Generation of α-acetolactone and the acetoxyl diradical •CH2COO• in the gas phase

Catalytic Properties of Caseinolytic Protease Subunit of Plasmodium knowlesi and Its Inhibition by a Member of δ-Lactone, Hyptolide

The caseinolytic protease (Clp) system plays an essential role in the protein homeostasis of the malaria parasite, particularly at the stage of apicoplast development. The inhibition of this protein is known to have a lethal effect on the parasite and is therefore considered an interesting avenue for antimalaria drugs discovery. The catalytic activity of the Clp system is modulated by its proteolytic subunit (ClpP), which belongs to the serine protease family member and is therefore extensively studied for further inhibitors development. Among many inhibitors, the group of β-lactone is known to be a specific inhibitor for ClpP. Nevertheless, other groups of lactones have never been studied. This study aims to characterize the catalytic properties of ClpP of Plasmodium knowlesi (Pk-ClpP) and the inhibition properties of a δ-lactone hyptolide against this protein. Accordingly, a codon-optimized synthetic gene encoding Pk-ClpP was expressed in Escherichia coli BL21(DE3) and purified under a single step of Ni²⁺-affinity chromatography, yielding a 2.20 mg from 1 L culture. Meanwhile, size-exclusion chromatography indicated that Pk-ClpP migrated primarily as homoheptameric with a size of 205 kDa. The specific activity of pure Pk-ClpP was 0.73 U µg^-1, with a catalytic efficiency k_cat/K_M of 0.05 µM^-1 s^-1, with optimum temperature and pH of 50 °C and 7.0-7.5, respectively. Interestingly, hyptolide, a member of δ-lactone, was shown to inhibit Pk-ClpP with an IC₅₀ value of 17.36 ± 1.44 nM. Structural homology modelling, secondary structure prediction, and far-UV CD spectra revealed that helical structures dominate this protein. In addition, the structural homology modeling showed that this protein forms a barrel-shaped homoheptamer. Docking simulation revealed that the inhibition was found to be a competitive inhibition in which hyptolide was able to dock into the catalytic site and block the substrate. The competitiveness of hyptolide is due to the higher binding affinity of this molecule than the substrate.

Regio- and sequence-controlled conjugated topological oligomers and polymers via boronate-tag assisted solution-phase strategy

The regulation of polymer topology and the precise control over the monomer sequence is crucial and challenging in polymer science. Herein, we report an efficient solution-phase synthetic strategy to prepare regio- and sequence-controlled conjugated polymers with topological variations via the usage of methyliminodiacetic acid (MIDA) boronates. Based on the solubility of MIDA boronates and their unusual binary affinity for silica gel, the synthesized regio- and sequence-defined conjugated oligomers can be rapidly purified via precipitation or automatic liquid chromatography. These synthesized discrete oligomers can be used for iterative exponential and sequential growth to obtain linear and dendrimer-like star polymers. Moreover, different topological sequence-controlled conjugated polymers are conveniently prepared from these discrete oligomers via condensation polymerization. By investigating the structure-property relationship of these polymers, we find that the optical properties are strongly influenced by the regiochemistry, which may give inspiration to the design of optoelectronic polymeric materials.

Structure Elucidation of the spiro-Polyketide Svalbardine B from the Arctic Fungal Endophyte Poaceicola sp. E1PB with Support from Extensive ESI-MSn Interpretation

Svalbardines A and B (1 and 2) and annularin K (3) were isolated from cultures of Poaceicola sp. E1PB, an endophyte isolated from the petals of Papaver dahlianum from Svalbard, Norway. Svalbardine A (1) is a pyrano[3,2-c]chromen-4-one, a new analogue of citromycetin. Svalbardine B (2) displays an unprecedented carbon skeleton based on a 5'-benzyl-spiro[chroman-3,7'-isochromene]-4,8'-dione core. Annularin K (3) is a hydroxylated derivative of annularin D. The structure of these new polyketides, along with those of known compounds 4-6, was established by spectrometric analysis, including extensive ESI-CID-MSⁿ processing in the case of svalbardine B (2).

