XFEL Microcrystallography of Self-Assembling Silver n-Alkanethiolates.

New synthetic hybrid materials and their increasing complexity have placed growing demands on crystal growth for single-crystal X-ray diffraction analysis. Unfortunately, not all chemical systems are conducive to the isolation of single crystals for traditional characterization. Here, small-molecule serial femtosecond crystallography (smSFX) at atomic resolution (0.833 Å) is employed to characterize microcrystalline silver n-alkanethiolates with various alkyl chain lengths at X-ray free electron laser facilities, resolving long-standing controversies regarding the atomic connectivity and odd-even effects of layer stacking. smSFX provides high-quality crystal structures directly from the powder of the true unknowns, a capability that is particularly useful for systems having notoriously small or defective crystals. We present crystal structures of silver n-butanethiolate (C4), silver n-hexanethiolate (C6), and silver n-nonanethiolate (C9). We show that an odd-even effect originates from the orientation of the terminal methyl group and its role in packing efficiency. We also propose a secondary odd-even effect involving multiple mosaic blocks in the crystals containing even-numbered chains, identified by selected-area electron diffraction measurements. We conclude with a discussion of the merits of the synthetic preparation for the preparation of microdiffraction specimens and compare the long-range order in these crystals to that of self-assembled monolayers.

Single-ion adsorption and switching in carbon nanotubes.

Single-ion detection has, for many years, been the domain of large devices such as the Geiger counter, and studies on interactions of ionized gasses with materials have been limited to large systems. To date, there have been no reports on single gaseous ion interaction with microelectronic devices, and single neutral atom detection techniques have shown only small, barely detectable responses. Here we report the observation of single gaseous ion adsorption on individual carbon nanotubes (CNTs), which, because of the severely restricted one-dimensional current path, experience discrete, quantized resistance increases of over two orders of magnitude. Only positive ions cause changes, by the mechanism of ion potential-induced carrier depletion, which is supported by density functional and Landauer transport theory. Our observations reveal a new single-ion/CNT heterostructure with novel electronic properties, and demonstrate that as electronics are ultimately scaled towards the one-dimensional limit, atomic-scale effects become increasingly important.

Förster resonance energy transfer as a probe of membrane protein folding.

The folding reaction of a ß-barrel membrane protein, outer membrane protein A (OmpA), is probed with Förster resonance energy transfer (FRET) experiments. Four mutants of OmpA were generated in which the donor fluorophore, tryptophan, and acceptor molecule, a naphthalene derivative, are placed in various locations on the protein to report the evolution of distances across the bilayer and across the protein pore during a folding event. Analysis of the FRET efficiencies reveals three timescales for tertiary structure changes associated with insertion and folding into a synthetic bilayer. A narrow pore forms during the initial stage of insertion, followed by bilayer traversal. Finally, a long-time component is attributed to equilibration and relaxation, and may involve global changes such as pore expansion and strand extension. These results augment the existing models that describe concerted insertion and folding events, and highlight the ability of FRET to provide insight into the complex mechanisms of membrane protein folding. This article is part of a Special Issue entitled: Membrane protein structure and function.

Protein structure prediction: do hydrogen bonding and water-mediated interactions suffice?

The many-body physics of hydrogen bond formation in alpha-helices of globular proteins was investigated using a simple physics-based model. Specifically, a context-sensitive hydrogen bond potential, which depends on residue identity and degree of solvent exposure, was used in the framework of the Associated Memory Hamiltonian codes developed previously but without using local-sequence structure matches ("memories"). Molecular dynamics simulations employing the energy function using the context-sensitive hydrogen bond potential alone (the "amnesiac" model) were used to generate low energy structures for three alpha-helical test proteins. The resulting structures were compared to both the X-ray crystal structures of the test proteins and the results obtained using the full Associated Memory Hamiltonian previously used. Results show that the amnesiac Hamiltonian was able to generate structures with reasonably high structural similarity (Q approximately 0.4) to that of the native protein but only with the use of predicted secondary structure information encoding local steric signals. Low energy structures obtained using the amnesiac Hamiltonian without any a priori secondary structure information had considerably less similarity to the native protein structures (Q approximately 0.3). Both sets of results utilizing the amnesiac Hamiltonian are poorer than when local-sequence structure matches are used.

