Attractive Interaction Energy Research Articles

Control of the Structure of Self-Spreading Lipid Membrane by Changing Electrolyte Concentration

We have controlled the structure of self-spreading lipid bilayer membranes prepared on surface-oxidized silicon substrates by changing electrolyte concentration. Analysis of the fluorescence intensity, considering the optical interference effect, clarified the stacking structure of the lipid membrane. By varying the electrolyte concentration, we can vary the number of single multilamellar lobes adsorbed on the underlying self-spreading bilayer. This dependence of the stacking ability on the electrolyte concentration was investigated on the basis of changes in the bilayer-lobe interaction energies, including van der Waals, electrostatic double layer, and hydration interaction energies. Theoretical estimation suggests that the observed electrolyte concentration dependence can be explained by the combination of the van der Waals attractive interaction energy and the repulsive double-layer interaction energy.

Control of the interaction in a Fermi-Bose mixture

We control the interspecies interaction in a two-species atomic quantum mixture by tuning the magnetic field at a Feshbach resonance. The mixture is composed by fermionic 40K and bosonic 87Rb. We observe effects of the large attractive and repulsive interaction energy across the resonance, such as collapse or a reduced spatial overlap of the mixture, and we accurately locate the resonance position and width. Understanding and controlling instabilities in this mixture opens the way to a variety of applications, including formation of heteronuclear molecular quantum gases.

Theoretical Evidence of PtSn Alloy Efficiency for CO Oxidation

The efficiency of PtSn alloy surfaces toward CO oxidation is demonstrated from first-principles theory. Oxidation kinetics based on atomistic density-functional theory calculations shows that the Pt3Sn surface alloy exhibits a promising catalytic activity for fuel cells. At room temperature, the corresponding rate outstrips the activity of Pt(111) by several orders of magnitude. According to the oxidation pathways, the activation barriers are actually lower on Pt3Sn(111) and Pt3Sn/Pt(111) surfaces than on Pt(111). A generalization of Hammer's model is proposed to elucidate the key role of tin on the lowering of the barriers. Among the energy contributions, a correlation is evidenced between the decrease of the barrier and the strengthening of the attractive interaction energy between CO and O moieties. The presence of tin modifies also the symmetry of the transition states which are composed of a CO adsorbate on a Pt near-top position and an atomic O adsorption on an asymmetric mixed PtSn bridge site. Along the reaction pathways, a CO2 chemisorbed surface intermediate is obtained on all the surfaces. These results are supported by a thorough vibrational analysis including the coupling with the surface phonons which reveals the existence of a stretching frequency between the metal substrate and the CO2 molecule.

Role of the Fermi Surface in Adsorbate−Metal Interactions: An Energy Decomposition Analysis

We present the result of a fragment-based energy decomposition analysis on some molecule-surface interactions. The analysis allows us to quantify the Pauli repulsion, its relief, and the attractive orbital interaction energy. In a metal, the existence of incompletely occupied energy bands causes significant relief of the Pauli repulsion due to escape of antibonding electrons to unoccupied states at the Fermi energy. This is the key electronic structure feature of metals that causes metal-molecule bond energies to be stronger and dissociation barriers of chemisorbed molecules to be much lower than those in comparable systems with no or one metal atom. As examples, we discuss the energy decomposition for the activated dissociation of hydrogen on the Cu surface and its unactivated dissociation on Pd, and for the (activated) chemisorption of N2 on W. We show that in all cases the relief of Pauli repulsion is of crucial importance for the chemisorption energy and for the low (or nonexistent) dissociation barriers. The barrier to the chemisorption well for nitrogen on tungsten is clearly related to a late relief of the Pauli repulsion. The relief of Pauli repulsion is important in lowering the barrier to dissociation of H2 on both Cu and Pd, but the difference in barrier heights for Cu and Pd appears to not be due to stronger relief of Pauli repulsion on Pd but primarily to the Pauli repulsion itself being stronger on Cu than on Pd, the relief energy being quite comparable on the two metals.

