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At least 523 records · Page 29

Introducing metal–sulfur active sites in metal–organic frameworks via post-synthetic modification for hydrogenation catalysis

Metal–sulfur active sites play a central role in catalytic processes such as hydrogenation and dehydrogenation, yet the majority of active sites in these compounds reside on the surfaces and edges of catalyst particles, limiting overall efficiency. Here we present a strategy to embed metal–sulfur active sites into metal–organic frameworks (MOFs) by converting bridging or terminal chloride ligands into hydroxide and subsequently into sulfide groups through post-synthetic modification. We apply this method to two representative MOF families: one featuring one-dimensional metal–chloride chains and another containing discrete multinuclear metal clusters. Crystallographic and spectroscopic analyses confirm structural integrity and sulfide incorporation, and the transformation is monitored by in situ total scattering methods. The sulfided MOFs display enhanced catalytic activity in the selective hydrogenation of nitroarenes using molecular hydrogen. Density functional theory calculations indicate that sulfur incorporation promotes homolytic metal–ligand bond cleavage and facilitates H 2 activation. This work establishes an approach to construct MOFs featuring accessible metal–sulfide sites.

Catalyst synthesis↗

In search of molecular ions for optical cycling: a difficult road

Optical cycling, a continuous photon scattering off atoms or molecules, plays a central role in the quantum information science. While optical cycling has been experimentally achieved for many neutral species, few molecular ions have been investigated. We present a systematic theoretical search for diatomic molecular ions suitable for optical cycling using equation-of-motion coupled-cluster methods. Inspired by the electronic structure patterns of laser-cooled neutral molecules, we establish the design principles for molecular ions and explore various possible cationic molecular frameworks. The results show that finding a perfect molecular ion for optical cycling is challenging, yet possible. Among various possible diatomic molecules we suggest several candidates, which require further attention from both theory and experiment: YF + , SiO + , PN + , SiBr + , and BO + .

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Velocity dispersion and dynamical masses for 388 galaxy clusters and groups

The second catalogue of Planck Sunyaev-Zeldovich (SZ) sources, hereafter PSZ2, represents the largest galaxy cluster sample selected by means of their SZ signature in a full-sky survey. For this work, using telescopes at the Canary Island observatories, we conducted the long-term observational program 128- MULTIPLE-16/15B (hereafter LP15), a large and complete optical follow-up campaign of all the unidentified PSZ2 sources in the northern sky, with declinations above –15° and no correspondence in the first Planck catalogue PSZ1. This paper is the third and last in the series of LP15 results, after Streblyanska et al. (2019, A&A, 628, A13) and Aguado-Barahona et al. (2019, A&A, 631, A148), and presents all the spectroscopic observations of the full program. We complement these LP15 spectroscopic results with Sloan Digital Sky Survey archival data and other observations from a previous program (ITP13-08), and present a catalogue of 388 clusters and groups of galaxies including estimates of their velocity dispersion. The majority of them (356) are optical counterparts of PSZ2 sources. A subset of 297 of those clusters are used to construct the M SZ – M dyn scaling relation based on the estimated SZ mass from Planck measurements and our dynamical mass estimates. We discuss and correct for different statistical and physical biases in the estimation of the masses, such as the Eddington bias when estimating M SZ and the aperture and the number of galaxies used to calculate M dyn . The SZ-to-dynamical mass ratio for those 297 PSZ2 clusters is (1 – B) = 0.80 ± 0.04 (stat) ± 0.05 (sys), with only marginal evidence for a possible mass dependence for this factor. Our value is consistent with previous results in the literature, but is associated with a significantly smaller uncertainty due to the use of the largest sample size for this type of study.

79 ASTRONOMY AND ASTROPHYSICS↗

A coupled cluster framework for electrons and phonons

Here, we describe a coupled cluster framework for coupled systems of electrons and harmonic phonons. Neutral and charged excitations are accessed via the equation-of-motion version of the theory. Benchmarks on the Hubbard–Holstein model allow us to assess the strengths and weaknesses of different coupled cluster approximations, which generally perform well for weak to moderate coupling. Finally, we report progress toward an implementation for ab initio calculations on solids and present some preliminary results on finite-size models of diamond with a linear electron–phonon coupling. We also report the implementation of electron–phonon coupling matrix elements from crystalline Gaussian type orbitals within the PySCF program package.

