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At least 433 records · Page 24

Toward Fast and Reliable Potential Energy Surfaces for Metallic Pt Clusters by Hierarchical Delta Neural Networks

Data-driven machine learning force fields (MLF) are more and more popular in atomistic simulations, and exploit machine learning methods to predict energies and forces for unknown structures based on the knowledge learned from an existing reference database. The latter usually comes from density functional theory calculations. One main drawback of MLFs is that physical laws are not incorporated in the machine learning models and instead, MLFs are designed to be very flexible to simulate complex quantum chemistry potential energy surface (PES). In general, MLFs have poor transferability, and hence a very large trainset is required to span all the target feature space to get a reliable MLF. This procedure becomes more troublesome when the PES is complicated, with a large number of degrees of freedom, in which building a large database is inevitable and very expensive, especially when accurate but costly exchange-correlation functionals have to be used. In this manuscript, we exploit a high dimensional neural network potential (HDNNP) on Pt clusters of size 6 to 20 as one example. Furthermore, our standard level of energy calculation is DFT GGA (PBE) using a plane wave basis set. We introduce an approximate but fast level with the PBE functional and a minimal atomic orbital basis set, then a more accurate but expensive level, using a hybrid functional or non-local vdw functional and a plane wave basis set, is reliably predicted by learning the difference with HDNNP. Findings show that such a differential approach (named ΔHDNNP) can deliver very accurate predictions (error < 10 meV/atom) in reference to converged basis set energies as well as more accurate but expensive xc functional. The overall speedup can be as large as 900 for 20 atom Pt cluster. More importantly, ΔHDNNP shows much better transferability due to the intrinsic smoothness of delta potential energy surface, and accordingly one can use much smaller trainset data to obtain better accuracy than the conventional HDNNP. A multi-layer ΔHDNNP is thus proposed to obtain very accurate predictions versus expensive non-local vdW functional calculations in which the required trainset is further reduced. The approach can be easily generalized to any other machine learning methods and opens a path to study the structure and dynamics of Pt clusters and nanoparticles.

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Efficient Modeling of Structural, Electronic, and Optical Properties of Silver and Gold Metal Nanoclusters and Alloys Using Optimized SCC-DFTB Parameters

Computation of optical properties using conventional time-dependent density functional theory (TD-DFT) is time-consuming and memory-intensive. In this study, we investigate the accuracy and efficiency of the density functional tight binding (DFTB) framework with newly optimized Slater–Koster (SK) parameters for modeling the structural, electronic properties, and absorption spectra of silver and gold nanoclusters and their alloys. Our investigation of the ground state (GS) properties demonstrates that the newly developed GS-SK parameters enable DFTB to closely approximate DFT-calculated bond lengths for octahedron, tetrahedron, icosahedra, and truncated octahedron with sizes Ag n /Au n (n = 19, 20, 38, 55), nanoclusters and Ag 20 /Au 20 nanoalloys, with a maximum deviation of approximately 0.15 Å. Formation energy results indicate that the GS-SK parameters can closely estimate changes in formation energies with alloy composition, and the comparison of electronic structures for Ag 20 , Au 20 , and AgAu alloy nanoclusters using the DFTB approximation reveals good agreement in the projected density of states (DOS) profiles and energy levels. A second set of SK parameters, ES-SK, has been developed to describe excited state (ES) properties, including the absorption spectra of silver octahedron Ag 19 , tetrahedral Ag n (n = 20, 56, 84), truncated octahedron Ag 38 , and icosahedra Ag 55 closed-shell clusters and their gold and alloy counterparts over a broad range of alloy compositions. This parametrization uses TD-DFTB calculations and fine-tunes the d and p eigenvalues by comparing them to reference absorption spectra from first-principles TD-DFT. This enables the generation of absorption spectra that closely match the reference spectra when plasmon excitation is dominant, as demonstrated by studying the plasmonic properties of icosahedral Ag n and Au n (n = 309 and 561) nanoparticles. This includes the rapid loss in plasmon quality when Au partially replaces Ag in alloy clusters. Furthermore, these results provide a foundation for addressing computational bottlenecks in plasmonics and with new prospects for applications in the quantum plasmonics for bimetallic alloys.

