Protection-deprotection chemistry to control styrene self-directed line growth on hydrogen-terminated Si(100)

TEMPO, 2,2,6,6-tetramethylpiperidinyloxy, was used in a series of protection-deprotection chemical reactions in order to gain single molecule-level control over the extent of styrene line growth on hydrogen-terminated Si(100). The mechanism involves the reaction of TEMPO with the dangling bond at the end of individual styrene lines. The TEMPO cap protects the dangling bond from further reaction with styrene resulting in the termination of line growth. TEMPO is then selectively removed from desired lines, deprotecting the dangling bond, using the scanning tunneling microscope. Further exposure of the surface to styrene ensures that only the deprotected areas continue to grow while the protected lines do not. All lines can then be capped with TEMPO, and this allows for the generation of stable styrene lines of varying lengths.     

Templated surfactant readsorption on polyelectrolyte-induced depleted surfactant surfaces

Changes in the structure of a surfactant adsorbed on oxidized silicon arising from interaction with a polyelectrolyte have been studied using polarized infrared attenuated total reflection spectroscopy. Specifically, the cationic surfactant cetyltrimethylammonium bromide (CTAB) was found to form a highly ordered layer on oxidized silicon at a concentration of 5.5 x 10(-5) M and a pH of 9.6. Addition of a solution of the anionic polyelectrolyte poly(styrenesulfonate) to the ordered CTAB layer resulted in a rapid and dramatic decrease in the surface excess of CTAB. Interestingly however, the interfacial order of the residual surfactant was retained for a time period greater than 1 h, before decreasing. Reintroduction of a surfactant solution prior to destabilization of the residual interfacial CTAB resulted in the readsorption of the surfactant, the recovery of the initial equilibrium coverage, and the maintenance of an ordered CTAB conformation. This desorption/readsorption process may be subsequently repeated without destroying the order of the CTAB on the surface. If however sufficient time is allowed for the residual interfacial surfactant to destabilize prior to readdition of CTAB, the degree of surfactant order remains low, despite the rapid reobtainment of a surface excess equal to or greater than that initially measured. These results are interpreted in terms of polymer/surfactant interfacial complexation and the removal of adsorbed surfactant into solution. The ordering behavior of the residual surfactant suggests that CTAB is left on the surface in isolated patches of highly ordered species that maintain their order until two-dimensional diffusion leads to a more homogeneous surfactant surface distribution and hence the loss of conformational order. The degree of orientation order assumed by surfactant readsorbing on a depleted surface appears to be templated by the order of the residual interfacial surfactant, suggestive of a two-dimensional epitaxial growth mechanism for CTAB readsorption.     

Lattice-Boltzmann simulations of the dynamics of polymer solutions in periodic and confined geometries

A numerical method to simulate the dynamics of polymer solutions in confined geometries has been implemented and tested. The method combines a fluctuating lattice-Boltzmann model of the solvent [Ladd, Phys. Rev. Lett. 70, 1339 (1993)] with a point-particle model of the polymer chains. A friction term couples the monomers to the fluid [Ahlrichs and Dunweg, J. Chem. Phys. 111, 8225 (1999)], providing both the hydrodynamic interactions between the monomers and the correlated random forces. The coupled equations for particles and fluid are solved on an inertial time scale, which proves to be surprisingly simple and efficient, avoiding the costly linear algebra associated with Brownian dynamics. Complex confined geometries can be represented by a straightforward mapping of the boundary surfaces onto a regular three-dimensional grid. The hydrodynamic interactions between monomers are shown to compare well with solutions of the Stokes equations down to distances of the order of the grid spacing. Numerical results are presented for the radius of gyration, end-to-end distance, and diffusion coefficient of an isolated polymer chain, ranging from 16 to 1024 monomers in length. The simulations are in excellent agreement with renormalization group calculations for an excluded volume chain. We show that hydrodynamic interactions in large polymers can be systematically coarse-grained to substantially reduce the computational cost of the simulation. Finally, we examine the effects of confinement and flow on the polymer distribution and diffusion constant in a narrow channel. Our results support the qualitative conclusions of recent Brownian dynamics simulations of confined polymers [Jendrejack et al., J. Chem. Phys. 119, 1165 (2003) and Jendrejack et al., J. Chem. Phys. 120, 2513 (2004)].     

A self-assembled multivalent pseudopolyrotaxane for binding galectin-1

A self-assembled pseudopolyrotaxane consisting of lactoside-displaying cyclodextrin (CD) "beads" threaded onto a linear polyviologen "string" was investigated for its ability to inhibit galectin-1-mediated T-cell agglutination. The CDs of the pseudopolyrotaxane are able to spin around the axis of the polymer chain as well as to move back and forth along its backbone to alter the presentation of its ligand. This supramolecular superstructure incorporates all the advantages of polymeric structures, such as the ability to span large distances, along with a distinctively dynamic presentation of its lactoside ligands to afford a neoglycoconjugate that can adjust to the relative stereochemistries of the lectin's binding sites. The pseudopolyrotaxane exhibited a valency-corrected 10-fold enhancement over native lactose in the agglutination assay, which was greater than the enhancements observed for lactoside-bearing trivalent glycoclusters and a lactoside-bearing chitosan polymer tested using the same assay. The experimental results indicate that supramolecular architectures, such as the pseudopolyrotaxane, provide tools for investigating protein-carbohydrate interactions.     

