ChemRxiv
Not a member yet
27047 research outputs found
Sort by
Intermolecular Bending States and Tunneling Splittings of Water Trimer from Rigorous 9D Quantum Calculations: I. Methodology, Energy Levels, and Low-Frequency Spectrum
No full textWe present the computational methodology that enables the first rigorous nine-dimensional (9D) quantum calculations of the intermolecular bending states of the water trimer, as well as its low-frequency spectrum for direct comparison with experiment. The water monomers, treated as rigid, have their centers of mass (cm\u27s) at the corners of an equilateral triangle, and the intermonomer cm-to-cm distance is set to a value slightly larger than that in the equilibrium geometry of the trimer. The remaining nine strongly coupled large-amplitude bending (angular) degrees of freedom (DOFs) enter the 9D bend Hamiltonian of the three coupled 3D rigid-water hindered rotors. Its 9D eigenstates encompass excited librational vibrations of the trimer, as well as their torsional and bifurcation tunneling splittings which have been the subject of much interest. For this reason, the calculation of these eigenstates by diagonalizing the 9D bend Hamiltonian represents the most rigorous high-dimensional quantum treatment to date of the intermolecular vibrational states of the water trimer and its excited-state tunneling splittings. Such calculations are extremely demanding, and a sophisticated computational scheme is developed that exploits the molecular symmetry group of the water trimer, G48, in order to make them feasible in a reasonable amount of time. The spectrum of the low-frequency vibrations of the water trimer simulated using the eigenstates of the 9D bend Hamiltonian agrees remarkably well with the experimentally observed far-infrared (FIR) spectrum of the trimer in helium nanodroplets over the entire frequency range of the measurements from 70 to 620 cm−1. This shows that most peaks in the experimental FIR spectrum are associated with the intermolecular bending vibrations of the trimer. Moreover, the ground-state torsional tunneling splittings from the present 9D calculations are in excellent agreement with the spectroscopic data. These results demonstrate the high quality of the ab initio 2+3-body PES employed for the DOFs included in the bound-state calculations
Prioritization of Novel Anti-infective Stilbene derivatives by Combining Metabolomic Data Organization and a Stringent 3R-infection Model in a Knowledge Graph
No full textThe rising threat of Multidrug-Resistant Tuberculosis (MDR-TB), caused by Mycobacterium tuberculosis (Mtb), underscores the urgent need for new therapeutic solutions to tackle the challenge of antibiotics resistance. The current study utilized an innovative 3R infection model featuring the amoeba Dictyostelium discoideum infected with Mycobacterium marinum, serving as stand-ins for macrophages and Mtb, respectively. This high-throughput phenotypic assay allowed for the evaluation of more specific anti-infective activities that may be less prone to resistance mechanisms. To discover novel anti-infective compounds, a diverse collection of 1,600 plant extracts from the Pierre Fabre Library (PFL) was screened using the latter assay. Concurrently, these extracts underwent untargeted UHPLC-HRMS/MS analysis. The biological screening flagged the extract from Stauntonia brunoniana as one of the anti-infective hit extracts. High-resolution HPLC micro-fractionation coupled with bioactivity profiling was employed to highlight the natural products (NPs) driving this bioactivity. Stilbenes were eventually identified as the primary active compounds in the bioactive fractions. A knowledge graph (KG) was then used to leverage the heterogeneous data integrated into it to make a rational selection of stilbene-rich extracts. Using both CANOPUS chemical classes and Jaccard similarity indices (JSIs) to compare features within the metabolome of the 1600 NEs set, 14 extracts rich in stilbenes were retrieved. Among those, the roots of Gnetum edule were flagged as possessing broader chemo-diversity in their stilbene content, along with the corresponding extract also being a strict anti-infective. Eventually, a total of 11 stilbene oligomers were isolated from G. edule and fully characterized by NMR with their absolute stereochemistry established through electronic circular dichroism (ECD). Six of these compounds are new since they possess a stereochemistry which was never described in the literature to the best of our knowledge. All of them were assessed for their anti-infective activity and (-)-Gnetuhainin M was reported as having the highest anti-infective activity with an IC50 of 22.22 μM
Experimentally Guided Neural Network and Statistical Forecasting of Membrane Water/Salt Selectivity with Minimal Mean Errors
