A reinvestigation of the boron cluster B15+/0/-: a benchmark of density functionals and consideration of aromaticity models.

This study presents a thorough reinvestigation of the B15+/0/- isomers, first employing coupled-cluster theory CCSD(T) calculations to validate the performance of different DFT functionals. The B15+ cation has two planar lowest-lying isomers, while the first 3D isomer is less stable than the global minimum by ∼10 kcal mol-1. The PBE functional, within this benchmark survey, has proved to be reliable in predicting relative energies for boron isomers. Other functionals such as the TPSSh, PBE0 and HSE06 result in good energy ordering of isomers but warrant reconsideration when distinguishing between 2D and 3D forms. Caution is needed for structures having high spin contamination, as it may lead to significant errors. The anomalously lower stability of the B15- anion with respect to its neighbours, in terms of electron detachment energy, was explained through a competition between both rectangle and disk models for its geometry. This elucidates its stability with 12 electrons in rectangle model and instability with 10 electrons in disk-shaped structure, emphasizing the value of employing such geometric models. The proximity of the σ* LUMO to the π HOMO also contributes to the weakening of the B15- stability.

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.

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.

Acetylene as an essential building block for prebiotic formation of pyrimidine bases on Titan.

Prebiotic building blocks for the formation of biomolecules are important in understanding the abiotic origin of biomolecules. However, there is a limited choice of the building blocks as precursors for the biomolecules. Acetylene (HCCH) is found in Titan's atmosphere and is an abiotic-precursor of pyrimidine bases. HCCH reacts with urea to form both cytosine and uracil. The mechanisms for the formation of both cytosine and uracil were studied by density functional theory at B3LYP/6-311G(d,p) level. Ethynyl radicals (˙CCH) are relevant for the chemistry of Titan's atmosphere therefore both HCCH and ˙CCH were evaluated as carbon sources. The pathways, for both HCCH and ˙CCH, lead to intermediates with an unsaturated-group that facilitate the formation of the six-membered ring of the pyrimidine bases. The predicted structures for cytosine and uracil were compared with labeled cytosine and uracil that were formed from the reaction of DCCD with urea. The results suggest that cytosine is formed from HCCH while uracil is formed from ˙CCH. The mechanisms are energetically feasible and there is no conclusive evidence for the preferred pathway (HCCH or ˙CCH). The pathways were further extended for the formation of both uric acid and 8-oxoguanine from HCCH and urea, and demonstrate the utility of HCCH as a carbon source for diverse biomolecules. Biuret is identified as a precursor for the pyridimine bases, and it unifies the free radical pathways for the pyrimidine bases with those of triazines. The pathways are appropriate for the reducing atmosphere that creates both radicals and electrons due to ionizing radiation on Titan. The mechanisms are feasible for the extraterrestrial formation of the pyrimidine bases.

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.

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.

Free radical routes for prebiotic formation of DNA nucleobases from formamide.

Modeling the complicated chemical reactions in the interstellar medium and surface materials of Titan is nontrivial. Since both the atmosphere and the surface are rich in organic molecules, the chemistry may have important implications for the origin of biomolecules. Prebiotic synthesis of DNA nucleobases from simple molecules such as formamide has been known for more than half a century. In this study, new free radical pathways leading to the synthesis of guanine, hypoxanthine, purine, and adenine have been studied using density functional theory (B3LYP with the 6-311G(d,p) basis set). The pathways of the selected nucleobases demonstrate the importance of free radicals in the production of useful biomolecules under conditions appropriate for the interstellar medium or on Titan. The pathways may be universal in nature and proceed without solvent requirements. Calculations indicate that radical pathways yield lower reaction barriers as compared to previously reported pathways. Overall, these results suggest that the chemistry on Titan's surface and/or the growth of organic particulates in the haze layers in Titan's atmosphere likely involve free radicals. The mechanisms demonstrate that important prebiotic precursors can be predicted. The reaction sequences reported here may lead to the production and build-up of molecules with prebiotic relevance.

Density functional theory and mass spectrometry of phthalate fragmentations mechanisms: modeling hyperconjugated carbocation and radical cation complexes with neutral molecules.

This is the first ab initio study of the energetics of the fragmentation mechanisms of phthalate, by mass spectrometry, leading to protonated phthalic anhydride (m/z 149). Phthalates fragment by two major pathways; namely, the McLafferty + 1 rearrangement and the loss of alkoxy. Both pathways involve a carbonyl oxygen attack to the ortho-carbonyl carbon leading to structures with tetrahedral carbon intermediates that eventually give m/z 149. These pathways were studied by collision induced dissociation (CID) using triple quadrupole mass spectrometry. The proposed McLafferty + 1 pathway proceeds through a distonic M(•+), leading to the loss of an allylic-stabilized alkene radical. The McLafferty rearrangement step proceeds through a six-membered ring transition state with a small activation energy ranging 0.4-6.2 kcal/mol; the transfer of a second H from the distonic ion of the rearrangement step proceeds through a radical cation molecule complex. Based on quantum chemical modeling of the cation molecule complexes, two kinds of cation molecule complexes were identified as radical cation molecule complex and hyperconjugated cation molecule complex. This distinction is based on the cation and simplifies future modeling of similar complexes. Optimization of important fragments in these pathways showed cyclized and hydrogen-bonded structures to be favored. An exception was the optimized structure of the protonated phthalic anhydride (m/z 149) that showed a structure with an open anhydride ring.

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).

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.