Van der Waals-corrected density functional theory: benchmarking for hydrogen-nanotube and nanotube-nanotube interactions

Density functional theory (DFT) is a powerful approach to electronic structure calculations in extended systems, but suffers currently from inadequate incorporation of long-range dispersion, or Van der Waals (VdW) interactions. VdW-corrected DFT is tested for interactions involving molecular hydrogen, graphite, single-walled carbon nanotubes (SWCNTs), and SWCNT bundles. The energy correction, based on an empirical London dispersion term with a damping function at short range, allows a reasonable physisorption energy and equilibrium distance to be obtained for H-2 on a model graphite surface. The VdW-corrected DFT calculation for an (8, 8) nanotube bundle reproduces accurately the experimental lattice constant. For H-2 inside or outside an (8, 8) SWCNT, we find the binding energies are respectively higher and lower than that on a graphite surface, correctly predicting the well known curvature effect. We conclude that the VdW correction is a very effective method for implementing DFT calculations, allowing a reliable description of both short-range chemical bonding and long-range dispersive interactions. The method will find powerful applications in areas of SWCNT research where empirical potential functions either have not been developed, or do not capture the necessary range of both dispersion and bonding interactions.

XPS study of basic aluminum sulphate and basic aluminium nitrate

Basic aluminium sulphate and nitrate crystals were prepared by forced hydrolysis of aluminium salt solution followed by precipitation with a sulphate solution or by evaporation for the basic aluminium nitrate. X-ray Photoelectron Spectroscopy (XPS) confirms the chemical composition determined by ICP-AES in earlier work. High resolution XPS scans of the individual elements allow the identification of both the central (AlO4)-Al-IV group and the 12 aluminium octahedra in the [IVAlO4AlVI(OH)(24)(H2O)(12)] building unit by two Al 2p transitions with binding energies of 73.7 and 74.2 eV in both the basic aluminium sulphate and nitrate. Four different types of oxygen atoms were identified in the basic aluminium sulphate associated with the central AlO4, OH, H2O and SO4 groups in the crystal structure with transitions at 529.4, 530.1, 530.7 and 531.8 eV, respectively. (c) 2005 Elsevier B.V. All rights reserved.

Explicit derivation of the relativistic mass-energy relation for internal kinetic and potential energies of a composite system

A straightforward derivation of relativistic expressions for the mechanical momentum, kinetic and total energies, and mass-energy equivalence (including potential energy) which does not require any knowledge of the energy-momentum relation for electromagnetic waves or consideration of elastic collisions, but is directly based on Newton's second law and Lorentz's transformations, is presented in this paper. The existence of an invariant force is shown to be important for the validity of the relativistic mechanics.

XPS study of the major minerals in bauxite: Gibbsite, bayerite and (pseudo-)boehmite

Synthetic corundum (Al2O3), gibbsite (Al(OH)(3)), bayerite (Al(OH)(3)), boehmite (AlO(OH)) and pseudoboehmite (AlO(OH)) have been studied by high resolution XPS. The chemical compositions based on the XPS survey scans were in good agreement with the expected composition. High resolution A12p scans showed no significant changes in binding energy, with all values between 73.9 and 74.4 eV. Only bayerite showed two transitions, associated with the presence of amorphous material in the sample. More information about the chemical and crystallographic environment was obtained from the 0 Is high resolution spectra. Here a clear distinction could be made between oxygen in the crystal structure, hydroxyl groups and adsorbed water. Oxygen in the crystal structure was characterised by a binding energy of about 530.6 eV in all minerals. Hydroxyl groups, present either in the crystal structure or on the surface, exhibited binding energies around 531.9 eV, while water on the surface showed binding energies around 533.0 eV. A distinction could be made between boehmite and pseudoboehmite based on the slightly lower ratio of oxygen to hydroxyl groups and water in pseudoboehmite. (c) 2005 Elsevier Inc. All rights reserved.

