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Synthesis of the bulky phosphanide (iPr3Si)2P− and its stabilisation of low-coordinate group 12 complexes.
No full textHere, we report the first practical synthesis of the bulky phosphanide anion [P(SiiPr3)2]− in synthetically useful yields, and its complexation to Group 12 metals. The ligand is obtained as the sodium salt NaP(SiiPr3)2 1 in a 42% isolated yield and a single step from red phosphorus and sodium. This is a significant improvement on the previously reported synthesis of this ligand, and we have thus applied 1 to the synthesis of the two-coordinate complexes M[P(SiiPr3)2]2 (M = Zn, Cd, Hg). These Group 12 complexes are all monomeric and with non-linear P–M–P angles in the solid state, with DFT calculations suggesting that this bending is due to the steric demands of the ligand. Multinuclear NMR spectroscopy revealed complex 2nd order splitting patterns due to strong PP’ coupling. This work demonstrates that the synthesis of 1 is viable and provides a springboard for the synthesis of low-coordinate d-block complexes featuring this unusual bulky ligand
What is the exchange-repulsion energy? Insight by partitioning into physically meaningful contributions
No full textExchange repulsion, the dominant repulsive contribution to intermolecular interaction energies, is caused by the Pauli principle, which enforces that electrons with the same spin must not be located at the same place. Starting from the Heitler-London expression of the exchange-repulsion energy, Exr, we investigate how it can be partitioned into physically relevant and comprehensible contributions. We demonstrate that a division of Exr into a positive kinetic and a negative potential part is possible. However, these contributions correlate only poorly with the actual exchange-repulsion energy. A meaningful partitioning of Exr is derived, where the kinetic energy contribution belongs to a term that vanishes for exact Hartree-Fock wave functions. The remaining pure potential energy terms are distinguished into an exchange integral contribution, Exi, as well as contributions to the repulsion-energy with two, three and four orbital indices (Exr2, Exr3, and Exr4). Qualitative explanations of these terms and their physical origin are proposed. The forms, relationships and absolute sizes of the four parts of Exr suggest an intuitive partitioning of the exchange-repulsion energy into orbital-pair contributions. Insight into the analytic form and quantitative size of the contributions to Exr is provided by considering the 3Sigma+u (1sigma g 1sigma u) state of the H2 molecule, the water dimer, as well as an argon atom interacting with Cl2 and N2. It is demonstrated that Exr is best described as a contribution due to the potential energy and that its leading contribution, Exr2, provides an intuitive qualitative and quantitative approach towards the exchange-repulsion energy
Thermodynamic stability and diffusion mechanism of LiMXCl4 superionic conductors
No full textLiMXCl4 is a recently discovered lithium superionic conductor reported with a Li conductivity up to 12.4 mS/cm at room temperature. In this work, we explore various types of M-cation and X-anion substitutions in the LiMXCl4 system. We find that fluoro-chlorides may provide promising thermodynamic and electrochemical stability without compromising ionic conductivity. Ab-initio molecular dynamics simulations on seven substitutions and three lithium concentrations for each substitution suggest that even higher conductivity may be achieved in LiMXCl4 than has been reported. A Meyer-Neldel analysis comparing LiMXCl4, close-packed halides, and LaCl3-type systems demonstrates the potential of the LiMXCl4 family due to their high Meyer-Neldel energy, high prefactor, and low activation energy, projecting a range of conductivity of 10-100 mS/cm. An analysis of the correlation between lithium-ion hops and small-angle tilting events finds that LiMXCl4 systems exhibit a strong cradle effect where weakly bound M-octahedra often tilt their orientation in conjunction with a nearby Li-ion hop to flatten the lithium-ion energy landscape. Such an advantage originates from the fact that in the LiMXCl4 structure, one-dimensional M-octahedral chains are bound via weak van der Waals interactions which can accommodate for reduction in free volume via rotational correlation of the octahedra. Our work demonstrates an exciting direction towards further improving this class of materials in terms of ionic conductivity and electrochemical stability and provides a fundamental understanding of the factors that lead to high ionic conductivity in non-close-packed oxyhalide systems
