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The Analyst Jun 2024Plant hormones are important in the control of physiological and developmental processes including seed germination, senescence, flowering, stomatal aperture, and...
Plant hormones are important in the control of physiological and developmental processes including seed germination, senescence, flowering, stomatal aperture, and ultimately the overall growth and yield of plants. Many currently available methods to quantify such growth regulators quickly and accurately require extensive sample purification using complex analytic techniques. Herein we used ultra-performance liquid chromatography-high-resolution mass spectrometry (UHPLC-HRMS) to create and validate the prediction of hormone concentrations made using attenuated total reflection Fourier-transform infrared (ATR-FTIR) spectral profiles of both freeze-dried ground leaf tissue and extracted xylem sap of Japanese knotweed () plants grown under different environmental conditions. In addition to these predictions made with partial least squares regression, further analysis of spectral data was performed using chemometric techniques, including principal component analysis, linear discriminant analysis, and support vector machines (SVM). Plants grown in different environments had sufficiently different biochemical profiles, including plant hormonal compounds, to allow successful differentiation by ATR-FTIR spectroscopy coupled with SVM. ATR-FTIR spectral biomarkers highlighted a range of biomolecules responsible for the differing spectral signatures between growth environments, such as triacylglycerol, proteins and amino acids, tannins, pectin, polysaccharides such as starch and cellulose, DNA and RNA. Using partial least squares regression, we show the potential for accurate prediction of plant hormone concentrations from ATR-FTIR spectral profiles, calibrated with hormonal data quantified by UHPLC-HRMS. The application of ATR-FTIR spectroscopy and chemometrics offers accurate prediction of hormone concentrations in plant samples, with advantages over existing approaches.
Topics: Spectroscopy, Fourier Transform Infrared; Plant Growth Regulators; Least-Squares Analysis; Plant Leaves; Chromatography, High Pressure Liquid; Support Vector Machine; Mass Spectrometry; Principal Component Analysis
PubMed: 38712606
DOI: 10.1039/d3an01817b -
The Journal of Physical Chemistry. A May 2024Recent work in combustion and atmospheric chemistry has revealed cases in which diastereomers must be distinguished to accurately model a reacting flow. This paper...
Recent work in combustion and atmospheric chemistry has revealed cases in which diastereomers must be distinguished to accurately model a reacting flow. This paper presents an open-source framework for introducing such stereoisomer resolution into a kinetic mechanism. We detail our definitions and algorithms for labeling and enumerating the stereoisomers of a molecule and then generalize our system to describe the transition state (TS) of a reaction. This allows for the stereospecific enumeration of reactants and products while accounting for "fleeting" stereochemistry that is unique to the TS. We also present the AutoMech Chemical Identifier (AMChI), an InChI-like string identifier that accounts for stereocenters omitted by InChI. This identifier is extended to describe the TSs of reactions, providing a universal lookup key for specific reaction channels. The final piece of our methodology is an analytic formula to remove redundancy from a stereoresolved mechanism when its enantiomers exist as a racemic mixture, making it as compact as possible while fully accounting for the differences between diastereomers. In applying our methodology to two subsets of the NUIGMech1.1 mechanism, we find that our approach reduces the extra species added for large-fuel oxidation from 2231 (133%, full expansion) to 694 (41%, nonredundant expansion). We also find that for pyrolysis more than a quarter of the species in the expanded mechanism cannot be properly described by an InChI string, requiring an AMChI string to communicate their identity. Finally, we find that roughly one-quarter of the large-fuel oxidation reactions and one-third of the pyrolysis reactions include fleeting TS stereochemistry, which may have relevant effects on their kinetics.
PubMed: 38683599
DOI: 10.1021/acs.jpca.4c01060 -
Astrobiology May 2024Solar radiation that arrives on the surface of Mars interacts with organic molecules present in the soil. The radiation can degrade or transform the organic matter and...
Solar radiation that arrives on the surface of Mars interacts with organic molecules present in the soil. The radiation can degrade or transform the organic matter and make the search for biosignatures on the planet's surface difficult. Therefore, samples to be analyzed by instruments on board Mars probes for molecular content should be selectively chosen to have the highest organic preservation content. To support the identification of organic molecules on Mars, the behavior under UV irradiation of two organic compounds, undecanoic acid and L-phenylalanine, in the presence of vermiculite and two chloride salts, NaCl and MgCl, was studied. The degradation of the molecule's bands was monitored through IR spectroscopy. Our results show that, while vermiculite acts as a photoprotective mineral with L-phenylalanine, it catalyzes the photodegradation of undecanoic acid molecules. On the other hand, both chloride salts studied decreased the degradation of both organic species acting as photoprotectors. While these results do not allow us to conclude on the preservation capabilities of vermiculite, they show that places where chloride salts are present could be good candidates for analytic experiments on Mars due to their organic preservation capacity under UV radiation.
