In situ chemical modification of peptide microarrays: application to the study of the antibody responses to methylated antigens.

Peptide microarrays are useful tools for characterizing the humoral response against methylated antigens. They are usually prepared by printing unmodified and methylated peptides on substrates such as functionalized microscope glass slides. The preferential capture of antibodies by methylated peptides suggests the specific recognition of methylated epitopes. However, unmodified peptide epitopes can be masked due to their interaction with the substrate. The accessibility of unmodified peptides and thus the specificity of the recognition of methylated peptide epitopes can be probed using the in situ methylation procedure described here. Alternately, the in situ methylation of peptide microarrays allows probing the presence of antibodies directed toward methylated epitopes starting from easy-to-make and cost-effective unmodified peptide libraries. In situ methylation was performed using formaldehyde in the presence of sodium cyanoborohydride and nickel chloride. This chemical procedure converts lysine residues into mono- or dimethyl lysines.

Surface area, porosity and water adsorption properties of fine volcanic ash particles

Our understanding on how ash particles in volcanic plumes react with coexisting gases and aerosols is still rudimentary, despite the importance of these reactions in influencing the chemistry and dynamics of a plume. In this study, six samples of fine ash (<100 μm) from different volcanoes were measured for their specific surface area, as, porosity and water adsorption properties with the aim to provide insights into the capacity of silicate ash particles to react with gases, including water vapour. To do so, we performed high-resolution nitrogen and water vapour adsorption/desorption experiments at 77 K and 303 K, respectively. The nitrogen data indicated as values in the range 1.1-2.1 m2/g, except in one case where as of 10 m2/g was measured. This high value is attributed to incorporation of hydrothermal phases, such as clay minerals, in the ash surface composition. The data also revealed that the ash samples are essentially non-porous, or have a porosity dominated by macropores with widths >500 Å All the specimens had similar pore size distributions, with a small peak centered around 50 Å These findings suggest that fine ash particles have relatively undifferentiated surface textures, irrespective of the chemical composition and eruption type. Adsorption isotherms for water vapour revealed that the capacity of the ash samples for water adsorption is systematically larger than predicted from the nitrogen adsorption as values. Enhanced reactivity of the ash surface towards water may result from (i) hydration of bulk ash constituents; (ii) hydration of surface compounds; and/or (iii) hydroxylation of the surface of the ash. The later mechanism may lead to irreversible retention of water. Based on these experiments, we predict that volcanic ash is covered by a complete monolayer of water under ambient atmospheric conditions. In addition, capillary condensation within ash pores should allow for deposition of condensed water on to ash particles before water reaches saturation in the plume. The total mass of water vapour retained by 1 g of fine ash at 0.95 relative water vapour pressure is calculated to be ∼10-2 g. Some volcanic implications of this study are discussed. © Springer-Verlag 2004.

Molecular dynamics simulation of adsorption of Ag particles on a graphite substrate

We have performed for the first time a molecular dynamics simulation of the adsorption of gas-phase Ag particles on a graphite substrate to provide an insight into the results of a comprehensive STM-based experiment on this system. Both pair-wise and many-body interatomic potentials have been employed, and a Morse-type Ag–C potential was specifically constructed to describe the interactions at the interface. Our simulation has successfully reproduced a significant portion of the experimental findings. We have also observed the intercalation of silver in graphite.

Modelling the adsorption and imaging of C60 molecules on a graphite substrate

The adsorption of a C60 monolayer on a graphite substrate was modelled via molecular dynamics simulation covering a significant period of 160 picoseconds. The final configuration of C60s agrees closely with that observed in a scanning tunnelling microscopy (STM) experiment. Clusters of adsorbed molecules were then selected and their STM-like images were computed via the Keldysh Green function method.

Numerical modelling of adsorption of metallic particles on graphite substrate via molecular dynamics simulation

A computer-based numerical modelling of the adsorption process of gas phase metallic particles on the surface of a graphite substrate has been performed via the application of molecular dynamics simulation method. The simulation relates to an extensive STM-based experiment performed in this field, and reproduces part of the experimental results. Both two-body and many-body inter-atomic potentials have been employed. A Morse-type potential describing the metal-carbon interactions at the interface was specifically formulated for this modelling. Intercalation of silver in graphite has been observed as well as the correct alignments of monomers, dimers and two-dimensional islands on the surface. PACS numbers: 02.60.Cb, 07.05.Tp, 68.55.-a, 81.05.Tp

Vibrational spectroscopy and DFT calculations of the di-amino acid peptide L-aspartyl-L-glutamic acid in the zwitterionic state

Solid state IR and Raman as well as aqueous solution state Raman spectra are reported for the linear di-amino acid peptide L-aspartyl-L-glutamic acid (L-Asp-L-Glu); the solution state Raman spectrum has also been obtained for the N,O-deuterated derivative. SCF-DFT calculations at the B3-LYP/cc-pVDZ level established that the structure and vibrational spectra of L-Asp-L-Glu can be interpreted using a model of the peptide with ten hydrogen-bonded water molecules, in conjunction with the conductor-like polarizable continuum solvation method. The DFT calculations resulted in the computation of a stable zwitterionic structure, which displays trans-amide conformation. The vibrational spectra were computed at the optimised molecular geometry, enabling normal coordinate analysis, which yielded satisfactory agreement with the experimental IR and Raman data. Computed potential energy distributions of the normal modes provided detailed vibrational assignments.

Vibrational spectra and crystal structure of the di-amino acid peptide cyclo(L-Met-L-Met): Comparison of experimental data and DFT calculations

Experimental Raman and FT-IR spectra of solid-state non-deuterated and N-deuterated samples of cyclo(L-Met-L-Met) are reported and discussed. The Raman and FT-IR results show characteristic amide I vibrations (Raman: 1649 cm-1, infrared: 1675 cm-1) for molecules exhibiting a cis amide conformation. A Raman band, assigned to the cis amide II vibrational mode, is observed at sim1493 cm-1 but no IR band is observed in this region. Cyclo(L-Met-L-Met) crystallises in the triclinic space group P1 with one molecule per unit cell. The overall shape of the diketopiperazine (DKP) ring displays a (slightly distorted) boat conformation. The crystal packing employs two strong hydrogen bonds, which traverse the entire crystal via translational repeats. B3-LYP/cc-pVDZ calculations of the structure of the molecule predict a boat conformation for the DKP ring, in agreement with the experimentally determined X-ray structure. Copyright © 2009 John Wiley & Sons, Ltd.

Vibrational spectroscopy and crystal structure analysis of two polymorphs of the di-amino acid peptide cyclo(L-Glu-L-Glu)

Cyclo(L-Glu-L-Glu) has been crystallised in two different polymorphic forms. Both polymorphs are monoclinic, but form 1 is in space group P21 and form 2 is in space group C2. Raman scattering and FT-IR spectroscopic studies have been conducted for the N,O-protonated and deuterated derivatives. Raman spectra of orientated single crystals, solid-state and aqueous solution samples have also been recorded. The different hydrogen-bonding patterns for the two polymorphs have the greatest effect on vibrational modes with N&bond;H and C&dbond;O stretching character. DFT (B3-LYP/cc-pVDZ) calculations of the isolated cyclo(L-Glu-L-Glu) molecule predict that the minimum energy structure, assuming C2 symmetry, has a boat conformation for the diketopiperazine ring with the two L-Glu side chains being folded above the ring. The calculated geometry is in good agreement with the X-ray crystallographic structures for both polymorphs. Normal coordinate analysis has facilitated the band assignments for the experimental vibrational spectra. Copyright © 2009 John Wiley & Sons, Ltd.