Yassin A. Jeilani

Positive chemical ionization triple-quadrupole mass spectrometry and ab initio computational studies of the multi-pathway fragmentation of phthalates

We report the first positive chemical ionization (PCI) fragmentation mechanisms of phthalates using triple-quadrupole mass spectrometry and ab initio computational studies using density functional theories (DFT). Methane PCI spectra showed abundant [M + H](+), together with [M + C(2)H(5)](+) and [M + C(3)H(5)](+). Fragmentation of [M + H](+), [M + C(2)H(5)](+) and [M + C(3)H(5)](+) involved characteristic ions at m/z 149, 177 and 189, assigned as protonated phthalic anhydride and an adduct of phthalic anhydride with C(2)H(5)(+) and C(3)H(5)(+), respectively. Fragmentation of these ions provided more structural information from the PCI spectra. A multi-pathway fragmentation was proposed for these ions leading to the protonated phthalic anhydride. DFT methods were used to calculate relative free energies and to determine structures of intermediate ions for these pathways. The first step of the fragmentation of [M + C(2)H(5)](+) and [M + C(3)H(5)](+) is the elimination of [R-H] from an ester group. The second ester group undergoes either a McLafferty rearrangement route or a neutral loss elimination of ROH. DFT calculations (B3LYP, B3PW91 and BPW91) using 6-311G(d,p) basis sets showed that McLafferty rearrangement of dibutyl, di(-n-octyl) and di(2-ethyl-n-hexyl) phthalates is an energetically more favorable pathway than loss of an alcohol moiety. Prominent ions in these pathways were confirmed with deuterium labeled phthalates.

Radical Pathways for the Prebiotic Formation of Pyrimidine Bases from Formamide

The prebiotic formation of nucleobases, the building blocks of RNA/DNA, is of current interest. Highly reactive radical species present in the atmosphere under irradiation have been suggested to be involved in the prebiotic synthesis of nucleobases from formamide (FM). We studied several free radical reaction pathways for the synthesis of pyrimidine bases (cytosine, uracil, and thymine) from FM under cold conditions. These pathways are theoretically determined using density functional theory (DFT) computations to examine their kinetic and thermodynamic feasibilities. These free radical reaction pathways share some common reaction types such as H-rearrangement, (•)H/(•)OH/(•)NH2 radical loss, and intramolecular radical cyclization. The rate-determining steps in these pathways are characterized with low energy barriers. The energy barriers of the ring formation steps are in the range of 3-7 kcal/mol. Although DFT methods are known to significantly underestimate the barriers for addition of (•)H radical to neutral species, many of these reactions are highly exergonic with energy release of -15 to -52 kcal/mol and are thus favorable. Among the suggested pathways for formation of cytosine (main route, routes 7a and 1a), uracil (main route, routes 7b and 1b), and thymine (main route and route 26a), the main routes are in general thermodynamically more exergonic and more kinetically favored than other alternative routes with lower overall energy barriers. The reaction energies released following formation of cytosine, uracil, and thymine from FM via the main radical routes amount to -59, -81, and -104 kcal/mol, respectively. Increasing temperature induces unfavorable changes in both kinetic and thermodynamic aspects of the suggested routes. However, the main routes are still more favored than the alternative pathways at the temperature up to the boiling point of FM.

Prebiotic synthesis of triazines from urea: a theoretical study of free radical routes to melamine, ammeline, ammelide and cyanuric acid

Prebiotic formation of triazines from urea was studied using density functional theory methods with the aim of understanding some of the neutral precursors that can lead to a mixture of triazines. The proposed mechanisms are based on free radical routes without solvent requirements that are appropriate for prebiotic scenarios occurring under highly non-equilibrium conditions. These include spark discharge or ultraviolet driven reactions taking place on or within low temperature ice or reactions simulated by meteoritic impact on organic surfaces on Titan and possibly early Earth. The ice increases radical lifetimes while the impact events produce sufficient heat to generate useful free radical densities in the impact zones. The mechanisms proceed through relatively low energy barriers. The pathways predict that biuret is a precursor for cyanuric acid, and guanylurea is a precursor for both melamine and ammeline. Based on the predicted precursors of the triazines, the established mechanisms provide theoretical support for previous thermal synthesis of the triazines from urea and biuret.

Hydrogen rearrangement and ring cleavage reactions study of progesterone by triple quadrupole mass spectrometry and density functional theory.

The fragmentation mechanisms of progesterone have been studied by triple quadrupole tandem mass spectrometry (MSMS) and density functional theory (DFT). Mechanisms leading to major product ions are proposed. The data suggest that progesterone fragments preferentially via hydrogen and other rearrangements lead to neutral losses. These fragmentations are quite complex and are preceded by σ-bond cleavages in most cases. Four major pathways for progesterone fragmentation are proposed involving: (1) cleavage of ring B at C9-C10, (2) cleavage of C6-C7 bond in ring B through m/z 191, (3) two types of cleavages of ring D, and (4) ketene elimination in ring A. Pathways (1)-(3) proceed via charge-remote fragmentations while pathway (4) proceeds via charge-site initiated mechanism. The geometry of product ions in these pathways were optimized using DFT at the B3LYP/6-311G(d,p) level of theory from which the free energies of the pathways were calculated. The effect that the choice of basis sets and density functionals has on the results was tested by performing additional calculations using B3LYP/6-31G(d) and B3PW91/6-311G(d,p).

