Reactivity Of Pph3 Toward Ruiiruiiicl(O2car)4 - Syntheses, Molecular-Structures, And Spectroscopic And Electrochemical Properties Of Ruiiruiii(Oh2)Cl(Mecn)(O2car)4(Pph3)2 And Ruii2(Oh2)(Mecn)2(O2car)4(Pph3)2

By the reaction of Ru2Cl(O2CAr)4 (1) and PPh3 in MeCN-H2O the diruthenium(II,III) and diruthenium(II) compounds of the type Ru2(OH2)Cl(MeCN)(O2CAr)4(PPh3)2 (2) and Ru2(OH2)(MeCN)2(O2CAr)4(PPh3)2 (3) were prepared and characterized by analytical, spectral, and electrochemical data (Ar is an aryl group, C6H4-p-X; X = H, OMe, Me, Cl, NO2). The molecular structure of Ru2(OH2)Cl(MeCN)(O2CC6H4-p-OMe)4(PPh3)2 was determined by X-ray crystallography. Crystal data are as follows: triclinic, P1BAR, a = 13.538 (5) angstrom, b = 15.650 (4) angstrom, c = 18.287 (7) angstrom, alpha = 101.39 (3)-degrees, beta = 105.99 (4)-degrees, gamma = 97.94 (3)-degrees, V = 3574 angstrom 3, Z = 2. The molecule is asymmetric, and the two ruthenium centers are clearly distinguishable. The Ru(III)-Ru(II), Ru(III)-(mu-OH2), and Ru(II)-(mu-OH2) distances and the Ru-(mu-OH2)-Ru angle in [{Ru(III)Cl(eta-1-O2CC6H4-p-OMe)(PPh3)}(mu-OH2)(mu-O2CC6H4-p-OMe)2{Ru(II)(MeCN)(eta-1-O2CC6H4-p-OMe)(PPh3)}] are 3.604 (1), 2.127 (8), and 2.141 (10) angstrom and 115.2 (5)-degrees, respectively. The compounds are paramagnetic and exhibit axial EPR spectra in the polycrystalline form. An intervalence transfer (IT) transition is observed in the range 900-960 nm in chloroform in these class II type trapped mixed-valence species 2. Compound 2 displays metal-centered one-electron reduction and oxidation processes near -0.4 and +0.6 V (vs SCE), respectively in CH2Cl2-TBAP. Compound 2 is unstable in solution phase and disproportionates to (mu-aquo)diruthenium(II) and (mu-oxo)diruthenium(III) complexes. The mechanistic aspects of the core conversion are discussed. The molecular structure of a diruthenium(II) compound, Ru2(OH2)(MeCN)2(O2CC6H4-p-NO2)4(PPh3)2.1.5CH2Cl2, was obtained by X-ray crystallography. The compound crystallizes in the space group P2(1)/c with a = 23.472 (6) angstrom, b = 14.303 (3) angstrom, c = 23.256 (7) angstrom, beta = 101.69 (2)-degrees, V = 7645 angstrom 3, and Z = 4. The Ru(II)-Ru(II) and two Ru(II)-(mu-OH2) distances and the Ru(II)-(mu-OH2)-Ru(II) angle in [{(PPh3)-(MeCN)(eta-1-O2CC6H4-p-NO2)Ru}2(mu-OH2)(mu-O2CC6H4-p-NO2)2] are 3.712 (1), 2.173 (9), and 2.162 (9) angstrom and 117.8 (4)-degrees, respectively. In both diruthenium(II,III) and diruthenium(II) compounds, each metal center has three facial ligands of varying pi-acidity and the aquo bridges are strongly hydrogen bonded with the eta-1-carboxylato facial ligands. The diruthenium(II) compounds are diamagnetic and exhibit characteristic H-1 NMR spectra in CDCl3. These compounds display two metal-centered one-electron oxidations near +0.3 and +1.0 V (vs SCE) in CH2Cl2-TBAP. The overall reaction between 1 and PPh3 in MeCN-H2O through the intermediacy of 2 is of the disproportionation type. The significant role of facial as well as bridging ligands in stabilizing the core structures is observed from electrochemical studies.

