Chemically-assisted fragmentation combined with multi-dimensional liquid chromatography and matrix-assisted laser desorption/ionization post source decay, matrix-assisted laser desorption/ionization tandem time-of flight or matrix-assisted laser desorption/ionization tandem mass spectrometry for improved sequencing of tryptic peptides

Derivatization of tryptic peptides using an Ettan CAF matrix-assisted laser desorption/ionization (MALDI) sequencing kit in combination with MALDI-post source decay (PSD) is a fast, accurate and convenient way to obtain de novo or confirmative peptide sequencing data. CAF (chemically assisted fragmentation) is based on solid-phase derivatization using a new class of water stable sulfonation agents, which strongly improves PSD analysis and simplifies the interpretation of acquired spectra. The derivatization is performed on solid supports, ZipTip(microC18, limiting the maximum peptide amount to 5 microg. By performing the derivatization in solution enabled the labeling of tryptic peptides derived from 100 microg of protein. To increase the number of peptides that could be sequenced, derivatized peptides were purified using multidimensional liquid chromatography (MDLC) prior to MALDI sequencing. Following the first dimension strong cation exchange (SCX) chromatography step, modified peptides were separated using reversed-phase chromatography (RPC). During the SCX clean up step, positively charged peptides are retained on the column while properly CAF-derivatized peptides (uncharged) are not. A moderately complex tryptic digest, prepared from six different proteins of equimolar amounts, was CAF-derivatized and purified by MDLC. Fractions from the second dimension nano RPC step were automatically sampled and on-line dispensed to MALDI sample plates and analyzed using MALDI mass spectrometry fragmentation techniques. All proteins in the derivatized protein mixture digest were readily identified using MALDI-PSD or MALDI tandem mass spectrometry (MS/MS). More than 40 peptides were unambiguously sequenced, representing a seven-fold increase in the number of sequenced peptides in comparison to when the CAF-derivatized protein mix digest was analyzed directly (no MDLC-separation) using MALDI-PSD. In conclusion, MDLC purification of CAF-derivatized peptides significantly increases the success rate for de novo and confirmative sequencing using various MALDI fragmentation techniques. This new approach is not only applicable to single protein digests but also to more complex digests and could, thus, be an alternative to electrospray ionization MS/MS for peptide sequencing.     

Excited-state dynamics of fac-[ReI(L)(CO)3(phen)]+ and fac-[ReI(L)(CO)3(5-NO2-phen)]+ (L = imidazole, 4-ethylpyridine; phen = 1,10-phenanthroline) complexes

The nature and dynamics of the lowest excited states of fac-[Re(I)(L)(CO)(3)(phen)](+) and fac-[Re(I)(L)(CO)(3)(5-NO(2)-phen)](+) [L = Cl(-), 4-ethyl-pyridine (4-Etpy), imidazole (imH); phen = 1,10-phenanthroline] have been investigated by picosecond visible and IR transient absorption spectroscopy in aqueous (L = imH), acetonitrile (L = 4-Etpy, imH), and MeOH (L = imH) solutions. The phen complexes have long-lived Re(I) --> phen (3)MLCT excited states, characterized by CO stretching frequencies that are upshifted relative to their ground-state values and by widely split IR bands due to the out-of-phase A'(2) and A"nu(CO) vibrations. The lowest excited states of the 5-NO(2)-phen complexes also have (3)MLCT character; the larger upward nu(CO) shifts accord with much more extensive charge transfer from the Re(I)(CO)(3) unit to 5-NO(2)-phen in these states. Transient visible absorption spectra indicate that the excited electron is delocalized over the 5-NO(2)-phen ligand, which acquires radical anionic character. Similarly, involvement of the -NO(2) group in the Franck-Condon MLCT transition is manifested by the presence of an enhanced nu(NO(2)) band in the preresonance Raman spectrum of [Re(I)(4-Etpy)(CO)(3)(5-NO(2)-phen)](+). The Re(I) --> 5-NO(2)-phen (3)MLCT excited states are very short-lived: 7.6, 170, and 43 ps for L = Cl(-), 4-Etpy, and imH, respectively, in CH(3)CN solutions. The (3)MLCT excited state of [Re(I)(imH)(CO)(3)(5-NO(2)-phen)](+) is even shorter-lived in MeOH (15 ps) and H(2)O (1.3 ps). In addition to (3)MLCT, excitation of [Re(I)(imH)(CO)(3)(5-NO(2)-phen)](+) populates a (3)LLCT (imH --> 5-NO(2)-phen) excited state. Most of the (3)LLCT population decays to the ground state (time constants of 19 (H(2)O), 50 (MeOH), and 72 ps (CH(3)CN)); in a small fraction, however, deprotonation of the imH.+ ligand occurs, producing a long-lived species, [Re(I)(im.)(CO)(3)(5-NO(2)-phen).-]+.     

