Diffusion trapping times and dynamic percolation in an Ising system

We address the problem of diffusion through dynamic Ising network structures using random walkers (RWs) whose net displacements are partitioned into two contributions, arising from (1) transport through neighboring "conducting" clusters and (2) self-diffusion of the site on which the RW finds itself, respectively. At finite temperatures, the conducting clusters in the network exhibit correlated dynamic behavior, making our model system different to most prior published work, which has largely been at the random percolation limit. We also present a novel heuristic scaling analysis for this system that utilizes a new scaling exponent theta(z) for representing RW trapping time as a function of "distance" from the dynamic percolation transition. Simulation results in two-dimensional networks show that when theta(z) = 2, a value found from independent physical arguments, our scaling equations appear to capture universal behavior in the system, at both the random percolation (infinite temperature) and finite temperature conditions studied. This study suggests that the model and the scaling approach given here should prove useful for studying transport in physical systems showing dynamic disorder.     

A versatile "multiple fishhooks" approach for the study of ligand-receptor interactions using single-molecule atomic force microscopy

Despite the powerfulness of atomic force microscopy (AFM)-based single-molecule force spectroscopy in the study of ligand-receptor interactions, complicated cantilever functionalization and data interpretation have often been a great hurdle for its widespread application. Here, we present a much simplified experimental scheme by using a "multiple fishhooks" approach. In this strategy, multiple ligands are labeled on a single polymer chain, which forms complexes with receptors anchored on the substrate surface. Therefore, multiple single-bond rupture events can be captured in the same force-extension curves, similar to the widely used polyprotein approach. This method also allows nonsingle-molecule events and nonspecific interactions between cantilever and surface to be readily excluded from real data pool and greatly increases the quality and quantity of single-molecule data. The biggest advantage of our approach over the previously reported one is the choice of a naturally occurring polysaccharide, hyaluronan, the conformation of which in solution can be fine-tuned by pH, as the polymer backbone of the "multiple fishhooks" handle. Furthermore, our approach greatly simplifies the chemical synthesis of the polymer handle, allowing bioactive molecules to be easily one-step labeled on the handles in aqueous solution. We validate this strategy using the widely studied streptavidin-biotin system, and our single-molecule AFM results are in good agreement with previously reported ones. We anticipate that this novel strategy can be used as a versatile tool to study other complex and challenging ligand-receptor interactions.     

An efficient implementation of the "cluster-in-molecule" approach for local electron correlation calculations

An efficient implementation of the "cluster-in-molecule" (CIM) approach is presented for performing local electron correlation calculations in a basis of orthogonal occupied and virtual localized molecular orbitals (LMOs). The main idea of this approach is that significant excitation amplitudes can be approximately obtained by solving the coupled cluster (or Moller-Plesset perturbation theory) equations of a series of "clusters," each of which contains a subset of occupied and virtual LMOs. In the present implementation, we have proposed a simple approach for constructing virtual LMOs of clusters, and new ways of constructing clusters and extracting the correlation contributions from calculations on clusters, which are more efficient than those suggested in the original work. More importantly, linear scaling of computational time of the CIM approach is achieved by evaluating the transformed two-electron integrals over LMOs using simple truncation techniques in limited operations (independent of the molecular size). With typical thresholds, for a variety of molecules our test calculations demonstrate that more than 99% of the conventional MP2 or coupled cluster with doubles correlation energies can be recovered in the present CIM approach.     

Tight-binding "dihedral orbitals" approach to the degree of folding of macromolecular chains

We develop a tight-binding molecular approach to quantify the degree of folding of a macromolecular chain. This approach is based on the linear combination of "dihedral" orbitals to give molecular orbitals (LCDO-MO). The dihedral orbitals are a set of orbitals situated in each dihedral angle of the chain. The LCDO-MO approach remains basically topological, and we display its direct relation to known graph theoretical concepts. Using this approach, we define the dihedral electronic energy and the dihedral electronic partition function of a linear macromolecular chain. We show that the partition function per dihedral angle quantifies the degree of folding of the dihedral graph. We analyze the empirical relationship between these two functions by using a series of 100 proteins. We also study the relation between these two functions and the percentages of secondary structure for these proteins. Finally, we illustrate the use of the dihedral energy and the partition function in structure-property studies of proteins by analyzing the binding of steroids to DB3 antibody.     

Chemoselective formation of successive triazole linkages in one pot: "click-click" chemistry

A methodology for the successive regiospecific "clicking" together of three components in one pot via two triazole linkages is reported. The protocol utilizes copper(I)-mediated alkyne-azide cycloaddition reactions combined with a silver(I)-catalyzed TMS-alkyne deprotection under mild hydroalcoholic conditions. We exemplify the approach with peptide-based components to illustrate its compatibility with polyfunctionalized biomolecules. The method constitutes a promising tool for peptide ligation. We also provide a procedure for directly using TMS-alkynes as the cycloaddition partner in classical "click" chemistry.     

