Synthesis and structure of ruthenium(IV) complexes featuring N-heterocyclic ligands with an N-H group as the hydrogen-bond donor: hydrogen interactions in solution and in the solid state

The synthesis and characterization of novel ruthenium(IV) complexes [Ru(η(3):η(3)-C(10)H(16))Cl(2)L] [L = 3-methylpyrazole (2b), 3,5-dimethylpyrazole (2c), 3-methyl-5-phenylpyrazole (2d), 2-(1H-pyrazol-5-yl)phenol (2e), 6-azauracile (3), and 1H-indazol-3-ol (4)] are reported. Complex 2e is converted to the chelated complex [Ru(η(3):η(3)-C(10)H(16))Cl(κ(2)-N,O-2-(1H-pyrazol-3-yl)phenoxy)] (5) by treatment with an excess of NaOH. All of the ligands feature N-H, O-H, or C═O as the potential hydrogen-bonding group. The structures of complexes 2a-2c, 2e, 3, and 5 in the solid state have been determined by X-ray diffraction. Complexes 2a-2c and 3, which contain the pyrazole N-H group, exhibit intra- and intermolecular hydrogen bonds with chloride ligands [N-H···Cl distances (?): intramolecular, 2.30-2.78; intermolecular, 2.59-2.77]. Complexes 2e and 3 bearing respectively O-H and C═O groups also feature N-H···O interactions [intramolecular (2e), 2.27 ?; intermolecular (3), 2.00 ?]. Chelated complex 5, lacking the O-H group, only shows an intramolecular N-H···Cl hydrogen bonding of 2.42 ?. The structure of complex 3, which turns out to be a dimer in the solid state through a double intermolecular N-H···O hydrogen bonding, has also been investigated in solution (CD(2)Cl(2)) by NMR diffusion studies. Diffusion-ordered spectroscopy experiments reveal an equilibrium between monomer and dimer species in solution whose extension depends on the temperature, concentration, and coordinating properties of the solvent. Preliminary catalytic studies show that complex 3 is highly active in the redox isomerization of the allylic alcohols in an aqueous medium under very mild reaction conditions (35 °C) and in the absence of a base.     

Assessment of the electronic structure of 2,2'-pyridylpyrrolides as ligands

The ligand class 2,2'-pyridylpyrrolide is surveyed, both for its structural features and its electronic structure, when attached to monovalent K, Cu, Ag, Au, and Rh. The influence of pyrrolide ring substituents is studied, as well as the question of push/pull interaction between the pyridyl and pyrrolide halves. The π donor ability of the pyrrolide is found to be less than that of an analogous phenyl. However, in contrast to the phenyl analog, the HOMO is pyrrolide π in character for pyridylpyrrolide complexes of copper and rhodium, while it is conventionally metal localized for planar, d(8) rhodium pyridylphenyl. Monovalent three-coordinate copper complexes show great deviations from Y-shaped toward T-shaped structures, including cases where the pyridyl ligand bonds only weakly.     

Liquid-vapor interfacial properties of vibrating square well chains

Liquid-vapor interfacial properties of square well chains are calculated. Surface tension, orthobaric densities, and vapor pressures are reported. Spinodal decomposition with a discontinuous molecular dynamics simulation program is used to obtain the results which are compared to previously published data for orthobaric densities and vapor pressures. In order to analyze the effect of the chain stiffness results for near tangent and overlapping linear chains as well as angled chains are obtained. Properties are calculated for linear chains of 2, 4, and 8 spheres for intramolecular distances of 0.97, 0.6, and 0.4 as well as for angled chains of 4 and 8 spheres and intramolecular distances of 0.4. The complete series of fully flexible near tangent square well chains is also studied (chains of 2, 4, 8, 12, and 16 particles with intramolecular distances of 0.97). The corresponding states principle applies to most of the systems considered. Critical properties values are reported as obtained from orthobaric densities, surface tensions, and vapor pressures. For the near tangent chains the critical temperatures increase with chain length but the rate of increment tends to zero for the longest chains considered. When the stiffness of the chain increases (intramolecular distance from 1 , 0.6, and 0.4) this saturation effect is either not present or reverses itself. The surface tension increases with the length of the chain while the width of the interface decreases.     

