cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.y7xy5k
title: Occurrence Download

description: A dataset containing 1 species occurrences available in GBIF matching the query:
{
 "and" : [
 "DatasetKey is Review of Neoleptastacus Nicholls, 1945 (Harpacticoida, Arenopontiidae), including an updated key to species and proposal of Phreatipontia gen. nov.",
 "Country is Croatia"
 ]
}

 The dataset includes 1 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008074-241107131044228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.7274/25599828
title: Development of a Low-Cost Solid-Phase Extraction Method for the Rapid Measurement of PFAS in Environmental Waters

description: A large class of synthetic compounds known as per- and polyfluoroalkyl substances (PFAS) has become ubiquitous in the environment due to their widespread use and extreme persistence. They pose risks to the environment and human health, drawing significant attention in recent years. Contaminated water consumption has emerged as one of the major pathways for human exposure, and studies have identified elevated PFAS concentrations in human blood linked to polluted drinking water sources. In response to the escalating concern surrounding PFAS, the U.S. EPA has proposed new maximum contaminant levels for six PFAS, notably setting stringent limits of 4 ppt each for PFOA and PFOS. This regulatory advancement, while crucial for public health, introduces challenges in the routine and regular monitoring and detection of PFAS in water samples.

Despite the development of various methods for total fluorine measurement and targeted PFAS analysis, those techniques often fall short in achieving the low ppt level required for efficient PFAS measurement or are time-consuming and expensive. As an innovative alternative, particle-induced gamma-ray emission (PIGE) spectroscopy has been developed and employed as a rapid, sensitive, and cost-effective method for screening total adsorbable organic fluorine (AOF) in water samples. The PIGE analysis is integrated with a solid-phase extraction (SPE) method utilizing commercially available and low-cost graphite activated carbon fiber (GACF) felt to pre-concentrate and extract PFAS from water samples before analysis. To accommodate diverse water sample types studied in this research, including drinking water, groundwater, and surface water, the method has been further developed to address various challenges. Specifically, a methanol rinse method distinguishes inorganic fluoride and organic fluorine from PIGE analysis, an acid rinse method differentiates inorganic fluoride and ultrashort-chain PFAS from longer-chain PFAS, and Fenton’s reagent is employed to eliminate water matrix interference.
DOI: 10.7274/25599828.v1
title: Development of a Low-Cost Solid-Phase Extraction Method for the Rapid Measurement of PFAS in Environmental Waters

description: A large class of synthetic compounds known as per- and polyfluoroalkyl substances (PFAS) has become ubiquitous in the environment due to their widespread use and extreme persistence. They pose risks to the environment and human health, drawing significant attention in recent years. Contaminated water consumption has emerged as one of the major pathways for human exposure, and studies have identified elevated PFAS concentrations in human blood linked to polluted drinking water sources. In response to the escalating concern surrounding PFAS, the U.S. EPA has proposed new maximum contaminant levels for six PFAS, notably setting stringent limits of 4 ppt each for PFOA and PFOS. This regulatory advancement, while crucial for public health, introduces challenges in the routine and regular monitoring and detection of PFAS in water samples.

Despite the development of various methods for total fluorine measurement and targeted PFAS analysis, those techniques often fall short in achieving the low ppt level required for efficient PFAS measurement or are time-consuming and expensive. As an innovative alternative, particle-induced gamma-ray emission (PIGE) spectroscopy has been developed and employed as a rapid, sensitive, and cost-effective method for screening total adsorbable organic fluorine (AOF) in water samples. The PIGE analysis is integrated with a solid-phase extraction (SPE) method utilizing commercially available and low-cost graphite activated carbon fiber (GACF) felt to pre-concentrate and extract PFAS from water samples before analysis. To accommodate diverse water sample types studied in this research, including drinking water, groundwater, and surface water, the method has been further developed to address various challenges. Specifically, a methanol rinse method distinguishes inorganic fluoride and organic fluorine from PIGE analysis, an acid rinse method differentiates inorganic fluoride and ultrashort-chain PFAS from longer-chain PFAS, and Fenton’s reagent is employed to eliminate water matrix interference.
DOI: 10.7274/25602495
title: Structure and Reactivity of Bis(iminoxolene) Ruthenium Complexes

