Microviscoelasticity of soft repulsive sphere dispersions: tracer particle microrheology of triblock copolymer micellar liquids and soft crystals

Tracer particle microrheology using diffusing wave spectroscopy-based microrheology is demonstrated to be a useful method to study the dynamics of aqueous Pluronic? F108 solutions, which are viewed as solutions of repulsive soft spheres. The measured zero-shear microviscosity of noncrystallizing micellar dispersions indicates micelle corona dehydration upon increasing temperature. Colloidal sphere thermal motion is shown to be exquisitely sensitive to the onset of crystallization in these micellar dispersions. High temperature dynamics are dominated by an apparent soft repulsive micelle-micelle interaction potential indicating the important role played by lubrication forces and ultimately micelle corona interpenetration and compression at sufficiently high concentrations. The measured microscopic viscoelastic storage and loss moduli are qualitatively similar to those experimentally observed in mechanical measurements on colloidal dispersions and crystals, and calculated from mode coupling theory of colloidal suspensions. The observation of subdiffusive colloidal sphere thermal motion at short time-scales is strong evidence that the observed microscopic viscoelastic properties reflect the dynamics of individual micelles rather than a dispersion of micellar crystallites.     

Trajectory study of supercollision relaxation in highly vibrationally excited pyrazine and CO2

Classical trajectory calculations were performed to simulate state-resolved energy transfer experiments of highly vibrationally excited pyrazine (E(vib) = 37,900 cm(-1)) and CO(2), which were conducted using a high-resolution transient infrared absorption spectrometer. The goal here is to use classical trajectories to simulate the supercollision energy transfer pathway wherein large amounts of energy are transferred in single collisions in order to compare with experimental results. In the trajectory calculations, Newton's laws of motion are used for the molecular motion, isolated molecules are treated as collections of harmonic oscillators, and intermolecular potentials are formed by pairwise Lennard-Jones potentials. The calculations qualitatively reproduce the observed energy partitioning in the scattered CO(2) molecules and show that the relative partitioning between bath rotation and translation is dependent on the moment of inertia of the bath molecule. The simulations show that the low-frequency modes of the vibrationally excited pyrazine contribute most to the strong collisions. The majority of collisions lead to small DeltaE values and primarily involve single encounters between the energy donor and acceptor. The large DeltaE exchanges result from both single impulsive encounters and chattering collisions that involve multiple encounters.     

Stress tensor in model polymer systems with periodic boundaries

The calculation of the stress tensor from molecular simulations of atomistic model polymer systems employing periodic boundary conditions is discussed. Starting from the dynamical equations governing the motion of sites, correct double summation forms of the atomic and the molecular virial equations are derived, which are valid for flexible, infinitely stiff and rigid chain models even in the presence of interactions between different images of the same parent macromolecule. A new expression for the true instantaneous stress (flux of momentum through the faces of the simulation box) is derived and shown to exhibit large fluctuations when applied in molecular dynamics simulations. A new equation for the thermodynamic stress, cast exclusively in terms of intermolecular forces on interaction sites, is also derived. Application to Monte Carlo simulations shows that the molecular virial expression exhibits the smallest fluctuations among all stress expressions discussed, and thus allows computation of the thermodynamic stress with least uncertainty. A scheme is developed for the calculation of surface tension from intermolecular forces only.     

Adsorption of single DNA molecules at the water/fused-silica interface

We applied total internal reflection fluorescence microscopy (TIRFM) to study intermolecular interactions at the water/fused-silica interface at the single-molecule level. Real-time molecular motion at the interface was recorded to reveal adsorption behavior and conformational dynamics of three DNAs with sticky ends of different numbers of unpaired bases. Features of DNA motion at the interface, such as evanescent-field residence time, linear velocity and frequency of adsorption/desorption events were measured to assess the relative affinities of the oligonucleotides for the surface. The general trend of stronger interaction with the surface for longer sticky ends confirmed hydrophobic interaction and hydrogen bonding as the driving forces of DNA adsorption to fused-silica at pH 5. For DNAs of different sizes, different conformational dynamics and the accessibility of sticky ends give rise to a nonlinear relationship with respect to affinity. Such information may prove valuable for chromatography studies as well as for the design of DNA microarrays and drug delivery systems.     

