Ionic Forces Research Articles

Homology modeling and molecular dynamics simulation of human prothrombin fragment 1.

The crystallographic structure of bovine prothrombin fragment 1 bound with calcium ions was used to construct the corresponding human prothrombin structure (hf1/Ca). The model structure was refined by molecular dynamics to estimate the average solution structure. Accommodation of long-range ionic forces was essential to reach a stable solution structure. The gamma-carboxyglutamic acid (Gla) domain and the kringle domain of hf1/Ca independently equilibrated. Likewise, the hydrogen bond network and the calcium ion coordinations were well preserved. A discussion of the phospholipid binding of the vitamin K-dependent coagulation proteins in the context of the structure and mutational data of the Gla domain is presented.

Effects of ionic strength and pH on the binding of medium-chain fatty acids to human serum albumin.

Binding equilibria for the interactions of the medium-chain fatty acid anions, laurate and myristate, with defatted human serum albumin have been investigated under varying environmental conditions such as ionic strength and pH. Since these ligands bind strongly to albumin (Kass approximately 10(7) M-1), conventional equilibrium dialysis is not a feasible method for these investigations. Consequently, we employed a dialysis method, allowing determination of very low concentrations of unbound ligand by measuring the rate of exchange of labelled ligand across a dialysis membrane under conditions of chemical equilibrium. Over a range of ionic strength, 8-68 mM, the binding of the first few molecules of laurate to albumin was weakened with increasing ionic strength, whereas the binding of subsequent molecules seemed to proceed independently of ionic strength. The binding of myristate by albumin, however, appeared to be independent of ionic strength in the observed range of concentrations. The influence of pH in the range 5.1-9.0 on the binding of the two fatty acid anions by albumin was more complicated. The first molecule of laurate appeared to bind with a slightly weaker affinity to albumin at low pH, compared to pH 7 and high pH, while the trends for the following molecules varied. The binding of myristate (irrespective of concentration) seemed to strengthen monotonously with pH, but this conclusion depends critically on the interpretation of the kinetic behaviour of the myristate anion. We have previously shown [Pedersen, A. O., Honoré, B. & Brodersen, R. (1990) Eur. J. Biochem. 190, 497-502] that the strength of binding of the first few molecules of the two fatty acid anions to albumin decreases with increasing temperature, whereas binding of subsequent molecules seems to proceed independently of temperature. We explain these findings as follows. The binding of the first few (3 or 4) molecules of the C12 laurate anion is clearly driven by formation of ionic bonds between the fatty acid anion and positively charged groups, such as lysine residues, in the albumin molecule, whereas the binding of subsequent molecules of laurate seems to depend more on hydrophobic interactions. In the case of the C14 myristate anion, the binding of the first few (only 1 or 2) molecules may depend on ionic forces, but binding of the following molecules of myristate seems to depend on hydrophobic interactions only.(ABSTRACT TRUNCATED AT 250 WORDS)

Removal of endotoxins by affinity sorbents.

Histidine, histamine and polymyxin B affinity sorbents were employed for the removal of Escherichia coli-derived endotoxins. Their effectiveness was compared with those of poly-L-lysine-Sepharose and DEAE-Sepharose. All sorbents reduced the concentration of endotoxins from an E. coli culture filtrate to tolerable levels. However, their effectiveness was not higher than that of the anion exchanger, which displayed clearance rates of up to 15,000. Endotoxin removal from protein solutions depended on the net charge of the desired protein. Lysozyme as a model for positively charged proteins enhanced endotoxin removal. In contrast, only low initial contamination levels (< 34 EU/ml) were reduced to tolerable levels from bovine serum albumin (BSA) as the negatively charged protein model owing to competition of BSA and endotoxins for adsorption sites. Hence also a low BSA recovery was observed after the treatment whereas the lysozyme recovery was almost 100%. At pH values below the isoelectric point of BSA, endotoxin removal was also more effective. The best conditions for the decontamination were found at neutral pH and low ionic strength (< or = 20 mM phosphate). Ionic forces between ligands and endotoxins are dominant at this ionic strength; hydrophobic interactions are not very effective. Hence the selectivities of all sorbents towards endotoxins are not exceptionally high. DEAE-anion exchangers are the most suitable sorbents for the removal of endotoxins from solutions accommodating positively charged proteins owing to their low cost and high capacity. Poly-L-lysine-Sepharose was most effective for the removal of small amounts of endotoxins from solutions of negatively charged proteins. The "affinity ligands" histamine, histidine and polymyxin B were effective for the removal of endotoxins from E. coli filtrate; however, their effectiveness decreased dramatically in the presence of BSA and it was lower than for poly-L-lysine- and DEAE-Sepharose in the presence of lysozyme.

