Analysis of EXAFS data of multiphasic heterogeneous catalysts

Cu K-edge EXAFS spectra of Cu-Ni/Al2O3 and Cu-ZnO catalysts, both of which contain more than one Cu species, have been analysed making use of an additive relation for the EXAFS function. The analysis, which also makes use of residual spectra for identifying the species, shows good agreement between experimental and calculated spectra.

Valence bond analysis of the Kondo chain Hamiltonian

Accurate extrapolations for the ground state energy per site of the one - dimensional Kondo chain system is obtained from exact finite system calculations carried out employing a valence bond scheme. An analysis of the ground state wave function indicates that the localized spin is quenched for all nonzero values of the Kondo exchange constant in one dimension.

Structural effects of a dimer interface mutation on catalytic activity of triosephosphate isomerase.The role of conserved residues and complementary mutations

The active site of triosephosphate isomerase (TIM, EC: 5.3.1.1), a dimeric enzyme, lies very close to the subunit interface. Attempts to engineer monomeric enzymes have yielded well-folded proteins with dramatically reduced activity. The role of dimer interface residues in the stability and activity of the Plasmodium falciparum enzyme, PfTIM, has been probed by analysis of mutational effects at residue 74. The PfTIM triple mutant W11F/W168F/Y74W (Y74W*) has been shown to dissociate at low protein concentrations, and exhibits considerably reduced stability in the presence of denaturants, urea and guanidinium chloride. The Y74W* mutant exhibits concentration-dependent activity, with an approximately 22-fold enhancement of kcat over a concentration range of 2.5–40 μm, suggesting that dimerization is obligatory for enzyme activity. The Y74W* mutant shows an approximately 20-fold reduction in activity compared to the control enzyme (PfTIM WT*, W11F/W168F). Careful inspection of the available crystal structures of the enzyme, together with 412 unique protein sequences, revealed the importance of conserved residues in the vicinity of the active site that serve to position the functional K12 residue. The network of key interactions spans the interacting subunits. The Y74W* mutation can perturb orientations of the active site residues, due to steric clashes with proximal aromatic residues in PfTIM. The available crystal structures of the enzyme from Giardia lamblia, which contains a Trp residue at the structurally equivalent position, establishes the need for complementary mutations and maintenance of weak interactions in order to accommodate the bulky side chain and preserve active site integrity.

Analysis of proteins with the `hot dog' fold: Prediction of function and identification of catalytic residues of hypothetical proteins

Background: The hot dog fold has been found in more than sixty proteins since the first report of its existence about a decade ago. The fold appears to have a strong association with fatty acid biosynthesis, its regulation and metabolism, as the proteins with this fold are predominantly coenzyme A-binding enzymes with a variety of substrates located at their active sites. Results: We have analyzed the structural features and sequences of proteins having the hot dog fold. This study reveals that though the basic architecture of the fold is well conserved in these proteins, significant differences exist in their sequence, nature of substrate and oligomerization. Segments with certain conserved sequence motifs seem to play crucial structural and functional roles in various classes of these proteins. Conclusion: The analysis led to predictions regarding the functional classification and identification of possible catalytic residues of a number of hot dog fold-containing hypothetical proteins whose structures were determined in high throughput structural genomics projects.

Finite element analysis of curved anisotropic laminated hollow bars

Curved hollow bars of laminated anisotropic construction are used as structural members in many industries. They are used in order to save weight without loss of stiffness in comparison with solid sections. In this paper are presented the details of the development of the stiffness matrices of laminated anisotropic curved hollow bars under line member assumptions for two typical sections, circular and square. They are 16dof elements which make use of one-dimensional first-order Hermite interpolation polynomials for the description of assumed displacement state. Problems for which analytical or other solutions are available are first solved using these elements. Good agreement was found between the results. In order to show the capability of the element, application is made to carbon fibre reinforced plastic layered anisotropic curved hollow bars.

Structural assignment of monothiocarbonohydrazones by 1H NMR spectroscopy

Analysis of the 1H NMR spectra of several monothiocarbonohydrazones, some of them synthesized for the first time, shows that they exist as two structural isomers. Whereas, in general, the derivatives of aromatic aldehydes conform to a linear structure, the aliphatic carbonyl derivatives conform to heterocyclic or linear structures, depending on the size of the substituent groups. This dual behaviour is explained in terms of extended conjugation and steric hindrance.

Lower Bound Limit Analysis of Rectangular Slabs

A general method for the development of valid lower bound solutions to uniformly distributed and orthotropically reinforced rectangular concrete slabs obeying normal moment criterion is described. General expressions for moment field have been obtained for nine cases of slabs having all combinations of simply supported and clamped-edge conditions. The lower bound collapse loads have been compared with the upper bound values obtained by the yield line theory. The paper also focuses attention to the need for the development of valid upper bound solutions with the satisfaction of kinematical admissibility and the flow rules associated with the normal moment criterion.

