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At least 991 records · Page 55
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

Materials Data on CoH3(CN)6 by Materials Project

Co(H(CN)2)3 crystallizes in the trigonal P-31m space group. The structure is zero-dimensional and consists of one cobalt molecule and three H(CN)2 clusters. In each H(CN)2 cluster, C+2.33+ is bonded in a single-bond geometry to one N3- atom. The C–N bond length is 1.17 Å. N3- is bonded in a linear geometry to one C+2.33+ and one H1+ atom. The N–H bond length is 1.27 Å. H1+ is bonded in a linear geometry to two equivalent N3- atoms.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Materials Data on Eu2Si3Ni8 by Materials Project

Eu2(Ni2Si)3(Ni)2 crystallizes in the tetragonal P4_2/nmc space group. The structure is three-dimensional and consists of eight nickel molecules and one Eu2(Ni2Si)3 framework. In the Eu2(Ni2Si)3 framework, Eu2+ is bonded in a distorted single-bond geometry to two equivalent Ni1+ and one Si4- atom. Both Eu–Ni bond lengths are 2.79 Å. The Eu–Si bond length is 2.83 Å. There are two inequivalent Ni1+ sites. In the first Ni1+ site, Ni1+ is bonded in a 2-coordinate geometry to one Eu2+ and two equivalent Si4- atoms. There are one shorter (2.32 Å) and one longer (2.33 Å) Ni–Si bond lengths. In the second Ni1+ site, Ni1+ is bonded in a 4-coordinate geometry to four Si4- atoms. There are a spread of Ni–Si bond distances ranging from 2.18–2.55 Å. There are two inequivalent Si4- sites. In the first Si4- site, Si4- is bonded in a 10-coordinate geometry to six Ni1+ atoms. In the second Si4- site, Si4- is bonded in a 4-coordinate geometry to two equivalent Eu2+ and four equivalent Ni1+ atoms.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Materials Data on Zr6BH42C12I13O12 by Materials Project

Zr6BC6H18(OI2)6(CH3OH)6I crystallizes in the trigonal R-3 space group. The structure is zero-dimensional and consists of three hydriodic acid molecules, eighteen methanol molecules, and three Zr6BC6H18(OI2)6 clusters. In each Zr6BC6H18(OI2)6 cluster, Zr is bonded in a distorted single-bond geometry to one B, one O, and four I atoms. The Zr–B bond length is 2.69 Å. The Zr–O bond length is 1.93 Å. There are two shorter (2.91 Å) and two longer (2.95 Å) Zr–I bond lengths. B is bonded in an octahedral geometry to six equivalent Zr atoms. C is bonded in a tetrahedral geometry to three H and one O atom. All C–H bond lengths are 1.10 Å. The C–O bond length is 1.41 Å. There are three inequivalent H sites. In the first H site, H is bonded in a single-bond geometry to one C atom. In the second H site, H is bonded in a single-bond geometry to one C atom. In the third H site, H is bonded in a single-bond geometry to one C atom. O is bonded in a bent 150 degrees geometry to one Zr and one C atom. There are two inequivalent I sites. In the first I site, I is bonded in an L-shaped geometry to two equivalent Zr atoms. In the second I site, I is bonded in an L-shaped geometry to two equivalent Zr atoms.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Materials Data on HW2C9NO10 by Materials Project

W2HW2H(NO)2(CO)18 crystallizes in the monoclinic C2 space group. The structure is zero-dimensional and consists of thirty-six formaldehyde molecules, two W2H clusters, and two W2H(NO)2 clusters. In each W2H cluster, W5+ is bonded in a single-bond geometry to one H1+ atom. The W–H bond length is 1.92 Å. H1+ is bonded in a bent 120 degrees geometry to two equivalent W5+ atoms. In each W2H(NO)2 cluster, W5+ is bonded in a linear geometry to one N3- and one H1+ atom. The W–N bond length is 1.90 Å. The W–H bond length is 1.95 Å. N3- is bonded in a linear geometry to one W5+ and one O2- atom. The N–O bond length is 1.17 Å. H1+ is bonded in a bent 120 degrees geometry to two equivalent W5+ atoms. O2- is bonded in a single-bond geometry to one N3- atom.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Amino‐Functionalised Hybrid Ultramicroporous Materials that Enable Single‐Step Ethylene Purification from a Ternary Mixture