Common interatomic potential model for the lattice dynamics of several cuprates.

A common empirical model is developed for the lattice dynamics of the cuprates ${\mathrm{La}}_{2}$${\mathrm{CuO}}_{4}$, (La,Sr${)}_{2}$${\mathrm{CuO}}_{4}$, ${\mathrm{Nd}}_{2}$${\mathrm{CuO}}_{4}$, ${\mathrm{YBa}}_{2}$${\mathrm{Cu}}_{3}$${\mathrm{O}}_{6}$, and ${\mathrm{YBa}}_{2}$${\mathrm{Cu}}_{3}$${\mathrm{O}}_{7}$, which is also consistent with their crystal structures. Starting from the idea that the binding in these compounds is primarily ionic in character, the interatomic interactions were modeled using shell models with short-range repulsive potentials of the Born-Mayer type. For the metallic members of the series, screening of the ionic forces by free carriers was taken into account. There is clear evidence for an anisotropic Cu-O potential whereas the polarizabilities could be kept isotropic. The Cu(1)-O(4) bond in ${\mathrm{YBa}}_{2}$${\mathrm{Cu}}_{3}$${\mathrm{O}}_{6}$ could not be treated on a common footing, as there is too little charge on the Cu(1). The present study demonstrates that the lattice dynamics of all the compounds investigated can be described quite satisfactorily by a common model and it offers a basis for extensions to related compounds. On the other hand, we found clear indications that a description of the lattice vibrations with purely ionic forces has its limits for this class of compounds.

Enhanced electron-phonon coupling and phonon-plasmon mixing in the high-temperature superconductors

It is shown, using La2CuO4 as an example, that the already large (nonlocal) electron-phonon coupling as calculated in the adiabatic approximation is further strongly enhanced for certain phonons in the nonadiabatic regime, where dynamical screening comes into play. At the same time, a low-lying plasmon mode of the electronic system appears for wave vectors in the (0,0,1) direction which mixes strongly with the phonons of appropriate symmetry and leads in addition to the phonons to very large changes of the crystal potential. Such a coexistence of phononlike and plasmonlike modes in the same frequency range is argued to be a specific feature of the high-temperature superconductors(HTSC's) related to their layered structure and weak screening of the strong ionic forces in c direction. It leads to a significant increase of the retarded attractive interaction.

Atomic force microscopy: a key to direct wafer bonding technology

Wafer bonding is the dedicated joining of two semiconductor wafer surfaces without the use of adhesives. Specific applications include silicon-oninsulator (SOI), sensors and actuators, and threedimensional integrated microstructures [1-5]. Although a complete theory has not been presented to explain the bonding process, it is generally accepted that the attractive interfacial force between the two surfaces that are separated only by atomic distances is responsible for the initial bonding. These attractive interracial forces are believed to be either electrostatic or chemical in nature. When the two wafers are contacted a relatively weak adhesive force is developed between the surfaces. This initial bond can be strengthened by additional processing such as thermal annealing. The sum of the attractive chemical or ionic interfacial forces balance against the mechanical forces exerted by surface contaminants, roughness, waviness, and wafer bow to determine if an initial bond will form [6]. It is obvious, therefore, that surface-related defects such as particulate contamination, surface roughness, and surface waviness must be minimized and controlled in order to optimize the initial contact for successful bonding to take place. Due to this fact the development of wafer bonding has been highly focused on smooth films such as thermal oxides and bare silicon surfaces. Chemically vapour deposited (CVD) oxides are widely used for the development of integrated circuit (IC) technologies. These CVD oxides may be good candidates for low-temperature wafer bonded surfaces. Structures that do not have surfaces that naturally bond may still be bonded by using deposited films such as oxides as an intermediate layer. P r e v i o u s l y , Si3N 4 and TiN deposited films have been found to form low-temperature bonds [7, 8]. Two other possibilities for low-temperature bondable deposited films are borophosphosilicate glass (BPSG), and low pressure chemically vapour deposited (LPCVD) undoped SiO2. BPSG is used extensively in microelectronics device fabrication as an interlayer dielectric film due to its excellent planarization, gettering and flow properties [9]; LPCVD SiO2 is used in applications where there are stringent step coverage and gap-filling requirements [10]. The successful and reliable bonding of these films would be a very important milestone in the realization of novel structures such as three-dimensional ICs

