Model Of Intermolecular Interactions Research Articles

1-methyl-3-propylimidazolium chlorideにおける分子間相互作用のPottsモデル

1-methyl-3-propylimidazolium chlorideにおける分子間相互作用のPottsモデル

Insight into the Structure of Photosynthetic LH2 Aggregate from Spectroscopy Simulations

Using the electrostatic model of intermolecular interactions, we obtain the Frenkel exciton Hamiltonian parameters for the chlorophyll Qy band of a photosynthetic peripheral light harvesting complex LH2 of a purple bacteria Rhodopseudomonas acidophila from structural data. The intermolecular couplings are mostly determined by the chlorophyll relative positions, whereas the molecular transition energies are determined by the background charge distribution of the whole complex. The protonation pattern of titratable residues is used as a tunable parameter. By studying several protonation state scenarios for distinct protein groups and comparing the simulated absorption and circular dichroism spectra to experiment, we determine the most probable configuration of the protonation states of various side groups of the protein.

Coherent and Incoherent Interactions between Cofacial Π-Conjugated Oligomer Dimers in Macrocycle Templates

The interactions between two π-conjugated oligomers templated in molecular scaffolds are revealed as a function of separation and orientation, providing models of intermolecular interactions in bulk organic semiconductor materials. For a variety of dimer geometries (acyclic and macrocyclic) of the same model oligomer, no change in fluorescence spectra, fluorescence dynamics, or low-temperature single-molecule emission characteristics is observed. A small red-shift and slowing of fluorescence in the most closely spaced macrocyclic dimer structure is thought to arise both due to an intramolecular solvatochromic shift as well as from weak intramolecular aggregate formation. No corresponding effect is observed in bulk films of the acyclic model oligomer, implying the absence of intermolecular aggregate or excimer formation due to random relative dipole orientations. The largest effect of intramolecular geometry of the model dimer structures is seen in transient fluorescence depolarization, where an open ring geometry leads to rapid depolarization, compared to the corresponding macrocycle, due to the presence of a range of molecular transition dipole moment orientations. Self-assembled monolayers of the molecules on HOPG investigated by scanning-tunneling microscopy further illustrate the conformational variability of the open dimers in contrast to the fixed conformation of the closed dimers.

Wetting on a spherical wall: Influence of liquid-gas interfacial properties

We study the equilibrium of a liquid film on an attractive spherical substrate for an intermolecular interaction model exhibiting both fluid-fluid and fluid-wall long-range forces. We first reexamine the wetting properties of the model in the zero-curvature limit, i.e., for a planar wall, using an effective interfacial Hamiltonian approach in the framework of the well known sharp-kink approximation (SKA). We obtain very good agreement with a mean-field density functional theory (DFT), fully justifying the use of SKA in this limit. We then turn our attention to substrates of finite curvature and appropriately modify the so-called soft-interface approximation (SIA) originally formulated by Napiórkowski and Dietrich [Phys. Rev. B34, 6469 (1986)] for critical wetting on a planar wall. A detailed asymptotic analysis of SIA confirms the SKA functional form for the film growth. However, it turns out that the agreement between SKA and our DFT is only qualitative. We then show that the quantitative discrepancy between the two is due to the overestimation of the liquid-gas surface tension within SKA. On the other hand, by relaxing the assumption of a sharp interface, with, e.g., a simple "smoothing" of the density profile there, markedly improves the predictive capability of the theory, making it quantitative and showing that the liquid-gas surface tension plays a crucial role when describing wetting on a curved substrate. In addition, we show that in contrast to SKA, SIA predicts the expected mean-field critical exponent of the liquid-gas surface tension.

A transferable electrostatic model for intermolecular interactions between polycyclic aromatic hydrocarbons

This work builds on our recently published anisotropic potential for polycyclic aromatic hydrocarbons (PAH) [T.S. Totton, A.J. Misquitta, M. Kraft, J. Chem. Theory Comput. 6 (2010) 683] by developing a new transferable electrostatic model for PAH molecules. Using this model, the atomic charge parameters used in the PAH anisotropic potential may be rapidly calculated from a set of predefined parameters rather than from molecule-specific ab initio calculations. The importance of the out-of-the-plane quadrupolar moments is highlighted and they are used as the basis for an accurate and transferable electrostatic model for PAHs. This model exhibits an r.m.s. deviation of 1.7kJmol-1 - an order of magnitude less than previous models.