Topics: Mars; Ultraviolet Rays; Phenylalanine; Exobiology; Aluminum Silicates; Extraterrestrial Environment; Photolysis; Fatty Acids
PubMed: 38669050
DOI: 10.1089/ast.2023.0088 -
Biosensors Mar 2024Covalent organic frameworks (COFs) are porous crystals that have high designability and great potential in designing, encapsulating, and immobilizing nanozymes. COF... (Review)
Review
Covalent organic frameworks (COFs) are porous crystals that have high designability and great potential in designing, encapsulating, and immobilizing nanozymes. COF nanozymes have also attracted extensive attention in analyte sensing and detection because of their abundant active sites, high enzyme-carrying capacity, and significantly improved stability. In this paper, we classify COF nanozymes into three types and review their characteristics and advantages. Then, the synthesis methods of these COF nanozymes are introduced, and their performances are compared in a list. Finally, the applications of COF nanozymes in environmental analysis, food analysis, medicine analysis, disease diagnosis, and treatment are reviewed. Furthermore, we also discuss the application prospects of COF nanozymes and the challenges they face.
Topics: Metal-Organic Frameworks; Biosensing Techniques; Nanostructures; Chemistry, Analytic; Food Analysis; Chemistry Techniques, Analytical
PubMed: 38667156
DOI: 10.3390/bios14040163 -
The Journal of Chemical Physics Apr 2024This study presents a population balance model for the kinetics of nucleation and growth in covalent organic framework (COF) synthesis. The model incorporates...
This study presents a population balance model for the kinetics of nucleation and growth in covalent organic framework (COF) synthesis. The model incorporates second-order nucleation and first-order growth rates, consistent with proposals in the literature. Despite having non-linear terms, an implicit analytic solution is derived and then converted to explicit solutions for the monomer concentration and size distribution of COF flakes as a function of time. For experimental definitions of the induction time and the initial growth rate based on yield (y) vs time (t) curves, the model predicts power-law relationships: tind=0.409kN-1/3kG-2/3cA0-1 and dy/dtmax=0.965kN1/3kG2/3cA0, respectively. We discuss the implications for the interpretation of Arrhenius plots. We also discuss key discrepancies with experiments, including the predicted attainment of 100% yield instead of 30%-40% as observed and the value of the yield at the inflection point in the yield vs time curve. We suggest extensions to the model, including nucleation and growth kinetics with equilibrium solubility limitations and two-dimensional nucleation for the formation of multilayer COF particles.
PubMed: 38666576
DOI: 10.1063/5.0197656 -
Water Environment Research : a Research... Apr 2024Wastewater management decision-making is complicated because of: (1) a complex regulatory structure, (2) the wide variety of conflicting expectations by stakeholders... (Review)
Review
Wastewater management decision-making is complicated because of: (1) a complex regulatory structure, (2) the wide variety of conflicting expectations by stakeholders external and internal to the responsible utility, and (2) constrains including regulatory requirements, available technologies and practices, and customer willingness to pay. This review synthesizes the results from over 200 papers published since 2000 and presents a decision-making structure and process which is (1) science and fact-based, (2) reflects sustainability, (3) clear and transparent, (4) inclusive, (5) produces an objective-oriented decision, (6) scalable, (7) repeatable, and (8) efficient. Tools supporting the decision-making process are reviewed, including Multi-Criteria Decision Analysis (MCDA), Data Envelopment Analysis (DEA), Analytic Hierarchy Process (AHP), process modeling, economic assessments, Life Cycle Assessment (LCA), and Social Life Cycle Assessment (SLCA). Ultimately it was determined that engagement of decision-makers and relevant stakeholders to assess their values and preferences, coupled with supporting data and analyses, is necessary to reach a decision that, critically, has the support needed for it to be implemented. The results demonstrate that an understanding of the components of the decision process, coupled with an orderly process, enables good wastewater management decision-making. PRACTITIONER POINTS: A decision-making structure and process leading to the selection of implementable solutions is presented. The process possesses the following attributes: (1) science and fact-based, (2) reflect sustainability, (3) clear and transparent, (4) inclusive, (5) produce an objective-oriented decision, (6) scalable, (7) repeatable, and (8) efficient An extensive summary and analysis of tools supporting the decision process are provided, including Multi-Criteria Decision Analysis (MCDA), Data Envelopment Analysis (DEA), Analytic Hierarchy Process (AHP), process modeling, economic assessments, Life Cycle Assessment (LCA), and Social Life Cycle Assessment (SLCA). The critical role of internal and external stakeholders and differentiating their involvement relative to decision-makers is emphasized.
