Theoretical study on small clusters of BaTiO3 using DFT calculations

Using density functional theory with the generalised gradient approximation, the structural and electronic properties of small (BaTiO₃)_n (n = 1–4) clusters have been studied. All the analysed growth modes were observed to consist of the same unit block, which in turn is similar to the well-known (TiO₂)₂ cluster. The BaTiO₃ and (BaTiO₃)₂ systems were observed to adopt analogous geometries to the ground state of (TiO₂)_n clusters with C_s and D_2h symmetries, respectively. The calculated value of the energy gap for the studied (BaTiO₃)_n clusters tends to approach that observed for its tetragonal bulk BaTiO₃ counterpart when n ≥ 3 is considered; the same tendency is observed for the Ba–Ba, Ba–Ti, Ti–O and Ba–Ti interatomic distances. For all the (BaTiO₃)_n clusters, the structural characteristics of their respective isomers were explored.     

Temperature-dependence of protein hydrogen bond properties as studied by high-resolution NMR

The temperature-dependence of a large number of NMR parameters describing hydrogen bond properties in the protein ubiquitin was followed over a range from 5 to 65 degrees C. The parameters comprise hydrogen bond (H-bond) scalar couplings, h3JNC', chemical shifts, amide proton exchange rates, 15N relaxation parameters as well as covalent 1JNC' and 1JNH couplings. A global weakening of the h3JNC' coupling with increasing temperature is accompanied by a global upfield shift of the amide protons and a decrease of the sequential 1JNC' couplings. If interpreted as a linear increase of the N...O distance, the change in h3JNC' corresponds to an average linear thermal expansion coefficient for the NH-->O hydrogen bonds of 1.7 x 10(-4)/K, which is in good agreement with overall volume expansion coefficients observed for proteins. A residue-specific analysis reveals that not all hydrogen bonds are affected to the same extent by the thermal expansion. The end of beta-sheet beta1/beta5 at hydrogen bond E64-->Q2 appears as the most thermolabile, whereas the adjacent hydrogen bond I3-->L15 connecting beta-strands beta1 and beta2 is even stabilized slightly at higher temperatures. Additional evidence for the stabilization of the beta1/beta2 beta-hairpin at higher temperatures is found in reduced hydrogen exchange rates for strand end residue V17. This reduction corresponds to a stabilizing change in free energy of 9.7 kJ/mol for the beta1/beta2 hairpin. The result can be linked to the finding that the beta1/beta2 hairpin behaves as an autonomously folding unit in the A-state of ubiquitin under changed solvent conditions. For several amide groups the temperature-dependencies of the amide exchange rates and H-bond scalar couplings are uncorrelated. Therefore, amide exchange rates are not a sole function of the hydrogen bond "strength" as given by the electronic overlap of donors and acceptors, but are clearly dependent on other blocking mechanisms.     

Chemical shift as a probe of molecular interfaces: NMR studies of DNA binding by the three amino-terminal zinc finger domains from transcription factor IIIA

We report the NMR resonance assignments for a macromolecular protein/DNA complex containing the three amino-terminal zinc fingers (92 amino acid residues) of Xenopus laevis TFIIIA (termed zf1-3) bound to the physiological DNA target (15 base pairs), and for the free DNA. Comparisons are made of the chemical shifts of protein backbone¹ H^N, ¹⁵N,¹³ C and¹³ C and DNA base and sugar protons of the free and bound species. Chemical shift changes are analyzed in the context of the structures of the zf1-3/DNA complex to assess the utility of chemical shift change as a probe of molecular interfaces. Chemical shift perturbations that occur upon binding in the zf1-3/DNA complex do not correspond directly to the structural interface, but rather arise from a number of direct and indirect structural and dynamic effects.     

