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At least 145 records · Page 8

Dicopper( i ) complexes of a binucleating, dianionic, naphthyridine bis(amide) ligand

The dinucleating ligand, 1,8-naphthyridine-2,7-bis(2,6-diisopropylphenyl)carboxamide (NBDA), was synthesized by palladium-catalyzed aminocarbonylation. This ligand was treated with two equivalents of mesitylcopper(I) in the presence of [nBu4N]X (X = Cl, N3) to give the anionic complexes [nBu4N][Cu2(NBDA)(μ-Cl)] and [nBu4N][Cu2(NBDA)(μ-N3)]. Treatment of H2NBDA with mesitylcopper(I) and two equivalents of xylyl isocyanide led to the formation of a charge-neutral dicopper(I) complex, [Cu2(NBDA)(CNXyl)2], displaying two isocyanide ligands, each terminally bound to one of the copper atoms. The complexes were characterized by NMR and IR spectroscopy, as well as by single-crystal X-ray diffraction analysis. Electrochemical characterization of the complexes using cyclic voltammetry revealed a reversible ligand-based reduction between -1.65 and -2.0 V vs. Fc/Fc+. DFT calculations suggest a more ionic bonding character and weaker Cu-Cu interactions in the NBDA complexes compared to those with other 1,8-naphthyridine-based ligands. This is congruent with intermetallic separations of over 3 Å induced by relatively strong coordination of the copper atoms to the amide nitrogen donor atoms observed in the solid state molecular structures.

Sévery, Laurent↗

Erratum: “Breaking covalent bonds in the context of the many-body expansion (MBE). I. The purported ‘first row anomaly’ in XH n (X = C, Si, Ge, Sn; n = 1–4)” [J. Chem. Phys. 156, 244303 (2022)]

We have noted typographical errors in TABLE V of J. Chem. Phys. 156, 244303 (2022). Specifically, the values of the angles φ HχH for the XH 2 species in both the ( 3 B 1 ) and ( 1 A 1 ) states were incorrectly reported as half of the correct values. Additionally, the values of the same angles for the XH 3 and XH 4 species were reported correctly.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Bivalent recognition of fatty acyl-CoA by a human integral membrane palmitoyltransferase

S-acylation, also known as palmitoylation, is the most abundant form of protein lipidation in humans. This reversible posttranslational modification, which targets thousands of proteins, is catalyzed by 23 members of the DHHC family of integral membrane enzymes. DHHC enzymes use fatty acyl-CoA as the ubiquitous fatty acyl donor and become autoacylated at a catalytic cysteine; this intermediate subsequently transfers the fatty acyl group to a cysteine in the target protein. Protein S-acylation intersects with almost all areas of human physiology, and several DHHC enzymes are considered as possible therapeutic targets against diseases such as cancer. These efforts would greatly benefit from a detailed understanding of the molecular basis for this crucial enzymatic reaction. Here, in this study, we combine X-ray crystallography with all-atom molecular dynamics simulations to elucidate the structure of the precatalytic complex of human DHHC20 in complex with palmitoyl CoA. The resulting structure reveals that the fatty acyl chain inserts into a hydrophobic pocket within the transmembrane spanning region of the protein, whereas the CoA headgroup is recognized by the cytosolic domain through polar and ionic interactions. Biochemical experiments corroborate the predictions from our structural model. We show, using both computational and experimental analyses, that palmitoyl CoA acts as a bivalent ligand where the interaction of the DHHC enzyme with both the fatty acyl chain and the CoA headgroup is important for catalytic chemistry to proceed. This bivalency explains how, in the presence of high concentrations of free CoA under physiological conditions, DHHC enzymes can efficiently use palmitoyl CoA as a substrate for autoacylation.

59 BASIC BIOLOGICAL SCIENCES↗

X-ray scattering signatures of early-time accelerations in iodine dissociation

Ultrafast time-resolved x-ray scattering (TRXS) from a photoexcited molecular ensemble measures a distribution $S(Q, τ)$ of the x-ray momentum transfer Q and pump-probe delay τ in which all modes of motion induced by the excitation overlap. Frequency-resolved x-ray scattering (FRXS) based on $\tilde {S}\left(Q,\omega \right)$ separates each oscillation and dissociation channel in the TRXS data, enabling measurements of vibrational frequencies and phases, and dissociation velocities and time shifts. In this work, we extend FRXS analysis to study early-time accelerations as well. We show how these appear as diffuse scattering patterns with characteristic phase evolution in FXRS and we develop a set of transformations that isolate individual channels to measure the early-time accelerated motion. This procedure is used to analyze diatomic iodine x-ray scattering data with multiple dissociations, and the ability of this technique to characterize early-time accelerations of one dissociation channel even in the presence of another dissociation is demonstrated.

