A solid-state NMR study of the dynamics and interactions of phenylalanine rings in a statherin fragment bound to hydroxyapatite crystals

Extracellular matrix proteins regulate hard tissue growth by acting as adhesion sites for cells, by triggering cell signaling pathways, and by directly regulating the primary and/or secondary crystallization of hydroxyapatite, the mineral component of bone and teeth. Despite the key role that these proteins play in the regulation of hard tissue growth in humans, the exact mechanism used by these proteins to recognize mineral surfaces is poorly understood. Interactions between mineral surfaces and proteins very likely involve specific contacts between the lattice and the protein side chains, so elucidation of the nature of interactions between protein side chains and their corresponding inorganic mineral surfaces will provide insight into the recognition and regulation of hard tissue growth. Isotropic chemical shifts, chemical shift anisotropies (CSAs), NMR line-width information, (13)C rotating frame relaxation measurements, as well as direct detection of correlations between (13)C spins on protein side chains and (31)P spins in the crystal surface with REDOR NMR show that, in the peptide fragment derived from the N-terminal 15 amino acids of salivary statherin (i.e., SN-15), the side chain of the phenylalanine nearest the C-terminus of the peptide (F14) is dynamically constrained and oriented near the surface, whereas the side chain of the phenylalanine located nearest to the peptide's N-terminus (F7) is more mobile and is oriented away from the hydroxyapatite surface. The relative dynamics and proximities of F7 and F14 to the surface together with prior data obtained for the side chain of SN-15's unique lysine (i.e., K6) were used to construct a new picture for the structure of the surface-bound peptide and its orientation to the crystal surface.     

A REDOR NMR study of a phosphorylated statherin fragment bound to hydroxyapatite crystals

Hydroxyapatite (HAP) is the main mineral component of teeth. It is well-known that several salivary proteins and peptides bind strongly to HAP to regulate crystal growth. Interactions between a peptide derived from the N-terminal fragment of the salivary protein statherin and HAP were measured utilizing rotational-echo double-resonance (REDOR) nuclear magnetic resonance (NMR). The REDOR measurement from the side chain of the salivary peptide to the HAP surface is complicated by two effects: a possible additional dipolar coupling to a phosphorylated side chain and the potential proximity of phosphorus atoms to each other, resulting in a homonuclear dipolar interaction. Both of these effects were addressed, and the smallest model applicable to our system includes the nitrogen-15 (15N) spin in the lysine side chain and two phosphorus-31 (31P) spins, at least one of which must be from the surface phosphates of the HAP.     

Homonuclear and heteronuclear NMR studies of a statherin fragment bound to hydroxyapatite crystals

Acidic proteins found in mineralized tissues act as nature's crystal engineers, where they play a key role in promoting or inhibiting the growth of minerals such as hydroxyapatite (HAP), Ca10(PO4)6(OH)2, the main mineral component of bone and teeth. Key to understanding the structural basis of protein-crystal recognition and protein control of hard tissue growth is the nature of interactions between the protein side chains and the crystal surface. In an earlier work we have measured the proximity of the lysine (K6) side chain in an SN-15 peptide fragment of the salivary protein statherin adsorbed to the Phosphorus-rich surface of HAP using solid-state NMR recoupling experiments. 15N{31P} rotational echo double resonance (REDOR) NMR data on the side-chain nitrogen in K6 gave rise to three different models of protein-surface interaction to explain the experimental data acquired. In this work we extend the analysis of the REDOR data by examining the contribution of interactions between surface phosphorus atoms to the observed 15N REDOR decay. We performed 31P-31P recoupling experiments in HAP and (NH4)2HPO4 (DHP) to explore the nature of dipolar coupled 31P spin networks. These studies indicate that extensive networks of dipolar coupled 31P spins can be represented as stronger effective dipolar couplings, the existence of which must be included in the analysis of REDOR data. We carried out 15N{31P} REDOR in the case of DHP to determine how the size of the dephasing spin network influences the interpretation of the REDOR data. Although use of an extended 31P coupled spin network simulates the REDOR data well, a simplified 31P dephasing system composed of two spins with a larger dipolar coupling also simulates the REDOR data and only perturbs the heteronuclear couplings very slightly. The 31P-31P dipolar couplings between phosphorus nuclei in HAP can be replaced by an effective dipolar interaction of 600 Hz between two 31P spins. We incorporated this coupling and applied the above approach to reanalyze the 15N{31P} REDOR of the lysine side chain approaching the HAP surface and have refined the binding models proposed earlier. We obtain 15N-31P distances between 3.3 and 5 A from these models that are indicative of the possibility of a lysine-phosphate hydrogen bond.     

