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PubMed2005

Surface-enhanced infrared ellipsometry of self-assembled undecanethiol and dodecanethiol monolayers on disordered gold nanoisland substrates.

Infrared spectroscopic ellipsometry (IRSE) is a powerful optical probe of various chemical and physical properties of molecules adsorbed onto solid surfaces. In particular, IRSE can be useful for detecting adsorption-induced changes in the IR spectra of self-assembled monolayers (SAMs), and unlike traditional IR absorption spectroscopies, IRSE provides useful information about the phase of the reflected radiation from the SAMs. However, in the standard IRSE experimental geometry using flat substrates for SAMs, the detectable signal containing these phase data is considerably weaker than the corresponding absorbance data. In our present work, we demonstrate that enhancing the local optical fields at the sample surface through the use of a disordered Au nanoisland substrate can substantially increase both these absorbance and phase signals. We also demonstrate how this surface-enhanced infrared spectroscopic ellipsometry (SEIRSE) can be utilized for straightforward analysis of absorption peak widths, as well as to obtain information about the orientation of the terminal methyl on adsorbed SAMs. As model SAMs for this study, we use undecanethiol (UDT) containing 10 CH(2) units and a terminal CH(3) group, as well as dodecanethiol (DDT) containing 11 CH(2) units with its terminal CH(3) at a different orientation than UDT. We show that surface-enhanced IRSE is sensitive to subtle vibrational signatures of the differently oriented terminal methyls of these two homologous alkanethiol SAMs.

Journal Article↗
PubMed2006

Reaction of 5-40 eV ions with self-assembled monolayers.

The reaction of 5-40 eV O(+) and Ne(+) ions with alkanethiolate and semifluorinated alkanethiolate self-assembled monolayers (SAMs) is studied under ultrahigh vacuum (UHV) conditions. Whereas Ne(+) simply sputters fragments from the surface, O(+) can also abstract surface atoms and break C-C bonds in both the hydrocarbon and fluorocarbon SAM chains. Isotopic labeling experiments reveal that O(+) initially abstracts hydrogen atoms from the outermost two carbon atoms on an alkanethiolate SAM chain. However, the position of the isotopic label quickly becomes scrambled along the chain as the SAM is damaged through continuous ion bombardment. Scanning tunneling microscopy (STM) monitors changes in the SAM conformational structure at various stages during 5 eV ion bombardment. STM images indicate that O(+) reacts less efficiently with dodecanethiolate molecules packed internally within a structural domain than it does with molecules adsorbed at domain boundaries or near defect sites. STM images recorded after Ne(+) bombardment suggest that Ne(+) attacks the SAM exclusively near the domain boundaries. Taken collectively, these experiments advance our understanding of the degradation pathways suffered by polymeric satellite materials in the low-earth orbit (LEO) space environment.

Gold↗
PubMed2006

Dynamics of the interaction of vapor-deposited copper with alkanethiolate monolayers: bond insertion, complexation, and penetration pathways.

We have investigated the interaction of vapor-deposited copper with -CH3, -OH, -OCH3, -COOH, and -CO2CH3 terminated alkanethiolate self-assembled monolayers (SAMs) adsorbed on polycrystalline Au using time-of-flight secondary ion mass spectrometry and density functional theory calculations. For -OH, -COOH, and -CO2CH3 terminated SAMs measurements indicate that for all copper coverages there is a competition between Cu atom bond insertion into C-O bonds, stabilization at the SAM/vacuum interface, and penetration to the Au/S interface. In contrast, on a -OCH3 terminated SAM Cu only weakly interacts with the methoxy group and penetrates to the Au substrate, while for a -CH3 terminated SAM deposited copper only penetrates to the Au/S interface. The insertion of copper into C-O terminal group bonds is an activated process. We estimate that the barriers for Cu insertion are 55 +/- 5 kJ mol(-1) for the ester, 50 +/- 5 kJ mol(-1) for the acid, and 55 +/- 5 kJ mol(-1) for the hydroxyl terminated SAMs. The activation barrier for the copper insertion is much higher for the -OCH3 SAM. Copper atoms with energies lower than the activation barrier partition between complexation (weak interaction) with the terminal groups and penetration through the monolayer to the Au/S interface. Weakly stabilized copper atoms at the SAM/vacuum interface slowly penetrate through the monolayer. In contrast to the case of Al deposition, C-O bond insertion is favored over C=O, C-H, and C-C bond insertion.