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Accelerating the Global Arrays ComEx Runtime using Multiple Progress Ranks

Partitioned Global Address Space (PGAS) models are part of system software that are being designed to support communication runtime for exascale applications. Suitability of using MPI as a scalable PGAS communication subsystem has been shown as a viable option due to its standardization and higher performance. We used MPI two-sided semantics with a combination of automatic and user defined splitting of MPI communicators to achieve asynchronous progress. Our implementation can make use of multiple asynchronous progress ranks (PR) per node that can be mapped to the computing architecture of a node in a distributed cluster. We are able to show significant speed up of over 2.0X and scaling of communication bound computational chemistry application over 1024 nodes of state- of-the-art HPC clusters. Our results show that while running a communication bound application workload on a certain number of cluster nodes, a use of optimum number of ranks dedicated for communication may be used to achieve asynchronous communication progress and obtain highest performance.

PGAS, global-arrays, NWCHEM, NWChemEx, HPC, GPGPU↗

Accelerated Simulation of Air Pollution Using NVIDIA RAPIDS

Atmospheric chemistry models are a central tool to study and forecast the impact of air pollution on the environment, vegetation, and human health. However, the numerical simulation of chemical kinetics is computationally expensive due to the stiffness of the system of ordinary differential equations that describes atmospheric chemistry. Here we present an alternative approach to the computation of atmospheric chemistry based on machine learning. Our training data set is produced using the NASA Goddard Earth Observing System (GEOS) model with GEOS-Chem chemistry, run on the NASA Center for Climate Simulation (NCCS) Discover supercomputing cluster on 384 Intel Xeon Haswell cores. This model spends more than 50% of total run time on solving atmospheric chemistry. The data set contains as input features the air pollution concentrations before solving the differential equations, together with some key physical parameters such as temperature and sun intensity. As target variables we define the air pollution concentrations after solving the differential equations. Using Dask-cuDF and Dask-XGBoost on the NVIDIA RAPIDS platform on 8 Tesla V100 GPUs, we generate from this training set gradient boosted decision tree models that can reproduce the simulation of chemical kinetics. We do this on the NCCS Advanced Data Analytics Platform (ADAPT) science cloud environment. Our application takes full advantage of recent advances in Dask-XGBoost, such as multi-node and multi-GPU scaling for distributed training with large data sets. The increase in training data size enabled by this is critical to capture the full range of chemical environments encountered across the globe and all annual seasons.The boosted tree models offer good predictability and show many of the features of the full chemistry reference simulation. Further improvements can be achieved through mass balance considerations and by accounting for error correlations. We incorporate the boosted tree models into the GEOS reference model using XGBoost's C API. This enables a seamless integration of the GPU trained models into GEOS-Chem, which is written in Fortran and optimized for use in a massively parallel CPU environment. We show the benefits of this approach and discuss the potential speedup of this machine learning accelerated atmospheric chemistry model.

Keller, Christoph A.↗

Navier: Dataflow Architecture for Computation Chemistry

Navier’s objectives were two evaluate the use of emerging technologies, especially dataflow accelerators, for high-performance computing (HPC) applications, specifically in the domain of chemistry, and to develop a prototype software stack to support such applications. Navier builds on capabilities previously developed by synergistic projects, such as PNNL Data Model Convergence (DMC) LDRD Hardware Advanced Workflows (HAW) and DuOMO, as well as DOE ARIAA. Throughout its 18 months, the Navier team developed new capabilities and artifacts at all levels of the HW/SW stack, provided a seamless way to integrate novel computing architectures (Sambanova SN10 and Xilinx Versal AI) into an existing software stack, developed chemistry workflows, data analytics tools, and HPC molecular dynamics workflows that leverage the developed stack and PNNL institutional investments in emerging architectures. Navier also explored the use of active learning to accelerate a computational chemistry workflow for organic molecules on PNNL Junction cluster (in collaboration with AMD/Xilinx). Navier developed tools, methodologies, and studies for hardware software co-design and (sparse) dataflow accelerators that are composable and can be used together or separately. These methodologies are now used in other projects, such as DOE AMAIS and HPDA. This report describes Navier’s achievement, the developed tools and methodologies, and the research findings and conclusions.

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Iron-sulfur clusters: the road to room temperature

Abstract Iron-sulfur proteins perform a wide variety of reactions central to the metabolisms of all living organisms. Foundational to their reaction chemistry are the rich electronic structures of their constituent Fe-S clusters, which differ in important ways from the active sites of mononuclear Fe enzymes. In this perspective, we summarize the essential electronic structure features that make Fe-S clusters unique, and point to the need for studies aimed at understanding the electronic basis for their reactivity under physiological conditions. Specifically, at ambient temperature, both the ground state and a large number of excited states are thermally populated, and thus a complete understanding of Fe-S cluster reactivity must take into account the properties, energies, and reactivity patterns of these excited states. We highlight prior research toward characterizing the low-energy excited states of Fe-S clusters that has established what is now a consensus model of these excited state manifolds and the bonding interactions that give rise to them. In particular, we discuss the low-energy alternate spin states and valence electron configurations that occur in Fe-S clusters of varying nuclearities, and finally suggest that there may be unrecognized functional roles for these states. Graphical abstract

