Ionic Recognition by 7-Nitro-1,3,5-triaza Adamantane: First Thermodynamic Study

A thermodynamic study involving 7-nitro-1,3,5-triaza adamantane, 1, and its interaction with metal cations in nonaqueous media is first reported. Solubility data of 1 in various solvents were used to derive the standard Gibbs energies of solution, Delta G(s)degrees in these solvents. The effect of solvation in the different media was assessed from the Gibbs energy of transfer taking acetonitrile as a reference solvent. (1)H NMR studies of the interaction of 1 and metal cations were carried out in CD(3)CN and CD(3)OD and the data are reported. Conductance measurements revealed that this ligand forms lead(II) or zinc complexes of 1: 1 stoichiometry in acetonitrile. It also revealed a stoichiometry of two molecules of 1 per mercury(II) and two cadmiu (II) ions per molecule of 1. The addition of silver salt to 1 led to the precipitation of the silver-1 complex which was isolated and characterized by X-ray crystallography. At variance with conductance measurements in solution, in the solid state the X-ray structure show`s a 1:1 stoichiometry in the Hg(II) complex. The themiodynamics of complexation of 1 and these cations provide a quantitative assessment of the selective behavior of this ligand for ions of environmental relevance.

Dependence of Response Functions and Orbital Functionals on Occupation Numbers

Explicitly orbital-dependent approximations to the exchange-correlation energy functional of density functional theory typically not only depend on the single-particle Kohn-Sham orbitals but also on their occupation numbers in the ground-state Slater determinant. The variational calculation of the corresponding exchange-correlation potentials with the optimized effective potential (OEP) method therefore also requires a variation of the occupation numbers with respect to a variation in the effective single-particle potential, which is usually not taken into account. Here it is shown under which circumstances this procedure is justified.

Tightened Lieb-Oxford Bound for Systems of Fixed Particle Number

The Lieb-Oxford bound is a constraint upon approximate exchange-correlation functionals. We explore a nonempirical tightening of that bound in both universal and electron number-dependent form. The test functional is PBE. Regarding both atomization energies (slightly worsened) and bond lengths (slightly improved), we find the PBE functional to be remarkably insensitive to the value of the Lieb-Oxford bound. This both rationalizes the use of the original Lieb-Oxford constant in PBE and suggests that enhancement factors more sensitive to sharpened constraints await discovery.

Copper(II) and zinc(II) complexes with 2-benzoylpyridine-methyl hydrazone

2-Benzoylpyridine-methyl hydrazone (HBzMe) has been obtained as well as its copper(II) [Cu(HBzMe)Cl(2)] (1) and zinc(II) [Zn(HBzMe)Cl(2)] (2) complexes. Upon re-crystallization in 1 - 9 DMSO:acetone conversion of I into dimeric [Cu(BzMe)Cl](2) (1a) occurred. The crystal structures of HBzMe, 1, 1a, and 2 were determined. HBzMe adopts the ZE conformation in the solid. In all complexes the hydrazone adopts the E configuration to attach to the metal through the N(py)-N2-O chelating system. In 1 and 2 a neutral hydrazone coordinates to the metal center while in 1a deprotonation occurs with coordination of an anionic ligand. la presents a dimeric structure. having two copper(II) ions per asymmetric unit. Two chlorides are also present in the copper coordination sphere, which act as bridging ligands and connect the copper centers to each other. (C) 2008 Elsevier B.V. All rights reserved.

Structural effects and hydrogen bonds on N,N `-di(methoxycarbonylsulfenyl)urea, [CH(3)OC(O)SNH](2)CO, studied by experimental and theoretical methods

