The acyl chains of phosphoinositide PIP3 alter the structure and function of nuclear receptor steroidogenic factor-1.

Nuclear receptors are transcription factors that bind lipids, an event that induces a structural conformation of the receptor that favors interaction with transcriptional coactivators. The nuclear receptor steroidogenic factor-1 (SF-1, NR5A1) binds the signaling phosphoinositides PI(4,5)P2 (PIP2) and PI(3,4,5)P3 (PIP3), and our previous crystal structures showed how the phosphoinositide headgroups regulate SF-1 function. However, what role the acyl chains play in regulating SF-1 structure remains unaddressed. Here, we used X-ray crystallography with in vitro binding and functional assays to examine how the acyl chains of PIP3 regulate human SF-1 ligand-binding domain structure and function. Altering acyl chain length and unsaturation regulates apparent binding of all tested phosphoinositides to SF-1. Mass spectrometry-based lipidomics data suggest C16 and C18 phospholipids preferentially associate with SF-1 expressed ectopically in bacteria. We then solved the 2.5 Å crystal structure of SF-1 bound to dioleoyl PIP3(18:1/18:1) to compare it with a matched structure of SF-1 bound to dipalmitoyl PIP3(16:0/16:0). The dioleoyl-bound structure was severely disordered in a specific SF-1 region associated with pathogenic human polymorphisms and within the coactivator-binding region critical for SF-1 function while inducing increased sensitivity to protease digestion in solution. Validating these structural observations, in vitro functional studies showed dioleoyl PIP3 induced 6-fold poorer affinity of a peroxisome proliferator-activated receptor gamma coactivator 1-alpha coactivator peptide for SF-1 compared with dipalmitoyl PIP3. Together, these data suggest the chemical nature of the phosphoinositide acyl chains controls the ordered state of specific, clinically important structural regions in SF-1, regulating SF-1 function in vitro.

Design and Characterization of a Novel Blood Collection and Transportation Device for Proteomic Applications.

A major hurdle for blood-based proteomic diagnostics is efficient transport of specimens from the collection site to the testing laboratory. Dried blood spots have shown utility for diagnostic applications, specifically those where red blood cell hemolysis and contamination of specimens with hemoglobin is not confounding. Conversely, applications that are sensitive to the presence of the hemoglobin subunits require blood separation, which relies on centrifugation to collect plasma/serum, and then cold-chain custody during shipping. All these factors introduce complexities and potentially increased costs. Here we report on a novel whole blood-collection device (BCD) that efficiently separates the liquid from cellular components, minimizes hemolysis in the plasma fraction, and maintains protein integrity during ambient transport. The simplicity of the design makes the device ideal for field use. Whole blood is acquired through venipuncture and applied to the device with an exact volume pipette. The BCD design was based on lateral-flow principles in which whole blood was applied to a defined area, allowing two minutes for blood absorption into the separation membrane, then closed for shipment. The diagnostic utility of the device was further demonstrated with shipments from multiple sites (n = 33) across the U.S. sent to two different centralized laboratories for analyses using liquid chromatography/mass spectrometry (LC/MS/MS) and matrix assisted laser desorption/ionization-time of flight (MALDI-ToF) commercial assays. Specimens showed high levels of result label concordance for the LC/MS/MS assay (Negative Predictive Value = 98%) and MALDI-ToF assay (100% result concordance). The overall goal of the device is to simplify specimen transport to the laboratory and produce clinical test results equivalent to established collection methods.

Gas-Phase Reactions of Deprotonated Nucleobases with H, N, and O Atoms.

Complex organic molecules, the hallmark of terrestrial life, are increasingly detected in exotic environments throughout the universe. Our studies probe the ion chemistry of these biomolecules. We report gas-phase reaction rate constants for five deprotonated nucleobases (adenine, cytosine, guanine, thymine, and uracil) reacting with the atomic species H, N, and O. Hydrogen atoms react at moderate rates via associative electron detachment. Oxygen atom reactions occur more rapidly, generating complex product distributions; reaction pathways include associative electron detachment, substitution of the hydrogen atom by an oxygen atom, and generation of OCN-. Nitrogen atoms do not react with the nucleobase anions. The reaction thermodynamics were investigated computationally, and reported product channels are exothermic. Many of the proposed products have been observed in various astrochemical environments. These reactions provide insight into chemical processes that may occur at the boundaries between diffuse and dense interstellar clouds and in complex extraterrestrial ionospheres.