No full textMembrane life and performance are the key determining factors in the adoption of membrane-based processes for water treatment and separations. This work investigated various time series models following hold-out validation of experimentally generated water vapor flux and saltwater rejection rates. The membrane properties were optimized by incorporating nanomaterials to induce wetting and porosity and develop correlations between membrane properties and high fluxes. The fine-tuned Autoregressive integrated moving average (ARIMA), Prophet, Exponential Smoothing, and Neural Prophet models were trained on the experimental dataset (N= 434) collected over 36 hours to forecast for 72 hrs. The results demonstrate the suitability of the Exponential Smoothing statistical model for predicting and forecasting membrane performance with the lowest value of root mean square error (RMSE) at 0.006 and mean absolute error (MAE) at 0.007. This is attributed to the intrinsic features of attributed to its non-linear data fitting approach, which employs weighted averages to mitigate nonstationary behavior of data. The modeling approach proposed in this study could be a more efficient alternative to traditional experimental studies, potentially leading to significant cost and time savings in the research and development phase of membrane distillation processes
Key Developments in Magnesiothermic Reduction of Silica: Insights into Reactivity and Future Prospects
No full textPorous Si (p-Si) nanomaterials are an exciting class of inexpensive and abundant materials within the field of energy storage. Specifically, porous Si has been explored in battery anodes to improve charge storage capacity, to generate clean fuels through photocatalysis and photoelectrochemical processes, for the stoichiometric conversion of CO2 to value added chemicals, and as a chemical H2 storage material. p-Si can be made from synthetic, natural, and waste SiO2 sources through a facile and inexpensive method called magnesiothermic reduction (MgTR). This yields a material with tunable properties and excellent energy storage capabilities. In order to tune the physical properties that affect performance metrics of p-Si, a deeper understanding of the mechanism of the MgTR and factors affecting it is required. In this perspective, we review the key developments in MgTR and discuss the thermal management strategies used to control the properties of p-Si. Additionally, we explore future research directions and approaches to bridge the gap between laboratory-scale experiments and industrial applications
Photo-induced Energy Transfer Polymerization
No full textIn conventional photo-induced polymerization strategies, the active species that initiate the reaction tend to be exogenous radical species. Inspired by photo-induced cycloaddition reactions, in this study we investigated photo-induced polymerization from the perspective of energy transfer processes. Utilizing low-energy, highly reactive triplet species of olefin molecules as energy acceptors, a polymerization strategy without the need for exogenous active components was developed. Triplet species from various sources were able to induce polymerization, demonstrating the excellent versatility of this strategy. The reaction mechanism was thoroughly investigated with controlled experiments and spectroscopic methods using thiochromanone as a template. It was clearly established that the key to polymerization is an active triplet species rather than a conventional radical species. As a result, the findings of this study stimulate further discussion on the role of monomers in photo-induced polymerization
Ribosomal Synthesis of Ketone-containing Peptide Backbone via O to C Acyl Shift
No full textDespite tremendous efforts to engineer translational machinery, replacing the encoded peptide backbone with new-to-Nature structures remains a significant and largely unmet challenge. C, H, O, and N are the elements of life, and yet ribosomes are only capable of forming C–N bonds as amides, C–O bonds as esters, and C–S bonds as thioesters; there is no current strategy to form C–C bonds as ketones embedded in the backbone of ribosomal products. We discovered that peptides containing a dehydrolactic acid motif rapidly isomerize to generate a backbone-embedded α,γ-diketoamide via a spontaneous formal O to C acyl shift. The dehydrolactic acid motif can be introduced into peptides ribosomally or via solid-phase synthesis using α-hydroxy phenylselenocysteine followed by oxidation. Subsequent incubation at physiological pH produces an α,γ-diketoamide that can be diversified using a variety of nucleophiles, including hydrazines and hydroxylamines to form pyrazoles and oximes, respectively. All of these groups remain embedded directly within the polypeptide backbone. This general strategy, predicated on an intricate cascade of acyl rearrangements, provides the first example of a C–C bond forming reaction to take place within the peptide backbone, as well as the first ribosomal strategy for generating protein-like materials with diverse, backbone-embedded heterocycles. The genetically encoded, new-to-nature biopolymers produced should accelerate the discovery of genetically encoded molecules whose properties better resemble those of bioactive natural products
