Two highly unsymmetrical tetradentate (N3O) Schiff base copper(II) complexes: Template synthesis, structural characterization, magnetic and computational studies

Two new copper(II) complexes, [Cu-2(L-1)(2)](ClO4)(2) (1) and [Cu(L-2)(ClO4)] (2), of the highly unsymmetrical tetradentate (N3O) Schiff base ligands HL1 and HL2 (where HL1 = N-(2-hydroxyacetophenone)-bis-3-aminopropylamine and HL2 = N-(salicyldehydine)-bis-3-aminopropylamine) have been synthesised using a template method. Their single crystal X-ray structures show that in complex 1 two independent copper(II) centers are doubly bridged through sphenoxo-O atoms (O1A and O1B) of the two ligands and each copper atom is five-coordinated with a distorted square pyramidal geometry. The asymmetric unit of complex 2 consists of two crystallographically independe N-(salicylidene) bis(aminopropyl)amine-copper(II) molecules, A and B, with similar square pyramidal geometries. Cryomagnetic susceptibility measurements (5-300 K) on complex 1 reveal a distinct antiferromagnetic interaction with J=-23.6 cm(-1), which is substantiated by a DFT calculation (J=-27.6 cm(-1)) using the B3LYP functional. Complex 1, immobilized over highly ordered hexagonal mesoporous silica, shows moderate catalytic activity for the epoxidation of cyclohexene and styrene in the presence of TBHP as an oxidant.

Recognition of Interaction Interface Residues in Low-Resolution Structures of Protein Assemblies Solely from the Positions of C alpha Atoms

Background: The number of available structures of large multi-protein assemblies is quite small. Such structures provide phenomenal insights on the organization, mechanism of formation and functional properties of the assembly. Hence detailed analysis of such structures is highly rewarding. However, the common problem in such analyses is the low resolution of these structures. In the recent times a number of attempts that combine low resolution cryo-EM data with higher resolution structures determined using X-ray analysis or NMR or generated using comparative modeling have been reported. Even in such attempts the best result one arrives at is the very course idea about the assembly structure in terms of trace of the C alpha atoms which are modeled with modest accuracy. Methodology/Principal Findings: In this paper first we present an objective approach to identify potentially solvent exposed and buried residues solely from the position of C alpha atoms and amino acid sequence using residue type-dependent thresholds for accessible surface areas of C alpha. We extend the method further to recognize potential protein-protein interface residues. Conclusion/Significance: Our approach to identify buried and exposed residues solely from the positions of C alpha atoms resulted in an accuracy of 84%, sensitivity of 83-89% and specificity of 67-94% while recognition of interfacial residues corresponded to an accuracy of 94%, sensitivity of 70-96% and specificity of 58-94%. Interestingly, detailed analysis of cases of mismatch between recognition of interface residues from C alpha positions and all-atom models suggested that, recognition of interfacial residues using C alpha atoms only correspond better with intuitive notion of what is an interfacial residue. Our method should be useful in the objective analysis of structures of protein assemblies when positions of only C alpha positions are available as, for example, in the cases of integration of cryo-EM data and high resolution structures of the components of the assembly.

2-Chloro-3-hydroxymethyl-7,8-dimethylquinoline

All non-H atoms of the title compound, C12H12ClNO, are co-planar (r.m.s. deviation = 0.055 angstrom). The hydroxy H atom is disordered over two positions of equal occupancy. In the crystal, molecules are linked by O-H center dot center dot center dot O hydrogen bonds, generating zigzag chains running along the b axis.

Vertex-Fused Metallaborane Clusters: Synthesis, Characterization and Electronic Structure of [(eta(5)-C5Me5Mo)(3)MoB9H18]

The reaction of the [(eta(5)-C5Me5)MoCl4] complex with [LiBH4 - TH F] in toluene at - 70 degrees C, followed by pyrolysis at 110 degrees C, afforded dark brown [(eta(5)-C5Me5Mo)(3)MoB9H18], 2, in parallel with the known [(eta(5)-C5Me5Mo)(2)B5H9], 1. Compound 2 has been characterized in solution by H-1, B-11, and C-13 NMR spectroscopy and elemental analysis, and the structural types were unequivocally established by crystallographic studies. The title compound represents a novel class of vertex-fused clusters in which a Mo atom has been fused in a perpendicular fashion between two molybdaborane clusters. Electronic structure calculations employing density functional theory yield geometries in agreement with the structure determinations, and on grounds of density functional theory calculations, we have analyzed the bonding patterns in the structure,

