 strain and the highest mnP activities were detected in the cultures grown at 25 °C and 200 rpm with an initial pH of 4.5. Effects of soy protein, skim milk, and bovine serum albumin on mnP production were investigated; 5 g/L of soy proteins or skim milk had comparable effects to 2.5 g/L bHg, while cultures with bovine serum albumin had diminished mnP activity. Disruption of both prtT and vsm1 substantially augmented the mnP production and its activity reached 575 U/L. Trametes sp. C30 laccase hybrid lac131 was strongly expressed in either A. niger gmnp2 (1975 U/L) or 11414prtT∆ (3895 U/L) strain. Both mnP and laccase in the culture supernatants effectively decolorized selected phenolic compounds (dyes) and cleaved tagged model lignin dimers. Conclusion The mnP was successfully produced in A. niger by optimizing the culture conditions and host strain. Co-expression of all four mnp genes in the same expression host by multiplex CRISPR will lead to the mnP production reaching levels comparable to P. chrysosporium, while only requiring 36 h at 25 °C. The Lac131 activity in transgenic A. niger strain is 4- to 7-times higher than that in previous studies. Co-production of mnP and laccase in A. niger will enhance the lignin bioconversion efficiency.

Aspergillus niger↗

Small Molecule Interactions with Membranes (CRADA No. TC02321 Final Report)

This was a collaborative effort between Lawrence Livermore National Security, LLC (LLNS) as manager and operator of Lawrence Livermore National Laboratory (LLNL) and Procter & Gamble (P&G) to develop and use a multiscale simulation method to explore and evaluate the nature of industrially relevant compounds in the presence of models that represent microbial membranes.

59 BASIC BIOLOGICAL SCIENCES↗

Small Molecule Interactions with Membranes. Final CRADA Report

Final Report CRADA No. TC02321 Date Technical Work Ended: 1/29/20. This was a collaborative effort between Lawrence Livermore National Security, LLC (LLNS) as manager and operator of Lawrence Livermore National Laboratory (LLNL) and Procter & Gamble (P&G) to develop and use a multiscale simulation method to explore and evaluate the nature of industrially relevant compounds in the presence of models that represent microbial membranes.

59 BASIC BIOLOGICAL SCIENCES↗

Dark Matter Reconstruction in LBAI Experiments with Imperfect Data

Long-baseline atom interferometer (LBAI) experiments offer unprecedented sensitivity to ultralight scalar dark matter (DM) [1], however reconstruction of a putative DM signal with traditional frequency-domain analysis requires ``perfect data (i.e., regularly-sampled with no missing samples). In a real LBAI experiment, there will undoubtedly be imperfections in the data leading to downtime. This downtime can arise from operational considerations (e.g., maintenance), the operational environment (motion of people and animals [2] or elevators), and robustness of the experimental apparatus (e.g., bad atom launches). In this work, we investigate the impact of various downtime models on the overall DM sensitivity of such an experiment. We compare the sensitivity for each downtime model as determined by a ``compound FFT analysis to a baseline no-downtime case. We also show how much sensitivity can be regained by moving to a Lomb-Scargle frequency analysis, as in [2]. Furthermore, we demonstrate reconstruction of the DM wave s phase as well as its frequency. [1] D. Antypas, et al, ``New Horizons: Scalar and Vector Ultralight Dark Matter (2022). arXiv:2203.14915 [2] J. Carlton and C. McCabe, ``From RATs to riches: mitigating anthropogenic and synanthropic noise in atom interferometer searches for ultra-light dark matter (2023). arXiv:2308.101731

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Crystal Structure Prediction of Binary Alloys via Deep Potential