Plasma steroids and steroid-binding capacity in male semelparous dasyurid marsupials (Phascogale tapoatafa) that survive beyond the breeding season in captivity

The semelparous dasyurids display a unique life history, in that all males die within a few weeks of the completion of the breeding season. Studies of several semelparous species have revealed that the male die-off is stress-related, and accompanied by increased plasma androgen and cortisol levels and decreased corticosteroid binding capacity, resulting in suppression of immune and inflammatory responses. This study examines the endocrine profile of male brush-tailed phascogales (Phascogale tapoatafa) that survive beyond the breeding season in captivity. Plasma cortisol, corticosteroid binding globulin and albumin levels were monitored in both males and females and steroid partitioning calculated. Captive males surviving beyond the breeding season did not show the elevation in plasma cortisol and decrease in corticosteroid binding capacity reported in wild males. Plasma albumin concentrations also remained constant during the sampling period. These data indicate that captive males do not undergo the same stress response described in wild populations. (c) 2006 Elsevier Inc. All rights reserved.

Structural determinants for binding to CGRP receptors expressed by human SK-N-MC and Col 29 cells:Studies with chimeric and other peptides

1. Structure-activity relationships for the binding of human α-calcitonin gene-related peptide 8-37 (hαCGRP8-37) have been investigated at the CGRP receptors expressed by human SK-N-MC (neuroblastoma) and Col 29 (colonic epithelia) cells by radioligand binding assays and functional assays (hαCGRP stimulation of adenylate cyclase). 2. On SK-N-MC cells the potency order was hαCGRP8-37 > hαCGRP19-37 = AC187 > rat amylin8-37 > hα[Tyr0]-CGRP28-37 (apparent pKBS of 7.49 ± 0.25, 5.89 ± 0.20, 6.18 ± 0.19, 5.85 ± 0.19 and 5.25 ± 0.07). The SK-N-MC receptor appeared CGRP1-like. 3. On Col 29 cells, only hαCGRP8-37 of the above compounds was able to antagonize the actions of hαCGRP (apparent pKB = 6.48 ± 0.28). Its receptor appeared CGRP2-like. 4. hα[Ala11,18]-CGRP8-37, where the amphipathic nature of the N-terminal α-helix has been reduced, bound to SK-N-MC cells a 100 fold less strongly than hαCGRP8-37. 5. On SK-N-MC cells, hαCGRP(8-18, 28-37) (M433) and mastoparan-hαCGRP28-37 (M432) had apparent pKBS of 6.64 ± 0.16 and 6.42 ± 0.26, suggesting that residues 19-27 play a minor role in binding. The physico-chemical properties of residues 8-18 may be more important than any specific side-chain interactions. 6. M433 was almost as potent as hαCGRP8-37 on Col 29 cells (apparent pKB = 6.17 ± 0.20). Other antagonists were inactive.

Controlled RAFT polymerization and zinc binding performance of catechol-inspired homopolymers

Incorporation of catechols into polymers has long been of interest due to their ability to chelate heavy metals and their use in the design of adhesives, metal-polymer nanocomposites, antifouling coatings, and so on. This paper reports, for the first time, the reversible addition-fragmentation chain transfer (RAFT) polymerization of a protected catechol-inspired monomer, 3,4-dimethoxystyrene (DMS), using commercially available trithiocarbonate, 2-(dodecylthiocarbonothioylthio)-2-methylpropionic acid (DDMAT), as a chain transfer agent. Our identified RAFT system produces well-defined polymers across a range of molecular weights (5-50 kg/mol) with low molar mass dispersities (Mw/Mn < 1.3). Subsequent facile demethylation of poly(3,4-dimethoxystyrene) (PDMS) yields poly(3,4-dihydroxystyrene) (PDHS), a catechol-bearing polymer, in quantitative yields. Semiquantitative zinc binding capacity analysis of both polymers using SEM/EDXA has demonstrated that both PDMS and PDHS have considerable surface binding (65% and 87%, respectively), although the films deposited from PDMS are of a better quality and processability due to solubility and lower processing temperatures. © 2014 American Chemical Society.

