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At least 1,045 records · Page 58
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

Solution Chemistry of Copper(II) Binding to Substituted 8-Hydroxyquinolines

8-Hydroxyquinolines (8HQs) are a family of lipophilic metal ion chelators that have been used in a range of analytical and pharmaceutical applications over the last 100 years. More recently, CQ (clioquinol; 5-chloro-7-iodo-8-hydroxyquinoline) and PBT2 (5,7-dichloro-2-[(dimethylamino)methyl]-8-hydroxyquinoline) have undergone clinical trials for the treatment of Alzheimer’s disease and Huntington’s disease. Because CQ and PBT2 appear to redistribute metals into cells, these compounds have been redefined as copper and zinc ionophores. Despite the attention surrounding the clinical trials and the clear link between 8HQs and metals, the fundamental solution chemistry of how these compounds bind divalent metals such as copper and zinc, as well as their mechanism(s) of action in mammalian systems, remains poorly understood. Here, we used a combination of X-ray absorption spectroscopy (XAS), high-energy resolution fluorescence detected (HERFD) XAS, electron paramagnetic resonance (EPR), and UV–visible absorption spectroscopies to investigate the aqueous solution chemistry of a range of 8HQ derivatives. To circumvent the known solubility issues with 8HQ compounds and their complexes with Cu(II), and to avoid the use of abiological organic solvents, we have devised a surfactant buffer system to investigate these Cu(II) complexes in aqueous solution. Our study comprises the first comprehensive investigation of the Cu(II) complexes formed with many 8HQs of interest in aqueous solution, and it provides the first structural information on some of these complexes. We find that halogen substitutions in 8HQ derivatives appear to have little effect on the Cu(II) coordination environment; 5,7-dihalogenated 8HQ conformers all have a pseudo square planar Cu(II) bound by two quinolin-8-olate anions, in agreement with previous studies. Conversely, substituents in the 2-position of the 8HQ moiety appear to cause significant distortions from the typical square-planar-like coordination of most Cu(II)-bis-8HQ complexes, such that the 8HQ moieties in the Cu(II)-bis-8HQ complex are rotated approximately 30–40° apart in a “propeller-like” arrangement.

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

Complexes of Platinum Group Metals with a Conformationally Locked Scorpionate in a Metal–Organic Framework: An Unusually Close Apical Interaction of Palladium(II)

Here, we report synthetic strategies for installing platinum group metals (PGMs: Pd, Rh, Ir, and Pt) on a scorpionate-derived linker (TpmC*) within a metal–organic framework (MOF), both by room-temperature postsynthetic metalation and by direct solvothermal synthesis, with a wide range of metal loadings relevant for fundamental studies and catalysis. In-depth studies for the palladium adduct Pd(II)@Zr-TpmC* by density-functional-theory-assisted extended X-ray absorption fine structure spectroscopy reveals that the rigid MOF lattice enforces a close Pd(II)–N apical interaction between the bidentate palladium complex and the third uncoordinated pyrazole arm of the TpmC* ligand (Pd–N apical = 2.501 ± 0.067 Å), an interaction that is wholly avoided in molecular palladium scorpionates.

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

Role of Pairwise Reactions on the Synthesis of Li 0.3 La 0.57 TiO 3 and the Resulting Structure–Property Correlations

The performance of single-ion conductors is highly sensitive to the material’s defect chemistry. Tuning these defects is limited for solid-state reactions as they occur at particle–particle interfaces, which provide a complex evolving energy landscape for atomic rearrangement and product formation. In this report, we investigate the (1) order of addition and (2) lithium precursor decomposition temperature and their effect on the synthesis and grain boundary conductivity of the perovskite lithium lanthanum titanium oxide (LLTO). We use an intimately mixed sol–gel, a solid-state reaction of Li precursor + La 2 O 3 + TiO 2 , and Li precursor + amorphous La 0.57 TiO x as different chemical routes to change the way in which the elements are brought together. The results show that the perovskite can accommodate a wide range of Li deficiencies (upward of 50%) while maintaining the tetragonal LLTO structure, indicating that X-ray diffraction (XRD) is insufficient to fully characterize the chemical nature of the product (i.e., Li-deficient LLTO may behave differently than stoichiometric LLTO). Variations in the relative intensities of different reflections in XRD suggest variations in the La ordering within the crystal structure between synthesis methods. Furthermore, the choice of the precursor and the order of addition of the reactants lower the time required to form a pure phase. Density functional theory calculations of the formation energy of possible reaction intermediates support the hypothesis that a greater thermodynamic driving force to form LLTO leads to a greater LLTO yield. Here, the retention of lithium is correlated with the thermal decomposition temperature of the Li precursor and the starting material mixing strategy. Taking the results together suggests that cations that share a site with Li should be mixed early to avoid ordering. Such cation ordering inhibits Li motion, leading to higher Li ion resistance.

