A microscopic study of structural and electronic properties of functionalized silicon surfaces based on first-principles

Surface modification of silicon with organic monolayers tethered to the surface by different linkers is an important process in realizing future (opto-)electronic devices. Understanding the role played by the nature of the linking group and the chain length on the adsorption structures and electronic properties of these assemblies is vital to advance this technology. This Thesis is a study of such properties and contributes in particular to a microscopic understanding of induced changes in the work function of experimentally studied functionalized silicon surfaces. Using first-principles density functional theory (DFT), at the first step, we provide predictions for chemical trends in the work function of hydrogenated silicon (111) surfaces modified with various terminations. For nonpolar terminating atomic species such as F, Cl, Br, and I, the change in the work function is directly proportional to the amount of charge transferred from the surface, thus relating to the difference in electronegativity of the adsorbate and silicon atoms. The change is a monotonic function of coverage in this case, and the work function increases with increasing electronegativity. Polar species such as −TeH, −SeH, −SH, −OH, −NH2, −CH3, and −BH2 do not follow this trend due to the interaction of their dipole with the induced electric field at the surface. In this case, the magnitude and sign of the surface dipole moment need to be considered in addition to the bond dipole to generally describe the change in work function. Compared to hydrogenated surfaces, there is slight increase in the work function of H:Si(111)-XH, where X = Te, Se, and S, whereas reduction is observed for surfaces covered with −OH, −CH3, and −NH2. Next, we study the hydrogen passivated Si(111) surface modified with alkyl chains of the general formula H:Si–(CH2)n–CH2 and H:Si–X–(CH2)n–CH3, where X = NH, O, S and n = (0, 1, 3, 5, 7, 9, 11), at half coverage. For (X)–Hexyl and (X)–Dodecyl functionalization, we also examined various coverages up to full monolayer grafting in order to validate the result of half covered surface and the linker effect on the coverage. We find that it is necessary to take into account the van der Waals interaction between the alkyl chains. The strongest binding is for the oxygen linker, followed by S, N, and C, irrespective of chain length. The result revealed that the sequence of the stability is independent of coverage; however, linkers other than carbon can shift the optimum coverage considerably and allow further packing density. For all linkers apart from sulfur, structural properties, in particular, surface-linker-chain angles, saturate to a single value once n > 3. For sulfur, we identify three regimes, namely, n = 0–3, n = 5–7, and n = 9–11, each with its own characteristic adsorption structures. Where possible, our computational results are shown to be consistent with the available experimental data and show how the fundamental structural properties of modified Si surfaces can be controlled by the choice of linking group and chain length. Later we continue by examining the work function tuning of H:Si(111) over a range of 1.73 eV through adsorption of alkyl monolayers with general formula -[Xhead-group]-(CnH2n)-[Xtail-group], X = O(H), S(H), NH(2). The work function is practically converged at 4 carbons (8 for oxygen), for head-group functionalization. For tail-group functionalization and with both head- and tail-groups, there is an odd-even effect in the behavior of the work function, with peak-to-peak amplitudes of up to 1.7 eV in the oscillations. This behavior is explained through the orientation of the terminal-group's dipole. The shift in the work function is largest for NH2-linked and smallest for SH-linked chains and is rationalized in terms of interface dipoles. Our study reveals that the choice of the head- and/or tail-groups effectively changes the impact of the alkyl chain length on the work function tuning using self-assembled monolayers and this is an important advance in utilizing hybrid functionalized Si surfaces. Bringing together the understanding gained from studying single type functionalization of H:Si(111) with different alkyl chains and bearing in mind how to utilize head-group, tail-group or both as well as monolayer coverage, in the final part of this Thesis we study functionalized H:Si(111) with binary SAMs. Aiming at enhancing work function adjustment together with SAM stability and coverage we choose a range of terminations and linker-chains denoted as –X–(Alkyl) with X = CH3, O(H), S(H), NH(2) and investigate the stability and work function of various binary components grafted onto H:Si(111) surface. Using binary functionalization with -[NH(2)/O(H)/S(H)]-[Hexyl/Dodecyl] we show that work function can be tuned within the interval of 3.65-4.94 eV and furthermore, enhance the SAM’s stability. Although direct Si-C grafted SAMs are less favourable compared to their counterparts with O, N or S linkage, regardless of the ratio, binary functionalized alkyl monolayers with X-alkyl (X = NH, O) is always more stable than single type alkyl functionalization with the same coverage. Our results indicate that it is possible to go beyond the optimum coverage of pure alkyl functionalized SAMs (50%) by adding a linker with the correct choice of the linker. This is very important since dense packed monolayers have fewer defects and deliver higher efficiency. Our results indicate that binary anchoring can modify the charge injection and therefore bond stability while preserving the interface electronic structure.

