Theoretical Studies on the Structure and Bonding of Metallacyclocumulenes, -cyclopentynes, and -cycloallenes

In this paper, we compare the electronic structure of the hafnacycloallene complex Cp(2)HfC(4)Rr'(2)R `' (5Hf), which was previously described by Erker et al., with those of the titanium, zirconium, and hafnium complexes Cp(2)M(eta(4)-RHC(4)HR) (3M; i.e. metallacyclopent-2,3,4-trienes, metallacyclocumulenes) and Cp(2)M(eta(2)-R(2)C(4)R(2)) (4M; i.e. 1-metallacyclopent-3-ynes) using density functional theory (BP86/LANL2DZ) calculations. Moreover, the eta(3)-phenylallenyl zirconocene complex 7Zr, which was synthesized by Wojcicki et al., is included for the comparison. These calculations and extended Huckel calculations show that the bonding in complex 5Hf is remarkably similar to that of complexes 4M and 7Zr. An analysis of the structural parameters and bonding reveals that the unique interaction of the internal carbon atoms along with the terminal carbon atoms with the bent-metallocene moiety is the reason for the unusual stability of these metallacycles. The molecular orbital analysis further suggests that complex 5Hf can react with another metal fragment to give the bimetallic complexes 9 and 10. The electronic structures of complexes 3M, 4M, 5Hf, and 7Zr have been comparatively studied to get a general understanding of the bonding in these metallacycles.

Novel double insertion of carbon disulfide into two Ru-H bonds of [(dppm)(2)Ru(H)(2)] (dppm = Ph2PCH2PPh2): Synthesis and crystal structure of a methanedithiolate complex

Addition of excess carbon disulfide to cis/trans-[(dPPM)(2)Ru(H)(2)] results in the methanedithiolate complex [(dppm)(2)Ru(eta(2)-S2CH2)] 4 via the intermediacy of cis-[(dppm)(2)Ru(H)(SC(S)H)] 2. The X-ray crystal structure of this species has been determined.

Pyrene appended bile acid conjugates: Synthesis and a structure-gelation property study

A wide variety of novel compounds obtained by combining two types of known organogelators, viz., bile acid alkyl amides and pyrene alkanoic acids, were synthesized and screened for their gelation ability. The 3 alpha esters of 1-pyrene butyric acid (PBA) of alkylamides of deoxycholic acid (DCA) turned out to be effective in the gel formation with many organic solvents although the gelation has to be triggered by the addition of a charge transfer (CT) agent 2,4,7-trinitrofluorenone (TNF). The special feature of these molecules is that the organogelation is achieved only after derivatizing the acid moiety of the 1-pyrenealkanoic acids. Additionally, the gelation properties can be fine-tuned by inserting different functional groups at the bile acid side chain. The gels obtained are deep red in colour and optically transparent up to 2% w/v. The SEM studies of the obtained xerogels revealed bundled rod-like morphology without specialized branching.

Synthesis, Structure, Negative Thermal Expansion, and Photocatalytic Property of Mo Doped ZrV(2)O(7)

A new series of compounds identified in the phase diagram of ZrO(2)-V(2)O(8)-MoO(3) have been synthesized via the solution combustion method. Single crystals of one of the compounds in the series, ZrV(1.50)Mo(0.50)O(7.25), were grown by the melt-cool technique from the starting materials with double the MoO(3) quantity. The room temperature average crystal structure of the grown crystals was solved using the single crystal X-ray diffraction technique. The crystals belong to the cubic crystal system, space group Pa (3) over bar (No. 205) with a = 8.8969 (4) angstrom, V = 704.24 (6) angstrom(3), and Z = 4. The final R(1) value of 0.0213 was achieved for 288 independent reflections during the structure refinement. The Zr(4+) occupies the special position (4a) whereas V(5+) and Mo(6+) occupy two unique (8c) Wyckoff positions. Two fully occupied O atoms, (24d) and (4b), one partially occupied 0 atom (8c) have been identified for this molybdovanadate, which is a unique feature for these crystals. The structure is related to both ZrV(2)O(7) and cubic ZrMo(2)O(8). The temperature dependent single crystal studies show negative thermal expansion above 370 K. The compounds have been characterized by powder X-ray diffraction, solid-state UV-vis diffuse reflectance spectra, scanning electron microscopy (SEM), and transmission electron microscopy (TEM). The photocatalytic activity of these compounds has been investigated for the degradation of various dyes, and these compounds show specificity toward the degradation of non-azoic dyes.