Shear-thickening in aqueous surfactant-associative thickener mixtures

Associative thickeners represent an important class of rheology modifiers used in waterborne coatings. Understanding molecular level interactions between associative thickeners and surfactants has been the subject of a number of prior studies. Our recent studies focused on the behavior of a hydrophobically modified, aminoplast ether (HEAT) associative thickener and a highly hydrophobic ethoxylated octylphenol surfactant in aqueous solution. Aqueous blends of these two materials exhibit shear-thinning, as well as rarely reported, transient, shear-induced thickening behavior. In addition, the same compositions exhibit both thixotropy and antithixotropy. The shear-induced thickening is shown to be the result of transient aggregated structures formed under shear. Addition of a third component, β-cyclodextrin—a molecule known to disrupt hydrophobic associations—to the mixture helped us advance the understanding of the nature of associative thickener–surfactant interactions that cause the transient shear-thickening behavior. Results indicate that, while overall viscosity of the HEAT/surfactant mixtures is decreased by β-cyclodextrin, the shear-induced thickening is unaffected. An intermolecular interaction model to describe the transient thickening mechanism is presented.

Intermolecular repulsive–dispersive potentials explain properties of impurity spectra in soft solids

Abstract Behavior of optical impurity spectra in van der Waals glasses is rationalized with the aid of a two-particle Lennard–Jones model of intermolecular interactions. Simple mathematical manipulations with the 6–12 potential yield inhomogeneous distribution functions (IDFs) of zero phonon lines (ZPLs) at different compressions, and the expressions for wavelength dependent pressure shift coefficients of ZPLs (or holes), local phonon frequencies, and linear and quadratic coupling constants. Experimentally, the ZPL to phonon wing intensity ratios (Huang–Rhys or Debye–Waller factors) are measured for bacteriochlorophyll a in glass-forming triethylamine 5 K. Enhancement of coupling strength with increasing transition wavelength is observed, in qualitative agreement with the model.

Molecular dynamics simulation based evaluation of glass transition temperatures of polystyrene in the presence of carbon dioxide

This paper develops a detailed molecular dynamics (MD) simulation model to study the glass transition temperature (Tg) of a finite polystyrene (PS) system in the presence of high pressure carbon dioxide (CO2). Validated inter-atomic potentials for pure PS and CO2 are used for these simulations. Specific parameters and combinations rules are introduced to accurately model the intermolecular interactions between PS and CO2. The intermolecular interaction model has a strong effect on the Tg of the PS–CO2 system. The MD model comprises PS and CO2 molecules confined in a finite walled system to manifest the effects of high pressure CO2. The effectiveness of the simulation model is established by comparison with experimental free-volume data from positronium annihilation lifetime spectroscopy (PALS). An important outcome of this study is the identification of clearly demarcated regions for bulk and surface analysis. Physical properties such as density, free volume, segmental motion across the thickness and end group mobility are also studied to gain insight into the polymer dynamics. As is expected, the simulations show that the presence of high pressure CO2 reduces the Tg of PS significantly due to an increase in chain mobility. Additionally, the simulation data show a remarkable effect of CO2 on the extent and characteristics of the surface layer.

Interaction of Alcohols with [Val5]angiotensin in Alcohol−Water Mixtures

Intermolecular solvent-solute NOE experiments have been used to probe interactions of various alcohols with the peptide hormone [val(5)]angiotensin II at 0 degrees C. It is found that these NOEs are detectable but dependent on the kind of alcohol present and the conformation of the peptide. Solvent-solute NOEs in 100% methanol and 89% methanol-water are basically those predicted by a hard sphere model for intermolecular spin dipole interactions. NOEs at the peptide backbone (N-H, C alpha-H) protons in 25% methanol-water and 36% ethylene glycol-water mixtures indicate that alcohol interactions near these groups are also adequately described by this model. However, in 35% ethanol-water, interactions of alcohol methyl protons with the peptide result in unexpectedly negative NOEs, probably signaling that peptide-alcohol interactions in this solvent take place on a significantly slower time scale than that defined by mutual diffusion of these species. Some side chain-alcohol interactions result in NOEs up to 8 times larger than expected. Possible reasons for these enhanced effects are discussed.

Charge separation in Na+Cl-(H2O) n clusters in water vapors. 1. Intermolecular interactions

Charge separation in “soft” nanoparticles composed of water molecules, as well as sodium and chlorine ions, is studied by computer simulation. The detailed model of intermolecular interactions that includes, in addition to Coulomb, exchange, and dispersion forces, many-particle polarization and covalent interactions, as well as the effect due to the transfer of excess ion charges and influence of ion field on molecular interactions, is constructed. Model potentials are calibrated using experimental data on the free energy and enthalpy of the addition of vapor molecules to the hydration shells of ions, as well as the data of quantum-chemical calculations for stable cluster configurations and the vibration frequency of interionic bonds. The allowance for many-particle interactions makes it possible to improve the agreement between experimental and quantum-chemical data by more than an order of magnitude. The disregard for many-particle interactions leads to the significant overestimation of cluster stability.

