A Mixed Ligand Platinum(II) Complex: Spectral Analysis, Crystal Structure, Steric Demand of the Ligand, and Bioactivity of cis-[Pt(PPh3)2(L1-O,S)]PF6 (L1-O,S = N,N-Morpholine-N′-benzoylthiourea)

A novel mixed platinum(II) complex with general formula [Pt(PPh3)2(L1-O,S)]PF6 has been synthetized and characterized by elemental analysis, molar conductivity, and by IR and NMR (1H, 13C and 31P) spectroscopic methods. The crystal structure has been determined by single-crystal X-ray crystallography. The molecule presents an almost ideal square-planar geometry, and the crystal is stabilized by weak C?H···O and C?H···F hydrogen bonds, and C?H···π stacking interactions. The steric congestion of ligands is described by ?exact? cone and solid cone angles, and the percentage of metal surface shielded by the ligands. The results are compared to closely related palladium complexes. The X-ray structure revealed the proximity of the ortho phenyl proton of one PPh3 ligand to platinum(II) showing rare intramolecular C?H···Pt anagostic binding interaction. The title complex was determined to be active against tumor cells, and it also showed a moderate inhibitory action against mycobacterium tuberculosis.Fil: Pérez, Hiram. Universidad de La Habana; CubaFil: Ramos, Raúl. Universidad de La Habana; CubaFil: Plutín, Ana M.. Universidad de La Habana; CubaFil: Mocelo, Raúl. Universidad de La Habana; CubaFil: Erben, Mauricio Federico. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Centro de Química Inorgánica "Dr. Pedro J. Aymonino". Universidad Nacional de La Plata. Facultad de Ciencias Exactas. Centro de Química Inorgánica "Dr. Pedro J. Aymonino"; ArgentinaFil: Castellano, Eduardo E.. Universidade de Sao Paulo; BrasilFil: Batista, Alzir A.. Universidade Federal do São Carlos; Brasi

Computational Ligand Descriptors for Catalyst Design

Ligands, especially phosphines and carbenes, can play a key role in modifying and controlling homogeneous organometallic catalysts, and they often provide a convenient approach to fine-tuning the performance of known catalysts. The measurable outcomes of such catalyst modifications (yields, rates, selectivity) can be set into context by establishing their relationship to steric and electronic descriptors of ligand properties, and such models can guide the discovery, optimization, and design of catalysts. In this review we present a survey of calculated ligand descriptors, with a particular focus on homogeneous organometallic catalysis. A range of different approaches to calculating steric and electronic parameters are set out and compared, and we have collected descriptors for a range of representative ligand sets, including 30 monodentate phosphorus­(III) donor ligands, 23 bidentate P,P-donor ligands, and 30 carbenes, with a view to providing a useful resource for analysis to practitioners. In addition, several case studies of applications of such descriptors, covering both maps and models, have been reviewed, illustrating how descriptor-led studies of catalysis can inform experiments and highlighting good practice for model comparison and evaluation

Self-assembled platinum(II) complexes for anion recognition.

The focus of this thesis is the development of novel anion receptors possessing conformational flexibility through the use of a simple inorganic framework. The complex cation, [PtL4]2+, can adopt four conformations inspired by calix[4]arene-based receptors: \u27cone\u27, \u27partial cone\u27, \u271,2-alternate\u27 or \u271,3-alternate\u27. The first part of the thesis involves the synthesis, characterization and examination of the binding properties of three generations of anion receptors using 1H NMR spectroscopy and X-ray crystallography. The first generation receptor is [PtL4]2+ where L = 3-nbutylnicotinamide. Solution studies show moderate binding constants in polar solvents with preference for 1:2 binding of planar bidentate anions such as CH3CO2- and NO3-. Conformational flexibility is removed in the second generation receptor. The receptor is preorganized for 1:2 binding of planar bidendate anions with two bis-3,5-nbutylnicotinamide ligands coordinated to [Pt(2,2\u27-bipy)]2+. The results show diminished receptor:anion interactions in both solution and solid state. The third generation receptor consists of [PtL4]2+ where L = 8nbutylureaisoquinoline. The association constants are high in very polar solvent with the 1,2-alternate conformation preferred for the binding of spherical halide anions. The cone conformation is seen when binding tetrahedral shaped oxo-anions. This trend is also confirmed by X-ray crystal structure data. The second part of the thesis investigates the conformational stability and interconversion barriers of several rotameric model complexes using 1H NMR spectroscopy and molecular mechanics. The number of possible conformations in most of the compounds is simplified to two, syn and anti. The anti conformation is the most stable and interconversion barriers range from 69 - 76 kJ/mol. Finally, the last section of the thesis explores the use of mass spectrometry and fluorescence spectroscopy as tools for qualitative analysis of the binding interactions between our third generation receptor and several different anions. Trends in anion selectivity are monitored. Source: Dissertation Abstracts International, Volume: 66-11, Section: B, page: 5971. Thesis (Ph.D.)--University of Windsor (Canada), 2005