Multivariate analysis of extremely large ToFSIMS imaging datasets by a rapid PCA method

Principal component analysis (PCA) and other multivariate analysis methods have been used increasingly to analyse and understand depth profiles in X‐ray photoelectron spectroscopy (XPS), Auger electron spectroscopy (AES) and secondary ion mass spectrometry (SIMS). These methods have proved equally useful in fundamental studies as in applied work where speed of interpretation is very valuable. Until now these methods have been difficult to apply to very large datasets such as spectra associated with 2D images or 3D depth‐profiles. Existing algorithms for computing PCA matrices have been either too slow or demanded more memory than is available on desktop PCs. This often forces analysts to ‘bin’ spectra on much more coarse a grid than they would like, perhaps even to unity mass bins even though much higher resolution is available, or select only part of an image for PCA analysis, even though PCA of the full data would be preferred. We apply the new ‘random vectors’ method of singular value decomposition proposed by Halko and co‐authors to time‐of‐flight (ToF)SIMS data for the first time. This increases the speed of calculation by a factor of several hundred, making PCA of these datasets practical on desktop PCs for the first time. For large images or 3D depth profiles we have implemented a version of this algorithm which minimises memory needs, so that even datasets too large to store in memory can be processed into PCA results on an ordinary PC with a few gigabytes of memory in a few hours. We present results from ToFSIMS imaging of a citrate crystal and a basalt rock sample, the largest of which is 134GB in file size corresponding to 67 111 mass values at each of 512 × 512 pixels. This was processed into 100 PCA components in six hours on a conventional Windows desktop PC. © 2015 The Authors. Surface and Interface Analysis published by John Wiley & Sons Ltd.     

Use of monomer fraction data in the parametrization of association theories

Association theories such as the CPA (cubic-plus-association), NRHB (non-random hydrogen bonding) equations of state and the various variants of SAFT (statistical associating fluid theory) have been extensively applied to phase equilibrium calculations. Such models can also be used for estimating the monomer fraction of hydrogen bonding compounds and their mixtures. Monomer fraction data are obtained from spectroscopic measurements and they are available for a few compounds such as pure water and alcohols as well as for some alcohol–alkane and similar mixtures. These data are useful for an understanding of the capabilities and limitations of association models. The purpose of this work is two-fold: (i) to compare the performance of three models, CPA, NRHB and sPC-SAFT, in predicting the monomer fraction of water, alcohols and mixtures of alcohol-inert compounds and (ii) to investigate whether “improved” model parameters can be obtained if monomer fraction data are included in the parameter estimation together with vapor pressures and liquid densities. The expression “improved” implies parameters which can represent several pure compound properties as well as monomer fraction data for pure compounds and mixtures. The accuracy of experimental monomer fraction data is discussed, as well as the role of monomer fraction data in clarifying which association scheme should be used in these equations of state. The results reveal that the investigated association models (CPA, sPC-SAFT and NRHB) can predict, at least qualitatively correct, monomer fractions of associating compounds and mixtures. Only, small differences are observed between the models. In addition, it has been shown that, using a suitable association scheme, a single set of parameters can describe satisfactorily vapor pressures, liquid densities and monomer fractions of water and alcohols. The 4C scheme is the best choice for water, while for methanol there is small difference between the 2B and 3B association schemes.     

Slow dynamics of a colloidal lamellar phase

We used x-ray photon correlation spectroscopy to study the dynamics in the lamellar phase of a platelet suspension as a function of the particle concentration. We measured the collective diffusion coefficient along the director of the phase, over length scales down to the interparticle distance, and quantified the hydrodynamic interaction between the particles. This interaction sets in with increasing concentration and can be described qualitatively by a simplified model. No change in the microscopic structure or dynamics is observed at the transition between the fluid and the gel-like lamellar phases.     

