A gas electron diffraction and ab initio quantum-mechanical investigation into the molecular structure of tricyclo-(3.1.002,4)-hexane

The structure of tricyclo-(3.1.00^2,4)exane has been determined by gas phase electron diffraction. The molecule has an inversion centre. The mean carbon—carbon bond length, averaged over both three- and four-membered rings is 1.508 A. A model with equal C-C bond lengths fits to the measured diffraction intensities. The four-membered ring is planar with valency angles of 90°, while the carbon atoms of the three-membered rings form isosceles triangles. Ab initio quantum mechanical calculations at the STO-3G level support this geometry. The valency angle CCC (between three- and four-membered rings) for the equilateral four-membered ring model has been found experimentally to be 109.9°. The average C-H bond distance (1.080 Å) is small as a result of increased s-character in these bonds in agreement with reported INDO—LMO calculations.     

Activation energy of single-stranded DNA moving through cross-linked polyacrylamide gels at 300 V/cm effect of temperature on sequencing rate in high-electric-field capillary gel electrophoresis

In DNA sequencing, single-stranded DNA fragments are separated by gel electrophoresis. This separation is based on a sieving mechanism where DNA fragments are retarded as they pass through pores in the gel. In this paper, we present the mobility of DNA sequencing fragments as a function of temperature; mobility is determined in 4% T LongRanger gels at an electric field of 300 V/cm. The temperature dependence is compared with the predictions of the biased reptation model. The model predicts that the fragment length for the onset of biased reptation with stretching increases with the square of temperature; the data show that the onset of biased reptation with stretching decreases with temperature. Biased reptation fails to model accurately the temperature dependence of mobility. We analyzed the data and extracted the activation energy for passage of sequencing fragments through the gel. For fragments containing less than ca. 200 bases, the activation energy increases linearly with the number of bases at a rate of 25 J/mol per base; for longer fragments, the activation energy increases at a rate of 6.5 J/mol per base. This transition in the activation energy presumably reflects a change in conformation of the DNA fragments; small fragments exist in a random coil configuration and larger fragments migrate in an elongated configuration.     

On-line strong cation exchange micro-HPLC-ESI-MS/MS for protein identification and process optimization

We have developed an on-line strong cation exchange (SCX)-ESI-MS/MS platform for the rapid identification of proteins contained in mixtures. This platform consists of a SCX precolumn followed by a nanoflow SCX column on-line with an electrospray ion trap mass spectrometer. We also used this platform to study the dynamics of peptide separation/extraction by SCX, in particular to understand the parameters affecting the performance of SCX in multidimensional chromatography. For example, we have demonstrated that the buffer typically used for tryptic digestion of protein mixtures can have a detrimental effect on the chromatographic behaviour of peptides during SCX separations, thereby affecting certain peptide quantitation approaches that rely on reproducible peptide fractionation. We have also demonstrated that band broadening results when a step (discontinuous) gradient approach is used to displace peptides from the SCX precolumn, reducing the separation power of SCX in multidimensional chromatography. In contrast, excellent chromatographic peak shapes are observed when a defined (continuous) gradient is used. Finally, using a tryptic digest of a protein extract derived from human K562 cells, we observed that larger molecular weight peptides are identified using this on-line SCX approach compared to the more conventional reverse phase (RP) LC/MS approach. Both methods used in tandem complement each other and can lead to a greater number of peptide identifications from a given sample.     

Highly sensitive detection of S-nitrosylated proteins by capillary gel electrophoresis with laser induced fluorescence

S-nitrosylated proteins are biomarkers of oxidative damage in aging and Alzheimer's disease (AD). Here, we report a new method for detecting and quantifying nitrosylated proteins by capillary gel electrophoresis with laser induced fluorescence detection (CGE-LIF). Dylight 488 maleimide was used to specifically label thiol group (SH) after switching the S-nitrosothiol (S-NO) to SH in cysteine using the "fluorescence switch" assay. In vitro nitrosylation model-BSA subjected to S-nitrosoglutathione (GSNO) optimized the labeling reactions and characterized the response of the LIF detector. The method proves to be highly sensitive, detecting 1.3 picomolar (pM) concentration of nitrosothiols in nanograms of proteins, which is the lowest limit of detection of nitrosothiols reported to date. We further demonstrated the direct application of this method in monitoring protein nitrosylation damage in MQ mediated human colon adenocarcinoma cells. The nitrosothiol amounts in MQ treated and untreated cells are 14.8±0.2 and 10.4±0.5 pmol/mg of proteins, respectively. We also depicted nitrosylated protein electrophoretic profiles of brain cerebrum of 5-month-old AD transgenic (Tg) mice model. In Tg mice brain, 15.5±0.4 pmol of nitrosothiols/mg of proteins was quantified while wild type contained 11.7±0.3 pmol/mg proteins. The methodology is validated to quantify low levels of S-nitrosylated protein in complex protein mixtures from both physiological and pathological conditions.     

