Modified density matrix renormalization group algorithm for the zigzag spin-1/2 chain with frustrated antiferromagnetic exchange: Comparison with field theory at large J(2)/J(1)

A modified density matrix renormalization group (DMRG) algorithm is applied to the zigzag spin-1/2 chain with frustrated antiferromagnetic exchange J(1) and J(2) between first and second neighbors. The modified algorithm yields accurate results up to J(2)/J(1) approximate to 4 for the magnetic gap Delta to the lowest triplet state, the amplitude B of the bond order wave phase, the wavelength lambda of the spiral phase, and the spin correlation length xi. The J(2)/J(1) dependences of Delta, B, lambda, and xi provide multiple comparisons to field theories of the zigzag chain. The twist angle of the spiral phase and the spin structure factor yield additional comparisons between DMRG and field theory. Attention is given to the numerical accuracy required to obtain exponentially small gaps or exponentially long correlations near a quantum phase transition.

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.

Characterization of the interaction of lipid A and lipopolysaccharide with human serum albumin: implications for an endotoxin carrier function for albumin

The interactions of lipid A and lipopolysaccharide (LPS) with human serum albumin (HSA) were examined using fluorescence methods. Lipid A binds HSA with a stoichiometry of 2:1 with dissociation constants of 1.0 µM and 6.0 µM for the high- and low-affinity interactions, respectively. Lipid A displaces HSA-bound dansylsarcosine competitively, but not HSA-bound warfarin, suggesting that domain III-A, and not domain 11-A, is a lipid A binding site. Domain I does not contribute a site for lipid A. Based on these data, and the structural similarity between subdomains III-A and III-B, it is proposed that these two regions of HSA represent the high- and low-affinity sites of interaction of lipid A. Whole LPS also binds HSA, displacing dansylsarcosine, and its lipid A moiety appears to be the interaction site. However, there are differences between LPS and free lipid A. Polymyxin B forms ternary complexes with LPS bound to HSA, suggesting that the regions on LPS recognized by HSA and polymyxin B are different. The observed affinity of lipid A for HSA and mass action effects due to its abundance in the circulation would imply a major LPS carrier function for HSA.

Charge density based classification of intermolecular interactions in molecular crystals

Evaluation of intermolecular interactions in terms of both experimental and theoretical charge density analyses has produced a unified picture with which to classify strong and weak hydrogen bonds, along with van der Waals interactions, into three regions.

Backbone chemical shift assignments of the acyl-acyl carrier protein intermediates of the fatty acid biosynthesis pathway of Plasmodium falciparum

We report the backbone chemical shift assignments of the acyl-acyl carrier protein (ACP) intermediates of the fatty acid biosynthesis pathway of Plasmodium falciparum. The acyl-ACP intermediates butyryl (C4), -octanoyl (C8), -decanoyl (C10), -dodecanoyl (C12) and -tetradecanoyl (C14)-ACPs display marked changes in backbone HN, Cα and Cβ chemical shifts as a result of acyl chain insertion into the hydrophobic core. Chemical shift changes cast light on the mechanism of expansion of the acyl carrier protein core.

Structural Insights into the Acyl Intermediates of the Plasmodium falciparum Fatty Acid Synthesis Pathway THE MECHANISM OF EXPANSION OF THE ACYL CARRIER PROTEIN CORE

Acyl carrier protein (ACP) plays a central role in fatty acid biosynthesis. However, the molecular machinery that mediates its function is not yet fully understood. Therefore, structural studies were carried out on the acyl-ACP intermediates of Plasmodium falciparum using NMR as a spectroscopic probe. Chemical shift perturbation studies put forth a new picture of the interaction of ACP molecule with the acyl chain, namely, the hydrophobic core can protect up to 12 carbon units, and additional carbons protrude out from the top of the hydrophobic cavity. The latter hypothesis stems from chemical shift changes observed in C-alpha and C-beta of Ser-37 in tetradecanoyl-ACP. C-13, N-15-Double-filtered nuclear Overhauser effect (NOE) spectroscopy experiments further substantiate the concept; in octanoyl (C-8)- and dodecanoyl (C-12)-ACP, a long range NOE is observed within the phosphopantetheine arm, suggesting an arch-like conformation. This NOE is nearly invisible in tetradecanoyl (C-14)-ACP, indicating a change in conformation of the prosthetic group. Furthermore, the present study provides insights into the molecular mechanism of ACP expansion, as revealed from a unique side chain-to-backbone hydrogen bond between two fairly conserved residues, Ile-55 HN and Glu-48 O. The backbone amide of Ile-55 HN reports a pK(a) value for the carboxylate, similar to 1.9 pH units higher than model compound value, suggesting strong electrostatic repulsion between helix II and helix III. Charge-charge repulsion between the helices in combination with thrust from inside due to acyl chain would energetically favor the separation of the two helices. Helix III has fewer structural restraints and, hence, undergoes major conformational change without altering the overall-fold of P. falciparum ACP.