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.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Transferability of data-driven, many-body models for CO 2 simulations in the vapor and liquid phases

Here, extending on the previous work by Riera et al. [J. Chem. Theory Comput. 16, 2246–2257 (2020)], we introduce a second generation family of data-driven many-body MB-nrg models for CO 2 and systematically assess how the strength and anisotropy of the CO 2 –CO 2 interactions affect the models’ ability to predict vapor, liquid, and vapor–liquid equilibrium properties. Building upon the many-body expansion formalism, we construct a series of MB-nrg models by fitting one-body and two-body reference energies calculated at the coupled cluster level of theory for large monomer and dimer training sets. Advancing from the first generation models, we employ the charge model 5 scheme to determine the atomic charges and systematically scale the two-body energies to obtain more accurate descriptions of vapor, liquid, and vapor–liquid equilibrium properties. Challenges in model construction arise due to the anisotropic nature and small magnitude of the interaction energies in CO 2 , calling for the necessity of highly accurate descriptions of the multidimensional energy landscape of liquid CO 2 . These findings emphasize the key role played by the training set quality in the development of transferable, data-driven models, which, accurately representing high-dimensional many-body effects, can enable predictive computer simulations of molecular fluids across the entire phase diagram.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Real-time equation-of-motion CC cumulant and CC Green’s function simulations of photoemission spectra of water and water dimer

Newly developed coupled-cluster (CC) methods enable simulations of ionization potentials and spectral functions of molecular systems in a wide range of energy scales ranging from core-binding to valence. This paper discusses the results obtained with the real-time equation-of-motion CC cumulant (RT-EOM-CC) approach and CC Green’s function (CCGF) approaches in applications to the water and water dimer molecules. Here, we compare the ionization potentials obtained with these methods for the valence region with the results obtained with the coupled-cluster with singles, doubles, and perturbative triples formulation as a difference of energies for N and N – 1 electron systems. All methods show good agreement with each other. They also agree well with the experiment with errors usually below 0.1 eV for the ionization potentials. We also analyze unique features of the spectral functions, associated with the position of satellite peaks, obtained with the RT-EOM-CC and CCGF methods employing single and double excitations, as a function of the monomer OH bond length and the proton transfer coordinate in the dimer. Finally, we analyze the impact of the basis set effects on the quality of calculated ionization potentials and find that the basis set effects are less pronounced for the augmented-type sets.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Geometric phase in coupled cluster theory

It has been well-established that the topography around conical intersections between excited electronic states is incorrectly described by coupled cluster and many other single reference theories (the intersections are “defective”). Despite this, we show both analytically and numerically that the geometric phase effect (GPE) is correctly reproduced upon traversing a path around a defective excited-state conical intersection (CI) in coupled cluster theory. The theoretical analysis is carried out by using a non-Hermitian generalization of the linear vibronic coupling approach. Interestingly, the approach qualitatively explains the characteristic (incorrect) shape of the defective CIs and CI seams. Moreover, the validity of the approach and the presence of the GPE indicate that defective CIs are local (and not global) artifacts. This implies that a sufficiently accurate coupled cluster method could predict nuclear dynamics, including geometric phase effects, as long as the nuclear wavepacket never gets too close to the conical intersections.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Coarsening dynamics of ternary polymer solutions with mobility and viscosity contrasts

Using phase-field simulations, we investigate the bulk coarsening dynamics of ternary polymer solutions undergoing a glass transition for two models of phase separation: diffusion only and with hydrodynamics. The glass transition is incorporated in both models by imposing mobility and viscosity contrasts between the polymer-rich and polymer-poor phases of the evolving microstructure. For microstructures composed of polymer-poor clusters in a polymer-rich matrix, the mobility and viscosity contrasts significantly hinder coarsening, effectively leading to structural arrest. For microstructures composed of polymer-rich clusters in a polymer-poor matrix, the mobility and viscosity contrasts do not impede domain growth; rather, they change the transient concentration of the polymer-rich phase, altering the shape of the discrete domains. This effect introduces several complexities to the coarsening process, including percolation inversion of the polymer-rich and polymer-poor phases—a phenomenon normally attributed to viscoelastic phase separation.

