A critical comparison of approximation methods and models for equilibrium properties of low-barrier hydrogen bonds

Recent experimental evidence has led to the conclusion that short, strong hydrogen bonds can stabilize transition states of enzyme catalyzed biochemical reactions. Evidence for such hydrogen bonds is the low value of the isotopic fractionation factor, phi, which is defined as the equilibrium constant for the generic reaction, R-H + DOH <--> R-D + HOH, where H is the hydrogen atom participating in the low-barrier hydrogen bond in a molecule R-H. In this work we assess two approximation methods for computing the isotopic fractionation factors for single and multidimensional systems containing a low-barrier hydrogen bond. These methods are WKB and an approach that corrects the classical partition function via a quantum correction factor. We find that the latter approach is universally accurate and applicable in both single and multidimensional systems containing a low-barrier hydrogen bond. We also assess two different models for the coupling of a molecule's low-barrier hydrogen bond to other degrees of freedom, both internal and external to the molecule, and show that each leads to a lowering of the fractionation factor.     

Unrestricted perfect pairing: the simplest wave-function-based model chemistry beyond mean field

The perfect pairing (PP) approximation from generalized valence bond theory is formulated in an unrestricted fashion for both closed- and open-shell systems using a coupled cluster ansatz. In the model chemistry proposed here, active electron pairs are correlated, but the unpaired or radical electrons remain uncorrelated, leading to a linear number of decoupled cluster amplitudes which can be solved for analytically. The alpha and beta spatial orbitals are variationally optimized independently. This minimal treatment of electron-electron correlation noticeably improves upon symmetry-breaking problems and other pathologies in Hartree-Fock (HF) theory and may be computed using the resolution of the identity approximation at only a factor of several times more effort than HF itself. PP also generally predicts improved molecular structures over HF. This compact, correlated wave function potentially provides a useful starting point for dynamical correlation corrections.     

Converting the sacrificial DNA repair protein N-ada into a catalytic methyl phosphotriester repair enzyme

Mutation of the active-site residue Cys38 of N-Ada converts it from a sacrificial DNA repair protein to an enzyme that uses methanethiol as an external sacrificial reagent to repair DNA methyl phosphotriesters catalytically.     

Unique spatial heterogeneity in ionic liquids

A multiscale coarse-graining model for ionic liquids has been extended to investigate the unique aggregation of cations in ionic liquids through computer simulation. It has been found that, with sufficiently long side chains, the tail groups of cations aggregate to form spatially heterogeneous domains, while headgroups of the cations and the anions distribute as uniformly as possible. This is understood as the result of competition between the charged electrostatic interactions between headgroups and anions and the collective short-range interactions between the neutral tail groups. This aggregation can help to explain a number of experimentally observed physical phenomena in ionic liquids.     

Stereochemical assignments of the 7-phenyl-3-oxabicyclo[4.1.0]heptanes

A method for making stereochemical assignments based on nmr data for the 7-phenyl-3-oxabicyclo[4.1.0]-heptanes is described.     

Chitosan-mediated and spatially selective electrodeposition of nanoscale particles

Nanoscale particles offer a variety of interesting properties, and there is growing interest in their assembly into higher ordered structures. We report that the pH-responsive aminopolysaccharide chitosan can mediate the electrodeposition of model nanoparticles. Chitosan is known to electrodeposit at the cathode surface in response to a high localized pH. To demonstrate that chitosan can mediate nanoparticle deposition, we suspended fluorescently labeled latex nanoparticles (100 nm diameter spheres) in a chitosan solution (1%) and performed electrodeposition (0.05 mA/cm2 for several minutes). Results demonstrate that chitosan is required for nanoparticle electrodeposition; chitosan confers spatial selectivity to electrodeposition; and nanoparticles distribute throughout the electrodeposited chitosan film. Additionally, we observed that the deposited films reversibly swell upon rehydration. This work indicates that chitosan provides a simple means to assemble nanoparticles at addressable locations and provides further evidence that stimuli-responsive biological materials may facilitate fabrication at the microscale.     

Analysis of uniform binary subdivision schemes for curve design

The paper analyses the convergence of sequences of control polygons produced by a binary subdivision scheme of the form