Advancements in Thermochemical Predictions: A Multi-Output Thermodynamics-Informed Neural Network Approach
No full textThe Gibbs free energy of an inorganic material represents its maximum reversible work potential under constant temperature and pressure. Its calculation is crucial for understanding material stability, phase transitions, and chemical reactions, thus guiding optimization for diverse applications like catalysis and energy storage. In this study, we have developed a Physics-Informed Neural Network model that leverages the Gibbs free energy equation. The overall loss function is adjusted to allow the model to simultaneously predict all three thermodynamic quantities, including Gibbs free energy, total energy, and entropy, thus transforming it into a multi-output model. In recent literature, there is a growing emphasis on evaluating machine learning models under challenging conditions, such as small datasets and out-of-distribution predictions. Reflecting this trend, we have rigorously benchmarked our model across these scenarios, demonstrating its robustness and adaptability. It turns out that our model demonstrates a 43% improvement for normal scenario and even more in out-of-distribution regime compared to the next-best model
GlyCombo enables rapid, complete glycan composition identification across diverse glycomic sample types
No full textGlycans are sugar-based polymers found to modify biomolecules including lipids and proteins, as well as occur unconjugated as free polysaccharides. Due to their ubiquitous cellular presentation, glycans mediate crucial biological processes and are frequently sought after as biomarkers for a wide range of diseases. Identification of glycans present in samples acquired with mass spectrometry (MS) is a cornerstone of glycomics research, thus, the ability to rapidly identify glycans in each acquisition is integral to glycomics analysis pipelines. Here we introduce GlyCombo (https://github.com/Protea-Glycosciences/GlyCombo), an open-source, freely available software tool designed to rapidly assign monosaccharide combinations to glycan precursor masses including those subjected to MS2 in LC-MS/MS experiments.
GlyCombo was evaluated across six diverse datasets, demonstrating MS vendor, derivatization, and glycan-type neutrality. Compositional assignments using GlyCombo are shown to be faster than the current, predominant approach, GlycoMod, a closed-source web application. Two unique features of GlyCombo, multiple adduct search and off-by-one error anticipation, reduced unassigned MS2 scans in a benchmark dataset by 40%. Finally, the comprehensiveness of glycan feature identification is exhibited in Skyline, a software that requires pre-defined transitions that are derived from GlyCombo output files
OPLS5: Addition of Polarizability and Improved Treatment of Metals
No full textWe report on the development and validation of the OPLS5 force field. OPLS5 further extends the accuracy of our previous model (OPLS4) with the addition of explicit polarization to improve model accuracy for molecular ions and cation-pi interactions. OPLS5 also includes advances to the functional form for metals achieving significant improvements across benchmarks assessing the structure and energetics of metal-organic complexes. Together these advances lead to improved accuracy on our protein-ligand binding benchmarks
A Software Tool for Rapid and Automated Pre-Processing of Large-Scale Serum Metabolomic Data by Multisegment Injection-Capillary Electrophoresis-Mass Spectrometry
No full textMass spectrometry (MS)-based metabolomics often rely on separation techniques when analyzing complex biological specimens to improve method resolution, metabolome coverage, quantitative performance, and/or unknown identification. However, low sample throughput and complicated data pre-processing procedures remain major barriers to affordable metabolomic studies that are also scalable to large populations. Herein, we introduce PeakMeister as a new software tool in the R statistical environment to enable the automated processing of serum metabolomic data acquired by multisegment injection-capillary electrophoresis-mass spectrometry (MSI-CE-MS) under positive ion mode. MSI-CE-MS takes advantage of a multiplexed separation format involving serial injection of 13 serum/plasma filtrate samples, quality controls, calibrants and/or blanks introduced within a single analytical run ( 99.9%), acceptable intermediate precision (median CV = 16.0 %), consistent metabolite peak integration (mean bias = 2.1%), and good mutual agreement when quantifying 16 plasma metabolites from NIST SRM-1950 (mean bias = -1.3%). We also report reference intervals for 40 serum metabolites in a national nutritional survey of children under 5 years of age (ENANI-2019). MSI-CE-MS in conjunction with PeakMeister allows for rapid and automated data pre-processing of large-scale metabolomic studies while tolerating long-term migration time shifts without the need for complicated dynamic time warping or effective mobility scale transformations