Chemistry↗

Improving gas adsorption modeling for MOFs by local calibration of Hubbard U parameters

While computational screening with density functional theory (DFT) is frequently employed for the screening of metal–organic frameworks (MOFs) for gas separation and storage, commonly applied generalized gradient approximations (GGAs) exhibit self-interaction errors, which hinder the predictions of adsorption energies. We investigate the Hubbard U parameter to augment DFT calculations for full periodic MOFs, targeting a more precise modeling of gas molecule–MOF interactions, specifically for N2, CO2, and O2. We introduce a calibration scheme for the U parameter, which is tailored for each MOF, by leveraging higher-level calculations on the secondary building unit (SBU) of the MOF. When applied to the full periodic MOF, the U parameter calibrated against hybrid HSE06 calculations of SBUs successfully reproduces hybrid-quality calculations of the adsorption energy of the periodic MOF. The mean absolute deviation of adsorption energies reduces from 0.13 eV for a standard GGA treatment to 0.06 eV with the calibrated U, demonstrating the utility of the calibration procedure when applied to the full MOF structure. Furthermore, attempting to use coupled cluster singles and doubles with perturbative triples calculations of isolated SBUs for this calibration procedure shows varying degrees of success in predicting the experimental heat of adsorption. It improves accuracy for N2 adsorption for cases of overbinding, whereas its impact on CO2 is minimal, and ambiguities in spin state assignment hinder consistent improvements of O2 adsorption. Our findings emphasize the limitations of cluster models and advocate the use of full periodic MOF systems with a calibrated U parameter, providing a more comprehensive understanding of gas adsorption in MOFs.

Chemistry↗

Quantifying rupture characteristics of microearthquakes in the Parkfield Area using a high-resolution borehole network

It is well known that large earthquakes often exhibit significant rupture complexity such as well separated subevents. With improved recording and data processing techniques, small earthquakes have been found to exhibit rupture complexity as well. Studying these small earthquakes offers the opportunity to better understand the possible causes of rupture complexities. Specifically, if they are random or are related to fault properties. We examine microearthquakes (M < 3) in the Parkfield, California, area that are recorded by a high-resolution borehole network. We quantify earthquake complexity by the deviation of source time functions and source spectra from simple circular (omega-square) source models. We establish thresholds to declare complexity, and find that it can be detected in earthquakes larger than magnitude 2, with the best resolution above M2.5. Comparison between the two approaches reveals good agreement (>90 per cent), implying both methods are characterizing the same source complexity. For the two methods, 60–80 per cent (M 2.6–3) of the resolved events are complex depending on the method. The complex events we observe tend to cluster in areas of previously identified structural complexity; a larger fraction of the earthquakes exhibit complexity in the days following the M w 6 2004 Parkfield earthquake. Ignoring the complexity of these small events can introduce artefacts or add uncertainty to stress drop measurements. Focusing only on simple events however could lead to systematic bias, scaling artefacts and the lack of measurements of stress in structurally complex regions.

58 GEOSCIENCES↗

Cryo-EM structures of DNA-free and DNA-bound BsaXI: architecture of a Type IIB restriction–modification enzyme

Abstract We have determined multiple cryogenic electron microscopy (cryo-EM) structures of the Type IIB restriction–modification enzyme BsaXI. Such enzymes cleave DNA on both sides of their recognition sequence and share features of Types I, II, and III restriction systems. BsaXI forms a heterotrimeric (RM)2S assemblage in the presence and absence of bound DNA. Two unique structural motifs—a multi-helical “knob” and a long antiparallel double-helical “paddle”—are involved in DNA binding and cleavage. Binding of the DNA target triggers a large conformational change from an ‘open’ to ‘closed’ configuration, resulting in a mixture of two different conformations with respect to the positioning of the S subunit and its target recognition domains on the enzyme’s bipartite DNA target site. Structure-guided mutagenesis studies implicated two clusters of residues in the RM subunit as being critical for DNA cleavage, both are located proximal to a DNA cleavage site. One corresponds to a canonical PD-(D/E)xK endonuclease site in the N-terminal endonuclease domain, while the other corresponds to residues clustered within the paddle motif (near to the C-terminal end of the RM subunit). This analysis facilitates a comparison of three potential mechanisms by which such enzymes cleave DNA on each side of the bound target.