"Competitive quenching": a mechanism by which perihydroxylated perylenequinone photosensitizers can prevent adverse phototoxic damage caused by verteporfin during photodynamic therapy

Incorporation of photodynamic therapy into clinical practice for induction of vascular photo-occlusion highlights the need to prevent adverse phototoxicity to sensitive juxtaposed tissues, particularly in the retina. We developed a system termed "competitive quenching" to prevent adverse phototoxic damage. It involves differential compartmentalization of a photoactivator to the intravascular compartment for photoexcitation and delivery of phototoxicity to targeted vessels. A different photodynamic agent is partitioned to the extravascular retinal space to quench reactive oxygen species generated by photosensitization, thereby protecting the adjacent retinal tissues from adverse phototoxicity. The absorption spectra of quenchers must span wavelengths that are shorter and excluded from the spectral range of photoexcitation light to prevent photoactivation of the quencher. Perihydroxylated perylenequinones were found to be suitable to function as "competitive quenchers" with the prototype hypericin identified as a potent quencher. Here we examined the mechanisms operative in competitive quenching and suggest that hypericin forms a complex with verteporfin, thereby quenching singlet oxygen formation. Furthermore, we show that hypericin, with six phenolic hydroxyls, protects retinal and endothelial hybridoma cells from phototoxicity more effectively than the dimethyl tetrahydroxy helianthrone structural analog with only four such phenolic hydroxyls. The findings suggest that hydroxyl numbers contribute to the efficacy of competitive quenching.     

"Orthogonal" separations for reversed-phase liquid chromatography

A general procedure is proposed for the rapid development of a reversed-phase liquid chromatographic (RP-LC) separation that is "orthogonal" to a pre-existing ("primary") method for the RP-LC separation of a given sample. The procedure involves a change of the mobile-phase organic solvent (B-solvent), the replacement of the primary column by one of very different selectivity, and (only if necessary) a change in mobile phase pH or the use of a third column. Following the selection of the "orthogonal" B-solvent, column and mobile phase pH, further optimization of peak spacing and resolution can be achieved by varying separation temperature and either isocratic %B or gradient time. The relative "orthogonality" of the primary and "orthogonal" RP-LC methods is then evaluated from plots of retention for one method versus the other. The present procedure was used to develop "orthogonal" methods for nine routine RP-LC methods from six pharmaceutical analysis laboratories. The relative success of this approach can be judged from the results reported here.     

Amphiphilic Janus gold nanoparticles via combining "solid-state grafting-to" and "grafting-from" methods

Despite the great efforts that have been made toward obtaining Janus architectures, synthesizing sub-10 nanometer Janus nanoparticles (NPs) modified with different types of polymers remains a challenging task. In this Communication, "solid-state grafting-to" and "grafting-from" methods were combined to obtain Janus gold NPs (AuNPs) modified with two types of polymer chains on the opposite sides of the NP. We used functionalized polymer single crystals as the solid substrates to immobilize AuNPs. We then used atom transfer radical polymerization to grow polymer chains on the "free" side of the AuNPs. Amphiphilic polyethylene oxide (PEO)-Au-poly(methyl methacrylate), PEO-Au-poly(tert-butyl acrylate) and hydrophilic PEO-Au-poly(acrylic acid) were synthesized. The Janus nature was demonstrated using a platinum-nanoparticle-decoration method. Using polymer single crystals as the reaction substrates is advantageous because they afford higher throughput compared with self-assembled monolayers. Dissolution of the single crystal also leads to NPs with defined polymer patches. We anticipate that our approach could serve as a generic method for synthesizing polymer-functionalized, sub-10 nm Janus NPs. This unique system holds promises for achieving controlled assembly and tunable optic and electronic properties of NPs.     

Solute- and temperature-responsive "smart" grafts and supported membranes formed by covalent layer-by-layer assembly

Polymers like poly(N-isopropylacrylamide) (PNIPAM) exhibit lower critical solution temperature (LCST) behavior. A variety of reports have shown that brush grafts of PNIPAM on surfaces exhibit similar temperature responsiveness. We recently described an alternative synthetic approach to such surfaces that affords surfaces with similar LCST-like behavior. We also noted how such surfaces' wettability can change in response to the identity and concentration of solutes. Here we show that this synthetic procedure can be extended to glass surfaces and to more complex surfaces present in porous glass frits. Functionalized glass surfaces exhibit solute-dependent wetting behavior analogous to that previously reported. We further show that the resulting responsive nanocomposite grafts on such frits exhibit "smart" responsive permeability with a greater than 1000-fold difference in permeability to water versus aqueous solutions of sodium sulfate. This "smart" permeability is ascribed to the solute-dependent wettability behavior of the responsive PNIPAM component of the nanocomposite graft, which is sensitive both to the identity and concentration of the solute anion and to temperature.     