Understanding the effect of cobalt particle size on Fischer-Tropsch synthesis: surface species and mechanistic studies by SSITKA and kinetic isotope effect

Co/γ-Al(2)O(3) catalysts with particle sizes in the range of 4-15 nm were investigated by isothermal hydrogenation (IH), temperature programmed hydrogenation (TPH), and steady-state isotopic transient kinetic analysis (SSITKA). Kinetic isotope effect experiments were used to probe possible mechanisms on Co/γ-Al(2)O(3) with different particle size. It was found that CO dissociated on Co/γ-Al(2)O(3) catalysts at 210 °C. The total amount of CO(2) formed following the dissociation depends on the cobalt crystal size. O-Co binding energy was found to be highly dependent on the Co metal particle size, whereas similar C-Co binding energy was found on catalysts with different Co particle size. Very strongly bonded carbon and oxygen surface species increased with decreasing particle size and acted as site blocking species in the methanation reaction. SSITKA experiments showed that the intrinsic activity (1/τ(CH(x))) remained constant as the particle size increased from 4 to 15 nm. The number of surface intermediates (N(CH(x))) increased with increasing particle size. The apparent activation energies were found similar for these catalysts, about 85 kJ/mol. D(2)-H(2) switches further confirmed that the particle size did not change the kinetically relevant steps in the reaction. The reactivity of the active sites on the 4 nm particles was the same as those on the 8, 11, and 15 nm particles, and only the number of total available surface active sites was less on the 4 nm particles than on the others.     

2D SMARTCyp reactivity-based site of metabolism prediction for major drug-metabolizing cytochrome P450 enzymes

Cytochrome P450 (CYP) 3A4, 2D6, 2C9, 2C19, and 1A2 are the most important drug-metabolizing enzymes in the human liver. Knowledge of which parts of a drug molecule are subject to metabolic reactions catalyzed by these enzymes is crucial for rational drug design to mitigate ADME/toxicity issues. SMARTCyp, a recently developed 2D ligand structure-based method, is able to predict site-specific metabolic reactivity of CYP3A4 and CYP2D6 substrates with an accuracy that rivals the best and more computationally demanding 3D structure-based methods. In this article, the SMARTCyp approach was extended to predict the metabolic hotspots for CYP2C9, CYP2C19, and CYP1A2 substrates. This was accomplished by taking into account the impact of a key substrate-receptor recognition feature of each enzyme as a correction term to the SMARTCyp reactivity. The corrected reactivity was then used to rank order the likely sites of CYP-mediated metabolic reactions. For 60 CYP1A2 substrates, the observed major sites of CYP1A2 catalyzed metabolic reactions were among the top-ranked 1, 2, and 3 positions in 67%, 80%, and 83% of the cases, respectively. The results were similar to those obtained by MetaSite and the reactivity + docking approach. For 70 CYP2C9 substrates, the observed sites of CYP2C9 metabolism were among the top-ranked 1, 2, and 3 positions in 66%, 86%, and 87% of the cases, respectively. These results were better than the corresponding results of StarDrop version 5.0, which were 61%, 73%, and 77%, respectively. For 36 compounds metabolized by CYP2C19, the observed sites of metabolism were found to be among the top-ranked 1, 2, and 3 sites in 78%, 89%, and 94% of the cases, respectively. The computational procedure was implemented as an extension to the program SMARTCyp 2.0. With the extension, the program can now predict the site of metabolism for all five major drug-metabolizing enzymes with an accuracy similar to or better than that achieved by the best 3D structure-based methods. Both the Java source code and the binary executable of the program are freely available to interested users.     