Ultrafast dynamics of myoglobin without the distal histidine: stimulated vibrational echo experiments and molecular dynamics simulations

Ultrafast protein dynamics of the CO adduct of a myoglobin mutant with the polar distal histidine replaced by a nonpolar valine (H64V) have been investigated by spectrally resolved infrared stimulated vibrational echo experiments and molecular dynamics (MD) simulations. In aqueous solution at room temperature, the vibrational dephasing rate of CO in the mutant is reduced by approximately 50% relative to the native protein. This finding confirms that the dephasing of the CO vibration in the native protein is sensitive to the interaction between the ligand and the distal histidine. The stimulated vibrational echo observable is calculated from MD simulations of H64V within a model in which vibrational dephasing is driven by electrostatic forces. In agreement with experiment, calculated vibrational echoes show slower dephasing for the mutant than for the native protein. However, vibrational echoes calculated for H64V do not show the quantitative agreement with measurements demonstrated previously for the native protein.     

Application of a high-performance,special-purpose computer,GRAPE-2A,to molecular dynamics

The special-purpose computer GRAPE-2A accelerates the calculation of pairwise interactions in many-body systems. This computer is a back-end processor connected to a host computer through a Versa Module Europe (VME) bus. GRAPE-2A receives coordinates and other physical data for particles from the host and then calculates the pairwise interactions. The host then integrates an equation of motion by using these interactions. We did molecular dynamics simulations for two systems of liquid water: System 1 (1000 molecules), and System 2 (1728 molecules). The time spent for one step of molecular dynamics was 3.9 s (System l), and 10.2 s (System 2). The larger the molecular system, the higher the performance. The speed of GRAPE-2A did not depend on the formula describing the pairwise interaction. The cost performance was about 20 times better than that of the fastest workstations available today, and GRAPE-2A cost only $22,000. © 1994 by John Wiley & Sons, Inc.     

Intermolecular motion in strong infrared laser fields

The effect of a strong infrared laser field on the collision between two rare gas atoms is examined as a model of intermolecular motion under such conditions. After examination of the classical collision dynamics, three novel classes of collisions are identified, all of which result from interaction with the angular potential well. The signatures of these “collision mechanisms” in the classical deflection function and differential cross-section are determined. The generality of the results and the feasibility of using a modified crossed molecular beam experiment to observe these laser-induced effects are discussed.     

On the lattice dynamics of solid nitrogen

Lattice statics and dynamics calculations for α-nitrogen have been done using the 6-exp atom-atom interaction to derive intermolecular forces. The three parameters of this interaction are reduced to one by constraining them so that the unit cell and sublimation energy are calculated to agree with experiment. Choice of the one parameter is then made using spectroscopic data. This 'best' potential is then used to calculate the statics and dynamics of β-nitrogen. This is stable only under pressure, and the calculation of the lattice dynamics under pressure gives a satisfactory agreement with experiment.     

Two-dimensional pentacene:3,4,9,10-perylenetetracarboxylic dianhydride supramolecular chiral networks on Ag(111)

Self-assembly of the binary molecular system of pentacene and 3,4,9,10-perylenetetracarboxylic dianhydride (PTCDA) on Ag(111) has been investigated by low-temperature scanning tunneling microscopy, molecular dynamics (MD), and density functional theory (DFT) calculations. Well-ordered two-dimensional (2D) pentacene:PTCDA supramolecular chiral networks are observed to form on Ag(111). The 2D chiral network formation is controlled by the strong interfacial interaction between adsorbed molecules and the underlying Ag(111), as revealed by MD and DFT calculations. The registry effect locks the adsorbed pentacene and PTCDA molecules into specific adsorption sites due to the corrugation of the potential energy surface. The 2D supramolecular networks are further constrained through the directional CO...H-C multiple intermolecular hydrogen bonding between the anhydride groups of PTCDA and the peripheral aromatic hydrogen atoms of the neighboring pentacene molecules.     

