Percolation in strongly correlated systems: The massless Gaussian field

We derive a number of new results for correlated nearest neighbor site percolation onZ ^d. We show in particular that in three dimensions the strongly correlated massless harmonic crystal, i.e., the Gaussian random field with mean zero and covariance –, has a nontrivial percolation behavior: sites on whichS _x h percolate if and only ifh _c . with0 _c < . This provides the first rigorous example of a percolation transition in a system with infinite susceptibility.     

Resolving Component Overlap in Multiwavelength Kinetic Spectroscopy: Application to Raman Scattering from Intermediates in Triplet-State Photoreactions

Abstract— Understanding of reaction mechanisms in photochemistry is advanced both by kinetic measurements to determine rates of reaction and by spectroscopic studies of the structures of precursors and photoproducts. When kinetics and spectroscopy are combined in a time-resolved, multiwavelength spectroscopic measurement on a reacting system, spectra and structures of intermediates can also be determined. In this paper, the application of multidimensional least-squares and factor analysis techniques for resolving overlapped spectra from intermediates in photochemical kinetics are discussed. The methods are employed specifically to resolve Raman spectra of intermediates in triplet-state photoreactions. By varying excitation intensity, spectra of excited-triplet states are resolved from ground states and solvent. By varying the concentration of a triplet quencher in the sample, the Raman spectrum of a sensitizer excited state (benzophe-none) can be resolved from those of acceptor-triplet states or radical photoproducts. Applications of these concepts in other areas of photochemical kinetics are addressed.     

Composite alignment media for the measurement of independent sets of NMR residual dipolar couplings

The measurement of independent sets of NMR residual dipolar couplings (RDCs) in multiple alignment media can provide a detailed view of biomolecular structure and dynamics, yet remains experimentally challenging. It is demonstrated here that independent sets of RDCs can be measured for ubiquitin using just a single alignment medium composed of aligned bacteriophage Pf1 particles embedded in a strained polyacrylamide gel matrix. Using this composite medium, molecular alignment can be modulated by varying the angle between the directors of ordering for the Pf1 and strained gel matrix, or by varying the ionic strength or concentration of the Pf1 particles. This approach offers significant advantages in that greater experimental control can be exercised over the acquisition of multi-alignment RDC data while a homogeneous chemical environment is maintained across all of the measured RDC data.     

Mono- and di-substituted urea derivatives of cyclodiphosphazane: [ClP(μ-NBu)2PN(Me)CON(H)Me] and [Me(H)NCON(Me)P(μ-NBu)]2

The reaction of cis-[ClP(μ-N^tBu)]₂ with N,N′-dimethylurea leads to the formation of both mono- and di-substituted derivatives [ClP(μ-N^tBu)₂P(NMeCON(H)Me)] and [(μ-N^tBu)P(NMeCON(H)Me)]₂, instead of monomeric, dimeric or higher oligomeric macrocycles. The structure of [ClP(μ-N^tBu)₂P(NMeCON(H)Me)] shows rare non-bonded P?Cl and intermolecular hydrogen bonding interactions leading to a 2D-sheet like structure.     

Silver and palladium complexes of some aromatic azo and azoxy compounds

The complexing ability of derivatives of azobenzene (I) is well known (I) and responsible for the production of a wide variety of dyestuffs and analytical chemicals. While the azo group generally participates in the coordination, the determination of the degree of its interaction is complicated by other functional groups which are also coordinated with the transition metal. In a previous publication (2), we reported the preparation of the silver and palladium complexes of benzo[c]cinnoline (II) and proposed that these results might be used to explain the electron donor properties of azobenzene. We are now reporting the preparation of some additional complexes with ligands containing the azo group.     

The complex of a bivalent derivative of galanthamine with torpedo acetylcholinesterase displays drastic deformation of the active-site gorge: implications for structure-based drug design

Bifunctional derivatives of the alkaloid galanthamine, designed to interact with both the active site of the enzyme acetylcholinesterase (AChE) and its peripheral cation binding site, have been assayed with Torpedo californica AChE (TcAChE), and the three-dimensional structures of their complexes with the enzyme have been solved by X-ray crystallography. Differences were noted between the IC(50) values obtained for TcAChE and those for Electrophorus electricus AChE. These differences are ascribed to sequence differences in one or two residues lining the active-site gorge of the enzyme. The binding of one of the inhibitors disrupts the native conformation of one wall of the gorge, formed by the loop Trp279-Phe290. It is proposed that flexibility of this loop may permit the binding of inhibitors such as galanthamine, which are too bulky to penetrate the narrow neck of the gorge formed by Tyr121 and Phe330 as seen in the crystal structure.     

