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At least 199 records · Page 11

One fold, many functions—M23 family of peptidoglycan hydrolases

Bacterial cell walls are the guards of cell integrity. They are composed of peptidoglycan that provides rigidity to sustain internal turgor and ensures isolation from the external environment. In addition, they harbor the enzymatic machinery to secure cell wall modulations needed throughout the bacterial lifespan. The main players in this process are peptidoglycan hydrolases, a large group of enzymes with diverse specificities and different mechanisms of action. They are commonly, but not exclusively, found in prokaryotes. Although in most cases, these enzymes share the same molecular function, namely peptidoglycan hydrolysis, they are leveraged to perform a variety of physiological roles. A well-investigated family of peptidoglycan hydrolases is M23 peptidases, which display a very conserved fold, but their spectrum of lytic action is broad and includes both Gram- positive and Gram- negative bacteria. In this review, we summarize the structural, biochemical, and functional studies concerning the M23 family of peptidases based on literature and complement this knowledge by performing large-scale analyses of available protein sequences. This review has led us to gain new insight into the role of surface charge in the activity of this group of enzymes. We present relevant conclusions drawn from the analysis of available structures and indicate the main structural features that play a crucial role in specificity determination and mechanisms of latency. Our work systematizes the knowledge of the M23 family enzymes in the context of their unique antimicrobial potential against drug-resistant pathogens and presents possibilities to modulate and engineer their features to develop perfect antibacterial weapons.

Razew, Alicja↗

Predicting Drug Effects from High-dimensional Asymmetric Drug Data Sets using Graph Neural Networks: A Comprehensive Analysis of Multi-target Drug Effect Prediction

Graph neural networks (GNNs) have emerged as one of the most effective Machine learning (ML) techniques for drug effect prediction from drug molecular graphs. Despite having immense potential, GNN models lack performance when using data sets that contain high dimensional asymmetrically co-occurrent drug effects as targets with complex correlations between them. Training individual learning models for each drug effect and incorporating every prediction result for a wide spectrum of drug effects is beyond practicality. Such an implication provides a testbed to address this challenge as multi-target prediction problems, aiming to predict all drug effects at a time. We develop standard and hybrid graph neural networks (GNNs)to perform two separate tasks that are multi-regression for continuous values and multi-label classification for categorical values contained in our data sets. Since this step makes the target data even more sparse and introduces asymmetric label co-occurrence, the learning of multi-label classification models becomes difficult and heavily impacts the GNN's performance. To address these challenges, we propose a new data oversampling technique to improve multi-label classification performances on all the given imbalanced molecular graph data sets. Using the technique, we improve the data imbalance ratio of the drug effects better than before while protecting the data set's integrity. Finally, we evaluate multi-label classification performance using the best-performant hybrid GNN model on all the oversampled data sets obtained from the proposed oversampling technique. These results outperform those of other ML models including GNN models when they are trained on the original data sets or oversampled data sets using MLSMOTE (a well-known oversampling technique) in all evaluation metrics precision, recall, and F1 score by a significant margin.

Bose, Avishek [ORNL]↗

Raman spectrum and polarizability of liquid water from deep neural networks

We introduce a scheme based on machine learning and deep neural networks to model the environmental dependence of the electronic polarizability in insulating materials. Application to liquid water shows that training the network with a relatively small number of molecular configurations is sufficient to predict the polarizability of arbitrary liquid configurations in close agreement with ab initio density functional theory calculations. In combination with a neural network representation of the interatomic potential energy surface, the scheme allows us to calculate the Raman spectra along 2-nanosecond classical trajectories at different temperatures for H 2 O and D 2 O. The vast gains in efficiency provided by the machine learning approach enable longer trajectories and larger system sizes relative to ab initio methods, reducing the statistical error and improving the resolution of the low-frequency Raman spectra. Decomposing the spectra into intramolecular and intermolecular contributions elucidates the mechanisms behind the temperature dependence of the low-frequency and stretch modes.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Interfacial thermal conductance between multi-layer graphene sheets and solid/liquid octadecane: A molecular dynamics study