Pure N,N`-di(methoxycarbonylsulfenyl)urea, [CH(3)OC(O)SNH](2)CO, is quantitatively prepared by the hydrolysis reaction of CH(3)OC(O)SNCO and characterized by (1)H NMR, GC-MS and FTIR spectroscopy techniques. Structural and conformational properties are analyzed using a combined approach with data obtained from X-ray diffraction, vibrational spectra and theoretical calculation methods. The IR and Raman spectra for normal and deuterated species are reported. The crystal structure of [CH(3)OC(O)SNH](2)CO was determined by X-ray diffraction methods. The substance crystallizes in the orthorhombic P2(1)2(1)2 space group with a = 9.524(2), b = 12.003(1), c = 4.481 (1) angstrom, and Z = 2 moieties in the unit cell. The molecule is sited on a twofold crystallographic axis (C(2)) parallel to c and shows the anti-anti conformation (S-N single bonds antiperiplanar with respect to the opposite C-N single bonds in sulfenyl-urea-sic group). Neighboring molecules are arranged in a chain motif that extends along the C(2)-axis and is held by bifurcated NH center dot center dot center dot O center dot center dot center dot HN intermolecular bonds. A local planar symmetry is observed in the crystal for the central -SN(H)C(O)N(H)S- skeleton. Experimental and calculated data allow to trace this structural feature to the occurrence of N-H center dot center dot center dot O=C hydrogen bonding interactions. Calculated vibrational and structural properties are in good agreement with the experimentally determined features. (C) 2008 Elsevier B.V. All rights reserved.

Structural and spectroscopic characterization of 2,2 `-methylenedi-8-quinolinol dihydrochloride dihydrate

The crystal structure of the title compound, a promising ligand for chelatoterapies in the treatment of Alzheimer`s disease, has been determined by single crystal X-ray diffractometry. The compound crystallized in the monoclinic space group C2/c with Z = 4. The dimeric 8-quinolinol molecule is sited on a crystallographic twofold axis passing through the CH(2) carbon atom that links the symmetry related molecular halves, giving rise to a two-bladed propeller-like conformation. The (1)H and (13)C NMR as well as the IFT-IR and Raman spectra of the compound were also recorded and are briefly discussed. Some comparisons with spectra of related species are made. (C) 2008 Elsevier B.V. All rights reserved.

Analyzing Ru(III)-dmso and Ru(III)-dms motifs in compounds used in the synthesis of the antimetastatic agents

The chemistry of Ru(III) complexes containing dmso as a ligand has become an interesting area in the cancer treatment field. Because of this, structural knowledge and chemistry of the moiety Ru(III)-dmso have become important to cancer research. The crystal structures of the compounds mer-[RuCl(3)(dms)(3)] (1) and mer-[RuCl(3)(dms)(2)(dmso)]:mer-[RuCl(3)(dms)(3)] (2) were determined by X-ray crystallography and a speciation of the presence of intramolecular hydrogen bond in these structures has been studied. Compound (1) crystallizes in the orthorhombic space group, Pna2(1); a = 16.591(8) angstrom, b = 8.724(2) angstrom. c = 10.547(3) angstrom; Z = 12 and (2) crystallizes in the space group, P2(1)/C: a = 11.9930(2) angstrom, b = 7.9390(2) angstrom, c = 15.8700(3) angstrom, beta = 93.266(1)degrees, Z = 2. From the X-ray structures solved in this work, were possible to suggest an interpretation for the broad lines observed in the EPR spectra of the Ru(III) compounds explored here. Also, the exchange interactions detected by EPR spectroscopy in solid state and in solution, confirm the presence of van der Waals interactions such as C-H center dot center dot center dot Cl in the compounds (1), (2) and (3). The use of techniques such as IR, UV-vis, (1)H NMR and EPR Spectroscopy and Cyclic Voltammetry were applied in this work to analyze the behavior of these metallocompounds. (c) 2008 Elsevier B.V. All rights reserved.

Combined Crystallographic and Solution Molecular Dynamics Study of Allosteric Effects in Ester and Ketone p-tert-Butylcalix[4]arene Derivatives and Their Complexes with Acetonitrile, Cd(II), and Pb(II)

We describe here a procedure to bridge the gap in the field of calixarene physicochemistry between solid-state atomic-resolution structural information and the liquid-state low-resolution thermodynamics and spectroscopic data. We use MD simulations to study the kinetics and energetics involved in the complexation of lower rim calix[4]arene derivatives (L), containing bidentate ester (1) and ketone (2) pendant groups, with acetonitrile molecule (MeCN) and Cd2+ and Pb2+ ions (M2+) in acetonitrile solution. On one hand, we found that the prior inclusion of MeCN into the calix to form a L(MeCN) adduct has only a weak effect in preorganizing the hydrophilic cavity toward metal ion binding. On the other hand, the strong ion-hydrophilic cavity interaction produces a wide open calix which enhances the binding of one MeCN molecule (allosteric effect) to stabilize the whole (M2+)1(MeCN) bifunctional complex. We reach two major conclusions: (i) the MD results for the (M2+)1(MeCN) binding are in close agreement with the ""endo"", fully encapsulated, metal complex found by X-ray diffraction and in vacuo MD calculations, and (ii) the MD structure for the more flexible 2 ligand, however, differs from the also endo solid-state molecule. In fact, it shows strong solvation effects at the calixarene lower bore by competing MeCN molecules that share the metal coordination sphere with the four C=O oxygens of an ""exo"" (M2+)2(MeCN) complex.