Journal Article↗
PubMed2006

Time-dependent organization and wettability of decanethiol self-assembled monolayer on Au(111) investigated with STM.

A detailed study on the time-dependent organization of a decanethiol self-assembled monolayer (SAM) at a designed solution concentration onto a Au(111) surface has been performed with scanning tunneling microscopy (STM). The SAMs were prepared by immersing Au(111) into an ethanol solution containing 1 microM decanethiol with different immersion times. STM images revealed the formation process and adlayer structure of the SAMs. It was found that the molecules self-organized into adlayers from random separation to a well-defined structure. From 10 s, small domains with ordered molecular organization appeared, although random molecules could be observed on Au(111) at the very initial stage. At 30 s, the SAM consisted of uniform short stripes. Each stripe consisted of sets of decanethiol mainly containing eight molecules. With the immersion time increasing, the length of the stripes increased. At 5 min, the alkyl chains overlapped each other between the adjacent stripes, indicating the start of a stacked process. After immersing Au(111) in decanethiol solution for 3 days, a densely packed adlayer with a (radical 3 x radical 3)R30 degrees structure was observed. The formation process and structure of decanethiol SAMs are well related to sample preparation conditions. The wettability of the decanethiolate SAM-modified Au(111) surface was also investigated.

Journal Article↗
PubMed2006

Controlled amine functionality in self-assembled monolayers via the hidden amine route: chemical and electronic tunability.

A synthetic strategy for fabricating a dense amine functionalized self-assembled monolayer (SAM) on hydroxylated surfaces is presented. The assembly steps are monitored by X-ray photoelectron spectroscopy, Fourier transform infrared- attenuated total reflection, atomic force microscopy, variable angle spectroscopic ellipsometry, UV-vis surface spectroscopy, contact angle wettability, and contact potential difference measurements. The method applies alkylbromide-trichlorosilane for the fabrication of the SAM followed by surface transformation of the bromine moiety to amine by a two-step procedure: S(N)2 reaction that introduces the hidden amine, phthalimide, followed by the removal of the protecting group and exposing the free amine. The use of phthalimide moiety in the process enabled monitoring the substitution reaction rate on the surface (by absorption spectroscopy) and showed first-order kinetics. The simplicity of the process, nonharsh reagents, and short reaction time allow the use of such SAMs in molecular nanoelectronics applications, where complete control of the used SAM is needed. The different molecular dipole of each step of the process, which is verified by DFT calculations, supports the use of these SAMs as means to tune the electronic properties of semiconductors and for better synergism between SAMs and standard microelectronics processes and devices.

Journal Article↗
PubMed2006

Room-temperature isolation of V(benzene)2 sandwich clusters via soft-landing into n-alkanethiol self-assembled monolayers.

The adsorption state and thermal stability of V(benzene)2 sandwich clusters soft-landed onto a self-assembled monolayer of different chain-length n-alkanethiols (Cn-SAM, n = 8, 12, 16, 18, and 22) were studied by means of infrared reflection absorption spectroscopy (IRAS) and temperature-programmed desorption (TPD). The IRAS measurement confirmed that V(benzene)2 clusters are molecularly adsorbed and maintain a sandwich structure on all of the SAM substrates. In addition, the clusters supported on the SAM substrates are oriented with their molecular axes tilted 70-80 degrees off the surface normal. An Arrhenius analysis of the TPD spectra reveals that the activation energy for the desorption of the supported clusters increases linearly with the chain length of the SAMs. For the longest chain C22-SAM, the activation energy reaches approximately 150 kJ/mol, and the thermal desorption of the supported clusters can be considerably suppressed near room temperature. The clear chain-length-dependent thermal stability of the supported clusters observed here can be explained well in terms of the cluster penetration into the SAM matrixes.