Ultrafast intermolecular dynamics of liquid water: a theoretical study on two-dimensional infrared spectroscopy

Physical and chemical properties of liquid water are dominated by hydrogen bond structure and dynamics. Recent studies on nonlinear vibrational spectroscopy of intramolecular motion provided new insight into ultrafast hydrogen bond dynamics. However, our understanding of intermolecular dynamics of water is still limited. We theoretically investigated the intermolecular dynamics of liquid water in terms of two-dimensional infrared (2D IR) spectroscopy. The 2D IR spectrum of intermolecular frequency region (<1000 cm(-1)) is calculated by using the equilibrium and nonequilibrium hybrid molecular dynamics method. We find the ultrafast loss of the correlation of the libration motion with the time scale of approximately 110 fs. It is also found that the energy relaxation from the libration motion to the low frequency motion takes place with the time scale of about 180 fs. We analyze the effect of the hindered translation motion on these ultrafast dynamics. It is shown that both the frequency modulation of libration motion and the energy relaxation from the libration to the low frequency motion significantly slow down in the absence of the hindered translation motion. The present result reveals that the anharmonic coupling between the hindered translation and libration motions is essential for the ultrafast relaxation dynamics in liquid water.     

Theoretical unimolecular kinetics for CH4 + M ⇄ CH3 + H + M in eight baths, M = He, Ne, Ar, Kr, H2, N2, CO, and CH4

Ensembles of classical trajectories are used to study collisional energy transfer in highly vibrationally excited CH(4) for eight bath gases. Several simplifying assumptions for the CH(4) + M interaction potential energy surface are tested against full dimensional direct dynamics trajectory calculations for M = He, Ne, and H(2). The calculated energy transfer averages are confirmed to be sensitive to the shape of the repulsive wall of the intermolecular potential, with an exponential repulsive wall required for quantitative predictions. For the diatomic baths, the usual "separable pairwise" approximation for the interaction potential is unable to describe the orientation dependence of the interaction potential accurately, and the ambiguity in the resulting parametrizations contributes an additional uncertainty to the predicted energy transfer averages of 20-40%. On the other hand, the energy transfer averages are shown to be insensitive to the level of theory used to describe the intramolecular CH(4) potential, with a computationally efficient semiempirical tight binding potential for hydrocarbons performing equally well as an MP2 potential. The relative collisional energy transfer efficiencies of the eight bath gases are discussed and shown to be a function of temperature. The ensemble-averaged energy transferred in deactivating collisions <ΔE(d)> for each bath is used to parametrize a single-exponential-down model for collisional energy transfer in master equation calculations. The predicted decomposition rate coefficients for CH(4) agree well with available experimental rate coefficients for M = He, Ar, Kr, and CH(4). The effect of vibrational anharmonicity on the predicted rate coefficients is considered briefly.     

Single-molecule force spectroscopy of β-peptides that display well-defined three-dimensional chemical patterns

Oligomers of β-amino acids ("β-peptides") can be designed to fold into stable helices that display side chains with a diverse range of chemical functionality in precise arrangements. We sought to determine whether the predictable, three-dimensional side-chain patterns generated by β-peptides could be used in combination with single-molecule force spectroscopy to quantify how changes in nanometer-scale chemical patterns affect intermolecular interactions. To this end, we synthesized β-peptides that were designed to be either globally amphiphilic (GA), i.e., display a global segregation of side chains bearing hydrophobic and cationic functional groups, or non-globally amphiphilic (iso-GA), i.e., display a more uniform distribution of hydrophobic and cationic functional groups in three-dimensions. Single-molecule force measurements of β-peptide interactions with hydrophobic surfaces through aqueous solution (triethanolamine buffer, pH 7.2) reveal that the GA and iso-GA isomers give rise to qualitatively different adhesion force histograms. The data are consistent with the display of a substantial nonpolar domain by the GA oligomer, which leads to strong hydrophobic interactions, and the absence of a comparable domain on the iso-GA oligomer. This interpretation is supported by force measurements in the presence of methanol, which is known to disrupt hydrophobic interactions. Our ability to associate changes in measured forces with changes in three-dimensional chemical nanopatterns projected from conformationally stable β-peptide helices highlights a contrast between this system and conventional peptides (α-amino acid residues): conventional peptides are more conformationally flexible, which leads to uncertainty in the three-dimensional nanoscopic chemical patterns that underlie measured forces. Overall, we conclude that β-peptide oligomers provide a versatile platform for quantifying intermolecular interactions that arise from specific functional group nanopatterns.     