Structural Modes of Stabilization of Permissive Phosphorylation Sites in Protein Kinases: Distinct Strategies in Ser/Thr and Tyr Kinases

Protein kinases phosphorylate several cellular proteins providing control mechanisms for various signalling processes. Their activity is impeded in a number of ways and restored by alteration in their structural properties leading to a catalytically active state. Most protein kinases are subjected to positive and negative regulation by phosphorylation of Ser/Thr/Tyr residues at specific sites within and outside the catalytic core. The current review describes the analysis on 3D structures of protein kinases that revealed features distinct to active states of Ser/Thr and Tyr kinases. The nature and extent of interactions among well-conserved residues surrounding the permissive phosphorylation sites differ among the two classes of enzymes. The network of interactions of highly conserved Arg preceding the catalytic base that mediates stabilization of the activation segment exemplifies such diverse interactions in the two groups of kinases. The N-terminal and the C-terminal lobes of various groups of protein kinases further show variations in their extent of coupling as suggested from the extent of interactions between key functional residues in activation segment and the N-terminal αC-helix. We observe higher similarity in the conformations of ATP bound to active forms of protein kinases compared to ATP conformations in the inactive forms of kinases. The extent of structural variations accompanying phosphorylation of protein kinases is widely varied. The comparison of their crystal structures and the distinct features observed are hoped to aid in the understanding of mechanisms underlying the control of the catalytic activity of distinct subgroups of protein kinases.

Structural Investigation of Activated Lattice Oxygen in Ce1-xSnxO2 and Ce1-x-ySnxPdyO2-delta by EXAFS and DFT calculation

Substitution of Sn4+ ion in CeO2 creates activated oxygen in Ce0.8Sn0.2O2 leading to higher oxygen storage capacity compared to Ce0.8Zr0.2O2. With Pd ion substitution in Ce0.8Sn0.2O2,activation of oxygen is further enhanced as observed from the H-2/TPR study. Both EXAFS analysis and DFT calculation reveal that in the solid solution Ceexhibits 4 + 4 coordination, Sri exhibits 4 + 2 + 2 coordination and Pd has 4 + 3 coordination. While the oxygen in the First four coordination with short M-O bonds are strongly held in the lattice, the oxygens in the second and higher coordinations with long M-O bonds are weakly bound, and they are the activated oxygen ill the lattice. Bond valence analysis shows that oxygen with valencies as low its 1.65 are created by the Sn and Pd ion Substitution. Another interesting observation is that H-2/TPR experiment of Ce1-xSnxO2 shows a broad peak starting from 200 to 500 degrees C, while the same reduction is achieved in a single step at similar to 110 degrees C in presence Pd2+ on. Substitution of Pd2+ ion thus facilitates synergistic reduction of the catalyst at lower temperature. We have shown that simultaneous reduction of the Ce4+ and Sr4+ ions by Pd-0 is the synergistic interaction leading to high oxygen storage capacity at low temperature.

Quantum phase analysis of 1D superconducting quantum dot lattice using extended Bose-Hubbard model

We have obtained the quantum phase diagram of a one-dimensional superconducting quantum dot lattice using the extended Bose-Hubbard model for different commensurabilities. We describe the nature of different quantum phases at the charge degeneracy point. We find a direct phase transition from the Mott insulating phase to the superconducting phase for integer band fillings of Cooper pairs. We predict explicitly the presence of two kinds of repulsive Luttinger liquid phases, besides the charge density wave and superconducting phases for half-integer band fillings. We also predict that extended range interactions are necessary to obtain the correct phase boundary of a one-dimensional interacting Cooper system. We have used the density matrix renormalization group method and Abelian bosonization to study our system.

Hydrothermal synthesis and structural characterization of novel alpha-Keggin unit-supported Cu(II)- and Mn(II)-bipyridine complexes from a tri-lacunary precursor

Blue [{Cu(2,2'-bipy)(2)}(2){alpha-SiW12O40}] (bipy = bipyridyl) (1) and pale yellow [Mn(2,2'-bipy)(3)](2)[alpha-SiW12O40] (2) have been synthesized hydrothermally and characterized by IR spectroscopy and single crystal X-ray structure analysis. In 1, the [alpha-SiW12O40](4-) ion acts as a bridge between the two [{Cu(2,2'-bipy)(2)](2+) moieties via coordination through the terminal oxygen atoms, while in 2, the [Mn(2,2'-bipy)(3)](2+) ion balances the charge on the polyoxo anion without forming any covalent bond. To the best of our knowledge, this is the first example of transition metal-mediated transformation of [alpha-SiW9O34](10-) to [alpha-SiW12O40](4-).