Large-scale molecular dynamics simulations of HLA-A*0201 complexed with a tumor-specific antigenic peptide:can the α3 and β2m domains be neglected?

Large-scale massively parallel molecular dynamics (MD) simulations of the human class I major histo-compatibility complex (MHC) protein HLA-A*0201 bound to a decameric tumor-specific antigenic peptide GVY-DGREHTV were performed using a scalable MD code on high-performance computing platforms. Such computational capabilities put us in reach of simulations of various scales and complexities. The supercomputing resources available Large-scale massively parallel molecular dynamics (MD) simulations of the human class I major histocompatibility complex (MHC) protein HLA-A*0201 bound to a decameric tumor-specific antigenic peptide GVYDGREHTV were performed using a scalable MD code on high-performance computing platforms. Such computational capabilities put us in reach of simulations of various scales and complexities. The supercomputing resources available for this study allow us to compare directly differences in the behavior of very large molecular models; in this case, the entire extracellular portion of the peptide–MHC complex vs. the isolated peptide binding domain. Comparison of the results from the partial and the whole system simulations indicates that the peptide is less tightly bound in the partial system than in the whole system. From a detailed study of conformations, solvent-accessible surface area, the nature of the water network structure, and the binding energies, we conclude that, when considering the conformation of the α1–α2 domain, the α3 and β2m domains cannot be neglected. © 2004 Wiley Periodicals, Inc. J Comput Chem 25: 1803–1813, 2004

Degradation, receptor binding, insulin secreting and antihyperglycaemic actions of palmitate-derivatised native and Ala8-substituted GLP-1 analogues

The hormone glucagon-like peptide-1(7-36)amide (GLP-1) is released in response to ingested nutrients and acts to promote glucose-dependent insulin secretion ensuring efficient postprandial glucose homeostasis. Unfortunately, the beneficial actions of GLP-1 which give this hormone many of the desirable properties of an antidiabetic drug are short lived due to degradation by dipeptidylpeptidase IV (DPP IV) and rapid clearance by renal filtration. In this study we have attempted to extend GLP-1 action through the attachment of palmitoyl moieties to the E-amino group in the side chain of the LyS26 residue and to combine this modification with substitutions of the Ala 8 residue, namely Val or amino-butyric acid (Abu). In contrast to native GLP-1, which was rapidly degraded, [Lys(pal) 26]GLP-1, [Abu8,Lys(pal)26]GLP-1 and [Val8,Lys-(pal)26]GLP-1 all exhibited profound stability during 12 h incubations with DPP IV and human plasma. Receptor binding affinity and the ability to increase cyclic AMP in the clonal β-cell line BRIN-BD11 were decreased by 86- to 167-fold and 15- to 62-fold, respectively compared with native GLP-1. However, insulin secretory potency tested using BRIN-BD11 cells was similar, or in the case of [Val8,Lys(pal)26]GLP-1 enhanced. Furthermore, when administered in vivo together with glucose to diabetic (ob/ob) mice, [Lys(pal)26]GLP-1, [Abu8,Lys(pal) 26]GLP-1 and [Val8,Lys(pal) 26]GLP-1 did not demonstrate acute glucose-lowering or insulinotropic activity as observed with native GLP-1. These studies support the potential usefulness of fatty acid linked analogues of GLP-1 but indicate the importance of chain length for peptide kinetics and bioavailability. Copyright © by Walter de Gruyter.