Mass-spectrometric identification of interaction sites for cytochrome P450 2b4/nadph cytochrome P450 reductase

We determined the interaction sites of the cytochrome P450's protein-partners: 2B4 (d-2B4) and NADPH-cytochrome P450 of reductase (d-Fp). While in operation, these proteins are forming the complexes. We used 4-4'-dithio(bisphenyl)azide linker for non-specific covalent coupling of d-2B4 complexes with d-Fp in Emulgen-913-monomerized system. Covalently-linked peptides in this complex were identified with ESI-MS/MS. Several sites of these proteins' binding with each other were revealed. Based on them, a model of intermolecular protein interactions was created. The model includes 5 cross-linker-stabilized contact sites of d-2B4 with d-Fp involving the following peptides of d-2B4 and d-Fp: (1) d-2B4423-433 and d-Fp 102-109; (2) d-2B4324-336 and d-Fp570-585; (3) d-2B4327-336 and d-Fp452-464; (4) d-2B4 192-197 and d-Fp456-464; (5) d-2B4 134-139 and d-Fp406-425. Herein, in the latter two cases, the peptides of d-Fp are located in their inter-domain slit and stabilize protein-protein complex via nanoprobe cross-linker; therefore, the formation of d-2B4/d-Fp complexes in these sites may involve aminoacid residues d-Fp456-464 and d-Fp406-425 surrounding inter-domain slit.

Development of a flow cytometric co‐immunoprecipitation technique for the study of multiple protein—protein interactions and its application to T‐cell receptor analysis

Co-immunoprecipitation is the classical approach for investigating protein-protein interactions. Analysis is generally conducted using the Western blot approach. We set out to investigate whether flow cytometry was a feasible alternative to Western blotting. Using the TCR-CD3 complex as a model for intermolecular interactions in the MA5.8 cell line, FLAG-tagged CD3zeta-scFv fusion proteins could be captured on anti-FLAG coupled beads and associated TCRbeta molecules could be detected by flow cytometry. This association was abrogated by mutations to the CD3zeta transmembrane domain. Using multicolor flow cytometry, TCRbeta, CD3epsilon, and the scFv region of the CD3zeta fusion molecule could all be detected from a single sample. This multicolor analysis was then applied to demonstrate the importance of correct lysis conditions for extraction of the TCR complex. In summary, this flow cytometric immunoprecipitation technique is a feasible alternative to classical co-immunoprecipitation analysis technique and offers many potential advantages including rapid analysis with increased target sensitivity, reduced technical demands, amenable to multiple protein analysis from a single sample, and provides a framework that may facilitate the development of high throughput analytical assays investigating protein-protein interactions.

Proton disorder and energetics of gas hydrate frameworks

A method of combinatorial optimization of gas hydrate frameworks based on the discrete model of intermolecular interaction is proposed. The stability of a large number of expected frameworks of high-pressure gas hydrates is analyzed.

A high energy barrier to charge recombination in ionized water vapor

A quantitative kinetic theory has been developed to explain the results of experimental observation of the abnormally intense clustering of water molecules in the vapor phase in an ionizing radiation field at a moderate dose rate. The recombination is impeded because of the hydration of ion pairs and the formation of an abnormally high energy barrier (∼100 k B T) in molecular clusters. The buildup of the clusters of water molecules stabilized in the electric field of ion pairs results in a dramatic enhancement of the effect of ionizing radiation on the electric properties of the vapor. The values of the coefficients to the rate equation of ionization-recombination equilibrium were calculated on the molecular level by computer simulation of the hydration of the H3O+(H2O) n OH− ion pair using the detailed model of intermolecular interactions.

Collective dynamics and molecular interactions in liquidCO2by inelastic neutron scattering and computer simulations

We report an inelastic neutron scattering determination of the dynamic structure factor of liquid carbon dioxide in the wave-vector range $3<Q<17\text{ }{\text{nm}}^{\ensuremath{-}1}$ and molecular dynamics simulations performed using several site-site intermolecular interaction models. The comparison of neutron and simulation dynamical spectra allows effective model-potential selection. The good performance of some of the ${\text{CO}}_{2}$ anisotropic interaction models enables a thorough investigation of the collective properties, taking full advantage of the direct access that simulations provide to the purely translational modes of a molecular liquid. Center-of-mass collective excitations of liquid ${\text{CO}}_{2}$ can be fully described through a viscoelastic modeling of the second-order memory function if a free $Q$ dependence of the parameters is allowed. The system behaves in a hydrodynamiclike way up to about $Q\ensuremath{\simeq}5\text{ }{\text{nm}}^{\ensuremath{-}1}$, where the thermal relaxation has a dominant role. A rather different situation is found at higher $Q$, ruled by both structural and dynamical effects, namely, the rapid growth of the static structure peak, the increased damping of the Brillouin lines, and the shortening of the relaxation time. Acoustic excitations propagate up to $Q\ensuremath{\simeq}14\text{ }{\text{nm}}^{\ensuremath{-}1}$, while beyond this value a transition to overdamped modes takes place.