Control of surface properties using fluorinated polymer brushes produced by surface-initiated controlled radical polymerization

Surface-grafted styrene-based homopolymer and diblock copolymer brushes bearing semifluorinated alkyl side groups were synthesized by nitroxide-mediated controlled radical polymerization on planar silicon oxide surfaces. The polymer brushes were characterized by X-ray photoelectron spectroscopy (XPS), near-edge X-ray absorption fine structure (NEXAFS), and time-dependent water contact angle measurements. Angle-resolved XPS studies and water contact angle measurements showed that, in the case of the diblock copolymer brushes, the second block to be added was always exposed at the polymer-air interface regardless of its surface energy. Values of z*/Rg were estimated based on the radius of gyration, Rg, of the grafted homopolymer or block copolymer chains for the grafted brushes and thickness of the brush, z*. The fact that z*/Rg > 1 suggests that all these brushes are stretched. These results support the idea that after grafting the first block onto the surface the nitroxide-end capped polymer chains were able to polymerize the second block in a "living" fashion and the stretched brush so formed was dense enough that the outermost block in all cases completely covers the surface. NEXAFS analysis showed a relationship between the surface orientation of the fluorinated side chains and brush thickness with thicker brushes having more oriented side chains. Time-dependent water contact angle measurements revealed that the orientation of the side chains of the brush improved the surface stability toward reconstruction upon prolonged exposure to water.     

Solvent dependence of the molecular order in ion-exchanged self-assembled dialkylammonium monolayers on mica studied with soft X-ray absorption

Dialkyldimethylammonium films on mica prepared via ion exchange from solution have been reported to be of high quality in terms of their density and molecular orientation. Different preparation procedures are described in the literature. The molecular order and the inclination of the alkyl chains, however, are often deduced from indirect experimental evidence such as the wettability and the film thickness. In the present study we employed near edge X-ray absorption fine structure spectroscopy (NEXAFS) to determine directly the order of the molecules adsorbed from different solvents (water, methanol, water/methanol 1:1, cyclohexanol, and chloroform). It was found that films prepared from different solvents are displaying large differences in the established surface coverage and orientation. In particular, NEXAFS disclosed that the orientation of the alkyl chains can differ significantly even when similar water contact angle values are observed.     

Semifluorinated side group poly(oxyethylene) derivatives having extremely low surface energy: Synthesis, characterization, and surface properties

Poly[oxy[[2-(perfluorooctyl)ethyl]thiomethyl]ethylene]s (H2F8TP-Xs, where X is mole% of perfluorooctyl groups in the side chain) with different levels of conversion were synthesized using polymer analogous reactions from poly[oxy(chloromethyl)ethylene] and 2-perfluorooctyl ethane thioacetate. H2F8TP-20, 41, 64, and 85 were obtained by changing the poly[oxy(chloromethyl)ethylene] to 2-perfluorooctyl ethane thioacetate mole ratio in the reaction from 0.35 to 1.50. H2F8TP-85 (85% conversion) was found to have an extremely low surface energy of 6.2 mN/m at room temperature, which was attributed to the highly ordered perfluorinated alkyl groups on the surface as a result of phase separation between the perfluorinated side chain part and the hydrogenated flexible backbone. The films of the polymers were characterized by electron spectroscopy for chemical analysis (ESCA) and near edge X-ray absorption fine structure (NEXAFS).     

Measuring molecular order in poly(3-alkylthiophene) thin films with polarizing spectroscopies

We measured the molecular order of poly(3-alkylthiophene) chains in thin films before and after melting through the combination of several polarized photon spectroscopies: infrared (IR) absorption, variable angle spectroscopic ellipsometry (SE), and near-edge X-ray absorption fine structure (NEXAFS). The data from the various techniques can be uniformly treated in the context of the dielectric constant tensor epsilon for the film. The combined spectroscopies allow determination of the orientation distribution of the main-chain axis (SE and IR), the conjugated pi system normal (NEXAFS), and the side-chain axis (IR). We find significant improvement in the backbone order of the films after recrystallization of the material at temperatures just below the melting temperature. Less aggressive thermal treatments are less effective. IR studies show that the changes in backbone structure occur without significant alteration of the structure of the alkyl side chains. The data indicate that the side chains exhibit significant disorder for all films regardless of the thermal history of the sample.     