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

A Low-Temperature Structural Transition in Canfieldite, Ag 8 SnS 6 , Single Crystals

Canfieldite, Ag 8 SnS 6 , is a semiconducting mineral notable for its high ionic conductivity, photosensitivity, and low thermal conductivity. In this paper, we report the solution growth of large single crystals of Ag 8 SnS 6 of mass up to 1 g from a ternary Ag–Sn–S melt. On cooling from high temperature, Ag 8 SnS 6 undergoes a known cubic ($F\bar{4}3m$) to orthorhombic ($Pna2_1$) phase transition at ≈460 K. By studying the magnetization and thermal expansion between 5–300 K, we discover a second structural transition at ≈120 K. Single crystal X-ray diffraction reveals the low-temperature phase adopts a different orthorhombic structure with space group $Pmn2_1$ ($\textit{a}$ = 7.662 9(5) Å, $\textit{b}$ = 7.539 6(5) Å, $\textit{c}$ = 10.630 0(5) Å, Z = 2 at 90 K) that is isostructural to the room-temperature forms of the related Se-based compounds Ag 8 SnSe 6 and Ag 8 GeSe 6 . The 120 K transition is first-order and has a large thermal hysteresis. On the basis of the magnetization and thermal expansion data, the room-temperature polymorph can be kinetically arrested into a metastable state by rapidly cooling to temperatures below 40 K. We last compare the room- and low-temperature forms of Ag8SnS6 with its argyrodite analogues, Ag 8 TQ 6 ($\textit{T}$ = Si, Ge, Sn; $\textit{Q}$ = S, Se), and identify a trend relating the preferred structures to the unit cell volume, suggesting smaller phase volume favors the $Pna2_1$ arrangement. We support this picture by showing that the transition to the $Pmn2_1$ phase is avoided in Ge alloyed Ag 8 Sn 1–x Ge x S 6 samples as well as in pure Ag 8 GeS 6 .

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Changing Directions: Influence of Ligand Electronics on the Directionality and Kinetics of Photoinduced Charge Transfer in Cu(I)Diimine Complexes

A key challenge to the effective utilization of solar energy is to promote efficient photoinduced charge transfer, specifically avoiding unproductive, circuitous electron-transfer pathways and optimizing the kinetics of charge separation and recombination. We hypothesize that one way to address this challenge is to develop a fundamental understanding of how to initiate and control directional photoinduced charge transfer, particularly for earth-abundant first-row transition-metal coordination complexes, which typically suffer from relatively short excited-state lifetimes. Here, in this paper, we report a series of functionalized heteroleptic copper(I)bis(phenanthroline) complexes, which have allowed us to investigate the directionality of intramolecular photoinduced metal-to-ligand charge transfer (MLCT) as a function of the substituent Hammett parameter. Ultrafast transient absorption suggests a complicated interplay of MLCT localization and solvent interaction with the Cu(II) center of the MLCT state. This work provides a set of design principles for directional charge transfer in earth-abundant complexes and can be used to efficiently design pathways for connecting the molecular modules to catalysts or electrodes and integration into systems for light-driven catalysis.

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

Infrared Spectroelectrochemical Insights into Rhenium-Based Supramolecular Assemblies for Electron Storage and Transfer

Three supramolecular square assemblies featuring Re(CO)3Cl corners and monodentate pyridyl linkers [4,4′-bipyridine, (1a), pyrazine (2a), and 1,2-di(4-pyridyl)ethylene (3a), where a denotes the native state] were synthesized and studied via infrared spectroelectrochemistry (IR-SEC). IR-SEC revealed that the length of the bridging ligand and degree of electronic coupling in rhenium squares greatly impact the reduction pathway in both inert and CO2 atmospheres; notably, the squares are capable of interacting with CO2 after only ligand reduction, thereby avoiding the need for an additional reductive event to generate the rhenium anion. This mechanism differs from that of mononuclear complexes, highlighting how unique redox properties can be endowed by electronic coupling in supramolecular systems.