Role of the triplet state in the green emission peak of polyfluorene films: A time evolution study

The blue emission of ethyl-hexyl substituted polyfluorene (PF2/6) films is accompanied by a low energy green emission peak around 500 nm in inert atmosphere. The intensity of this 500 nm peak is large in electroluminescence (EL) compared to photoluminescence (PL)measurements. Furthermore, the green emission intensity reduces dramatically in the presence of molecular oxygen. To understand this, we have modeled various nonradiative processes by time dependent quantum many body methods. These are (i) intersystem crossing to study conversion of excited singlets to triplets leading to a phosphorescence emission, (ii) electron-hole recombination (e-hR) process in the presence of a paramagnetic impurity to follow the yield of triplets in a polyene system doped with paramagnetic metal atom, and (iii) quenching of excited triplet states in the presence of oxygen molecules to understand the low intensity of EL emission in ambient atmosphere, when compared with that in nitrogen atmosphere. We have employed the Pariser-Parr-Pople Hamiltonian to model the molecules and have invoked electron-electron repulsions beyond zero differential approximation while treating interactions between the organic molecule and the rest of the system. Our time evolution methods show that there is a large cross section for triplet formation in the e-hR process in the presence of paramagnetic impurity with degenerate orbitals. The triplet yield through e-hR process far exceeds that in the intersystem crossing pathway, clearly pointing to the large intensity of the 500 nm peak in EL compared to PL measurements. We have also modeled the triplet quenching process by a paramagnetic oxygen molecule which shows a sizable quenching cross section especially for systems with large sizes. These studies show that the most probable origin of the experimentally observed low energy EL emission is the triplets.

5-Phenyl-3-(2-thienyl)-1,2,4-triazolo[3,4-a]isoquinoline

In the title molecule, C20H13N3S, the triazoloisoquinoline ring system is approximately planar, with an r.m.s. deviation of 0.045 angstrom and a maximum deviation of 0.090 (2) angstrom from the mean plane for the triazole ring C atom which is bonded to the thiophene ring. The phenyl ring is twisted by 52.0 (1)degrees with respect to the mean plane of the triazoloisoquinoline ring system. The thiophene ring is rotationally disordered by approximately 180 degrees over two sites, the ratio of refined occupancies being 0.73 (1): 0.27 (1).

2,6-Bis(3-methoxyphenyl)-3-methylpiperidin-4-one

In the molecule of the title compound, C20H23NO3, the bulky methoxyphenyl substituents at the equatorial 2,6-positions crowd the vicinity of the equatorial amino H atom and prevent it from forming intermolecular hydrogen bonds. The piperidine ring adopts a distorted chair conformation.

Inter-helical Interactions in Membrane Proteins: Analysis Based on the Local Backbone Geometry and the Side Chain Interactions

The availability of a significant number of the Structures of helical membrane proteins has prompted us to investigate the mode of helix-helix packing. In the present study, we have considered a dataset of alpha-helical membrane proteins representing Structures solved from all the known superfamilies. We have described the geometry of all the helical residues in terms of local coordinate axis at the backbone level. Significant inter-helical interactions have been considered as contacts by weighing the number of atom-atom contacts, including all the side-chain atoms. Such a definition of local axis and the contact criterion has allowed us to investigate the inter-helical interaction in a systematic and quantitative manner. We show that a single parameter (designated as alpha), which is derived from the parameters representing the Mutual orientation of local axes, is able to accurately Capture the details of helix-helix interaction. The analysis has been carried Out by dividing the dataset into parallel, anti-parallel, and perpendicular orientation of helices. The study indicates that a specific range of alpha value is preferred for interactions among the anti-parallel helices. Such a preference is also seen among interacting residues of parallel helices, however to a lesser extent. No such preference is seen in the case of perpendicular helices, the contacts that arise mainly due to the interaction Of Surface helices with the end of the trans-membrane helices. The Study Supports the prevailing view that the anti-parallel helices are well packed. However, the interactions between helices of parallel orientation are non-trivial. The packing in alpha-helical membrane proteins, which is systematically and rigorously investigated in this study, may prove to be useful in modeling of helical membrane proteins.