Structures of the hexafluorocyclopropane, octafluorocyclobutane, and decafluorocyclopentane radical anions probed by experimental and computational studies of anisotropic electron spin resonance (ESR) spectra

Anisotropic electron spin resonance (ESR) spectra are reported for the radical anions of hexafluorocyclopropane (c-C(3)F(6)(-)), octafluorocyclobutane (c-C(4)F(8)(-)), and decafluorocyclopentane (c-C(5)F(10)(-)) generated via gamma-irradiation in plastically crystalline tetramethylsilane (TMS) and rigid 2-methyltetrahydrofuran (MTHF) matrices. By combining the analysis of these experimental ESR spectra involving anisotropic hyperfine (hf) couplings with a series of quantum chemical computations, the geometrical and electronic structure of these unusual perfluorocycloalkane radical anions have been characterized more fully than in previous studies that considered only the isotropic couplings. Unrestricted Hartree-Fock (UHF) computations with the 6-311+G(d,p) basis set predict planar ring structures for all three radical anions, the ground electronic states being (2)A(2)(") for c-C(3)F(6)(-) (D(3h) symmetry), (2)A(2u) for c-C(4)F(8)(-) (D(4h)), and (2)A(2)(") for c-C(5)F(10)(-) (D(5h)), in which the respective six, eight, and ten 19F-atoms are equivalent by symmetry. A successful test of the theoretical computation is indicated by the fact that the isotropic 19F hf couplings computed by the B3LYP method with the 6-311+G(2df,p) basis set for the optimized geometries are in almost perfect agreement with the experimental values: viz., 19.8 mT (exp) vs 19.78 mT (calc) for c-C(3)F(6)(-); 14.85 mT (exp) vs 14.84 mT (calc) for c-C(4)F(8)(-); 11.6 mT (exp) vs 11.65 mT (calc) for c-C(5)F(10)(-). Consequently, the same computation method has been applied to calculate the almost axially symmetric anisotropic 19F hf couplings for the magnetically equivalent 19F atoms: (-4.90 mT, -4.84 mT, 9.75 mT) for c-C(3)F(6), (-3.54 mT, -3.48 mT, 7.02 mT) for c-C(4)F(8)(-), and (-2.62 mT, -2.56 mT, 5.18 mT) for c-C(5)F(10)(-). ESR spectral simulations performed using the computed principal values of the hf couplings and the spatial orientations of the 19F nuclei as input parameters reveal an excellent fit to the experimental anisotropic ESR spectra of c-C(3)F(6)(-), c-C(4)F(8)(-), and c-C(5)F(10)(-), thereby providing a convincing proof of the highly symmetric D(nh) structures that are predicted for these negative ions. Furthermore, using the computed 19F principal values and their orientations, the effective 19F anisotropic hf couplings along the molecular symmetry axes were evaluated for c-C(3)F(6)(-) and c-C(4)F(8)(-) and successfully correlated with the positions of the characteristic outermost features in both the experimental and calculated anisotropic spectra. In addition, the electronic excitation energies and oscillator strengths for the c-C(3)F(6)(-) , c-C(4)F(8)(-), and c-C(5)F(10)(-) radical anions were computed for the first time using time-dependent density functional theory (TD-DFT) methods.     

A p‐Type NiO‐Based Dye‐Sensitized Solar Cell with an Open‐Circuit Voltage of 0.35 V

In tandem : Employing a molecular dyad and a cobalt‐based electrolyte gives a threefold‐increase in open‐circuit voltage (V_OC) for a p‐type NiO device (V_OC=0.35 V), and a fourfold better energy conversion efficiency. Incorporating these improvements in a TiO₂/NiO tandem dye‐sensitized solar cell (TDSC), results in a TDSC with a V_OC=0.91 V (see figure; CB=conductance band, VB= valence band).

     

Increased fraction of low-density structures in aqueous solutions of fluoride

X-ray absorption spectroscopy (XAS) and small angle x-ray scattering (SAXS) were utilized to study the effect of fluoride (F(-)) anion in aqueous solutions. XAS spectra show that F(-) increases the number of strong H-bonds, likely between F(-) and water in the first hydration shell. SAXS data show a low-Q scattering intensity increase similar to the effect of a temperature decrease, suggesting an enhanced anomalous scattering behavior in F(-) solutions. Quantitative analysis revealed that fluoride solutions have larger correlation lengths than chloride solutions with the same cations but shorter compared to pure water. This is interpreted as an increased fraction of tetrahedral low-density structures in the solutions due to the presence of the F(-) ions, which act as nucleation centers replacing water in the H-bonding network and forming stronger H-bonds, but the presence of the cations restricts the extension of strong H-bonds.