关于限域离子液体吸附CO_2的密度泛函理论(DFT)的研究

近年来,温室效应日趋严重,因此吸收CO_2的材料受到了广泛的关注.采用了密度泛函理论(DFT)研究以SiO_2为载体的限域离子液体对CO_2的吸附.对比纯净离子液体(ILs)以及限域离子液体与CO_2的相互作用情况,在这两种状态下两种体系的吸附情况大不相同.从几何结构、相互作用以及电荷分析等方面对ILs、 SiO_2以及ILs/SiO_2复合结构进行研究.计算结果表明,载体、离子液体和CO_2之间都存在较强的相互作用.离子液体的负载不仅改变了SiO_2载体的结构,而且受载体的影响阴阳离子之间的相互作用力也发生了改变.计算结果为进一步深入限域离子液体对CO_2的吸附打下了理论基础.     

Intermolecular interaction in water hexamer

The origin of the intermolecular interaction, especially the many-body interaction, in eight low-lying water hexamer structures (prism, cage, book-1, book-2, cyclic-chair, bag, cyclic-boat-1, and cyclic-boat-2) is unraveled using the localized molecular orbital energy decomposition analysis (LMO-EDA) method at the second-order M?ller-Plesset perturbation (MP2) level of theory with a large basis set. It is found that the relative stabilities of these hexamer structures are determined by delicate balances between different types of interaction. According to LMO-EDA, electrostatic and exchange interactions are strictly pairwise additive. Dispersion interaction in these water hexamer structures is almost pairwise additive, with many-body effects varying from -0.13 to +0.05 kcal/mol. Repulsion interaction is roughly pairwise additive, with many-body effects varying from -0.84 to -0.62 kcal/mol. Polarization interaction is not pairwise additive, with many-body effects varying from -13.10 to -8.85 kcal/mol.     

The geometry and vibrational frequency shift of CO molecules in an argon matrix studied by force-field calculations

In this paper, the CO·Ar interaction potential including pairwise and three-body contributions which reproduces the experimental CO vibrational frequency shift, Δω = ?4.7 cm^?1 in a static force-field approximation, is presented. The geometry of the COAr solid system is described in detail. The frequency shift is obtained when the CO molecule is oriented along the (0, 0, 1) crystal axis, with its center of mass shifted by 0.25 Å from the center of interaction, and with the surrounding first shell argon atoms relaxed into an approximately ellipsoidal cage. The semi-axes of the ellipsoid deviate from the radius of the undistorted first shell, 3.756 Å, by only 0.06 Å. The second shell of the argon atoms is also distorted into an ellipsoidal cage but the deviations from the sphere in this case are an order of magnitude smaller than for the first shell. Distortions of more distant crystal sites are negligible. Substitution of an Ar atom by a CO molecule with subsequent lattice relaxations into the minimum potential energy configuration results in a decrease in potential energy of 0.16 kJ mol^?1. The three-body contributions to the CO·Ar potential have only a negligible influence on the geometry of the COAr system (including the lattice relaxations) but a strong influence on the vibrational frequency shift.     

Calculation of the Maxwell stress tensor and the Poisson-Boltzmann force on a solvated molecular surface using hypersingular boundary integrals

The electrostatic interaction among molecules solvated in ionic solution is governed by the Poisson-Boltzmann equation (PBE). Here the hypersingular integral technique is used in a boundary element method (BEM) for the three-dimensional (3D) linear PBE to calculate the Maxwell stress tensor on the solvated molecular surface, and then the PB forces and torques can be obtained from the stress tensor. Compared with the variational method (also in a BEM frame) that we proposed recently, this method provides an even more efficient way to calculate the full intermolecular electrostatic interaction force, especially for macromolecular systems. Thus, it may be more suitable for the application of Brownian dynamics methods to study the dynamics of protein/protein docking as well as the assembly of large 3D architectures involving many diffusing subunits. The method has been tested on two simple cases to demonstrate its reliability and efficiency, and also compared with our previous variational method used in BEM.     