Untargeted Molecular Discovery in Primary Metabolism: Collision Cross Section as a Molecular Descriptor in Ion Mobility-Mass Spectrometry.

In this work, we established a collision cross section (CCS) library of primary metabolites based on analytical standards in the Mass Spectrometry Metabolite Library of Standards (MSMLS) using a commercially available ion mobility-mass spectrometer (IM-MS). From the 554 unique compounds in the MSMLS plate library, we obtained a total of 1246 CCS measurements over a wide range of biochemical classes and adduct types. Resulting data analysis demonstrated that the curated CCS library provides broad molecular coverage of metabolic pathways and highlights intrinsic mass-mobility relationships for specific metabolite superclasses. The separation and characterization of isomeric metabolites were assessed, and all molecular species contained within the plate library, including isomers, were critically evaluated to determine the analytical separation efficiency in both the mass ( m/ z) and mobility (CCS/ΔCCS) dimension required for untargeted metabolomic analyses. To further demonstrate the analytical utility of CCS as an additional molecular descriptor, a well-characterized biological sample of human plasma serum (NIST SRM 1950) was examined by LC-IM-MS and used to provide a detailed isomeric analysis of carbohydrate constituents by ion mobility.

Photoelectron spectroscopy and thermochemistry of o-, m-, and p-methylenephenoxide anions.

The anionic products following (H + H+) abstraction from o-, m-, and p-methylphenol (cresol) are investigated using flowing afterglow-selected ion flow tube (FA-SIFT) mass spectrometry and anion photoelectron spectroscopy (PES). The PES of the multiple anion isomers formed in this reaction are reported, including those for the most abundant isomers, o-, m- and p-methylenephenoxide distonic radical anions. The electron affinity (EA) of the ground triplet electronic state of neutral m-methylenephenoxyl diradical was measured to be 2.227 ± 0.008 eV. However, the ground singlet electronic states of o- and p-methylenephenoxyl were found to be significantly stabilized by their resonance forms as a substituted cyclohexadienone, resulting in measured EAs of 1.217 ± 0.012 and 1.096 ± 0.007 eV, respectively. Upon electron photodetachment, the resulting neutral molecules were shown to have Franck-Condon active ring distortion vibrational modes with measured frequencies of 570 ± 180 and 450 ± 80 cm-1 for the ortho and para isomers, respectively. Photodetachment to excited electronic states was also investigated for all isomers, where similar vibrational modes were found to be Franck-Condon active, and singlet-triplet splittings are reported. The thermochemistry of these molecules was investigated using FA-SIFT combined with the acid bracketing technique to yield values of 341.4 ± 4.3, 349.1 ± 3.0, and 341.4 ± 4.3 kcal mol-1 for the o-, m-, and p-methylenephenol radicals, respectively. Construction of a thermodynamic cycle allowed for an experimental determination of the bond dissociation energy of the O-H bond of m-methylenephenol radical to be 86 ± 4 kcal mol-1, while this bond is significantly weaker for the ortho and para isomers at 55 ± 5 and 52 ± 5 kcal mol-1, respectively. Additional EAs and vibrational frequencies are reported for several methylphenyloxyl diradical isomers, the negative ions of which are also formed by the reaction of cresol with O-.

Automated flow injection method for the high precision determination of drift tube ion mobility collision cross sections.

The field of ion mobility-based omics studies requires high-quality collision cross section (CCS) libraries to effectively utilize CCS as a molecular descriptor. Absolute CCS values with the highest precision are obtained on drift tube instruments by measuring the drift time of ions at multiple drift voltages, commonly referred to as a 'stepped field' experiment. However, generating large scale absolute CCS libraries from drift tube instruments is time consuming due to the current lack of high-throughput methods. This communication reports a fully automated stepped-field method to acquire absolute CCS on commercially available equipment. Using a drift tube ion mobility-mass spectrometer (DTIM-MS) coupled to a minimally modified liquid chromatography (LC) system, CCS values can be measured online with a carefully timed flow injection analysis (FIA) experiment. Results demonstrate that the FIA stepped-field method yields CCS values which are of high analytical precision (<0.4% relative standard deviation, RSD) and accuracy (≤0.4% difference) comparable to CCS values obtained using traditional direct-infusion stepped-field experiments. This high-throughput CCS method consumes very little sample volume (20 µL) and will expedite the generation of large-scale CCS libraries to support molecular identification within global untargeted studies.