Journal Article↗
PubMed2004

Surface stress, kinetics, and structure of alkanethiol self-assembled monolayers.

The surface stress induced during the formation of alkanethiol self-assembled monolayers (SAMs) on gold from the vapor phase was measured using a micromechanical cantilever-based chemical sensor. Simultaneous in situ thickness measurements were carried out using ellipsometry. Ex situ scanning tunneling microscopy was performed in air to ascertain the final monolayer structure. The evolution of the surface stress induced during coverage-dependent structural phase transitions reveals features not apparent in average ellipsometric thickness measurements. These results show that both the kinetics of SAM formation and the resulting SAM structure are strongly influenced both by the surface structure of the underlying gold substrate and by the impingement rate of the alkanethiol onto the gold surface. In particular, the adsorption onto gold surfaces having large, flat grains produces high-quality self-assembled monolayers. An induced compressive surface stress of 15.9 +/- 0.6 N/m results when a c(4x2) dodecanethiol SAM forms on gold. However, the SAMs formed on small-grained gold are incomplete and an induced surface stress of only 0.51 +/- 0.02 N/m results. The progression to a fully formed SAM whose alkyl chains adopt a vertical (standing-up) orientation is clearly inhibited in the case of a small-grained gold substrate and is promoted in the case of a large-grained gold substrate.

Journal Article↗
PubMed2004

Immobilization of the nanoparticle monolayer onto self-assembled monolayers by combined sterically enhanced hydrophobic and electrophoretic forces.

The immobilization of surface-derivatized gold nanoparticles onto methyl-terminated self-assembled monolayers (SAMs) on gold surface was achieved by the cooperation of hydrophobic and electrophoretic forces. Electrochemical and scanning probe microscopy techniques were utilized to explore the influence of the SAM's structure and properties of the nanoparticle/SAM/gold system. SAMs prepared from 1-decanethiol (DT) and 2-mercapto-3-n-octylthiophene (MOT) were used as hydrophobic substrates. The DT SAM is a closely packed and organized monolayer, which can effectively block the underlying gold and inhibit a variety of solution species including organic and inorganic molecules from penetrating, whereas the MOT monolayer is poorly packed or disorganized (because of a large difference in dimension between the thiophene head and the alkylchain tail) and permeable to many organic probes in aqueous solution but not to inorganic probes. Thus, the MOT monolayer provides a more energetically favorable hydrophobic surface for the penetration and adsorption of organic species than the DT monolayer. This hypothesis is supported by experiments in which the density of hydrophobically immobilized nanoparticles on the MOT SAM is much larger than that on the DT SAM. The results also suggest new approaches for modification of macroscopic surfaces with nanoscopic particles.

Electrochemistry↗
PubMed2004

Molecular simulation study of water interactions with oligo (ethylene glycol)-terminated alkanethiol self-assembled monolayers.

Molecular simulations were performed to study a system consisting of protein (e.g., lysozyme) and self-assembled monolayers (SAMs) terminating with different chemical groups in the presence of explicit water molecules and ions. Mixed SAMs of oligo (ethylene glycol) [S(CH2)4(OCH2CH2)4OH, (OEG)] and hydroxyl-terminated SAMs [S(CH2)4OH] with a mole fraction of OEG at chiOEG = 0.2, 0.5, 0.8, and 1.0 were used in this study. In addition, methyl-terminated SAMs [S(CH2)11CH3] were also studied for comparison. The structural and dynamic behavior of hydration water, the flexibility and conformation state of SAMs, and the orientation and conformation of protein were examined. Simulation results were compared with those of experiments. It appears that there is a correlation between OEG surface resistance to protein adsorption and the surface density of OEG chains, which leads to a large number of tightly bound water molecules around OEG chains and the rapid mobility of hydrated SAM chains.

Journal Article↗
PubMed2005

Systematic control of the packing density of self-assembled monolayers using bidentate and tridentate chelating alkanethiols.