Predicting crystal structure has been a challenging problem in physics and materials science for a long time. A reliable energy calculation engine combined with an efficient global search algorithm, such as particle swarm optimization algorithm or genetic algorithm, is needed to conduct crystal structure prediction. In recent years, machine learning-based interatomic potential energy surface models have been proposed, potentially allowing us to perform crystal structure prediction for systems with the accuracy of density functional theory (DFT) and the speed of empirical force fields. In this paper, we employ a previously developed Deep Potential model to predict the intermetallic compound of the aluminum–magnesium system, and find six meta-stable phases with negative or nearly zero formation energy. In particular, Mg 12 Al 8 shows excellent ductility and Mg 5 Al 27 has a high Young's modulus. Based on our benchmark results, we propose a relatively robust structure screening criterion that selects potentially stable structures from the Deep Potential-based convex hull and performs DFT refinement. By using this criterion, the computational cost needed to construct the convex hull with ab initio accuracy can be dramatically reduced.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Enantioselectivity of Pentedrone and Methylone on Metabolic Profiling in 2D and 3D Human Hepatocyte-like Cells

Pentedrone and methylone can express stereoselectivity in toxicokinetic and toxicodynamic processes. Similarly, their chiral discrimination in metabolism, which was not yet evaluated, can result in different metabolic profiles and subsequent hepatotoxic effects. Therefore, the aim of this work was to assess, for the first time, both the hepatic cytotoxic and metabolic profile of pentedrone and methylone enantiomers using physiologically relevant in vitro models. The hepatotoxicity of these compounds was observed in a concentration-dependent manner in human stem-cell-derived hepatocyte-like cells (HLCs) cultured under 3D (3D-HLCs) and 2D (2D-HLCs) conditions. Enantioselectivity, on the other hand, was only shown for pentedrone (1 mM) in 3D-HLCs, being R-(−)-pentedrone the most cytotoxic. Furthermore, the metabolic profile was initially evaluated in human liver microsomes (HLM) and further demonstrated in 3D-HLCs and 2D-HLCs applying a gas chromatography coupled to a mass spectrometer (GC–MS) technique. Methylone and pentedrone showed distinct and preferential metabolic routes for their enantiomers, resulting in the production of differentiated metabolites; R-(+)-methylone and R-(−)-pentedrone are the most metabolized enantiomers. In conclusion, the results demonstrated enantioselectivity for pentedrone and methylone in the metabolic processes, with enantioselectivity in cytotoxicity for pentedrone.

Silva, Bárbara (ORCID:0000000173990197)↗

Global anthropogenic emissions (CAMS-GLOB-ANT) for the Copernicus Atmosphere Monitoring Service simulations of air quality forecasts and reanalyses

Anthropogenic emissions are the result of many different economic sectors, including transportation, power generation, industrial, residential and commercial activities, waste treatment and agricultural practices. Air quality models are used to forecast the atmospheric composition, analyze observations and reconstruct the chemical composition of the atmosphere during the previous decades. In order to drive these models, gridded emissions of all compounds need to be provided. This paper describes a new global inventory of emissions called CAMS-GLOB-ANT, developed as part of the Copernicus Atmosphere Monitoring Service (CAMS; https://doi.org/10.24380/eets-qd81, Soulie et al., 2023). The inventory provides monthly averages of the global emissions of 36 compounds, including the main air pollutants and greenhouse gases, at a spatial resolution of 0.1° × 0.1° in latitude and longitude, for 17 emission sectors. The methodology to generate the emissions for the 2000–2023 period is explained, and the datasets are analyzed and compared with publicly available global and regional inventories for selected world regions. Depending on the species and regions, good agreements as well as significant differences are highlighted, which can be further explained through an analysis of different sectors as shown in the figures in the Supplement.

54 ENVIRONMENTAL SCIENCES↗

Volatile organic compound emissions from 4D printing: Effects of material composition and external stimulus