Electronic Structure Calculations on a Real-Space Mesh with Multigrid Acceleration

AbstractWe have developed a set of techniques for performing large scale ab initio calculations using multigrid accelerations and a real-space grid as a basis. The multigrid methods permit efficient calculations on ill-conditioned systems with long length scales or high energy cutoffs. We discuss the design of pseudopotentials for real-space grids, and the computation of ionic forces. The technique has been applied to several systems, including an isolated C60 molecule, the wurtzite phase of GaN, a 64-atom cell of GaN with the Ga d-states in valence, and a 443-atom protein. The method has been implemented on both vector and parallel architectures. We also discuss ongoing work on O(N) implementations and solvated biomolecules.

The Structure of Na3SbTe3: How Ionic and Covalent Bonding Forces Work Together

The compound Na3SbTe3 has been synthesized from the elements and characterized by single crystal X-ray diffraction. Na3SbTe3 is cubic, crystallizing in the cP28 structure type (isomorphous with Na3AsS3); space group P 213 (No. 198); a = 9.6114(9) Å; Z = 4; R 1 = 0.0324; wR2 = 0.0561 (I ≥ 2σ(I)). The structure consists of isolated sodium cations and trigonal pyramidal [SbTe3]-3 anions with a Sb-Te bond length of 2.787(1) Å and a Te-Sb-Te bond angle of 100.0(1)°. The structure is related to both the Li3Bi and K3AsS4-type structures. Both lattice energy and semiempirical electronic structure calculations are utilized to evaluate various local and long-range structural aspects of this Zintl phase.

Nonadiabatic and nonlocal electron-phonon interaction and phonon-plasmon mixing in the high-temperature superconductors.

Within the framework of an electronic density response approach, recently worked out to describe screening, lattice dynamics, and the electron-phonon interaction in the high-temperature superconductors, it is shown, using ${\mathrm{La}}_{2}$${\mathrm{CuO}}_{4}$ as an example, that the already large (nonlocal) electron-phonon coupling as calculated in the adiabatic approximation is further strongly enhanced for certain phonons in the high-temperature superconductors (HTSC's) in the nonadiabatic regime where dynamical screening comes into play. At the same time, a low-lying plasma mode of the electronic system appears for wave vectors in the (0,0,1) direction which mixes strongly with the phonons of appropriate symmetry and leads in addition to the phonons to very large changes of the crystal potential. Such a coexistence of phononlike and plasmonlike modes in the same frequency range is argued to be a specific feature of the HTSC's related to their layered structure and weak screening of the strong ionic forces in the c direction. It leads to a significant increase of the retarded attractive interaction and provides, at least in part, an understanding of the reduction of the oxygen isotope effect in these materials, which is difficult to explain for a pure (harmonic) electron-phonon superconductor.

Cyclic hexapeptide NK-2 antagonists.

The synthesis of 11 cyclic hexapeptides, some of which contain a carbohydrate side chain moiety, is described in this paper. A glycosylamine was coupled without hydroxyl protecting groups either directly or via a butyric acid spacer to the side chain of glutamic acid, leading to beta-N-glycosylated peptides. All peptides described are selective NK-2 antagonists. The binding affinity to the NK-2-receptor ranges from 7 x 10(-7) to 1 x 10(-8) M, whereas at the NK-1 receptor the IC50 was > 10(-5) M with the exception of cyclo(-Lys(Boc)-Trp-Phe-Gly-Leu-D-Leu-) (I), which shows low affinity to the NK-1 receptor (IC50 = 9 x 10(-6) M). The antagonist activity is determined in the hamster trachea assay. pA2-Values range from 7.1 to 7.8. The results demonstrate the broad range of side chains which can be accommodated at the glutamine position without a major drop in activity. The different charges of the lysine and the glutamic acid peptides indicate that the interaction with the receptor at this position is not determined by ionic forces. Rather, we expect that conformational flexibility allows differently charged amino acid residues to be accommodated by the receptor.