Computational assessment on the Tolman cone angles for P-ligands

The Tolman cone angle (θ), the par excellence descriptor of the steric measure of a phosphine, has been recomputed for a set of 119 P-ligands, including simple phosphines and phosphites, as well as bulky biaryl species often employed in catalytic processes. The computed cone angles have been obtained from three different transition metal coordination environments: linear [AuCl(P)] (θL), tetrahedral [Ni(CO)3(P)] (θT) and octahedral [IrCl3(CO)2(P)] (θO), allowing us to observe the steric behavior of the ligand when increasing the steric hindrance around the metal center. The computed cone angles have been extracted from the lowest-energy conformer geometry obtained with a combined MM/DFT methodology. A conformational screening has been done using MM, which allows us to identify the lowest energy structure of each ligand in each coordination environment. These low energy conformers have been subsequently reoptimized at the DFT theory level, from which the cone angle value can be extracted. The computed cone angles have been compared with the original Tolman cone angles, and with other steric parameters such as solid angles (Θ), percent buried volumes (%Vbur), and angular symmetric deformation coordinate (S′4). This new set of values correlates with phosphine ligand dissociation enthalpies in titanocene complexes of the general formula [Ti(2,4-C7H11)2(PR3)], and with reaction barriers in the Suzuki-Miyaura reaction between [Pd-PR3] and bromobenzene, proving that this newly proposed set of cone angles can be employed to establish linear correlations between different experimental and calculated properties for systems in which phosphine ligands play a significant role

Optical study of the anisotropic erbium spin flip-flop dynamics

We investigate the erbium flip-flop dynamics as a limiting factor of the electron spin lifetime and more generally as an indirect source of decoherence in rare-earth doped insulators. Despite the random isotropic arrangement of dopants in the host crystal, the dipolar interaction strongly depends on the magnetic field orientation following the strong anisotropy of the $g$-factor. In Er$^{3+}$:Y$_2$SiO$_5$, we observe by transient optical spectroscopy a three orders of magnitude variation of the erbium flip-flop rate (10ppm dopant concentration). The measurements in two different samples, with 10ppm and 50ppm concentrations, are well-supported by our analytic modeling of the dipolar coupling between identical spins with an anisotropic $g$-tensor. The model can be applied to other rare-earth doped materials. We extrapolate the calculation to Er$^{3+}$:CaWO$_4$, Er$^{3+}$:LiNbO$_3$ and Nd$^{3+}$:Y$_2$SiO$_5$ at different concentrations

Selective optical addressing of nuclear spins through superhyperfine interaction in rare-earth doped solids

In Er$^{3+}$:Y$_2$SiO$_5$, we demonstrate the selective optical addressing of the $^{89}$Y$^{3+}$ nuclear spins through their superhyperfine coupling with the Er$^{3+}$ electronic spins possessing large Land\'e $g$-factors. We experimentally probe the electron-nuclear spin mixing with photon echo techniques and validate our model. The site-selective optical addressing of the Y$^{3+}$ nuclear spins is designed by adjusting the magnetic field strength and orientation. This constitutes an important step towards the realization of long-lived solid-state qubits optically addressed by telecom photons.Comment: 5 pages, 4 figures, supplementary material (3 pages

Coating thickness and coverage effects on the forces between silica nanoparticles in water