Mixtures of paraffin and carbon nanofillers have promising potential for thermal storage, as paraffin (the matrix) possesses high latent heat and the nanofillers compensate for the low thermal conductivity (TC) of paraffin. Understanding thermal transport in these materials is essential for practical applications, as weak thermal transport hinders fast charge/discharge of thermal energy. Here, we use non-equilibrium molecular dynamics (NEMD) simulations to study the interfacial thermal conductance (ITC) between graphene sheets and octadecane (C18H38) matrix under the limiting conditions of the sheets being parallel or perpendicular to the direction of the imposed heat flux. The findings show that the systems containing thin graphene layers exhibit higher values of ITC. This study captures the asymptotic saturation of thermal conductance for the liquid phase of the perpendicular structure. Besides, given the greater number of structured layers of paraffin upon phase change, the ITC for the solid paraffin-graphene system is higher than the conductance of the liquid paraffin-graphene interface. We use the Pearson correlation coefficients of the vibrational power spectrum (VPS) of interfacing materials to explain the orders of magnitude variations of the observed ITC.

25 ENERGY STORAGE↗

Ferrocene Bis(Sulfonate) Salt as Redoxmer for Fast and Steady Redox Flow Desalination

Desalination is considered a promising solution to alleviate water shortages, yet current methods are often restricted, due to challenges like high energy consumption, significant cost, or limited desalination capacity. In this study, we present a novel approach of redox flow desalination (RFD) utilizing the highly aqueous-soluble and reversible redox-active compound, potassium 1,1'-bis(sulfonate) ferrocene (1,1'-FcDS). This water-soluble organic compound yielded stable and rapid desalination, sustaining extended operation without notable decay and achieving an impressive desalination rate of up to 457.5 mmol·h -1 ·m -2 and energy consumption as low as 40.2 kJ·mol NaCl -1 . Specifically, the RFD device effectively desalinated a 50 mM NaCl solution to potable standards within 6000 s using 1,1'-FcDS. It maintained an average energy consumption of 178.16 kJ·mol NaCl -1 and exhibited negligible deterioration in desalination rate, energy efficiency, and charge efficiency throughout a rigorous 12,000 s cycling test. Furthermore, the versatility of this method was demonstrated by effectively treating saline water with varying initial concentrations from 10 mM to 50 mM, showcasing its potential across a broad spectrum of applications.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Status on Genetic Resistance to Rice Blast Disease in the Post-Genomic Era

Rice blast, caused by Magnaporthe oryzae, is a major threat to global rice production, necessitating the development of resistant cultivars through genetic improvement. Breakthroughs in rice genomics, including the complete genome sequencing of japonica and indica subspecies and the availability of various sequence-based molecular markers, have greatly advanced the genetic analysis of blast resistance. To date, approximately 122 blast-resistance genes have been identified, with 39 of these genes cloned and molecularly characterized. The application of these findings in marker-assisted selection (MAS) has significantly improved rice breeding, allowing for the efficient integration of multiple resistance genes into elite cultivars, enhancing both the durability and spectrum of resistance. Pangenomic studies, along with AI-driven tools like AlphaFold2, RoseTTAFold, and AlphaFold3, have further accelerated the identification and functional characterization of resistance genes, expediting the breeding process. Future rice blast disease management will depend on leveraging these advanced genomic and computational technologies. Emphasis should be placed on enhancing computational tools for the large-scale screening of resistance genes and utilizing gene editing technologies such as CRISPR-Cas9 for functional validation and targeted resistance enhancement and deployment. These approaches will be crucial for advancing rice blast resistance, ensuring food security, and promoting agricultural sustainability.

Pedrozo, Rodrigo↗

Dimensionally reduced machine learning model for predicting single component octanol–water partition coefficients