Correlation between conductivity or diffusivity and activation energy in amorphous solids

There exist many investigations of ionic transport in a variety of glasses. These studies exhibit strong correlation between ionic conductivity and activation energy: Typically, it is found that higher conductivity is associated with lower activation energies and vice versa. Although there are explanations for this at a phenomenological level, there is no consistent physical picture to explain the correlation between conductivity and activation energy. We have carried out molecular dynamics simulation as a function of the size of the impurity atom or diffusant (both neutral and charged) in a host amorphous matrix. We find that there is a maximum in self-diffusivity as a function of the size of the impurity atom suggesting that there is an appropriate size for which the diffusivity is maximum. The activation energy is found to be the lowest for this size of the impurity. A similar maximum has been previously found in other condensed phases, such as confined fluids and dense liquids, and has its origin in the levitation effect. The implications of this result for understanding ionic conductivity in glasses are discussed. Our results suggest that there is a relation between microscopic structure of the amorphous solid, diffusivity or conductivity, and activation energy. The nature of this relationship is discussed in terms of the levitation parameter showing that diffusivity is maximum when the size of the neck or doorway radius is comparable with the size of the diffusant. Our computational results here are in excellent agreement with independent experimental results of Nascimento et al. [Braz. J. Phys. 35, 626 (2005)] that structural features of the glass are important in determining the ionic conductivity.

Direct probe of end-segment distribution in tethered polymer chains

End-tethered chains made of an adsorbed diblock copolymer of polystyrene (PS)-polyisoprene (PI) bearing an end-segment including a Ge atom are built by the Langmuir-Schaeffer technique. They are studied both in the dry state and in a good solvent for the PI chain using grazing incidence X-ray standing waves. The analysis of the signal provides a direct measurement of the end-segment distribution which is found to be singular and mostly localized to a plane in the dry case. In the good solvent case, end-segments are found to span the entire assembly and compare very well with results obtained by Kreer et al.

Antithyroid Drugs and their Analogues Protect Against Peroxynitrite-Mediated Protein Tyrosine Nitration-A Mechanistic Study

In this paper, the effect of some commonly used antithyroid drugs and their analogues on peroxynitrite-mediated nitration of proteins is described. The nitration of tyrosine residues in bovine serum albumin (BSA) and cytochromec was studied by Western blot analysis. These studies reveal that the antithyroid drugs methimazole (MMI), 6-n-propyl-2-thiouracil (PTU), and 6-methyl-2-thiouracil (MTU), which contain thione moieties, significantly reduce the tyrosine nitration of both BSA and cytochrome c. While MMI exhibits good peroxynitrite (PN) scavenging activity, the thiouracil compounds PTU and MTU are slightly less effective than MMI. The S- and Se-methylated compounds show a weak inhibitory effect in the nitration of tyrosine, indicating that the presence of a thione or selone moiety is important for an efficient inhibition. Similarly, the replacement of N-H moiety in MMI by N-methyl or N-m-methoxybenzyl substituents dramatically reduces the antioxidant activity of the parent compound. Theoretical studies indicate that the substitution of N-H moiety by N-Me significantly increases the energy required for the oxidation of sulfur center by PN. However, such substitution in the selenium analogue of MMI increases the activity of parent compound. This is due to the facile oxidation of the selone moiety to the corresponding selenenic and seleninic acids. Unlike N,N'-disubstituted thiones, the corresponding selones efficiently scavenge PN, as they predominantly exist in their zwitterionic forms in which the selenium atom carries a large negative charge.

3-Benzyl-6-benzylamino-1-methyl-5-nitro-1,2,3,4-tetrahydropyrimidine

In the title compound, C19H22N4O2, the tetrahydropyrimidine ring adopts an envelope conformation (with the N atom connected to the benzyl group representing the flap). This benzyl group occupies a quasi-axial position. The two benzyl groups lie over the tetrahydropyridimidine ring. The amino group is a hydrogen-bond donor to the nitro group.