Theoretical investigation of the chemical bonds in metal chelates as emitting material for OLED

Geometries of ground (S 0) states of mer-tris(8-hydroxyquinolinato)metal (Mq3, M = Al 3+, Ga 3+, In 3+, Tl 3+) are optimized by B3LYP/6-31G(d) methods. In order to investigate the distribution for unequal individual ligands in mer-Mq3 as key materials for OLED, the bonding interactions either between the metal fragment Mq2 and a single ligand q have been analyzed with the energy decomposition scheme. The bonding analysis has been carried out at the BP86 level using TZ2P quality basis functions with small core. All the calculated results suggest that the HOMOs for Mq3 are mainly localized on A-quinolate ligand, which are responsible to the optical characteristics. The calculated phenomena about optical and structural properties of mer-Mq3 can be simply traced back to the lowest electrostatic attractive interaction energy between fragments A-quinolate ligand and the Mq2 due to the special arrangement, resulting in the easy of geometry relaxation for excited state or interaction with metal atoms.

Molecular Dynamics Study of the Methanol Effect on the Membrane Morphology of Perfluorosulfonic Ionomers

The membranes of a perfluorosulfonic acid polymer swollen in 10-80 wt % methanol solution were investigated to elucidate the methanol effect on their morphologies, such as size of the solvent cluster, solvent location, and polymer structure, by using isothermal-isobaric molecular dynamics simulations. In higher methanol concentrations, we found less-spherical solvent aggregation and a more spread polymer structure because of the ampholytic nature of methanol. The partial radial distribution functions between solvent oxygen and fluorocarbons, which are composed of the main chain, clearly show that methanol is located closer to the polymer matrix than water. On the other hand, water is preferentially located in the vicinity of an acidic headgroup, SO(3)(-), compared with methanol, although both have similar attractive interaction energies to the acidic group. Furthermore, we discussed solvent dynamics and hydrogen bonding between sulfonic oxygen and solvent O-H groups.

MC simulation of a physical gel

The sol–gel transition of a solution of linear polymer chains interacting at low temperatures through the formation of triple helices is studied by means of a fully developed dynamic MC algorithm that incorporates excluded volume conditions. The algorithm includes local movements, to induce dynamic behaviour of the polymer system, and a small set of parameters (helix seeds fraction, polymer volume fraction, gelation strength parameter) that control the final structure of the network. The sol–gel transition is a temperature driven process that we accomplish in our simulation by changing the polymer attractive interaction energy. Results obtained for this model are in good agreement with experimental data of sol–gel transitions in gelatine gels. Therefore, the model can be further used to gain local and global information of the sol–gel process, which can be used as a guide for interpreting experimental results.

Macro- and Nanoscale Observations of Adhesive Behavior for Several E. coli Strains (O157:H7 and Environmental Isolates) on Mineral Surfaces

Subsurface biobarriers can be conceived to attenuate the migration of pathogens by adhesion to mineral surfaces. Candidate biobarrier materials of varied surface characteristics (dolomite, alpha-alumina, silica, pyrophyllite, and Pyrax (a composite form of pyrophyllite, mica, and silica)) were tested for Escherichia coli adhesive capacity in macroscale continuous-flow columns. Atomic force microscopy (AFM) was used to determine nanoscale interaction energies. Predicted attractive interaction energies correlated well with macroscale adhesive behavior for tested E. coli strains. AFM measurements confirmed ExDLVO model predictions of attachment in the primary minima for E. coli O157:H7 and two environmental isolates E. coli (UCFL339 and UCFL-348) with MOPS conditioned Pyrax. In macroscale column experiments, pyrophyllite and Pyrax demonstrated significantly higher bacterial retention, higher deposition coefficients and lower initial cell breakthrough values for E. coli O157:H7 than did alpha-alumina, silica, or dolomite (pyrophyllite, 0.93, 3.56 h(-1), 3.2% ODo; Pyrax, 0.95, 3.73 h(-1), 2.8% ODo; alpha-alumina, 0.74, 1.60 h(-1), 33% ODo; silica, 0.63, 0.43 h(-1), 73% ODo; and dolomite, 0.33, 0.17 h(-1), 89% ODo, respectively). Bacterial hydrophilicity impacted cell retention in Pyrax columns with the relatively hydrophobic E. coli isolate UCFL-339 (0.99, 6.13 h(-1), 0.4% ODo) retained better than the more hydrophilic E. coli isolate UCFL348 (0.94, 3.70 h(-1), 3.6% ODo). The strong adhesive behavior of Pyrax was attributed to the hydrophobic (deltaGiwi = -32.4 mJ/m2) pyrophyllite component of the mineral. Vicinal water appears poised between the bacterial and the mineral surface during initial attachment. Overall, observed behavior of the various E. coli strains and the selected mineral surfaces was consistent with surface analyses, conducted at both the macro- and nanoscale.

