Metabolic profiling of Escherichia coli by ion mobility-mass spectrometry with MALDI ion source

Comprehensive metabolome analysis using mass spectrometry (MS) often results in a complex mass spectrum and difficult data analysis resulting from the signals of numerous small molecules in the metabolome. In addition, MS alone has difficulty measuring isobars and chiral, conformational and structural isomers. When a matrix-assisted laser desorption ionization (MALDI) source is added, the difficulty and complexity are further increased. Signal interference between analyte signals and matrix ion signals produced by MALDI in the low mass region (<1500 Da) cause detection and/or identification of metabolites difficult by MS alone. However, ion mobility spectrometry (IMS) coupled with MS (IM-MS) provides a rapid analytical tool for measuring subtle structural differences in chemicals. IMS separates gas-phase ions based on their size-to-charge ratio. This study, for the first time, reports the application of MALDI to the measurement of small molecules in a biological matrix by ion mobility-time of flight mass spectrometry (IM-TOFMS) and demonstrates the advantage of ion-signal dispersion in the second dimension. Qualitative comparisons between metabolic profiling of the Escherichia coli metabolome by MALDI-TOFMS, MALDI-IM-TOFMS and electrospray ionization (ESI)-IM-TOFMS are reported. Results demonstrate that mobility separation prior to mass analysis increases peak-capacity through added dimensionality in measurement. Mobility separation also allows detection of metabolites in the matrix-ion dominated low-mass range (m/z < 1500 Da) by separating matrix signals from non-matrix signals in mobility space.     

On the controversy of metal ion composition on amine oxygenase (AurF): a computational investigation

An energetics-spectroscopic approach based on DFT method reveals that the active site structure of AurF has {Fe(III)(2)O} central core with one protonated terminal glutamate.     

Hydrogen bonding in substituted formic acid dimers

The hydrogen-bonded dimers of formic acid derivatives XCOOH (X = H, F, Cl, and CH3) have been investigated using density functional theory (B3LYP) and second-order M?ller-Plesset perturbation (MP2) methods, with the geometry optimization carried out using 6-311++G(2d,2p) basis set. The dimerization energies calculated using aug-cc-pVXZ (with X = D and T) basis have been extrapolated to infinite basis set limit using the standard methodology. The results indicate that the fluorine-substituted formic acid dimer is the most stable one in comparison to the others. Topological analysis carried out using Bader's atoms in molecules (AIM) theory shows good correlation of the values of electron density and its Laplacian at the bond critical points (BCP) with the hydrogen bond length in the dimers. Natural bond orbital (NBO) analysis carried out to study the charge transfer from the proton acceptor to the antibonding orbital of the X-H bond in the complexes reveals that most of the dimers are associated with conventional H-bonding except a few, where improper blue-shifting hydrogen bonds are found to be present.     

Ultrasonic and DFT study of intermolecular association through hydrogen bonding in aqueous solutions of d(−)-arabinose

The experimental measurements of density, viscosity and ultrasonic velocity of aqueous d-arabinose solutions were carried out as functions of concentration (0.1 ≤ m [mol kg^? 1] ≤ 1.0) and temperature (303.15 ≤ T [K] ≤ 323.15). The isentropic compressibility (β_s), acoustic impedance (Z), hydration number (H_n), intermolecular free length (L_f), classical sound absorption (α/f²)_class and shear relaxation time (τ) were calculated by using the measured data. These parameters have been interpreted in terms of solute–solvent interactions. The quantum chemical calculations were performed to study the hydrogen bonding in interacting complex formed between α-D-arabinopyranose in ¹C₄ conformation and water molecules. Computations have been done by using Density Functional Theory (DFT) method at B3LYP/6-31+g(d) level of theory to study the equilibrium structure of α-d-arabinose, α-D-arabinopyranose–water interacting complex and vibrational frequencies. The solution phase study was carried out using Onsager's reaction field model in water solvent. The computed and scaled vibrational frequencies are in good agreement with the main features of the experimental spectrum when seven water molecules are considered explicitly with α-D-arabinopyranose in ¹C₄ conformation. The interaction energy (E_total), hydrogen bond lengths and dipole moment (μ_m) of the interacting complex are also presented and discussed with in the light of solute–solvent interactions.     