Topics: Decision Making; Wastewater; Waste Disposal, Fluid; Decision Support Techniques
PubMed: 38666418
DOI: 10.1002/wer.11024 -
JACS Au Apr 2024We investigated room-temperature metal and ligand K-edge X-ray absorption (XAS) spectra of a complete redox series of cubane-type iron-sulfur clusters. The Fe K-edge...
We investigated room-temperature metal and ligand K-edge X-ray absorption (XAS) spectra of a complete redox series of cubane-type iron-sulfur clusters. The Fe K-edge position provides a qualitative but convenient alternative to the traditional spectroscopic descriptors used to identify oxidation states in these systems, which we demonstrate by providing a calibration curve based on two analytic methods. Furthermore, high energy resolution fluorescence detected XAS (HERFD-XAS) at the S K-edge was used to measure Fe-S bond covalencies and record their variation with the average valence of the Fe atoms. While the Fe-S(thiolate) covalency evolves linearly, gaining 11 ± 0.4% per bond and hole, the Fe-S(μ) covalency evolves asystematically, reflecting changes in the magnetic exchange mechanism. A strong discontinuity manifested for superoxidation to the all-ferric state, distinguishing its electronic structure and its potential (bio)chemical role from those of its redox congeners. We highlight the functional implications of these trends for the reactivity of iron-sulfur cubanes.
PubMed: 38665672
DOI: 10.1021/jacsau.4c00213 -
Global Epidemiology Jun 2024Evidence triangulation may help identify the impact of study design elements on study findings and to tease out biased results when evaluating potential causal...
Evidence triangulation may help identify the impact of study design elements on study findings and to tease out biased results when evaluating potential causal relationships; however, methods for triangulating epidemiologic evidence are evolving and have not been standardized. Building upon key principles of epidemiologic evidence triangulation and risk of bias assessment, and responding to the National Academies of Sciences, Engineering, and Medicine (NASEM) call for applied triangulation examples, the objective of this manuscript is to propose a triangulation framework and to apply it as an illustrative example to epidemiologic studies examining the possible relationship between occupational formaldehyde exposure and risk of myeloid leukemias (ML) including acute (AML) and chronic (CML) types. A nine-component triangulation framework for epidemiological evidence was developed incorporating study quality and ROB guidance from various federal health agencies (i.e., US EPA TSCA and NTP OHAT). Several components of the triangulation framework also drew from widely used epidemiological analytic tools such as stratified meta-analysis and sensitivity analysis. Regarding the applied example, fourteen studies were identified and assessed using the following primary study quality domains to explore potential key sources of bias: 1) study design and analysis; 2) study participation; 3) exposure assessment; 4) outcome assessment; and 5) potential confounding. Across studies, methodological limitations possibly contributing to biased results were observed within most domains. Interestingly, results from one study - often providing the largest and least-precise relative risk estimates, likely reflecting study biases, deviated from most primary study findings indicating no such associations. Triangulation of epidemiological evidence appears to be helpful in exploring inconsistent results for the identification of study results possibly reflecting various biases. Nonetheless, triangulation methodologies require additional development and application to real-world examples to enhance objectivity and reproducibility.
PubMed: 38659700
DOI: 10.1016/j.gloepi.2024.100143 -
Organic Letters May 2024Switchable enantioselectivity was uncovered in the enantioselective catalytic conjugate addition of β,γ-unsaturated α-keto esters with terminal alkynes to the chiral...
Switchable enantioselectivity was uncovered in the enantioselective catalytic conjugate addition of β,γ-unsaturated α-keto esters with terminal alkynes to the chiral Lewis acid complex of In(BF) and chiral phosphoric acid.
PubMed: 38656195
DOI: 10.1021/acs.orglett.4c01101 -
Journal of Chemical Theory and... May 2024Accurately modeling photochemical reactions is difficult due to the presence of conical intersections and locally avoided crossings, as well as the inherently...
Accurately modeling photochemical reactions is difficult due to the presence of conical intersections and locally avoided crossings, as well as the inherently multiconfigurational character of excited states. As such, one needs a multistate method that incorporates state interaction in order to accurately model the potential energy surface at all nuclear coordinates. The recently developed linearized pair-density functional theory (L-PDFT) is a multistate extension of multiconfiguration PDFT, and it has been shown to be a cost-effective post-MCSCF method (as compared to more traditional and expensive multireference many-body perturbation methods or multireference configuration interaction methods) that can accurately model potential energy surfaces in regions of strong nuclear-electronic coupling in addition to accurately predicting Franck-Condon vertical excitations. In this paper, we report the derivation of analytic gradients for L-PDFT and their implementation in the PySCF-forge software, and we illustrate the utility of these gradients for predicting ground- and excited-state equilibrium geometries and adiabatic excitation energies for formaldehyde, --butadiene, phenol, and cytosine.
PubMed: 38639604
DOI: 10.1021/acs.jctc.4c00095