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The development of glass capillary gas chromatography/real-time, high-resolution mass spectrometry for the analysis of complex organic mixtures
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Design, implementation, and performance of a high resolution gas chromatography/high resolution mass spectrometry/real-time computer system for the analysis of complex organic mixtures
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Chemical Reaction and Flow Modeling in Fullerene and Nanotube Production
The development of processes to produce fullerenes and carbon nanotubes has largely been empirical. Fullerenes were first discovered in the soot produced by laser ablation of graphite [1]and then in the soot of electric arc evaporated carbon. Techniques and conditions for producing larger and larger quantities of fullerenes depended mainly on trial and error empirical variations of these processes, with attempts to scale them up by using larger electrodes and targets and higher power. Various concepts of how fullerenes and carbon nanotubes were formed were put forth, but very little was done based on chemical kinetics of the reactions. This was mainly due to the complex mixture of species and complex nature of conditions in the reactors. Temperatures in the reactors varied from several thousand degrees Kelvin down to near room temperature. There are hundreds of species possible, ranging from atomic carbon to large clusters of carbonaceous soot, and metallic catalyst atoms to metal clusters, to complexes of metals and carbon. Most of the chemical kinetics of the reactions and the thermodynamic properties of clusters and complexes have only been approximated. In addition, flow conditions in the reactors are transient or unsteady, and three dimensional, with steep spatial gradients of temperature and species concentrations. All these factors make computational simulations of reactors very complex and challenging. This article addresses the development of the chemical reaction involved in fullerene production and extends this to production of carbon nanotubes by the laser ablation/oven process and by the electric arc evaporation process. In addition, the high-pressure carbon monoxide (HiPco) process is discussed. The article is in several parts. The first one addresses the thermochemical aspects of modeling; and considers the development of chemical rate equations, estimates of reaction rates, and thermodynamic properties where they are available. The second part addresses modeling of the arc process for fullerene and carbon nanotube production using O-D, 1-D and 2-D fluid flow models. The third part addresses simulations of the pulsed laser ablation process using time-dependent techniques in 2-D, and a steady state 2-D simulation of a continuous laser ablation process. The fourth part addresses steady state modeling in O-D and 2-D of the HiPco process. In each of the simulations, there is a variety of simplifications that are made that enable one to concentrate on one aspect or another of the process. There are simplifications that can be made to the chemical reaction models , e.g. reduction in number of species by lumping some of them together in a representative species. Other simulations are carried out by eliminating the chemistry altogether in order to concentrate on the fluid dynamics. When solving problems with a large number of species in more than one spatial dimension, it is almost imperative that the problem be decoupled by solving for the fluid dynamics to find the fluid motion and temperature history of "particles" of fluid moving through a reactor. Then one can solve the chemical rate equations with complex chemistry following the temperature and pressure history. One difficulty is that often mixing with an ambient gas is involved. Therefore, one needs to take dilution and mixing into account. This changes the ratio of carbon species to background gas. Commercially available codes may have no provision for including dilution as part of the input. One must the write special solvers for including dilution in decoupled problems. The article addresses both ful1erene production and single-walled carbon nanotube (SWNT) production. There are at least two schemes or concepts of SWNT growth. This article will only address growth in the gas phase by carbon and catalyst cluster growth and SW T formation by the addition of carbon. There are other models that conceive of SWNT growth as a phase separation process from clusters me up carbon and metal catalyst, with the carbon precipitating from the cluster as it cools. We will not deal with that concept in this article. Further research is needed to determine the rates at which these composite clusters form, evaporate, and segregate.
High phase resolution: Probing interactions in complex interfaces with sum frequency generation
An often-quoted statement attributed to Wolfgang Pauli is that God made the bulk, but the surface was invented by the devil. Although humorous, the statement really reflects frustration in developing a detailed picture of a surface. In the last several decades, that frustration has begun to abate with numerous techniques providing clues to interactions and reactions at surfaces. Often these techniques require considerable prior knowledge. Complex mixtures on irregular or soft surfaces—complex interfaces—thus represent the last frontier. Two optical techniques: sum frequency generation (SFG) and second harmonic generation (SHG) are beginning to lift the veil on complex interfaces. Of these techniques, SFG with one excitation in the infrared has the potential to provide exquisite molecular- and moiety-specific vibrational data. This Perspective is intended both to aid newcomers in gaining traction in this field and to demonstrate the impact of high-phase resolution. It starts with a basic description of light-induced surface polarization that is at the heart of SFG. The sum frequency is generated when the input fields are sufficiently intense that the interaction is nonlinear. This nonlinearity represents a challenge for disentangling data to reveal the molecular-level picture. Three, high-phase-resolution methods that reveal interactions at the surface are described.