Two- and Three-Dimensional Open-Framework Uranium Arsenates: Synthesis, Structure, and Characterization

Hydrothermal reactions between uranium salts and arsenic pentoxide in the presence of two different amines yielded six new uranium arsenate phases exhibiting open-framework structures, ethylenediamine (en): [C2N2H9]-[(UO2)(ASO(4))] I; [C2N2H10][(UO2)F(HASO(4))]2 center dot 4H(2)O, II; [C2N2H9][U2F5(HASO(4))(2)], III; [C2N2H9][UF2(ASO(4))], IV; diethylenetriamine (DETA), [C4N3H16][U2F3(ASO(4))(2)(HAsO4)] V; and [C4N3H16][U2F6(AsO4)(HAsO4)], VI. The structures were determined using single crystal studies, which revealed two- (I, II, V) and three-dimensional (III, IV, VI) structures for the uranium arsenates. The uranium atom, in these compounds, exhibits considerable variations in the coordination (6 to 9) that appears to have some correlation with the synthetic conditions. The water molecules in [C2N2H10][(UO2)F(HAsO4)](2 center dot)4H(2)O, II, could be reversibly removed, and the dehydrated phase, [C2N2H10][(UO2)F(HAsO4)](2), IIa, was also characterized using single crystal studies. The observation of many mineralogical structures in the present compounds suggests that the hydrothermal method could successfully replicate the geothermal conditions. As part of this study, we have observed autunite, Ca[(UO2)(PO4)](2)(H2O)(11), metavauxite, [Fe(H2O)(6)][Al(OH)(H2O)(PO4)](2), finarite, PbCU(SO4)(OH)(2), and tancoite, LiNa2H[Al(PO4)(2)(OH)], structures. The repeated observation of the secondary building unit, SBU-4, in many of the uranium arsenate structures suggests that these are viable building units. Optical studies on the uranium arsenate compound, [C4N3H16][U2F6(AsO4)(HASO(4))), VI, containing uranium in the +4 oxidation state indicates a blue emission through an upconversion process. The compound also exhibits antiferromagnetic behavior.

Synthesis of Cu@ZnO Core−Shell Nanocomposite through Digestive Ripening of Cu and Zn Nanoparticles

The synthesis of colloids of copper and zinc nanoparticles by solvated metal atom dispersion (SMAD) is described. The as-prepared colloids with a large size distribution of the particles are transformed into colloidal nanoparticles of a narrow size distribution by the digestive ripening process which involves refluxing the colloid at or near the boiling point of the solvent in the presence of a passivating ligand. The copper nanoparticles of 2.1 ± 0.3 nm and zinc nanoparticles of 3.9 ± 0.3 nm diameters have thus been obtained. Digestive ripening of the as-prepared copper and zinc colloids together in the presence of a passivating agent gave Cu@ZnO core−shell nanoparticles, with an average diameter of 3.0 ± 0.7 nm. Particles synthesized in this manner were characterized by UV−visible spectroscopy, high-resolution electron microscopy, energy-filtered electron microscopy, and powder X-ray diffraction methods which confirm the core−shell structure.

Vibrational phase relaxation of O–H stretch in bulk water: Role of large amplitude angular jumps and negative cross-correlations among the forces on the O–H bond

The ultrafast vibrational phase relaxation of O–H stretch in bulk water is investigated in molecular dynamics simulations. The dephasing time (T2) of the O–H stretch in bulk water calculated from the frequency fluctuation time correlation function (Cω(t)) is in the range of 70–80 femtosecond (fs), which is comparable to the characteristic timescale obtained from the vibrational echo peak shift measurements using infrared photon echo [W.P. de Boeij, M.S. Pshenichnikov, D.A. Wiersma, Ann. Rev. Phys. Chem. 49 (1998) 99]. The ultrafast decay of Cω(t) is found to be responsible for the ultrashort T2 in bulk water. Careful analysis reveals the following two interesting reasons for the ultrafast decay of Cω(t). (A) The large amplitude angular jumps of water molecules (within 30–40 fs time duration) provide a large scale contribution to the mean square vibrational frequency fluctuation and gives rise to the rapid spectral diffusion on 100 fs time scale. (B) The projected force, due to all the atoms of the solvent molecules on the oxygen (FO(t)) and hydrogen (FH(t)) atom of the O–H bond exhibit a large negative cross-correlation (NCC). We further find that this NCC is partly responsible for a weak, non-Arrhenius temperature dependence of the dephasing rate.