Visual Analysis of Biomolecular Surfaces

Surface models of biomolecules have become crucially important for the study and understanding of interaction between biomolecules and their environment. We argue for the need for a detailed understanding of biomolecular surfaces by describing several applications in computational and structural biology. We review methods used to model, represent, characterize, and visualize biomolecular surfaces focusing on the role that geometry and topology play in identifying features on the surface. These methods enable the development of efficient computational and visualization tools for studying the function of biomolecules.

Experimental and Theoretical Charge Density Analysis of Polymorphic Structures: The Case of Coumarin 314 Dye

Experimental charge density distributions in two known conformational polymorphs (orange and yellow) of coumarin 314 dye are analyzed based on multipole modeling of X-ray diffraction data collected at 100 K. The experimental results are compared with the charge densities derived from multipole modeling of theoretical structure factors obtained from periodic quantum calculation with density functional theory (DFT) method and B3LYP/6-31G(d,p) level of theory. The presence of disorder at the carbonyl oxygen atom of ethoxycarbonyl group in the yellow form, which was not identified earlier, is addressed here. The investigationof intermolecular interactions, based on Hirshfeld surface analysis and topological properties via quantum theory of atoms in molecule and total electrostatic interaction energies, revealed significant differences between the polymorphs. The differences of electrostatic nature in these two polymorphic forms were unveiled via construction of three-dimensional deformation electrostatic potential maps plotted over the molecular surfaces. The lattice energies evaluated from ab initio calculations on the two polymorphic forms indicate that the yellow form is likely to be the most favorable thermodynamically. The dipole moments derived from experimental and theoretical charge densities and also from Lorentz tensor approach are compared with the single-molecule dipole moments. In each case, the differences of dipole moments between the polymorphs are identified.

Stereochemical analysis of the antigenic tip of the V3 loop peptide of HIV-1 gp120

A novel multiple turn conformation has been observed for a segment GPGRAFY in the crystal structure of a complex of HIV-1 gp120 V3 loop peptide with the Fab fragment of a neutralizing antibody [Ghiara ct al. (1994) Science 264, 82-85]. A structural motif has been defined for the peptide segment, employing idealized backbone conformations characterized by ranges of virtual C-alpha torsion angles and bond angles. A search of 122 high-resolution protein crystal structures has permitted identification of 24 examples of similar structural motifs. Two major conformational families have been identified, which differ primarily in the conformation at residue 3. The observed conformation at residue 3 in family 1 is left-handed helical (alpha(L)) and that in family 2 is right-handed helical (alpha(R)). Of the 10 examples in family 1, 9 examples have Gly residues at position 3. Of the 12 examples in family 2, 7 examples have Asn/Asp at position 3. Computer modeling of the V3 loop tip sequence using the two backbone conformational families as starting points leads to minimum-energy conformations in which antigenically important side-chains occupy similar spatial arrangements. This stereochemical analysis of the V3 loop tip sequence suggests a rational basis for the design of synthetic analog peptides for use as viral antagonists or synthetic antigens. (C) Munksgaard 1995.

Local structure in LaMnO3 and CaMnO3 perovskites: A quantitative structural refinement of mn K-edge XANES data

Hole-doped perovskites such as La1-xCaxMnO3 present special magnetic and magnetotransport properties, and it is commonly accepted that the local atomic structure around Mn ions plays a crucial role in determining these peculiar features. Therefore experimental techniques directly probing the local atomic structure, like x-ray absorption spectroscopy (XAS), have been widely exploited to deeply understand the physics of these compounds. Quantitative XAS analysis usually concerns the extended region [extended x-ray absorption fine structure (EXAFS)] of the absorption spectra. The near-edge region [x-ray absorption near-edge spectroscopy (XANES)] of XAS spectra can provide detailed complementary information on the electronic structure and local atomic topology around the absorber. However, the complexity of the XANES analysis usually prevents a quantitative understanding of the data. This work exploits the recently developed MXAN code to achieve a quantitative structural refinement of the Mn K-edge XANES of LaMnO3 and CaMnO3 compounds; they are the end compounds of the doped manganite series LaxCa1-xMnO3. The results derived from the EXAFS and XANES analyses are in good agreement, demonstrating that a quantitative picture of the local structure can be obtained from XANES in these crystalline compounds. Moreover, the quantitative XANES analysis provides topological information not directly achievable from EXAFS data analysis. This work demonstrates that combining the analysis of extended and near-edge regions of Mn K-edge XAS spectra could provide a complete and accurate description of Mn local atomic environment in these compounds.