Molecular association of heteronuclear vibrating square-well dumbbells in liquid-vapor phase equilibrium

Molecular aggregates are formed by heteronuclear vibrating square-well dumbbells. In a recent article [G. A. Chapela and J. Alejandre, J. Chem. Phys., 132(10), 104704 (2010)], it is shown that heteronuclear vibrating square-well dumbbells with a diameter ratio between particles of 1/2 and interacting potential ratio of 4 form micelles of different sizes and shapes which manifest themselves in both the liquid and vapor phases, up to and above the critical point. This means that micellization and phase separation are present simultaneously in this simple model. These systems present a maximum in the critical temperature when plotted against the potential well depth of the second particle ε(2). In the same publication, it was speculated that the formation of micelles was responsible for the appearance of the maximum. A thorough study on this phenomena is presented here and it is found that there is a threshold on the size of the second particle and its corresponding depth of interaction potential, where the micelles are formed. If the diameter and well depth of the second particle are small enough for the first and deep enough for the second, micelles are formed. For σ(2)/σ(1) between 0.25 and 0.65 and ε(2)/ε(1) larger than 5.7, micelles are formed up to and above the critical temperature. Outside these ranges micelles appear only at temperatures lower than the critical point. There is a strong temperature dependence on the formation and persistence of the aggregates. For the deepest wells and large enough second particles, a gel interconnected aggregate is obtained. In this work, the micelles are formed at temperatures as low as the triple point and as high as the critical point and, in some cases, persist well above it. The presence of these maxima in critical temperatures T(c) when plotted against ε(2) as follows. At lower values of ε(2), an increase of T(c) is obtained as is expected by the increase of the attractive volume as indicated by the principle of corresponding states. As ε(2) increases further, the formation of molecular aggregates produce a saturation effect of the deepening of the potential well by encapsulating the particles of the second kind inside the micelles, so the resulting T(c) represents a new poly disperse system of molecular aggregates and not the original heteronuclear vibrating square-well dumbbells. The surface tension is also analyzed for these systems, and it is shown that decreases with increasing attraction due to the formation of molecular aggregates.     

A semi-analytical description of protein folding that incorporates detailed geometrical information

Much has been done to study the interplay between geometric and energetic effects on the protein folding energy landscape. Numerical techniques such as molecular dynamics simulations are able to maintain a precise geometrical representation of the protein. Analytical approaches, however, often focus on the energetic aspects of folding, including geometrical information only in an average way. Here, we investigate a semi-analytical expression of folding that explicitly includes geometrical effects. We consider a Hamiltonian corresponding to a Gaussian filament with structure-based interactions. The model captures local features of protein folding often averaged over by mean-field theories, for example, loop contact formation and excluded volume. We explore the thermodynamics and folding mechanisms of beta-hairpin and alpha-helical structures as functions of temperature and Q, the fraction of native contacts formed. Excluded volume is shown to be an important component of a protein Hamiltonian, since it both dominates the cooperativity of the folding transition and alters folding mechanisms. Understanding geometrical effects in analytical formulae will help illuminate the consequences of the approximations required for the study of larger proteins.     

Stabilization and study of SrFe(1-x)Mn(x)O2 oxides with infinite-layer structure

A series of layered oxides of nominal composition SrFe(1-x)Mn(x)O(2) (x = 0, 0.1, 0.2, 0.3) have been prepared by the reduction of three-dimensional perovskites SrFe(1-x)Mn(x)O(3-δ) with CaH(2) under mild temperature conditions of 583 K for 2 days. The samples with x = 0, 0.1, and 0.2 exhibit an infinite-layer crystal structure where all of the apical O atoms have been selectively removed upon reduction. A selected sample (x = 0.2) has been studied by neutron powder diffraction (NPD) and X-ray absorption spectroscopy. Both techniques indicate that Fe and Mn adopt a divalent oxidation state, although Fe(2+) ions are under tensile stress whereas Mn(2+) ions undergo compressive stress in the structure. The unit-cell parameters progressively evolve from a = 3.9932(4) ? and c = 3.4790(4) ? for x = 0 to a = 4.00861(15) ? and c = 3.46769(16) ? for x = 0.2; the cell volume presents an expansion across the series from V = 55.47(1) to 55.722(4) ?(3) for x = 0 and 0.2, respectively, because of the larger effective ionic radius of Mn(2+) versus Fe(2+) in four-fold coordination. Attempts to prepare Mn-rich compositions beyond x = 0.2 were unsuccessful. For SrFe(0.8)Mn(0.2)O(2), the magnetic properties indicate a strong magnetic coupling between Fe(2+) and Mn(2+) magnetic moments, with an antiferromagnetic temperature T(N) above room temperature, between 453 and 523 K, according to temperature-dependent NPD data. The NPD data include Bragg reflections of magnetic origin, accounted for with a propagation vector k = ((1)/(2), (1)/(2), (1)/(2)). A G-type antiferromagnetic structure was modeled with magnetic moments at the Fe/Mn position. The refined ordered magnetic moment at this position is 1.71(3) μ(B)/f.u. at 295 K. This is an extraordinary example where Mn(2+) and Fe(2+) ions are stabilized in a square-planar oxygen coordination within an infinite-layer structure. The layered SrFe(1-x)Mn(x)O(2) oxides are kinetically stable at room temperature, but in air at ~170 °C, they reoxidize and form the perovskites SrFe(1-x)Mn(x)O(3-δ). A cubic phase is obtained upon reoxidation of the layered compound, whereas the starting precursor SrFeO(2.875) (Sr(8)Fe(8)O(23)) was a tetragonal superstructure of perovskite.     