Koehne, Sydney Marie↗
DOE OSTI2020

Nature of Hyperfine Interactions in TbPc 2 Single-Molecule Magnets: Multiconfigurational Ab Initio Study

Lanthanide-based single-ion magnetic molecules can have large magnetic hyperfine interactions as well as large magnetic anisotropy. Recent experimental studies reported tunability of these properties by changes of chemical environments or by application of external stimuli for device applications. In order to provide insight onto the origin and mechanism of such tunability, here we investigate the magnetic hyperfine and nuclear quadrupole interactions for a 159 Tb nucleus in TbPc 2 (Pc = phthalocyanine) single-molecule magnets using multiconfigurational ab initio methods including spin–orbit interaction. Since the electronic ground and first-excited (quasi)doublets are well separated in energy, the microscopic Hamiltonian can be mapped onto an effective Hamiltonian with an electronic pseudospin S = 1/2. From the ab initio calculated parameters, we find that the magnetic hyperfine coupling is dominated by the interaction of the Tb nuclear spin with electronic orbital angular momentum. The asymmetric 4f-like electronic charge distribution leads to a strong nuclear quadrupole interaction with significant transverse terms for the molecule with low symmetry. The ab initio calculated electronic–nuclear spectrum including the magnetic hyperfine and quadrupole interactions is in excellent agreement with the experiment. We further find that the transverse quadrupole interactions significantly influence the avoided level crossings in magnetization dynamics and that the molecular distortions affect mostly the Fermi contact terms as well as the transverse quadrupole interactions. Synopsis Hyperfine interactions for 159 Tb nucleus in TbPc 2 single-molecule magnets are investigated from first-principles using multiconfigurational calculations. Strong nuclear quadrupole and magnetic hyperfine coupling are found, with the latter being dominated by the paramagnetic spin-orbital mechanism. Furthermore, we construct an ab initio pseudospin Hamiltonian and obtain the electronic-nuclear spectrum that is in excellent agreement with experiment. The Zeeman diagram is calculated, and the magnetization dynamics is discussed. The effects of molecular distortions are researched.

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

Speed of Sound Measurements of Binary Mixtures of trans -1,2-Difluoroethylene (R-1132(E)) with Difluoromethane (R-32) or 2,3,3,3-Tetrafluoropropene (R-1234yf)

The speed of sound of two binary mixtures containing 0.336 mole fraction trans-1,2- difluoroethylene (R-1132(E)) with difluoromethane (R-32) and 0.435 mole fraction R-1132(E) with 2,3,3,3-tetrafluoropropene (R-1234yf) were measured with a dual-path pulse-echo instrument. The speed of sound was measured along several pseudo-isochores for each blend at temperatures ranging from 230 K to 325 K for blends with R-32 and to 342 K for blends with R- 1234yf. Measurements started at pressures just above each mixtures bubble point pressure and were limited to 8 MPa to avoid potential disproportionation reactions of the R-1132(E). The data were compared to multi-fluid models incorporating Helmholtz-energy-explicit equations of state (EOS) for each pure fluid.

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

Machine Learning Algorithm Identifies an Antibiotic Vocabulary for Permeating Gram-Negative Bacteria

Drug discovery faces a crisis. The industry has used up the “obvious” space in which to find novel drugs for biomedical applications, and productivity is declining. One strategy to combat this is rational approaches to expand the search space without relying on chemical intuition, to avoid rediscovery of similar spaces. Here, we present proof of concept of an approach to rationally identify a “chemical vocabulary” related to a specific drug activity of interest without employing known rules. We focus on the pressing concern of multidrug resistance in Pseudomonas aeruginosa by searching for submolecules that promote compound entry into this bacterium. By synergizing theory, computation, and experiment, we validate our approach, explain the molecular mechanism behind identified fragments promoting compound entry, and select candidate compounds from an external library that display good permeation ability.