Synthesis, Characterization, and Electronic Structure of New Type of Heterometallic Boride Clusters

The reaction of [Cp*TaCl(4)], 1 (Cp* = eta(5)-C(5)Me(5)), with [LiBH(4)center dot THF] at -78 degrees C, followed by thermolysis in the presence of excess [BH(3)center dot THF], results in the formation of the oxatantalaborane cluster [(Cp*Ta)(2)B(4)H(10)O], 2 in moderate yield. Compound 2 is a notable example of an oxatantalaborane cluster where oxygen is contiguously bound to both the metal and boron. Upon availability of 2, a room temperature reaction was performed with [Fe(2)(CO)(9)], which led to the isolation of [(Cp*Ta)(2)B(2)H(4)O{H(2)Fe(2)(CO)(6)BH} ] 3. Compound 3 is an unusual heterometallic boride cluster in which the [Ta(2)Fe(2)] atoms define a butterfly framework with one boron atom lying in a semi-interstitial position. Likewise, the diselenamolybdaborane, [(Cp*Mo)(2)B(4)H(4)Se(2)], 4 was treated with an excess of [Fe(2)(CO)(9)] to afford the heterometallic boride cluster [(Cp*MoSe)(2)Fe(6)(CO)(13)B(2)(BH)(2)], 5. The cluster core of 5 consists of a cubane [Mo(2)Se(2)Fe(2)B(2)] and a tricapped trigonal prism [Fe(6)B(3)] fused together with four atoms held in common between the two subclusters. In the tricapped trigonal prism subunit, one of the boron atoms is completely encapsulated and bonded to six iron and two boron atoms. Compounds 2, 3, and 5 have been characterized by mass spectrometry, IR, (1)H, (11)B, (13)C NMR spectroscopy, and the geometric structures were unequivocally established by crystallographic analysis. The density functional theory calculations yielded geometries that are in close agreement with the observed structures. Furthermore, the calculated (11)B NMR chemical shifts also support the structural characterization of the compounds. Natural bond order analysis and Wiberg bond indices are used to gain insight into the bonding patterns of the observed geometries of 2, 3, and 5.

Relation between Local Structure and Glass Forming Ability of Liquid Alloys

An attempt has been made to describe the glass forming ability (GFA) of liquid alloys, using the concepts of the short range order (SRO) and middle range order (MRO) characterizing the liquid structure.A new approach to obtain good GFA of liquid alloys is based on the following four main factors: (1) formation of new SRO and competitive correlation with two or more kinds of SROs for crystallization, (2) stabilization of dense random packing by interaction between different types of SRO, (3) formation of stable cluster (SC) or middle range order (MRO) by harmonious coupling of SROs, and (4) difference between SRO characterizing the liquid structure and the near-neighbor environment in the corresponding equilibrium crystalline phases. The atomic volume mismatch estimated from the cube of the atomic radius was found to be a close relation with the minimum solute concentration for glass formation. This empirical guideline enables us to provide the optimum solute concentration for good GFA in some ternary alloys. Model structures, denoted by Bernal type and the Chemical Order type, were again tested in the novel description for the glass structure as a function of solute concentration. We illustrated the related energetics of the completion between crystal embryo and different types of SRO. Recent systematic measurements also provide that thermal diffusivity of alloys in the liquid state may be a good indicator of their GFA.

Structure of the Pyridine-Chloranil Complex in Solution: A Surprise from Depolarized Hyper-Rayleigh Scattering Measurements

In this article, we report the structure of a 1:1 charge transfer complex between pyridine (PYR) and chloranil (CHL) in solution (CHCl(3)) from the measurement of hyperpolarizability (beta(HRS)) and linear and circular depolarization ratios, D and D', respectively, by the hyper-Rayleigh scattering technique and state-of-the-art quantum chemical calculations. Using linearly (electric field vector along X) and circularly polarized incident light, respectively, we have measured two macroscopic depolarization ratios D = I(X,X)(2 omega)/I(X,Z)(2 omega) and D' = I(X,C)(2 omega)/I(Z,C)(2 omega) in the laboratory fixed XYZ frame by detecting the second harmonic (SH) scattered light in a polarization resolved fashion. The stabilization energy and the optical gap calculated through the MP2/cc-pVDZ method using Gaussian09 were not significantly different to distinguish between the cofacial and T-shape structures. Only when the experimentally obtained beta(HRS) and the depolarization ratios, D and D', were matched with the theoretically computed values from single and double configuration interaction (SDCI) calculations performed using the ZINDO-SCRF technique, we concluded that the room temperature equilibrium structure of the complex is cofacial. This is in sharp contrast to an earlier theoretical prediction of the T-shape structure of the complex.