Abstract Pyrazine‐linked hybrid ultramicroporous (pore size <7 Å) materials (HUMs) offer benchmark performance for trace carbon capture thanks to strong selectivity for CO 2 over small gas molecules, including light hydrocarbons. That the prototypal pyrazine‐linked HUMs are amenable to crystal engineering has enabled second generation HUMs to supersede the performance of the parent HUM, SIFSIX‐3‐Zn , mainly through substitution of the metal and/or the inorganic pillar. Herein, we report that two isostructural aminopyrazine‐linked HUMs, MFSIX‐17‐Ni (17=aminopyrazine; M=Si, Ti), which we had anticipated would offer even stronger affinity for CO 2 than their pyrazine analogs, unexpectedly exhibit reduced CO 2 affinity but enhanced C 2 H 2 affinity. MFSIX‐17‐Ni are consequently the first physisorbents that enable single‐step production of polymer‐grade ethylene (>99.95 % for SIFSIX‐17‐Ni ) from a ternary equimolar mixture of ethylene, acetylene and CO 2 thanks to coadsorption of the latter two gases. We attribute this performance to the very different binding sites in MFSIX‐17‐Ni versus SIFSIX‐3‐Zn .

Mukherjee, Soumya↗
DOE OSTI2021

Amino‐Functionalised Hybrid Ultramicroporous Materials that Enable Single‐Step Ethylene Purification from a Ternary Mixture

Abstract Pyrazine‐linked hybrid ultramicroporous (pore size <7 Å) materials (HUMs) offer benchmark performance for trace carbon capture thanks to strong selectivity for CO 2 over small gas molecules, including light hydrocarbons. That the prototypal pyrazine‐linked HUMs are amenable to crystal engineering has enabled second generation HUMs to supersede the performance of the parent HUM, SIFSIX‐3‐Zn , mainly through substitution of the metal and/or the inorganic pillar. Herein, we report that two isostructural aminopyrazine‐linked HUMs, MFSIX‐17‐Ni (17=aminopyrazine; M=Si, Ti), which we had anticipated would offer even stronger affinity for CO 2 than their pyrazine analogs, unexpectedly exhibit reduced CO 2 affinity but enhanced C 2 H 2 affinity. MFSIX‐17‐Ni are consequently the first physisorbents that enable single‐step production of polymer‐grade ethylene (>99.95 % for SIFSIX‐17‐Ni ) from a ternary equimolar mixture of ethylene, acetylene and CO 2 thanks to coadsorption of the latter two gases. We attribute this performance to the very different binding sites in MFSIX‐17‐Ni versus SIFSIX‐3‐Zn .

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2026

Viral Nuclease Inhibitors: Small molecule disruptors of the UL12 alkaline nuclease display broad anti-herpes virus activity

Herpes simplex virus 1 (HSV-1) UL12 encodes a highly conserved 5′ → 3′ alkaline exonuclease that is essential for the production of infectious virus. Together with the viral single-stranded DNA-binding/annealing protein ICP8, UL12 functions as a two-component recombinase that mediates recombination-dependent viral DNA replication. Here, we present the crystal structure of the catalytic domain of the HSV alkaline nuclease (UL12), which provides the first view of an α-herpesvirus alkaline nuclease. Using this structure, we optimized a series of small-molecule viral nuclease inhibitors (VNIs) that target the UL12 active site and potently inhibit UL12 exonuclease activity in vitro. We have thus established a robust platform for structure-based docking, SAR analysis and rational inhibitor design. Because UL12 orthologs are conserved across all human herpesviruses, we examined the activity of these compounds against the β- and γ-herpesvirus alkaline nucleases UL98 and SOX and found that they inhibit all three enzymes. The VNIs also exhibit antiviral activity against HSV-1 and HCMV in cell culture. EC 50 and IC 50 values were in the nanomolar to low micromolar range. Together, these findings establish herpesvirus alkaline nucleases as conserved, druggable antiviral targets and provide a foundation for the development of broad-spectrum anti-herpesvirus therapeutics, either as standalone agents or in combination with existing nucleoside analogs.