The structural and interfacial properties of self-assembled monolayers (SAMs) on gold derived from the adsorption of a series of 1,1,1-tris(mercaptomethyl)alkanes (i.e., CH3(CH2)mC[CH2SH]3, where m = 9, 11, 13, 15) were investigated. The new SAMs, which possess uniformly low densities of alkyl chains, were characterized by ellipsometry, contact angle goniometry, and polarization modulation infrared reflection absorption spectroscopy. Additional analysis of the SAMs by X-ray photoelectron spectroscopy permitted a direct calculation of the packing densities of the SAMs on gold. The results as a whole, when compared to those obtained on SAMs generated from normal alkanethiols (CH3(CH2)m+2SH), 2-alkylpropane-1,3-dithiols (CH3(CH2)mCH[CH2SH]2), and 2-alkyl-2-methylpropane-1,3-dithiols (CH3(CH2)mC(CH3)[CH2SH]2) having analogous chain lengths, demonstrate that the 1,1,1-tris(mercaptomethyl)alkanes afford SAMs with alkyl chains having the lowest packing density and least conformational order.

Journal Article↗
PubMed2004

Fabrication of microarrays on fused silica plates using the laser-induced backside wet etching method.

A novel approach in the fabrication of microarrays of dye and protein on fused silica plates using the laser-induced backside wet etching (LIBWE) technique is described. The surface of fused silica plates was initially precoated using trimethoxysilane self-assembled monolayers (SAMs) and then etched using the LIBWE method to obtain the desired microstructures on the plate surface. Using this technique, the SAMs on the nonirradiated areas were able to survive the LIBWE process and were used as templates for the subsequent deposition of dye molecules or proteins via chemical bonding or physical adsorption. In the case of fused silica plates precoated with fluorinated SAMs, the LIBWE method is used to remove the SAMs to expose the etched silica surfaces, on which a thin layer of pyranine molecules can be site-selectively deposited using an aqueous solution of pyranine. In another application, an ethanol solution of rhodamine 6G was preferentially deposited onto the nonirradiated areas. In yet another application, bovine serum albumin was preferentially deposited onto the laser-irradiated areas; in this case, the fused silica plates were precoated with poly(ethylene oxide) SAMs. Interestingly, when an aqueous suspension of polystyrene (PS) microbeads was cast onto the fused silica precoated with the fluorinated SAMs, hexagonally close-packed PS microbeads were deposited into the etched cavities. Depositions of the dye, protein, and microbeads were confirmed by visualization using a fluorescence microscope and scanning electron microscope.

Journal Article↗
PubMed2006

Designing highly specific biosensing surfaces using aptamer monolayers on gold.

To build highly specific surfaces using aptamer affinity reagents, the effects of linker and coadsorbents were investigated for maximizing target binding and specificity for aptamer-based self-assembled monolayers (SAMs) supported on gold. An aptamer that binds the protein thrombin was utilized as a model system to compare different mixed monolayer systems toward maximizing binding and selectivity to the immobilized aptamer. Important factors used to optimize binding characteristics of thrombin to the aptamer-based monolayer films include changes in design elements of the linker and different coadsorbent thiols. Binding events measured by surface plasmon resonance (SPR) and ellipsometry showed that the binding performance of the aptamer SAMs depends principally on the linker and to a lesser extent on the coadsorbent. SAMs formed with HS-(CH2)6-OP(O)2O-(CH2CH2O)6-TTTTT-aptamer exhibited a 4-fold increase in binding capacity versus SAMs made using HS-(CH2)6-TTTTT-aptamer. Furthermore, SAMs made using HS-(CH2)6-OP(O)2O-(CH2CH2O)6-TTTTT-aptamer showed nearly complete specificity for thrombin versus bovine serum albumin (BSA, less than 2% bound), while a SAM incorporating a random DNA fragment (HS-(CH2)6-OP(O)2O-(CH2CH2O)6-TTTTT-RANDOM) showed little binding of thrombin. Irrespective of the aptamer-linker system, use of HS-(CH2)11(OCH2CH2)3OH, referred to as EG(3), as a coadsorbent enhanced binding of thrombin by approximately 2.5-fold compared to that of HS-(CH2)6-OH (mercaptohexanol, MCH).