Spectroscopy of Electroproduced Light to Medium Mass Lambda Hypernuclei

The E01-011 experiment at Jefferson Laboratory (JLab) studied light-to-medium mass Λ hypernuclei via the AZ + e → [special characters omitted] + e' + K+ electroproduction reaction. Precise measurement of hypernuclear ground state masses and excitation energies provides information about the nature of hyperon-nucleon interactions. Until recently, hypernuclei were studied at accelerator facilities with intense π+ and K- meson beams. The poor quality of these beams limited the resolution of the hypernuclear excitation energy spectra to about 1.5 MeV (FWHM). This resolution is not sufficient for resolving the rich structure observed in the excitation spectra. By using a high quality electron beam and employing a new high resolution spectrometer system, this study aims to improve the resolution to a few hundred keV with an absolute precision of about 100 keV for excitation energies. In this work the high-resolution excitation spectra of [special characters omitted], and [special characters omitted] hypernuclei are presented. In an attempt to emphasize the presence of the core-excited states we introduced a novel likelihood approach to particle identification (PID) to serve as an alternative to the commonly used standard hard-cut PID. The new method resulted in almost identical missing mass spectra as obtained by the standard approach. An energy resolution of approximately 400–500 keV (FWHM) has been achieved, an unprecedented value in hypernuclear reaction spectroscopy. For [special characters omitted] the core-excited configuration has been clearly observed with significant statistics. The embedded Λ hyperon increases the excitation energies of the 11B nuclear core by 0.5–1 MeV. The [special characters omitted] spectrum has been observed with significant statistics for the first time. The ground state is bound deeper by roughly 400 keV than currently predicted by theory. Indication for the core-excited doublet, which is unbound in the core itself, is observed. The measurement of [special characters omitted] provides the first study of a d-shell hypernucleus with sub-MeV resolution. Discrepancies of up to 2 MeV between measured and theoretically predicted binding energies are found. Similar disagreement exists when comparing to the [special characters omitted] mirror hypernucleus. Also the core-excited structure observed between the major s-, p- and d-shell Λ orbits is not consistent with the available theoretical calculations. In conclusion, the discrepancies found in this study will provide valuable input for the further development of theoretical models.

Simultaneous high-resolution pH and spectrophotometric recordings of oxygen binding in native blood microvolumes, link to supplementary material

Oxygen equilibrium curves have been widely used to understand oxygen transport in numerous organisms. A major challenge has been to monitor oxygen binding characteristics and concomitant pH changes as they occur in vivo, in limited sample volumes. Here we report a technique allowing highly resolved and simultaneous monitoring of pH and blood pigment saturation in minute blood volumes. We equipped a gas diffusion chamber with a broad range fibre optic spectrophotometer and a micro-pH optode and recorded changes of pigment oxygenation along PO2 and pH gradients to test the setup. Oxygen binding parameters derived from measurements in only 15 µl of haemolymph from the cephalopod Octopus vulgaris showed low instrumental error (0.93%) and good agreement with published data. Broad range spectra, each resolving 2048 data points, provided detailed insight into the complex absorbance characteristics of diverse blood types. After consideration of photobleaching and intrinsic fluorescence, pH optodes yielded accurate recordings and resolved a sigmoidal shift of 0.03 pH units in response to changing PO2 from 0-21 kPa. Highly resolved continuous recordings along pH gradients conformed to stepwise measurements at low rates of pH changes. In this study we showed that a diffusion chamber upgraded with a broad range spectrophotometer and an optical pH sensor accurately characterizes oxygen binding with minimal sample consumption and manipulation. We conclude that the modified diffusion chamber is highly suitable for experimental biologists who demand high flexibility, detailed insight into oxygen binding as well as experimental and biological accuracy combined in a single set up.

Effect of dipole polarizability on positron binding by strongly polar molecules

A model for positron binding to polar molecules is considered by combining the dipole potential outside the molecule with a strongly repulsive core of a given radius. Using existing experimental data on binding energies leads to unphysically small core radii for all of the molecules studied. This suggests that electron–positron correlations neglected in the simple model play a large role in determining the binding energy. We account for these by including the polarization potential via perturbation theory and non-perturbatively. The perturbative model makes reliable predictions of binding energies for a range of polar organic molecules and hydrogen cyanide. The model also agrees with the linear dependence of the binding energies on the polarizability inferred from the experimental data (Danielson et al 2009 J. Phys. B: At. Mol. Opt. Phys. 42 235203). The effective core radii, however, remain unphysically small for most molecules. Treating molecular polarization non-perturbatively leads to physically meaningful core radii for all of the molecules studied and enables even more accurate predictions of binding energies to be made for nearly all of the molecules considered.