Sharma, Nidhi↗
DOE OSTI2025

Attosecond control and measurement of chiral photoionization dynamics

Many chirality-sensitive light–matter interactions are governed by chiral electron dynamics. Therefore, the development of advanced technologies making use of chiral phenomena would critically benefit from measuring and controlling chiral electron dynamics on their natural attosecond timescales. Such endeavours have so far been hampered by the lack of characterized circularly polarized attosecond pulses, an obstacle that has recently been overcome. Here we introduce chiroptical spectroscopy with attosecond pulses and demonstrate attosecond coherent control over photoelectron circular dichroism (PECD), as well as the measurement of chiral asymmetries in the forward–backward and angle-resolved photoionization delays of chiral molecules. We show that co-rotating attosecond and near-infrared (IR) pulses can nearly double the PECD and even change its sign compared with single-photon ionization. We demonstrate that chiral photoionization delays depend on both polar and azimuthal angles of photoemission in the light-propagation frame, requiring 3D momentum resolution. We measure forward–backward chiral-sensitive delays of up to 60 as and polar-angle-resolved photoionization delays of up to 240 as, which include an asymmetry of about 60 as originating from chirality in the continuum–continuum transitions. Attosecond chiroptical spectroscopy opens the door to quantitatively understanding and controlling the dynamics of chiral molecules on the electronic timescale.

Atomic and molecular interactions with photons↗
DOE OSTI2021

Local-Field Effects in Linear Response Properties within a Polarizable Frozen Density Embedding Method

In this work, we present a polarizable frozen density embedding (FDE) method for calculating polarizabilities of coupled subsystems. The method (FDE-pol) combines a FDE method with an explicit polarization model such that the expensive freeze/thaw cycles can be bypassed, and approximate nonadditive kinetic potentials are avoided by enforcing external orthogonality between the subsystems. To describe the polarization of the frozen environment, we introduce a Hirshfeld partition-based density-dependent method for calculating the atomic polarizabilities of atoms in molecules, which alleviates the need to fit the atomic parameters to a specific system of interest or to a larger general set of molecules. Further, we show that the Hirshfeld partition-based method predicts molecular polarizabilities close to the basis set limit, and thus, a single basis set-dependent scaling parameter can be introduced to improve the agreement against the reference polarizability data. To test the model, we characterized the uncoupled and coupled response of small interacting molecular complexes. Here, the coupled response properties include the perturbation of the frozen system due to the external perturbation which is ignored in the uncoupled response. We show that FDE-pol can accurately reproduce both the exact uncoupled polarizability and the coupled polarizabilities of the supermolecular systems. Using damped response theory, we also demonstrate that the coupled frequency-dependent polarizability can be described by including local field effects. The results emphasize the necessity of including local-field effects for describing the response properties of coupled subsystems, as well as the importance of accurate atomic polarizability models.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Robust control of the minima of high-order harmonics by fine-tuning the alignment of CO 2 molecules for shaping attosecond pulses and probing molecular alignment

In a recent paper, we reported that the position and depth of the minima in the harmonic spectra of CO 2 molecules can be dramatically manipulated by a slight change of the degree of alignment, thus providing a convenient method of shaping attosecond pulses which could lead to the splitting of a typical single attosecond burst into two. Here, we demonstrate that harmonic minima can also be dramatically controlled by changing the pump-probe angles to shape attosecond pulses. In the meanwhile, since the pump-probe angle-dependent harmonic spectra are very sensitive to the degree of alignment, harmonic spectra can also be used to calibrate the alignment distribution of molecules. In this work we identify such robust control of harmonic generation is due to the optical property of CO 2 and the coherent harmonic emission from the oriented molecules. The photoionization transition dipoles (PITDs) of CO 2 exhibit deep minima that change rapidly with molecular orientations accompanied by large phase changes of π in PITDs, thus leading to strong interference when the dipoles are added up coherently.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2022

Methods to Calculate Electronic Excited-State Dynamics for Molecules on Large Metal Clusters with Many States: Ensuring Fast Overlap Calculations and a Robust Choice of Phase

Here, we present an efficient set of methods for propagating excited-state dynamics involving a large number of configuration interaction singles (CIS) or Tamm-Dancoff approximation (TDA) single-reference excited states. Specifically, (i) following Head-Gordon et al., we implement an exact evaluation of the overlap of singly-excited CIS/TDA electronic states at different nuclear geometries using a biorthogonal basis and (ii) we employ a unified protocol for choosing the correct phase for each adiabat at each geometry. For many-electron systems, the combination of these techniques significantly reduces the computational cost of integrating the electronic Schrodinger equation and imposes minimal overhead on top of the underlying electronic structure calculation. As a demonstration, we calculate the electronic excited-state dynamics for a hydrogen molecule scattering off a silver metal cluster, focusing on high-lying excited states, where many electrons can be excited collectively and crossings are plentiful. Interestingly, we find that the high-lying, plasmon-like collective excitation spectrum changes with nuclear dynamics, highlighting the need to simulate non-adiabatic nuclear dynamics and plasmonic excitations simultaneously. In the future, the combination of methods presented here should help theorists build a mechanistic understanding of plasmon-assisted charge transfer and excitation energy relaxation processes near a nanoparticle or metal surface.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Device and Method for Parallel Measurement of Phosphoproteome and Proteome from Single Cells