Effect of glycophorin on lipid polymorphism: A 31P-NMR study

(1) The effect of glycophorin, a major intrinsic glycoprotein of the human erythrocyte membrane, on lipid polymorphism has been investigated by ³¹P-NMR (at 36.4 MHz) and by freeze-fracture electron microscopy. (2) Incorporation of glycophorin into vesicles of 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC) results in the formation of unilamellar vesicles (1000–5000 Å diameter) which exhibit ³¹P-NMR bilayer spectra over a wide range of temperature. A reduction in the chemical shift anisotropy (Δσ_csa^eff) and an increase in spectral linewidth in comparison to dioleoylphosphatidylcholine liposomes may suggest a decrease in phospholipid headgroup order. (3) 1,2-Dioleoyl-sn-glycero-3-phosphoethanolamine (DOPE), in the presence of excess water, undergoes a bilayer to hexagonal (H_II) phospholipid arrangement as the temperature is increased above 0°C. Incorporation of glycophorin into this system stabilizes the bilayer configuration, prohibiting the formation of the H_II phase. (4) Cosonication of glycophorin with DOPE in aqueous solution (pH 7.4) produces small, stable unilamellar vesicles (300–1000 Å diameter), unlike DOPE alone which is unstable and precipitates from solution. (5) The current study demonstrates the bilayer stabilizing capacity of an intrinsic membrane protein, glycophorin, most likely by means of a strong hydrophobic interaction between the membrane spanning portion of glycophorin and the hydrophobic region of the phospholipid.     

A DFT study of the effects of donor-to-acceptor ratio on the electronic properties of copolymers based on tricyclic non-classical thiophene

The geometries and electronic properties of the 1D polymers composed of thieno[3,2-b]thiophene (TT), thiophene (T), pyrrole (P), furan (F) and tricyclic non-classical thiophenes ([1,2,5]thiadiazolo[3,4-b]thieno-[3,4-e]pyrazine, TTP) are investigated systematically by the density functional theory method at the B3LYP level with 6-31G(d) basis set. The theoretical study suggests that the ratio of donor-to-acceptor (D-A ratio) plays a crucial role in the geometric and electronic properties for the alternating donor–acceptor polymers. The increase in the D-A ratio leads to an increase in the bridge bond length and an inverse change in the bond-length alternation. Furthermore, the increase in the portion of donor units can lead to an obvious reduction in band gap for these studied polymers. The TT-containing polymer possessing the D-A ratio of 2:1 (p-BTTTTP) that is predicted to have a small band gap of 0.25 eV and a relatively small effective mass of carriers is a good candidate for an intrinsic conducting polymer. Therefore, the tricyclic non-classical thiophenes (TTP) and TT are good building blocks that can lead to small band gap polymers.     

Extended structures of three new coordination polymers based on 1,10-phenanthroline derivatives and 1,4-benzenedicarboxylate mixed ligands: Preparation, structural characterization and properties

Three coordination polymers, namely, [Cd(HOIP)₂(1,4-bdc)] (1), [Cu(HOIP)(1,4-bdc)] (2) and [Cu(PDIP)(1,4-bdc)] (3) (HOIP = 2-(4-hydroxylbenzene) imidazo[4,5-f]1,10-phenanthroline, PDIP = 2-(3-pyridine) imidazo[4,5-f]1,10-phenanthroline, and 1,4-bdc = 1,4-benzenedicarboxylate), have been synthesized under the hydrothermal conditions. All complexes have been characterized by elemental analyses, IR and single-crystal X-ray diffraction. Structural analyses reveal that complex 1 possesses infinite one-dimensional (1D) chain bridged by 1,4-bdc ligands, complexes 2 and 3 both exhibit two-dimensional (2D) (4,4) network structures based on dinuclear [Cu₂O₂] units. However, the weak interactions are different in complexes 1-3. Moreover, the thermal properties of all complexes, fluorescence property of 1, and the electrochemical behavior of 3 are also reported in this paper.     

Determination of the orientation of the axial ligands and of the magnetic properties of the haems in the tetrahaem ferricytochrome from Shewanella frigidimarina

The unambiguous assignment of the nuclear magnetic resonance (NMR) signals of the alpha-substituents of the haems in the tetrahaem cytochrome isolated from Shewanella frigidimarina NCIMB400, was made using a combination of homonuclear and heteronuclear experiments. The paramagnetic (13)C shifts of the nuclei directly bound to the porphyrin of each haem group were analysed in the framework of a model for the haem electronic structure. The analysis yields g-tensors for each haem, which allowed the assignment of some electron paramagnetic resonance (EPR) signals to specific haems, and the orientation of the magnetic axes relative to each haem to be established. The orientation of the axial ligands of the haems was determined semi-empirically from the NMR data, and the structural results were compared with those of the homologous tetrahaem cytochrome from Shewanella oneidensis MR-1 showing significant similarities between the two proteins.     

