Biomedical subjects

Simon E Lappi

Publications and source records attributed to Simon E Lappi.

6 recordsLinked to original sources

PubMed2007

Study of the packing density and molecular orientation of bimolecular self-assembled monolayers of aromatic and aliphatic organosilanes on silica.

Bimolecular self-assembled monolayers (SAMs) of aromatic and aliphatic chlorosilanes were self-assembled onto silica, and their characteristics were established by contact angle measurement, near-edge X-ray absorption fine structure spectroscopy, and Fourier transform infrared spectroscopy. Three aromatic constituents (phenyltrichlorosilane, benzyltrichlorosilane, and phenethyltrichlorosilane) were studied in combination with four aliphatic coadsorbates (butyltrichlorosilane, butyldimethylchlorosilane, octadecyltrichlorosilane, and octadecyldimethylchlorosilane). Our results demonstrate that whereas SAMs made of trichlorinated organosilanes are densely packed, SAMs prepared from monochlorinated species are less dense and poorly ordered. In mixed systems, trichlorinated aromatics and trichlorinated aliphatics formed SAMs with highly tunable compositions; their surfaces were compositionally homogeneous with no large-scale domain separation. The homogeneous nature of the resulting SAM was a consequence of the formation of in-plane siloxane linkages among neighboring molecules. In contrast, when mixing monochlorinated aliphatics with trichlorinated aromatics, molecular segregation occurred. Although the two shortest aromatic species did not display significant changes in orientation upon mixing with aliphatics, the aromatic species with the longest polymethylene spacer, phenethyltrichlorosilane, displayed markedly different orientation behavior in mixtures of short- and long-chain aliphatics.

Journal Article↗

PubMed2004

Characterization of single- and double-stranded DNA on gold surfaces.

Single- and double-stranded deoxy ribonucleic acid (DNA) molecules attached to self-assembled monolayers (SAMs) on gold surfaces were characterized by a number of optical and electronic spectroscopic techniques. The DNA-modified gold surfaces were prepared through the self-assembly of 6-mercapto-1-hexanol and 5'-C(6)H(12)SH -modified single-stranded DNA (ssDNA). Upon hybridization of the surface-bound probe ssDNA with its complimentary target, formation of double-stranded DNA (dsDNA) on the gold surface is observed and in a competing process, probe ssDNA is desorbed from the gold surface. The competition between hybridization of ssDNA with its complimentary target and ssDNA probe desorption from the gold surface has been investigated in this paper using X-ray photoelectron spectroscopy, chronocoulometry, fluorescence, and polarization modulation-infrared reflection absorption spectroscopy (PM-IRRAS). The formation of dsDNA on the surface was identified by PM-IRRAS by a dsDNA IR signature at approximately 1678 cm(-)(1) that was confirmed by density functional theory calculations of the nucleotides and the nucleotides' base pairs. The presence of dsDNA through the specific DNA hybridization was additionally confirmed by atomic force microscopy through colloidal gold nanoparticle labeling of the target ssDNA. Using these methods, strand loss was observed even for DNA hybridization performed at 25 degrees C for the DNA monolayers studied here consisting of attachment to the gold surfaces by single Au-S bonds. This finding has significant consequence for the application of SAM technology in the detection of oligonucleotide hybridization on gold surfaces.

DNA↗

PubMed2004

Infrared detection of a phenylboronic acid terminated alkane thiol monolayer on gold surfaces.

Polarization modulation infrared reflectance absorption spectroscopy (PM-IRRAS) and infrared reflectance absorption spectroscopy (IRRAS) have been used to characterize the formation of a self-assembled monolayer of N-(3-dihydroxyborylphenyl)-11-mercaptoundecanamide) (abbreviated PBA) on a gold surface and the subsequent binding of various sugars to the PBA adlayer through the phenylboronic acid moiety to form a phenylboronate ester. Vibrationally resonant sum frequency generation (VR-SFG) spectroscopy confirmed the ordering of the substituted phenyl groups of the PBA adlayer on the gold surface. Solution FTIR spectra and density functional theory were used to confirm the identity of the observed vibrational modes on the gold surface of PBA with and without bound sugar. The detection of the binding of glucose on the gold surface was confirmed in part by the presence of a C-O stretching mode of glucose and the observed O-H stretching mode of glucose that is shifted in position relative to the O-H stretching mode of boronic acid. An IR marker mode was also observed at 1734 cm(-1) upon the binding of glucose. Additionally, changes in the peak profile of the B-O stretching band were observed upon binding, confirming formation of a phenylboronate ester on the gold surface. The binding of mannose and lactose were also detected primarily through the IR marker mode at approximately 1736 to 1742 cm(-1) depending on the identity of the bound sugar.