Shen, Betty W.↗

Efficient time-dependent orbital-free density functional theory: Semilocal adiabatic response

Orbital-free density functional theory and its time-dependent extension are efficient ab initio methods for calculating the electronic structure and dynamics of large systems. Through the calculation of the optical spectra of selected clusters, we reach three important conclusions: (1) The quality of the spectra is strongly affected by the quality of the corresponding ground-state electron density; (2) the adiabatic part of the electronic response to external perturbations can be safely evaluated at the semilocal level; and (3) the nonadiabatic, current-dependent part of the time-dependent Pauli potential is key to recover correct spectral envelopes.

36 MATERIALS SCIENCE↗

Cosmological constraints from DES Y1 cluster abundances and SPT multiwavelength data

We perform a joint analysis of the counts of redMaPPer clusters selected from the Dark Energy Survey (DES) year 1 data and multiwavelength follow-up data collected within the 2500 deg2 South Pole Telescope (SPT) Sunyaev-Zel’dovich (SZ) survey. The SPT follow-up data, calibrating the richness-mass relation of the optically selected redMaPPer catalog, enable the cosmological exploitation of the DES cluster abundance data. To explore possible systematics related to the modeling of projection effects, we consider two calibrations of the observational scatter on richness estimates: a simple Gaussian model which account only for the background contamination (BKG), and a model which further includes contamination and incompleteness due to projection effects (PRJ). Assuming either a ΛCDM+∑mν or wCDM+∑mν cosmology, and for both scatter models, we derive cosmological constraints consistent with multiple cosmological probes of the low and high redshift Universe, and in particular with the SPT cluster abundance data. This result demonstrates that the DES Y1 and SPT cluster counts provide consistent cosmological constraints, if the same mass calibration data set is adopted. It thus supports the conclusion of the DES Y1 cluster cosmology analysis which interprets the tension observed with other cosmological probes in terms of systematics affecting the stacked weak lensing analysis of optically selected low–richness clusters. Finally, we analyze the first combined optically SZ selected cluster catalog obtained by including the SPT sample above the maximum redshift probed by the DES Y1 redMaPPer sample (z=0.65). Besides providing a mild improvement of the cosmological constraints, this data combination serves as a stricter test of our scatter models: the PRJ model, providing scaling relations consistent between the two abundance and multiwavelength follow-up data, is favored over the BKG model.

79 ASTRONOMY AND ASTROPHYSICS↗

Constraining the galaxy-halo connection of infrared-selected unWISE galaxies with galaxy clustering and galaxy-CMB lensing power spectra

We present the first detailed analysis of the connection between galaxies and their dark matter halos for the unWISE galaxy catalog—a full-sky, infrared-selected sample built from WISE data, containing over 500 million galaxies. Using unWISE galaxy-galaxy autocorrelation and Planck CMB lensing-galaxy cross-correlation measurements down to 10 arcmin angular scales, we constrain the halo occupation distribution (HOD), a model describing how central and satellite galaxies are distributed within dark matter halos, for three unWISE galaxy samples at mean redshifts z ¯ ≈ 0.6 , 1.1, and 1.5, assuming a fixed cosmology at the best-fit Planck Λ CDM values. We constrain the characteristic minimum halo mass to host a central galaxy, M min HOD = 1.8 3 - 1.63 + 0.41 × 10 12 M ⊙ / h , 5.22 - 4.80 + 0.34 × 10 12 M ⊙ / h , 6.60 - 1.11 + 0.30 × 10 13 M ⊙ / h and the mass scale at which one satellite galaxy per halo is found, M 1 ' = 1.1 3 - 0.70 + 0.32 × 10 13 M ⊙ / h , 1.18 - 1.11 + 0.30 × 10 13 M ⊙ / h , 1.23 - 1.17 + 0.14 × 10 14 M ⊙ / h for the unWISE samples at z ¯ ≈ 0.6 , 1.1, and 1.5, respectively. We find that all three samples are dominated by central galaxies, rather than satellites. Using our constrained HOD models, we infer the effective linear galaxy bias for each unWISE sample, and find that it does not evolve as steeply with redshift as found in previous perturbation-theory-based analyses of these galaxies. We discuss possible sources of systematic uncertainty in our results, the most significant of which is the uncertainty on the galaxy redshift distribution. Our HOD constraints provide a detailed, quantitative understanding of how the unWISE galaxies populate the underlying dark matter halo distribution. These constraints will have a direct impact on future studies employing the unWISE galaxies as a cosmological and astrophysical probe, including measurements of ionized gas thermodynamics and dark matter profiles via Sunyaev-Zel’dovich and lensing cross-correlations.

