Machine Learning Quantum Mechanical/Molecular Mechanical Potentials: Evaluating Transferability in Dihydrofolate Reductase-Catalyzed Reactions.

Integrating machine learning potentials (MLPs) with quantum mechanical/molecular mechanical (QM/MM) free energy simulations has emerged as a powerful approach for studying enzymatic catalysis. However, its practical application has been hindered by the time-consuming process of generating the necessary training, validation, and test data for MLP models through QM/MM simulations. Furthermore, the entire process needs to be repeated for each specific enzyme system and reaction.

Resolving tissue complexity by multimodal spatial omics modeling with MISO.

Spatial molecular profiling has provided biomedical researchers valuable opportunities to better understand the relationship between cellular localization and tissue function. Effectively modeling multimodal spatial omics data is crucial for understanding tissue complexity and underlying biology. Furthermore, improvements in spatial resolution have led to the advent of technologies that can generate spatial molecular data with subcellular resolution, requiring the development of computationally efficient methods that can handle the resulting large-scale datasets.

Precision fetal cardiology detects cyanotic congenital heart disease using maternal saliva metabolome and artificial intelligence.

Prenatal sonographic diagnosis of congenital heart disease (CHD) can lead to improved morbidity and mortality. However, the diagnostic accuracy of ultrasound, the sole prenatal screening tool, remains limited. Failed prenatal or early newborn detection of cyanotic CHD (CCHD) can have disastrous consequences.

Transcription factor EB (TFEB) activity increases resistance of TNBC stem cells to metabolic stress.

Breast cancer stem cells (CSCs) are difficult to therapeutically target, but continued efforts are critical given their contribution to tumor heterogeneity and treatment resistance in triple-negative breast cancer. CSC properties are influenced by metabolic stress, but specific mechanisms are lacking for effective drug intervention. Our previous work on TFEB suggested a key function in CSC metabolism.

Targeting TRPC channels for control of arthritis-induced bone erosion.

Arthritis leads to bone erosion due to an imbalance between osteoclast and osteoblast function. Our prior investigations revealed that the Ca-selective ion channel, Orai1, is critical for osteoclast maturation. Here, we show that the small-molecule ELP-004 preferentially inhibits transient receptor potential canonical (TRPC) channels.

Pan-cancer secreted proteome and skeletal muscle regulation: insight from a proteogenomic data-driven knowledge base.

Large-scale, pan-cancer analysis is enabled by data driven knowledge bases that link tumor molecular profiles with phenotypes. A debilitating cancer-related phenotype is skeletal muscle loss, or cachexia, which occurs partly from tumor products secreted into circulation. Using the LinkedOmicsKB knowledge base assembled from the Clinical Proteomics Tumor Analysis Consortium proteogenomic analysis, along with catalogs of human secretome proteins, ligand-receptor pairs and molecular signatures, we sought to identify candidate pan-cancer proteins secreted to blood that could regulate skeletal muscle phenotypes in multiple solid cancers.

Investigation of the Gas-Phase N + CHCN Reaction at Low Temperatures.

Rate coefficients for ion-polar-molecule reactions between acetonitrile molecules (CHCN) and nitrogen molecular ions (N), which are of importance to the upper atmospheric chemistry of Saturn's moon Titan, were measured for the first time at low translational temperatures. In the experiments, the reaction between sympathetically cooled N ions embedded in laser-cooled Ca Coulomb crystals and velocity-selected acetonitrile molecules generated using a wavy Stark velocity filter was studied to determine the reaction rate coefficients. Capture rate coefficients calculated by the Su-Chesnavich approach and by the perturbed rotational state theory considering the rotational state distribution of CHCN were compared to the experimental rate coefficients.

Effective repulsive interaction between Janus polymer-grafted nanoparticles adhering to lipid vesicles.

The adhesion of nanoparticles to lipid vesicles causes curvature deformations to the membrane to an extent determined by the competition between the adhesive interaction and the membrane's elasticity. These deformations can extend over length scales larger than the size of a nanoparticle, leading to an effective membrane-curvature-mediated interaction between nanoparticles. Nanoparticles with uniform surfaces tend to aggregate into unidimensionally close-packed clusters at moderate adhesion strengths and endocytose at high adhesion strengths.

Enhancing the accuracy of XPS calculations: Exploring hybrid basis set schemes for CVS-EOMIP-CCSD calculations.

Reliable computational methodologies and basis sets for modeling x-ray spectra are essential for extracting and interpreting electronic and structural information from experimental x-ray spectra. In particular, the trade-off between numerical accuracy and computational cost due to the size of the basis set is a major challenge, since molecular orbitals undergo extreme relaxation in the core-hole state. To gain clarity on the changes in electronic structure induced by the formation of a core-hole, the use of sufficiently flexible basis for expanding the orbitals, particularly for the core region, has been shown to be essential.