Metal−Olefin Interactions in M(CO)5(cycloolefin) (M = Cr, Mo, W; Cycloolefin = Cyclopropene to Cyclooctene): Strain Relief and Metal−Olefin Bond Strength

Density functional theory calculations on the title compounds indicate that metal−olefin bond strengths follow the trend for cyclic olefin strain energies. It was found, however, that the proportionality between metal−olefin bond energy and strain energy is not evenly distributed throughout the olefin series. For instance, cyclopropene and cyclobutene are expected to bind to the metal much more weakly than would be anticipated on the basis of their strain energies. A bond energy decomposition analysis reveals that the metal−olefin interaction is responsible for strain relief in the cycloolefins by means of the rehybridization of the olefinic carbons. However, the geometrical changes accompanying this rehybridization, namely CC elongation and olefin pyramidalization, involve an energetic cost that is paid at the expense of the bonding interaction energy. Nonpyramidalized strained olefins such as cyclopropene and cyclobutene undergo large conformational changes, to the detriment of their large attractive interaction energies. It was found that a cyclic olefin that is already deformed, such as trans-cyclooctene, interacts strongly with a metal to relieve strain but does not suffer much energy-costly reorganizations. This, thus, constitutes an energy benefit to the metal−trans-cyclooctene bond strength.

Prediction of the Orientations of Adsorbed Protein Using an Empirical Energy Function with Implicit Solvation

When simulating protein adsorption behavior, decisions must first be made regarding how the protein should be oriented on the surface. To address this problem, we have developed a molecular simulation program that combines an empirical adsorption free energy function with an efficient configurational search method to calculate orientation-dependent adsorption free energies between proteins and functionalized surfaces. The configuration space is searched systematically using a quaternion rotation technique, and the adsorption free energy is evaluated using an empirical energy function with an efficient grid-based calculational method. In this paper, the developed method is applied to analyze the preferred orientations of a model protein, lysozyme, on various functionalized alkanethiol self-assembled monolayer (SAM) surfaces by the generation of contour graphs that relate adsorption free energy to adsorbed orientation, and the results are compared with experimental observations. As anticipated, the adsorbed orientation of lysozyme is predicted to be dependent on the discrete organization of the functional groups presented by the surface. Lysozyme, which is a positively charged protein, is predicted to adsorb on its 'side' on both hydrophobic and negatively charged surfaces. On surfaces with discrete positively charged sites, attractive interaction energies can also be obtained due to the presence of discrete local negative charges present on the lysozyme surface. In this case, 'end-on' orientations are preferred. Additionally, SAM surface models with mixed functionality suggest that the interactions between lysozyme and surfaces could be greatly enhanced if individual surface functional groups are able to access the catalytic cleft region of lysozyme, similar to ligand-receptor interactions. The contour graphs generated by this method can be used to identify low-energy orientations that can then be used as starting points for further simulations to investigate conformational changes induced in protein structure following initial adsorption.

