CoLn dinuclear complexes (Ln = Gd,Tb, Dy,Ho and Er) as platforms for 1,5-dicyanamide-bridged tetranuclear Co2Ln2 complexes: A magneto-structural and theoretical study

Five acetate-diphenoxo triply-bridged Co^II-Ln^III complexes (Ln^III = Gd, Tb, Dy, Ho, Er) of formula [Co(μ-L)(μ-Ac)Ln(NO₃)₂] and two diphenoxo doubly-bridged Co^II-Ln^III complexes (Ln^III = Gd, Tb) of formula [Co(H₂O)(μ-L)Ln(NO₃)₃]·S (S = H₂O or MeOH), were prepared in one pot reaction from the compartmental ligand N,N′,N′′-trimethyl-N,N′′-bis(2-hydroxy-3-methoxy-5-methylbenzyl)diethylene triamine (H₂L). The diphenoxo doubly-bridged Co^II-Ln^III complexes were used as platforms to obtain 1,5-dicyanamide-bridged tetranuclear Co^II-Ln^III complexes (Ln^III = Gd, Tb, Dy, Ho, Er). All exhibit ferromagnetic interactions between the Co^II and Ln^III ions and in the case of the Gd^III complexes, the J_CoGd were estimated to be ∼+0.7 cm⁻¹. Compound 3 exhibits slow relaxation of the magnetization.     

ChemInform Abstract: Structural Principles of Semiconducting Group 14 Clathrate Frameworks.

The basic clathrate frameworks, together with their polytypes, intergrowth clathrate frameworks, and extended frameworks based on larger icosahedral building blocks of carbon, silicon, germanium, and tin are investigated by quantum chemical DFT computations.     

Cellular elements for seeing in the dark: voltage-dependent conductances in cockroach photoreceptors

ABSTRACT: BACKGROUND: The importance of voltage-dependent conductances in sensory information processing is well-established in insect photoreceptors. Here we present the characterization of electrical properties in photoreceptors of the cockroach (Periplaneta americana), a nocturnal insect with a visual system adapted for dim light. RESULTS: Whole-cell patch-clamped photoreceptors had high capacitances and input resistances, indicating large photosensitive rhabdomeres suitable for efficient photon capture and amplification of small photocurrents at low light levels. Two voltage-dependent potassium conductances were found in the photoreceptors: a delayed rectifier type (KDR) and a fast transient inactivating type (KA). Activation of KDR occurred during physiological voltage responses induced by light stimulation, whereas KA was nearly fully inactivated already at the dark resting potential. In addition, hyperpolarization of photoreceptors activated a small-amplitude inward-rectifying (IR) current mediated at least partially by chloride. Computer simulations showed that KDR shapes light responses by opposing the light-induced depolarization and speeding up the membrane time constant, whereas KA and IR have a negligible role in the majority of cells. However, larger KA conductances were found in smaller and rapidly adapting photoreceptors, where KA could have a functional role. CONCLUSIONS: The relative expression of KA and KDR in cockroach photoreceptors was opposite to the previously hypothesized framework for dark-active insects, necessitating further comparative work on the conductances. In general, the varying deployment of stereotypical K+ conductances in insect photoreceptors highlights their functional flexibility in neural coding.     

Hydrolytic reactions of cyclic bis(3′‐5′)diadenylic acid (c‐di‐AMP)

Hydrolytic reactions of cyclic bis(3′‐5′)diadenylic acid (c‐di‐AMP) have been followed by Reversed phase high performance liquid chromatography (RP‐HPLC) over a wide pH range at 90 °C. Under neutral and basic conditions (pH ≥ 7), disappearance of the starting material (first‐order in [OH^?]) was accompanied by formation of a mixture of adenosine 2′‐monophosphate and 3′‐monophosphate (2′‐AMP and 3′‐AMP). Under very acidic conditions (from H₀ = ?0.7 to 0.2), c‐di‐AMP undergoes two parallel reactions (first‐order in [H⁺]): the starting material is cleaved to 2′‐AMP and 3′‐AMP and depurinated to adenine (i.e., cleavage of the N‐glycosidic bond), the former reaction being slightly faster than the latter one. At pH 1–3, isomerization to cyclic bis(2′‐5′)diadenylic acid competes with the depurination. Copyright © 2012 John Wiley & Sons, Ltd.     