Structure of valinomycin by molecular dynamics studies

Valinomycin is an important ionophore which exhibits a high conformational flexibility. The study of various conformations adopted by this molecule together with the study of flexibility in a given conformation can throw light on the ion transport by the ionophore across the membrane. Molecular dynamics (MD) studies are ideal to characterize the flexibility in different parts of the molecule and can also give an idea of various conformations adopted by the molecule at a given temperature. Hence MD studies at 100K have been carried out on the minimized crystal structure of the molecule to scan the possible conformations in the neighbourhood of the well known 'bracelet' like structure of uncomplexed Valinomycin, Properties, like the flexibility, average values, r.m.s. fluctuations of the various intramolecular hydrogen bonds are discussed. Energy minimization has been carried out on selected MD simulated points to analyze the characteristics of the unique conformation adopted by this molecule at this temperature.

Crystal and molecular structure of putrescine DL- glutamic acid complex

The polyamines spermine, spermidine, putrescine, cadaverine, etc. have been implicated in a variety of cellular functions. However, details of their mode of interaction with other ubiquitous biomolecules is not known. We have solved a few structures of polyamine-amino acid complexes to understand the nature and mode of their interactions. Here we report the structure of a complex of putrescine with DL-glutamic acid. Comparison of the structure with the structure of putrescine-L-glutamic acid complex reveals the high degree of similarity in the mode of interaction in the two complexes. Despite the presence of a centre of symmetry in the present case, the arrangement of molecules is strikingly similar to the L-glutamic acid complex.

Temperature and concentration dependence of adsorption properties of methane in NaY: a molecular dynamics study

Molecular dynamics calculations on methane sorbed in NaY (Si/Al = 3.0) employing realistic methane-methane and methane-zeolite intermolecular potential functions at different temperatures (50, 150, 220, and 300 K) and concentrations (2, 4, 6, and 8 molecules/cage) are reported. The thermodynamic results are in agreement with the available experimental data. Guest-guest and guest-host radial distribution functions (rdfs), energy distribution functions, distribution of cage occupancy, center-of-cage-center-of-mass (coc-com) rdfs, velocity autocorrelation functions for com and angular motion and the Fourier transformed power spectra, and diffusion coefficients are presented as a function of temperature and concentration. At 50 K, methane is localized near the adsorption site. Site-site migration and essentially free rotational motion are observed at 150 K. Molecules preferentially occupy the region near the inner surface of the alpha-cage. The vibrational frequencies for the com of methane shift toward higher values with decreasing temperature and increasing adsorbate concentration. The observed frequencies for com motion are 36, 53, and 85 cm-1 and for rotational motion at 50 K, 95 and 150 cm-1 in agreement with neutron scattering data. The diffusion coefficients show a type I behavior as a function of loading in agreement with NMR measurements. Cage-to-cage diffusion is found to be always mediated by the surface.

The crystal and molecular structure of putrescine - di-glutamic acid complexes

The polyamines spermine, spermidine, putrescine, cadaverine, etc. have been implicated in a variety of cellular functions. However, details of their mode of interaction with other ubiquitous biomolecules is not known. We have solved a few structures of polyamine-amino acid complexes to understand the nature and mode of their interactions. Here we report the structure of a complex of putrescine with DL-glutamic acid. Comparison of the structure with the structure of putrescine-L-glutamic acid complex reveals the high degree of similarity in the mode of interaction in the two complexes. Despite the presence of a centre of symmetry in the present case, the arrangement of molecules is strikingly similar to the L-glutamic acid complex.

The velocity dispersion of giant molecular clouds. II - Mathematical and numerical refinements

The energy input to giant molecular clouds is recalculated, using the proper linearized equations of motion, including the Coriolis force and allowing for changes in the guiding center. Perturbation theory yields a result in the limit of distant encounters and small initial epicyclic amplitudes. Direct integration of the motion equations allows the strong encounter regime to be studied. The present perturbation theory result differs by a factor of order unity from that of Jog and Ostriker (1988). The result of present numerical integrations for the 2D (planar) velocity dispersion is presented. The accretion rate for a molecular cloud in the Galactic disk is calculated.