19F NMR study of protein-induced rhombic perturbations on the electronic structure of the active site of myoglobin

 A novel C ₂-symmetric ring-fluorinated hemin, 13,17-bis(2-carboxyethyl)-2,8,12,18-tetramethyl-3,7-difluoroporphyrinatoiron(III), has been synthesized and was incorporated into sperm whale apomyoglobin to investigate protein-induced rhombic perturbations on the electronic structure of the active site of myoglobin (Mb) using ¹⁹F NMR spectroscopy. NMR signals for ¹⁹F atoms introduced as substituents on the present heme in ferrous low-spin and high-spin and ferric low-spin complexes have been observed and their shifts sharply reflect not only the electronic nature of the heme iron, but also in-plane asymmetry of the heme electronic structure. The two-fold symmetric electronic structure of the ring-fluorinated hemin is clearly manifested in the ¹⁹F and ¹H NMR spectra of its dicyano complex. The chemical equivalence of the two fluorine atoms of the heme is removed in the active site of myoglobin and the splitting of the two ¹⁹F NMR signals provides a quantitative probe for characterizing the rhombic perturbation of the heme electronic structure induced by the heme-protein interaction. The in-plane asymmetry of heme electronic structures in carbonmonoxy and deoxy Mbs have been analyzed for the first time on the basis of the shift difference between the two ¹⁹F NMR signals of the heme and is interpreted in terms of iron-ligand binding and/or the orbital ground state of the heme. A potential utility of ¹⁹F NMR, combined with the use of a symmetric fluorinated hemin, in characterizing the heme electronic structure of myoglobin in a variety of iron oxidation, spin, and ligation states, is presented. Received: 23 December 1999 / Accepted: 3 April 2000     

Theoretical study of the infrared spectrum of 5-phenyl-1,3,4-oxadiazole-2-thiol by using DFT calculations

We have carried out a structural and vibrational study for 5-phenyl-1,3,4-oxadiazole-2-thiol by using the infrared (IR) spectrum and theoretical calculations. For a complete assignment of the compound IR spectrum, density functional theory calculations were combined with Pulay's scaled quantum mechanical force field methodology in order to fit the theoretical wavenumber values to the experimental ones. An agreement between theoretical and available experimental results was found. The theoretical vibrational calculations allowed us to obtain a set of scaled force constants fitting the observed wavenumbers. The results were then used to predict the Raman spectra, for which there are no experimental data. The nature of the benzyl and oxadiazole rings was studied by means of natural bond order and atoms in molecules theory calculations. In addition, the frontier molecular (highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO)) orbitals were analysed and compared with those calculated for the oxadiazole molecule.     

Orientation of the axial ligands and magnetic properties of the hemes in the triheme ferricytochrome PpcA from G. sulfurreducens determined by paramagnetic NMR

The geometry of the axial ligands of the hemes in the triheme cytochrome PpcA from Geobacter sulfurreducens was determined in solution for the ferric form using the unambiguous assignment of the NMR signals of the α-substituents of the hemes. The paramagnetic ¹³C shifts of the hemes can be used to define the heme electronic structure, the geometry of the axial ligands, and the magnetic susceptibility tensor. The latter establishes the magnitude and geometrical dependence of the pseudocontact shifts, which are crucial to warrant reliable structural constraints for a detailed structural characterization of this paramagnetic protein in solution.     

Primary structure of three cationic peptides from porcine neutrophils Sequence determination by the combined usage of electrospray ionization mass spectrometry and Edman degradation

The primary structure of three major cationic peptides from porcine neutrophils has been determined. The sequencing was made by the combined use of electrospray ionization mass spectrometry and Edman degradation. The determined sequences unambiguously show that these peptides can not be considered as defensins.     

Synthesis, structures and luminescent properties of novel coordination polymers constructed by lanthanide salts and benzimidazole-5,6-dicarboxylic acid

Two three-dimensional (3D) novel lanthanide complexes with the H₂Lbenzimidazole-5,6-dicarboxylate [Ln₂L₃(H₂O)] [Ln = Eu (1), Tb (2)] and one two-dimensional (2D) novel lanthanide complex [Pr(L)(HL)H₂O]·H₂O (3) were synthesized by hydrothermal reaction at 180 °C and characterized by elemental analysis, infrared spectra and single-crystal X-ray diffraction. The result showed that complexes 1 and 2 are isostructural and build porous 3D networks by L²⁻ groups linking Ln(III) atoms via tetradentate (bridging and bridging) and pentadentate (bridging/chelating and bridging) coordination modes. Complex 3 is a eight-coordinated Pr(III) chain complex, exhibiting a 2D polymeric network with parallel Pr-carboxylate chains along the crystallographic c-axis. In addition, it is found that in these structures, coordination modes of L²⁻ and HL⁻ are versatile and can adopt different conformations according to distinct dimensions of polymeric structures. The photoluminescent properties of 1, 2 and thermogravimetric analyses of the three complexes were discussed in detail.     