Carbon monoxide formation from trimethylamine-boranecarboxylate: DFT studies of SNi and chelotropic mechanisms

Trimethylamine-boranecarboxylic acid (CH₃)₃N-BH₂COOH and other amine carboxyboranes have been observed to undergo slow decarbonylation in neutral aqueous solution. This reaction, when it occurs in vivo, may have a therapeutic effect by delivering low concentrations of carbon monoxide over an extended period. In order to identify a possible mechanistic pathway for decarbonylation, the smallest tertiary amine derivative and its corresponding carboxylate ion were studied using CCSD(T)/PCM/6-311++G(2d,p)//M06-2X/PCM/6-311++G(2d,p) model chemistry. The proposed mechanistic pathway begins with a trimethylamine boranecarboxylate ion, which first undergoes an internal substitution reaction (S_Ni) to give free amine and the carboxyborane anion BH₂COO⁻. The latter cyclic ion then releases CO via a rapid chelotropic fragmentation. The role of water solvent in these reactions was explored by structural and energetic analysis of hydrogen-bonded complexes. It was found that complexation with water inhibits dissociation of trimethylamine by stabilizing the trimethylamine carboxyborane anion, whereas water accelerates CO loss by stabilizing the polar chelotropic transition state.

According to a DFT model, CO is formed from trimethylamine boranecarboxylate, a carbon monoxide releasing molecular pro-drug (CORM), via initial S_Ni subsitution followed by chelotropic fragmentation of the resulting cyclic carboxyborane anion.

Competing fragmentation processes of β-substituted propanoate ions upon collision-induced dissociation

RATIONALE

When subjected to collisional activation, gas-phase carboxylate ions typically undergo decarboxylation. However, alternative fragmentation processes dominate when the carboxylate group is located within certain structural motifs. In this work, the fragmentation processes of β-substituted carboxylate ions are characterized to improve correlations between reactivity and structure.

METHODS

Mass spectra were collected using both ion trap and triple quadrupole mass spectrometers operating in the negative ion mode; collision-induced dissociation (CID) of ions was used to study the relationship between product ions and the structures of their precursor ions. Quantum mechanical computations were performed on a full range of reaction geometries at the MP2/6-311++G(2d,p)//B3LYP/6-31++G(2d,p) level of theory.

RESULTS

For a series of β-substituted carboxylate ions, a product ion corresponding to the anion of the β-substituent was obtained upon CID. Detailed computations indicated that decarboxylative elimination and at least one other fragmentation mechanism had feasible energetics for the formation of substituent anions differing in their gas-phase basicities. Predicted energetics for anti- and synperiplanar alignments in the transition structures for decarboxylative elimination correlated with the positions of crossover points in breakdown curves acquired for conformationally constrained ions.

CONCLUSIONS

The feasibility of more than one mechanism was established for the fragmentation of β-substituted propanoates. The contribution of each mechanistic pathway to the formation of the substituent anion was influenced by structural variations and conformational constraints, but mostly depended on the nature of the substituent. Copyright © 2016 John Wiley & Sons, Ltd.

Phenyl group participation in rearrangements during collision-induced dissociation of deprotonated phenoxyacetic acid

RATIONALE

The identification of trace constituents in biological and environmental samples is frequently based on the fragmentation patterns resulting from the collision-induced dissociation (CID) of gas-phase ions. Credible mechanistic characterization of fragmentation processes, including rearrangements, is required to make reliable assignments for structures of precursor and product ions.

METHODS

Mass spectra were collected using both ion trap and triple quadrupole mass spectrometers operating in the negative ion mode. Precursor ion scans and CID of ions generated in-source were used to establish precursor-product ion relationships. Density functional theory (DFT) computations were performed at the MP2/6-311++G(2d,p)//B3LYP/6-31++G(2d,p) level of theory.

RESULTS

Product ions at m/z 93 and 107 obtained upon CID of phenoxyacetate were attributed to phenoxide and o-methylphenoxide, respectively. An isotopic labeling experiment and computations showed that the phenoxide ion was formed by intramolecular displacement with formation of an α-lactone and also by a Smiles rearrangement. Rearrangement of phenoxyacetate via the ion-neutral complex formed in the α-lactone displacement pathway gave the isomeric o-hydroxyphenylacetate ion which yielded o-methylphenoxide upon decarboxylation. Computations provided feasible energetics for these pathways.

CONCLUSIONS

Previously unrecognized and energetically favorable rearrangements during the collision-induced fragmentation of phenoxyacetate have been characterized using isotopic labeling and DFT computations. Notably, the phenyl substituent plays an indispensable role in each rearrangement process resulting in multiple pathways for the fragmentation of phenoxyacetate.

Three-membered ring amides — a calculational and conceptual study of the structure and energetics of 1,2-oxaziridine-3-one and aziridine-2,3-dione

Species with three-membered rings and the amide linkage are well studied. A quick perusal of the literature with SciFinder finds some 50 000 references to cyclopropanes and almost 300 000 references to amides. In the current paper, we discuss the structure and energetics of two understudied three-membered ring amides, 1,2-oxaziridine-3-one (5) (simultaneously describable as the simplest cyclic carbamate and simplest hydroxamate) and aziridine-2,3-dione (7) (simultaneously describable as the simplest imide and simplest α-ketoamide), with but 5 and nearly 10 references, respectively, for these two classes of compounds. Neither 1,2-oxaziridine-3-one (5) nor aziridine-2,3-dione (7), nor any derivative thereof, has been isolated. Calculational theory ameliorates the paucity of experimental information. The current study reports our computational findings for these and related species (e.g., enols and imidols) where we have used the G3(MP2)//B3LYP method.