Investigation of the local composition enhancement and related dynamics in supercritical CO2-cosolvent mixtures via computer simulation: the case of ethanol in CO2

The supercritical mixture ethanol-carbon dioxide (EtOH-CO2) with mole fraction of ethanol X(EtOH) congruent with 0.1 was investigated at 348 K, by employing the molecular dynamics simulation technique in the canonical ensemble. The local intermolecular structure of the fluid was studied in terms of the calculated appropriate pair radial distribution functions. The estimated average local coordination numbers and mole fractions around the species in the mixture reveal the existence of local composition enhancement of ethanol around the ethanol molecules. This finding indicates the nonideal mixing behavior of the mixture due to the existence of aggregation between the ethanol molecules. Furthermore, the local environment redistribution dynamics have been explored by analyzing the time correlation functions (TCFs) of the total local coordination number (solvent, cosolvent) around the cosolvent molecules in appropriate parts. The analysis of these total TCFs in the auto-(solvent-solvent, cosolvent-cosolvent) and cross-(solvent-cosolvent, cosolvent-solvent) TCFs has shown that the time dependent redistribution process of the first solvation shell of ethanol is mainly determined by the redistribution of the CO2 solvent molecules. These results might be explained on the basis of the CO2-CO2 and EtOH-CO2 intermolecular forces, which are sufficiently weaker in comparison to the EtOH-EtOH hydrogen bonding interactions, creating in this way a significantly faster redistribution of the CO2 molecules in comparison with EtOH. Finally, the self-diffusion coefficients and the single reorientational dynamics of both the cosolvent and solvent species in the mixture have been predicted and discussed in relationship with the local environment around the species, which in the case of the EtOH molecules seem to be strongly affected.     

Strong Short-Range Cooperativity in Hydrogen-Bond Chains

Chains of hydrogen bonds such as those found in water and proteins are often presumed to be more stable than the sum of the individual H bonds. However, the energetics of cooperativity are complicated by solvent effects and the dynamics of intermolecular interactions, meaning that information on cooperativity typically is derived from theory or indirect structural data. Herein, we present direct measurements of energetic cooperativity in an experimental system in which the geometry and the number of H bonds in a chain were systematically controlled. Strikingly, we found that adding a second H-bond donor to form a chain can almost double the strength of the terminal H bond, while further extensions have little effect. The experimental observations add weight to computations which have suggested that strong, but short-range cooperative effects may occur in H-bond chains.     

Ligand rearrangement reactions of Cr(CO)6 in alcohol solutions: experiment and theory

The ligand rearrangement reaction of Cr(CO)6 is studied in a series of alcohol solutions using ultrafast infrared spectroscopy and Brownian dynamics simulations. Excitation with 266 nm light gives Cr(CO)5 which is quickly solvated by a ligand from the bath. In alcohol solutions, solvation by an alkyl or hydroxyl site can occur; all alkyl bound complexes eventually rearrange to hydroxyl bound complexes. This rearrangement has been described using both an intermolecular (stochastic) and intramolecular (chainwalk) mechanism. Experiments alone do not allow for characterization of the mechanism, and therefore, theoretical calculations were carried out for the first time by modeling the ligand rearrangement as a diffusive walk along a potential defined by the different interaction possibilities. Experiments and simulations were carried out for Cr(CO)6 in 1-propanol, 2-propanol, 1-butanol, 2-butanol, isobutanol, 1-pentanol, 2-pentanol, 2-methylbutanol, and 3-methylbutanol. The trends in the theoretical and experimental rearrangement times are similar for all simulations carried out indicating that the two mechanisms have very similar ensemble behavior when bath effects are taken into account. The nature of the mechanism responsible for motion along the alcohol chain is not of primary importance in isolating the kinetic behavior because of the highly diffusive nature of the reaction. Future experimental and theoretical work will be directed at identifying a definitive assignment of the reaction mechanism.