Abstract MF-LOGP, a new method for determining a single component octanol–water partition coefficients ( $$LogP$$ LogP ) is presented which uses molecular formula as the only input. Octanol–water partition coefficients are useful in many applications, ranging from environmental fate and drug delivery. Currently, partition coefficients are either experimentally measured or predicted as a function of structural fragments, topological descriptors, or thermodynamic properties known or calculated from precise molecular structures. The MF-LOGP method presented here differs from classical methods as it does not require any structural information and uses molecular formula as the sole model input. MF-LOGP is therefore useful for situations in which the structure is unknown or where the use of a low dimensional, easily automatable, and computationally inexpensive calculations is required. MF-LOGP is a random forest algorithm that is trained and tested on 15,377 data points, using 10 features derived from the molecular formula to make $$LogP$$ LogP predictions. Using an independent validation set of 2713 data points, MF-LOGP was found to have an average $$RMSE$$ RMSE = 0.77 ± 0.007, $$MAE$$ MAE = 0.52 ± 0.003, and $${R}^{2}$$ R 2 = 0.83 ± 0.003. This performance fell within the spectrum of performances reported in the published literature for conventional higher dimensional models ( $$RMSE$$ RMSE = 0.42–1.54, $$MAE$$ MAE = 0.09–1.07, and $${R}^{2}$$ R 2 = 0.32–0.95). Compared with existing models, MF-LOGP requires a maximum of ten features and no structural information, thereby providing a practical and yet predictive tool. The development of MF-LOGP provides the groundwork for development of more physical prediction models leveraging big data analytical methods or complex multicomponent mixtures. Graphical Abstract

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Ab Initio Molecular Dynamics Simulations of Amorphous Calcium Carbonate: Interpretation of Pair Distribution Function and X-Ray Absorption Spectroscopy Data

The structure and transformation of hydrous amorphous calcium carbonate (ACC) are key to understanding biomineralization pathways and their relationship with the properties of the resulting material. Quantitative interpretation of scattering experiments aimed at elucidating the structure of ACC is challenging, due to the amorphous nature of this material, and, therefore, requires models for the structure and the scattering physics. Here, we generate physically realistic ensembles of hydrated ACC structures and their vibrational disorder from ab initio molecular dynamics (AIMD) simulations with an emphasis on enabling the consistent interpretation of the finer details of three complementary structural probes: neutron and x-ray pair distribution experiments and x-ray absorption spectroscopy (XAS). In each case, we simulate the signal directly in reciprocal space and then manipulate it into the real-space pair distribution function (PDF) or spectrum using the same procedures for the experimental and theoretical data. Good agreement with experiment was obtained across the three techniques with the simulations accounting well for all features in the spectra. Remaining small discrepancies pointed to differences between real samples and the idealized simulated systems such as deviations from the nominal CaCO3·nH2O stoichiometry. Additionally, the simulations offered a more accurate description of the local coordination environment of calcium than previous shell-by-shell fits to spectra of synthetic ACC and classical molecular dynamics simulations. This work demonstrates that AIMD is a powerful approach for extracting detailed structural information from neutron PDF, x-ray PDF, and XAS of amorphous carbonate phases.

Prange, Micah P.↗

Quantum computation solves a half-century-old enigma: Elusive vibrational states of magnesium dimer found

The high-lying vibrational states of the magnesium dimer (Mg 2 ), which has been recognized as an important system in studies of ultracold and collisional phenomena, have eluded experimental characterization for half a century. Until now, only the first 14 vibrational states of Mg 2 have been experimentally resolved, although it has been suggested that the ground-state potential may support five additional levels. Here, we present highly accurate ab initio potential energy curves based on state-of-the-art coupled-cluster and full configuration interaction computations for the ground and excited electronic states involved in the experimental investigations of Mg 2 . Our ground-state potential unambiguously confirms the existence of 19 vibrational levels, with ~1 cm -1 root mean square deviation between the calculated rovibrational term values and the available experimental and experimentally derived data. Our computations reproduce the latest laser-induced fluorescence spectrum and provide guidance for the experimental detection of the previously unresolved vibrational levels.

74 ATOMIC AND MOLECULAR PHYSICS↗

A novel approach to characterize the full spectrum and radiative properties of aerosols

Organic aerosols play a significant role in the absorption and radiative budget of the atmosphere, but current modeling approaches do not adequately capture the photo-chemical and oxidative bleaching that occurs during their lifetimes. Most climate models inaccurately assume constant optical properties of these particles, therefore leading to errors in their predictions. In this study we present an approach to better parameterize the optical properties of atmospheric aerosols, including brown carbon (BrC). Using thin-film spectrometry, the full spectrum of reflectivity and emissivity was used to calculate the complex refractive index for multiple species of organic aerosols. This is in contrast to previous techniques which only probe single wavelengths. Since BrC is a complex molecular mixture, we initially focused on single species absorption using four molecular surrogates. Dye-doped polyacrylic-acid thin-films were prepared on glass slides and compared to an aerosolized collection method. Verification of the collection method will open the door to characterizing the complex refractive index of smoke and ambient aerosol.