Aptamers, Nucleotide↗
PubMed2006

Gating current flowing through molecules in metal-molecules-metal junctions.

We have assembled two junctions that incorporate redox sites between Hg electrodes by different interactions. In the first junction, Hg-SAM-R//R-SAM-Hg, the redox site (R) are covalently linked to each electrode in self assembled monolayers (SAM-R). In the second junction, Hg-SAM//R//SAM-Hg, the redox sites dissolved in solution are trapped by electrostatic interaction at the SAM formed at the electrodes. The current flowing through these junctions can be controlled by adjusting the potential applied at the electrodes with respect to the redox potential of the species by using an electrochemical system. The current flowing in these two junctions is mediated by the redox sites through different mechanisms. In particular, the current flowing through the Hg-SAM-R//R-SAM-Hg junction occurs through a self exchange mechanism between the redox sites organized at each electrode, while the current flowing through the Hg-SAM//R//SAM-Hg junction is dominated by a redox-cycling mechanism. The systems described here are easy to assemble, well-characterized, yield reproducible data and make it easy to modify the electrical properties of the junctions by changing the nature of the redox centres. For these characteristics they are well suited for collecting fundamental information relevant to the fabrication of molecular switches.

Journal Article↗
PubMed2006

Ozonolysis and photolysis of alkene-terminated self-assembled monolayers on quartz nanoparticles: implications for photochemical aging of organic aerosol particles.

Photolysis of alkene-terminated self assembled monolayers (SAM) deposited on Degussa SiO(2) nanoparticles is studied following oxidation of SAM with a gaseous ozone/oxygen mixture. Infrared cavity ring-down spectroscopy is used to observe gas-phase products generated during ozonolysis and subsequent photolysis of SAM in real time. Reactions taking place during ozonolysis transform alkene-terminated SAM into a photochemically active state capable of photolysis in the tropospheric actinic window (lambda > 295 nm). Formaldehyde and formic acid are the observed photolysis products. Photodissociation action spectra of oxidized SAM and the observed pattern of gas-phase products are consistent with the well-established Criegee mechanism of ozonolysis of terminal alkenes. There is strong evidence for the presence of secondary ozonides (1,3,4-trioxalones) and other peroxides on the oxidized SAM surface. The data imply that photolysis plays a role in atmospheric aging of primary and secondary organic aerosol particles.

Journal Article↗
PubMed2004

Identification of the human mitochondrial S-adenosylmethionine transporter: bacterial expression, reconstitution, functional characterization and tissue distribution.

The mitochondrial carriers are a family of transport proteins that, with a few exceptions, are found in the inner membranes of mitochondria. They shuttle metabolites and cofactors through this membrane, and connect cytoplasmic functions with others in the matrix. SAM (S-adenosylmethionine) has to be transported into the mitochondria where it is converted into S-adenosylhomocysteine in methylation reactions of DNA, RNA and proteins. The transport of SAM has been investigated in rat liver mitochondria, but no protein has ever been associated with this activity. By using information derived from the phylogenetically distant yeast mitochondrial carrier for SAM and from related human expressed sequence tags, a human cDNA sequence was completed. This sequence was overexpressed in bacteria, and its product was purified, reconstituted into phospholipid vesicles and identified from its transport properties as the human mitochondrial SAM carrier (SAMC). Unlike the yeast orthologue, SAMC catalysed virtually only countertransport, exhibited a higher transport affinity for SAM and was strongly inhibited by tannic acid and Bromocresol Purple. SAMC was found to be expressed in all human tissues examined and was localized to the mitochondria. The physiological role of SAMC is probably to exchange cytosolic SAM for mitochondrial S-adenosylhomocysteine. This is the first report describing the identification and characterization of the human SAMC and its gene.

Amino Acid Sequence↗
PubMed2002

The Pneumocystis carinii drug target S-adenosyl-L-methionine:sterol C-24 methyl transferase has a unique substrate preference.