Reversible Formation of a Planar Chiral Ferrocenylboroxine and Its Supramolecular Structure

The boronic acid (pS)-1,2-NpFcB(OH)(2) (1) was obtained by treatment of the lithiated species (pS)-1,2-NpFcLi with B(O(i)Pr)(3), followed by acidic workup; subsequent dehydration gave the enantiomerically pure boroxine [(pS)-1,2-NpFcBO](3) (2) in 49% isolated yield. Multinuclear and 2D NMR spectroscopies, single-crystal X-ray diffraction, and elemental analysis served to confirm the structure of 2. In the solid-state structure, all three of the naphthyl groups point in one direction and all of the ferrocenyl moieties are placed on the opposite face of the boroxine ring, which is also the preferred conformation in solution according to a (1)H, (1)H-NOESY experiment. Cyclic voltammetry revealed three separate reversible oxidation events, which suggests significant communication between the ferrocenyl moieties. These redox processes experience a cathodic shift upon addition of 4-dimethylaminopyridine (DMAP) as a Lewis base. The six-membered ring is opened upon treatment with hot CHCl(3)/MeOH to form the methoxy species (pS)-1,2-NpFcB(OH)(OMe) (3), which can be converted back to the cycle 2 by dissolution in wet CHCl(3), followed by column chromatography on silica gel.

Structure and dynamics of protein excited states with millisecond lifetimes

An in-depth understanding of biological processes often requires detailed atomic resolution structures of the molecules involved. However in solution where most of these processes occur the conformation of biomolecules like RNA, DNA and proteins is not static but fluctuates. Routinely used structural techniques like X-ray crystallography, NMR spectroscopy and cryo-electron microscopy have almost always been used to determine the structure of the dominant conformation or obtain an average structure of the biomolecule in solution with very little detailed information regarding the dynamics of these molecules in solution. Over the last few years, NMR based methods have been developed to study the dynamics of these biomolecules in solution in a site-specific manner with the aim of generating structures of the different conformations that these molecules can adopt in solution. One powerful technique is the Carr-Purcell-Meiboom-Gill (CPMG) relaxation dispersion experiment, which can be used to detect and characterize protein excited states that are populated for as less as 0.5% of the time with ∼0.5–10 millisecond lifetimes. Due to recent advances in NMR pulse sequences and labeling methodology, it is now possible to determine the structures of these transiently populated excited states with millisecond lifetimes by obtaining accurate chemical shifts, residual dipolar couplings (RDCs) and residual chemical shift anisotropies (RCSAs) of these excited states. In these excited states the dynamics of some methyl containing residues can also be studied.

The Structure of the Thioredoxin-Triosephosphate Isomerase Complex Provides Insights into the Reversible Glutathione-Mediated Regulation of Triosephosphate Isomerase

Protein-protein interactions are crucial for many biological functions. The redox interactome encompasses numerous weak transient interactions in which thioredoxin plays a central role. Proteomic studies have shown that thioredoxin binds to numerous proteins belonging to various cellular processes, including energy metabolism. Thioredoxin has cross talk with other redox mechanisms involving glutathionylation and has functional overlap with glutaredoxin in deglutathionylation reactions. In this study, we have explored the structural and biochemical interactions of thioredoxin with the glycolytic enzyme, triosephosphate isomerase. Nuclear magnetic resonance chemical shift mapping methods and molecular dynamics-based docking have been applied in deriving a structural model of the thioredoxin-triosephosphate isomerase complex. The spatial proximity of active site cysteine residues of thioredoxin to reactive thiol groups on triosephosphate isomerase provides a direct link to the observed deglutathionylation of cysteine 217 in triosephosphate isomerase, thereby reversing the inhibitory effect of S-glutathionylation of triosephosphate isomerase.

The Structure of the Thioredoxin−Triosephosphate Isomerase Complex Provides Insights into the Reversible Glutathione-Mediate Regulation of Triosephosphate Isomerase

Protein−protein interactions are crucial for many biological functions. The redox interactome encompasses numerous weak transient interactions in which thioredoxin plays a central role. Proteomic studies have shown that thioredoxin binds to numerous proteins belonging to various cellular processes, including energy metabolism. Thioredoxin has cross talk with other redox mechanisms involving glutathionylation and has functional overlap with glutaredoxin in deglutathionylation reactions. In this study, we have explored the structural and biochemical interactions of thioredoxin with the glycolytic enzyme, triosephosphate isomerase. Nuclear magnetic resonance chemical shift mapping methods and molecular dynamics-based docking have been applied in deriving a structural model of the thioredoxin−triosephosphate isomerase complex. The spatial proximity of active site cysteine residues of thioredoxin to reactive thiol groups on triosephosphate isomerase provides a direct link to the observed deglutathionylation of cysteine 217 in triosephosphate isomerase, thereby reversing the inhibitory effect of S-glutathionylation of triosephosphate isomerase.