58 GEOSCIENCES↗

Polyyne production is regulated by the transcriptional regulators PgnC and GacA in Pseudomonas protegens Pf-5

ABSTRACT Polyynes produced by bacteria have promising applications in agriculture and medicine due to their potent antimicrobial activities. Polyyne biosynthetic genes have been identified inPseudomonasandBurkholderia. However, the molecular mechanisms underlying the regulation of polyyne biosynthesis remain largely unknown. In this study, we used a soil bacteriumPseudomonas protegensPf-5, which was recently reported to produce polyyne called protegenin, as a model to investigate the regulation of bacterial polyyne production. Our results show that Pf-5 controls polyyne production at both the pathway-specific level and a higher global level. Mutation ofpgnC, a transcriptional regulatory gene located in the polyyne biosynthetic gene cluster, abolished polyyne production. Gene expression analysis revealed that PgnC directly activates the promoter of polyyne biosynthetic genes. The production of polyyne also requires a global regulator GacA. Mutation ofgacAdecreased the translation of PgnC, which is consistent with the result thatpgnCleader mRNA bound directly to RsmE, an RNA-binding protein negatively regulated by GacA. These results suggest that GacA induces the expression of the PgnC regulator, which in turn activates polyyne biosynthesis. Additionally, the polyyne-producing strain of Pf-5, but not the polyyne-nonproducing strain, could inhibit a broad spectrum of bacteria including both Gram-negative and Gram-positive bacteria. IMPORTANCE Antimicrobial metabolites produced by bacteria are widely used in agriculture and medicine to control plant, animal, and human pathogens. Although bacteria-derived polyynes have been identified as potent antimicrobials for decades, the molecular mechanisms by which bacteria regulate polyyne biosynthesis remain understudied. In this study, we found that polyyne biosynthesis is directly activated by a pathway-specific regulator PgnC, which is induced by a global regulator GacA through the RNA-binding protein RsmE inPseudomonas protegens. To our knowledge, this work is the first comprehensive study of the regulatory mechanisms of bacterial polyyne biosynthesis at both pathway-specific level and global level. The discovered molecular mechanisms can help us optimize polyyne production for agricultural or medical applications.

Biotechnology & Applied Microbiology↗

The Low-Lying Electronic States of NO 2 : Potential Energy and Dipole Surfaces, Bound States, and Electronic Absorption Spectrum

Nitrogen dioxide, NO 2 , is a free radical composed of the two most abundant elements in Earth’s atmosphere, nitrogen and oxygen, and is relevant to atmospheric and combustion chemistry. The electronic structure of even its lowest-lying states is remarkably complex, with various conical intersections and Renner–Teller pairings, giving rise to complex and perturbed vibronic states. Here we report some analysis of the 18 molecular states of doublet spin-multiplicity formed by combining ground-state N( 4 S u ) and O( 3 P g ) atoms. In this work, three-dimensional potential energy surfaces were fit at the MRCI(Q)-F12/VTZ-F12 level, describing the lowest four ($\tilde X$, $\tilde A$, $\tilde B$, and $\tilde C$) electronic states. A properties-based diabatization procedure was applied to accommodate the intersections, producing energies in a quasidiabatic representation and yielding couplings that were also fit into surfaces. The low-lying vibrational levels on the ground $\tilde X$ state were computed and compared with experimental measurements. Compared to experiment, the lowest 125 calculated vibrational levels (up to 8500 cm –1 above the zero-point energy) have a root-mean-squared error of 16.5 cm –1 . In addition, dipole moments for each of the lowest four electronic states—and the transition dipoles between them—were also computed and fit. With the coupled energy and dipole surfaces, the electronic spectrum was calculated in absolute intensity and compared with experimental measurements. Detailed structure in the experimental spectrum was successfully reproduced, and the total integrated intensity matches experiment to an accuracy of ~1.5% with no empirical adjustments.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Vibronic Relaxation Pathways in Molecular Spin Qubit Na 9 [Ho(W 5 O 18 ) 2 ]·35H 2 O under Pressure