Unusual hydroxyl migration in the fragmentation of β-alanine dication in the gas phase

Experimental and theoretical investigations show that hydroxyl migration leads to unexpected fragmentation dynamics of β-alanine dication in the gas phase.

Experimental investigation of the absolute enthalpies of formation of 2,3-, 2,4-, and 3,4-pyridynes

The absolute enthalpies of formation of 3,4-, 2,3-, and/or 2,4-didehydropyridines (3,4-, 2,3- and 2,4-pyridynes) have been determined by using energy-resolved collision-induced dissociation of deprotonated 2- and 3-chloropyridines. Bracketing experiments find the gas-phase acidities of 2- and 3-chloropyridines to be 383 ± 2 and 378 ± 2 kcal/mol, respectively. Whereas deprotonation of 3-chloropyridine leads to formation of a single ion isomer, deprotonation of the 2-chloro isomer results in a nearly 60:40 mixture of regioisomers. The enthalpy of formation of 3,4-pyridyne is measured to be 121 ± 3 kcal/mol by using the chloride dissociation energy for deprotonated 3-chloropyridine. The structure of the product formed upon dissociation of the ion from 2-chloropyridine cannot be unequivocally assigned because of the isomeric mixture of reactant ions and the fact that the potential neutral products (2,3-pyridyne and 2,4-pyridyne) are predicted by high level spin-flip coupled-cluster calculations to be nearly the same in energy. Consequently, the enthalpies of formation for both neutral products are assigned to be 130 ± 3 kcal/mol. Comparison of the enthalpies of dehydrogenation of benzene and pyridine indicates that the nitrogen in the pyridine ring does not have any effect on the stability of the aryne triple bond in 3,4-pyridyne, destabilizes the aryne triple bond in 2,3-pyridyne, and stabilizes the 1,3-interaction in 2,4-pyridyne compared to that in m-benzyne. Natural bond order calculations show that the effects on the 2,3- and 2,4-pyridynes result from polarization of the electrons caused by interaction with the lone pair. The polarization in 2,4-pyridyne is stabilizing because it creates a 1,2-interaction between the nitrogen and dehydrocarbons that is stronger than the 1,3-interaction between the dehydrocarbons.

Gas-phase fragmentation of deprotonated p-hydroxyphenacyl derivatives

Electrospray ionization of methanolic solutions of p-hydroxyphenacyl derivatives HO-C(6)H(4)-C(O)-CH(2)-X (X = leaving group) provides abundant signals for the deprotonated species which are assigned to the corresponding phenolate anions (-)O-C(6)H(4)-C(O)-CH(2)-X. Upon collisional activation in the gas phase, these anions inter alia undergo loss of a neutral "C(8)H(6)O(2)" species concomitant with formation of the corresponding anions X(-). The energies required for the loss of the neutral roughly correlate with the gas phase acidities of the conjugate acids (HX). Extensive theoretical studies performed for X = CF(3)COO in order to reveal the energetically most favorable pathway for the formation of neutral "C(8)H(6)O(2)" suggest three different routes of similar energy demands, involving a spirocyclopropanone, epoxide formation, and a diradical, respectively.

Mild route to generate gaseous metal anions

Gaseous metal anions such as Na(-), K(-), Cs(-), and Ag(-) can be generated at ambient temperatures by the collision-induced dissociation of the anions of several dicarboxylic acid salts, including oxalate, maleate, fumarate, succinate, and glutamate salts. The formation of gaseous metal anions in this way is unprecedented because the metal is initially present in its cationic form. The mild process described here could facilitate novel applications of metal anions as selective reagents for gas-phase ion-molecule and ion-ion reactions. Ab initio calculations were used to describe the dissociation process for anions of the oxalate salts. The formation of alkalides occurs via production of a metal-carbon dioxide anion intermediate with a bidentate three-center two-electron bond to the metal. The metal atom acquires a partial negative charge in the intermediate structure.