Anti-biofouling properties of comblike block copolymers with amphiphilic side chains

Surfaces of novel block copolymers with amphiphilic side chains were studied for their ability to influence the adhesion of marine organisms. The surface-active polymer, obtained by grafting fluorinated molecules with hydrophobic and hydrophilic blocks to a block copolymer precursor, showed interesting bioadhesion properties. Two different algal species, one of which adhered strongly to hydrophobic surfaces, and the other, to hydrophilic surfaces, showed notably weak adhesion to the amphiphilic surfaces. Both organisms are known to secrete adhesive macromolecules, with apparently different wetting characteristics, to attach to underwater surfaces. The ability of the amphiphilic surface to undergo an environment-dependent transformation in surface chemistry when in contact with the extracellular polymeric substances is a possible reason for its antifouling nature. Near-edge X-ray absorption fine structure spectroscopy (NEXAFS) was used, in a new approach based on angle-resolved X-ray photoelectron spectroscopy (XPS), to determine the variation in chemical composition within the top few nanometers of the surface and also to study the surface segregation of the amphiphilic block. A mathematical model to extract depth-profile information from the normalized NEXAFS partial electron yield is developed.     

Adsorption geometry and core excitation spectra of three phenylpropene isomers on Cu(111)

Theoretical C 1s near edge x-ray absorption fine structure (NEXAFS) spectra for the C(9)H(10) isomers trans-methylstyrene, alpha-methylstyrene, and allylbenzene in gas phase and adsorbed at Cu(111) surfaces have been obtained from density functional theory calculations where adsorbate geometries were determined by corresponding total energy optimizations. The three species show characteristic differences in widths and peak shapes of the lowest C 1s-->pi(*) transitions which are explained by different coupling of the pi-electron system of the C(6) ring with that of the side chain in the molecules as well as by the existence of nonequivalent carbon centers. The adsorbed molecules bind only weakly with the substrate which makes the use of theoretical NEXAFS spectra of the oriented free molecules meaningful for an interpretation of experimental angle-resolved NEXAFS spectra of the adsorbate systems obtained in this work. However, a detailed quantitative account of relative peak intensities requires theoretical angle-resolved NEXAFS spectra of the complete adsorbate systems which have been evaluated within the surface cluster approach. The comparison with experiment yields almost perfect agreement and confirms the reliability of the calculated equilibrium geometries of the adsorbates. This can help to explain observed differences in the catalytic epoxidation of the three molecules on Cu(111) based on purely geometric considerations.     

Orientational relationship among main and side chains of a polyimide alignment layer,liquid crystals monolayer and bulk pretilt angle

We have determined the orientational distribution of cyano-substituted side chains of a rubbed polyimide film, and a liquid crystal monolayer adsorbed on the film, by means of optical second harmonic generation. With the orientational distribution of a main chain that was measured in a previous study by means of near-edge X-ray absorption fine structure (NEXAFS) spectroscopy, we have obtained the correlation of all the orientational distributions contributing to the alignment of LC molecules, i.e. pretilt angle. We find that the side chain plays a role in increasing the pretilt angle, but in the case of rubbing strength dependence, the main chain has stronger correlation with the pretilt angle than has the side chain.     

Self-assembled carbon nanotubes on gold: polarization-modulated infrared reflection-absorption spectroscopy, high-resolution X-ray photoemission spectroscopy, and near-edge X-ray absorption fine structure spectroscopy study