description: Redox-active iminoxolenes, the mono-aza analogues of dioxolenes, can undergo three formal oxidation states, from the fully reduced amidophenoxide, a radical anion iminosemiquinonate, to the neutral iminoquinone. The variability of these oxidation states arises from the redox-active orbital (RAO), which is close in energy to the 4d and 5d metals. Therefore, metal iminoxolene interaction is at its peak in group 8 of the periodic table, and provides an opportunity for compounds with unusual bonding and reactivity.
DOI: 10.7274/25602495.v1
title: Structure and Reactivity of Bis(iminoxolene) Ruthenium Complexes

description: Redox-active iminoxolenes, the mono-aza analogues of dioxolenes, can undergo three formal oxidation states, from the fully reduced amidophenoxide, a radical anion iminosemiquinonate, to the neutral iminoquinone. The variability of these oxidation states arises from the redox-active orbital (RAO), which is close in energy to the 4d and 5d metals. Therefore, metal iminoxolene interaction is at its peak in group 8 of the periodic table, and provides an opportunity for compounds with unusual bonding and reactivity.
DOI: 10.7274/25607784
title: Advancements in Mid-Infrared Imaging and Spectroscopic Techniques for the Study of Phase Separating Peptides

description: Liquid-liquid phase separating (LLPS) proteins have been the center of concentrated research efforts over the past decade due to their relevance in many biological functions and systems, as well as their involvement in various neurodegenerative diseases. While current evidence links condensates formed by LLPS proteins to a number of mechanisms for biological function, the role of these condensates has proven difficult to study directly. Model peptides that undergo phase separation have been designed to help facilitate the study of these systems. It has been proposed that these peptides, when in condensate phase, undergo changes in secondary structure.

While research has been done to show that the condensates can cause changes to protein and peptide behavior, work on structural changes is limited, especially in situ. The majority of these studies are computational work or utilize the addition of fluorescent labels or tags. Infrared (IR) spectroscopy and microscopy techniques are uniquely qualified to detect secondary structural changes, among other characteristics, in complex environments.

To study these changes, two-dimensional infrared spectroscopy (2DIR) experiments have been done to compare structural differences in bulk solution versus condensate-forming conditions for several model peptide systems. The spectra resulting from these studies, however, do not always show any noticeable differences. While it is plausible in these cases that there is no substantial difference in overall secondary structure between bulk solution and condensate phase for these particular peptide systems, it is also possible that we were unable to collect 2DIR of the condensates specifically.

With the use of two-dimensional infrared hyperspectral imaging, secondary structural information can be distinctly gathered on the proteins both within and outside of the LLPS condensates. At this time, however, the technology to perform such an experiment is underdeveloped. Mid-infrared light lacks the ability to measure anything smaller than a few microns due to the classical resolution limit and its long wavelengths. Additionally, the broadband light necessary for 2DIR spectroscopic measurements causes chromatic dispersion, further worsening the actual experimental resolution.

The work presented here progresses the instrumental development necessary for super resolution, two-dimensional infrared hyperspectral imaging of liquid-liquid phase separating systems, as well as presents preliminary studies on several model LLPS systems.
DOI: 10.7274/25607784.v1
title: Advancements in Mid-Infrared Imaging and Spectroscopic Techniques for the Study of Phase Separating Peptides

description: Liquid-liquid phase separating (LLPS) proteins have been the center of concentrated research efforts over the past decade due to their relevance in many biological functions and systems, as well as their involvement in various neurodegenerative diseases. While current evidence links condensates formed by LLPS proteins to a number of mechanisms for biological function, the role of these condensates has proven difficult to study directly. Model peptides that undergo phase separation have been designed to help facilitate the study of these systems. It has been proposed that these peptides, when in condensate phase, undergo changes in secondary structure.