74 ATOMIC AND MOLECULAR PHYSICS↗

Relationship between molecular structure and corrugations in self-assembled polypeptoid nanosheets revealed by cryogenic electron microscopy

Designing conformationally dynamic molecules that self-assemble into predictable nanostructures remains an important unmet challenge. This paper describes how atomic-scale cryogenic transmission electron microscopy (cryo-TEM) can be used to explore the relationship between molecular structure and self-assembly of block copolymers. We examined sheetlike micelles formed in water using a series of diblock copolypeptoids with the same hydrophilic block and three distinct crystalline hydrophobic blocks. Our cryo-TEM images revealed all the structures share nansoscale features, but differ in their intermolecular packing geometries. Different molecular arrangements, parallel and antiparallel V-shaped crystal motifs, were revealed by two-dimensional atomic-scale through-plane images. However, images from tilted samples revealed an unexpected feature when the hydrophobic polypeptoid block comprised phenyl rings with substituted bromine atoms at the para position. The nanosheets contained atomic-scale corrugations that were absent in the other systems which comprised unsubstituted aliphatic and aromatic side chains. We hypothesize that these corrugations are due to the dipolar characteristics of the brominated phenyl group and interactions between this group and water molecules. Published by the American Physical Society 2024

36 MATERIALS SCIENCE↗

Clifford transformations for fermionic quantum systems: From Pauli and Majorana operators to Dirac fermions

Clifford gates and transformations, which map products of elementary Pauli or Majorana operators to other such products, are foundational in quantum computing, underpinning the stabilizer formalism, error-correcting codes, magic state distillation, quantum communication and cryptography, and qubit tapering. Moreover, circuits composed entirely of Clifford gates are classically simulatable, highlighting their computational significance. In this article we extend the concept of Clifford transformations to Dirac fermions. We demonstrate that discrete Clifford transformations are generated by half-body and pair operators while continuous Clifford transformations are generated by number operators, providing a systematic framework for their characterization. Additionally, we establish connections with fermionic mean-field theories and applications in qubit tapering, offering insights into their broader implications in quantum computing.

74 ATOMIC AND MOLECULAR PHYSICS↗

femto-PIXAR: a self-supervised neural network method for reconstructing femtosecond X-ray free electron laser pulses

X-ray Free Electron Lasers (X-FELs) operate in a wide range of lasing configurations for a broad variety of scientific applications at ultrafast time-scales such as structural biology, materials science, and atomic and molecular physics. Shot-by-shot characterization of the X-FEL pulses is crucial for analysis of many experiments as well as tuning the X-FEL performance. However, for the weak pulses found in advanced configurations, e.g. those needed for coherent, two-pulse studies of quantum materials, there is no current method for reliably resolving pulse profiles. Here we show that a physics-based U-net model can reconstruct the individual pulse power profiles for sub-picosecond pulse separation without the need for simulations. Using experimental data from weak X-FEL pulse pairs, we demonstrate we can learn the pulse characteristics on a shot-by-shot basis when conventional methods fail.

43 PARTICLE ACCELERATORS↗

The hTERT core promoter forms three parallel G-quadruplexes

The structure of the 68 nt sequence with G-quadruplex forming potential within the hTERT promoter is disputed. One model features a structure with three stacked parallel G-quadruplex units, while another features an unusual duplex hairpin structure adjoined to two stacked parallel and antiparallel quadruplexes. We report here the results of an integrated structural biology study designed to distinguish between these possibilities. As part of our study, we designed a sequence with an optimized hairpin structure and show that its biophysical and biochemical properties are inconsistent with the structure formed by the hTERT wild-type sequence. By using circular dichroism, thermal denaturation, nuclear magnetic resonance spectroscopy, analytical ultracentrifugation, small-angle X-ray scattering, molecular dynamics simulations and a DNase I cleavage assay we found that the wild type hTERT core promoter folds into a stacked, three-parallel G-quadruplex structure. The hairpin structure is inconsistent with all of our experimental data obtained with the wild-type sequence. All-atom models for both structures were constructed using molecular dynamics simulations. These models accurately predicted the experimental hydrodynamic properties measured for each structure. We found with certainty that the wild-type hTERT promoter sequence does not form a hairpin structure in solution, but rather folds into a compact stacked three-G-quadruplex conformation.

