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.     

Palladium-catalyzed Suzuki cross-coupling of aryl halides with aryl boronic acids in the presence of glucosamine-based phosphines

Carbohydrate-substituted phosphines are easily obtained in quite good yields by coupling of protected or non-protected d-glucosamine with the corresponding diphenylphosphino acid. These neutral ligands, in association with palladium acetate, are very active catalysts in the Suzuki cross-coupling reaction. The polyhydroxy phosphines are more active than the peracetylated phosphines. The process tolerates electron-rich as well as electron-poor substituents. Excellent turnovers, up to 97?000 are observed.     

A very large diversity space of synthetically accessible compounds for use with drug design programs

We have constructed a very large virtual diversity space containing more than 10¹³ chemical compounds. The diversity space is built from about 400 combinatorial libraries, which have been expanded by choosing sizeable collections of suitable R-groups that can be attached to each link point of their scaffolds. These R-group collections have been created by selecting reagents that have drug-like properties from catalogs of available chemicals. As members of known combinatorial libraries, the compounds in the diversity space are in general synthetically accessible and useful as potential drug leads. Hence, the diversity space can be used as a vast source of compounds by a de novo drug design program. For example, we have used such a program to generate inhibitors of HIV integrase enzyme that exhibited activity in the micromolar range.     

The study and characterization of nucleosides by mass spectrometry—I: The mass spectra of pyrimidine 2,2′-anhydronucleosides and their derivatives

The mass spectra of 2,2′-anhydrouridine, 2,2′-anhydrothymidine and 2,2′-anhydro-4-thiouridine are reported. The acetyl, trifluoroacetyl, trityl, pivaloyl and trimethylsilyl ether derivatives were also studied. Deuterium labeling in acetyl and trimethylsilyl groups aided characterization of many ions in the spectra, as well as helping to clarify hydrogen migration processes. The anhydronucleosides and their derivatives are readily distinguished from natural nucleosides by the presence of an ion containing the base moiety plus the anhydro-ring plus one hydrogen atom from the rest of the molecule. As for natural nucleosides the [base + H]⁺ and [base + 2H]⁺ ions are usually prominent, but in contrast to natural nucleosides, ions characteristic of the sugar moiety do not retain the 2′-oxygen atom (i.e. the oxygen atom of the anhydro-ring). The mass spectra of deuterium labeled derivatives suggest a test for the presence of a 3′-O-acetyl function (the O-acetyl group is lost from the molecular ion much more readily from the 3′- than from the 5′-carbon atom). The trimethylsilyl derivatives showed evidence in their mass spectra for migration of trimethylsilyl groups in addition to hydrogen atoms.     

Accurate measurement of the exciton diffusion length in a conjugated polymer using a heterostructure with a side-chain cross-linked fullerene layer

Exciton diffusion and photoluminescence quenching in conjugated polymer/fullerene heterostructures are studied by time-resolved photoluminescence. It is observed that heterostructures consisting of a spin-coated poly(p-phenylene vinylene) (PPV)-based derivative and evaporated C60 are ill-defined because of diffusion of C60 into the polymer, leading to an overestimation of the exciton diffusion length. This artifact is resolved by the use of a novel, thermally side-chain polymerizing and cross-linking fullerene derivative (F2D) containing two diacetylene moieties, forming a completely immobilized electron acceptor layer. With this heterostructure test system, an exciton diffusion length of 5 +/- 1 nm is derived for this PPV derivative from time-integrated luminescence quenching data.     

Synthesis and characterization of molybdenum oxo complexes of two tripodal ligands: reactivity studies of a functional model for molybdenum oxotransferases

Reaction of the tetradentate ligand N-(2-hydroxybenzyl)-N,N-bis(2-pyridylmethyl)amine (L-OH) with MoO2Cl2 in methanol in the presence of NaOMe and PF6- results in the formation of [MoO2(L-O)]PF6. Similarly, the reaction of N-(2-mercaptobenzyl)-N,N-bis(2-pyridylmethyl)amine (L-SH) with MoO2(acac)2 leads to the formation of [MoO2(L-S)]+. The dioxo-molybdenum complex [MoO2(L-O)]+ reacts with phosphines in methanol to afford phosphine oxides and an air-sensitive molybdenum complex, tentatively identified as [Mo(IV)O(L-O)(OCH3)]. The latter complex is capable of reducing biological oxygen donors such as DMSO or nitrate, thereby mimicking the activity of DMSO reductase and nitrate reductase. Reaction of [MoO2(L-O)]PF6 with PPh3 in other solvents than methanol leads to the formation of the Mo(V) dimer [(L-O)OMo(micro-O)MoO(L-O)](PF6)2. The crystal structures of [MoO2(L-O)]PF6 and the micro-oxo bridged dimer are presented.     