Experimental and Theoretical Studies of the Reactivity and Thermochemistry of Dicyanamide: N(CN)(2)(-).

Dicyanamide [N(CN)2(-)] is a common anionic component of ionic liquids, several of which have shown hypergolic reactivity upon mixing with white-fuming nitric acid. In this study, we explore the thermochemistry of dicyanamide and its reactivity with nitric acid and other molecules to gain insight into the initial stages of the hypergolic phenomenon. We have developed and utilized an electrospray ion source for our selected ion flow tube (SIFT) to generate the dicyanamide anion. We have explored the general reactivity of this ion with several neutral molecules and atoms. Dicyanamide does not show reactivity with O2, H2SO4, H2O2, DBr, HCl, NH3, N2O, SO2, COS, CO2, CH3OH, H2O, CH4, N2, CF4, or SF6 (k < 1 × 10(-12) cm(3)/s); moreover, dicyanamide does not react with N atom, O atom, or electronically excited molecular oxygen (k < 5 × 10(-12) cm(3)/s), and our previous studies showed no reactivity with H atom. However, at 0.45 Torr helium, we observe the adduct of dicyanamide with nitric acid with an effective bimolecular rate constant of 2.7 × 10(-10) cm(3)/s. Intrinsically, dicyanamide is a very stable anion in the gas phase, as illustrated by its lack of reactivity, high electron-binding energy, and low proton affinity. The lack of reactivity of dicyanamide with H2SO4 gives an upper limit for the gas-phase deprotonation enthalpy of the parent compound (HNCNCN; <310 ± 3 kcal/mol). This limit is in agreement with theoretical calculations at the MP2/6-311++G(d,p) level of theory, finding that ΔH298 K(HNCNCN) = 308.5 kcal/mol. Dicyanamide has two different proton acceptor sites. Experimental and computational results indicate that it is lower in energy to protonate the terminal nitrile nitrogen than the central nitrogen. Although proton transfer to dicyanamide was not observed for any of the acidic molecules investigated here, the calculations on dicyanamide with one to three nitric acid molecules reveal that higher-order solvation can favor exothermic proton transfer. Furthermore, the formation of 1,5-dinitrobiuret, proposed to be the key intermediate during the hypergolic ignition of dicyanamide ionic liquids with nitric acid, is investigated by calculation of the reaction coordinate. Our results suggest that solvation dynamics of dicyanamide with nitric acid play an important role in hypergolic ignition and the interactions at the droplet/condensed-phase surface between the two hypergolic liquids are very important. Moreover, dicyanamide exists in the atmosphere of Saturn's moon, Titan; the intrinsic stability of dicyanamide strongly suggests that it may exist in molecular clouds of the interstellar medium, especially in regions where other stable carbon-nitrogen anions have been detected.

Gas-phase acidities of nitrated azoles as determined by the extended kinetic method and computations.

Making use of the extended kinetic method and the alternative method for data analysis, we have experimentally determined ΔH°acid (kcal/mol) for six mononitrated azole species (2-nitropyrrole = 337.0, 3-nitropyrrole = 335.8, 3-nitropyrazole = 330.5, 4-nitropyrazole = 329.5, 2-nitroimidazole = 327.4, and 4-nitroimidazole = 325.0). We report an absolute uncertainty of ±2.2 kcal/mol that arises from the uncertainties of the reference acids; the relative values are known within 0.4 kcal/mol. Combining these experimental ΔH°acid values with ΔS°acid values calculated at the B3LYP/aug-cc-pVTZ level of theory, we report ΔG°acid (kcal/mol) for the nitroazoles (2-nitropyrrole = 329.4, 3-nitropyrrole = 328.4, 3-nitropyrazole = 323.1, 4-nitropyrazole = 322.0, 2-nitroimidazole = 319.7, and 4-nitroimidazole = 317.6); the absolute uncertainties are ±2.4 kcal/mol. In addition to the experimental studies, we have computationally investigated the gas-phase acidities and electron affinities of the azoles in this work, as well as higher-order aza- and dinitro-substituted azoles. We discuss trends in the stabilities of the deprotonated azoles based on aza substitution and nitro group placement. 4-Nitroimidazole has already found use as the anionic component in ionic liquids, and we propose that the additional nitrated azolate ions are potential candidates for the anionic component of ionic liquids.