Solution structures of conformationally equilibrium forms of holo-acyl carrier protein (PfACP) from Plasmodium falciparum provides insight into the mechanism of activation of ACPs

Acyl Carrier Protein (ACP) from the malaria parasite, Plasmodium falciparum (PfACP) in its holo form is found to exist in two conformational states in solution. Unique 3D solution structures of holo-PfACP have been determined for both equilibrium conformations, using high-resolution NMR methods. Twenty high-resolution solution structures for each of the two forms of holo-PfACP have been determined on the basis of 1226 and 1218 unambiguously assigned NOEs (including NOEs between 4 '-phosphopantetheine prosthetic group (4 '-PP) and protein), 55 backbone dihedral angles and 26 hydrogen bonds. The atomic rmsd values of the determined structures of two equilibrium forms, about the mean coordinates of the backbone and heavy atoms, are 0.48 +/- 0.09 and 0.92 +/- 0.10 and 0.49 +/- 0.08 and 0.97 +/- 0.11 angstrom, respectively. The interaction of 4 '-PP with the polypeptide backbone is reported here for the first time for any of the ACPs. The structures of holo-PfACP consist of three well-defined helices that are tightly packed. The structured regions of the molecule are stabilized by extensive hydrophobic interactions. The difference between the two forms arises from a reorientation of the 4 '-PP group. The enthalpy difference between the two forms, although small, implies that a conformational switch is essential for the activation of holo-ACP. Sequence and structures of holo-PfACP have been compared with those of the ACPs from type I and type II fatty acid biosynthesis pathways (FAS), in particular with the ACP from rat and the butyryl-ACP from E. coli. The PfACP structure, thus determined has several novel features hitherto not seen in other ACPs.

Exploring the interaction energies for the binding of hydroxydiphenyl ethers to enoyl-acyl carrier protein reductases

It is now well established that the potent anti-microbial compound, triclosan, interrupts the type II fatty acid synthesis by inhibiting the enzyme enoyl-ACP reductase in a number of organisms. Existence of a high degree of similarity between the recently discovered enoyl-ACP reductase from R falciparum and B. napus enzyme permitted building of a satisfactory model for the former enzyme that explained some of the key aspects of the enzyme such as its specificity for binding to the cofactor and the inhibitor. We now report the interaction energies between triclosan and other hydroxydiphenyl ethers with the enzymes from B. napus, E. coli and R falciparum. Examination of the triclosan-enzyme interactions revealed that subtle differences exist in the ligand binding sites of the enzymes from different sources i.e., B. napus, E. coli and P falciparum. A comparison of their binding propensities thus determined should aid in the design of effective inhibitors for the respective enzymes.

Low density polyethylene and grafted lignin polyblends using epoxy-functionalized compatibilizer: mechanical and thermal properties

Lignin was graft copolymerized with methyl methacrylate using manganic pyrophosphate as initiator. This modified lignin was then blended (up to 50 wt%) with low density polyethylene (LDPE) using a small quantity of poly[ethylene-co-(glycidyl methacrylate)] (PEGMA) compatibilizer. The mechanical properties of the blend were substantially improved by using modified lignin in contrast to untreated lignin. Differential scanning calorimetry studies showed loss of crystallinity of the LDPE phase owing to the interaction between the blend components. Thermogravimetric analysis showed higher thermal stability of modified lignin in the domain of blend processing. This suggested that there is scope for useful utilization of lignin, which could also lead to the development of eco-friendly products. (c) 2005 Society of Chemical Industry.

Note: Creep behaviour of high density polyethylene

The Ramberg-Osgood type constitutive law for creep suggested by Iyengar2 has been verified on high-density polyethylene. The time functions are evaluated from the experimental data of Scheweiker and Sidebottom3. It is found that the creep behaviour of the above material can be represented by the Ramberg-Osgood type law.

Simplified theory of carrier back-scattering in semiconducting carbon nanotubes: A Kane's model approach

We present a simplified yet analytical formulation of the carrier backscattering coefficient for zig-zag semiconducting single walled carbon nanotubes under diffusive regime. The electron-phonon scattering rate for longitudinal acoustic, optical, and zone-boundary phonon emissions for both inter- and intrasubband transition rates have been derived using Kane's nonparabolic energy subband model.The expressions for the mean free path and diffusive resistance have been formulated incorporating the aforementioned phonon scattering. Appropriate overlap function in Fermi's golden rule has been incorporated for a more general approach. The effect of energy subbands on low and high bias zones for the onset of longitudinal acoustic, optical, and zone-boundary phonon emissions and absorption have been analytically addressed. 90% transmission of the carriers from the source to the drain at 400 K for a 5 mu m long nanotube at 105 V m(-1) has been exhibited. The analytical results are in good agreement with the available experimental data. (c) 2010 American Institute of Physics.

Crystalline ethane-1,2-diol does not have intra-molecular hydrogen bonding: Experimental and theoretical charge density studies

The X-ray structure and electron density distribution of ethane-1,2-diol (ethylene glycol), obtained at a resolution extending to 1.00 Å−1 in sin θ/λ (data completion = 100% at 100 K) by in situ cryocrystallization technique is reported. The diol is in the gauche (g′Gt) conformation with the crystal structure stabilised by a network of inter-molecular hydrogen bonds. In addition to the well-recognized O–H···O hydrogen bonds there is topological evidence for C–H···O inter-molecular interactions. There is no experimental electron density based topological evidence for the occurrence of an intra-molecular hydrogen bond. The O···H spacing is not, vert, similar0.45 Å greater than in the gas-phase with an O–H···O angle close to 90°, calling into question the general assumption that the gauche conformation of ethane-1,2-diol is stabilised by the intra-molecular oxygen–hydrogen interaction.