Water concentration profiles in membranes measured by ESEEM of spin-labeled lipids

Electron spin-echo envelope modulation (ESEEM) spectroscopy of phospholipids spin-labeled systematically down the sn-2 chain was used to detect the penetration of water (D2O) into bilayer membranes of dipalmitoyl phosphatidylcholine with and without 50 mol % cholesterol. Three-pulse stimulated echoes allow the resolution of two superimposed 2H-ESEEM spectral components of different widths, for spin labels located in the upper part of the lipid chains. Quantum chemical calculations (DFT) and ESEEM simulations assign the broad spectral component to one or two D2O molecules that are directly hydrogen bonded to the N-O group of the spin label. Classical ESEEM simulations establish that the narrow spectral component arises from nonbonded water (D2O) molecules that are free in the hydrocarbon chain region of the bilayer membrane. The amplitudes of the broad 2H-ESEEM spectral component correlate directly with those of the narrow component for spin labels at different positions down the lipid chain, reflecting the local H-bonding equilibria. The D2O-ESEEM amplitudes decrease with position down the chain toward the bilayer center, displaying a sigmoidal dependence on position that is characteristic of transmembrane polarity profiles established by other less direct spin-labeling methods. The midpoint of the sigmoidal profile is shifted toward the membrane center for membranes without cholesterol, relative to those with cholesterol, and the D2O-ESEEM amplitude in the outer regions of the chain is greater in the presence of cholesterol than in its absence. For both membrane types, the D2O amplitude is almost vanishingly small at the bilayer center. The water-penetration profiles reverse correlate with the lipid-chain packing density, as reflected by 1H-ESEEM intensities from protons of the membrane matrix. An analysis of the H-bonding equilibria provides essential information on the binding of water molecules to H-bond acceptors within the hydrophobic interior of membranes. For membranes containing cholesterol, approximately 40% of the nitroxides in the region adjacent to the lipid headgroups are H bonded to water, of which ca. 15% are doubly H bonded. Corresponding H-bonded populations in membranes without cholesterol are ca. 20%, of which ca. 6% are doubly bonded.     

Measurements and Utilization of Consistent Gibbs Energies of Transfer of Single Ions: Towards a Unified Redox Potential Scale for All Solvents

Utilizing the “ideal” ionic liquid salt bridge to measure Gibbs energies of transfer of silver ions between the solvents water, acetonitrile, propylene carbonate and dimethylformamide results in a consistent data set with a precision of 0.6 kJ mol⁻¹ over 87 measurements in 10 half-cells. This forms the basis for a coherent experimental thermodynamic framework of ion solvation chemistry. In addition, we define the solvent independent - and the values that account for the electronating potential of any redox system similar to the value of a medium that accounts for its protonating potential. This scale is thermodynamically well-defined enabling a straightforward comparison of the redox potentials (reducities) of all media with respect to the aqueous redox potential scale, hence unifying all conventional solvents′ redox potential scales. Thus, using the Gibbs energy of transfer of the silver ion published herein, one can convert and unify all hitherto published redox potentials measured, for example, against ferrocene, to the scale.     

Measurement of lactate in whole human blood with near-infrared transmission spectroscopy

We have evaluated the potential of near-infrared spectroscopy (NIRS) as a technique for rapid analysis of lactate in whole blood. To test the NIRS technique, a comparison was made with a standard clinical method using whole blood samples taken from five exercising human subjects at three different stage of exercise. To expand lactate concentration within the physiological range, standard additions method was used to generate 45 unique data points. Spectra were collected over the 2050-2400 nm spectral range with a 1 mm optical path length quartz cell. Reference lactate concentrations in the samples were determined by enzymatic measurements. Estimates and calibration of the lactate concentration with NIRS was made using partial least squares (PLS) regression analysis and leave-N-out cross validation on second derivative spectra. Separate calibrations were determined from each of the subject samples and cumulative PRESS was used to determine the number of PLS factors in the final model. The results from the PLS model presented are generated from the five individual calibration coefficient vectors and provided a correlation coefficient of 0.978 and a standard error of cross validation of 0.65 mmol l⁻¹ between the enzymatic assay and the NIRS technique. To study the parameters that impact the spectra baseline and the correlation between the calculated model and the data, referenced measurements of lactate against baseline spectrum were made for each individual. A correlation coefficient of 0.992 and a standard error of cross validation of 0.21 mmol l⁻¹ were found. The results suggest that NIRS may provide a valuable tool to assess physiological status for both research and clinical needs.     

Semiempirical calculations of TiO2 (rutile) clusters

The densities of states for small (TiO₂)_x-clusters, x = 1, 3, 6, 9, and 14, have been calculated by means of the INDO method. The shape of the valence bands' density of states (DOS ) are discussed in terms of the distribution of coordination numbers. A one-slab cluster with uniform distribution of the coordination numbers was used to compare our calculations with experimental spectra. The photoelectric DOS and DOS for a cluster with an oxygen vacancy are in very good agreement with experimental findings for the TiO₂ (001) surface. O1s core level shifts between a surfacelike and a bulklike oxygen atom have been estimated. It is concluded that the observed surface–bulk shift for the TiO₂ (001) surface contains a substantial relaxation contribution. © 1992 John Wiley & Sons, Inc.