Structure and magnetic properties of polynuclear chloro- and hydroxo-bridged copper(II) complexes formed by a tetramacrocyclic derivative of 1,4,7-triazacyclononane

Two new copper(II) complexes of the ligand 1,2,4,5-tetrakis(1,4,7-triazacyclononan-1-ylmethyl)benzene (L^dur) have been synthesized and characterized by single crystal X-ray studies. The first, [Cu₄L^dur(μ₂-OH)₄]Cl₂(PF₆)₂ · 8H₂O (1), was isolated from a solution of L^dur and Cu²⁺ at pH 9. Under acidic conditions (pH 3), a polymeric complex, {[Cu₄L^dur(μ₂-Cl)₆](PF₆)₂ · 10H₂O}_n (2), crystallized from solution. In both complexes, each of the four triazacyclononane (tacn) rings of the L^dur ligand facially coordinate to separate metal centres. Pairs of Cu(II) centres are then doubly-bridged by hydroxo groups in 1, leading to tetranuclear complex cation units featuring pairs of isolated copper(II) dimers with Cu₂(μ₂-OH)₂ cores folded at the O?O lines. Two forms of the tetranuclear units, featuring slightly different Cu₂(μ₂-OH)₂ core geometries, are present in equal amounts within the crystal lattice. In complex 2, chloro bridging ligands link pairs of Cu(II) centres from neighbouring tetranuclear units, forming a 1D helical polymeric structure. Variable-temperature magnetic susceptibility measurements suggest that the hydroxo-bridged copper(II) centres within one of the tetranuclear units in 1 are weakly antiferromagnetically coupled (J = −27 cm⁻¹), whilst those in the other interact ferromagnetically (J = +19 cm⁻¹). Similar measurements indicate weak ferromagnetic coupling (J = +16 cm⁻¹) for the chloro-bridged copper(II) centres in 2.     

Hydrogen exchange properties of proteins in native and denatured states monitored by mass spectrometry and NMR.

The extent of deuterium labeling of hen lysozyme, its three-disulfide derivative, and the homologous alpha-lactalbumins, has been measured by both mass spectrometry and NMR. Different conformational states of the proteins were produced by varying the solution conditions. Alternate protein conformers were found to contain different numbers of 2H atoms. Furthermore, measurement in the gas phase of the mass spectrometer or directly in solution by NMR gave consistent results. The unique ability of mass spectrometry to distinguish distributions of 2H atoms in protein molecules is exemplified using samples prepared to contain different populations of 2H-labeled protein. A comparison of the peak widths of bovine alpha-lactalbumin in alternate solution conformations but containing the same average number of 2H atoms showed dramatic differences due to different 2H distributions in the two protein conformers. Measurement of 2H distributions by ESI-MS enabled characterization of conformational averaging and structural heterogeneity. In addition, a time course for hydrogen exchange was examined and the variation in distributions of 2H atom compared with simulations for different hydrogen exchange models. The results clearly show that exchange from the native state of bovine alpha-lactalbumin at 15 degrees C is dominated by local unfolding events.     

Physicochemical characterization and antimicrobial properties of rhamnolipids produced by Pseudomonas aeruginosa 47T2 NCBIM 40044