Red-Light Photocatalytic Activation Of Pt(IV) Anticancer Prodrugs Using Methylene Blue
No full textCatalysis-based approaches offer versatile strategies for activating anticancer prodrugs, potentially allowing precise control over drug release and localization within tumor tissues, while reducing systemic toxicity. In this study, we explore the role of the phenothiazine dye methylene blue (MB+) as a photocatalyst in conjunction with biologically relevant electron donors to facilitate the red-light conversion of two Pt(IV) complexes, denoted as cis,cis,trans-[PtCl2(NH3)2(O2CCH2CH2COOH)2] (1) and trans-[Pt(O2CCH2CH2COOH)21R,2R-(DACH)(ox)] (2), into cisplatin and oxaliplatin, respectively. Combining spectroscopic techniques (NMR, UV-Vis, flash photolysis) with computational methods, we reveal that the doubly reduced MB+ (leucomethylene blue, LMB) triggers the reductive elimination of axial ligands in the two Pt(IV) precursors, generating the corresponding Pt(II) anticancer drugs. In vitro experiments conducted on the human cervical cancer cell line CaSki, which harbors multiple copies of the integrated HPV-16 genome, and on non-tumoral cells (HaCat) demonstrate that co-administration with Pt(IV) prodrugs improves MB+\u27s antiproliferative efficacy in cancer cells, particularly under red light exposure. This enhancement could be attributed to the catalytic production of Pt(II) species within the cellular environment
The Chemistry of Henna: A Module for High School Students
No full textHere we present a hands-on module for high school students to explore the chemistry of henna dye. This lesson is affordable, accessible, adaptable, and engaging for students. In this lesson, students are shown how henna paste is derived from the henna shrub, discuss the chemical structure of the main dye component lawsone (2-hydroxy-1,4-napthoquinone), apply the henna paste to their skin, and discuss the darkening of the dye over time as a result of lawsone oxidation. Through understanding the chemistry of henna, students are encouraged to consider the influence of chemical reactions in their daily lives. This module also promotes diversity and inclusion in science by increasing the representation of non-Western cultures in the chemistry curriculum. In this work, the module is presented in detail, and student reactions are discussed
High pressure microreactor for minute amounts of catalyst on planar supports: a case study of CO2 hydrogenation over Pd0.25Zn0.75Ox nanoclusters
No full textHigh-pressure studies of catalyst quantities down to a few hundred nanograms, particularly well-defined catalysts prepared using physical methods in ultra-high vacuum on planar supports can potentially bridge the surface science and applied catalysis approaches to catalyst development. However, the chemical reactors required for such investigations are lacking.
We present the novel design and evaluation of a 50 µL rectangular microchannel reactor capable of testing small quantities of catalyst at pressures up to 40 bar and temperatures up to 250°C. To evaluate the microreactor\u27s performance, Pd0.25Zn0.75Ox nanoclusters soft-landed on SiO2-coated mica sheets using the cluster beam deposition technique, were tested for the reverse water-gas shift reaction through a series of kinetic experiments.
Experimental results, combined with computational fluid dynamics and mass transport analysis, demonstrate that the proposed microreactor setup allows for testing minute quantities of catalysts with high sensitivity at industrially relevant temperatures and pressures. Although not restricted to a particular catalyst preparation method, the setup is an excellent platform for conducting catalytic tests on composition-controlled, mass-selected, gas-phase nanoparticles deposited on planar substrates, facilitating the development of reliable structure-activity relationships and enabling a more rational design of catalysts