Biodegradable microspheres as depot system for patenteral delivery of peptide drugs

Synthetic biodegradable polymers of lactic and glycolic acid have been extensively investigated for sustained drug delivery. Drug release from lactide/glycolide polymers can be either diffusion controlled or matrix erosion controlled. Polymer degradation was dependent on the molecular weight of the polymer and matrix structure of the delivery system. High surface area, lower particle size and lower bulk density increased the rate of degradation. Gamma irradiation of the delivery system also increased the rate of matrix erosion by reduction of molecular weight. Microspheres containing peptide, salmon calcitonin (sCT), were prepared by solvent extraction techniques using temperature or dilution. sCT was also incorporated into pre-formed microspheres by adsorption. sCT has a strong hydrophobic region and hence can bind to the polymer by a combination of hydrophobic and ionic forces, resulting in high incorporation from an aqueous medium. Adsorption appeared to result in multiple layers of adsorbed peptide on the polymer surface. The microspheres with entrapped sCT exhibited in vivo release of sCT between days 5 and 9, whereas microspheres with adsorbed sCT showed low but detectable in vivo release for 3–4 days. Combination of microspheres with different release properties can be used to achieve various in vivo serum profiles.

Acid and enzymatic degradation of cell wall from epicotyls of Cicer arietinum L.

In epicotyls of Cicer arietinum, there is a specific release of sugars when the cell wall is incubated at pH 1 (acid degradation). This process is distinct from the enzymatic cell wall autolysis which takes place at pH 5.5. The release is faster during the acid degradation and the products released are mainly polysaccharides with a high proportion of uronic acids, suggesting that this process may be due to a direct effect of protons on some pH-susceptible bonds between galacturonic acid-rich pectic polysaccharides, bound by ionic forces mainly by calcium type linkages. The main neutral sugar released is arabinose with lesser amounts of galactose. These results indicate the involvement of different substrates than in the autolysis or enzymatc degradation where mainly galactose is released as a monosaccharide component. Cell walls previously subjected to an exhaustive enzymatic degradation, underwent the sam edegree of acid degradation as in the case in which the walls were intact, without prior enzymatic treatment, confirm that both substrates are not localized in the same polysaccharides. Thus, they would be two different and independent processes.

Calculated effects of charge fluctuations on the phonon dispersion of YBa2Cu3O6 and YBa2Cu3O7. II. Results