59 BASIC BIOLOGICAL SCIENCES↗

Multiscale and Multimodal Characterization of 2D Titanium Carbonitride MXene

Here, a comprehensive study on the prototype solid solution phase carbonitride MXene Ti 3 CN is conducted using nuclear magnetic resonance, electron spin resonance, total and quasi-elastic neutron scattering, combined with density functional theory-based electronic structure and molecular dynamic calculations. The combination of experiment and theory lead toward rational atomic structural models of Ti 3 CN. The remnant Al ions from the etching process significantly tune the interlayer spacing, distinct from the more typical MXene, Ti 3 C 2 , prepared similarly. Neutron scattering indicates the surface terminations of Ti 3 CN display high oxygen and fluorine concentrations and rather low hydroxyl and hydrogen concentrations. Calculations show that the structure including both the residual Al ions and mixed surface terminations give the best agreement with the measurements. The water molecules in Ti 3 CN are highly immobile, in strong contrast to those in Ti 3 C 2 . The analysis of the electronic structure suggests that the nitride MXene displays higher conductivity than the carbides. Finally, the absence of hydroxyl groups in terminations, the solid-solution in the anion sites, the remnants within layers, and immobile water altogether make the carbonitrides a unique series in the MXene family, implying a further exploration of their exotic properties and applications in energy storage.

36 MATERIALS SCIENCE↗

Melting and transport properties of Al 2⁢ O 3 at extreme conditions

The high-pressure, temperature phase diagram and transport properties of materials are of broad interest to planetary sciences and high-energy-density sciences and applications. Alumina (Al 2 O 3 ) or its various forms (e.g., solutions with other oxides or silicates) are important constituents in Earth’s and super-Earths’ mantles, common window materials in dynamic compression experiments, and standard pressure calibrators in diamond-anvil-cell experiments. Its structures and transport properties are of particular importance but have not been well studied at above 100 GPa pressures. Based on extensive first-principles molecular dynamics calculations, we obtain atomic level insights on structural differences and accurate results on electrical conductivity (σ dc ), thermal conductivity (κ), and reflectivity of Al 2 O 3 in several phases at pressures of ~130–1300 GPa and temperatures of 4000–20,000 K. We find the solid-to-liquid state changes of Al 2 O 3 are accompanied by an insulator-to-semimetal transition with enhanced σ dc and κ, which is similar to other silicates and oxides and can facilitate magnetic field generation in deep interiors of rocky planets. We also find the solid-to-solid transition (from Rh 2 O 3 (II) to CaIrO 3 ) is accompanied by negligible changes in σ dc and κ at 160 GPa, contrary to previous expectations, whereas another higher pressure phase transition (CaIrO 3 to U 2 S 3 at 450 GPa) is associated with increases in σ dc and κ. Furthermore, we show the transport properties can be enhanced by oxygen vacancy in Al 2 O 3 , but are not significantly affected by forming solutions with MgSiO 3 , particularly when in the solid states.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Atomistic structure of the SARS-CoV-2 pseudoknot in solution from SAXS-driven molecular dynamics

SARS-CoV-2 depends on -1 programmed ribosomal frameshifting (-1 PRF) to express proteins essential for its replication. The RNA pseudoknot stimulating -1 PRF is thus an attractive drug target. However, the structural models of this pseudoknot obtained from cryo-EM and crystallography differ in some important features, leaving the pseudoknot structure unclear. We measured the solution structure of the pseudoknot using small-angle X-ray scattering (SAXS). The measured profile did not agree with profiles computed from the previously solved structures. Beginning with each of these solved structures, we used the SAXS data to direct all atom molecular dynamics (MD) simulations to improve the agreement in profiles. In all cases, this refinement resulted in a bent conformation that more closely resembled the cryo-EM structures than the crystal structure. Applying the same approach to a point mutant abolishing -1 PRF revealed a notably more bent structure with reoriented helices. This work clarifies the dynamic structures of the SARS-CoV-2 pseudoknot in solution.