Gd(III) chelates as NMR probes of protein-protein interactions. Case study: rubredoxin and cytochrome c3

Two cyclen-derived Gd probes, [Gd-DOTAM](3+) and [Gd-DOTP](5-) (DOTAM = 1,4,7,10-tetraazacyclododecane-1,4,7,10-tetraacetamide; DOTP = 1,4,7,10-tetraazacyclododecane-1,4,7,10-tetrakis(methylenephosphonate)), were assessed as paramagnetic relaxation enhancement (PRE)-inducing probes for characterization of protein-protein interactions. Two proteins, Desulfovibrio gigas rubredoxin and Desulfovibrio gigas cytochrome c(3), were used as model partners. In a (1)H NMR titration it was shown that [Gd-DOTP](5-) binds to cytochrome c(3) near heme IV, causing pronounced PREs, characterized by line width broadenings of the heme methyl resonances at ratios as low as 0.08. A K(d) of 23 ± 1 μM was calculated based on chemical shift perturbation of selected heme methyl resonances belonging to three different heme groups, caused by allosteric effects upon [Gd-DOTP](5-) binding to cytochrome c(3) at a molar ratio of 2. The other probe, [Gd-DOTAM](3+), caused PREs on a well-defined patch near the metal center of rubredoxin (especially the patch constituted by residues D19-G23 and W37-S45, which broaden beyond detection). This effect was partially reversed for some resonances (C6-Y11, in particular) when cytochrome c(3) was added to this system. Both probes were successful in causing reversible PREs at the partner binding site, thus showing to be good probes to identify partners' binding sites and since the interaction is reversible to structurally characterize protein complexes by better defining the complex interface.     

Novel small stable gold nanoparticles bearing fluorescent cysteine-coumarin probes as new metal-modulated chemosensors

Emissive molecular probes based on amino acid moieties are very appealing because of their application as new building blocks in peptide synthesis. Two new bioinspired coumarin probes (L1 and L2) were synthesized and fully characterized by elemental analysis, infrared, (1)H NMR, (13)C NMR, UV-vis absorption and emission spectroscopy, matrix-assisted laser desorption-ionization time-of-flight mass spectrometry (MALDI-TOF-MS), lifetime measurements, and X-ray crystal diffraction. Their sensing ability toward alkaline earth, transition, and post-transition metal ions (Ca(2+), Zn(2+), Cd(2+), Cu(2+), Ni(2+), Hg(2+), Ag(+), and Al(3+)) and their acid-base behavior (H(+), OH(-)) were explored in absolute ethanol by absorption and fluorescence spectroscopy. Compound L1 shows a strong complexation constant with the soft metal ions Zn(2+), Cd(2+), and Ag(+). Compound L2 shows a high fluorescence quantum yield, and it could be used as a non-pH-dependent fluorescent biological probe. Very small gold nanoparticles (AuNPs) using compounds L1 and L2 as stabilizers were obtained by using a reductive method and were characterized by UV-vis, light scattering, and transmission electron microscopy (TEM). Dynamic light scattering and TEM studies show that the formation of small nanoparticles is around 4.27 ± 0.64 nm for L1 and around 2.69 ± 0.96 nm for L2. The new stable Cou@AuNPs behaved as supramolecular chemosensors, which have been selective for the heavy element Hg(2+), with a concomitant change of color from pink to dark red/brown and an increase of size up to 100-fold.     

Synthetic hosts for molecular recognition of ureas

Four hosts (7-10) containing 2,6-bisamidopyridine- and 2,5-bisamidopyrrole-bearing pyridyl or 1,8-naphthyridyl groups have been prepared and their structures studied by a combination of multinuclear NMR spectroscopy and X-ray crystallography. Their behavior in molecular recognition of urea derivatives, including (+)-biotin methyl ester, has been approached by molecular modeling (Monte Carlo conformational search, AMBER force field). The minimum energy values for the complexes are correlated with the experimental binding energies determined by means of (1)H NMR titrations.