Ion mobility-mass correlation trend line separation of glycoprotein digests without deglycosylation

A high-throughput ion mobility mass spectrometer (IMMS) was used to rapidly separate and analyze peptides and glycopeptides derived from glycoproteins. Two glycoproteins, human α-1-acid glycoprotein and antithrombin III were digested with trypsin and subjected to electro-spray traveling wave IMMS analysis. No deglycosylation steps were performed; samples were complex mixtures of peptides and glycopeptides. Peptides and glycosylated peptides with different charge states (up to 4 charges) were observed and fell on distinguishable trend lines in 2-D IMMS spectra in both positive and negative modes. The trend line separation patterns matched between both modes. Peptide sequence was identified based on the corresponding extracted mass spectra and collision induced dissociation (CID) experiments were performed for selected compounds to prove class identification. The signal-to-noise ratio of the glycopeptides was increased dramatically with ion mobility trend line separation compared to non-trend line separation, primarily due to selection of precursor ion subsets within specific mobility windows. In addition, isomeric mobility peaks were detected for specific glycopeptides. IMMS demonstrated unique capabilities and advantages for investigating and separating glycoprotein digests in this study and suggests a novel strategy for rapid glycoproteomics studies in the future.     

Conventional strain energies of 1,2-dihydroazete, 2,3-dihydroazete, 1,2-dihydrophosphete, and 2,3-dihydrophosphete

The conventional strain energies of 1,2-dihydroazete, 2,3-dihydroazete, 1,2-dihydrophosphete, and 2,3-dihydrophosphete are determined within the isodesmic, homodesmotic, and hyperhomodesmotic models. Optimum equilibrium geometries, harmonic vibrational frequencies, and corresponding electronic energies and zero-point vibrational energies are computed for all pertinent molecular systems using SCF theory, second-order perturbation theory, and density functional theory and employing the correlation consistent basis sets cc-pVDZ, cc-pVTZ, and cc-pVQZ. Single-point fourth-order perturbation theory, CCSD, and CCSD(T) calculations employing the cc-pVTZ and the cc-pVQZ basis sets are computed using the MP2/cc-pVTZ and MP2/cc-pVQZ optimized geometries, respectfully, to ascertain the contribution of higher order correlation. Three DFT functionals, B3LYP, wB97XD, and M06-2X, are employed to determine whether they can yield results similar to those obtained at the CCSD(T) level.     

Neuronal metabolomics by ion mobility mass spectrometry: cocaine effects on glucose and selected biogenic amine metabolites in the frontal cortex, striatum, and thalamus of the rat

We report results of studies of global and targeted neuronal metabolomes by ambient pressure ion mobility mass spectrometry. The rat frontal cortex, striatum, and thalamus were sampled from control nontreated rats and those treated with acute cocaine or pargyline. Quantitative evaluations were made by standard additions or isotopic dilution. The mass detection limit was ～100 pmol varying with the analyte. Targeted metabolites of dopamine, serotonin, and glucose followed the rank order of distribution expected between the anatomical areas. Data was evaluated by principal component analysis on 764 common metabolites (identified by m/z and reduced mobility). Differences between anatomical areas and treatment groups were observed for 53 % of these metabolites using principal component analysis. Global and targeted metabolic differences were observed between the three anatomical areas with contralateral differences between some areas. Following drug treatments, global and targeted metabolomes were found to shift relative to controls and still maintained anatomical differences. Pargyline reduced 3,4-dihydroxyphenylacetic acid below detection limits, and 5-HIAA varied between anatomical regions. Notable findings were: (1) global metabolomes were different between anatomical areas and were altered by acute cocaine providing a broad but targeted window of discovery for metabolic changes produced by drugs of abuse; (2) quantitative analysis was demonstrated using isotope dilution and standard addition; (3) cocaine changed glucose and biogenic amine metabolism in the anatomical areas tested; and (4) the largest effect of cocaine was on the glycolysis metabolome in the thalamus confirming inferences from previous positron emission tomography studies using 2-deoxyglucose.

Gaussian basis sets for molecular applications

The choice of basis set in quantum chemical calculations can have a huge impact on the quality of the results, especially for correlated ab initio methods. This article provides an overview of the development of Gaussian basis sets for molecular calculations, with a focus on four popular families of modern atom‐centered, energy‐optimized bases: atomic natural orbital, correlation consistent, polarization consistent, and def2. The terminology used for describing basis sets is briefly covered, along with an overview of the auxiliary basis sets used in a number of integral approximation techniques and an outlook on possible future directions of basis set design. © 2012 Wiley Periodicals, Inc.     