Tandem mass spectrometry and density functional theory of RDX fragmentation pathways: Role of ion-molecule complexes in loss of NO3 and lack of molecular ion peak.

RATIONALE Hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) is an explosive compound that finds a wide range of military and civilian applications. RDX has been a target in environmental matrices by gas chromatography/tandem mass spectrometry (GC/MS/MS). MS/MS in negative chemical ionization (NCI) mode of RDX provides important fragmentation patterns that are useful for structural elucidation. The fragmentation patterns are needed for proper identification of precursor and product ions in analytical methods that depend on MS/MS approaches for a reliable identification of RDX. METHODS This study focuses on the MS fragmentation mechanisms of RDX in NCI mode using both MS/MS and density functional theory (DFT). The DFT studies were performed at the B3LYP/6-311G(d,p) level of theory. RESULTS The DFT results showed that NCI of RDX leads to the formation of an anion-molecule complex that was energetically more stable than the RDX anion. The fragmentation proceeds through two pathways, leading to the loss of NO(2) and NO(3). The loss of NO(3) takes place in an anion-molecule complex leading to the formation of characteristic nitroso group fragment ions. Using the fragmentation schemes, important ion structures are proposed including structures for m/z 160, 129, 102, and 86. CONCLUSIONS The results demonstrate the importance of both charge-induced and charge-remote dissociations in RDX pathways. The ion structures identified along the pathways could be used as targets in analytical methods for reliable identification purposes.

Assessing Bioremediation of Acid Mine Drainage in Coal Mining Sites Using a Predictive Neural Network-Based Decision Support System (NNDSS)

In this study, an Artificial Neural Network (ANN) was developed as a predictive tool for identifying optimal remediation conditions for groundwater contaminants that include selected metals found at coal mining sites. The ANN was developed from a previous field data obtained from a bioremediation project at an abandoned mine at Cane Creek in Alabama, and from a coal pile run off at a Department of Energy’s site in Aiken, South Carolina. The evaluative parameters included pH, redox, nutrients, bacterial strain (MRS-1), and type of microbial growth process (aerobic, anaerobic or sequential aerobic-anaerobic conditions). Using the conditions predicted by the Neural Networks, significant levels of As, Pb, and Se were precipitated and removed over eight days in remediation assays containing 10 mg/L of each metal in cultures that include MRS-1. The results showed 85%, 100%, and 87% reductions of As, Pb, and Se, respectively. The results from these ANN- driven assays are significant. It provides a roadmap for reducing the technical risks and uncertainties in clean-up programs. Continuous success in these efforts will require a strong and responsive research that provides a decision support system for long-term restoration efforts.

Reaction Routes for Experimentally Observed Intermediates in the Prebiotic Formation of Nucleobases under High-Temperature Conditions

The prebiotic synthesis of nucleobases is of particular interest, given the experimental evidence that indicated formation of the nucleobases under abiotic conditions on the Early Earth under high-temperature conditions. Biomolecules have been formed under meteoritic impact scenarios that lead to high temperature and the generation of high energy. Free radical pathways for the formation of biomolecules are appropriate under these conditions. Density functional theory computations were used to study the free radical routes for the formation of nucleobases at the UB3LYP/6-311G(d,p) level. We have found that both 5-aminoimidazole-4-carboxamide (AICA) and 5-(formylamino)imidazole-4-carboxamide (fAICA) are formed first from formamide then the nucleobases are formed. Calculated results show the radical reaction routes of AICA as a precursor for guanine. Both hypoxanthine and xanthine are formed from radical pathways of fAICA. In addition, generation of imino-AICA and imino-fAICA has been shown for the first time to be needed for the production of adenine, purine, and isoguanine. Formation of hypoxanthine and adenine/purine from fAICA and imino-fAICA, respectively, is consistent with experiments performed nearly seven decades ago.

Collision induced dissociations of non‐derivatized and trimethylsilyl‐derivatized estradiols: similarities in fragmentation patterns

Fragmentation mechanisms of estradiol and trimethylsilyl (TMS)-derivatized estradiol were studied by triple quadrupole tandem mass spectrometry (MSMS) and density functional theory (DFT) at B3LYP/6-311G(d,p) level. Collision induced dissociations (CID) of estradiol give product ions that are associated with the cleavage of B, C and D rings. Characteristic fragments from the cleavage of the aromatic ring A were not identified, and this was confirmed with both labeled estradiol and trimethylsilyl (TMS)-derivatized estradiol. The mechanisms are based on charge-site directed, radical-directed and charge remote fragmentations that are consistent with previous studies of steroids. CID spectra show ion pairs at m/z: 145/146, 157/158, 185/186, 211/213 and 225/226 with significant intensities, suggesting that these pairs are not from isotopic contributions. The mechanisms show similarities with some minor differences in the fragmentation patterns between the non-derivatized and the TMS-derivatized estradiol.