Skeel, Brighton A. (ORCID:000000018458088X)↗

Polarizable Frozen Density Embedding with External Orthogonalization

In this work, we report a polarizable subsystem density functional theory to describe electronic properties of molecules embedded on a metal cluster. Interaction between the molecule and metal cluster is described using frozen density embedding (FDE). Substituting the nonadditive kinetic potential (NAKP) by approximate functionals is circumvented by enforcing external orthogonality (EO) through a projection operator. The computationally expensive freeze/thaw (FT) cycles are bypassed by including a polarization term in the embedding operator. Furthermore, the combination of polarization and EO permits supermolecular basis set calculations, which was not possible for strongly interacting systems with existing kinetic energy functionals. To test the method, we described the ground state density of pyridine, water, and benzene on a silver cluster. Performing FT on top of EO results in exact density embedding for this category of systems and is thus used for benchmarking the method. We find that the density is reproduced to within 0.15e, and the dipole and quadrupole moments are within 18% of the reference points for subsystem separations ranging from bonding to noninteracting distances. Additionally, our formalism allows the flexibility of incorporating different density functionals to the molecular and the metallic subsystems reducing the overall computational cost.

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Computational studies of structural, energetic, and electronic properties of pure Pt and Mo and mixed Pt/Mo clusters: Comparative analysis of characteristics and trends

The added technological potential of bimetallic clusters and nanoparticles, as compared to their pure (i.e., one-component) counterparts, stems from the ability to further fine-tune their properties and, consequently, functionalities through a simultaneous use of the “knobs” of size and composition. The practical realization of this potential can be greatly advanced by the knowledge of the correlations and relationships between the various characteristics of bimetallic nanosystems on the one hand and those of their pure counterparts as well as pure constituent components on the other hand. Here, in this study, we present results of a density functional theory based study of pure Pt n and Mo n clusters aimed at revisiting and exploring further their structural, electronic, and energetic properties. These are then used as a basis for analysis and characterization of the results of calculations on two-component Pt n-m Mo m clusters. The analysis also includes establishing relationships between the properties of the Pt n-m Mo m clusters and those of their Pt n-m and Mo m components. One of the particularly intriguing findings suggested by the calculated data is a linear dependence of the average binding energy per atom in sets of Pt n-m Mo m clusters that have the same fixed number m of Mo atoms and different number n-m of Pt atoms on the fractional content (n-m)/n of Pt atoms. We derive an analytical model that establishes the fundamental basis for this linearity and expresses its parameters—the m-dependent slope and intercept—in terms of characteristic properties of the constituent components, such as the average binding energy per atom of Mo m and the average per-atom adsorption energy of the Pt atoms on Mo m . The conditions of validity and degree of robustness of this model and of the linear relationship predicted by it are discussed.

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Lewis Acid Supported Nickel Nitrenoids

Metalation of the polynucleating ligand F,tbs LH 6 (1,3,5-C 6 H 9 (NC 6 H 3 −4-F−2-NSiMe 2 t Bu) 3 ) with two equivalents of Zn(N(SiMe 3 ) 2 ) 2 affords the dinuclear product ( F,tbs LH 2 )Zn 2 (1), which can be further deprotonated to yield ( F,tbs L)Zn 2 Li 2 (OEt 2 ) 4 (2). Transmetalation of 2 with NiCl 2 (py) 2 yields the heterometallic, trinuclear cluster ( F,tbs L)Zn 2 Ni(py) (3). Reduction of 3 with KC 8 affords [KC 222 ][( F,tbs L)Zn 2 Ni] (4) which features a monovalent Ni centre. Addition of 1-adamantyl azide to 4 generates the bridging μ 3 -nitrenoid adduct [K(THF) 3 ][( F,tbs L)Zn 2 Ni(μ 3 -NAd)] (5). EPR spectroscopy reveals that the anionic cluster possesses a doublet ground state (S = 1/2). Cyclic voltammetry of 5 reveals two fully reversible redox events. The dianionic nitrenoid [K 2 (THF) 9 ][( F,tbs L)Zn 2 Ni(μ 3 -NAd)] (6) was isolated and characterized while the neutral redox isomer was observed to undergo both intra- and intermolecular H-atom abstraction processes. Here, Ni K-edge XAS studies suggest a divalent oxidation state for the Ni centres in both the monoanionic and dianionic [Zn 2 Ni] nitrenoid complexes. However, DFT analysis suggests Ni-borne oxidation for 5.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Spatiotemporal Studies of Soluble Inorganic Nanostructures with X‐rays and Neutrons