A novel syndrome of severe neutrophil dysfunction: unresponsiveness confined to chemotaxin-induced functions.

We have identified a patient with a number of neutrophil dysfunctions. The patient was a female baby who lived for 8 months. During her life, she developed severe bacterial infections and showed omphalitis, impaired wound healing, and a pronounced leukocytosis. She was not a patient with leukocyte adhesion deficiency, because all leukocyte CD18 complex proteins were expressed at normal levels. Yet, neutrophil polarization and chemotaxis to platelet-activating factor, leukotriene B4, or formyl-methionyl-leucyl-phenylalanine (FMLP) were completely absent. We found a strong defect in actin polymerization in response to chemotactic stimuli, but only a retarded or even normal reaction with other stimuli. This indicates that the cellular dysfunctions were not due to an intrinsic defect in actin metabolism. Instead, the regulation of actin polymerization with chemotactic stimuli seemed to be defective. We concentrated on FMLP-induced responses in the patient's neutrophils. Functions dependent on activation of complement receptor type 3, such as aggregation or adherence to endothelial cells, were normally induced. Binding to serum-coated coverslips was normal in cell number; however, spreading was not observed. Exocytosis from the specific granules was readily induced. In contrast, FMLP failed to induce a respiratory burst activity or degranulation of the azurophil granules. FMLP induced a normal increase in free intracellular Ca2+, but a decreased formation of diglycerides (especially the 1-O-alkyl,2-acyl compounds). Thus, we have described a patient whose neutrophils show a severe defect in functional activation via chemotaxin receptors, resulting in a selective absence of NADPH oxidase activity, exocytosis from the azurophil granules, and actin polymerization. Our findings show that actin polymerization for neutrophil spreading and locomotion is regulated differently from that for phagocytosis. Also, the release of azurophil and specific granule contents is clearly shown to be regulated in a different way.

Genome-wide association study of Lp-PLA(2) activity and mass in the Framingham Heart Study.

Lipoprotein-associated phospholipase A(2) (Lp-PLA(2)) is an emerging risk factor and therapeutic target for cardiovascular disease. The activity and mass of this enzyme are heritable traits, but major genetic determinants have not been explored in a systematic, genome-wide fashion. We carried out a genome-wide association study of Lp-PLA(2) activity and mass in 6,668 Caucasian subjects from the population-based Framingham Heart Study. Clinical data and genotypes from the Affymetrix 550K SNP array were obtained from the open-access Framingham SHARe project. Each polymorphism that passed quality control was tested for associations with Lp-PLA(2) activity and mass using linear mixed models implemented in the R statistical package, accounting for familial correlations, and controlling for age, sex, smoking, lipid-lowering-medication use, and cohort. For Lp-PLA(2) activity, polymorphisms at four independent loci reached genome-wide significance, including the APOE/APOC1 region on chromosome 19 (p = 6 x 10(-24)); CELSR2/PSRC1 on chromosome 1 (p = 3 x 10(-15)); SCARB1 on chromosome 12 (p = 1x10(-8)) and ZNF259/BUD13 in the APOA5/APOA1 gene region on chromosome 11 (p = 4 x 10(-8)). All of these remained significant after accounting for associations with LDL cholesterol, HDL cholesterol, or triglycerides. For Lp-PLA(2) mass, 12 SNPs achieved genome-wide significance, all clustering in a region on chromosome 6p12.3 near the PLA2G7 gene. Our analyses demonstrate that genetic polymorphisms may contribute to inter-individual variation in Lp-PLA(2) activity and mass.

Partitioning, bioavailability and effects of oestrogens and xeno-oestrogens in the aquatic environment

This review provides insights into the distribution and impact of oestrogens and xeno-oestrogens in the aquatic environment and highlights some significant knowledge gaps in our understanding of endocrine disrupting chemicals. Key areas of uncertainty in the assessment of risk include the role of estuarine sediments in mediating the fate and bioavailability of environmental (xeno)oestrogens (notably their transfer to benthic organisms and estuarine food chains), together with evidence for endocrine disruption in invertebrate populations. Emphasis is placed on using published information to interpret the behaviour and effects of a small number of model compounds thought to contribute to oestrogenic effects in nature; namely, the natural steroid 17 beta -oestradiol (E2) and the synthetic hormone 17 alpha -ethinyloestradiol (EE2), together with the alkyl-phenols octyl- and nonyl-phenol (OP, NP) as oestrogen mimics. Individual sections of the review are devoted to sources and concentrations of (xeno)oestrogens in waterways, sediment partitioning and persistence, bioaccumulation rates and routes, assays and biomarkers of oestrogenicity, and, finally, a synopsis of reproductive and ecological effects in aquatic species.