Structure and Photocatalytic Activity of Ti 1- x M x O 2±δ (M = W, V, Ce, Zr, Fe, and Cu) Synthesized by Solution Combustion Method

The W, V, Ce, Zr, Fe, and Cu metal ion substituted nanocrystalline anatase TiO2 was prepared by solution combustion method and characterized by XRD, Raman, BET, EPR, XPS, IR TGA, UV absorption, and photoluminescence measurements. The structural studies indicate that the solid solution formation was limited to a narrow range of concentrations of the dopant ions. The photocatalytic degradation of 4-nitrophenol under UV and solar exposure was investigated with Ti1-xMxO2±δ. The degradation rates of 4-nitrophenol with these catalysts were lesser than the degradation rates of 4-nitrophenol with undoped TiO2 both with UV exposure and solar radiation. However, the photocatalytic activities of most metal ion doped TiO2 are higher than the activity of the commercial TiO2, Degussa P25. The decrease in photocatalytic activity is correlated with decrease in photoluminescence due to electron states of metal ions within the band gap of TiO2.

A comparative study of erbium oxide and gadolinium oxide high-k dielectric thin films grown by low-pressure metalorganic chemical vapour deposition (MOCVD) using beta-Diketonates as precursors

In this paper, a comparative study of thin films of Er2O3 and Gd2O3 grown on n-type Si(100) by low-pressure metalorganic chemical vapour deposition (MOCVD) under the identical conditions has been presented. beta-Diketonate complex of rate earth metals was used as precursor. Description on the evolution of the morphology, structure, optical, and electrical characteristics of films with respect to growth parameters and post-deposition annealing process has been presented. As-gown Gd2O3 films grow with <111> texture, whereas the texture of Er2O3 films strongly depends on the growth temperature (either <100> or <111>). Compositional analysis reveals that the Gd2O3 films grown at or above 500degreesC are carbon free whereas Er2O3 films at upto 525degreesC show the presence of heteroatoms and Er2O3 films grown above 525degreesC are carbon five. The effective dielectric constant is in the range of 7-24, while the fixed charge density is in the range - 10(11) to 10(10) CM-2 as extracted from the C-V characteristics. DC I-V study was carried out to examine the leakage behaviour of films. It reveals that the as-grown Gd2O3 film was very leakey in nature. Annealing of the films in oxidizing ambient for a period of 20 min results in a drastic improvement in the leakage behaviour. The presence of heteroatoms (such as carbon) and their effect on the properties of films are discussed.

From anomalies in neat liquid to structure, dynamics and function in the biological world

Water brings its remarkable thermodynamic and dynamic anomalies in the pure liquid state to biological world where water molecules face a multitude of additional interactions that frustrate its hydrogen bond network. Yet the water molecules participate and control enormous number of biological processes in manners which are yet to be understood at a molecular level. We discuss thermodynamics, structure, dynamics and properties of water around proteins and DNA, along with those in reverse micelles. We discuss the roles of water in enzyme kinetics, in drug-DNA intercalation and in kinetic-proof reading ( the theory of lack of errors in biosynthesis). We also discuss how water may play an important role in the natural selection of biomolecules. (C) 2011 Elsevier B. V. All rights reserved.

Designed Cyclic Permutants of HIV-1 gp120: Implications for Envelope Trimer Structure and Immunogen Design

Most HIV-1 broadly neutralizing antibodies are directed against the gp120 subunit of the env surface protein. Native env consists of a trimer of gp120-gp41 heterodimers, and in contrast to monomeric gp120, preferentially binds CD4 binding site (CD4bs)-directed neutralizing antibodies over non-neutralizing ones. Some cryo-electron tomography studies have suggested that the V1V2 loop regions of gp120 are located close to the trimer interface. We have therefore designed cyclically permuted variants of gp120 with and without the h-CMP and SUMO2a trimerization domains inserted into the V1V2 loop. h-CMP-V1cyc is one such variant in which residues 153 and 142 are the N- and C-terminal residues, respectively, of cyclically permuted gp120 and h-CMP is fused to the N-terminus. This molecule forms a trimer under native conditions and binds CD4 and the neutralizing CD4bs antibodies b12 with significantly higher affinity than wild-type gp120. It binds non-neutralizing CD4bs antibody F105 with lower affinity than gp120. A similar derivative, h-CMP-V1cycl, bound the V1V2 loop-directed broadly neutralizing antibodies PG9 and PG16 with similar to 20-fold higher affinity than wild-type JRCSF gp120. These cyclic permutants of gp120 are properly folded and are potential immunogens. The data also support env models in which the V1V2 loops are proximal to the trimer interface.