Facile "green" synthesis, characterization, and catalytic function of beta-D-glucose-stabilized Au nanocrystals

We present a straightforward, economically viable, and "green" approach for the synthesis and stabilization of relatively monodisperse Au nanocrystals with an average diameter of 8.2 nm (standard deviation, SD=2.3 nm) by using nontoxic and renewable biochemical of beta-D-glucose and by simply adjusting the pH environment in aqueous medium. The beta-D-glucose acts both as reducing agent and capping agent for the synthesis and stabilization of Au nanocrystals in the system. The UV/Vis spectroscopy, Fourier transform infrared (FT-IR) spectroscopy, transmission electron microscopy (TEM), electron diffraction (ED), and X-ray diffraction (XRD) techniques were employed to systematically characterize Au nanocrystals synthesized. Additionally, it is shown that these beta-D-glucose-stabilized Au nanocrystals function as effective catalyst for the reduction of 4-nitrophenol in the presence of NaBH4 (otherwise unfeasible if only the strong reducing agent NaBH4 is employed), which was reflected by the UV/Vis spectra of the catalytic reaction kinetics.     

"Liquid-phase calcination" of colloidal mesoporous silica nanoparticles in high-boiling solvents

We report on a novel high temperature liquid phase "calcination" method with trioctylphosphine oxide (TOPO), tri-n-octylamine (TOA), and squalene for removing the template and strengthening the silica network in colloidal mesoporous silica (CMS) nanoparticles. For such materials, the common calcination procedure in air would result in strong agglomeration, thus preventing their use in colloidal suspensions. The highest efficiency of the new approach is obtained by thermal calcination in TOPO at only 275 °C, as shown by an increasing degree of silica condensation, and the retention of the high colloidal stability of the CMS nanoparticles. Moreover, we also show the ability of the TOPO treatment to remove the template, thus saving a preparation step. The resulting CMS nanoparticles retain the ordered mesostructure, high porosity, and large surface area of the original mesoporous nanoparticles, while showing a much greater degree of silica condensation and high stability. The concept of "liquid calcination" represents a powerful general approach for the preparation of stable colloidal porous nanoparticles.     

An efficient approach for ab initio energy calculation of biopolymers

We present a new method for efficient total-energy calculation of biopolymers using the density-matrix (DM) scheme based on the molecular fractionation with conjugate caps (MFCC) approach. In this MFCC-DM method, a biopolymer such as a protein is partitioned into properly capped fragments whose density matrices are calculated by conventional ab initio methods which are then assembled to construct the full system density matrix. The assembled full density matrix is then employed to calculate the total energy and dipole moment of the protein using Hartree-Fock or density-functional theory methods. Using this MFCC-DM method, the self-consistent-field procedure for solving the full Hamiltonian problem is avoided and an efficient approach for ab initio energy calculation of biopolymers is achieved. Two implementations of the approach are presented in this paper. Systematic numerical studies are carried out on a series of extended polyglycines CH3CO-(GLY)n-NHCH3(n = 3-25) and excellent results are obtained.     

Synergistic approach to improve "alchemical" free energy calculation in rugged energy surface

The authors present an integrated approach to "alchemical" free energy simulation, which permits efficient calculation of the free energy difference on rugged energy surface. The method is designed to obtain efficient canonical sampling for rapid free energy convergence. The proposal is motivated by the insight that both the exchange efficiency in the presently designed dual-topology alchemical Hamiltonian replica exchange method (HREM), and the confidence of the free energy determination using the overlap histogramming method, depend on the same criterion, viz., the overlaps of the energy difference histograms between all pairs of neighboring states. Hence, integrating these two techniques can produce a joint solution to the problems of the free energy convergence and conformational sampling in the free energy simulations, in which lambda parameter plays two roles to simultaneously facilitate the conformational sampling and improve the phase space overlap for the free energy determination. Specifically, in contrast with other alchemical HREM based free energy simulation methods, the dual-topology approach can ensure robust conformational sampling. Due to these features (a synergistic solution to the free energy convergence and canonical sampling, and the improvement of the sampling efficiency with the dual-topology treatment), the present approach, as demonstrated in the model studies of the authors, is highly efficient in obtaining accurate free energy differences, especially for the systems with rough energy landscapes.     