We present the development of an immobilized metal affinity chromatography (IMAC) chip designed to enable nanoscale phosphopeptide enrichment within microfabricated nanowells. This novel platform leverages surface chemistry to immobilize high-density Nickel-Nitrilotriacetic Acid (Ni-NTA) molecules on nanowells, followed by applying Fe 3+ . The nanowell surface serves as a capture media to enrich phosphopeptides based on IMAC. The system's efficiency was validated using ß-casein as a model protein, demonstrating the chip’s capability to significantly enrich phosphopeptides. Future applications of this technology are anticipated to enable the detection of over 100 phosphopeptides from individual cells and more than 500 phosphopeptides from pools of 100 cells, offering exciting potential for single-cell phosphoproteomics. We will next apply an integrated proteomics workflow to perform multi-omics measurements, including single-cell isolation, protein digestion, and phosphopeptide enrichment, followed by LC-MS analysis of both the global proteome and phosphoproteome. Future research will explore the use of this technology to study phosphorylation dynamics in cancer cells, enhancing our understanding of cellular signaling and disease mechanisms.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

A physics-informed multi-agents model to predict thermo-oxidative/hydrolytic aging of elastomers

This paper introduces a novel physics-informed multi-agents constitutive model to propose prediction in quasi-static constitutive behavior of cross-linked elastomer and the loss of mechanical performance during environmental aging. The presented model is used to simulate the effect of single-mechanism chemical aging (i.e. thermal-inducedor hydrolytic aging) on the behavior of the material in this hybrid framework. Those environmental single-mechanism damages change the polymer matrix over time due to massive chain scission, chain formations, and changing the arrangement of molecules in the polymer matrix. Here we propose a data-driven super-constrained machine-learned engine to represent damage in the polymer matrix and capture the changes in material behavior, including its inelastic features such as Mullins effect and permanent set in the course of aging. We have simplified the 3D stress–strain tensor mapping problem into a small number of super-constrained 1D mapping problems by means of a sequential order reduction. An assembly of multiple replicated conditional neural-network learning-agents (L-agents) is trained to systematically simplify the high-dimensional mapping problem into multiple 1D problems, each represented by a different type of agent. Our hybrid framework is designed to capture the effect of deformation history, aging time, and aging temperature. The model is validated with respect to a comprehensive set of experiments specifically designed to benchmark model capabilities and also against available data in the literature. Thermodynamic consistency and frame independency have been verified. Besides acceptable predictive abilities, a significant reduction of computational cost to predict behavior at multiple states of deformation is the most significant feature of this model.

42 ENGINEERING↗
DOE OSTI2022

Process-Specific Effects of Sulfate on CaCO 3 Formation in Environmentally Relevant Systems

Additives, such as ions, small molecules, and macromolecules, have been found to regulate the formation of CaCO 3 and control its morphologies and properties. However, a single additive usually affects dominantly one process in CaCO 3 's formation and is seldom found to significantly affect multiple CaCO 3 formation processes. In this work, we used in situ grazing incidence X-ray techniques to observe the heterogeneous formation of CaCO 3 and found that a series of formation processes (i.e., nucleation, growth, and Ostwald ripening) were modulated by sulfate. In the nucleation process, increased interfacial free energy and bulk free energy cooperatively increased the nucleation barrier and decreased nucleation rates. In the growth process, sulfate reduced the electrostatic repulsion between CaCO 3 precursors and nuclei, promoting CaCO 3 growth. This influence on the growth counteracted the inhibition effect in the nucleation process, causing a nearly 100% increase in the volume of heterogeneously formed CaCO 3 . Meanwhile, adsorbed sulfate on CaCO 3 nuclei may poison the surface of smaller CaCO 3 nuclei, inhibiting Ostwald ripening. These revealed sulfate's active roles in controlling CaCO 3 formation advance our understanding of sulfate-incorporated biomineralization and scaling phenomena in natural and engineered aquatic environments.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Benchmarking Correlation-Consistent Basis Sets for Frequency-Dependent Polarizabilities with Multiresolution Analysis

