Investigation of nucleation processes under the influence of magnetic fields

The present work demonstrates the possibilities and the limits of the in situ electrochemical scanning tunneling microscopy for investigation of nucleation processes in magnetic fields on the examples of Cu and Co electrodeposition onto Au(111) electrodes from sulfate electrolytes with pH 3. Cyclic voltammograms of Cu in the underpotential range (UPD) exhibit no significant change in the cathodic and anodic peaks recorded in magnetic fields parallel to the surface. In magnetic fields of a permanent magnet, the reconstruction of Au has been annihilated during UPD of Cu. In the overpotential range, the dissolution of Cu is inhibited. This triggers the formation of a Cu–Au surface alloy. The UPD deposition of Co onto Au(111) could be proven without magnetic field, which leads to the formation of two monolayers. The nucleation in an applied field could not be observed due to higher induced fluctuations and microconvective effects. Contribution to special issue “Magnetic field effects in Electrochemistry”.     

Structure and formation of gaseous [C4H5O]+ Ions. II–Ions of the type HCC?\documentclass{article}\pagestyle{empty}\begin{document}$ \mathop {\rm C}\limits^{\rm + } $\end{document}(OH)(CH3)

Loss of an alkyl group X? from acetylenic alcohols HC?C? CX(OH)(CH₃) and gas phase protonation of HC?C? CO? CH₃ are both shown to yield stable HC?C? \documentclass{article}\pagestyle{empty}\begin{document}$ \mathop {\rm C}\limits^{\rm + } $\end{document}(OH)(CH₃) ions. Ions of this structure are unique among all other [C₄H₅O]⁺ isomers by having m/z 43 [C₂H₃O]⁺ as base peak in both the metastable ion and collisional activation spectra. It is concluded that the composite metastable peak for formation of m/z 43 corresponds to two distinct reaction profiles which lead to the same product ion, CH₃\documentclass{article}\pagestyle{empty}\begin{document}$ \mathop {\rm C}\limits^{\rm + } $\end{document}?O, and neutral, HC?CH. It is further shown that the [C₄H₅O]⁺ ions from related alcohols (like HC?C? CH(OH)(CH₃)) which have an α-H atom available for isomerization into energy rich allenyl type molecular ions, consist of a second stable structure, H₂C?\documentclass{article}\pagestyle{empty}\begin{document}$ \mathop {\rm C}\limits^{\rm + } $\end{document}? C(OH)?CH₂.     

Binding and condensation of plasmid DNA onto functionalized carbon nanotubes: toward the construction of nanotube-based gene delivery vectors

Carbon nanotubes (CNTs) constitute a class of nanomaterials that possess characteristics suitable for a variety of possible applications. Their compatibility with aqueous environments has been made possible by the chemical functionalization of their surface, allowing for exploration of their interactions with biological components including mammalian cells. Functionalized CNTs (f-CNTs) are being intensively explored in advanced biotechnological applications ranging from molecular biosensors to cellular growth substrates. We have been exploring the potential of f-CNTs as delivery vehicles of biologically active molecules in view of possible biomedical applications, including vaccination and gene delivery. Recently we reported the capability of ammonium-functionalized single-walled CNTs to penetrate human and murine cells and facilitate the delivery of plasmid DNA leading to expression of marker genes. To optimize f-CNTs as gene delivery vehicles, it is essential to characterize their interactions with DNA. In the present report, we study the interactions of three types of f-CNTs, ammonium-functionalized single-walled and multiwalled carbon nanotubes (SWNT-NH3+; MWNT-NH3+), and lysine-functionalized single-walled carbon nanotubes (SWNT-Lys-NH3+), with plasmid DNA. Nanotube-DNA complexes were analyzed by scanning electron microscopy, surface plasmon resonance, PicoGreen dye exclusion, and agarose gel shift assay. The results indicate that all three types of cationic carbon nanotubes are able to condense DNA to varying degrees, indicating that both nanotube surface area and charge density are critical parameters that determine the interaction and electrostatic complex formation between f-CNTs with DNA. All three different f-CNT types in this study exhibited upregulation of marker gene expression over naked DNA using a mammalian (human) cell line. Differences in the levels of gene expression were correlated with the structural and biophysical data obtained for the f-CNT:DNA complexes to suggest that large surface area leading to very efficient DNA condensation is not necessary for effective gene transfer. However, it will require further investigation to determine whether the degree of binding and tight association between DNA and nanotubes is a desirable trait to increase gene expression efficiency in vitro or in vivo. This study constitutes the first thorough investigation into the physicochemical interactions between cationic functionalized carbon nanotubes and DNA toward construction of carbon nanotube-based gene transfer vector systems.     

Polymer-assisted laser desorption/ionization analysis of small molecular weight compounds

The use of non-polar, small polymers as matrices for the analysis of low molecular weight compounds in polymer-assisted laser desorption/ionization mass spectrometry (PALDI-MS) is demonstrated. The matrices evaluated were either based on an oligothiophene or a benzodioxin backbone. Metallocenes, polycyclic hydrocarbons, a fluorosurfactant, and a subset of small organic compounds with various functionalities, served as model analytes. The mechanism of ionization charge transfer is discussed and ionization potentials for the matrices in the study have been estimated using density functional theory (DFT) calculations. Some of the results are possibly contradictory to the generally accepted limiting conditions for gas-phase charge-transfer reactions. These results are interpreted in the light of energy pooling. Also a new mass calibration procedure for the low-mass region in positive ion mode is presented, and some aspects of the ionization/desorption process leading to radical cations are studied.     