Dehalogenation of arenes via SN2 reactions at bromine: competition with nucleophilic aromatic substitution.

The gas-phase reactions of carbon- and nitrogen-centered nucleophiles with polyfluorobromobenzenes were examined in a selected-ion flow tube (SIFT) and modeled computationally at the MP2/6-31+G(d,p)//MP2/6-31+G(d) level. In the gas-phase experiments, rate constants and branching ratios were determined. The carbon nucleophiles produce expected nucleophilic aromatic substitution (SNAr) and proton transfer products along with unexpected products that result from SN2 reactions at the bromine center (polyfluorophenide leaving group). With nitrogen nucleophiles, the SN2 at bromine channel is suppressed. In the SNAr channels, the "element effect" is observed, and fluoride loss competes with bromide loss. The computational modeling indicates that all the substitution barriers are well below the entrance channel and that entropy and dynamics effects control the product distributions.

The α-effect in gas-phase SN2 reactions of microsolvated anions: methanol as a solvent.

The α-effect, an enhanced reactivity of nucleophiles with a lone-pair adjacent to the reaction center, has been studied in solution for several decades. The gas-phase α-effect has recently been documented in studies of SN2 reactions as well as in competing reactions for both bare and microhydrated anions. In the present work we extend our studies of the significance of microsolvation on the α-effect, employing methanol as the solvent, in the expectation that the greater stability of the methanol cluster relative to the water cluster will lower the reactivity and thereby allow studies over a wider efficiency range. We compare the gas-phase reactivity of the microsolvated α-nucleophile HOO(-)(CH3OH) to that of microsolvated normal alkoxy nucleophiles, RO(-)(CH3OH) in reactions with CH3Cl and CH3Br. The results reveal enhanced reactivity of HOO(-)(CH3OH) toward both methyl halides relative to the normal nucleophiles, and clearly demonstrate the presence of an α-effect for the microsolvated α-nucleophile. The highly exothermic reactions with methyl bromide result in a smaller Brønsted ßnuc value than observed for methyl chloride, and the α-effect in turn influences the reactions with methyl chloride more than with methyl bromide. Computational investigations reveal that reactions with methyl bromide proceed through earlier transition states with less advanced bond formation compared to the related reactions of methyl chloride. In addition, solvent interactions for HOO(-) are quite different from those with the normal nucleophiles at the transition state, indicating that differential solvation may well contribute to the α-effect. The greater thermodynamic and kinetic stability of the anion-methanol clusters relative to the anion-water clusters accounts well for the differences in the influence of solvation with the two protic polar solvents.

The α-effect and competing mechanisms: the gas-phase reactions of microsolvated anions with methyl formate.

The enhanced reactivity of α-nucleophiles, which contain an electron lone pair adjacent to the reactive site, has been demonstrated in solution and in the gas phase and, recently, for the gas-phase S(N)2 reactions of the microsolvated HOO(-)(H2O) ion with methyl chloride. In the present work, we continue to explore the significance of microsolvation on the α-effect as we compare the gas-phase reactivity of the microsolvated α-nucleophile HOO(-)(H2O) with that of microsolvated normal alkoxy nucleophiles, RO(-)(H2O), in reactions with methyl formate, where three competing reactions are possible. The results reveal enhanced reactivity of HOO(-)(H2O) towards methyl formate, and clearly demonstrate the presence of an overall α-effect for the reactions of the microsolvated α-nucleophile. The association of the nucleophiles with a single water molecule significantly lowers the degree of proton abstraction and increases the S(N)2 and B(AC)2 reactivity compared with the unsolvated analogs. HOO(-)(H2O) reacts with methyl formate exclusively via the B(AC)2 channel. While microsolvation lowers the overall reaction efficiency, it enhances the B(AC)2 reaction efficiency for all anions compared with the unsolvated analogs. This may be explained by participation of the solvent water molecule in the B(AC)2 reaction in a way that continuously stabilizes the negative charge throughout the reaction.