AbstractUsing the model presented in the preceding paper we investigate the effects of charge fluctuations (CF) on the phonon dispersion of YBa2Cu3O6 (O6) and YBa2Cu3O7 (O7). Starting from an ab‐initio rigid‐ion model as a reference system, CF are allowed for at the copper‐ and oxygen ions. The CF are treated as adiabatic electronic degrees of freedom. Within the rigid‐ion model (RIM) the structural parameters are calculated by minimization of the energy. The results agree reasonably well with the experiment, indicating the suitability of the ionic model as a starting point and the importance of ionic forces for the properties of the high‐temperature superconductors (HTSC) in general.Next, the phonon dispersion is calculated in the RIM as well as including CF additionally and the renormalization of the individual modes is discussed. By restricting the CF optionally to the planes, effects arising specifically from CF in the planes on the one hand and from CF in the chain as well as at the axial bridging oxygens (O4) on the other hand can be separated. We find the oxygen axial modes at the γ‐ and Z point (A1g/A2μ in O6, Ag/B1μ in O7) particularly interesting. Most of these modes show considerable renormalizations. Moreover, the γ/Z‐axial modes are characterized by the possibility of having CF of the same sign in the whole CuO planes what distinguishes them from the modes at other symmetry points. In particular, the Z‐point axial modes are singular in having CF of alternating sign in consecutive structural units in c direction. Such a “c‐direction‐charge‐transfer” has been shown previously to be an effective screening mechanism in La2CuO4. Indeed, we find a drastic renormalization of the plane‐oxygen Ag mode at the Z point (Ag(O23;Z)) in O7 (oxygen ions in neighboring planes vibrating in‐phase), at least in the adiabatic approximation used here. In the insulating phase this mode exhibits, on the other hand, very large changes of the potential at the ion sites, whereas its renormalization is moderate only. The reason for this behaviour is that in the insulating phase in case of a two‐dimensional electronic structure the charge transfer (screening) is restricted locally in the structural unit and long‐range charge transfer is not possible as in the metal. However, a strong suppression of screening for this mode can also be expected for the metallic phase in O7 in case non‐adiabatic electron‐phonon coupling would be important. The Ag (O23;Z)‐mode thus seems to be by far the most interesting mode in O7. These features are directly related to the layered structure of the HTSC compounds considered here. The O4‐axial‐breathing modes show significant renormalizations too, and are characterized by plane‐chain charge transfer. Moreover, besides the O23‐ and O4‐modes, the yttrium modes appear to be important too. In addition to the phonon‐dispersion curves, we present values for the CF amplitudes and screened site‐potential changes at the copper‐and oxygen ions. Finally, we give transverse effective charges and dielectric constants for the insulating phase (O6) as calculated within our formalism.

The associative nature of lower rank coal

Initial volumetric swelling in tetrahydrofuran of pyridine-unextracted parts from subbituminous coal and lignite showed no dependence of their concentration, and was smaller than that of their pyridine extracts. These results are opposite to those obtained from high volatile bituminous coals and coincide with predictions for the cross-linked network model of coal. However, when ionic forces in these coals were reduced by acid washing or O-alkylation, these coals showed the same associative nature as did high volatile bituminous coals. Swelling kinetics were analysed on the basis of associative equilibria controlled by the ionic forces. It was concluded that solvation of the ionic forces was the rate determining step of volumetric swelling of lower rank coal rather than solvent diffusion into the coal, although diffusion has been proposed to be the most important factor in swelling.

Adsorption on polymer-coated fused-silica capillary electrophoresis columns using selected protein and peptide standards

Three series of basic proteins and peptides were selected for use in studying the adsorption behavior of fused-silica capillary electrophoresis columns. A comparative study of untreated and treated fused-silica columns was done. The polymers used as coating materials ranged from very hydrophobic to very hydrophilic. The average efficiency of weakly hydrophilic Ucon-coated capillaries for basic proteins was over 1 million theoretical plates at a buffer pH of 4.8. For this coating, it was found that the maximum column efficiency was obtained at a film thickness of approximately 100 nm. It was easily seen that both ionic and hydrophobic interaction forces can play important roles in protein adsorption onto the capillary walls. Furthermore, strongly hydrophilic polymer coatings may possibly lead to hydrogen-bonding interactions, which decrease column efficiency. Studies have been conducted using two series of polypeptides with varying chain lengths. One series was used to study the effect of polypeptide chain length on retention behavior. Efficient separations of bioactive peptide drugs on Ucon-coated columns were achieved. The results indicate that high efficiency and resolution of basic peptides tested can be realized on columns modified with weakly hydrophilic polymers at a pH value of about 5.

Lattice dynamics of La 2NiO 4 in the charge fluctuation model

The lattice dynamics of La 2NiO 4 is calculated in the framework of a description of the electronic density response recently applied to the high-temperature superconductors (HTSC). The local part of the density response is approximated by a proper ab initio ionic model of rigid ions to represent the effects of the ionic forces in the crystal. The structure parameters and the phonon dispersion curves are investigated in this model and are compared with recent interpretations of the experimental data. Additionally, nonlocal contributions to the density response in the form of charge fluctuations at the ions are considered and their influence on the dispersion is discussed. From our results we find that some corrections of the current interpretation of the experimental data may be appropriate. Finally, the importance of phonon-induced charge fluctuations for the HTSC is emphasized.

