Y(III) Interactions with Guanine Oligonucleotides Covalently Attached to Aqueous/Solid Interfaces

The binding of Y­(III) ions to surface-immobilized single-stranded 20-mers of guanine was studied using the Eisenthal χ⁽³⁾ technique and AFM. The free energy of binding for Y­(III) to the G₂₀ sequence was found to be −39.5(8) kJ/mol. Furthermore, yttrium binds much more strongly to surface-immobilized oligonucleotides than the divalent metals previously reported. At maximum surface coverage, Y­(III) ion densities range between one to three ions bound per strand. Comparatively, Mg­(II) binds to the G₂₀-functionalized interface in much higher ion densities. This result may be explained, in part, by the larger hydration sphere radius of Y­(III) compared to that of Mg­(II). The ion loading and binding free energy results, in conjunction with other surface and bulk aqueous phase studies, suggest that a fully hydrated +2 or +3 yttrium ion binds to the oligonucleotides through an outer-sphere mechanism. Tapping mode AFM results indicate that oligonucleotide height does not appreciably decrease following Y­(III) binding. These results, together with the low ion densities for Y­(III) ions, indicate that Y­(III) strand loading may not significantly decrease the intrastrand Coulombic repulsions in order to cause a significant decrease in oligomer height

Synthesis and Characterization of Chemically Pure Nanometer-Thin Zero-Valent Iron Films and Their Surfaces

The synthesis and characterization of 15, 25, 50, and 70 nm thin iron films having chemical impurities below the detection limit of various analytical techniques is reported. As established herein, the films are chemically pure and formed by electron beam deposition from inexpensive and readily available iron sources of 3N5 purity. Chemical purity of the thin films was achieved using mean deposition rates of 0.3 nm/s or higher, at which point the melting point of iron is reached at the iron source surface and a shutter is opened, from which point on the rate of transfer of impurities present in the source to the target is low enough that they are not observed in the film as confirmed via X-ray photoelectron spectroscopy (XPS), reported here for energies between 0 and 1200 eV. Nanoindentation measurements indicate the iron films to be 14 times harder than bulk iron. The iron films are shown by XPS to be coated with a 3 nm thin overlayer of Fe³⁺, which is possibly present in the form of Fe₃O₄, even though other forms of iron oxide are likely to be present as well, as indicated by Raman and XPS spectroscopy. Grazing incidence angle X-ray diffraction experiments indicate the presence of crystalline Fe⁰ with low index faces exposed but no crystallinity of the iron oxide overlayer. Atomic force microscopy of the iron film surfaces indicates narrowing and shifts to lower heights in the height distribution of nanoscale features formed during the film deposition process as the film thickness decreases. Second harmonic generation is then used to determine that the interfacial charge density of the thinnest iron film is −0.007(3) C/m² at pH 7

Importance of Length and Sequence Order on Magnesium Binding to Surface-Bound Oligonucleotides Studied by Second Harmonic Generation and Atomic Force Microscopy

The binding of magnesium ions to surface-bound single-stranded oligonucleotides was studied under aqueous conditions using second harmonic generation (SHG) and atomic force microscopy (AFM). The effect of strand length on the number of Mg­(II) ions bound and their free binding energy was examined for 5-, 10-, 15-, and 20-mers of adenine and guanine at pH 7, 298 K, and 10 mM NaCl. The binding free energies for adenine and guanine sequences were calculated to be −32.1(4) and −35.6(2) kJ/mol, respectively, and invariant with strand length. Furthermore, the ion density for adenine oligonucleotides did not change as strand length increased, with an average value of 2(1) ions/strand. In sharp contrast, guanine oligonucleotides displayed a linear relationship between strand length and ion density, suggesting that cooperativity is important. This data gives predictive capabilities for mixed strands of various lengths, which we exploit for 20-mers of adenines and guanines. In addition, the role sequence order plays in strands of hetero-oligonucleotides was examined for 5′-A₁₀G₁₀-3′, 5′-(AG)₁₀-3′, and 5′-G₁₀A₁₀-3′ (here the -3′ end is chemically modified to bind to the surface). Although the free energy of binding is the same for these three strands (averaged to be −33.3(4) kJ/mol), the total ion density increases when several guanine residues are close to the 3′ end (and thus close to the solid support substrate). To further understand these results, we analyzed the height profiles of the functionalized surfaces with tapping-mode atomic force microscopy (AFM). When comparing the average surface height profiles of the oligonucleotide surfaces pre- and post- Mg­(II) binding, a positive correlation was found between ion density and the subsequent height decrease following Mg­(II) binding, which we attribute to reductions in Coulomb repulsion and strand collapse once a critical number of Mg­(II) ions are bound to the strand