A History of Molecular Level Analysis of Natural Organic Matter by FTICR Mass Spectrometry and The Paradigm Shift in Organic Geochemistry
Natural organic matter (NOM) is a complex mixture of biogenic molecules resulting from the deposition and transformation of plant and animal matter. It has long been recognized that NOM plays an important role in many geological, geochemical, and environmental processes. Of particular concern is the fate of NOM in response to a warming climate in environments that have historically sequestered carbon (e.g., peatlands and swamps) but may transition to net carbon emitters. In this review, we will highlight developments in the application of high-field Fourier transform ion cyclotron resonance mass spectrometry (FTICR MS) in identifying the individual components of complex NOM mixtures, focusing primarily on the fraction that is dissolved in natural waters (dissolved organic matter or DOM). We will first provide some historical perspective on developments in FTICR technology that made molecular-level characterizations of DOM possible. In conclusion, a variety of applications of the technique will then be described, followed by our view of the future of high-field FTICR MS in carbon cycling research, including a particularly exciting metabolomic approach.
Finch: Toxicity Dose Response Curve Prediction of Chemical Compounds and Mixtures
A paradigm shift in chemical risk assessment is emphasizing mixture testing over single compound analysis, eliminating animal testing, and adopting advanced modeling approaches to understand mixture activity profiles. However, existing computational models largely focus on single chemicals, with few effective solutions for modeling complex mixtures that account for synergistic or antagonistic effects and multiple Modes of Action (MoA). Conventional methods like concentration addition (CA) and independent action (IA) are insufficient for this task as they are designed for simplistic interactions and struggle to account for the dynamic and multifaceted nature of chemical mixtures, such as overlapping MoA and non-linear interactions. Finch offers a novel approach utilizing deep learning (DL) embeddings and multi-task quantitative structure-activity relationship (QSAR) models to improve chemical exposure prediction. By leveraging molecular descriptors, physiochemical properties, and large language model (LLM) embeddings from SMILES inputs, Finch preserves critical information in a latent space thereby enhancing predictive accuracy. The multi-task learning aspect of Finch is highly advantageous, as it simultaneously optimizes multiple loss functions, leveraging all available data across tasks to develop generalized representations that effectively capture complex ingredient interactions within mixtures.
Carbon-rich aggregates in type 3 ordinary chondrites - Characterization, origins, and thermal history
Carbon-rich aggregates from three type 3.4-3.6 ordinary chondrites and two chondritic clasts have been characterized in detail, using TEM techniques. The aggregates in all the meteorites studied range in size from 5-1000 microns and consist of a fine scale intergrowth of poorly graphitized carbon, amorphous carbon, Fe,Ni metal, and minor chromite. Contrary to previous reports, well-crystallized graphite and magnetite are absent. The association of Fe,Ni metal and carbonaceous material suggests that the original carbonaceous material may have formed by Fischer-Tropsch (FT) type reactions at low temperatures (less than 400 K), possibly in the solar nebula. This carbonaceous material probably consisted of a complex mixture of hydrocarbons, kerogen-like material, and other complex organic molecules. The aggregates were subsequently accreted onto the ordinary chondrite parent bodies and underwent planetary thermal processing which resulted in the catalytic graphitization of hydrocarbons, in the presence of Fe,Ni metal, to produce poorly graphitized carbon. None of the meteorites studied experienced temperatures sufficiently high to produce crystalline, ordered graphite. Using the empirical geothermometer of Rietmeijer and Mackinnon (1985), the measured d(002) spacings of poorly graphitized carbon show that graphitization occurred at temperatures between 300 and 450 C. This range of temperatures is significantly lower than the generally quoted metamorphic temperatures for type 3.4-3.6 ordinary chondrites (about 450-500 C).
