Structural evolution of sulfur overlayers on Pd(1 1 1)

Low energy ion scattering spectroscopy (LEISS) has been used to characterize the evolution of ordered structures of S on the Pd(1 1 1) surface during annealing. During exposure of the Pd(1 1 1) surface to 0.7 L H₂S at 300 K—conditions that produce the S(√3 × √3)R30 overlayer—the intensity of the Pd LEIS signal decreases and a feature assigned to adsorbed S appears as the adsorbed layer forms. When the surface is held at 300 K after exposure to H₂S is stopped, the LEIS Pd intensity partially recovers and the S signal weakens, presumably as surface S atoms assume their equilibrium positions in the S(√3 × √3)R30 overlayer. Subsequent annealing of the S(√3 × √3)R30 structure at 700 K causes it to convert into a S(√7 × √7)R19 overlayer, whose LEIS spectrum is identical to that of clean Pd(1 1 1). The absence of LEIS evidence for S atoms at the exposed surface of the S(√7 × √7)R19 overlayer is at odds with published models of a mixed Pd-S top layer. Despite the similarity of the LEIS spectra of Pd(1 1 1) and Pd(1 1 1)-S(√7 × √7)R19, their activities for dissociative hydrogen adsorption are very different—the former readily adsorbs hydrogen at 100 K, while the latter does not—suggesting that S exerts its influence on surface chemistry from subsurface locations.     

Quasiracemic crystallization as a tool to assess the accommodation of noncanonical residues in nativelike protein conformations

Quasiracemic crystallization has been used to obtain high-resolution structures of two variants of the villin headpiece subdomain (VHP) that contain a pentafluorophenylalanine (F(5)Phe) residue in the hydrophobic core. In each case, the crystal contained the variant constructed from l-amino acids and the native sequence constructed from d-amino acids. We were motivated to undertake these studies by reports that racemic proteins crystallize more readily than homochiral forms and the prospect that quasiracemic crystallization would enable us to determine whether a polypeptide containing a noncanonical residue can closely mimic the tertiary structure of the native sequence. The results suggest that quasiracemic crystallization may prove to be generally useful for assessing mimicry of naturally evolved protein folding patterns by polypeptides that contain unnatural side-chain or backbone subunits.     

Parallel β-sheet secondary structure is stabilized and terminated by interstrand disulfide cross-linking

Disulfide bonds between Cys residues in adjacent strands of parallel β-sheets are rare among proteins, which suggests that parallel β-sheet structure is not stabilized by such disulfide cross-links. We report experimental results that show, surprisingly, that an interstrand disulfide bond can stabilize parallel β-sheets formed by an autonomously folding peptide in aqueous solution. NMR analysis reveals that parallel β-sheet structure is terminated beyond the disulfide bond, which causes deviation from the extended backbone conformation at one of the Cys residues.     

Uptake,transport, and release of hydrogen from Pd(100)

Understanding the interactions of hydrogen atoms with the surface and the subsurface regions of Pd is critical to the development of advanced energy technologies for hydrogen storage, hydrogen separations, and catalytic conversion processes. While many of the physical and chemical characteristics of the H₂–Pd system are known, the kinetics and thermodynamics of H atom absorption into the bulk, transport from the bulk back to the surface, and desorption from the surface remain unclear. In this work, the kinetics of D₂ release from Pd following exposure to D₂ over a range of pressures and temperatures were measured using temperature programmed desorption. To accurately simulate the kinetics of D₂ release, the continuum-based model of Mavrikakis, et al. (J. Chem. Phys 105, 8398, 1996) was extended to include activation barriers for desorption and transport that depend on D atom concentration in the surface, subsurface and bulk regions of the Pd. The use of concentration dependent barriers improves the ability of the model to predict the hydrogen uptake and release kinetics observed across temperatures ranging from 100 to 600 K.     

Segregation at the surfaces of CuxPd1 − x alloys in the presence of adsorbed S

The influence of adsorbed S on surface segregation in Cu_xPd_1 ? x alloys (S/Cu_xPd_1 ? x) was characterized over a wide range of bulk alloy compositions (x = 0.05 to 0.95) using high-throughput Composition Spread Alloy Film (CSAF) sample libraries. Top-surface and near-surface compositions of the CSAFs were measured as functions of bulk Cu composition, x, and temperature using spatially resolved low energy ion scattering spectroscopy (LEISS) and X-ray photoemission spectroscopy (XPS). Preferential segregation of Cu to the top-surface of the S/Cu_xPd_1 ? x CSAF was observed at all bulk compositions, x, but the extent of Cu segregation to the S/Cu_xPd_1 ? x surface was lower than the Cu segregation to the surface of a clean Cu_xPd_1 ? x CSAF, clear evidence of an S-induced “segregation reversal.” The Langmuir–McLean formulation of the Gibbs isotherm was used to estimate the enthalpy and entropy of Cu segregation to the top-surface, ΔH_seg(x) and ΔS_seg(x), at saturation sulfur coverages. While Cu segregation to the top-surface of the clean Cu_xPd_1 ? x is exothermic (ΔH_seg < 0) for all bulk Cu compositions, it is endothermic (ΔH_seg > 0) for S/Cu_xPd_1 ? x. Segregation to the S/Cu_xPd_1 ? x surface is driven by entropy. Changes in segregation patterns that occur upon adsorption of S onto Cu_xPd_1 ? x appear to be related to formation of energetically favored PdS bonds at the surface, which counterbalance the enthalpic driving forces for Cu segregation to the clean surface.     