Ocean-atmosphere trace gas exchange

The oceans contribute significantly to the global emissions of a number of atmospherically important volatile gases, notably those containing sulfur, nitrogen and halogens. Such gases play critical roles not only in global biogeochemical cycling but also in a wide range of atmospheric processes including marine aerosol formation and modification, tropospheric ozone formation and destruction, photooxidant cycling and stratospheric ozone loss. A number of marine emissions are greenhouse gases, others influence the Earth's radiative budget indirectly through aerosol formation and/or by modifying oxidant levels and thus changing the atmospheric lifetime of gases such as methane. In this article we review current literature concerning the physical, chemical and biological controls on the sea-air emissions of a wide range of gases including dimethyl sulphide (DMS), halocarbons, nitrogen-containing gases including ammonia (NH3), amines (including dimethylamine, DMA, and diethylamine, DEA), alkyl nitrates (RONO2) and nitrous oxide (N2O), non-methane hydrocarbons (NMHC) including isoprene and oxygenated (O)VOCs, methane (CH4) and carbon monoxide (CO). Where possible we review the current global emission budgets of these gases as well as known mechanisms for their formation and loss in the surface ocean.

Atmospheric pressure chemical ionisation liquid chromatography/mass spectrometry of bacteriochlorophylls from Chlorobiaceae: characteristic fragmentations

Atmospheric pressure chemical ionisation liquid chromatography/mass spectrometry/mass spectrometry (APCI-LC/MS/MS) has been applied to the study of bacteriochlorophylls c, d, and e of phototrophic prokaryotes. Cultures of Chlorobiaceae containing bacteriochlorophyll c, d or e were examined using a high-resolution high-performance liquid chromatography (HPLC) method and APCI-LC/MS/MS employing post-column addition of formic acid. The results reveal complex distributions of bacteriochlorophyll homologues, with some closely eluting species giving isobaric protonated molecules. On-line LC/MS/MS studies reveal characteristic fragment ions for bacteriochlorophylls c, d, and e. Fragmentations involving loss of the extended alkyl substituents that are unique to bacteriochlorophylls c, d and e and their derivatives have been rationalised by studying the phaeophorbides and the results applied to the direct study of the bacteriochlorophylls.

Predicting physical properties of ionic liquids

A simple method to predict the densities of a range of ionic liquids from their surface tensions, and vice versa, using a surface-tension-weighted molar volume, the parachor, is reported. The parachors of ionic liquids containing 1-alkyl-3-methylimidazolium cations were determined experimentally, but were also calculated directly from their structural compositions using existing parachor contribution data for neutral compounds. The calculated and experimentally determined parachors were remarkably similar, and the latter data were subsequently employed to predict the densities and surface tensions of the investigated ionic liquids. Using a similar approach, the molar refractions of ionic liquids were determined experimentally, as well as calculated using existing molar refraction contribution data for uncharged compounds. The calculated molar refraction data were employed to predict the refractive indices of the ionic liquids from their surface tensions. The errors involved in the refractive index predictions were much higher than the analogous predictions employing the parachor, but nevertheless demonstrated the potential for developing parachor and molar refraction contribution data for ions as tools to predict ionic liquid physical properties.

Biotransformation of Substituted Pyridines with Dioxygenase-containing Microorganisms.