Precipitates of Al(III), Sc(III), and La(III) at the Muscovite–Water Interface

The interaction of Al­(III), Sc­(III), and La­(III) with muscovite–water interfaces was studied at pH 4 and 10 mM NaCl using second harmonic generation (SHG) and X-ray photoelectron spectroscopy (XPS). SHG data for Sc­(III) and La­(III) suggest complete and/or partial irreversible adsorption that is attributed by XPS to the growth of Sc­(III) and La­(III) hydroxides/oxides on the muscovite surface. Al­(III) adsorption appears to coincide with the growth of gibbsite (Al­(OH)₃) deposits on the muscovite surface, as indicated by the magnitude of the interfacial potential computed from the SHG data. This interpretation of the data is consistent with previous studies reporting the epitaxial growth of gibbsite on the muscovite surface under similar conditions. The implication of our findings is that the surface charge density of mica may change (and in the case of Al­(III), even flip sign from negative (mica) to positive (gibbsite)) when Al­(III), Sc­(III), or La­(III) is present in aqueous phases in contact with heterogeneous geochemical media rich in mica-class minerals, even at subsaturation conditions

Hydrocarbon on Carbon: Coherent Vibrational Spectroscopy of Toluene on Graphite

The ability to study the interactions of hydrocarbons on carbon surfaces is an integral step toward gaining a molecular level understanding of the chemical reactions and physical properties occurring on them. Here, we apply vibrational sum frequency generation (SFG) to determine the tilt angle of toluene, a common organic solvent, on millimeter-thick highly oriented pyrolytic graphite (HOPG). The combination of a time-delay technique, which results in the successful suppression of the nonresonant SFG response, and a null angle method is shown to overcome the “strong optical absorber” problem posed by macroscopically thick carbon samples and yields a molecular tilt angle of toluene in the range of 37° to 42° from the surface normal. The implications of this approach for determining the orientation of organic species adsorbed on carbon interfaces, which are important for energy-relevant processes, are discussed

Investigations into Apopinene as a Biorenewable Monomer for Ring-Opening Metathesis Polymerization

The ring-opening metathesis polymerization (ROMP) of apopinene is reported. We find that apopinene reacts with Ru-based metathesis catalysts to provide an all <i>trans</i>-polymer with a polydispersity index (PDI) as low as 1.6 and molecular weights in the 1100 to 15 600 g·mol^–1 range (9–127 monomer units). Because apopinene is readily prepared in one-step from myrtenal or two-steps from α-pinene, both of which are commercially available and naturally abundant, these studies indicate that apopinene might find future use as a new biorenewable precursor for the sustainable production of ROMP-based materials

Zinc Ion–Hydroxyl Interactions at Undecanol-Functionalized Fused Silica/Water Interfaces Using the Eisenthal χ⁽³⁾ Technique

The interaction of Zn²⁺ ions with undecanol-functionalized fused silica/water interfaces was studied directly at the aqueous/solid interface. We characterized the surface functionalization using vibrational sum frequency generation (SFG) and X-ray photoelectron spectroscopy (XPS). We then employed the SHG χ⁽³⁾ technique to determine the degree of silane functionalization, track Zn²⁺ adsorption directly at the hydroxyl-terminated undecanol silane-functionalized fused silica/aqueous interface at pH 7 and 10 mM NaCl concentration, determine the electrostatic and thermodynamic binding parameters, quantify the change in interfacial potential upon zinc ion adsorption, and compare these values to our previous work with glucosamine-functionalized and bare fused silica/water interfaces. The results from the calculated adsorption free energy suggest that 2:1 hydroxyl/metal coordination complexes, which have not been observed with natural carbohydrates in the bulk aqueous phase, are possible in interfacial environments, with direct implications for controlling and predicting coordination chemistry

Uranyl Adsorption at the Muscovite (Mica)/Water Interface Studied by Second Harmonic Generation

Uranyl adsorption at the muscovite (mica)/water interface was studied by second harmonic generation (SHG). Using the nonresonant χ³ technique and the Gouy–Chapman model, the initial surface charge density of the mica surface was determined to be −0.022(1) C/m² at pH 6 and in the presence of dissolved carbonate. Under these same conditions, uranyl adsorption isotherms collected using nonresonant χ³ experiments and resonantly enhanced SHG experiments that probe the ligand-to-metal charge transfer bands of the uranyl cation yielded a uranyl binding constant of 3(1) × 10⁷ M^–1, corresponding to a Gibbs free energy of adsorption of −52.6(8) kJ/mol, and a maximum surface charge density at monolayer uranyl coverage of 0.028(3) C/m². These results suggest favorable adsorption of uranyl ions to the mica interface through strong ion-dipole or hydrogen interactions, with a 1:1 uranyl ion to surface site ratio that is indicative of monovalent cations ((UO₂)₃(OH)₅⁺, (UO₂)₄(OH)₇⁺, UO₂OH⁺, UO₂Cl⁺, UO₂(CH₃COO^–)⁺) binding at the interface, in addition to neutral uranyl species (UO₂(OH)₂ and UO₂CO₃). This work provides benchmark measurements to be used in the improvement of contaminant transport modeling