Coarse-grained rigid blob model for soft matter simulations

We have developed a coarse-grained multiscale molecular simulation method for soft matter systems that directly incorporates stereochemical information. We divide the material into disjoint groups of atoms or particles that move as separate rigid bodies; we call these groups "rigid blobs," hence the name coarse-grained rigid blob model. The method is enabled by the construction of transferable interblob potentials that approximate the net intermolecular interactions, as obtained from ab initio electronic structure calculations, other all-atom empirical potentials, experimental data, or any combination of the above. We utilize a multipolar expansion to obtain the interblob potential-energy functions. The series, which contains controllable approximations that allow us to estimate the errors, approaches the original intermolecular potential as the number of terms increases. Using a novel numerical algorithm, we can calculate the interblob potentials very efficiently in terms of a few interaction moment tensors. This reduces the labor well beyond what is required in standard molecular-dynamics calculations and allows large-scale simulations for temporal scales commensurate with characteristic times of nano- and mesoscale systems. A detailed derivation of the formulas is presented, followed by illustrative applications to several systems showing that the method can effectively capture realistic microscopic details and can easily extend to large-scale simulations.     

Relative energies of substituted benzene valence isomers

Ab initio calculations employing the STO-3G basis set are used to obtain the relative energies of the benzene valence isomers and some selected monosubstituted derivatives. We find that 3,3'-bicyclopropenyl, the least stable of the five (CH)₆ examined, is slightly more stable in the anti conformation than the gauche (Φ = 45°) conformation in agreement with experiment. Substituents are calculated to produce significant changes in the relative energies of the benzene valence isomers. The ground-state isomerization of 1-Dewar benzeneearbinyl cation to benzyl cation is more exothermic than the aromatization of Dewar benzene, but is, in contrast to the latter, symmetry-allowed.     

Shot noise sets the limit of quantification in electrochemical measurements

Detection of single molecules, particles, and rapid redox events is a challenge of electrochemical investigations and requires either an amplification strategy or significant averaging for the electrochemical current to exceed the noise level. We consider the minimum number of electrons required to reach the limit of quantification in these electrochemical measurements. A survey of the literature indicates that the state-of-the-art limit in current detection for different types of measurements (e.g. voltammetry, single-molecule redox cycling, ion channel recordings of single molecules, metal nanoparticle collision, and phase nucleation) is independent of the nature of the measurement and increases linearly with reciprocal response time, Δt^?1, over ～5 orders of magnitude (from ～10 to ～10⁶ s^?1). We demonstrate that the practical limit of quantification requires cumulative measurement of ～2100 electrons during Δt and is determined by statistics of counting electrons, that is, the shot noise in the current.     

Effects of As(III) binding on alpha-helical structure

As(III) displays a wide range of effects in cellular chemistry. Surprisingly, the structural consequences of arsenic binding to peptides and proteins are poorly understood. This study utilizes model alpha-helical peptides containing two cysteine (Cys) residues in various sequential arrangements and spatial locations to study the structural effects of arsenic binding. With i, and i + 1, i + 2, or i + 3 arrangements, CD spectroscopy shows that As(III) coordination causes helical destabilization when Cys residues are located at central or C-terminal regions of the helix. Interestingly, arsenic binding to i, i + 3 positions results in the elimination of helical structure and the formation of a relatively stable alternate fold. In contrast, helical stabilization is observed for peptides containing i, i + 4 Cys residues, with corresponding pseudo pairwise interaction energies (Delta G(pw) degrees) of -1.0 and -0.7 kcal/mol for C-terminal and central placements, respectively. Binding affinities and association rate constants show that As(III) binding is comparatively insensitive to the location of the Cys residues within these moderately stable helices. These data demonstrate that As(III) binding can be a significant modulator of helical secondary structure.