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

Machine Learning Models to Predict Inhibition of the Bile Salt Export Pump

Cholestatic liver injury is frequently associated with drug inhibition of bile salt transporters, such as the bile salt export pump (BSEP). Reliable in silico models to predict BSEP inhibition directly from chemical structures would significantly reduce costs during drug discovery and could help avoid injury to patients. We report our development of classification and regression models for BSEP inhibition with substantially improved performance over previously published models. We assessed the performance effects of different methods of chemical featurization, data set partitioning, and class labeling and identified the methods producing models that generalized best to novel chemical entities.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

CoarsenConf: Equivariant Coarsening with Aggregated Attention for Molecular Conformer Generation

Molecular conformer generation (MCG) is an important task in cheminformatics and drug discovery. The ability to efficiently generate low-energy 3D structures can avoid expensive quantum mechanical simulations, leading to accelerated virtual screenings and enhanced structural exploration. Several generative models have been developed for MCG, but many struggle to consistently produce high-quality conformers for meaningful downstream applications. To address these issues, we introduce CoarsenConf, which coarse-grains molecular graphs based on torsional angles and integrates them into an SE(3)-equivariant hierarchical variational autoencoder. Through equivariant coarse-graining, we aggregate the fine-grained atomic coordinates of subgraphs connected via rotatable bonds, creating a variable-length coarse-grained latent representation. Our model uses a novel aggregated attention mechanism to restore fine-grained coordinates from the coarse-grained latent representation, enabling efficient generation of accurate conformers. Furthermore, we evaluate the chemical and biochemical quality of our generated conformers on multiple downstream applications, including property prediction and large-scale oracle-based protein docking. Overall, CoarsenConf generates more accurate conformer ensembles compared to prior generative models.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
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 OSTI2023

Partitioning Quantum Chemistry Simulations with Clifford Circuits

Current quantum computing hardware is restricted by the availability of only few, noisy qubits which limits the investigation of larger, more complex molecules in quantum chemistry calculations on quantum computers in the near term. Here, in this work, we investigate the limits of their classical and near-classical treatment while staying within the framework of quantum circuits and the variational quantum eigensolver. To this end, we consider naive and physically motivated, classically efficient product ansatz for the parametrized wavefunction adapting the separable-pair ansatz form. We combine it with post-treatment to account for interactions between subsystems originating from this ansatz. The classical treatment is given by another quantum circuit that has support between the enforced subsystems and is folded into the Hamiltonian. To avoid an exponential increase in the number of Hamiltonian terms, the entangling operations are constructed from purely Clifford or near-Clifford circuits. While Clifford circuits can be simulated efficiently classically, they are not universal. In order to account for missing expressibility, near-Clifford circuits with only few, selected non-Clifford gates are employed. The exact circuit structure to achieve this objective is molecule-dependent and is constructed using simulated annealing and genetic algorithms. We demonstrate our approach on a set of molecules of interest and investigate the extent of our methodology’s reach.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Shadow Molecular Dynamics and Atomic Cluster Expansions for Flexible Charge Models

Here, a shadow molecular dynamics scheme for flexible charge models is presented where the shadow Born–Oppenheimer potential is derived from a coarse-grained approximation of range-separated density functional theory. The interatomic potential, including the atomic electronegativities and the charge-independent short-range part of the potential and force terms, is modeled by the linear atomic cluster expansion (ACE), which provides a computationally efficient alternative to many machine learning methods. The shadow molecular dynamics scheme is based on extended Lagrangian (XL) Born–Oppenheimer molecular dynamics (BOMD). XL-BOMD provides stable dynamics while avoiding the costly computational overhead associated with solving an all-to-all system of equations, which normally is required to determine the relaxed electronic ground state prior to each force evaluation. To demonstrate the proposed shadow molecular dynamics scheme for flexible charge models using atomic cluster expansion, we emulate the dynamics generated from self-consistent charge density functional tight-binding (SCC-DFTB) theory using a second-order charge equilibration (QEq) model. The charge-independent potentials and electronegativities of the QEq model are trained for a supercell of uranium oxide (UO 2 ) and a molecular system of liquid water. The combined ACE+XL-QEq molecular dynamics simulations are stable over a wide range of temperatures both for the oxide and for the molecular systems and provide a precise sampling of the Born–Oppenheimer potential energy surfaces. Accurate ground Coulomb energies are produced by the ACE-based electronegativity model during an NVE simulation of UO 2 , predicted to be within 1 meV of those from SCC-DFTB on average during comparable simulations.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Linearized Pair-Density Functional Theory for Vertical Excitation Energies