Electric-field control of the tautomerization and metal ion binding reactivity of 8-hydroxyquinoline immobilized to an electrode surface.

Surface-enhanced Raman scattering (SERS) spectra of a metal-complexing ligand, immobilized to a silver electrode surface, exhibits significant structural changes upon application of modest potentials. A detailed spectroscopic investigation shows that the potential applied to the electrode surface governs the tautomerization equilibrium of the immobilized ligand, p-((8-hydroxyquinoline)azo)benzenethiol (SHQ). Potential-dependent SERS spectra reveal that SHQ exists predominantly in a keto-hydrazone tautomeric form at applied potentials that are negative of -300 mV (vs Ag/AgCl), while the enol-azo tautomer is strongly favored at potentials positive of this value. The observed switching of the tautomer population occurs within a narrow range of applied potentials, approximately 200 mV (Ag/AgCl). Electrical control over the tautomerization equilibrium of immobilized SHQ governs the reactivity of the ligand toward metal ion complexation, where the enol-azo tautomer exhibits much greater affinity for metal ion binding compared to its keto-hydrazone counterpart. Accordingly, the potential applied to the electrode can be used to influence metal ion binding of immobilized SHQ through control over the tautomerization equilibrium, to produce an electrically switchable surface for metal ion complexation. Large differences in the electric dipole moment of the two tautomers, estimated from density functional theory calculations, suggested a model where the potential dependence arises from the interaction of the ligand dipole with electric fields that exist at a polarized electrode surface. This model accurately predicts the relative tautomer populations versus applied potential, at interfacial electric fields that are consistent with previous measurements of the vibrational Stark effect at polarized interfaces. Potential applications of this technology to several areas of analytical chemistry are considered.

Potential-dependent surface-enhanced Raman scattering from adsorbed thiocyanate for characterizing silver surfaces with improved reproducibility.

Surface-enhanced Raman scattering (SERS) spectroelectrochemistry is used to characterize electrochemically roughened and highly polished polycrystalline silver SERS-active substrates. Changes in the nitrile stretching vibrational mode of adsorbed thiocyanate are used as an in situ spectroscopic probe: the potential dependence of band position (Stark tuning), shape, and scattering intensity of this mode are measured in order to investigate differences between SERS-active sites found on smooth and roughened electrode surfaces. Results obtained from thiocyanate adsorbed onto two different types of highly polished Ag surfaces (alumina and diamond polishing) show discrete populations of SERS-active adsorption sites that remain stable over a wide potential range. This behavior stands in contrast to that observed on electrochemically roughened surfaces, where very strong Stark tuning, large vibrational bandwidths, and irreversible loss of SERS enhancement upon negative potential excursions can be attributed to a diverse population of labile SERSactive sites that exhibit strong charge-transfer interactions with the adsorbate and large chemical SERS enhancement.

SERS detection of the vibrational Stark effect from nitrile-terminated SAMs to probe electric fields in the diffuse double-layer.

The vibrational Stark effect is observed in the surface-enhanced Raman scattering spectra of self-assembled monolayers functionalized with pendant nitrile groups. Stark tuning of the nitrile-stretching frequency serves as a localized probe of the electric field in the diffuse double layer of a SAM-modified electrochemical interface. Stark-tuning rates at low ionic strength correspond to reasonable values of the local electric (E) field in the double layer. The nitrile-stretching frequency converges on its isotropic value at applied potentials approaching the PZC, which indicates that Stark-tuning of the frequency is a direct probe of the E field at the interface. Loss of the local electric field at high ionic strengths shows that the probe responds to changes in the Debye length of the double layer. The results demonstrate the applicability of this electric-field probe for characterizing the diffuse double-layer region.