Partial molar volume of methanol in water: Effect of polarizability

The available pairwise additive intermolecular interaction models used so far in simulations in combination with common combining rules do not seem to be able to reproduce the most distinct feature of aqueous solutions of alcohols, the minimum of the partial molar volume at low alcohol concentrations. Nonetheless, this fundamental failure seems to have been paid little attention to, partly because of very high requirements for accuracy and, hence, CPU time of simulations. As an attempt to go beyond empirical combining rules and account in a more physical and yet simple way for the cross interactions, a feasibility study has been undertaken using a polarizable model of water in molecular simulations of the water–methanol mixture at ambient conditions. It turns out that the inclusion of polarizability may qualitatively change the behavior of the mixture bringing the result in agreement with experiment.

Charge separation in water molecule clusters under thermal fluctuations: 1. Intermolecular interactions

A detailed model of intermolecular interactions in water molecule clusters is developed that makes it possible to describe their disintegration to ions under conditions of finite temperatures by the stochastic simulation methods. In this model, the Hamiltonian in explicit form includes Coulomb, dispersion, exchange, and polarization interactions; many-particle covalent interactions and hydrogen bonds; the interaction of induced dipoles; charge transfers from ions to molecules; and the recombination of counterion charges, as well as the effect of an ion field on the unpaired interactions of molecules. The model is consistent with experimental data on the free energy and entropy of ion hydration in water vapors and the free energy of the hydration of a recombined ion pair.

Solvent smectic order parameters from solute nematic order parameters

In liquid crystals, while the second and fourth rank orientational order parameters characterizing a nematic phase can be experimentally determined via several techniques, there is no straightforward experiment rendering the positional order parameters characterizing a smectic A phase. This work illustrates a novel method to estimate the positional order parameters of a smectogenic liquid crystal solvent from knowledge of the orientational order parameters of a number of solutes dissolved therein. The latter order parameters can be experimentally determined via liquid crystal NMR spectroscopy. These data can be then analyzed with a statistical-thermodynamic density functional theory, whose basic ingredient is a model for solute-solvent intermolecular interactions. Its parametrization and the subsequent fitting procedure eventually permit one to obtain the positional order parameters of the solvent besides the positional-orientational distribution function of the solutes. The method is applied to the smectogen 4,4(')-di-n-heptyl-azoxybenzene, in which the solutes 1,4-dichlorobenzene and naphthalene have been dissolved. With the help of this exploratory practical example, pros and cons of the method are pointed out and further developments prospected.

Bistability in Fc-PTM Crystals: The Role of Intermolecular Electrostatic Interactions

Fc-PTM is a valence tautomeric radical, where the ferrocene (Fc) group, a good electron donor, is linked by an ethylenic spacer to a perchlorotriphenylmethyl radical (PTM(*)), a good electron acceptor. In solution this compound exists mainly in the neutral Fc-PTM(*) form which can be photoexcited through an intramolecular electron transfer to the zwitterionic Fc(+*)-PTM(-) form. By contrast, in crystals of Fc-PTM at room temperature both the neutral and the zwitterionic forms coexist, pointing to a true bistability phenomenon. We rationalize these findings accounting for the role of intermolecular electrostatic interactions in Fc-PTM crystals. In fact the energy of the zwitterionic Fc(+*)-PTM(-) form is lowered in the crystal by attractive electrostatic intermolecular interactions and the cooperative nature of these interactions explains the observed coexistence of neutral Fc-PTM(*) and zwitterionic Fc(+*)-PTM(-) species. The temperature evolution of Mossbauer spectra of Fc-PTM is quantitatively reproduced adopting a bottom-up modeling strategy that combines a molecular model, derived from optical spectra of Fc-PTM in solution, with a model for intermolecular electrostatic interactions, supported by quantum-chemical calculations. Fc-PTM then offers the first experimental demonstration of bistability induced by electrostatic interactions in crystals of valence tautomeric donor-acceptor molecules.

Magnetic moment oscillation in ammonium perchlorate in a DC SQUID-based magnetic resonance experiment

In this work we describe experimental results in which a DC SQUID (superconducting quantum interference device) is used as free induction decay detector. Measurements of a solid ammonium perchlorate (NH 4ClO 4) sample were performed, in zero field, at 4.2 K. Unexpected magnetic moment oscillations were detected at 1.5 kHz. The computation of the magnetic fields suggests that the proton nuclear magnetic resonance may explain the measured resonance, considering reorientation of the ammonium group by quantum tunneling of protons and a magnetic proton dipole–dipole intermolecular interaction model.