Recently we reported noncovalent functionalization of nanotubes in an aqueous medium with ionic liquid-based surfactants, 1-dodecyl-3-methylimidazolium bromide (1) and 1-(12-mercaptododecyl)-3-methylimidazolium bromide (2), resulting in positively charged single-wall carbon nanotube (SWNT)-1,2 composites. Thiolation of SWNTs with 2 provides their self-assembly on gold as well as templating gold nanoparticles on SWNT sidewalls via a covalent -S-Au bond. In this investigation, we studied the electronic structure, intermolecular interactions, and packing within noncovalently thiolated SWNTs and also nanotube alignment in the bulk of SWNT-2 dried droplets and self-assembled submonolayers (SAMs) on gold by high-resolution X-ray photoemission spectroscopy (HRXPS), C K-edge X-ray absorption fine structure (NEXAFS) spectroscopy, and polarization-modulated infrared reflection-absorption spectroscopy (PM-IRRAS). HRXPS data confirmed the noncovalent nature of interactions within the nanocomposite of thiolated nanotubes. In PM-IRRAS spectra of SWNT SAMs on gold, the IR-active vibrational SWNT modes have been observed and identified. According to PM-IRRAS data, the hydrocarbon chains of 2 are oriented with less tilt angle to the bare gold normal in a SAM deposited from an SWNT-2 dispersion than those of 1 deposited from an SWNT-1 dispersion on the mercaptoethanesulfonic acid-primed gold. For both the dried SWNT-2 bulk and the SWNT-2 SAM on gold, the C K-edge NEXAFS spectra revealed the presence of CH-pi interactions between hydrocarbon chains of 2 and the pi electronic nanotube structure due to the highly resolved vibronic fine structure of carbon 1s --> R*/sigma*C-H series of states in the alkyl chain of 2. For the SWNT-2 bulk, the observed splitting and upshift of the SWNT pi* orbitals in the NEXAFS spectrum indicated the presence of pi-pi interactions. In the NEXAFS spectrum of the SWNT-2 SAM on gold, the upshifted values of the photon energy for R*/sigma*C-H transitions indicated close contact of 2 with nanotubes and with a gold surface. The angle-dependent NEXAFS for the SWNT-2 bulk showed that most of the molecules of 2 are aligned along the nanotubes, which are self-organized with orientation parallel to the substrate plane, whereas the NEXAFS for the SWNT-2 SAM revealed a more normal orientation of functionality 2 on gold compared with that in the SWNT-2 bulk.     

Synthesis of bis‐Phenylalanine,A Novel Eight‐Membered Cyclic Dipeptide

Cyclic eight‐membered ring lactams have been prepared which are formally analogs of Phe‐Ala or Ala‐Phe dipeptides joined together on their side chains. These are termed bis‐phenylalanines because they are phenylalanine with respect to both of the residues in which the phenyl ring is shared between the two. The key synthetic step was the Negishi coupling of Boc‐β‐I‐Ala methyl ester with a suitably protected 2′‐I phenylalanine.     

Orientational relationship among main and side chains of a polyimide alignment layer, liquid crystals monolayer and bulk pretilt angle

We have determined the orientational distribution of cyano-substituted side chains of a rubbed polyimide film, and a liquid crystal monolayer adsorbed on the film, by means of optical second harmonic generation. With the orientational distribution of a main chain that was measured in a previous study by means of near-edge X-ray absorption fine structure (NEXAFS) spectroscopy, we have obtained the correlation of all the orientational distributions contributing to the alignment of LC molecules, i.e. pretilt angle. We find that the side chain plays a role in increasing the pretilt angle, but in the case of rubbing strength dependence, the main chain has stronger correlation with the pretilt angle than has the side chain.     

Electronic structure of C60 on Au(887)

We present an analysis of the electronic structure of C60 adsorbed on a vicinal Au(111) surface at different fullerene coverages using photoemission, x-ray absorption, and scanning tunneling microscopy/spectroscopy (STS). STS provides a straightforward determination of the highest occupied molecular orbital (HOMO) and the lowest unoccupied molecular orbital (LUMO) levels with respect to the Fermi energy. At C60 coverages of 0.5 and 1 ML a 2.7 eV wide HOMO-LUMO gap is found. The near-edge x-ray absorption fine structure (NEXAFS) spectrum for the 0.5 ML C60 nanomesh structure displays a significant intensity at the low energy side of the LUMO exciton peak, which is explained as due to absorption into HOMO-LUMO gap states localized at individual C60 cluster edges. From 0.5 to 1 ML we observe a rigid shift of the HOMO-LUMO peaks in the STS spectra and an almost complete quenching of the gap states feature in NEXAFS.     

Geometric and electronic structures of NO dimer layers on Rh(111) studied with near edge x-ray absorption fine structure spectroscopy: experiment and theory

Adsorption of NO on the Rh(111) surface has been studied in the monolayer, bilayer, and multilayer regimes with near edge x-ray absorption fine structure (NEXAFS) spectroscopy. NO dimer layers are formed on a chemisorbed monomer layer. The polarization dependence in the NEXAFS spectra of the dimer components has contradicted the previous assignments. To determine the structure of the NO dimer layers from the polarization analysis of the NEXAFS spectra, ab initio configuration interaction calculations have been carried out for some low-lying core excited states of the weakly bound NO dimer with cis-ONNO planar geometry. It is revealed that the NO dimers in the multilayer are standing with the N-N bond perpendicular to the surface, while in the second layer they are rather lying on the first monomer layer.     