Non-Pinned, Reversible Spin Crossover in Self-Assembled Monolayers of a Functionalized Fe(II) Scorpionate Complex
No full textThe spin crossover (SCO) behaviour of molecules in (sub)monolayers is typically significantly altered from that of the bulk: in particular, the SCO can be quenched by direct contact between the SCO molecules and the substrate, known as pinning, which causes problems for potential device applications. Here, an Fe (II) complex is presented that exhibits fully reversible, non-pinned SCO in self-assembled monolayers (SAMs) on template stripped gold substrates. The complex, [Fe(Tp(4-NHCOC10H20SCOCH3))(Tp)] where Tp = tris(1H-pyrazol-1-yl borohydride), has a broad SCO with a T½ of 366 K. The SAMs are uniform and homogeneous, as indicated by Atomic Force Microscopy, and contain the target molecules in a well-oriented layer with the expected thickness for a monolayer of the complex, as revealed by polarization modulation infrared reflection-absorption spectroscopy, time-of-flight secondary ion mass spectrometry and cyclic voltammetry. Variable temperature X-ray photoelectron spectroscopy, as well as X-ray absorption spectroscopy at the Fe L2,3 edges, indicates a reversible SCO in the monolayers that is identical to the bulk behaviour
Emergence of Bulk Band Inversion in the Nanodomain and Relaxation Effects on the Surface States of the Bi2Se3 Topological Insulator Family
No full textTopological insulators (TIs) hold compelling promise for diverse applications in advanced nanodevices and catalysis, owing to their protected edge and surface states. Under operational conditions, TI materials are typically fabricated into (ultra-)thin films with highly crystalline nanodomains. The exposed facets exhibit distinct surface properties that vary with respect to the size of the nanocrystals. Herein, we investigate the finite-size effects on the surface states and the bulk band inversion within the Bi2Se3 family of three-dimensional (3D) TIs via first-principles calculations. Thin films exposing the three lowest-energy surfaces are simulated by two-dimensional (2D) semi-infinite slabs with tunable thicknesses. We propose that the finite-size effects originate from electron confinement in the cutoff direction. The increase in film thickness then counteracts these confinement effects, resulting in a monotonically decreasing band gap evaluated at the spin-orbit decoupled level. The dependence of the bulk gap on the thickness is found consistent for various surface slabs. This relationship is then utilized to predict the required thickness for maintaining the 3D TI phase in the bulk domain of the thin films. Our findings provide a unique understanding of the finite-size effects on various surfaces of the 3D TI materials. In addition, the actual manifestation of topological surface states on the side surfaces is affected significantly by the co-existing dangling bonds produced by surface cuts. Therefore, surface relaxation plays a crucial role in disentangling the trivial and nontrivial surface states
Formate Salt as a Bifunctional Reagent for Hydroxylation and Carbonylation Reactions Under Photochemically Driven Nickel Catalysis
No full textIn this study, we disclose for the first time that formate salt can be used as a bifunctional reagent for the synthesis of phenol derivatives and as a CO source for carbonylative cross-coupling processes using the COware gas reactor under activation free conditions. Key to this success is the in-situ synthesis of aryl formate via an unprecedented nickel/organophotocatalyst system under blue LED irradiation. This developed system demonstrated high applicability to various aryl iodide substrates for synthesizing phenol derivatives. Moreover, the generated CO could be utilized in a range of carbonylative C-heteroatom and C-C processes. Notably, commercially available H13COONa salt can serve as a bifunctional reagent for both synthesizing phenols and generating 13CO
A Refined Set of Universal Force Field Parameters for Some Metal Nodes in Metal-Organic Frameworks
No full textMetal-organic frameworks (MOFs) exhibit promise as porous materials for carbon capture due to their design versatility and large pore sizes. The generic force field (e.g. UFF and Dreiding) uses one set of Lennard-Jones parameters for each element, while MOFs have a much richer local chemical environment than those used to fit the UFF. When MOFs contain hard-Lewis acid metals, UFF systematically overestimates uptakes within MOFs. To address this, we developed a workflow to affordably and efficiently generate reliable force fields to predict \ce{CO2} adoption isotherms of MOFs containing metals from groups IIA (e.g. Mg, Ca, Sr, Ba) and IIIA (e.g., Al, Ga, In), connected to various carboxylate ligands. This method uses experimental isotherms as input. The optimal parameters are obtained by minimizing the loss function of the experimental and simulated isotherms, in which we use the Multistate Bennett Acceptance Ratio (MBAR) theory can be used to derive the functionality relationship of loss functions in terms of force field parameters