A model explaining declining rate in hydrolysis of lignocellulose substrates with cellobiohydrolase I (cel7A) and endoglucanase I (cel7B) of Trichoderma reesei

It is commonly observed that the rate of enzymatic hydrolysis of solid cellulose substrates declines markedly with time. In this work the mechanism behind the rate reduction was investigated using two dominant cellulases of Trichoderma reesei: exoglucanase Cel7A (formerly known as CBHI) and endoglucanase Cel7B (formerly EGI). Hydrolysis of steam-pretreated spruce (SPS) was performed with Cel7A and Cel7B alone, and in reconstituted mixtures. Throughout the 48-h hydrolysis, soluble products, hydrolysis rates, and enzyme adsorption to the substrate were measured. The hydrolysis rate for both enzymes decreases rapidly with hydrolysis time. Both enzymes adsorbed rapidly to the substrate during hydrolysis. Cel7A and Cel7B cooperate synergistically, and synergism was approximately constant during the SPS hydrolysis. Thermal instability of the enzymes and product inhibition was not the main cause of reduced hydrolysis rates. Adding fresh substrate to substrate previously hydrolyzed for 24 h with Cel7A slightly increased the hydrolysis of SPS; however, the rate increased even more by adding fresh Cel7A. This suggests that enzymes become inactivated while adsorbed to the substrate and that unproductive binding is the main cause of hydrolysis rate reduction. The strongest increase in hydrolysis rate was achieved by adding Cel7B. An improved model is proposed that extends the standard endo-exo synergy model and explains the rapid decrease in hydrolysis rate. It appears that the processive action of Cel7A becomes hindered by obstacles in the lignocellulose substrate. Obstacles created by disordered cellulose chains can be removed by the endo activity of Cel7B, which explains some of the observed synergism between Cel7A and Cel7B. The improved model is supported by adsorption studies during hydrolysis.     

Capillary electrophoretic detection in apolipoprotein E genotyping

We describe the application of capillary electrophoresis to detect DNA fragments, obtained after amplifying a part of the apolipoprotein E (apoE) gene with polymerase chain reaction (PCR). Compared to conventional agarose slab gel electrophoresis (AGE), CE appears the method of choice with regard to resolution and sensitivity, to detect DNA fragments in the range of 20-100 base pairs. Especially discrimination between apoE2/E2 and apoE2/E3 genotypes is more reliable with CE than with AGE, this being of great clinical value in the diagnosis of familiary dysbetalipoproteinemia.     

Density functionals for inorganometallic and organometallic chemistry

We present a database of 21 bond dissociation energies for breaking metal-ligand bonds. The molecules in the metal-ligand bond energy database are AgH, CoH, CoO+, CoOH+, CrCH3+, CuOH2+, FeH, Fe(CO)5, FeO, FeS, LiCl, LiO, MgO, MnCH3NiCH2+, Ni(CO)4, RhC, VCO+, VO, and VS. We have also created databases of metal-ligand bond lengths and atomic ionization potentials. The molecules used for bond lengths are AgH, BeO, CoH, CoO+, FeH, FeO, FeS, LiCl, LiO, MgO, RhC, VO, and VS and the ionization potentials are for the following atoms: C, Co, Cr, Cu, Ni, O, and V. The data were chosen based on their diversity and expected reliability, and they are used along with three previously developed databases (transition metal dimer bond energies and bond lengths and main-group molecular atomization energies) for assessing the accuracy of several kinds of density functionals. In particular, we report tests for 42 previously defined functionals: 2 local spin density approximation (LSDA) functionals, 14 generalized gradient approximation (GGA) methods, 13 hybrid GGA methods, 7 meta GGA methods, and 8 hybrid meta GGA methods. In addition to these functionals, we also examine the effectiveness of scaling the correlation energy by testing 13 functionals with scaled or no gradient-corrected correlation energy, and we find that functionals of this kind are more accurate for metal-metal and metal-ligand bonds than any of the functionals already in the literature. We also present a readjusted GGA and a hybrid GGA with parameters adjusted for metals. When we consider these 57 functionals for metal-ligand and metal-metal bond energies simultaneously with main-group atomization energies, atomic ionization potentials, and bond lengths we find that the most accurate functional is G96LYP, followed closely by MPWLYP1M (new in this article), XLYP, BLYP, and MOHLYP (also new in this article). Four of these five functionals have no Hartree-Fock exchange, and the other has only 5%. As a byproduct of this work we introduce a convenient diagnostic, called the B1 diagnostic, for ascertaining the multireference character in a bond.     

Expanding the genetic code

Although chemists can synthesize virtually any small organic molecule, our ability to rationally manipulate the structures of proteins is quite limited, despite their involvement in virtually every life process. For most proteins, modifications are largely restricted to substitutions among the common 20 amino acids. Herein we describe recent advances that make it possible to add new building blocks to the genetic codes of both prokaryotic and eukaryotic organisms. Over 30 novel amino acids have been genetically encoded in response to unique triplet and quadruplet codons including fluorescent, photoreactive, and redox-active amino acids, glycosylated amino acids, and amino acids with keto, azido, acetylenic, and heavy-atom-containing side chains. By removing the limitations imposed by the existing 20 amino acid code, it should be possible to generate proteins and perhaps entire organisms with new or enhanced properties.