While research has been done to show that the condensates can cause changes to protein and peptide behavior, work on structural changes is limited, especially in situ. The majority of these studies are computational work or utilize the addition of fluorescent labels or tags. Infrared (IR) spectroscopy and microscopy techniques are uniquely qualified to detect secondary structural changes, among other characteristics, in complex environments.

To study these changes, two-dimensional infrared spectroscopy (2DIR) experiments have been done to compare structural differences in bulk solution versus condensate-forming conditions for several model peptide systems. The spectra resulting from these studies, however, do not always show any noticeable differences. While it is plausible in these cases that there is no substantial difference in overall secondary structure between bulk solution and condensate phase for these particular peptide systems, it is also possible that we were unable to collect 2DIR of the condensates specifically.

With the use of two-dimensional infrared hyperspectral imaging, secondary structural information can be distinctly gathered on the proteins both within and outside of the LLPS condensates. At this time, however, the technology to perform such an experiment is underdeveloped. Mid-infrared light lacks the ability to measure anything smaller than a few microns due to the classical resolution limit and its long wavelengths. Additionally, the broadband light necessary for 2DIR spectroscopic measurements causes chromatic dispersion, further worsening the actual experimental resolution.

The work presented here progresses the instrumental development necessary for super resolution, two-dimensional infrared hyperspectral imaging of liquid-liquid phase separating systems, as well as presents preliminary studies on several model LLPS systems.
DOI: 10.7274/25607838
title: Infrared Spectroscopic Studies of Model Biophysical Peptide Systems

description: Characterization of protein structure is vital to our understanding of biological function and disease progression. While some proteins can be crystallized for structure determination, a vast majority are intrinsically disordered, lacking a well-defined structure. This class of proteins poses a major challenge for developing drugs, as there are limited techniques available to probe drug-target structures in solution. This dissertation sheds light on several infrared spectroscopic methods as promising techniques for studying intrinsically disordered proteins (IDPs) through the use of model peptides. Chapter 3 details insights that can be gained from (1) two-dimensional infrared (2DIR) spectroscopy, focusing on the intracellular neuronal protein, tau, an IDP known be involved in Alzheimer’s disease. Here we utilize backbone isotope labeling and reveal structural organization of toxic aggregated ß-sheets. Chapter 4 introduces (2) visible pump-infrared probe (Vis-IR) spectroscopy and lays the foundation for studying interactions between IDPs and chromophoric inhibitors of amyloid aggregation. Some IDPs undergo a method of liquid-liquid phase separation (LLPS), by which proteins sequester themselves into pockets, or visible droplets, creating two distinct phases within the same solvent. Chapter 5 introduces (3) cysteine cyanylation, a side-chain isotope labeling mechanism, that when combined with 2DIR has the potential to reveal key protein-solvent dynamics driving phase separation. Another area that presents a challenge in unraveling protein structure is the degree to which salts impact protein stability. Recent work has proposed that this effect arises from their direct contact with protein backbone. Chapter 6 introduces N-Methylacetamide, a common model of protein backbone, that in combination with 2DIR spectroscopy, reveals fundamental interactions and proposes structures that can be adopted under specific salt conditions. Chapter 7 expands on N-methylacetamide, utilizing its inhomogeneous nature as an illustration for Fabry-Perot cavity coupling and its use in disentangling quantum information science.
DOI: 10.7274/25607838.v1
title: Infrared Spectroscopic Studies of Model Biophysical Peptide Systems