Uncovering dissipation from coarse observables: A case study of a random walk with unobserved internal states.

Inferring underlying microscopic dynamics from low-dimensional experimental signals is a central problem in physics, chemistry, and biology. As a trade-off between molecular complexity and the low-dimensional nature of experimental data, mesoscopic descriptions such as the Markovian master equation are commonly used. The states in such descriptions usually include multiple microscopic states, and the ensuing coarse-grained dynamics are generally non-Markovian.

Retrieving the Stability and Practical Performance of Activation-Unstable Mesoporous Zr(IV)-MOF for Highly Efficient Self-Calibrating Acidity Sensing.

The practical applications of activation-unstable mesoporous metal-organic frameworks (MOFs) are often constrained by their structural instability. However, enhancing their stability could unlock valuable functionalities. Herein, we stabilized the otherwise unstable, post-activated structure of a novel mesoporous Zr(IV)-MOF, NKM-809, which uses a pyridine-containing amphiprotic linker (PPTB).

Combining Fourier Transform Ion Mobility with Charge Detection Mass Spectrometry for the Analysis of Multimeric Protein Complexes.

Charge detection mass spectrometry (CDMS) allows direct mass measurement of heterogeneous samples by simultaneously determining the charge state and the mass-to-charge ratio (/) of individual ions, unlike conventional MS methods that use large ensembles of ions. CDMS typically requires long acquisition times and the collection of thousands of spectra, each containing tens to hundreds of ions, to generate sufficient ion statistics, making it difficult to interface with the time scales of online separation techniques such as ion mobility. Here, we demonstrate the application of Fourier transform multiplexing and drift tube ion mobility joined with Orbitrap-based CDMS for the analysis of multimeric protein complexes.

Modular Construction of Multivariate Metal-Organic Frameworks for Luminescent Sensing.

Metal-organic frameworks (MOFs) have played a pivotal role as rapid and effective luminescent sensing materials. Numerous MOFs with diverse characteristics have been meticulously designed for target analytes. Previous studies have highlighted the factors of spectral characteristics, energy levels, interaction forces, and sensor stabilities for the luminescent sensing performance in response to a specific analyte.

Brain-derived tau oligomer polymorphs: distinct aggregations, stability profiles, and biological activities.

Aggregation of microtubule-associated tau protein is a distinct hallmark of several neurodegenerative disorders such as Alzheimer's disease (AD), dementia with Lewy bodies (DLB), and progressive supranuclear palsy (PSP). Tau oligomers are suggested to be the primary neurotoxic species that initiate aggregation and propagate prion-like structures. Furthermore, different diseases are shown to have distinct structural characteristics of aggregated tau, denoted as polymorphs.

Injectable ionic hydrogel conductors: Advancing material design to transform cardiac pacing.

Direct pacing of the mid myocardium where re-entry originates can be used to prevent ventricular arrhythmias and circumvent the need for painful defibrillation or cardiac ablation. However, there are no pacing electrodes small enough to navigate the coronary veins that cross these culprit scar regions. To address this need, we have developed an injectable ionically conductive hydrogel electrode that can fill the epicardial coronary veins and transform them into flexible electrodes.

Stereospecific Resistance to N2-Acyl Tetrahydro-β-carboline Antimalarials Is Mediated by a PfMDR1 Mutation That Confers Collateral Drug Sensitivity.

Half the world's population is at risk of developing a malaria infection, which is caused by parasites of the genus . Currently, resistance has been identified to all clinically available antimalarials, highlighting an urgent need to develop novel compounds and better understand common mechanisms of resistance. We previously identified a novel tetrahydro-β-carboline compound, PRC1590, which potently kills the malaria parasite.

Rational Electrolyte Design for Elevated-Temperature and Thermally Stable Lithium-Ion Batteries with Nickel-Rich Cathodes.

As the energy density of lithium-ion batteries (LIBs) increases, the shortened cycle life and the increased safety hazards of LIBs are drawing increasing concerns. To address such challenges, a series of localized high-concentration electrolytes (LHCEs) based on a solvating-solvent mixture of tetramethylene sulfone and trimethyl phosphate and a high flash-point diluent 1H,1H,5H-octafluoropentyl 1,1,2,2-tetrafluoroethyl ether were designed. The LHCEs exhibited nonflammability and greatly suppressed heat release at elevated temperatures, which would potentially improve the safety performance of the LIBs.

A computational study on the effect of structural isomerism on the excited state lifetime and redox energetics of archetype iridium photoredox catalyst platforms [Ir(ppy)2(bpy)]+ and Ir(ppy)3.

This study investigates the impact of structural isomerism on the excited state lifetime and redox energetics of heteroleptic [Ir(ppy)2(bpy)]+ and homoleptic Ir(ppy)3 photoredox catalysts using ground-state and time-dependent density functional theory methods. While the ground- and excited-state reduction potentials differ only slightly among the isomers of these complexes, our findings reveal significant variations in the radiative and non-radiative decay rates of the reactivity-controlling triplet 3MLCT states of these closely related species. The observed differences in radiative decay rates could be traced back to variations in the transition dipole moment, vertical energy gaps, and spin-orbit coupling of the isomers.