Selective neuronal cell attachment to a covalently patterned monoamine on fluorinated ethylene propylene films.

The patterned covalent surface addition of a monoamine to fluorinated ethylene propylene films (FEP) controls both cellular attachment and differentiation in defined media conditions. A radio frequency glow discharge (RFGD) process was used to replace FEP surface fluorine atoms with hydroxyl groups. The primary amine was then covalently attached by polymerizing aminopropyl-triethoxysilane (APTES) via the hydroxyl functionalities. The selective attachment of cells to the APTES regions was determined to be dependent upon the initial adsorption of albumin to the patterned FEP membrane. Albumin was determined to enhance cellular attachment to the APTES regions and prevent attachment to the unmodified FEP areas for both an NB2a neuroblastoma cell line and primary rat endothelial cells. If albumin were not preadsorbed onto the membrane, selective attachment to the modified regions would not occur. Radiolabeling albumin with 125I demonstrated the preference of albumin for adsorption onto the monoamine surface where the cells preferentially attached. Both hydrophobic and ionic forces contributed to the adsorption process. Although selective cellular attachment to the patterned APTES regions could be achieved by albumin preadsorption to the surface, the neuroblastoma cells did not significantly differentiate unless additional serum components were supplemented to the media.

The crystal structure of the addition compound of decavanadate and guanidine

NaVO 3 reacts with guanidine hydrochloride in aqueous solution to afford the title complex. The X-ray single crystal structure of the complex reveals that the molecular structure consists of a V 10O 6− 28 polyanion 10 VO 6 distorted octahedra, which form two octahedra sharing an edge. Six protons of each decavanadic acid are captured by guanidine. In the crystal, the isopolydecavanadate anion, guanidine and the crystal water are linked together by ionic forces and hydrogen bonding.

Electrostatic calculations on colloids with planar and spherical charge distributions

A model of the electrical double layer has been derived by assuming that a fraction of double layer counter-ions remains associated with the charged surface (Nature 1984 310: 396). The magnitude of this fraction, i.e. the degree of counter-ion association, can be derived from experimental data. E.g. the electrostatic repulsions in clay gels can be quantitatively explained with the degree of counter-ion association that is independent of plate separation. The dependence of the degree of counter-ion association on bulk ionic strength is obtained from Lubetkin'set al data (Philos Trans R Soc London (1984) A311∶133), which permits the derivation of a new limiting law that predicts large and ionic strength independent repulsive forces at close surface separations. Such forces have been usually attributed to “hydration forces”. Within the DLVO framework the theory perdicts reasonable values of the equilibrium separations of swelling clays with divalent counter-ions. The Stern potentials of clays are also consistently accounted for. New calculations for spherical surfaces predict that Stern potentials can have maxima at certain ionic strengths. These maxima, which are often observed in the case of polymer latices, disappear in the limit of infinite radius.

Electronic structure studies of the differences in ferroelectric behavior of batio3and PbTiO3

Abstract We have performed extensive self-consistent total energy calculations for PbTiO3 and BaTiO3 in order to better understand the origin of the ferroelectric instability in perovskites and the reasons for different ferroelectric behavior in the two materials. Physically reasonable ferroelectric instabilities are found for both materials at the experimental volume. However, the results are quite sensitive to volume and typical local density approximation (LDA) errors in volume can lead to significant errors in the potential surface for ferroelectric distortions. The sensitivity of the perovskite ferroelectrics to defects and chemistry, as well as the sensitivity to approximations in first principles calculations, stems from the delicate near-cancellation of long-range ionic forces which favor the instability with short-range repulsions that inhibit the ferroelectric state. The spontaneous strain is also an important feature of ferroelectrics, and we find that the large tetragonal strain stabilizes the tetragonal structure in PbTiO3. The differences in behavior between BaTiO3 and PbTiO3 stem from their different electronic structures: The Pb 6s and O 2p states are strongly hybridized in PbTiO3, whereas Ba is essentially a fully ionic Ba2+ ion in BaTiO3. In both materials the Ti 3d states hybridize with O 2p, and it is the Ti-O interaction that is responsible for the ferroelectric instability. We also discuss the nature of the ferroelectric phase transition, including effects of electrical boundary conditions.