Aromatic-aromatic interactions in crystal structures of helical peptide scaffolds containing projecting phenylalanine residues

Aromatic-aromatic interactions between phenylalanine side chains in peptides have been probed by the structure determination in crystals of three peptides: Boc-Val-Ala-Phe-Aib-Val-Ala-Phe-Aib-OMe, I; Boc-Val-Ala-Phe-Aib-Val-Ala-Phe-Aib-Val-Ala-Phe-Aib-OMe, II; Boc-Aib-Ala-Phe-Aib-Phe-Ala-Val-Aib-OMe, III. X-ray diffraction studies reveal that all three peptides adopt helical conformations in the solid state with the Phe side chains projecting outward. Interhelix association in the crystals is promoted by Phe-Phe interactions. A total of 15 unique aromatic pairs have been characterized in the three independent crystal structures. In peptides I and II, the aromatic side chains lie on the same face of the helix at i/i + 4 positions resulting in both intrahelix and interhelix aromatic interactions. In peptide III, the Phe side chains are placed on the opposite faces of the helix, resulting in exclusive intermolecular aromatic interactions. The distances between the centroids of aromatic pair ranges from 5.11 to 6.86 A, while the distance of closest approach of ring carbon atoms ranges from 3.27 to 4.59 A. Examples of T-shaped and parallel-displaced arrangements of aromatic pairs are observed, in addition to several examples of inclined arrangements. The results support the view that the interaction potential for a pair of aromatic rings is relatively broad and rugged with several minima of similar energies, separated by small activation barriers.     

Layer structure estimation of three‐dimensional crystal and two‐dimensional molecular film for fluorinated comb copolymers

Comb copolymers containing both hydrogenated and fluorinated side‐chains were prepared by copolymerization using acrylic or methacrylic monomers in several ratios. The crystal structures of these copolymers and layer structures of their organized molecular films were investigated by wide‐angle X‐ray diffraction (WAXD), small‐angle X‐ray scattering (SAXS), and out‐of plane X‐ray diffraction. Further, to selectively estimate the regularity of shorter fluorocarbon side‐chains, organized molecular films of copolymers were investigated by polarized near‐edge X‐ray adsorption fine structure (NEXAFS) spectroscopy. From the results of these measurements, it was inferred that these copolymers formed highly ordered layer structures, and a long spacing was predominantly determined by the arrangement of hydrogenated side‐chains, except in copolymers having extremely high fluorocarbon contents. In the case of the organized molecular films, the fluorinated side‐chains of methacrylate copolymers cannot form a highly ordered arrangement, whereas those of acrylate copolymers were oriented on monolayers. However, in both cases, the hydrogenated side‐chains predominantly formed layer structures in the organized films, and the fluorinated side‐chains did not contribute to the formation of the layer structures. © 2008 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 46: 534–546, 2008     

Synthesis of a chiral dioxo-cyclam derived from L-phenylalanine and its application to olefin oxidation chemistry

An optically active dioxo-cyclam macrocycle bearing two benzyl side chains derived from phenylalanine has been synthesized; its Ni(II) complex catalyzes the oxidation of olefins using hypochlorite under phase transfer conditions.     

An investigation of complexes of some model tripeptides containing phenylalanine and tyrosine residues with DNA by Fourier1H NMR spectroscopy

Complexes of native and denatured DNA with model tripeptides containing phenylalanine or tyrosine residues flanked by lysine or arginine residues, respectively have been investigated by pulsed Fourier¹H NMR spectroscopy. The existence of shifts into the strong-field region of the signals of aromatic protons of the model tripeptides in the complexes both with native and with denatured DNA has been shown. Results have been obtained that indicate the possibility of the intercalation of the side chains of aromatic amino acid residues into the DNA double helix.     

Rapid, high-yield, solid-phase synthesis of the antitumor antibiotic sansalvamide A using a side-chain-tethered phenylalanine building block

A 10-step solid-phase synthesis of the cytotoxic depsipeptide sansalvamide A (1) has been accomplished in an overall yield of 67% with >95% purity employing polymer-bound phenylalanine building block 2. Both the N- and C-termini of 2 are extended followed by on-resin head-to-tail macrocyclization of the linear peptide in a high yield. This should be a general stategy for the synthesis of diverse libraries of cyclic peptides and depsipeptides that contain exclusively phenylalanine and other hydrophobic side chains.