Evaluation of Poisson solvation models using a hybrid explicit/implicit solvent method

Implicit solvent methods have become popular tools in the field of protein dynamics simulations, yet evaluation of their validity has been primarily limited to comparisons with experimental and theoretical data for small molecules. In this paper, we use a recently developed hybrid explicit/implicit solvent methodology to evaluate the accuracy of several Poisson-based implicit solvent models. Specifically, we focus on the calculation of electrostatic solvation free energies of various fixed conformations for two proteins. We show that, among various dielectric boundary definitions, the Lee-Richards molecular surface has the best agreement with hybrid solvent results. Furthermore, certain modifications of the molecular surface Poisson protocol provide varied results. For instance, simple modifications of atomic radii on charged residues generally improve absolute errors but do not significantly reduce relative errors among conformations. On the other hand, using a water-probe radius of 1.0 A, as opposed to the standard value of 1.4 A, to generate the molecular surface, moderately improves both absolute and relative results.     

Multireference spin-adapted variant of density functional theory

A new Kohn-Sham formalism is developed for studying the lowest molecular electronic states of given space and spin symmetry whose densities are represented by weighted sums of several reference configurations. Unlike standard spin-density functional theory, the new formalism uses total spin conserving spin-density operators and spin-invariant density matrices so that the method is fully spin-adapted and solves the so-called spin-symmetry dilemma. The formalism permits the use of an arbitrary set of reference (noninteracting) configurations with any number of open shells. It is shown that the requirement of degeneracy of the total noninteracting energies of the reference configurations (or configuration state functions) is equivalent to the stationary condition of the exact energy relative to the weights of the configurations (or configuration state functions). Consequently, at any molecular geometry, the weights can be determined by minimization of the energy, and, for given reference weights, the Kohn-Sham orbitals can be determined. From this viewpoint, the developed theory can be interpreted as an analog of the multiconfiguration self-consistent field approach within density functional theory.     

Convenient Asymmetric Syntheses of anti-beta-Amino Alcohols

Condensation of allylborane reagents 9 and 12 with aldehydes gave anti-3-[(diphenylmethylene)amino]-1-alken-4-ols 10 and 13 with high relative and absolute stereocontrol. Subsequent deprotection gave the corresponding free anti-3-amino-1-alken-4-ols 11 and 14. Alternatively, reaction of imines 13a, 13f, and 13g with trifluoromethanesulfonic anhydride and acidic methanol gave, via rearrangement, double inversion, and hydrolysis, the isomeric anti-4-amino-1-alken-3-ols 22, 38a, and 38b in good yield. The stereochemistry of the rearrangement products has been established by a single crystal X-ray study of compound 37 and by chemical correlation.     

In vivo optical analysis of quantitative changes in collagen and elastin during arterial remodeling

Altered collagen and elastin content correlates closely with remodeling of the arterial wall after injury. Optical analytical approaches have been shown to detect qualitative changes in plaque composition, but the capacity for detection of quantitative changes in arterial collagen and elastin content in vivo is not known. We have assessed fluorescence spectroscopy for detection of quantitative changes in arterial composition in situ, in rabbit models of angioplasty and stent implant. Fluorescence emission intensity (FEI) recorded at sites remote from the primary implant site was correlated with immunohistochemical (IH) analysis and extracted elastin and collagen. FEI was significantly decreased (P<0.05) after treatment with anti-inflammatory agents, and plaque area decreased on comparison with saline-treated rabbits after stent implant or angioplasty (Por=0.961) analysis were detected by multiple regression (MR) analysis. Good correlations also were found for FEI with elastin and collagen measured by high-performance liquid chromatography; MR analysis provided highly predictive values for collagen and elastin (R2>or=0.994). Fluorescence spectroscopic analysis detects quantitative compositional changes in arterial connective tissue in vivo, demonstrating changes at sites remote from primary angioplasty and stent implant sites.     