4D printing of stimuli-responsive materials extends 3D printing by enabling the fabricated structures to transform their shapes and properties over time in response to external stimuli. Numerous research efforts have been dedicated to developing new smart materials, enhancing material printability, and ensuring time-evolving properties. Meanwhile, the use of smart materials and external stimuli in 4D printing has introduced the possibility of air emissions that can potentially deteriorate the indoor air quality at the workplace and pose continuous health hazards to users during the production and use phases. These potential air emissions caused by 4D printing have not yet been assessed in current literature, leading to unknown occupational hazards and human health effects. This study focuses on stereolithography-based 4D printing with constrained thermo-mechanics and builds an emission model to quantify the volatile organic compound emissions from printing, shape programming, and shape recovery stages. The established model mathematically links the emission characteristics with material compositional design and stimuli-response mechanisms. Additionally, shape fixity and recovery abilities are considered to analyze the trade-off between the air emissions and stimuli-response performance of 4D printed parts. Case study results suggest that the methacrylate-based thermo-responsive material with higher glass transition temperature leads to higher air emissions, surpassing the permissible exposure level in the indoor environment. By altering the thermo-temporal conditions, a 61.29% reduction in emission yield can be achieved while ensuring a satisfactory shape memory performance.

36 MATERIALS SCIENCE↗

Zinc chloride affects chondrogenesis via VEGF signaling

Highlights: • ZnCl2 increases expression of various chondrogenic signaling intermediates. • VEGF/VEGFR play a key role in modulating levels of chondrogenesis. • Insulin mimetics are an appealing option for improvement of fracture healing. • Axitinib + ZnCl2 treatment results in decreased transcription of chondrogenic genes. Insulin mimetics, including zinc containing compounds, have previously been shown to influence chondrogenesis as it relates to healing of fractures in various preclinical models. However, the mechanism by which these compounds drive chondrogenic differentiation is yet undefined. Here, via next-generation sequencing (NGS) and in vitro functional validation, we show that Zinc Chloride (ZnCl{sub 2}) induces expression of both chondrogenic genes (Sox9, Runx1, collagen) as well as genes associated with VEGF-mediated signal transduction, including VEGF receptors 1 and 2 and their ligands; VEGF-A and VEGF-B. Noticeably, although insulin was able to also induce expression of these pro-angiogenic and pro-chondrogenic genes, the impact of insulin on expression of VEGF receptor and ligand genes was marginal when compared to that of ZnCl{sub 2.} Furthermore, while the VEGFR antagonist, Axitinib, was able to attenuate the pro-chondrogenic effects of both insulin and ZnCl{sub 2}; a reduction in gene and protein expression was most profoundly observed when the antagonist was applied to cells treated with ZnCl{sub 2.} Taken together, these data suggest an important role for the VEGF-mediated signal transduction pathways in the positive effects observed when applying zinc-based compounds as adjuvants for chondrogenesis-mediated fracture healing. In this regard, further mechanistic evaluation of ZnCl{sub 2} and other zinc-containing insulin mimetics may support rational design of therapies targeted for disease indications associated with impaired fracture healing.

60 APPLIED LIFE SCIENCES↗

Compounding Uncertainties in Economic and Population Growth Increase Tail Risks for Relevant Outcomes Across Sectors

Understanding the long-term effects of population and GDP changes requires a multisectoral and regional understanding of the coupled human-Earth system, as the long-term evolution of this coupled system is influenced by human decisions and the Earth system. This study investigates the impact of compounding economic and population growth uncertainties on long-term multisectoral outcomes. We use the Global Change Analysis Model (GCAM) to explore the influence of compounding and feedback between future GDP and population growth on four key sectors: final energy consumption, water withdrawal, staple food prices, and CO 2 emissions. The results show that uncertainties in GDP and population compound, resulting in a magnification of tail risks for outcomes across sectors and regions. Compounding uncertainties significantly impact metrics such as CO 2 emissions and final energy consumption, particularly at the upper tail at both global and regional levels. However, the impact of staple food prices and water withdrawal depends on regional factors. Additionally, an alternative low-carbon transition scenario could compound uncertainties and increase tail risk, particularly in staple food prices, highlighting the influence of emergent constraints on land availability and food-energy competition for land use. The findings underscore the importance of considering and adequately accounting for compounding uncertainties in key drivers of multisectoral systems to enhance our comprehensive understanding of the complex nature of multisectoral systems. The paper provides valuable insights into the potential implications of compounding uncertainties.

54 ENVIRONMENTAL SCIENCES↗