This paper presents the first converged frequency-dependent HF polarizability results for general molecules, on a set of 89 closed-shell atoms and molecules. The solver employs multiresolution analysis (MRA) in a multiwavelet basis to compute both ground and response states to a guaranteed precision, which are validated against independent numerical grid calculations on atoms and linear molecules. The MRA ground-state energies and response properties are used to evaluate results in correlation-consistent basis sets up to 5Z augmented with either single or double diffuse functions and core-polarization functions. Systematic trends are revealed through consideration of chemical composition as well as the use of machine learning to cluster convergence trends, the latter suggesting the possibility of learning and correcting basis-set error.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Second Linear Response Theory and the Analytic Calculation of Excited-State Properties

We present a method based on second linear response time-dependent density func- tional theory (TDDFT) to calculate permanent and transition multipoles of excited states, which are required to compute excited-state absorption/emission spectra, multi- photon optical processes, among others. In previous work, we examined computations based on second linear response theory in which linear response TDDFT was employed twice. In contrast, the present methodology only requires information from a single linear response calculation to compute the excited-state properties. These are eval- uated analytically through various algebraic operations involving electron repulsion integrals and excitation vectors. The present derivation focuses on full many-body wave functions instead of single orbitals, as in our previous approach. Here, we test the proposed method by applying it to several diatomic and triatomic molecules. This shows that the computed excited-state dipoles are consistent with respect to reference equation-of-motion coupled cluster calculations.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

Theoretical study of the CO 2 –O 2 van der Waals complex: potential energy surface and applications

A four-dimensional-potential energy surface (4D-PES) of the atmospherically relevant carbon dioxide–oxygen molecule (CO 2 –O 2 ) van der Waals complex is mapped using the ab initio explicitly correlated coupled cluster method with single, double, and perturbative triple excitations (UCCSD(T)-F12b), and extrapolation to the complete basis set (CBS) limit using the cc-pVTZ-F12/cc-pVQZ-F12 bases and the l –3 formula. An analytic representation of the 4D-PES was fitted using the method of interpolating moving least squares (IMLS). These calculations predict that the most stable configuration of CO 2 –O 2 complex corresponds to a planar slipped-parallel structure with a binding energy of V ~ –243 cm –1 . Another isomer is found on the PES, corresponding to a non-planar cross-shaped structure, with V ~ –218 cm –1 . The transition structure connecting the two minima is found at V ~ –211 cm –1 . We also performed comparisons with some CO 2 –X van der Waals complexes. Moreover, we provide a SAPT analysis of this molecular system. Then, we discuss the complexation induced shifts of CO 2 and O 2 . Afterwards, this new 4D-PES is employed to compute the second virial coefficient including temperature dependence. A comparison between quantities obtained in our calculations and those from experiments found close agreement attesting to the high quality of the PES and to the importance of considering a full description of the anisotropic potential for the derivation of thermophysical properties of CO 2 –O 2 mixtures.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

Equation-of-motion internally contracted multireference unitary coupled-cluster theory

The accurate computation of excited states remains a challenge in electronic structure theory, especially for systems with a ground state that requires a multireference treatment. In this work, we introduce a novel equation-of-motion (EOM) extension of the internally contracted multireference unitary coupled-cluster framework (ic-MRUCC), termed EOM-ic-MRUCC. EOM-ic-MRUCC follows the transform-then-diagonalize approach, in analogy to its non-unitary counterpart. By employing a projective approach to optimize the ground state, the method retains additive separability and proper scaling with system size. We show that excitation energies are size-intensive if the EOM operator satisfies the “killer” and the projective conditions. Furthermore, we propose to represent changes in the reference state upon electron excitation via projected many-body operators that span the active orbitals and show that the EOM equations formulated in this way are invariant with respect to active orbital rotations. We test the EOM-ic-MRUCC method truncated to single and double excitations by computing the potential energy curves for several excited states of a BeH2 model system, the HF molecule, and water undergoing symmetric dissociation. Across these systems, our method delivers accurate excitation energies and potential energy curves within 5 mE h (∼0.14 eV) from full configuration interaction. Here, we find that truncating the Baker–Campbell–Hausdorff series to fourfold commutators contributes negligible errors (on the order of 10 −5 E h or less), offering a practical route to highly accurate excited-state calculations with reduced computational overhead.

74 ATOMIC AND MOLECULAR PHYSICS↗