Pseudomonas aeruginosa 47T2, grown in submerged culture with waste frying oil as a carbon source, produced a mixture of rhamnolipids with surface activity. Up to 11 rhamnolipid homologs (Rha-Rha-C(8)-C(10); Rha-C(10)-C(8)/Rha-C(8)-C(10);Rha-Rha-C(8)-C(12:1); Rha-Rha-C(10)-C(10); Rha-Rha-C(10)-C(12:1); Rha-C(10)-C(10); Rha-Rha-C(10)-C(12)/Rha-Rha-C(12)-C(10); Rha-C(10)-C(12:1)/Rha-C(12:1)-C(10); Rha-Rha-C(12:1)-C(12); Rha-Rha-C(10)-C(14:1); Rha-C(10)-C(12)/Rha-C(12)-C(10)) were isolated from cultures of P. aeruginosa 47T2 from waste frying oil and identified by HPLC-MS analysis. This article deals with the production, isolation, and chemical characterization of the rhamnolipid mixture RL(47T2). The physicochemical and biological properties of RL(47T2) as a new product were also studied. Its surface tension decreased to 32.8 mN/m; and the interfacial tension against kerosene to 1 mN/m. The critical micellar concentration for RL(47T2) was 108.8 mg/mL. The product showed excellent antimicrobial properties. Antimicrobial activity was evaluated according to the minimum inhibitory concentration (MIC), the lowest concentration of an antimicrobial agent that inhibits development of visible microbial growth. Low MIC values were found for bacteria Serratia marcescens (4 microg/mL), Enterobacter aerogenes (8 microg/mL), Klebsiella pneumoniae (0.5 microg/mL), Staphylococcus aureus and Staphylococcus epidermidis (32 microg/mL), Bacillus subtilis (16 microg/mL), and phytopathogenic fungal species: Chaetonium globosum (64 microg/mL), Penicillium funiculosum (16 microg/mL), Gliocadium virens (32 microg/mL) and Fusarium solani (75 microg/mL).     

Syntheses, structures and magnetic properties of three 1-D chain metal-nitroxide coordination polymers bridged by e,e-trans-1,4-cyclohexanedicarboxylate

Three new one-dimensional (1-D) chain metal-nitroxide complexes of the formula [M(NIT4Py)₂(e,e-trans-1,4-chdc)(H₂O)₂]_n (M = Co(II) 1, Ni(II) 2 and Zn(II) 3; NIT4Py = 2-(4′-pyridyl)-4,4,5,5-tetramethylimidazoline-1-oxyl-3-oxide and 1,4-chdc = 1,4-cyclohexanedicarboxylate dianion) have been synthesized and characterized structurally as well as magnetically. The X-ray crystal structure analyses of complexes 1, 2 and 3 reveal that they are isostructural. Three complexes all crystallize in neutral 1-D chains where metal-nitroxide units [M(NIT4Py)₂(H₂O)₂] are linked by the linear 1,4-cyclohexanedicarboxylate dianion. The 1,4-chdc completes the segregation and only possesses the e,e-trans-conformation, although there are both cis- and trans-isomers in the raw material. The magnetic measurements show that complexes 1 and 2 both exhibit weak antiferromagnetic interactions between the metal ions and the nitroxides.     

The thermosetting resin prepared by curing reaction of typical soybean oil and properties of the product network structures: a multiscale simulation study

With our multiscale simulation strategy developed previously, we study the curing reaction of soybean oil and styrene to prepare a thermosetting resin. From atomistic simulation details, we estimate the parameters used in coarse-grained (CG) simulations. Then, with the mesoscopic dissipative particle dynamics simulation, the CG network structure and average cross-linking density of a material can be obtained. Finally, the reverse-mapping scheme of the CG structure to atomistic representation is carried out to analyse the mechanical properties and the glass transition temperature of the system. We find in such a system that the molar ratio of double bonds in the two reactants plays a significant role in determining the physical properties of a product. These results shed light on improved control and design of thermosetting resin material via curing reaction of soybean oil.     

Mapping the binding site of full length HIV-1 Nef on human Lck SH3 by NMR spectroscopy

Summary The Nef protein of human immunodeficiency virus type 1 (HIV-1) is known to directly bind to the SH3 domain of human lymphocyte specific kinase (Lck) via a proline-rich region located in the amino terminal part of Nef. To address the question whether Nef binding to Lck SH3 involves residues outside the typical poly-proline peptide binding site and whether the Lck unique domain is involved in Nef–Lck interaction, we studied the direct interaction between both molecules using recombinant full-length HIV-1 Nef protein on one side and recombinantly expressed and uniformly ¹⁵N-isotope labeled Lck protein comprising unique and SH3 domains on the other side. Applying nuclear magnetic resonance spectroscopy we could show that only residues of Lck SH3, that are typically involved in binding poly-proline peptides, are affected by Nef binding. Further, for the first time we could rule out that residues of Lck unique domain are involved in binding to full length Nef protein. Thus, interactions of Lck unique domain to cellular partners e.g. CD4 or CD8, are not necessarily competitive with Lck binding to HIV-1 Nef.