description: Characterization of protein structure is vital to our understanding of biological function and disease progression. While some proteins can be crystallized for structure determination, a vast majority are intrinsically disordered, lacking a well-defined structure. This class of proteins poses a major challenge for developing drugs, as there are limited techniques available to probe drug-target structures in solution. This dissertation sheds light on several infrared spectroscopic methods as promising techniques for studying intrinsically disordered proteins (IDPs) through the use of model peptides. Chapter 3 details insights that can be gained from (1) two-dimensional infrared (2DIR) spectroscopy, focusing on the intracellular neuronal protein, tau, an IDP known be involved in Alzheimer’s disease. Here we utilize backbone isotope labeling and reveal structural organization of toxic aggregated ß-sheets. Chapter 4 introduces (2) visible pump-infrared probe (Vis-IR) spectroscopy and lays the foundation for studying interactions between IDPs and chromophoric inhibitors of amyloid aggregation. Some IDPs undergo a method of liquid-liquid phase separation (LLPS), by which proteins sequester themselves into pockets, or visible droplets, creating two distinct phases within the same solvent. Chapter 5 introduces (3) cysteine cyanylation, a side-chain isotope labeling mechanism, that when combined with 2DIR has the potential to reveal key protein-solvent dynamics driving phase separation. Another area that presents a challenge in unraveling protein structure is the degree to which salts impact protein stability. Recent work has proposed that this effect arises from their direct contact with protein backbone. Chapter 6 introduces N-Methylacetamide, a common model of protein backbone, that in combination with 2DIR spectroscopy, reveals fundamental interactions and proposes structures that can be adopted under specific salt conditions. Chapter 7 expands on N-methylacetamide, utilizing its inhomogeneous nature as an illustration for Fabry-Perot cavity coupling and its use in disentangling quantum information science.
DOI: 10.7274/25607841
title: Redox Transformations of Sulfane Sulfur at Zinc Thiolate Complexes and Other Metal Cations

description: This dissertation details investigations into the reactivity between Zn-S bonds in molecular zinc thiolate complexes and elemental sulfur. With spectroscopic, voltammetric, and crystallographic evidence, changes in both metal cation with benzenethiolate anion and the ligand environment of zinc thiolate complexes were observed to influence whether sulfur was inserted, resulting in zinc polysulfanide products, or reduced via thiolate oxidation.
Chapter 2 describes the comparison of nucleophilic reactivity between synthetic zinc dithiolate and zinc tetrasulfanide complexes. Comparing rates of catalytic thiolate-disulfide exchange as well as alkylation kinetics demonstrates that sulfane sulfur decreases the nucleophilic reactivity of the less basic tetrasulfanide moiety when compared to that of the zinc thiolate.
Chapter 3 describes the study of the shifts induced by redox-inert metal cations in the equilibria that results from reaction between thiolate anion and elemental sulfur, forming distributions of polysulfanide anions, polysulfide anions, and organic disulfide species. Spectroscopic characterization was used to track solution-phase speciation of reduced sulfur species and thiolate oxidation to organic disulfide. Electrochemical analysis reveals changes in equilibria in the presence of metal cations results from metal-sulfur interactions which shift the sulfur reduction and thiolate oxidation half-reaction potentials. Together with computational studies, the stability of strong, covalent metal polysulfide interactions of more highly-charged cations over those of metal thiolates or metal polysulfanides is shown to promote sulfur reduction and thiolate oxidation pathways over sulfur catenation at thiolate.
Chapter 4 describes the effects of ligand environment in zinc thiolate complexes on their reactivity with sulfur. Modulation of thiolate-containing ligand across a series of 4- and 5-coordinate platforms suggests a dissociative mechanism of thiolate nucleophilicity dependent on ligand electronics and chelation. More electron-rich and monodentate thiolate donors were observed to favor sulfur reduction and thiolate oxidation while electron-poor, chelating thiolate moieties selectively insert sulfur to form zinc polysulfanide complexes.
DOI: 10.7274/25607841.v1
title: Redox Transformations of Sulfane Sulfur at Zinc Thiolate Complexes and Other Metal Cations