Unprecedented cage-carbon to cage-boron NMe(3) transfer in a monocarbon Molybdenacarborane

The reagent Li(2)[7-NMe(3)-nido-7-CB(10)H(10)] reacts with [Mo(CO)(3)(NCMe)(3)] in THF-NCMe (THF = tetrahydrofuran) to give a molybdenacarborane intermediate which, upon oxidation by CH(2)[double bond]CHCH(2)Br or I(2) and then addition of [N(PPh(3))(2)]Cl, gives the salts [N(PPh(3))(2)][2,2,2-(CO)(3)-2-X-3-NMe(3)-closo-2,1-MoCB(10)H(10)] (X = Br (1) or I (2)). During the reaction, the cage-bound NMe(3) substituent is transferred from the cage-carbon atom to an adjacent cage-boron atom, a feature established spectroscopically in 1 and 2, and by X-ray diffraction studies on several of their derivatives. When [Rh(NCMe)(3)(eta(5)-C(5)Me(5))][BF(4)](2) is used as the oxidizing agent, the trimetallic compound [2,2,2-(CO)(3)-7-mu-H-2,7,11-[Rh(2)(mu-CO)(eta(5)-C(5)Me(5))(2)]-closo-2,1-MoCB(10)H(9)] (10) is formed, the NMe(3) group being lost. Reaction of 1 in CH(2)Cl(2) with Tl[PF(6)] in the presence of donor ligands L affords neutral zwitterionic compounds [2,2,2-(CO)(3)-2-L-3-NMe(3)-closo-2,1-MoCB(10)H(10)] for L = PPh(3) (4) or CNBu(t) (5), and [2-Bu(t)C[triple bond]CH-2,2-(CO)(2)-3-NMe(3)-closo-2,1-MoCB(10)H(10)] (6) when L = Bu(t)C[triple bond]CH. When 1 is treated with CNBu(t) and X(2), the metal center is oxidized, and in the products obtained, [2,2,2,2-(CNBu(t))(4)-2-Br-3-X-closo-2,1-MoCB(10)H(10)] (X = Br (7), I (8)), the B-NMe(3) bond is replaced by B-X. In contrast, treatment of 2 with I(2) and cyclo-1,4-S(2)(CH(2))(4) in CH(2)Cl(2) results in oxidative substitution of the cluster and retention of the NMe(3) group, giving [2,2,2-(CO)(3)-2-I-3-NMe(3)-6-[cyclo-1,4-S(2)(CH(2))(4)]-closo-2,1-MoCB(10)H(9)] (9). The unique structural features of the new compounds were confirmed by single-crystal X-ray diffraction studies upon 6, 7, 9 and 10.     

Folding, conformational changes, and dynamics of cytochromes C probed by NMR spectroscopy

NMR spectroscopy has become a vital tool for studies of protein conformational changes and dynamics. Oxidized Fe(III)cytochromes c are a particularly attractive target for NMR analysis because their paramagnetism (S = (1)/(2)) leads to high (1)H chemical shift dispersion, even for unfolded or otherwise disordered states. In addition, analysis of shifts induced by the hyperfine interaction reveals details of the structure of the heme and its ligands for native and nonnative protein conformational states. The use of NMR spectroscopy to investigate the folding and dynamics of paramagnetic cytochromes c is reviewed here. Studies of nonnative conformations formed by denaturation and by anomalous in vivo maturation (heme attachment) are facilitated by the paramagnetic, low-spin nature of native and nonnative forms of cytochromes c. Investigation of the dynamics of folded cytochromes c also are aided by their paramagnetism. As an example of this analysis, the expression in Escherichia coli of cytochrome c(552) from Nitrosomonas europaea is reported here, along with analysis of its unusual heme hyperfine shifts. The results are suggestive of heme axial methionine fluxion in N. europaea ferricytochrome c(552). The application of NMR spectroscopy to investigate paramagnetic cytochrome c folding and dynamics has advanced our understanding of the structure and dynamics of both native and nonnative states of heme proteins.     