A series of 2-, 3- and 4-substituted pyridines was metabolised using the mutant soil bacterium Pseudomonas putida UV4 which contains a toluene dioxygenase (TDO) enzyme. The regioselectivity of the biotransformation in each case was determined by the position of the substituent. 4-Alkylpyridines were hydroxylated exclusively on the ring to give the corresponding 4-substituted 3-hydroxypyridines, while 3-alkylpyridines were hydroxylated stereoselectively on C-1 of the alkyl group with no evidence of ring hydroxylation. 2-Alkylpyridines gave both ring and side-chain hydroxylation products. Choro- and bromo-substituted pyridines, and pyridine itself, while being poor substrates for P. putida UV4, were converted to some extent to the corresponding 3-hydroxypyridines. These unoptimised biotransformations are rare examples of the direct enzyme-catalysed oxidation of pyridine rings and provide a novel synthetic method for the preparation of substituted pyridinols. Evidence for the involvement of the same TDO enzyme in both ring and side-chain hydroxylation pathways was obtained using a recombinant strain of Escherichia coli (pKST11) containing a cloned gene for TDO. The observed stereoselectivity of the side-chain hydroxylation process in P. putida UV4 was complicated by the action of an alcohol dehydrogenase enzyme in the organism which slowly leads to epimerisation of the initial (R)-alcohol bioproducts by dehydrogenation to the corresponding ketones followed by stereoselective reduction to the (S)-alcohols.

Synthesis and characterisation of polymerisable photochromic spiropyrans: towards photomechanical biomaterials

A methodology for the synthesis of novel polymerisable spiropyrans with photomechanical properties suitable for subsequent copolymerisation with either vinyl or acrylate-based biomaterials is described. UV-vis spectroscopic characterisation of photoisomerism shows that photochromic behaviour with respect to related non-polymerisable compounds is retained and is solvent dependent. In acetone, conventional spiropyran-merocyanine photochromism is observed for nitro-spiropyran derivatives, whereas in dichloromethane both nitro-spiropyrans and spiropyrans isomerise to merocyanines which rapidly form H-aggregates. The monomers were designed such that an alkyl spacer of variable length, both electronically and sterically, separates the polymerisable moiety from the photochromic core and allows steric aspects of the resulting photomechanical behaviour to be explored. (c) 2006 Elsevier Ltd. All rights reserved.

Base free dynamic kinetic resolution of secondary alcohols using ‘piano stool’ complexes of N-heterocyclic carbenes

Piano stool complexes of rhodium and iridium activated by fluorinated and non-fluorinated N-heterocyclic carbene (NHC) ligands were shown to be catalysts for racemization in the one-pot chemoenzymic dynamic kinetic resolution (DKR) of secondary alcohols. Excellent conversions and good enantioselectivities were observed for alkyl aryl and dialkyl secondary alcohols.

Acoustic, volumetric, compressibility and refractivity properties and reduction parameters for the ERAS and Flory models of some homologous series of amines from 298.15 to 328.15 K

The speeds of sound u, densities ? and refractive indices nD of homologous series of mono-, di-, and tri-alkylamines were measured in the temperature range from 298.15 to 328.15 K. Isentropic and isothermal compressibilities ?S and ?T, molar refraction Rm, Eykman’s constant Cm, Rao’s molar sound function R, thermal expansion coefficient a, thermal pressure coefficient ?, and reduction parameters P*, V*, and T* in frameworks of the ERAS model for associated amines and Flory model for tertiary amines have been calculated from the measured experimental data. Applicability of the Rao theory and the ERAS and Flory models have been examined and discussed for the alkyl amines.

High-Pressure Densities and Derived Thermodynamic Properties of Imidazolium-Based Ionic Liquids

This work addresses the experimental measurements of the pressure (0.10 <p/MPa <10.0) and temperature (293.15 <T/K <393.15) dependence of the density and derived thermodynamic properties, such as the isothermal compressibility, the isobaric expansivity, the thermal pressure coefficient, and the pressure dependence of the heat capacity of several imidazolium-based ionic liquids (ILs), namely, 1-butyl-3-methylimidazolium tetrafluoroborate, [bmim][BF4]; 3-methyl-1-octylimidazolium tetrafluoroborate, [omim][BF4]; 1-hexyl-3-methylimidazolium hexafluorophosphate, [hmim][PF6]; 3-methyl-1-octylimidazolium hexafluorophosphate, [omim][PF6]; 1-butyl-2,3-dimethylimidazolium hexafluorophosphate, [bmmim][PF6]; and 1-butyl-3-methylimidazolium trifluoromethansulfonate, [bmim][CF3SO3]. These ILs were chosen to provide an understanding of the influence of the cation alkyl chain length, the number of cation substitutions, and the anion influence on the properties under study. The influence of water content in the density was also studied for the most hydrophobic IL used, [omim][PF6]. A simple ideal-volume model was employed for the prediction of the imidazolium molar volumes at ambient conditions, which proved to agree well with the experimental results.