Crystal and Molecular Structure of N-acetyl-L-glutamine

The crystal and molecular structure of the title compound has been determined by direct methods from diffractometer data. Crystals are orthorhombic, with Z= 4 in a unit cell of dimensions : a= 13.811 (10), b= 5.095(5), c= 12.914(10)Å, space group P212121. The structure was refined by least-squares to R 3.31% for 868 observed reflections. There is significant non-planarity of the peptide group and its nitrogen atom is significantly pyramidal. There is no correlation between the double-bond character and reactivity of the C–N bond of the terminal amide group in glutamine and acetamide

Communication pathways from the anti-codon region to the aminoacylation site in Methionyl tRNA Synthetase: Molecular dynamics simulations and the structure network analysis

The enzymes of the family of tRNA synthetases perform their functions with high precision by synchronously recognizing the anticodon region and the aminoacylation region, which are separated by ?70 in space. This precision in function is brought about by establishing good communication paths between the two regions. We have modeled the structure of the complex consisting of Escherichia coli methionyl-tRNA synthetase (MetRS), tRNA, and the activated methionine. Molecular dynamics simulations have been performed on the modeled structure to obtain the equilibrated structure of the complex and the cross-correlations between the residues in MetRS have been evaluated. Furthermore, the network analysis on these simulated structures has been carried out to elucidate the paths of communication between the activation site and the anticodon recognition site. This study has provided the detailed paths of communication, which are consistent with experimental results. Similar studies also have been carried out on the complexes (MetRS + activated methonine) and (MetRS + tRNA) along with ligand-free native enzyme. A comparison of the paths derived from the four simulations clearly has shown that the communication path is strongly correlated and unique to the enzyme complex, which is bound to both the tRNA and the activated methionine. The details of the method of our investigation and the biological implications of the results are presented in this article. The method developed here also could be used to investigate any protein system where the function takes place through long-distance communication.

Conformational studies of the triphenylphosphazenyl side chain in cyclophosphazenes. I. Crystal and molecular structure of N3P3C15(NPPh3)

The title compound, C t8H~sC15NaP4, crystallizes in the monoclinic space group P2~/n with a = 20.14 (2), b = 8.69 (1), c = 14.92 (2) A, fl = 98.8 (3) ° , Z = 4. The structure was determined from visual data and refined to R = 0-069 for 1450 reflections. The cyclophosphazene ring is non-planar. The exocyclic NPPh 3 group exhibits type I conformation [R. A. Shaw (1975). Pure Appl. Chem. 44, 317-341] in which the N-P bond is perpendicular to the adjacent P-CI bond.

Ruthenium-Oxygen Coordination-Driven Self-Assembly of a Ru-8(II) Incomplete Prism: Synthesis, Structure, and Shape-Selective Molecular Recognition Study

Coordination-driven self-assembly of 1,3,5-benzenetricarboxylate (tma; 1) and oxalato-bridged p-cymeneruthenium(II) building block Ru-2(mu-eta(4)-C2O4)(MeOH)(2)(eta(6)-p-cymene)(2)](O3SCF3)(2) (2) affords an unusual octanuclear incomplete prism Ru-8(eta(6)-p-cymene)(8)(tma)(2)(mu-eta(4)-C2O4)(2)(OMe)(4)](O3SCF3)( 2) (3), which exhibits a remarkable shape-selective binding affinity for neutral phenolic compounds via hydrogen-bonding interactions (p-cymene = p-(PrC6H4Me)-Pr-i). Such a binding was confirmed by single-crystal X-ray diffraction analysis using 1,3,5-trihydroxybenzene as an analyte.

Structural Relationships in 2,3-Bis-n-decyloxyanthracene and 12-Hydroxystearic Acid Molecular Gels and Aerogels Processed in Supercritical CO2

Supercritical carbon dioxide is used to prepare aerogels of two reference molecular organogelators, 2,3-bis-n-decyloxyanthracene (DDOA) (luminescent molecule) and 12-hydroxystearic acid (HSA). Electron microscopy reveals the fibrillar morphology of the aggregates generated by the protocol. SAXS and SANS measurements show that DDOA aerogels are crystalline materials exhibiting three morphs: (1) arrangements of the crystalline solid (2D p6m), (2) a second hexagonal morph slightly more compact, and (3) a packing specific of the fibers in the gel. Aggregates specific of the aerogel (volume fraction being typically phi approximate to 0.60) are developed over larger distances (similar to 1000 angstrom) and bear fewer defaults and residual strains than aggregates in the crystalline and gel phases. Porod, Scherrer and Debye-Bueche analyses of the scattering data have been performed. The first five diffraction peaks show small variations in position and intensity assigned to the variation of the number of fibers and their degree of vicinity within hexagonal bundles of the related SAFIN according to the Oster model. Conclusions are supported by the guidelines offered by the analysis of the situation in HSA aerogels for which the diffraction pattern can be described by two coexisting lamellar-like arrangements. The porosity of the aerogel, as measured by its specific surface extracted from the scattering invariant analysis, is only 1.8 times less than that of the swollen gel and is characteristic of a very porous material.