The structure and interactions of coated silica nanoparticles have been studied in water using molecular dynamics simulations. For 5 nm diameter amorphous silica nanoparticles we studied the effects of varying the chain length and grafting density of polyethylene oxide (PEO) on the nanoparticle coating's shape and on nanoparticle-nanoparticle effective forces. For short ligands of length $n=6$ and $n=20$ repeat units, the coatings are radially symmetric while for longer chains ($n=100$) the coatings are highly anisotropic. This anisotropy appears to be governed primarily by chain length, with coverage playing a secondary role. For the largest chain lengths considered, the strongly anisotropic shape makes fitting to a simple radial force model impossible. For shorter ligands, where the coatings are isotropic, we found that the force between pairs of nanoparticles is purely repulsive and can be fit to the form $(R/2r_\text{core}-1)^{-b}$ where $R$ is the separation between the center of the nanoparticles, $r_\text{core}$ is the radius of the silica core, and $b$ is measured to be between 2.3 and 4.1.Comment: 20 pages, 6 figure

EROS-DOCK: Protein-Protein Docking Using Exhaustive Branch-and-Bound Rotational Search

International audienceMotivation: Protein-protein docking algorithms aim to predict the 3D structure of a binary complex using the structures of the individual proteins. This typically involves searching and scoring in a six-dimensional space. Many docking algorithms use FFT techniques to exhaustively cover the search space and to accelerate the scoring calculation. However, FFT docking results often depend on the initial protein orientations with respect to the Fourier sampling grid. Furthermore, Fourier-transforming a physics-base force field can involve a serious loss of precision.Results: Here, we present EROS-DOCK, an algorithm to rigidly dock two proteins using a series of exhaustive 3D rotational searches in which non-clashing orientations are scored using the ATTRACT coarse-grained force field model. The rotational space is represented as a quaternion "π-ball", which is systematically subdivided in a "branch-and-bound" manner, allowing efficient pruning of rotations that will give steric clashes. The algorithm was tested on 173 Docking Benchmark complexes, and results were compared with those of ATTRACT and ZDOCK. According to the CAPRI quality criteria, EROS-DOCK typcially gives more acceptable or medium quality solutions than ATTRACT and ZDOCK.Availability: The EROS-DOCK program is available for download at http://erosdock.loria.fr

Cellular Mechanisms Underlying Retinoic Acid-Induced Growth Cone Guidance During Neuronal Regeneration

During the period of neuronal development, neurons must make correct synaptic connections with their appropriate targets. The intricate connections of the nervous system are established in part by growth cones, located at the tips of extending neurites. These unique structures are essential for axon pathfinding and target cell selection by sensing and integrating numerous guidance cues from their environment. Retinoic acid, the active metabolite of vitamin A, is an important regulator of neurite outgrowth during vertebrate development, but there is substantial evidence that it also plays a role in axon guidance. Previous studies have provided preliminary evidence of a potential role of retinoid receptors in mediating the chemotropic effects of retinoic acid. In this study, I demonstrated that a synthetic retinoic acid receptor agonist was able to mimic the effects of retinoic acid in inducing growth cone turning. I also examined the intracellular pathways activated by retinoic acid that induce changes in growth cone behaviour. Previously it has been shown that retinoic acid-induced growth cone turning of invertebrate motorneurons requires local protein synthesis and calcium influx, similar to other known guidance cues in the central nervous system. However, the signalling pathways that link calcium influx to the regulation of cytoskeletal dynamics involved in growth cone turning are not currently known. Here, I examined potential effectors downstream of retinoic acid and have provided evidence that the intracellular pathways likely involve the Rho GTPases, Rac and Cdc42. I demonstrated that the inhibition of Rac or Cdc42 prevented growth cone turning towards retinoic acid. However, it was shown that the involvement of Rac differed depending on whether the growth cones maintained communication with the cell body or not. Moreover, the inhibition of Cdc42 not only blocked growth cone turning towards retinoic acid, but also induced a switch in growth cone responsiveness from attraction to repulsion. Overall, these studies provide new knowledge of the mechanisms underlying growth cone pathfinding by retinoids during nervous system development and regeneration