Bonding trends in MCH2 systems: Simple orbital interpretation and evidence for double bonds

MCH₂ systems, where M is a metal from 4th up to 7th period, are studied at DFT level using B3LYP functional and small-core quasirelativistic pseudopotential or fully relativistic four-component methodology. We obtained structural data for 44 elements, M, and our results can be used to infer double-bond lengths for these elements. Our results also suggest that the bonding of these MCH₂ systems can be understood by a simple pictorial approach, even when spin–orbit effects are present.     

"Mass defect" tags for biomolecular mass spectrometry

We present a new class of "mass defect" tags with utility in biomolecular mass spectrometry. These tags, incorporating element(s) with atomic numbers between 17 (Cl) and 77 (Ir), have a substantially different nuclear binding energy (mass defect) from the elements common to biomolecules. This mass defect yields a readily resolvable mass difference between tagged and untagged species in high-resolution mass spectrometers. We present the use of a subset of these tags in a new protein sequencing application. This sequencing technique has advantages over existing mass spectral protein identification methodologies: intact proteins are quickly sequenced and unambiguously identified using only an inexpensive, robust mass spectrometer. We discuss the potential broader utility of these tags for the sequencing of other biomolecules, differential display applications and combinatorial methods.     

Analytical method for the representation of atoms-in-molecules densities

We present analytic refinements and applications of the deformed atomic densities method [Fernández Rico, J.; López, R.; Ramírez, G. J Chem Phys 1999, 110, 4213-4220]. In this method the molecular electron density is partitioned into atomic contributions, using a minimal deformation criterion for every two-center distributions, and the atomic contributions are expanded in spherical harmonics times radial factors. Recurrence relations are introduced for the partition of the two-center distributions, and the final radial factors are expressed in terms of exponential functions multiplied by polynomials. Algorithms for the practical implementation are developed and tested, showing excellent performances. The usefulness of the present approach is illustrated by examining its ability to describe the deformation of atoms in different molecular environments and the relationship between these atomic densities and some chemical properties of molecules.     

Polymer brushes grafted to "passivated" silicon substrates using click chemistry

We present herein a versatile method for grafting polymer brushes to passivated silicon surfaces based on the Cu(I)-catalyzed Huisgen 1,3-dipolar cycloaddition (click chemistry) of omega-azido polymers and alkynyl-functionalized silicon substrates. First, the "passivation" of the silicon substrates toward polymer adsorption was performed by the deposition of an alkyne functionalized self-assembled monolayer (SAM). Then, three tailor-made omega-azido linear brush precursors, i.e., PEG-N3, PMMA-N3, and PS-N3 (Mn approximately 20,000 g/mol), were grafted to alkyne-functionalized SAMs via click chemistry in tetrahydrofuran. The SAM, PEG, PMMA, and PS layers were characterized by ellipsometry, scanning probe microscopy, and water contact angle measurements. Results have shown that the grafting process follows the scaling laws developed for polymer brushes, with a significant dependence over the weight fraction of polymer in the grafting solution and the grafting time. The chemical nature of the brushes has only a weak influence on the click chemistry grafting reaction and morphologies observed, yielding polymer brushes with thickness of ca. 6 nm and grafting densities of ca. 0.2 chains/nm2. The examples developed herein have shown that this highly versatile and tunable approach can be extended to the grafting of a wide range of polymer (pseudo-) brushes to silicon substrates without changing the tethering strategy.     

Catalysis with phosphine-containing amino acids in various "turn" motifs

We have been actively involved in the development of parallel approaches for the discovery of phosphine ligands. Our approach has been based on the incorporation of phosphine-containing amino acids into peptide sequences that are designed to have stable secondary structures. We have examined helical and turn secondary structures and have reported that alkylation of cyclopentenyl acetate with dimethylmalonate can be catalyzed in high enantiomeric excess (ee) with a beta-turn-based ligand. The importance of the peptide secondary structure was demonstrated through the synthesis of a series of peptide ligands where the nature of the turn-forming residues was probed. Additionally, other turn-forming units and a variety of different phosphine-containing amino acids have been examined for their ability to control the selectivity of the allylation reaction. This paper reports the results obtained through the examination of different turn motifs as well as different phosphine substitutions on the "best" turn sequence, Pps-Pro-d-Xxx-Pps.     

Pauling resonant structures in real space through electron number probability distributions

A general hierarchy of the coarsed-grained electron probability distributions induced by exhaustive partitions of the physical space is presented. It is argued that when the space is partitioned into atomic regions the consideration of these distributions may provide a first step toward an orbital invariant treatment of resonant structures. We also show that, in this case, the total molecular energy and its components may be partitioned into structure contributions, providing a fruitful extension of the recently developed interacting quantum atoms approach (J. Chem. Theory Comput. 2005, 1, 1096). The above ideas are explored in the hydrogen molecule, where a complete statistical and energetic decomposition into covalent and ionic terms is presented.