Reaction pathways of 2-iodoacetic acid on Cu(100): coverage-dependent competition between C-I bond scission and COOH deprotonation and identification of surface intermediates

The chemistry of 2-iodoacetic acid on Cu(100) has been studied by a combination of reflection-absorption infrared spectroscopy (RAIRS), X-ray photoelectron spectroscopy (XPS), temperature-programmed reaction/desorption (TPR/D), and theoretical calculations based on density functional theory for the optimized intermediate structures. In the thermal decomposition of ICH(2)COOH on Cu(100) with a coverage less than a half monolayer, three surface intermediates, CH(2)COO, CH(3)COO, and CCOH, are generated and characterized spectroscopically. Based on their different thermal stabilities, the reaction pathways of ICH(2)COOH on Cu(100) at temperatures higher than 230 K are established to be ICH(2)COOH --> CH(2)COO + H + I, CH(2)COO + H --> CH(3)COO, and CH(3)COO --> CCOH. Theoretical calculations suggest that the surface CH(2)COO has the skeletal plane, with delocalized pi electrons, approximately parallel to the surface. The calculated Mulliken charges agree with the detected binding energies for the two carbon atoms in CH(2)COO on Cu(100). The CCOH derived from CH(3)COO decomposition has a CC stretching frequency at 2025 cm(-1), reflecting its triple-bond character which is consistent with the calculated CCOH structure on Cu(100). Theoretically, CCOH at the bridge and hollow sites has a similar stability and is adsorbed with the molecular axis approximately perpendicular to the surface. The TPR/D study has shown the evolution of the products of H(2), CH(4), H(2)O, CO, CO(2), CH(2)CO, and CH(3)COOH from CH(3)COO decomposition between 500 and 600 K and the formation of H(2) and CO from CCOH between 600 and 700 K. However, at a coverage near one monolayer, the major species formed at 230 and 320 K are proposed to be ICH(2)COO and CH(3)COO. CH(3)COO becomes the only species present on the surface at 400 K. That is, there are two reaction pathways of ICH(2)COOH --> ICH(2)COO + H and ICH(2)COO + H --> CH(3)COO + I (possibly via CH(2)COO), which are different from those observed at lower coverages. Because the C-I bond dissociation of iodoethane on copper single crystal surfaces occurs at approximately 120 K and that the deprotonation of CH(3)COOH on Cu(100) occurs at approximately 220 K, the preferential COOH dehydrogenation of monolayer ICH(2)COOH is an interesting result, possibly due to electronic and/or steric effects.

Competition of electron transfer, dissociation, and bond-forming processes in the reaction of the CO(2)(2+) dication with neutral CO(2)

The bimolecular reactivity of the CO(2)(2+) dication with neutral CO(2) is investigated using triple quadrupole and ion-ion coincidence mass spectrometry. Crucial for product analysis is the use of appropriate isotope labelling in the quadrupole experiments in order to distinguish the different reactive pathways. The main reaction corresponds to single-electron transfer from the neutral reagent to the dication, i.e. CO(2)(2+) + CO(2) --> 2CO(2)(+); this process is exothermic by almost 10 eV, if ground state monocations are formed. Interestingly, the results indicate that the CO(2)(+) ion formed when the dication accepts an electron dissociates far more readily than the CO(2)(+) ion formed from the neutral CO(2) molecule. This differentiation of the two CO(2)(+) products is rationalized by showing that the population of the key dissociative states of the CO(2)(+) monocation will be favoured from the CO(2)(2+) dication rather than from neutral CO(2). In addition, two bond-forming reactions are observed as minor channels, one of which leads to CO(+) and O(2)(+) as ionic products and the other affords a long-lived C(2)O(3)(2+) dication.

The effect of carbonyl substitution on the strain energy of small ring compounds and their six-member ring reference compounds

High level ab initio calculations have been applied to the estimation of ring strain energies (SE) of a series of three- and six-member ring compounds. The SE of cyclohexane has been estimated to be 2.2 kcal/mol at the CBS-APNO level of theory. The SE of cyclopropane has been increased to 28.6 kcal/mol after correction for the one-half of the SE of cyclohexane. The SEs of a series of carbonyl-containing three-member ring compounds have been estimated at the CBS-Q level by their combination with cyclopropane to produce a six-member ring reference compound. The SEs of cyclopropanone (5), the simplest alpha-lactone (6) [oxiranone], and alpha-lactam (7) [aziridinone] have been predicted to be 49, 47, and 55 kcal/mol, respectively, after correction for the SE of the corresponding six-member ring reference compound. The SEs of cyclohexanone, delta-valerolactone, and delta-valerolactam have been estimated to be 4.3, 11.3, and 5.1 kcal/mol, respectively. Marked increases in the SE of silacyclopropane and siladioxirane have been established, while significant decreases in the SEs of phosphorus, sulfur, dioxa- and diaza-containing three-member ring compounds were observed. The ring strain energies of the hydrocarbons (but not heterocycles) exhibit a strong correlation with their C-H bond dissociation energies.