In order to explore how spectral sparsity and vibronic decoherence pathways can be controlled in a model qubit system with atomic clock transitions, we combined diamond anvil cell techniques with synchrotron-based far infrared spectroscopy and first-principles calculations to reveal the vibrational response of Na 9 [Ho(W 5 O 18 ) 2 ]·35H 2 O under compression. Because the hole in the phonon density of states acts to reduce the overlap between the phonons and f manifold excitations in this system, we postulated that pressure might move the HoO 4 rocking, bending, and asymmetric stretching modes that couple with the M J = ±5, ±2, and ±7 levels out of resonance, reducing their interactions and minimizing decoherence processes, while a potentially beneficial strategy for some molecular qubits, pressure slightly hardens the phonons in Na 9 [Ho(W 5 O 18 ) 2 ]·35H 2 O and systematically fills in the transparency window in the phonon response. The net result is that the vibrational spectrum becomes less sparse and the overlap with the various M J levels of the Ho 3+ ion actually increases. These findings suggest that negative pressure, achieved using chemical means or elongational strain, could further open the transparency window in this rare earth-containing spin qubit system, thus paving the way for the use of device surfaces and interface elongational/compressive strains to better manage decoherence pathways.

36 MATERIALS SCIENCE↗

The Terahertz Dynamics of an Aqueous Nanoparticle Suspension: An Inelastic X-ray Scattering Study

We used the high-resolution Inelastic X-ray Scattering beamline of the Advanced Photon Source at Argonne National Laboratory to measure the terahertz spectrum of pure water and a dilute aqueous suspension of 15 nm diameter spherical Au nanoparticles (Au-NPs). We observe that, despite their sparse volume concentration of about 0.5%, the immersed NPs strongly influence the collective molecular dynamics of the hosting liquid. We investigate this effect through a Bayesian inference analysis of the spectral lineshape, which elucidates how terahertz transport properties of water change upon Au-NP immersion. In particular, we observe a nearly complete disappearance of the longitudinal acoustic mode and a mildly decreased ability to support shear wave propagation.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Modeling the Electronic Absorption Spectra of the Indocarbocyanine Cy3

Accurate modeling of optical spectra requires careful treatment of the molecular structures and vibronic, environmental, and thermal contributions. The accuracy of the computational methods used to simulate absorption spectra is limited by their ability to account for all the factors that affect the spectral shapes and energetics. The ensemble-based approaches are widely used to model the absorption spectra of molecules in the condensed-phase, and their performance is system dependent. The Franck–Condon approach is suitable for simulating high resolution spectra of rigid systems, and its accuracy is limited mainly by the harmonic approximation. In this work, the absorption spectrum of the widely used cyanine Cy3 is simulated using the ensemble approach via classical and quantum sampling, as well as, the Franck–Condon approach. The factors limiting the ensemble approaches, including the sampling and force field effects, are tested, while the vertical and adiabatic harmonic approximations of the Franck–Condon approach are also systematically examined. Our results show that all the vertical methods, including the ensemble approach, are not suitable to model the absorption spectrum of Cy3, and recommend the adiabatic methods as suitable approaches for the modeling of spectra with strong vibronic contributions. We find that the thermal effects, the low frequency modes, and the simultaneous vibrational excitations have prominent contributions to the Cy3 spectrum. The inclusion of the solvent stabilizes the energetics significantly, while its negligible effect on the spectral shapes aligns well with the experimental observations.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Terahertz Circular Dichroism Spectroscopy of Molecular Assemblies and Nanostructures