Empirical analysis of the Lieb-Oxford bound in ions and molecules

Universal properties of the Coulomb interaction energy apply to all many-electron systems. Bounds on the exchange-correlation energy, in particular, are important for the construction of improved density functionals. Here we investigate one such universal property-the Lieb-Oxford lower bound-for ionic and molecular systems. In recent work [J Chem Phys 127, 054106 (2007)], we observed that for atoms and electron liquids this bound may be substantially tightened. Calculations for a few ions and molecules suggested the same tendency, but were not conclusive due to the small number of systems considered. Here we extend that analysis to many different families of ions and molecules, and find that for these, too, the bound can be empirically tightened by a similar margin as for atoms and electron liquids. Tightening the Lieb-Oxford bound will have consequences for the performance of various approximate exchange-correlation functionals. (C) 2008 Wiley Periodicals Inc.

Orbital-polarization terms: From a phenomenological to a first-principles description of orbital magnetism in density-functional theory

Phenomenological orbital-polarizition (OP) terms have been repeatedly introduced in the single-particle equations of spin-density-functional theory, in order to improve the description of orbital magnetic moments in systems containing transition metal ions. Here we show that these ad hoc corrections can be interpreted as approximations to the exchange-correlation vector potential A(xc) of current-density functional theory (CDFT). This connection provides additional information on both approaches: phenomenological OP terms are connected to first-principles theory, leading to a rationale for their empirical success and a reassessment of their limitations and the approximations made in their derivation. Conversely, the connection of OP terms with CDFT leads to a set of simple approximations to the CDFT potential A(xc), with a number of desirable features that are absent from electron-gas-based functionals. (C) 2008 Wiley Periodicals, Inc.

Solid state NMR as a new approach for the structural characterization of rare-earth doped lead lanthanum zirconate titanate laser ceramics

To facilitate the design of laser host materials with optimized emission properties, detailed structural information at the atomic level is essential, regarding the local bonding environment of the active ions (distribution over distinct lattice sites) and their extent of local clustering as well as their population distribution over separate micro- or nanophases. The present study explores the potential of solid state NMR spectroscopy to provide such understanding for rare-earth doped lead lanthanum zirconate titanate (PLZT) ceramics. As the NMR signals of the paramagnetic dopant species cannot be observed directly, two complementary approaches are utilized: (1) direct observation of diamagnetic mimics using Sc-45 NMR and (2) study of the paramagnetic interaction of the constituent host lattice nuclei with the rare-earth dopant, using Pb-207 NMR lineshape analysis. Sc-45 MAS NMR spectra of scandium-doped PLZT samples unambiguously reveal scandium to be six-coordinated, suggesting that this rare-earth ion substitutes in the B site. Static Pb-207 spin echo NMR spectra of a series of Tm-doped PLZT samples reveal a clear influence of paramagnetic rare-earth dopant concentration on the NMR lineshape. In the latter case high-fidelity spectra can be obtained by spin echo mapping under systematic incrementation of the excitation frequency, benefiting from the signal-to-noise enhancement afforded by spin echo train Fourier transforms. Consistent with XRD data, the Pb-207 NMR lineshape analysis suggests that statistical incorporation into the PLZT lattice occurs at dopant levels of up to 1 wt.% Tm3+, while at higher levels the solubility limit is reached. (C) 2008 Elsevier Masson SAS. All rights reserved.