Covalent and non-covalent albumin binding of Au(i) bis-NHCs via post-synthetic amide modification

Recent decades have witnessed the emergence of Au(i) bis-N-heterocyclic carbenes (NHCs) as potential anticancer agents. However, these systems exhibit little interaction with serum proteins (e.g., human serum albumin), which presumably impacts their pharmacokinetic profile and tumor exposure. Anticancer drugs bound to human serum albumin (HSA) often benefit from significant advantages, including longer circulatory half-lives, tumor targeted delivery, and easier administration relative to the drug alone. In this work, we present Au(i) bis-NHCs complexes, 7 and 9, capable of binding to HSA. Complex 7 contains a reactive maleimide moiety for covalent protein conjugation, whereas its congener 9 contains a naphthalimide fluorophore for non-covalent binding. A similar drug motif was used in both cases. Complexes 7 and 9 were prepared from a carboxylic acid functionalized Au(i) bis-NHC (complex 2) using a newly developed post-synthetic amide functionalization protocol that allows coupling to both aliphatic and aromatic amines. Analytical, and in vitro techniques were used to confirm protein binding, as well as cellular uptake and antiproliferative activity in A549 human lung cancer cells. The present findings highlight a hitherto unexplored approach to modifying Au(i) bis-NHC drug candidates for protein ligation and serve to showcase the relative benefits of covalent and non-covalent HSA binding.

Au(i) bis-N-heterocyclic carbenes (NHCs) functionalized using an amide linker were found to bind to human serum albumin (HSA) in covalent and non-covalent fashion. The solubility and in vitro anti-cancer activity of these new conjugates were studied.     

Rotaxanated conjugated sensory polymers

Two highly emissive conjugated polymers with tethered rotaxane repeat units are reported. Hydrogen bonding between acidic alcohols and the N-heteroaromatic groups in the rotaxanes attenuates polymer fluorescence. In addition, the rotaxane groups create precise three-dimensional pockets for metal binding, which results in fluorescence quenching. Exposing thin films of Zn-doped polymers to alcohol vapors reverses the quenching by up to 25%.     

A convenient synthesis of diaminoglyoxime and diaminofurazan: Useful precursors for the synthesis of high density energetic materials

The reaction of glyoxime ( 4 ) and hydroxylamine hydrochloride in aqueous sodium hydroxide was found to be a safe and inexpensive method for the preparation of multigram quantities of diaminoglyoxime ( 5 ). Potassium hydroxide mediated dehydration of 5 furnished diaminofurazan ( 1 ) in good yield of exceptional purity. The ready availability of 1 and 5 has facilitated the synthesis of new energetic furazan derivative 8 .     

Molecular dynamics study of gas hydrate formation

Long-time-scale molecular dynamics simulations are presented of the spontaneous formation of methane hydrate at a methane/liquid water interface. The water film was prepared at 300 K, 30 bar and showed no significant hydrate order. On crash cooling to 250 K, 300 bar (about 20 K subcooling), the system showed a rapid growth of hydrate clusters. Contrary to popular models for hydrate nucleation, the clusters formed first as two-dimensional arrangements and only later into three-dimensional cage structures; the results are, however, consistent with the local order model proposed recently. The hydrate clusters showed clear signatures of the type II hydrate structure even though the type I structure is the thermodynamically stable form for methane hydrate; this is in accord with the results of recent diffraction experiments.     

Composition-controlled synthesis of bimetallic gold-silver nanoparticles

This paper reports findings of an investigation of the synthesis of monolayer-capped binary gold-silver (AuAg) bimetallic nanoparticles that is aimed at understanding the control factors governing the formation of the bimetallic compositions. The synthesis of alkanethiolate-capped AuAg nanoparticles was carried out using two related synthetic protocols using aqueous sodium borohydride as a reducing agent. One involves a two-phase reduction of AuCl(4)(-), which is dissolved in organic solution, and Ag(+), which is dissolved in aqueous solution. The other protocol involves a two-phase reduction of AuCl(4)(-) and AgBr(2)(-), both of which are dissolved in the same organic solution. AuAg nanoparticles of 2-3 nm core sizes with different compositions in the range of 0-100% Au have been synthesized. The two synthetic routes were compared in terms of bimetallic composition and size properties. Our new findings have allowed us to establish the correlation between synthetic feeding of metals and metal compositions in the bimetallic nanoparticles, which have important implications to the exploration of gold-based bimetallic nanoparticles for constructing sensing and catalytic nanomaterials.     

Synthesis and Structure of a 1,3-alternate-Thiacalix[4]arene diamide Derivative

A novel receptor possessing two complexation sites and bearing 1,3-alternate conformation based on thiacalix[4]arene, confirmed by single crystal X-ray analysis, was prepared. The tetrathiacalix[4]arene diamide shows strong intramolecular hydrogen bonding. The binding behavior towards K⁺ and halides has been examined by ¹H NMR titration experiments.