Ultrafine Coal Cleaning using Selective Hydrophobic Coagulation

ABSTRACT Studies have shown that ultrafine hydrophobic materials such as coal and graphite can be selectively coagulated and separated from hydrophilic impurities without using oily agglomerants, flocculants, or electrolytes. This process, which is referred to as Selective Hydrophobic Coagulation (SHC), has been used in laboratory tests to significantly reduce the ash and sulfur contents of several ultrafine, run-of-mine coal samples. The selective coagulation occurs at ζ-potentials significantly higher than those predicted by the classical DLVO theory due to the presence of an attractive interaction energy between hydrophobic particles such as coal. To account for this additional attraction, the interaction energies for the coal-mineral system have been calculated using an extended DLVO theory that incorporates the hydrophobic interaction energy in addition to the traditional dispersion and the electrostatic energies. The results of these theoretical calculations correlate well with separation response obtained using the SHC process.

Theoretical study of intramolecular interaction energies during dynamics simulations of oligopeptides by the fragment molecular orbital-Hamiltonian algorithm method

We analyzed the interaction energies between residues (fragments) in an oligopeptide occurring during dynamic simulations by using the fragment molecular orbital-Hamiltonian algorithm (FMO-HA) method, an ab initio MO-molecular dynamics technique. The FMO method enables not only calculation of large molecules based on ab initio MO but also easy evaluation of interfragment interaction energies. The glycine pentamer [(Gly)(5)] and decamer [(Gly)(10)] were divided into five and ten fragments, respectively. alpha-helix structures of (Gly)(5) and (Gly)(10) were stabilized by attractive interaction energies owing to intramolecular hydrogen bonds between fragments n and n+3 (and n+4), and beta-strand structures were characterized by repulsive interaction energies between fragments n and n+2. We analyzed interfragment interaction energies during dynamics simulations as the peptides' geometries changed from alpha helix to beta strand. Intramolecular hydrogen bonds between fragments 2-4 and 2-5 control the geometrical preference of (Gly)(5) for the beta-strand structure. The pitch of one turn of the alpha helix of (Gly)(10) elongated and thus weakened during dynamics due to a shifting of the intramolecular hydrogen bonds, and enabled the beta-strand structure to form. Changes in interaction energies due to the intramolecular hydrogen bonds controlled the tendency toward alpha-helix or beta-strand structure of (Gly)(5) and (Gly)(10). Evaluation of interfragment interaction energies during dynamics simulations thus enabled detailed analysis of the process of the geometrical changes occurring in oligopeptides.

Theoretical studies of cooperativity effects in the ternary complexes of nitrous acid with ammonia and water

Theoretical MP2 and B3LYP studies of the structures, energetics and vibrational spectra of the ternary complexes of nitrous acid with the ammonia and water molecules are presented. Six stable structures for the 1:1:1 HONO/NH 3/H 2O complexes were found. The lowest energy complexes formed by the trans- and cis-HONO isomers have cyclic seven- and eight-membered structures in which the mediating water molecule is strongly bound to the OH group of trans-HONO and to the nitrogen atom of NH 3. In the other eight-membered cyclic structure (formed by cis-HONO), two six-membered structures (formed by trans- and cis-HONO) and the chain structure (formed by trans-HONO) the main contribution to the complex stabilization comes form the interaction between the OH group of HONO and the nitrogen atom of ammonia, however, the other two weak bonds formed by the H 2O molecule with NH 3 and HONO give also nonegligible contributions. For all stable complexes the attractive three-body interaction energy terms, (Δ E 3), are calculated. The strongest cooperativity effects, as determined by Δ E 3 values, occur for the seven and eight-membered cyclic complexes, in the six-membered structures the cooperativity is reduced due to the strong distortion of the hydrogen bonds in the smaller rings. The analysis of the cooperative effects have been also performed for the ternary HONO/H 2O/H 2O complexes and the results are compared with those obtained for the HONO/H 2O/H 2O ones.