description: This dissertation details investigations into the reactivity between Zn-S bonds in molecular zinc thiolate complexes and elemental sulfur. With spectroscopic, voltammetric, and crystallographic evidence, changes in both metal cation with benzenethiolate anion and the ligand environment of zinc thiolate complexes were observed to influence whether sulfur was inserted, resulting in zinc polysulfanide products, or reduced via thiolate oxidation.
Chapter 2 describes the comparison of nucleophilic reactivity between synthetic zinc dithiolate and zinc tetrasulfanide complexes. Comparing rates of catalytic thiolate-disulfide exchange as well as alkylation kinetics demonstrates that sulfane sulfur decreases the nucleophilic reactivity of the less basic tetrasulfanide moiety when compared to that of the zinc thiolate.
Chapter 3 describes the study of the shifts induced by redox-inert metal cations in the equilibria that results from reaction between thiolate anion and elemental sulfur, forming distributions of polysulfanide anions, polysulfide anions, and organic disulfide species. Spectroscopic characterization was used to track solution-phase speciation of reduced sulfur species and thiolate oxidation to organic disulfide. Electrochemical analysis reveals changes in equilibria in the presence of metal cations results from metal-sulfur interactions which shift the sulfur reduction and thiolate oxidation half-reaction potentials. Together with computational studies, the stability of strong, covalent metal polysulfide interactions of more highly-charged cations over those of metal thiolates or metal polysulfanides is shown to promote sulfur reduction and thiolate oxidation pathways over sulfur catenation at thiolate.
Chapter 4 describes the effects of ligand environment in zinc thiolate complexes on their reactivity with sulfur. Modulation of thiolate-containing ligand across a series of 4- and 5-coordinate platforms suggests a dissociative mechanism of thiolate nucleophilicity dependent on ligand electronics and chelation. More electron-rich and monodentate thiolate donors were observed to favor sulfur reduction and thiolate oxidation while electron-poor, chelating thiolate moieties selectively insert sulfur to form zinc polysulfanide complexes.
DOI: 10.7274/25872196
title: Exploring Actinide Bonding and Crystal Chemistry in Acidic Media with Borate, Sulfate, Phosphate, and Arsenate Ligands

description: Herein we explore the vast coordination and crystal chemistry of the actinides by probing various ligand systems in acidic media. Unique solvothermal synthetic techniques were developed and implemented in order to synthesize new crystals yielding a variety of new structures containing the acidic solvent of choice. The main reaction medium used was oleum, or fuming sulfuric acid, which presented an uncommon avenue of study in the solid-state, given the lack of literature using these methods with actinide-bearing compounds. Additional research was done on the hydronium cation, a common cation in acidic aqueous systems, and the radiation stability of hydronium in uranium-bearing compounds.
The first area of research explored the development of methods required to synthesize new compounds in oleum, SO3 enriched sulfuric acid. The use of 20% free SO3 H2SO4 presented various unique challenges when combining with the safety necessary in handling the actinides. Once established, these methods were executed in order to synthesize the first actinide borosulfate compounds. The first two actinide borosulfate compounds were both synthesized using solvothermal techniques with oleum and are both uranium-bearing compounds. Two out of the three unique bridging modes within borosulfate chemistry were targeted in these structures, the conventional borate-to-sulfate (B-O-S) and the unconventional borate-to-borate (B-O-B) bridging modes.
The second area of research further expanded the synthetic methods of acidic media and the actinides by exploring with transuranic elements, neptunium and plutonium. These two elements have an extensive redox landscape and introduced more precautionary measures given the higher activity of the isotopes. Exploring neptunium and plutonium sulfate syntheses with oleum, concentration sulfuric acid, and H5[B(SO4)4] yielded some of the first anhydrous transuranic sulfates, as well as targeted an uncommon oxidation state sulfate, plutonium(III) sulfate.
The third area of study investigated the environmentally relevant minerals, hydronium uranyl phosphate (HUP) and hydronium uranyl arsenate (HUAs). Hydronium, H3O+, is extremely prevalent in acidic aqueous solutions, but is far less common in solid-state compounds. The presence and placement of hydronium in HUP was analyzed with neutron powder diffraction and was compared to density functional perturbation theory calculations. Radiation stability of these low solubility compounds was also explored.