Formation of positron-atom bound states in collisions between Rydberg Ps and neutral atoms

Predicted 20 years ago, positron binding to neutral atoms has not yet been observed experimentally. A scheme is proposed to detect positron-atom bound states by colliding Rydberg positronium (Ps) with neutral atoms. Estimates of the charge-transfer reaction cross section are obtained using the first Born approximation for a selection of neutral atom targets and a wide range of incident Ps energies and principal quantum numbers. We also estimate the corresponding Ps ionization cross section. The accuracy of the calculations is tested by comparison with earlier predictions for charge transfer in Ps collisions with hydrogen and antihydrogen. We describe an existing Rydberg Ps beam suitable for producing positron-atom bound states and estimate signal rates based on the calculated cross sections and realistic experimental parameters. We conclude that the proposed methodology is capable of producing such states and of testing theoretical predictions of their binding energies.

Dynamics and Heterogeneity of Pb(II) Binding by SiO2 Nanoparticles in an Aqueous Dispersion

Pb(II) binding by SiO2 nanoparticles in an aqueous dispersion was investigated under conditions where the concentrations of Pb2+ ions and nanoparticles are of similar magnitude. Conditional stability constants (log K) obtained at different values of pH and ionic strength varied from 4.4 at pH 5.5 and I = 0.1 M to 6.4 at pH 6.5 and I = 0.0015 M. In the range of metal to nanoparticle ratios from 1.6 to 0.3, log K strongly increases, which is shown to be due to heterogeneity in Pb(II) binding. For an ionic strength of 0.1 M the Pb2+/SiO2 nanoparticle system is labile, whereas for lower ionic strengths there is loss of lability with increasing pH and decreasing ionic strength. Theoretical calculations on the basis of Eigen-type complex formation kinetics seem to support the loss of lability. This is related to the nanoparticulate nature of the system, where complexation rate constants become increasingly diffusion controlled. The ion binding heterogeneity and chemodynamics of oxidic nanoparticles clearly need further detailed research.

Time-Dependent Density Functional Molecular Orbital and Excited State Calculations on Bis(porphyrinyl)butadiynes in the Monocationic, Neutral, Monoanionic, and Dianionic Oxidation States

We report a theoretical study of the multiple oxidation states (1+, 0, 1−, and 2−) of a meso,meso-linked diporphyrin, namely bis[10,15,20-triphenylporphyrinatozinc(II)-5-yl]butadiyne (4), using Time-Dependent Density Functional Theory (TDDFT). The origin of electronic transitions of singlet excited states is discussed in comparison to experimental spectra for the corresponding oxidation states of the close analogue bis{10,15,20-tris[3‘,5‘-di-tert-butylphenyl]porphyrinatozinc(II)-5-yl}butadiyne (3). The latter were measured in previous work under in situ spectroelectrochemical conditions. Excitation energies and orbital compositions of the excited states were obtained for these large delocalized aromatic radicals, which are unique examples of organic mixed-valence systems. The radical cations and anions of butadiyne-bridged diporphyrins such as 3 display characteristic electronic absorption bands in the near-IR region, which have been successfully predicted with use of these computational methods. The radicals are clearly of the “fully delocalized” or Class III type. The key spectral features of the neutral and dianionic states were also reproduced, although due to the large size of these molecules, quantitative agreement of energies with observations is not as good in the blue end of the visible region. The TDDFT calculations are largely in accord with a previous empirical model for the spectra, which was based simplistically on one-electron transitions among the eight key frontier orbitals of the C4 (1,4-butadiyne) linked diporphyrins.