Multiconfiguration pair-density functional theory (MC-PDFT) is a computationally efficient method that computes the energies of electronic states in a state specific or state average framework via an on-top functional. However, MC-PDFT does not include state interaction among these states since the final energies do not come from the diagonalization of an effective model-space Hamiltonian. Recently, multistate extensions such as linearized PDFT (L-PDFT) have been developed to accurately model the potentials near conical intersections and avoided crossings. However, there has not been any systematic study evaluating their performance for predicting vertical excitations at the equilibrium geometry of a molecule, when the excited states are generally well separated. In this paper, we report the performance of L-PDFT on the extensive QUESTDB data set of vertical excitations using a database of automatically selected active spaces. We show that L-PDFT performs well on all these excitations and successfully reproduces the performance of MC-PDFT. These results further demonstrate the potential of L-PDFT, as its scaling is constant with the number of states included in the state-average manifold, whereas MC-PDFT scales linearly in this regard.

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

Cholesky Decomposition-Based Implementation of Relativistic Two-Component Coupled-Cluster Methods for Medium-Sized Molecules

A Cholesky decomposition (CD)-based implementation of relativistic two-component coupled-cluster (CC) and equation-of-motion CC (EOM-CC) methods using an exact two-component Hamiltonian augmented with atomic-mean-field integrals (the X2CAMF scheme) is reported. Furthermore, the present CD-based implementation of X2CAMF-CC and EOM-CC methods employs atomic-orbital-based algorithms to avoid the construction of two-electron integrals and intermediates involving three and four virtual indices. The CD-based implementation extends the applicability of X2CAMF-CC and EOMCC methods to medium-sized molecules with the correlation of around 1000 spinors. Benchmark calculations for uranium-containing small molecules have been performed to assess the dependence of CC results with respect to the Cholesky threshold. A Cholesky threshold of 10 –4 is shown to maintain chemical accuracy. Example calculations to illustrate the capability of the CD-based relativistic CC methods are reported for the bond dissociation energy of the uranium hexafluoride molecule, UF 6 , with up to quadruple-zeta basis sets and the lowest excitation energy in solvated uranyl ion [UO 2 2+ (H 2 O) 12 ].

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

Enhanced Twist-Averaging Technique for Magnetic Metals: Applications Using Quantum Monte Carlo

In this study, we propose an improved twist-averaging (TA) scheme for quantum Monte Carlo methods that use converged Kohn–Sham or Hartree–Fock orbitals as the reference. This TA technique is tailored to sample the Brillouin zone of magnetic metals, although it naturally extends to nonmagnetic (NM) conducting systems. The proposed scheme aims to reproduce the reference magnetization and achieves charge neutrality by construction, thus avoiding the large energy fluctuations and the postprocessing needed to correct the energies. It shows the most robust convergence of total energy and magnetism to the thermodynamic limit (TDL) when compared to four other TA schemes. Diffusion Monte Carlo applications are shown on NM Al and ferromagnetic α-Fe. The cohesive energy of Al in the TDL shows an excellent agreement with the experimental result. Furthermore, the magnetic moments in α-Fe exhibit rapid convergence with an increasing number of twists.

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

Analytic Nuclear Gradients for Complete Active Space Linearized Pair-Density Functional Theory

Accurately modeling photochemical reactions is difficult due to the presence of conical intersections and locally avoided crossings, as well as the inherently multiconfigurational character of excited states. As such, one needs a multistate method that incorporates state interaction in order to accurately model the potential energy surface at all nuclear coordinates. The recently developed linearized pair-density functional theory (L-PDFT) is a multistate extension of multiconfiguration PDFT, and it has been shown to be a cost-effective post-MCSCF method (as compared to more traditional and expensive multireference many-body perturbation methods or multireference configuration interaction methods) that can accurately model potential energy surfaces in regions of strong nuclear–electronic coupling in addition to accurately predicting Franck–Condon vertical excitations. Here, in this paper, we report the derivation of analytic gradients for L-PDFT and their implementation in the PySCF-forge software, and we illustrate the utility of these gradients for predicting ground- and excited-state equilibrium geometries and adiabatic excitation energies for formaldehyde, s-trans-butadiene, phenol, and cytosine.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