P(rho)T Measurements of Imidazolium-Based Ionic Liquids

Experimental density measurements are reported, and the derived thermodynamic properties, such as the isothermal compressibility, the isobaric expansivity, and the thermal pressure coefficient are presented as Supporting Information for several imidazolium-based ionic liquids (ILs), namely, 1-ethyl-3-methyl-imidazolium bis(trifluoromethylsulfonyl)imide [C2mim][NTf2], 1-heptyl-3-methyl-imidazolium bis(trifluoromethylsulfonyl)imide [C7mim][NTf2], 1-octyl-3-methyl-imidazolium bis(trifluoromethylsulfonyl)imide [C8mim][NTf2], 1-ethyl-3-methyl-imidazolium tetrafluoroborate [C2mim][BF4], and 1-butyl-3-methyl-imidazolium tricyanomethane [C4mim][C(CN)3] in the pressure (0.10 <p/MPa <30.00) and temperature (293.15 <T/K <393.15) domains. These ILs were chosen to provide an understanding of the influence of the cation alkyl chain length and the anion influence on the properties under study. Experimental densities are correlated with the Tait equation with an average absolute deviation (AAD) less than 0.04 %. Experimental densities are in good agreement with the densities obtained by some recent predictive methods proposed in the literature.

Mutual Solubilities of Water and Hydrophobic Ionic Liquids

The ionic nature of ionic liquids (ILs) results in a unique combination of intrinsic properties that produces increasing interest in the research of these fluids as environmentally friendly "neoteric" solvents. One of the main research fields is their exploitation as solvents for liquid-liquid extractions, but although ILs cannot vaporize leading to air pollution, they present non-negligible miscibility with water that may be the cause of some environmental aquatic risks. It is thus important to know the mutual solubilities between ILs and water before their industrial applications. In this work, the mutual solubilities of hydrophobic yet hygroscopic imidazolium-, pyridinium-, pyrrolidinium-, and piperidinium-based ILs in combination with the anions bis(trifluoromethylsulfonyl)imide, hexafluorophosphate, and tricyanomethane with water were measured between 288.15 and 318.15 K. The effect of the ILs structural combinations, as well as the influence of several factors, namely cation side alkyl chain length, the number of cation substitutions, the cation family, and the anion identity in these mutual solubilities are analyzed and discussed. The hydrophobicity of the anions increases in the order [C(CN)3] <[PF6] <[Tf2N] while the hydrophobicity of the cations increases from [Cnmim] <[Cnmpy] [Cnmpyr] <[Cnmpip] and with the alkyl chain length increase. From experimental measurements of the temperature dependence of ionic liquid solubilities in water, the thermodynamic molar functions of solution, such as Gibbs energy, enthalpy, and entropy at infinite dilution were determined, showing that the solubility of these ILs in water is entropically driven and that the anion solvation at the IL-rich phase controls their solubilities in water. The COSMO-RS, a predictive method based on unimolecular quantum chemistry calculations, was also evaluated for the description of the water-IL binary systems studied, where it showed to be capable of providing an acceptable qualitative agreement with the experimental data.

Mutual Solubilities of Water and the [Cnmim][Tf2N] Hydrophobic Ionic Liquids

Ionic liquids (ILs) have recently garnered increased attention because of their potential environmental benefits as "green" replacements over conventional volatile organic solvents. While ILs cannot significantly volatilize and contribute to air pollution, even the most hydrophobic ones present some miscibility with water posing environmental risks to the aquatic ecosystems. Thus, the knowledge of ILs toxicity and their water solubility must be assessed before an accurate judgment of their environmental benefits and prior to their industrial applications. In this work, the mutual solubilities for [C2-C8mim][Tf2N] (n-alkyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide) and water between 288.15 and 318.15 K at atmospheric pressure were measured. Although these are among the most hydrophobic ionic liquids known, the solubility of water in these compounds is surprisingly large, ranging from 0.17 to 0.36 in mole fraction, while the solubility of these ILs in water is much lower ranging from 3.2 × 10-5 to 1.1 × 10-3 in mole fraction, in the temperature and pressure conditions studied. From the experimental data, the molar thermodynamic functions of solution and solvation such as Gibbs energy, enthalpy, and entropy at infinite dilution were estimated, showing that the solubility of these ILs in water is entropically driven. The predictive capability of COSMO-RS, a model based on unimolecular quantum chemistry calculations, was evaluated for the description of the binary systems investigated providing an acceptable agreement between the model predictions and the experimental data both with the temperature dependence and with the ILs structural variations.