Ultrahigh performance LC/FT-MS non-targeted screening for biomass burning organic aerosol with MZmine2 and MFAssignR
In recent years, ultrahigh performance liquid chromatography Fourier transform mass spectrometry (LC/FT-MS) based non-targeted screening (NTS) methods have become increasingly popular for comprehensive analysis of complex organic mixtures. However, applying these methods for environmental complex mixture analysis is challenging due to the extreme complexity of natural samples and a lack of standard samples or surrogates for environmental complex mixtures. Furthermore, limited molecular markers in the databases and insufficient data processing software workflows make the application of these methods more challenging for environmental complex mixtures. In this work, we implement a new NTS data processing workflow to process data collected from ultrahigh performance liquid chromatography and Fourier transform Orbitrap Elite Mass Spectrometry (LC/FT-MS) by combining MZmine2 and MFAssignR, two opensource data processing tools and commercial Mesquite liquid smoke as a surrogate for biomass burning organic aerosol. MZmine2.53 data extraction followed MFAssignR molecular formula assignment offered noise free and highly accurate 1733 individual molecular formulas presented in liquid smoke with 4906 molecular species, including isomers. The results of this new approach were consistent with the results of direct infusion FT-MS analysis confirming its reliability. Over 90% of the molecular formulas presented in mesquite liquid smoke were matched with the molecular formulas of ambient biomass burning organic aerosol. This suggests the potential use of commercial liquid smoke as a surrogate for biomass burning organic aerosol research. Furthermore, the presented method significantly improves the identification of the molecular composition of biomass burning organic aerosol by successfully addressing some of the limitations related to the data analysis and giving a semi quantitative insight into the analysis.
Apparatus and methodology for fire gas characterization by means of animal exposure
While there is a great deal of information available from small-scale laboratory experiments and for relatively simple mixtures of gases, considerable uncertainty exists regarding appropriate bioassay techniques for the complex mixture of gases generated in full-scale fires. Apparatus and methodology have been developed based on current state of the art for determining the effects of fire gases in the critical first 10 minutes of a full-scale fire on laboratory animals. This information is presented for its potential value and use while further improvements are being made.
Transient Pulse-Response Time-of-Flight Mass Spectrometry for Complex, Deactivating Heterogeneous Catalytic Systems: Application to Ethane Dehydroaromatization
The study of complex, multistep bond-forming and -breaking reactions in heterogeneous catalytic systems often encounters challenges associated with the involvement of large numbers of intermediates among branching pathways. Kinetic information obtained from traditional steady-state measurements can be complemented with that from time-resolved methods to uncover details of the underlying chemistry. Herein, we describe an approach for tracking the complete time-resolved chemical composition (ca. 4–200 u) of a reactor effluent in response to a reactant pulse. We use a six-port rotary valve with a metered sampling loop to pulse reactants at ambient pressure into a flow reactor packed with a catalyst bed within the isothermal region of a heated furnace. The temporal evolution of effluent species is tracked using time-resolved molecular-beam time-of-flight mass spectrometry. We highlight the possibilities that this method has to offer by studying the complex bifunctional mechanism of ethane dehydroaromatization over an HZSM-5-supported platinum catalyst. We demonstrate that energy-tunable ionization sources, which facilitate isomer resolution, enable the measurement of the full mass spectral time-dependent system response. This includes the evolution of major products and mechanistically relevant reactive intermediates such as 1,3-butadiene and cyclopentadiene; these species have not previously been observed from this reaction. In additional studies, we also assess the role of platinum in the catalyst by examining temporal responses to ethane and ethylene feeds. Results show that two temporally distinct formation pathways exist for methane and benzene, and that their importance depends on both catalyst composition and reactant identity. Additionally, characteristics of catalyst deactivation are uniquely observable in the time-resolved mass spectral response, including the selective deactivation of a benzene formation pathway. The combination of time-of-flight mass spectrometry with tunable ionization enables the simultaneous observation of all effluents in a complex mixture of intermediates with isomer/isobar differentiation capabilities that can be applied to any complex reaction system.