Chemical, physical, biological and materials engineering disciplines use a variety of chiroptical spectroscopies to probe geometrical and optical asymmetry in molecules and particles. Electronic (ECD) and vibrational (VCD) circular dichroism are the most common of these techniques and collectively enable the studies of electronic and vibronic transitions with energies between 0.1 and 5.0 eV. The vibrational states with characteristic energies in the range of 0.001–0.01 eV carry valuable information about concerted intermolecular motions in molecules and crystals involving multiple atoms. These vibronic transitions located in the terahertz (THz) part of the spectrum become increasingly more important for the chemistry, physics, and biology of complex molecules and materials However, the methodology and hardware of THz circular dichroism (TCD) are much less developed than the chiroptical spectroscopies for ultraviolet, visible, near- and mid infrared photons. In this report we provide theoretical foundations, practical implementations, comparative assessments, and exemplary applications of TCD spectroscopy. We show that the sign, intensity, and position of TCD peaks are highly sensitive to the three-dimensional structure and long-range organization of molecular crystals, which offer unique capabilities to study (bio) molecules, their crystals, and nanoscale assemblies and apply the novel data processing methodologies. TCD also offers a convenient toolbox to identify new physical phenomena, such as chiral phonons and their propagation in nanostructured matter. We also discuss the major challenges, emerging opportunities and promising research directions, including broad investigation of chiral phonons observed in chiral (nano) crystals and emerging machine learning methodologies for TCD in biological and nanoscale structures. Ubiquity of low-frequency vibrations with rotational components in biomolecular structures, combined with sharpness of peaks in TCD spectra, enables a variety of technological translations.

36 MATERIALS SCIENCE↗

Design, Control and Application of Next Generation Qubits

Design, Control and Application of Next Generation Qubits Arun Bansil, Northeastern University (Principal Investigator) Claudio Chamon, Boston University (Co-Investigator) Adrian Feiguin, Northeastern University (Co-Investigator) Liang Fu, MIT (Co-Investigator) Eduardo Mucciolo, Univ. of Central Florida (Co-Investigator) Qimin Yan, Temple University (Co-Investigator) The quest for developing technologies for manipulating and storing information quantum mechanically is currently led by approaches that include Josephson-junctions, ion-traps, and qubits generated by defect spins in solids. Topological qubits, however, are inherently more robust to decoherence by environmental effects, and should be able to sprint ahead once practical barriers have been overcome. At the present stage of the development of the field, it is important to explore a variety of architectures and materials beyond the conventional paradigms in order to seed breakthroughs toward building a scalable quantum computer. Our comprehensive theoretical research program involved four interconnected thrusts as follows. • A materials discovery effort in two-dimensional compounds in search of materials to support Majorana zero modes and defect structures suitable as qubits. • Exploration of architectures for topological quantum computation by investigating both superconducting Majorana qubits, and robust platforms for braiding with new “meta-materials” built of arrays of Majorana qubits. • Investigation of properties of hybrid metal-organic qubits based on transition-metal centers in graphene, and molecular crystals of polyaromatic complexes with embedded transition-metal atoms. • Development of tensor-network and semiclassical approaches to study decoherence in the presence of random and dispersive spin baths, and NV centers in diamond. The full spectrum of theoretical and numerical approaches was used to address the goals of this project including first-principles, density-matrix-renormalization group, tensor networks, and data-driven high-throughput approaches using materials database and machine-learning.

36 MATERIALS SCIENCE↗

Homoleptic Uranium–Bis(acyl)phosphide Complexes

Here, the first uranium bis(acyl)phosphide (BAP) complexes were synthesized from the reaction between sodium bis(mesitoyl)phosphide (Na( mes BAP)) or sodium bis(2,4,6-triisopropylbenzoyl)phosphide (Na( tripp BAP)) and UI 3 (1,4-dioxane) 1.5 . Thermally stable, homoleptic BAP complexes were characterized by single-crystal X-ray diffraction and electron paramagnetic resonance (EPR) spectroscopy, when appropriate, for the elucidation of the electronic structure and bonding of these complexes. EPR spectroscopy revealed that the BAP ligands on the uranium center retain a significant amount of electron density. The EPR spectrum of the trivalent U( tripp BAP) 3 has a rhombic signal near g = 2 (g 1 = 2.03; g 2 = 2.01; and g 3 = 1.98) that is consistent with the EPR-observed unpaired electron being located in a molecular orbital that appears ligand-derived. However, upon warming the complex to room temperature, no resonance was observed, indicating the presence of uranium character.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