Structures and anion-binding properties of M4L6 tetrahedral cage complexes with large central cavities

Reaction of the bis-bidentate bridging ligand L(3), in which two bidentate chelating 3(2-pyridyl)pyrazole units are separated by a 3,3'-biphenyl spacer, with Co(II) salts affords tetranuclear cage complexes of composition [Co(4)(L(3))(6)]X(8)(X =[BF(4)](-), [ClO(4)](-), [PF(6)](-) or I(-)) in which four 6-coordinate Co(II) ions in an approximately tetrahedral array are connected by six bis-bidentate bridging ligands, one spanning each of the six edges of the Co(4) tetrahedron. In every case, X-ray crystallography reveals that the 'apical' Co(II) ion has a fac tris-chelate geometry, whereas the other three Co(II) ions have mer tris-chelate geometries, resulting in (non-crystallographic)C(3) symmetry for the cages; that this structure is retained in solution is confirmed by (1)H NMR spectroscopy of the paramagnetic cages. In every case one of the anions is located inside the central cavity of the cage, with the remaining seven outside. We found no clear evidence for an anion-based templating effect. The cage superstructure is sufficiently large to leave gaps in the centres of the faces through which the internal and external anions can exchange. Variable-temperature (19)F NMR spectroscopy was used to investigate the dynamic behaviour of the cages with X =[BF(4)](-) and [PF(6)](-) in MeCN solution: in both cases two separate signals, corresponding to external and internal anions, are clear at 233 K which have coalesced to a single signal at room temperature. Analysis of the linewidth of the minor signal (for the internal anion) at various temperatures below coalescence gave an activation energy for anion exchange of ca. 50 kJ mol(-1) in each case, a figure which suggests that anion exchange can occur via a conformational rearrangement of the cage superstructure in solution rather than opening of the cavity by cleavage of metal-ligand bonds.     

Cross-correlated relaxation enhanced 1H[bond]13C NMR spectroscopy of methyl groups in very high molecular weight proteins and protein complexes

A comparison of HSQC and HMQC pulse schemes for recording (1)H[bond](13)C correlation maps of protonated methyl groups in highly deuterated proteins is presented. It is shown that HMQC correlation maps can be as much as a factor of 3 more sensitive than their HSQC counterparts and that the sensitivity gains result from a TROSY effect that involves cancellation of intra-methyl dipolar relaxation interactions. (1)H[bond](13)C correlation spectra are recorded on U-[(15)N,(2)H], Ile delta 1-[(13)C,(1)H] samples of (i) malate synthase G, a 723 residue protein, at 37 and 5 degrees C, and of (ii) the protease ClpP, comprising 14 identical subunits, each with 193 residues (305 kDa), at 5 degrees C. The high quality of HMQC spectra obtained in short measuring times strongly suggests that methyl groups will be useful probes of structure and dynamics in supramolecular complexes.     

Sampling unfolding intermediates in calmodulin by single-molecule spectroscopy

We used single-pair fluorescence resonance energy transfer (spFRET) measurements to characterize denatured and partially denatured states of the multidomain calcium signaling protein calmodulin (CaM) in both its apo and Ca(2+)-bound forms. The results demonstrate the existence of an unfolding intermediate. A CaM mutant (CaM-T34C-T110C) was doubly labeled with fluorescent probes AlexaFlour 488 and Texas Red at opposing globular domains. Single-molecule distributions of the distance between fluorophores were obtained by spFRET at varying levels of the denaturant urea. Multiple conformational states of CaM were observed, and the amplitude of each conformation was dependent on urea concentration, with the amplitude of an extended conformation increasing upon denaturation. The distributions at intermediate urea concentrations could not be adequately described as a combination of native and denatured conformations, showing that CaM does not denature via a two-state process and demonstrating that at least one intermediate is present. The intermediate conformations formed upon addition of urea were different for Ca(2+)-CaM and apoCaM. An increase in the amplitude of a compact conformation in CaM was observed for apoCaM but not for Ca(2+)-CAM upon the addition of urea. The changes in the single-molecule distributions of CaM upon denaturation can be described by either a range of intermediate structures or by the presence of a single unfolding intermediate that grows in amplitude upon denaturation. A model for stepwise unfolding of CaM is suggested in which the domains of CaM unfold sequentially.     

Effect of phase ratio on van't Hoff analysis in reversed-phase liquid chromatography,and phase-ratio-independent estimation of transfer enthalpy

In analysis of the thermodynamics of the transfer of a solute from the mobile phase to the stationary phase in reversed-phase liquid chromatography, it is nearly always assumed that the phase ratio is constant. This type of analysis is typically performed by applying a form of the van't Hoff equation, which relates the retention factor to temperature via the enthalpy and entropy of transfer. When non-linear van't Hoff plots are observed, it is often assumed that the enthalpy and entropy of transfer change with temperature. However, when the possibility of a change in the phase ratio is considered, it becomes apparent that non-linear van't Hoff behavior may or may not be due to changes in enthalpy or entropy. In this work, we present mathematical evidence that phase ratio changes, if they occur, can cause deviations from linearity in a van't Hoff plot. We also show that the phase ratio influence can be eliminated by considering the molecular difference between two solutes instead of the solutes themselves. The resulting selectivity van't Hoff plots may be linear, even when the van't Hoff plots of the two solutes are non-linear. In such cases, temperature-dependent phase ratio changes, and not necessarily changes in the transfer enthalpy, may be responsible for the curved van't Hoff plots of the individual solutes. In addition, we present chromatographic evidence that different solutes may "see" different thermodynamic phase ratios. It is clear that the concept of a phase ratio in reversed-phase chromatography is not nearly as well defined as a phase ratio in a bulk system like a liquid-liquid extraction.