Aminonitriles - Possible role in chemical evolution
The formation of HCN, ammonium cyanide, alkylnitriles, aminoacetonitrile and its C- and N-methyl homologs was demonstrated earlier in a simulated Jovian atmosphere. The polymeric material resulting in these experiments was shown to give glycine, alanine, sarcosine, aspartic acid and some imino dibasic acids on acid hydrolysis, suggesting thereby the participation of the monomeric nitriles in the formation of the polymeric product(s). Further examination of products resulting from semicorona and arc discharge through a mixture of methane and ammonia has provided evidence for the formation of alkylaminopropionitriles as a complex mixture and also some pyridyl and pyrimidyl type heterocyclic compounds. A gas chromatograph/mass spectrometer examination of the heterocyclics showed resemblance with those found in some carbonaceous chondrites. The significance of these findings in relation to chemical evolution is discussed.
An automated multi-component gas adsorption system (MC GAS)
The knowledge gap on adsorption of complex mixtures in the literature relative to single component data represents a persistent obstacle to developing accurate process models for adsorption separations. The collection of mixed gas adsorption data is an imminent need for improved understanding of the behavior of adsorbent systems in these diverse adsorption applications. Current approaches to understanding mixture adsorption using predictive theories based on pure component adsorption experiments often fail to capture the behavior of more complex, non-ideal systems. In this work, we present an automated volumetric instrument for the measurement of mixed gas adsorption isotherms. This instrument was validated by comparison to other in-house instruments and data available in the literature, and the binary adsorption measurements were found to be thermodynamically consistent. The automation of this instrument allows for rapid collection of high-quality mixture adsorption data.
Measuring Thermal Characteristics of Urban Landscapes
The additional heating of the air over the city is the result of the replacement of naturally vegetated surfaces with those composed of asphalt, concrete, rooftops and other man-made materials. The temperatures of these artificial surfaces can be 20 to 40 C higher than vegetated surfaces. Materials such as asphalt store much of the sun's energy and remains hot long after sunset. This produces a dome of elevated air temperatures 5 to 8 C greater over the city, compared to the air temperatures over adjacent rural areas. This effect is called the "urban heat island". Urban landscapes are a complex mixture of vegetated and nonvegetated surfaces. It is difficult to take enough temperature measurements over a large city area to characterize the complexity of urban radiant surface temperature variability. However, the use of remotely sensed thermal data from airborne scanners are ideal for the task. In a study funded by NASA, a series of flights over Huntsville, Alabama were performed in September 1994 and over Atlanta, Georgia in May 1997. Analysis of thermal energy responses for specific or discrete surfaces typical of the urban landscape (e.g., asphalt, building rooftops, vegetation) requires measurements at a very fine spatial scale (i.e., <15 m) to adequately resolve these surfaces and their attendant thermal energy regimes. Additionally, very fine scale spatial resolution thermal infrared data, such as that obtained from aircraft, are very useful for demonstrating to planning officials, policy makers, and the general populace, what the benefits are of the urban forest in both mitigating the urban heat island effect, in making cities more aesthetically pleasing and more habitable environments, and in overall cooling of the community. In this presentation we will examine the techniques of analyzing remotely sensed data for measuring the effect of various urban surfaces on their contribution to the urban heat island effect.
The Use of ATLAS Data to Quantify Surface Radiative Budget Alteration Through Urbanization for San Juan, Puerto Rico.
The additional heating of the air over the city is the result of the replacement of naturally vegetated surfaces with those composed of asphalt, concrete, rooftops and other manmade materials. The temperatures of these artificial surfaces can be 20 to 40 0 C higher than vegetated surfaces. Materials such as asphalt store much of the sun s energy and remains hot long after sunset. This produces a dome of elevated air temperatures 5 to 8 C greater over the city, compared to the air temperatures over adjacent rural areas. This effect is called the "urban heat island". Urban landscapes are a complex mixture of vegetated and nonvegetated surfaces. It is difficult to take enough temperature measurements over a large city area to characterize the complexity of urban radiant surface temperature variability. However, the use of remotely sensed thermal data from airborne scanners are ideal for the task. The NASA Airborne Thermal and Land Applications Sensor (ATLAS) operates in the visual and IR bands was used in February 2004 to collect data from San Juan, Puerto Rico with the main objective of investigating the Urban Heat Island (UHI) in tropical cities. In this presentation we will examine the techniques of analyzing remotely sensed data for measuring the effect of various urban surfaces on their contribution to the urban heat island effect. Results from data collected from other US cities of Sacramento, Salt Lake City and Baton Rouge will be used to compare the "urban fabric" among the cities.