Modelling interaction between ammonia and nitric oxide molecules and aquaporins

Aquaporin is a family of small membrane-proteins that are capable of transporting nano-sized materials. In the present paper, we investigate the structure of these channels and provide information about the mechanism of individual molecules being encapsulated into aquaglyceroporin (GlpF) and aquaporin-1 (AQP1) channels by calculating the potential energy. In particular, we presents a mathematical model to determine the total potential energy for the interaction of the ammonia and nitric oxide molecules and different aquaporin channels which we assume to have a symmetrical cylindrical structure. We propose to describe these interactions in two steps. Firstly, we model the nitrogen atom as a discrete point and secondly, we model the three hydrogen atoms on the surface of a sphere of a certain radius. Then, we find the total potential energy by summing these interactions. Next, by considering the nitric oxide molecule as two discrete atoms uniformly distributed interacting with GlpF and AQP1 channels then gathering all pairs of interaction to determine the potential energy. Our results show that the ammonia and nitric oxide molecules can be encapsulated into both GlpF and AQP1 channels.     

Theoretical Insights into the Nature of Halogen Bonding in Prereactive Complexes

Benchmark quality geometries and interaction energies for the prereactive halogen‐bonded complexes of dihalogens and ammonia, including hypothetical astatine containing dihalogens, have been produced via explicitly correlated coupled cluster methods. The application of local electron correlation partitioning reveals dispersion, electrostatics and ionic substitutions all contribute significantly to the interaction energy, with a linear relationship between the ionic substitutions and the degree of charge transfer. Potential energy curves for H₃N???ClF show that as the relative orientations of the two subunits are manipulated appreciable interactions can be found at considerably angular displaced geometries, signifying lower directionality in halogen bonding than previously supposed.     

C−H Activation of Inert Arenes using a Photochemically Activated Guanidinato-Magnesium(I) Compound

UV irradiation of solutions of a guanidinate coordinated dimagnesium(I) compound, [{(Priso)Mg}₂] 3 (Priso=[(DipN)₂CNPrⁱ₂]⁻, Dip=2,6-diisopropylphenyl), in either benzene, toluene, the three isomers of xylene, or mesitylene, leads to facile activation of an aromatic C−H bond of the solvent in all cases, and formation of aryl/hydride bridged magnesium(II) products, [{(Priso)Mg}₂(μ-H)(μ-Ar)] 4 – 9 . In contrast to similar reactions reported for β-diketiminate coordinated counterparts of 3 , these C−H activations proceed with little regioselectivity, though they are considerably faster. Reaction of 3 with an excess of the pyridine, p-NC₅H₄Bu^t (py^But), gave [(Priso)Mg(py^ButH)(py^But)₂] 10 , presumably via reduction of the pyridine to yield a radical intermediate, [(Priso)Mg(py^But⋅)(py^But)₂] 11 , which then abstracts a proton from the reaction solvent or a reactant. DFT calculations suggest two possible pathways to the observed arene C−H activations. One of these involves photochemical cleavage of the Mg−Mg bond of 3 , generating magnesium(I) doublet radicals, (Priso)Mg⋅. These then doubly reduce the arene substrate to give “Birch-like” products, which subsequently rearrange via C−H activation of the arene. Circumstantial evidence for the photochemical generation of transient magnesium radical species includes the fact that irradiation of a cyclohexane solution of 3 leads to an intramolecular aliphatic C−H activation process and formation of an alkyl-bridged magnesium(II) species, [{Mg(μ-Priso^−H)}₂] 12 . Furthermore, irradiation of a 1 : 1 mixture of 3 and the β-diketiminato dimagnesium(I) compound, [{(^DipNacnac)Mg}₂] (^DipNacnac=[HC(MeCNDip)₂]⁻), effects a “scrambling” reaction, and the near quantitative formation of an unsymmetrical dimagnesium(I) compound, [(Priso)Mg−Mg(^DipNacnac)] 13 . Finally, the EPR spectrum (77 K) of a glassed solution of UV irradiated 3 is dominated by a broad featureless signal, indicating the presence of a doublet radical species.     

Robust controlled-NOT gates from almost any interaction

There are many cases where the interaction between two qubits is not precisely known, but single-qubit operations are available. In this Letter we show how, regardless of an incomplete knowledge of the strength or form of the interaction between two qubits, it is often possible to construct a controlled-NOT gate which has arbitrarily high fidelity. In particular, we show that oscillations in the strength of the exchange interaction in solid state Si and Ge structures are correctable.