ULTRAFINE COAL CLEANING USING SELECTIVE HYDROPHOBIC COAGULATION

ABSTRACT Studies have shown that ultrafine hydrophobic materials such as coal and graphite can be selectively coagulated and separated from hydrophilic impurities without using oily agglomerants, flocculants, or electrolytes. This process, which is referred to as Selective Hydrophobic Coagulation (SHC), has been used in laboratory tests to significantly reduce the ash and sulfur contents of several ultrafine, run-of-mine coal samples. The selective coagulation occurs at ζ-potentials significantly higher than those predicted by the classical DLVO theory due to the presence of an attractive interaction energy between hydrophobic particles such as coal. To account for this additional attraction, the interaction energies for the coal-mineral system have been calculated using an extended DLVO theory that incorporates the hydrophobic interaction energy in addition to the traditional dispersion and the electrostatic energies. The results of these theoretical calculations correlate well with separation response obtained using the SHC process.

Quantum chemical analysis of the chemical bonds in Mq3 (M = Al III, Ga III) as emitting material for OLED

Geometries of ground and first excited states of mer-tris(8-hydroxyquinolinato)metal (Mq3, M = Al III, Ga III) are optimized at B3LYP/6-31G(d) and CIS/6-31G level, respectively. In order to investigate the difference for individual ligands in mer-Mq3, the energy partitioning analysis has been carried out at the BP86 level using TZ2P basis functions for the bonding interactions between each fragment Mq2 and single ligand q. HOMO and LUMO distribution fashion can be traced back to the lowest electrostatic attractive and highest orbital interaction energy between fragments A-quinolate ligand and Mq2 and B-ligand and Mq2, respectively.

(2×1)-(1×1) phase transition on Ge(001): quasi-chemical approximation and Monte Carlo simulations

Abstract This paper deals with the (2 × 1)-(1 × 1) phase transition that has been observed on the Ge(0 0 1) surface at temperatures 950–1000 K. The transition is described in terms of ordering and disordering in (2 × 1) arrays of surface Ge dimers. An analytical statistical mechanical theory is presented in the framework of the quasi-chemical approximation. The dimer formation energy allows dimers to dissociate into monomers and the attractive interaction energy between dimers realizes the (2 × 1) ordered array of dimers. The conventional order parameter reproduces at least qualitatively well the experimentally observed drastic disordering with increasing temperature. On the contrary the monomer density remains fairy low and increases quite modestly with temperature around the transition point, which is not in favor to the dimer break-up mechanism for the phase transition. Combined with suitable Monte Carlo simulations, the phase transition can be characterized by exhaustive recombination of dimers triggered by generation of a small number of monomers.

Insights into the Structures, Energetics, and Vibrations of Monovalent Cation−(Water)1-6Clusters

This study details the interactions prevailing in aqueous clusters of monovalent alkali metal, ammonium, and hydronium cations. The calculations involve a detailed evaluation of the structures, thermodynamic energies, andIR spectra of several plausible conformers of M + .(H 2 O) 1 - 6 (M = Li, Na, K, Rb, Cs, NH 4 , H 3 O) clusters at the second-order Miller-Plesset (MP2) and density functional levels of theory. A detailed decomposition of the interaction energies has been carried out for complexes involving one or two water molecules using symmetry adapted perturbation theory. Some of the salient insights on the structures include the emergence of the second solvent shell even before the realization of the maximal coordination number of the cation. This effect was more pronounced in clusters involving the larger cations. The quantitative estimates of various components of the interaction energy indicate the predominance of electrostatic energies in the binding of these cations to water molecules. Interestingly, for all the hydrated alkali metal cation complexes, the contribution of electrostatic energy is almost the same as the total attractive interaction energy, whereas the sum of the induction and dispersion energies are almost canceled out by exchange-repulsion energy. However, the contribution of dispersion energies slowly starts increasing as the size of the cation increases and is quite substantial in case of the Cs + complexes. In the organic cations, the dispersion energies become significant, though not comparable to the electrostatic energies. In addition to the evaluation of the harmonic frequencies of -OH stretching mode of all the structures, the anharmonic frequencies were evaluated for the smaller clusters. As the size of the cation and the size of the water cluster increases, the red shifts associated with the -OH stretching mode progressively become larger for the alkali metal cation containing complexes. For the organic cation (NH 4 +, H 3 O + ) containing complexes, an opposite trend is observed. Compared to the isolated water monomer, the ratio of the infrared intensities of the asymmetric and symmetric -OH stretching modes is very small. However, this ratio progressively becomes larger as the size of the cation increases.