79 ASTRONOMY AND ASTROPHYSICS↗

Overcoming photobleaching in imaging of single barium atoms in a solid xenon matrix

Neutrinoless double beta decay is one of the most sensitive probes for new physics beyond the Standard Model of particle physics. One of the isotopes under investigation is 136 Xe, which would double beta decay into 136 Ba. Detecting the single 136 Ba daughter provides a sort of ultimate tool in the discrimination against backgrounds. Previous work demonstrated the ability to perform single atom imaging of Ba atoms in a single-vacancy site of a solid xenon matrix. In this paper, the effort to identify signal from individual barium atoms is extended to Ba atoms in a hexa-vacancy site in the matrix and is achieved despite increased photobleaching in this site. Abrupt fluorescence turn-off of a single Ba atom is also observed. Significant recovery of fluorescence signal lost through photobleaching is demonstrated upon annealing of Ba deposits in the Xe ice. Following annealing, it is observed that Ba atoms in the hexa-vacancy site exhibit antibleaching while Ba atoms in the tetra-vacancy site exhibit bleaching. This may be evidence for a matrix site transfer upon laser excitation. Our findings offer a path of continued research toward tagging of Ba daughters in all significant sites in solid xenon.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Association between optically identified galaxy clusters and the underlying dark matter halos

Clusters of galaxies trace massive dark matter halos in the Universe, but they can include multiple halos projected along lines of sight. Here, we study the halos contributing to clusters using the Cardinal simulation, which mimics the Dark Energy Survey data. We use the red-sequence-based cluster finding algorithm redMaPPer as a case study. For each cluster, we identify the halos hosting its member galaxies, and we define the main halo as the one contributing the most to the cluster's richness ($λ$, the estimated number of member galaxies). At $z=0.3$, for clusters with $λ> 60$, the main halo typically contributes to $92\%$ of the richness, and this fraction drops to $67\%$ for $λ\approx 20$. Defining "clean" clusters as those with $\geq50\%$ of the richness contributed by the main halo, we find that $100\%$ of the $λ> 60$ clusters are clean, while $73\%$ of the $λ\approx 20$ clusters are clean. Three halos can usually account for more than $80\%$ of the richness of a cluster. The main halos associated with redMaPPer clusters have a completeness ranging from $98\%$ at virial mass $10^{14.6}~h^{-1}M_{\odot}$ to $64\%$ at $10^{14}~h^{-1}M_{\odot}$. In addition, we compare the inferred cluster centers with true halo centers, finding that $30\%$ of the clusters are miscentered with a mean offset $40\%$ of the cluster radii, in agreement with recent X-ray studies. These systematics worsen as redshift increases, but we expect that upcoming surveys extending to longer wavelengths will improve the cluster finding at high redshifts. Our results affirm the robustness of the redMaPPer algorithm and provide a framework for benchmarking other cluster-finding strategies.

79 ASTRONOMY AND ASTROPHYSICS↗

An invertible seven-dimensional Dirichlet cell characterization of lattices

Characterization of crystallographic lattices is an important tool in structure solution, crystallographic database searches and clustering of diffraction images in serial crystallography. Characterization of lattices by Niggli-reduced cells (based on the three shortest non-coplanar lattice vectors) or by Delaunay-reduced cells (based on four non-coplanar vectors summing to zero and all meeting at obtuse or right angles) is commonly performed. The Niggli cell derives from Minkowski reduction. The Delaunay cell derives from Selling reduction. All are related to the Wigner–Seitz (or Dirichlet, or Voronoi) cell of the lattice, which consists of the points at least as close to a chosen lattice point as they are to any other lattice point. The three non-coplanar lattice vectors chosen are here called the Niggli-reduced cell edges. Starting from a Niggli-reduced cell, the Dirichlet cell is characterized by the planes determined by 13 lattice half-edges: the midpoints of the three Niggli cell edges, the six Niggli cell face-diagonals and the four body-diagonals, but seven of the lengths are sufficient: three edge lengths, the three shorter of each pair of face-diagonal lengths, and the shortest body-diagonal length. These seven are sufficient to recover the Niggli-reduced cell.

Chemistry↗