Alkanes↗

PubMed2004

Covalent attachment of a nickel nitrilotriacetic acid group to a germanium attenuated total reflectance element.

The surface of a germanium internal reflectance element (IRE) was modified to bind 6X-histidine (his)-tagged biomolecules. The step-by-step surface modification was monitored via single-pass attenuated total reflectance Fourier transform infrared spectroscopy (ATR-FT-IR). Initially an adlayer of 7-octenyltrimethoxysilane (7-OTMS) was formed on the Ge crystal through the surface hydroxyl groups, which were produced via ozonolysis of the Ge surface. The vinyl moiety of 7-OTMS was oxidized to a carboxylic acid, which was activated by 1,1'-carbonydiimidazole (CDI) to produce a labile imidazole. The labile imidazole that resulted from the CDI coupling was then displaced by the primary amine of nitrilotriacetic acid (NTA). Nickel sulfate was added to the system, and it coordinated with the three carbonyl groups and the nitrogen on NTA, thus leaving the ability of Ni to coordinate with two adjacent histidine residues. Binding of his-tagged biotin to nickel nitrilotriacetic acid (Ni-NTA) was observed by ATR-FT-IR spectroscopy. The surface modification method presented in this paper had minimal nonspecific binding, the Ni-NTA surface was reusable if stored properly, and complete removal of the organic surface was achievable.

Journal Article↗

PubMed2004

Infrared spectra of H(2)16O, H(2)18O and D(2)O in the liquid phase by single-pass attenuated total internal reflection spectroscopy.

Mid-infrared attenuated total internal reflection (ATR) spectra of H(2)16O, H(2)18O and D(2)16O in the liquid state were obtained and normal coordinate analysis was performed based on the potential energy surface obtained from density functional theory (DFT) calculations. Fits of the spectra to multiple Gaussians showed a consistent fit of three bands for the bending region and five bands for the stretching region for three isotopomers, H(2)16O, H(2)18O and D(2)16O. The results are consistent with previous work and build on earlier studies by the inclusion of three isotopomers and mixtures using the advantage of single-pass ATR to obtain high quality spectra of the water stretching bands. DFT calculation of the vibrational spectrum of liquid water was conducted on seven model systems, two systems with periodic boundary conditions (PBC) consisting of four and nine H(2)16O molecules, and five water clusters consisting of 4, 9, 19, 27 and 32 H(2)16O molecules. The PBC and cluster models were used to obtain a representation of bulk water for comparison with experiment. The nine-water PBC model was found to give a good fit to the experimental line shapes. A difference is observed in the broadening of the water bending and stretching vibrations indicative of a difference in the rate of pure dephasing. The nine-water PBC calculation was also used to calculate the wavenumber shifts observed in the water isotopomers.

Deuterium Oxide↗

PubMed2004

Eigenvector mapping: a method for discerning solvent effects on vibrational spectra.

This paper reports a density functional theory (DFT) analysis of the adenine spectra in a hydrogen-bonding environment. We compare the theoretical vibrational spectra of 26 model systems in which water has been hydrogen bonded to adenine with the experimental frequencies of the solid state infrared spectra (150-1700 cm(-1)) of polycrystalline adenine and the experimental frequencies observed in matrix isolation spectra of adenine [J. Phys. Chem. 100 (1996) 3527]. The vibrational eigenvectors of adenine are compared by taking the dot product to determine how the normal modes of the 15-adenine atoms are affected by different hydrogen bonding geometries. Using the isolated adenine molecule as a reference permits a comparison of different calculated spectra in terms of the projections of various normal modes and the determination of the potential energy redistribution among normal modes. This method creates a map of the normal modes using the isolated adenine molecule as a reference. Improvement in agreement between the polycrystalline data and a model of adenine with four waters is most striking. The improvement in the fit between matrix isolation data and a model of adenine with a single water was not as dramatic as the fit seen for the polycrystalline data, but the fact that a single hydrogen-bonded water shifted the spectra of the model to a closer fit than that of isolated adenine is important. We call this method eigenvector mapping. The eigenvector mapping method can be used to extract the normal modes of a parent molecule from a solvent model system. The application of this method is important because it aids in the interpretation of complex molecular interactions in terms of the spectrum of an isolated molecule. The eigenvector mapping procedure will be shown to greatly improve the correspondence between the model and the experimental data.

Adenine↗