This Review addresses the use of X-ray and neutron scattering as well as X-ray absorption to describe how inorganic nanostructured materials assemble, evolve, and function in solution. We first provide an overview of techniques and instrumentation (both large user facilities and benchtop). We review recent studies of soluble inorganic nanostructure assembly, covering the disciplines of materials synthesis, processes in nature, nuclear materials, and the widely applicable fundamental processes of hydrophobic interactions and ion pairing. Reviewed studies cover size regimes and length scales ranging from sub-Ångström (coordination chemistry and ion pairing) to several nanometers (molecular clusters, i.e. polyoxometalates, polyoxocations, and metal-organic polyhedra), to the mesoscale (supramolecular assembly processes). Reviewed studies predominantly exploit 1) SAXS/WAXS/SANS (small- and wide-angle X-ray or neutron scattering), 2) PDF (pair-distribution function analysis of X-ray total scattering), and 3) XANES and EXAFS (X-ray absorption near-edge structure and extended X-ray absorption fine structure, respectively). While the scattering techniques provide structural information, X-ray absorption yields the oxidation state in addition to the local coordination. Our goal for this Review is to provide information and inspiration for the inorganic/materials science communities that may benefit from elucidating the role of solution speciation in natural and synthetic processes.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Rank-reduced coupled-cluster. III. Tensor hypercontraction of the doubles amplitudes

In this work, we develop a quartic-scaling implementation of coupled-cluster singles and doubles (CCSD) based on low-rank tensor hypercontraction (THC) factorizations of both the electron repulsion integrals (ERIs) and the doubles amplitudes. This extends our rank-reduced (RR) coupled-cluster method to incorporate higher-order tensor factorizations. The THC factorization of the doubles amplitudes accounts for most of the gain in computational efficiency as it is sufficient, in conjunction with a Cholesky decomposition of the ERIs, to reduce the computational complexity of most contributions to the CCSD amplitude equations. Further THC factorization of the ERIs reduces the complexity of certain terms arising from nested commutators between the doubles excitation operator and the two-electron operator. We implement this new algorithm using graphical processing units and demonstrate that it enables CCSD calculations for molecules with 250 atoms and 2500 basis functions using a single computer node. Furthermore, we show that the new method computes correlation energies with comparable accuracy to the underlying RR-CCSD method.

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Kinetics of Carbon Condensation in Detonation of High Explosives: First-Order Phase Transition Theory Perspective

We report the kinetics of carbon condensation, or carbon clustering, in detonation of carbon-rich high explosives is modeled by solving a system of rate equations for concentrations of carbon particles. Unlike previous efforts, the rate equations account not only for the aggregation of particles but also for their fragmentation in a thermodynamically consistent manner. Numerical simulations are performed, yielding the distribution of particle concentrations as a function of time. In addition to that, analytical expressions are obtained for all the distinct steps and regimes of the condensation kinetics, which facilitates the analysis of the numerical results and allows one to study the sensitivity of the kinetic behavior to the variation of system parameters. The latter is important because the numerical values of many parameters are not reliably known at present. The theory of the kinetics of first-order phase transitions is found adequate to describe the general kinetic trends of carbon condensation, as described by the rate equations. Such physical phenomena and processes as the coagulation, nucleation, growth, and Ostwald ripening are observed, and their dependence on various system parameters is studied and reported. It is believed that the present work will become useful when analyzing the present and future results for the kinetics of carbon condensation, obtained from experiments or atomistic simulations.

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Reversible CO 2 Hydrogenation, Neutron Crystallography, and Hydride Reactivity of a Triiridium Heptahydride Complex

Here, the authors report the structure, reactivity, and catalytic utility of a triiridium complex, [Ir 3 H 6 (μ 3 -H)(PN) 3 ] 2+ (2-H, PN = (2-pyridyl)CH 2 PBu t 2 ). Despite its unusual stability to unsaturated organics, electrophiles, and even CF 3 SO 3 D, they find that complex 2-H catalyzes hydrogenation of CO 2 to formate (TON Ir = 9600) and reverse formic acid dehydrogenation (TON Ir = 54 400). The hydrogenation operates via a reactive intermediate [Ir 3 H 4 (μ-H) 4 (PN) 3 ] + (5). Neutron crystallography and DFT-supported neutron vibrational spectroscopy of 2-H reveal Ir─H bond lengths and elucidate the vibration modes within the Ir 3 H 7 core. Stoichiometric oxidation of 2-H produces four classes of iridium complexes of varied nuclearity and hydride structure: tetra- and pentanuclear clusters [Ir 3 H 6 (μ 3 -AuPPh 3 )(PN) 3 ] 2+ (2-Au) and [Ag{Ir 2 H 4 (μ-OAc)(PN) 2 } 2 ] 3+ (6) are generated using AuPPh 3 + and AgOAc, respectively. Further oxidation to class [Ir 2 H 3 (μ-X) 2 (PN) 2 ] + is possible with AgOAc, Hg(OAc) 2 , or I 2 . Finally, a TEMPO/HCl system completely oxidizes the hydrides and gives [Ir 2 Cl 4 (μ-Cl) 2 (PN) 2 ] (11).