Only subtle protein conformational adaptations are required for ligand binding to thyroid hormone receptors: Simulations using a novel multipoint steered molecular dynamics approach

Thyroid hormone receptors (TR) are hormone-dependent transcription regulators that play a major role in human health, development, and metabolic functions. The thyroid hormone resistance syndrome, diabetes, obesity, and some types of cancer are just a few examples of important diseases that are related to TR malfunctioning, particularly impaired hormone binding. Ligand binding to and dissociation from the receptor ultimately control gene transcription and, thus, detailed knowledge of binding and release mechanisms are fundamental for the comprehension of the receptor`s biological function and development of pharmaceuticals. In this work, we present the first computational study of ligand entry into the ligand binding domain (LBD) of a nuclear receptor. We report molecular dynamics simulations of ligand binding to TRs using a generalization of the steered molecular dynamics technique designed to perform single-molecule pulling simulations along arbitrarily nonlinear driving pathways. We show that only gentle protein movements and conformational adaptations are required for ligand entry into the LBDs and that the magnitude of the forces applied to assist ligand binding are of the order of the forces involved in ligand dissociation. Our simulations suggest an alternative view for the mechanisms ligand binding and dissociation of ligands from nuclear receptors in which ligands can simply diffuse through the protein surface to reach proper positioning within the binding pocket. The proposed picture indicates that the large-amplitude protein motions suggested by the apo- and holo-RXR alpha crystallographic structures are not required, reconciling conformational changes of LBDs required for ligand entry with other nuclear receptors apo-structures that resemble the ligand-bound LBDs.

Structural role of fluoride in the ion-conducting glass system B(2)O(3)-PbO-LiF studied by single- and double-resonance NMR

The local structure of an ion-conducting glass with nominal composition 50B(2)O(3)-10PbO-40LiF has been investigated by complementary (7)Li, (11)B, (19)F, and (207)Pb single- and double-resonance experiments. The results give insight into the structural role of the lithium fluoride additive in borate glasses: (1) LiF is seen to actively participate in the network transformation process contributing to the conversion of three- into four-coordinate boron units, as shown by (11)B single-resonance as well as by (11)B{(19)F} and (19)F{(11)B} double-resonance experiments. (2) (19)F signal quantification experiments suggest substantial fluoride loss, presumably caused by formation of volatile BF(3). A part of the fluoride remains in the dopant role, possibly in the form of small LiF-like cluster domains, which serve as a mobile ion supply. (3) The extent of lithium-fluorine and lead-fluorine interactions has been characterized by (7)Li{(19)F} and (207)Pb{(19)F} REDOR and SEDOR experiments. On the basis of these results, a quantitative structural description of this system has been developed.

Structural stability and reversible unfolding of recombinant porcine S100A12

Porcine S100A12 is a member of the S100 proteins, family of small acidic calcium-binding proteins characterized by the presence of two EF-hand motifs. These proteins are involved in many cellular events such as the regulation of protein phosphorylation, enzymatic activity, protein-protein interaction, Ca(2+) homeostasis, inflammatory processes and intermediate filament polymerization. In addition, members of this family bind Zn(2+) or Ca(2+) with cooperative effect on binding. In this study, the gene sequence encoding porcine S100A12 was obtained by the synthetic gene approach using E. coli codon bias. Additionally, we report a thermodynamic study of the recombinant S100A12 using circular dichroism, fluorescence and isothermal titration calorimetry. The results of urea and temperature induced unfolding and refolding processes indicated a reversible two-state process. Also, the ANS fluorescence studies showed that in presence of divalent ions the protein exposes hydrophobic sites which could facilitate the interaction with other proteins and trigger the physiological responses. (c) 2008 Elsevier B.V. All rights reserved.

Preparation and characterization of new glassy system As2P2S8-Ga2S3

Glasses having the composition (100 - x)As2P2S8-xGa(2)S(3) with x ranging from 0 to 50% were investigated to determine the compositional effect on properties and local structure. The glass transition temperature (T-g) and the stability parameter against crystallization (T-x - T-g) increased with the addition of Ga2S3. The structure of these glasses was probed by Raman scattering, Fourier transform infrared (FT-IR) and P-31 nuclear magnetic resonance. On the basis of the observed vibrations and the strength of the P-31-P-31 homonuclear magnetic dipolar coupling, two scenarios can be proposed for the structural evolution induced by the addition of Ga2S3. For x <= 20% we may have the formation of GaS4E- groups (E = nonbonding electron), and for x >= 30% we have depolymerization of the As2P2S8 units and the formation of a network of GaPS4 units with each PS4/2 unit (Q(4)) species carrying a single positive formal charge.