Investigating the α-effect in gas-phase S(N)2 reactions of microsolvated anions.

The α-effect-enhanced reactivity of nucleophiles with a lone-pair adjacent to the attacking center-was recently demonstrated for gas-phase S(N)2 reactions of HOO(-), supporting an intrinsic component of the α-effect. In the present work we explore the gas-phase reactivity of microsolvated nucleophiles in order to investigate in detail how the α-effect is influenced by solvent. We compare the gas-phase reactivity of the microsolvated α-nucleophile HOO(-)(H2O) to that of microsolvated normal alkoxy nucleophiles, RO(-)(H2O), in reaction with CH3Cl using a flowing afterglow-selected ion flow tube instrument. The results reveal enhanced reactivity of HOO(-)(H2O) and clearly demonstrate the presence of an α-effect for the microsolvated α-nucleophile. The association of the nucleophile with a single water molecule results in a larger Brønsted ßnuc value than is the case for the unsolvated nucleophiles. Accordingly, the reactions of the microsolvated nucleophiles proceed through later transition states in which bond formation has progressed further. Calculations show a significant difference in solvent interaction for HOO(-) relative to the normal nucleophiles at the transition states, indicating that differential solvation may well contribute to the α-effect. The reactions of the microsolvated anions with CH3Cl can lead to formation of either the bare Cl(-) anion or the Cl(-)(H2O) cluster. The product distributions show preferential formation of the Cl(-) anion even though the formation of Cl(-)(H2O) would be favored thermodynamically. Although the structure of the HOO(-)(H2O) cluster resembles HO(-)(HOOH), we demonstrate that HOO(-) is the active nucleophile when the cluster reacts.

Gas-phase reactions of the atomic oxygen radical cation with halogenated compounds.

Rate constants and product distributions have been measured for the reactions of O(+)˙((4)S) with the methyl halides (CH(3)F, CH(3)Cl, CH(3)Br, CH(3)I) and three perfluorinated compounds (CF(4), SF(6), SF(5)CF(3)) at 300 K in a flowing afterglow-selected ion flow tube (FA-SIFT). The reactions occur with high efficiency, despite the necessity for spin conversion in some processes. The mechanisms include charge transfer, atom abstraction, and fragmentation reactions. Computational modeling was carried out to provide insight into these processes.

State-specific reactions of Cu(+)(1S, 3D) with CH3X and CF3X (X = Cl, Br, I): exploring the influence of dipole orientation on association and C-X bond activation.

The reactions of gas-phase Cu(+)((1)S) and Cu(+)((3)D) with CF(3)X and CH(3)X (X = Cl, Br, and I) have been examined experimentally using the drift cell technique at 3.5 Torr in He at room temperature. State-specific product channels and overall bimolecular rate constants for depletion of the two Cu(+) states were determined using electronic state chromatography. The results showed that Cu(+)((1)S) participates exclusively in association with all of these neutrals, whereas, depending on the neutral, Cu(+)((3)D) initiates up to three bimolecular processes, resulting in the formation of CuX(+), CuC(H/F)(3)(+), and C(H/F)(3)X(+). Possible structures for the singlet association products were explored using density functional methods. These calculations indicated that Cu(+) preferentially associates with the labile halogen (Cl, Br, I) with all neutrals except CF(3)Cl, for which a "backside" geometry occurs in which Cu(+)((1)S) is weakly bound to the -CF(3) end of the molecule. All products observed on the triplet reaction surface can be understood in terms of either known or calculated thermochemical requirements. Product distributions and overall reaction efficiencies for C-X bond activation (X = Br, I) through Cu(+)((3)D) suggest that the orientation of the neutral dipole has little or no effect in controlling access to specific product channels. Likewise, second-order rate constants for reactions with X = Br and I indicate efficient depletion of Cu(+)((3)D) and do not exhibit the dramatic variations in reaction efficiency previously observed with CH(3)Cl and CF(3)Cl. These results suggest that C-X bond activation proceeds through a bond-insertion mechanism as opposed to direct abstraction.