60 APPLIED LIFE SCIENCES↗

Uncovering fast solid-acid proton conductors based on dynamics of polyanion groups and proton bonding strength

Achieving high proton conductivity in inorganic solids is key for advancing many electrochemical technologies, including low-energy nano-electronics and energy-efficient fuel cells and electrolyzers. A quantitative understanding of the physical traits of a material that regulate proton diffusion is necessary for accelerating the discovery of fast proton conductors. In this work, we have mapped the structural, chemical and dynamic properties of solid acids to the elementary steps of the Grotthuss mechanism of proton diffusion. Our approach combines ab initio molecular dynamics simulations, analysis of phonon spectra and atomic structure calculations. We have identified the donor–hydrogen bond lengths and the acidity of polyanion groups as key descriptors of local proton transfer and the vibrational frequencies of the cation framework as the key descriptor of lattice flexibility. The latter facilitates rotations of polyanion groups and long-range proton migration in solid acid proton conductors. The calculated lattice flexibility also correlates with the experimentally reported superprotonic transition temperatures. Using these descriptors, we have screened the Materials Project database and identified potential solid acid proton conductors with monovalent, divalent and trivalent cations, including Ag + , Sr 2+ , Ba 2+ and Er 3+ cations, which go beyond the traditionally considered monovalent alkali cations (Cs + , Rb + , K + , and NH 4 + ) in solid acids.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Spectral Irradiance Measurements of Simulated Lightning in Planetary Atmospheres

Optical emissions from lightning provide information to estimate the altitude, latitude and longitude of lightning storms, the energy of the discharges, and the production of important trace species such as HCN and C2H2. Knowledge of the spectra of planetary lightning is needed to deduce the total energy dissipated by lightning (and thereby, the production of trace gases) and to help design experiments to detect and track lightning storms. Measurements of the spectral irradiance from approximately 380 to 820 nm are reported for laboratory simulations of lightning in the atmospheres of Venus, Jupiter, and Titan. In our laboratory, laser-induced plasmas (LIP) are used to simulate lightning discharges. This technique avoids contamination of the spectra by elect-ode material and maintains a safe environment while allowing the use of flammable gases, such as hydrogen and methane, found in outer planet atmospheres. The observations were made at I and 5 bars pressure for Venus and Jupiter and at 1 bar for the Titan mixture. At a pressure of one bar, our results show prominent lines from H(sub alpha), H(sub beta), H(sub gamma), and H(sub delta) lines of the Balmer Series of atomic hydrogen, a single line from Helium at 588 nm and strong continuum radiation. At pressures of 5 bars, the H(sub alpha) and H(sub beta) lines are wider, the H(sub gamma), and H(sub delta) lines merge into the continuum because of pressure broadening, and the helium line at 588 nm is no longer visible. The observed spectra of simulated lightning in the venusian atmosphere at 1 and 5 bars shows that the OI multiplet at 777.7 nm dominates the spectra, but weak features due to atomic carbon and singly excited and singly ionized oxygen atoms are also visible. Although lightning has not yet been observed on Titan, it conceivable that some form of lightning discharge could be occurring. Therefore experiments on a Titan atmosphere mixture were conducted. The most prominent features seen in the simulated spectra are the H(sub alpha) at 656 nm. from the dissociation of the methane and two strong features at 740 and 820 nm from singly excited nitrogen atoms. Most of the features between 400 and 656 nm are due to ionized nitrogen atoms. A broad, highly structured feature centered near 389 nm is molecular band radiation from CN molecules formed in the cooling plasma of atomic nitrogen, carbon, and hydrogen. It is observed in the lightning simulations of both the venusian and Titan atmospheres, For Venus, Jupiter, and Titan, narrow spectral features that are ideal for detecting lightning in the presence of sunlight are present in the spectra. These features could allow lightning to be detected and tracked by Earth-based instruments.