Pneumocystis is an opportunistic pathogen that can cause pneumonitis in immunodeficient people such as AIDS patients. Pneumocystis remains difficult to study in the absence of culture methods for luxuriant growth. Recombinant protein technology now makes it possible to avoid some major obstacles. The P. carinii expressed sequence tag (EST) database contains 11 entries of a sequence encoding a protein homologous to S-adenosyl-L-methionine (SAM):C-24 sterol methyl transferase (SMT), suggesting high activity of this enzyme in the organism. We sequenced the erg6 cDNA, identified the putative peptide motifs for the sterol and SAM binding sites in the deduced amino acid sequence and expressed the protein in Escherichia coli. Unlike SAM:SMT from other organisms, the P. carinii enzyme had higher affinities for lanosterol and 24-methylenelanosterol than for zymosterol, the preferred substrate in other fungi. Cycloartenol was not a productive substrate. With lanosterol and 24-methylenelanosterol as substrates, the major reaction products were 24-methylenelanosterol and pneumocysterol respectively. Thus, the P. carinii SAM:SMT catalysed the transfer of both the first and the second methyl groups to the sterol C-24 position, and the substrate preference was found to be a unique property of the P. carinii SAM:SMT. These observations, together with the absence of SAM:SMT among mammals, further support the identification of sterol C-24 alkylation reactions as excellent targets for the development of drugs specifically directed against this pathogen.

Alkylation↗
PubMed2002

High free-methionine and decreased lignin content result from a mutation in the Arabidopsis S-adenosyl-L-methionine synthetase 3 gene.

As an approach to understand the regulation of methionine (Met) metabolism, Arabidopsis Met over-accumulating mutants were isolated based on their resistance to selection by ethionine. One mutant, mto3, accumulated remarkably high levels of free Met - more than 200-fold that observed for wild type - yet showed little or no difference in the concentrations of other protein amino-acids, such as aspartate, threonine and lysine. Mutant plants did not show any visible growth differences compared with wild type, except a slight delay in germination. Genetic analysis indicated that the mto3 phenotype was caused by a single, recessive mutation. Positional cloning of this gene revealed that it was a novel S-adenosylmethionine synthetase, SAMS3. A point mutation resulting in a single amino-acid change in the ATP binding domain of SAMS3 was determined to be responsible for the mto3 phenotype. SAMS3 gene expression and total SAMS protein were not changed in mto3; however, both total SAMS activity and S-adenosylmethionine (SAM) concentration were decreased in mto3 compared with wild type. Lignin, a major metabolic sink for SAM, was decreased by 22% in mto3 compared with wild type, presumably due to the reduced supply of SAM. These results suggest that SAMS3 has a different function(s) in one carbon metabolism relative to the other members of the SAMS gene family.

Arabidopsis↗
PubMed2002

OsPNH1 regulates leaf development and maintenance of the shoot apical meristem in rice.

The Arabidopsis PINHEAD/ZWILLE (PNH/ZLL) gene is thought to play an important role in the formation of the shoot apical meristem (SAM) and in leaf adaxial cell specification. To investigate the molecular mechanisms of rice development, we have isolated a rice homologue of PNH/ZLL, called OsPNH1. Around the SAM, OsPNH1 was strongly expressed in developing leaf primordia, specifically in the presumptive vascular domains, developing vascular tissues, a few cell-layers of the adaxial region, and future bundle sheath extension cells. In the SAM, only weak expression was observed in the central region, whereas strong expression was detected in the mid-vein region of leaf founder cells in the peripheral SAM domain. We produced transgenic rice plants containing the antisense OsPNH1 strand. The antisense OsPNH1 plants developed malformed leaves with an altered vascular arrangement and abnormal internal structure. These plants also formed an aberrant SAM with reduced KNOX gene expression. We examined the subcellular localization of the OsPNH1-GFP fusion protein and found that it was localized in the cytoplasm. On the basis of these observations, we propose that OsPNH1 functions not only in SAM maintenance as previously thought, but also in leaf formation through vascular development.

Amino Acid Sequence↗