Metal-metal interactions in heterobimetallic d8-d10 complexes. Structures and spectroscopic investigation of [M'M' '(mu-dcpm)2(CN)2]+ (M' = Pt, Pd; M' ' = Cu, Ag, Au) and related complexes by UV-vis absorption and resonance Raman spectroscopy and ab initio calculations.

X-ray structural and spectroscopic properties of a series of heterodinuclear d(8)-d(10) metal complexes [M'M' '(mu-dcpm)(2)(CN)(2)](+) containing d(8) Pt(II), Pd(II), or Ni(II) and d(10) Au(I), Ag(I), or Cu(I) ions with a dcpm bridging ligand have been studied (dcpm = bis(dicyclohexylphosphino)methane; M' = Pt, M' ' = Au 4, Ag 5, Cu, 6; M' ' = Au, M' = Pd 7, Ni 8). X-ray crystal analyses showed that the metal...metal distances in these heteronuclear metal complexes are shorter than the sum of van der Waals radii of the M' and M' ' atoms. The UV-vis absorption spectra of 4-6 display red-shifted intense absorption bands from the absorption spectra of the mononuclear trans-[Pt(phosphine)(2)(CN)(2)] and [M' '(phosphine)(2)](+) counterparts, attributable to metal-metal interactions. The resonance Raman spectra confirmed assignments of (1)[nd(sigma)-->(n + 1)p(sigma)] electronic transitions to the absorption bands at 317 and 331 nm in 4 and 6, respectively. The results of theoretical calculations at the MP2 level reveal an attractive interaction energy curve for the skewed [trans-Pt(PH(3))(2)(CN)(2)-Au(PH(3))(2)(+)] dimer. The interaction energy of Pt(II)-Au(I) was calculated to be ca. 0.45 ev.

First‐principles study of inter‐nitrogen interaction energy of Cu(100)‐ c(2 × 2)N surface

AbstractEffective interaction energy among nitrogen atoms on Cu(100)‐c(2 × 2)N surface was obtained by a density functional plane‐wave pseudopotential calculation. For efficient calculation of metallic systems, a preconditioning method for the local potential in self‐consistent field iteration was proposed. Attractive interaction energy among nitrogen atoms consistent with a high‐temperature STM experiment was obtained. © 2002 Wiley Periodicals, Inc. Int J Quantum Chem, 2003

Metal Ion-Induced Lateral Aggregation of Filamentous Viruses fd and M13

We report a detailed comparison between calculations of inter-filament interactions based on Monte-Carlo simulations and experimental features of lateral aggregation of bacteriophages fd and M13 induced by a number of divalent metal ions. The general findings are consistent with the polyelectrolyte nature of the virus filaments and confirm that the solution electrostatics account for most of the experimental features observed. One particularly interesting discovery is resolubilization for bundles of either fd or M13 viruses when the concentration of the bundle-inducing metal ion Mg2+ or Ca2+ is increased to large (>100mM) values. In the range of Mg2+ or Ca2+ concentrations where large bundles of the virus filaments are formed, the optimal attractive interaction energy between the virus filaments is estimated to be on the order of 0.01 kT per net charge on the virus surface when a recent analytical prediction to the experimentally defined conditions of resolubilization is applied. We also observed qualitatively distinct behavior between the alkali-earth metal ions and the divalent transition metal ions in their action on the charged viruses. The understanding of metal ions-induced reversible aggregation based on solution electrostatics may lead to potential applications in molecular biology and medicine.