Reaction mechanism of O -acylhydroxamate with cysteine proteases

The gas-phase reaction mechanism of O-acylhydroxamate with cysteine proteases has been investigated using ab initio and density functional theory. On the irreversible process, after breakdown of tetrahedral intermediate (INT1), small 1–2 anionotropic has been formed and rearranged to give stable by-products sulfenamide (P1) and thiocarbamate (P2) with considerable energy loss. While, on the reversible part of this reaction mechanism, intermediate (INT2) breaks down on oxidation, to form a stable product (P3). Topological and AIM analyses have been performed for hydrogen bonded complex in this reaction profile. Intrinsic reaction coordinates [IRC, minimum-energy path (MEP)] calculation connects the transition state between R-INT1, INT1-P1 and INT1-P2. The products P1, P2 and P3 are energetically more stable than the reactant and hence the reaction enthalpy is found to be exothermic.     

Structure and ionization energies of some analogues of iron-only hydrogenases studied by density functional theory methods

Density functional theory calculations using both the B3LYP and BP86 functional in conjunction with a medium and large size basis set have been used to predict the structures and ionization energies of 12 models of iron-only hydrogenases. Although the structural predictions do not allow a clear discrimination between the different computational models, these models do yield significantly different adiabatic and vertical ionization energies. The closest agreement with experiment is given by the BP86 functional and the large all-electron basis. At this level of theory the adiabatic ionization energies are very close to experiment, but the vertical values are uniformly too small, leading to an underestimation of the reorganization energies. The calculations also suggest that measured ionization energies may help in identifying both the bridge-head group and whether CO bridging takes place upon ionization.     

Plasma-Spray Ionization (PLASI): A Multimodal Atmospheric Pressure Ion Source for Liquid Stream Analysis

A new ion generation method, named plasma-spray ionization (PLASI) for direct analysis of liquid streams, such as in continuous infusion experiments or liquid chromatography (LC), is reported. PLASI addresses many of the analytical limitations of electrospray ionization (ESI) and has potential for real time process stream analysis and reaction monitoring under atmospheric conditions in non-ESI friendly scenarios. In PLASI-mass spectrometry (MS), the liquid stream is pneumatically nebulized and partially charged at low voltages; the resultant aerosol is thus entrained with a gaseous plasma plume from a distal glow discharge prior to MS detection. PLASI-MS not only overcomes ESI-MS limitations but also generates simpler mass spectra with minimal adduct and cluster formation. PLASI utilizes the atomization capabilities of an ESI sprayer operated below the ESI threshold to generate gas-phase aerosols that are then ionized by the plasma stream. When operated at or above the ESI threshold, ionization by traditional ESI mechanisms is achieved. The multimodal nature of the technique enables readily switching between plasma and ESI operation. It is expected that PLASI will enable analyzing a wide range of analytes in complex matrices and less-restricted solvent systems, providing more flexibility than that achievable by ESI alone. Figure

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An Effective Approach for Coupling Direct Analysis in Real Time with Atmospheric Pressure Drift Tube Ion Mobility Spectrometry

Drift tube ion mobility spectrometry (DTIMS) has evolved as a robust analytical platform routinely used for screening small molecules across a broad suite of chemistries ranging from food and pharmaceuticals to explosives and environmental toxins. Most modern atmospheric pressure IM detectors employ corona discharge, photoionization, radioactive, or electrospray ion sources for efficient ion production. Coupling standalone DTIMS with ambient plasma-based techniques, however, has proven to be an exceptional challenge. Device sensitivity with near-ground ambient plasma sources is hindered by poor ion transmission at the source–instrument interface, where ion repulsion is caused by the strong electric field barrier of the high potential ion mobility spectrometry (IMS) inlet. To overcome this shortfall, we introduce a new ion source design incorporating a repeller point electrode used to shape the electric field profile and enable ion transmission from a direct analysis in real time (DART) plasma ion source. Parameter space characterization studies of the DART DTIMS setup were performed to ascertain the optimal configuration for the source assembly favoring ion transport. Preliminary system capabilities for the direct screening of solid pharmaceuticals are briefly demonstrated. Figure

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Synthesis and Spectroscopic Distinction of Benzonaphthonaphthyridine and Its Isomer

Distinction of benzo[h]naphtho[1,2-b][1,6]naphthyridine and its isomeric benzo[b]naphtho[1,2-h][1,6]naphthyridine is well explained on the basis of various spectroscopic techniques. Initially these isomers were prepared from their respective chloroquinolines via anilinoquinolines as potential intermediates. Spectroscopic dissimilarities of their precursors and intermediates have also been considered and compared with the final benzonaphthonaphthyridine isomers.