Analysis of The Surface Radiative Budget Using ATLAS Data for San Juan, Puerto Rico
The additional beating of the air over the city is the result of the replacement of naturally vegetated surfaces with those composed of asphalt, concrete, rooftops and other man-made materials. The temperatures of these artificial surfaces can be 20 to 40 C higher than vegetated surfaces. This produces a dome of elevated air temperatures 5 to 8 C greater over the city, compared to the air temperatures over adjacent rural areas. Urban landscapes are a complex mixture of vegetated and nonvegetated surfaces. It is difficult to take enough temperature measurements over a large city area to characterize the complexity of urban radiant surface temperature variability. The NASA Airborne Thermal and Land Applications Sensor (ATLAS) operates in the visual and IR bands was used in February 2004 to collect data from San Juan, Puerto Rico with the main objective of investigating the Urban Heat Island (UHI) in tropical cities.
A mixture parameterized biologically based dosimetry model to predict body burdens of polycyclic aromatic hydrocarbons in developmental zebrafish toxicity assays
Polycyclic aromatic hydrocarbons (PAHs) are a group of environmental toxicants found ubiquitously as complex mixtures in human-impacted environments. Developmental zebrafish exposures have been used widely to study PAH toxicity, but most studies report nominal exposure concentrations. Nominal exposure concentrations can be unreliable dose metrics due to differences in toxicant bioavailability resulting from disparate exposure methodologies and chemical properties. Toxicokinetic modeling can predict toxicant tissue doses to facilitate comparison between exposures of different chemicals, methodologies, and biological models. We parameterize a biologically based dosimetry model for developmental zebrafish toxicity assays for 9 PAHs. The model was optimized with measurements from media, tissue, and plastic plate walls throughout a static developmental exposure to a mixture of 10 PAHs of high abundance within the Portland Harbor Superfund Site. Plate binding, volatilization, zebrafish permeability, and tissue—media partitioning coefficients vary widely between PAHs. Model predictions accounted for 83% and 54% of 48 hpf body burdens within a factor of 2 resulting from exposures to mixtures and individual PAHs, respectively. Accounting for solubility significantly improves model performance. Competition for active sites in metabolizing enzymes may change biotransformation kinetics between individual PAH and mixture exposures. Area under the curve estimations of concentrations in zebrafish resulted in altered hazard rankings from nominal exposure concentrations. Future work will be oriented to generalizing the model to other PAHs. This PAH dosimetry model improves the interpretability of developmental zebrafish toxicity assays by providing time-resolved body burdens from nominal exposure concentrations.
Quantitative Separation of Unknown Organic–Metal Complexes by Liquid Chromatography–Inductively Coupled Plasma-Mass Spectrometry
Dissolved organic matter (DOM) is widely recognized to control the solubility and reactivity of trace metals in the environment. However, the mechanisms that govern metal-DOM complexation remain elusive, primarily due to the analytical challenge of fractionating and quantifying metal–organic species within the complex mixture of organic compounds that comprise DOM. Here, we describe a quantitative method for fractionation and element-specific detection of organic–metal complexes using liquid chromatography with online inductively coupled plasma mass spectrometry (LC–ICP-MS). The method implements a post-column compensation gradient to stabilize ICP–MS elemental response across the LC solvent gradient, thereby overcoming a major barrier to achieving quantitative accuracy with LC–ICP-MS. With external calibration and internal standard correction, the method yields concentrations of organic–metal complexes that were consistently within 6% of their true values, regardless of the complex’s elution time. We used the method to evaluate the effects of four stationary phases (C18, phenyl, amide, and pentafluoroylphenyl propyl) on the recovery and separation of environmentally relevant trace metals (Mn, Fe, Co, Ni, Cu, Zn, Cd, and Pb) in Suwannee River Fulvic Acid and Suwannee River Natural Organic Matter. The C18, amide, and phenyl phases generally yielded optimal metal recoveries (>75% for all metals except Pb), with the phenyl phase separating polar species to a greater extent than C18 or amide. We also fractionated organic-bound Fe, Cu, and Ni in oxidized and reduced soils, revealing divergent metal-DOM speciation across soil redox environments. Finally, by enabling quantitative fractionation of DOM-bound metals, our method offers a means for advancing a mechanistic understanding of metal–organic complexation throughout the environment.