Multiphase density functional theory parameterization of the interatomic potential for silver and gold

The ground state energies of Ag and Au in the face-centered cubic (FCC), body-centeredcubic (BCC), simple cubic (SC) and the hypothetical diamond-like phase, and dimer werecalculated as a function of bond length using density functional theory (DFT). Theseenergies were then used to parameterize the many-body Gupta potential for Ag and Au. Wepropose a new parameterization scheme that adopts coordination dependence of theparameters using the well-known Tersoff potential as its starting point. Thisparameterization, over several phases of Ag and Au, was performed to guaranteetransferability of the potentials and to make them appropriate for studies of relatednanostructures. Depending on the structure, the energetics of the surface atoms play acrucial role in determining the details of the nanostructure. The accuracy of theparameters was tested by performing a 2?ns MD simulation of a cluster of 55 Ag?atoms – awell studied cluster of Ag, the most stable structure being the icosahedral one. Withinthis time scale, the initial FCC lattice was found to transform to the icosahedralstructure at room temperature. The new set of parameters for Ag was then used in atemperature dependent atom-by-atom deposition of Ag nanoclusters of up to 1000 atoms. Wefind a deposition temperature of 500?±?50?K where low energy clusters are generated,suggesting an optimal annealing temperature of 500?K for Ag cluster synthesis. Surfaceenergies were also calculated via a 3 ns MD simulation.     

Synthesis, reactivity, and computational analysis of halophosphines supported by dianionic guanidinate ligands

The reported chemistry and reactivity of guanidinate supported group 15 elements in the +3 oxidation state, particularly phosphorus, is limited when compared to their ubiquity in supporting metallic elements across the periodic table. We have synthesized a series of chlorophosphines utilizing homo- and heteroleptic (dianionic)guanidinates and have completed a comprehensive study of their reactivity. Most notable is the reluctancy of these four-membered rings to form the corresponding N-heterocyclic phosphenium cations, the tendency to chemically and thermally eliminate carbodiimide, and the scarcely observed ring expansion by insertion of a chloro(imino)phosphine into a P-N bond of the P-N-C-N framework. Computational analysis has provided corroborating evidence for the unwillingness of the halide abstraction reaction by demonstrating the exceptional electron acceptor properties of the target phosphenium cations and the underscoring strength of the P-X bond.     

Long-time correlations and hydrophobe-modified hydrogen-bonding dynamics in hydrophobic hydration

The physical mechanisms behind hydrophobic hydration have been debated for over 65 years. Spectroscopic techniques have the ability to probe the dynamics of water in increasing detail, but many fundamental issues remain controversial. We have performed systematic first-principles ab initio Car-Parrinello molecular dynamics simulations over a broad temperature range and provide a detailed microscopic view on the dynamics of hydration water around a hydrophobic molecule, tetramethylurea. Our simulations provide a unifying view and resolve some of the controversies concerning femtosecond-infrared, THz-GHz dielectric relaxation, and nuclear magnetic resonance experiments and classical molecular dynamics simulations. Our computational results are in good quantitative agreement with experiments, and we provide a physical picture of the long-debated "iceberg" model; we show that the slow, long-time component is present within the hydration shell and that molecular jumps and over-coordination play important roles. We show that the structure and dynamics of hydration water around an organic molecule are non-uniform.     

Comparison of Secondary Structure Formation Using 10 Different Force Fields in Microsecond Molecular Dynamics Simulations

We have compared molecular dynamics (MD) simulations of a β-hairpin forming peptide derived from the protein Nrf2 with 10 biomolecular force fields using trajectories of at least 1 μs. The total simulation time was 37.2 μs. Previous studies have shown that different force fields, water models, simulation methods, and parameters can affect simulation outcomes. The MD simulations were done in explicit solvent with a 16-mer Nrf2 β-hairpin forming peptide using Amber ff99SB-ILDN, Amber ff99SB*-ILDN, Amber ff99SB, Amber ff99SB*, Amber ff03, Amber ff03*, GROMOS96 43a1p, GROMOS96 53a6, CHARMM27, and OPLS-AA/L force fields. The effects of charge-groups, terminal capping, and phosphorylation on the peptide folding were also examined. Despite using identical starting structures and simulation parameters, we observed clear differences among the various force fields and even between replicates using the same force field. Our simulations show that the uncapped peptide folds into a native-like β-hairpin structure at 310 K when Amber ff99SB-ILDN, Amber ff99SB*-ILDN, Amber ff99SB, Amber ff99SB*, Amber ff03, Amber ff03*, GROMOS96 43a1p, or GROMOS96 53a6 were used. The CHARMM27 simulations were able to form native hairpins in some of the elevated temperature simulations, while the OPLS-AA/L simulations did not yield native hairpin structures at any temperatures tested. Simulations that used charge-groups or peptide capping groups were not largely different from their uncapped counterparts with single atom charge-groups. On the other hand, phosphorylation of the threonine residue located at the β-turn significantly affected the hairpin formation. To our knowledge, this is the first study comparing such a large set of force fields with respect to β-hairpin folding. Such a comprehensive comparison will offer useful guidance to others conducting similar types of simulations.