Borucki, W. J.↗

Coordinate-based simulation of pair distance distribution functions for small and large molecular assemblies: implementation and applications

X-ray scattering has become a major tool in the structural characterization of nanoscale materials. Thanks to the widely available experimental and computational atomic models, coordinate-based X-ray scattering simulation has played a crucial role in data interpretation in the past two decades. However, simulation of real-space pair distance distribution functions (PDDFs) from small- and wide-angle X-ray scattering, SAXS/WAXS, has been relatively less exploited. This study presents a comparison of PDDF simulation methods, which are applied to molecular structures that range in size from β-cyclodextrin [1 kDa molecular weight (MW), 66 non-hydrogen atoms] to the satellite tobacco mosaic virus capsid (1.1 MDa MW, 81 960 non-hydrogen atoms). The results demonstrate the power of interpretation of experimental SAXS/WAXS from the real-space view, particularly by providing a more intuitive method for understanding of partial structure contributions. Furthermore, the computational efficiency of PDDF simulation algorithms makes them attractive as approaches for the analysis of large nanoscale materials and biological assemblies. The simulation methods demonstrated in this article have been implemented in stand-alone software, SolX 3.0 , which is available to download from https://12idb.xray.aps.anl.gov/solx.html.

Zuo, Xiaobing (ORCID:0000000201344804)↗

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↗

Targeting Aspergillus allergen oryzin with a chemical probe at atomic precision

We report the molecular basis of Aspergillus fumigatus oryzin, allergen Asp f 13, or alkaline proteinase ALP1, containing the sequence motif His–Asp–Ser of the subtilisin family, structure, and function at atomic detail. Given the resolution of the data (1.06 Å), we use fragment molecular replacement with ideal polyalanine α-helices to determine the first crystal structure of oryzin. We probe the catalytic serine through formation of an irreversible bond to a small molecule compound, specifically labeling it, describing the amino acid residues performing the catalytic function. Defined by a self-processed pro-peptide, the active site architecture shapes up pocket-like subsites that bind to and unveil the S1′–S4′ substrate binding preferences. We use molecular modeling to dock a model of the pro-peptide in the S1–S4 region and to dock collagen along the active site cleft. Opposite to the face harboring the catalytic serine, the enzyme binds to a calcium ion in a binding site created by backbone flipping. We use thermal unfolding to show that this metal ion provides structural stability. With no known host inhibitor identified thus far, this structure may hasten the progress of developing new therapeutic agents for diseases caused by pathogenic fungi.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Leiomodin creates a leaky cap at the pointed end of actin-thin filaments

Improper lengths of actin-thin filaments are associated with altered contractile activity and lethal myopathies. Leiomodin, a member of the tropomodulin family of proteins, is critical in thin filament assembly and maintenance; however, its role is under dispute. Using nuclear magnetic resonance data and molecular dynamics simulations, we generated the first atomic structural model of the binding interface between the tropomyosin-binding site of cardiac leiomodin and the N-terminus of striated muscle tropomyosin. Our structural data indicate that the leiomodin/tropomyosin complex only forms at the pointed end of thin filaments, where the tropomyosin N-terminus is not blocked by an adjacent tropomyosin protomer. This discovery provides evidence supporting the debated mechanism where leiomodin and tropomodulin regulate thin filament lengths by competing for thin filament binding. Data from experiments performed in cardiomyocytes provide additional support for the competition model; specifically, expression of a leiomodin mutant that is unable to interact with tropomyosin fails to displace tropomodulin at thin filament pointed ends and fails to elongate thin filaments. Together with previous structural and biochemical data, we now propose a molecular mechanism of actin polymerization at the pointed end in the presence of bound leiomodin. In the proposed model, the N-terminal actin-binding site of leiomodin can act as a “swinging gate” allowing limited actin polymerization, thus making leiomodin a leaky pointed-end cap. Results presented in this work answer long-standing questions about the role of leiomodin in thin filament length regulation and maintenance.

2D-NMR↗

Treatment of atomic and molecular line blanketing by opacity sampling

A sampling technique for treating the radiative opacity of large numbers of atomic and molecular lines in cool stellar atmospheres is subjected to several tests. In this opacity sampling (OS) technique, the global opacity is sampled at only a selected set of frequencies, and at each of these frequencies the total monochromatic opacity is obtained by summing the contribution of every relevant atomic and molecular line. In accord with previous results, we find that the structure of atmospheric models is accurately fixed by the use of 1000 frequency points, and 100 frequency points are adequate for many purposes. The effects of atomic and molecular lines are separately studied. A test model computed using the OS method agrees very well with a model having identical atmospheric parameters, but computed with the giant line (opacity distribution function) method.

Johnson, H. R.↗