Computational Tool for Determining Local Dielectric Constants in Heterogeneous Nanoscale Systems from Molecular Dynamics Trajectories.

In this work, we describe a computational tool designed to determine the local dielectric constants (ε) of charge-neutral heterogeneous systems by analyzing dipole moment fluctuations from molecular dynamics (MD) trajectories. Unlike conventional methods, our tool can calculate dielectric constants for dynamically evolving selections of molecules within a defined region of space, rather than for fixed sets of molecules. We validated our approach by computing the dielectric constants of TIP3P water nanospheres, achieving results consistent with literature values for bulk water.

NADH-bound AIF activates the mitochondrial CHCHD4/MIA40 chaperone by a substrate-mimicry mechanism.

Mitochondrial metabolism requires the chaperoned import of disulfide-stabilized proteins via CHCHD4/MIA40 and its enigmatic interaction with oxidoreductase Apoptosis-inducing factor (AIF). By crystallizing human CHCHD4's AIF-interaction domain with an activated AIF dimer, we uncover how NADH allosterically configures AIF to anchor CHCHD4's β-hairpin and histidine-helix motifs to the inner mitochondrial membrane. The structure further reveals a similarity between the AIF-interaction domain and recognition sequences of CHCHD4 substrates.

Transforming Detrimental Crystalline Zinc Hydroxide Sulfate to Homogeneous Fluorinated Amorphous Solid-Electrolyte Interphase on Zinc Anode.

The formation of non-ion conducting byproducts on zinc anode is notoriously detrimental to aqueous zinc-ion batteries (AZIBs). Herein, we successfully transform a representative detrimental byproduct, crystalline zinc hydroxide sulfate (ZHS) to fast-ion conducting solid-electrolyte interphase (SEI) via amorphization and fluorination induced by suspending CaF nanoparticles in dilute sulfate electrolytes. Distinct from widely reported nonhomogeneous organic-inorganic hybrid SEIs that exhibit structural and chemical instability, the designed single-phase SEI is homogeneous, mechanically robust, and chemically stable.

Organoboron-Functionalized Metal-organic Nanosheets for Highly Efficient CO2 Fixation Mediated by Frustrated Lewis Pairs.

Converting CO2 to high-value fine chemicals represents one of the most promising approaches to combat global warming and subsequently achieve a sustainable carbon cycle. Herein, we contribute an organoboron functionalized ultra-thin metal-organic nanosheet (MON), termed TCPB-Zr-NS, featuring an abundance of exposed Lewis acidic B and formate sites, which can effectively promote CO2 conversion upon the addition of Lewis basic o-phenylenediamines. Compared with the prototypical 3D analogue TCPB-Zr-3D, the resultant TCPB-Zr-NS showcases dramatically improved catalytic activity for the cyclization of o-phenylenediamine as a result of the highly exposed active sites and efficient substrates/products diffusion.

Overcoming the Conductance versus Crossover Trade-off in State-of-the-Art Proton Exchange Fuel-Cell Membranes by Incorporating Atomically Thin Chemical Vapor Deposition Graphene.

Permeance-selectivity trade-offs are inherent to polymeric membranes. In fuel cells, thinner proton exchange membranes (PEMs) could enable higher proton conductance and increased power density with lower area-specific resistance (ASR), smaller ohmic losses, and lower ionomer cost. However, reducing thickness is accompanied by an increase in undesired species crossover harming performance and long-term efficiency.

Gut bacterial sphingolipid production modulates dysregulated skin lipid homeostasis.

Sphingolipids are an essential lipid component of the skin barrier with alterations in skin sphingolipid composition associated with multiple skin disorders including psoriasis, atopic dermatitis, and ichthyosis. Contributions to skin sphingolipid abundance are not well characterized, thus the main method of modulating skin lipid levels is the topical application of creams rich with sphingolipids at the skin surface. Evidence that diet and gut microbiome function can alter skin biology proposes an intriguing potential for the modulation of skin lipid homeostasis through gut microbial metabolism, but potential mechanisms of action are not well understood.

Hydralazine inhibits cysteamine dioxygenase to treat preeclampsia and senesce glioblastoma.

The vasodilator hydralazine (HYZ) has been used clinically for ~ 70 years and remains on the World Health Organization's List of Essential Medicines as a therapy for preeclampsia. Despite its longstanding use and the concomitant progress toward a general understanding of vasodilation, the target and mechanism of HYZ have remained unknown. We show that HYZ selectively targets 2-aminoethanethiol dioxygenase (ADO) by chelating its metal cofactor and alkylating one of its ligands.