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Multi–Modular Design of Stable Pore–Space–Partitioned Metal–Organic Frameworks for Gas Separation Applications

Pore space partition (PSP) is an effective materials design method for developing high-performance small-pore materials for storage and separation of gas molecules. The continued success of PSP depends on broad availability and judicious choice of pore-partition ligands and better understanding of each structural module on stability and sorption properties. Here, by using substructural bioisosteric strategy (sub-BIS), a dramatic expansion of pore-partitioned materials is targeted by using ditopic dipyridyl ligands with non-aromatic cores or extenders, as well as by expanding heterometallic clusters to uncommon nickel–vanadium and nickel–indium clusters rarely known before in porous materials. The dual-module iterative refinement of pore-partition ligands and trimers leads to remarkable enhancement of chemical stability and porosity. Here a family of 23 pore-partitioned materials synthesized from five pore-partition ligands and seven types of trimeric clusters is reported. New materials with such compositionally and structurally diverse framework modules reveal key factors that dictate stability, porosity, and gas separation properties. Among these, materials based on heterometallic vanadium–nickel trimeric clusters give rise to the highest long-term hydrolytic stability and remarkable uptake capacity for CO 2 , C 2 H 2 /C 2 H 4 /C 2 H 6 , and C 3 H 6 /C 3 H 8 hydrocarbon gases. Here, the breakthrough experiment shows the potential application of new materials for separating gas mixtures such as C 2 H 2 /CO 2 .

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Experimental observation of hydrocarbon growth by resonance stabilized radical-radical chain reaction

Rapid molecular weight growth of hydrocarbons occurs in flames, in industrial synthesis, and potentially in cold astrochemical environments. A variety of high- and low-temperature chemical mechanisms have been proposed and confirmed, but more facile pathways may be needed to explain observations. Here, we provide laboratory confirmation in a controlled pyrolysis environment of a recently proposed mechanism, radical-radical chain reactions of resonance-stabilized species. The recombination reaction of phenyl (c-C 6 H 5 ) and benzyl (c-C 6 H 5 CH 2 ) radicals produces both diphenylmethane and diphenylmethyl radicals, the concentration of the latter increasing with rising temperature. A second phenyl addition to the product radical forms both triphenylmethane and triphenylmethyl radicals, confirming the propagation of radical-radical chain reactions under the experimental conditions of high temperature (1100-1600 K) and low pressure (~3 kPa). Similar chain reactions may contribute to particle growth in flames, the interstellar medium, and industrial reactors.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Spatiotemporal Studies of Soluble Inorganic Nanostructures with X‐rays and Neutrons

Abstract This Review addresses the use of X‐ray and neutron scattering as well as X‐ray absorption to describe how inorganic nanostructured materials assemble, evolve, and function in solution. We first provide an overview of techniques and instrumentation (both large user facilities and benchtop). We review recent studies of soluble inorganic nanostructure assembly, covering the disciplines of materials synthesis, processes in nature, nuclear materials, and the widely applicable fundamental processes of hydrophobic interactions and ion pairing. Reviewed studies cover size regimes and length scales ranging from sub‐Ångström (coordination chemistry and ion pairing) to several nanometers (molecular clusters, i.e. polyoxometalates, polyoxocations, and metal‐organic polyhedra), to the mesoscale (supramolecular assembly processes). Reviewed studies predominantly exploit 1) SAXS/WAXS/SANS (small‐ and wide‐angle X‐ray or neutron scattering), 2) PDF (pair‐distribution function analysis of X‐ray total scattering), and 3) XANES and EXAFS (X‐ray absorption near‐edge structure and extended X‐ray absorption fine structure, respectively). While the scattering techniques provide structural information, X‐ray absorption yields the oxidation state in addition to the local coordination. Our goal for this Review is to provide information and inspiration for the inorganic/materials science communities that may benefit from elucidating the role of solution speciation in natural and synthetic processes.

Yin, Jia‐Fu↗