Arylsilanated SiO_<i>x</i> Surfaces for Mild and Simple Two-Step Click Functionalization with Small Molecules and Oligonucleotides

The conversion of surface-bound aminophenyl groups to azidophenyl moieties on SiO_<i>x</i> surfaces was investigated as part of a mild, simple two-step strategy for “click”-based” surface functionalization with acetylene-functionalized reagents. Small terminal alkynes (phenylacetylene, 1-hexyne) and acetylene-modified single-stranded DNA 20-mers (T₂₀) were then used as model compounds to test the efficiency of the 1,3-dipolar cycloaddition reaction. The identities of surface species were verified, and their coverages were quantified using X-ray photoelectron spectroscopy in the C 1s, N 1s, F 1s, Cl 2p, and P 2p regions. Depending on conditions, the yield of the azidification was in the 30–90% range, and the efficiency of triazole formation depended significantly on the rigidity of the acetylene reactant. Vibrational sum frequency generation was applied to probe the C–H stretching region and test the platform’s viability for minimizing spectral interference in the C–H stretching region. Fluorescence spectroscopy was also performed to verify the presence of fluorescein-tagged DNA single strands that have been coupled to the surface, while label-free DNA hybridization studies by vibrational sum frequency generation spectroscopy readily show the occurrence of duplex formation. Our results suggest that the two-step azidification–click sequence is a viable strategy for readily functionalizing silica and glass surfaces with molecules spanning a wide range of chemical complexity, including biopolymers

Vibrational Sum Frequency Generation Spectroscopy of Secondary Organic Material Produced by Condensational Growth from α‑Pinene Ozonolysis

Secondary organic material (SOM) was produced in a flow tube from α-pinene ozonolysis, and collected particles were analyzed spectroscopically via a nonlinear coherent vibrational spectroscopic technique, namely sum frequency generation (SFG). The SOM precursor α-pinene was injected into the flow tube reactor at concentrations ranging from 0.125 ± 0.01 ppm to 100 ± 3 ppm. The oxidant ozone was varied from 0.15 ± 0.02 to 194 ± 2 ppm. The residence time was 38 ± 1 s. The integrated particle number concentrations, studied using a scanning mobility particle sizer (SMPS), varied from no particles produced up to (1.26 ± 0.02) × 10⁷ cm^–3 for the matrix of reaction conditions. The mode diameters of the aerosols increased from 7.7 nm (geometric standard deviation (gsd), 1.0) all the way to 333.8 nm (gsd, 1.9). The corresponding volume concentrations were as high as (3.0 ± 0.1) × 10¹⁴ nm³ cm^–3. The size distributions indicated access to different particle growth stages, namely condensation, coagulation, or combination of both, depending on reaction conditions. For filter collection and subsequent spectral analysis, reaction conditions were selected that gave a mode diameter of 63 ± 3 nm and 93 ± 3 nm, respectively, and an associated mass concentration of 12 ± 2 μg m^–3 and (1.2 ± 0.1) × 10³ μg m^–3 for an assumed density of 1200 kg m^–3. Teflon filters loaded with 24 ng to 20 μg of SOM were analyzed by SFG. The SFG spectra obtained from particles formed under condensational and coagulative growth conditions were found to be quite similar, indicating that the distribution of SFG-active C–H oscillators is similar for particles prepared under both conditions. The spectral features of these flow-tube particles agreed with those prepared in an earlier study that employed the Harvard Environmental Chamber. The SFG intensity was found to increase linearly with the number of particles, consistent with what is expected from SFG signal production from particles, while it decreased at higher mass loadings of 10 and 20 μg, consistent with the notion that SFG probes the top surface of the SOM material following the complete coverage of the filter. The linear increase in SFG intensity with particle density also supports the notion that the average number of SFG active oscillators per particle is constant for a given particle size, that the particles are present on the collection filters in a random array, and that the particles are not coalesced. The limit of detection of SFG intensity was established as 24 ng of mass on the filter, corresponding to a calculated density of about 100 particles in the laser spot. As established herein, the technique is applicable for detecting low particle number or mass concentrations in ambient air. The related implication is that SFG is useful for short collection times and would therefore provide increased temporal resolution in a locally evolving atmospheric environment