Studies in the Helicene Series NMR. Evidence of ‘Helicene-like’ Conformations in the cis 1,2-Diarylethylenes. Part XVII

The cis and trans isomers of eight 1,2-diarylethylenes, precursors of helicenes, have been studied by NMR. spectroscopy. The observed differences in chemical shifts, specific solvent effects and steric effects (bromo derivatives) can be explained by the contribution of ‘helicenelike’ conformers in the cis isomers.     

On the use of NDO approximate wavefunctions in the evaluation of momentum density and radial momentum density distributions in polyatomic molecules

The use of single determinantal approximate molecular wavefunctions of the LCAO MO NDO type for the calculation of the momentum densityρ(p) and the radial momentum density distributionJ(p) is discussed. In each case, these expressions should be orientationally invariant and the momentum density should be normalized. Combining these two requirements, it is shown that only two approximations are physically significant:

1. NDO wavefunctions are used andρ(p) andI(p) are approximated respectively up to an INDO and a CNDO level;
2. Overlap integrals are explicitly taken into account when solving the Roothaan SCF equations or deorthogonalized NDO functions are employed, together with the unapproximated expressions.

     

New ammunition for the proteomic reactor: strong anion exchange beads and multiple enzymes enhance protein identification and sequence coverage

The enrichment and processing of proteomic samples prior to multi-dimensional chromatography remain a challenge in ‘gel-free’ proteomics. We previously reported the development of a microfluidic device called the “proteomic reactor” that relied on enriching proteins by using strong cation exchange (SCX) followed by trypsin digestion in an interstitial volume as little as 50 nL. Here, we report a novel proteomic reactor that is based on polymeric strong anion exchange (SAX) material to analyse proteomic samples. We also compare the performance of the SAX proteomic reactor to our previously reported SCX proteomic reactor for analysing complex yeast proteomes. Our results indicate that the SAX protein reactor preferentially identifies more acidic peptides and proteins compared to the SCX reactor. We show that the SAX and SCX reactors are complementary and that their combination increases the number of unique peptides and proteins identified by 50%. Furthermore, we show that the number of protein identified can be increased further by up to 40% using different proteolytic enzymes on the proteomic reactor.     

An INDO-LMO and 13C NMR spectroscopic study of the C-H bonds in tetracyclo[3.2.0.02,7.04,6]heptane (quadricyclane) and tricyclo[3.1.0.02,4]hexane

Using an INDO approximation to Von Niessen's charge density localization method, the percent s character of the C atom hybrid orbitals engaged in C-H bonds is computed for a series of open-chain and cyclic saturated and unsaturated hydrocarbons. A semi-empirical linear relationship is found between these quantities and the experimental nuclear spin-spin coupling constants J_CH (standard deviation 4·98 Hz). The experimental values of J_CH were measured for quadricyclane (1) and tricyclo[3.1.0.0^2,4]hexane (2) and were shown to be in fair agreement with the theoretical predictions. An analogous relationship is also established between the percent s character of the involved C atom hybrid orbital and the C-H bond distance, the standard deviation being 0·0040Å. This relation is used in order to predict the different C-H bond lengths in the vibrational ground state of 1 and 2, for which equal CH distances were assumed in the analysis of electron diffraction experiments. The results indicate that molecular geometries can be refined with the use of semi-empirical correlations of the above mentioned type.     

Electronic excitations during grazing scattering of hydrogen atoms on KI(001) and LiF(001) surfaces

The energy loss of hydrogen atoms with energies of 400 eV and 1 keV is studied in coincidence with the number of emitted electrons during grazing scattering from atomically clean and flat KI(001) and LiF(001) surfaces. The energy loss spectra for specific numbers of emitted electrons are analyzed in terms of a binary interaction model based on the formation of transient negative ions via local capture of valence band electrons from anion sites. Based on computer simulations we derive for this interaction scenario probabilities for the production of surface excitons, for electron loss to the conduction band of KI, for emission of electrons, and for formation of negative hydrogen ions. The pronounced differences of data obtained for the two surfaces are attributed to the different electronic structures of KI and LiF.