Transition state for beta-hydride elimination in alkyl groups on Pt(111)

The transition state for beta-hydride elimination in alkyl groups on the Pt(111) surface has been probed by studying the effects of fluorine substitution on the barriers to beta-hydride elimination, DeltaE++(betaH). Four different fluoroalkyl groups have been formed on the Pt(111) surface by dissociative adsorption of four fluoroalkyl iodides: RCH(2)CH(2)-I (R = CF(3), CF(3)CH(2), and CF(3)CF(2)) and (CF(3))(2)CHCH(2)-I. In the absence of preadsorbed hydrogen, fluoroalkyl groups on the Pt(111) surface dehydrogenate via beta-hydride elimination to form unsaturated fluorocarbons and deposit hydrogen atoms onto the surface. Those hydrogen atoms then hydrogenate the remaining fluoroalkyl groups to produce fluoroalkanes that desorb rapidly from the surface. The kinetics of hydrogenation and fluoroalkane desorption are rate limited by the beta-hydride elimination step and thus serve as measures of the kinetics of beta-hydride elimination. The field effects of the fluorinated substituents increase the barriers to beta-hydride elimination with a reaction constant of rho(F) = 19 +/- 2 kJ/mol. The interpretation of this effect is that the beta-carbon atom in the transition state is cationic, [RC(delta+...)H]++, with respect to the reactant. The field effect of the fluorinated substituent energetically destabilizes the electron deficient beta-carbon atom in the transition state. This is consistent with observations made on the Cu(111) surface; however, the substituent effect is significantly smaller on the Pt(111) surface. On the Pt(111) surface, the transition state for beta-hydride elimination is less polarized with respect to the initial state alkyl group than on the Cu(111) surface.     

Structural mimicry of the α-helix in aqueous solution with an isoatomic α/β/γ-peptide backbone

Artificial mimicry of α-helices offers a basis for development of protein-protein interaction antagonists. Here we report a new type of unnatural peptidic backbone, containing α-, β-, and γ-amino acid residues in an αγααβα repeat pattern, for this purpose. This unnatural hexad has the same number of backbone atoms as a heptad of α residues. Two-dimensional NMR data clearly establish the formation of an α-helix-like conformation in aqueous solution. The helix formed by our 12-mer α/β/γ-peptide is considerably more stable than the α-helix formed by an analogous 14-mer α-peptide, presumably because of the preorganized β and γ residues employed.     

Sheet-like assemblies of charged amphiphilic α/β-peptides at the air-water interface

There is growing interest in the design of molecules that undergo predictable self-assembly. Bioinspired oligomers with well-defined conformational propensities are attractive from this perspective, since they can be constructed from diverse building blocks, and self-assembly can be directed by the identities and sequence of the subunits. Here we describe the structure of monolayers formed at the air-water interface by amphiphilic α/β-peptides with 1:1 alternation of α- and β-amino acid residues along the backbone. Two of the α/β-peptides, one a dianion and the other a dication, were used to determine differences between self-assemblies of the net negatively and positively charged oligomers. Two additional α/β-peptides, both zwitterionic, were designed to favor assembly in a 1:1 molar ratio mixture with parallel orientation of neighboring strands. Monolayers formed by these α/β-peptides at the air-water interface were characterized by surface pressure-area isotherms, grazing incidence X-ray diffraction (GIXD), atomic force microscopy and ATR-FTIR. GIXD data indicate that the α/β-peptide assemblies exhibited diffraction features similar to those of β-sheet-forming α-peptides. The diffraction data allowed the construction of a detailed model of an antiparallel α/β-peptide sheet with a unique pleated structure. One of the α/β-peptide assemblies displayed high stability, unparalleled among previously studied assemblies of α-peptides. ATR-FTIR data suggest that the 1:1 mixture of zwitterionic α/β-peptides assembled in a parallel arrangement resembling that of a typical parallel β-sheet secondary structure formed by α-peptides. This study establishes guidelines for design of amphiphilic α/β-peptides that assemble in a predictable manner at an air-water interface, with control of interstrand orientation through manipulation of Coulombic interactions along the backbone.     

Ketones from Nickel‐Catalyzed Decarboxylative,Non‐Symmetric Cross‐Electrophile Coupling of Carboxylic Acid Esters

Synthesis of the C?C bonds of ketones relies upon one high‐availability reagent (carboxylic acids) and one low‐availability reagent (organometallic reagents or alkyl iodides). We demonstrate here a ketone synthesis that couples two different carboxylic acid esters, N‐hydroxyphthalimide esters and S‐2‐pyridyl thioesters, to form aryl alkyl and dialkyl ketones in high yields. The keys to this approach are the use of a nickel catalyst with an electron‐poor bipyridine or terpyridine ligand, a THF/DMA mixed solvent system, and ZnCl₂ to enhance the reactivity of the NHP ester. The resulting reaction can be used to form ketones that have previously been difficult to access, such as hindered tertiary/tertiary ketones with strained rings and ketones with α‐heteroatoms. The conditions can be employed in the coupling of complex fragments, including a 20‐mer peptide fragment analog of Exendin(9–39) on solid support.