Flemming Y. Hansen

Methodological problems in pressure profile calculations for lipid bilayers

From molecular dynamics simulations of a dipalmitoyl-phosphatidyl-choline (DPPC) lipid bilayer in the liquid crystalline phase, pressure profiles through the bilayer are calculated by different methods. These profiles allow us to address two central and unresolved problems in pressure profile calculations: The first problem is that the pressure profile is not uniquely defined since the expression for the local pressure involves an arbitrary choice of an integration contour. We have investigated two different choices leading to the Irving-Kirkwood (IK) and Harasima (H) expressions for the local pressure tensor. For these choices we find that the pressure profile is almost independent of the contour used, which indicates that the local pressure is well defined for a DPPC bilayer in the liquid crystalline phase. This may not be the case for other systems and we therefore suggest that both the IK and H profiles are calculated in order to test the uniqueness of the profile. The second problem is how to include electrostatic interactions in pressure profile calculations when the simulations are conducted without truncating the electrostatic potential, i.e., using the Ewald summation technique. Based on the H expression for the local pressure, we present a method for calculating the contribution to the lateral components of the local pressure tensor from electrostatic interactions evaluated by the Ewald summation technique. Pressure profiles calculated with an electrostatic potential truncation (cutoff) from simulations conducted with Ewald summation are shown to depend on the cutoff in a subtle manner which is attributed to the existence of long-ranged charge ordering in the system. However, the pressure profiles calculated with relatively long cutoffs are qualitatively similar to the Ewald profile for the DPPC bilayer studied here.

Quasielastic neutron scattering and molecular dynamics simulation studies of the melting transition in butane and hexane monolayers adsorbed on graphite

~Received 14 May 1997; accepted 24 June 1997! Quasielastic neutron scattering experiments and molecular dynamics ~MD! simulations have been used to investigate molecular diffusive motion near the melting transition of monolayers of flexible rod-shaped molecules. The experiments were conducted on butane and hexane monolayers adsorbed on an exfoliated graphite substrate. For butane, quasielastic scattering broader than the experimental energy resolution width of 70 meV appears abruptly at the monolayer melting point of Tm 5116 K, whereas, for the hexane monolayer, it appears 20 K below the melting transition ( Tm 5170 K). To facilitate comparison with experiment, quasielastic spectra calculated from the MD simulations were analyzed using the same models and fitting algorithms as for the neutron spectra. This combination of techniques gives a microscopic picture of the melting process in these two monolayers which is consistent with earlier neutron diffraction experiments. Butane melts abruptly to a liquid phase where the molecules in the trans conformation translationally diffuse while rotating about their center of mass. In the case of the hexane monolayer, the MD simulations show that the appearance of quasielastic scattering below Tm coincides with transformation of some molecules from trans to gauche conformations. Furthermore, if gauche molecules are prevented from forming in the simulation, the calculated incoherent scattering function contains no quasielastic component below Tm . Modeling of both the neutron and simulated hexane monolayer spectra below Tm favors a plastic phase in which there is nearly isotropic rotational diffusion of the gauche molecules about their center of mass, but no translational diffusion. The elastic scattering observed above Tm is consistent with the coexistence of solid monolayer clusters with a fluid phase, as predicted by the simulations. For T/Tm>1.3, the elastic scattering vanishes from the neutron spectra where the simulation indicates the presence of a fluid phase alone. The qualitative similarities between the observed and simulated quasielastic spectra lend support to a previously proposed ‘‘footprint reduction’’ mechanism of melting in monolayers of flexible, rod-shaped molecules.

High-resolution ellipsometric study of an n-alkane film, dotriacontane, adsorbed on a SiO2 surface

Using high-resolution ellipsometry and stray light intensity measurements, we have investigated during successive heating-cooling cycles the optical thickness and surface roughness of thin dotriacontane (n-C32H66) films adsorbed from a heptane (n-C7H16) solution onto SiO2-coated Si(100) single-crystal substrates. Our results suggest a model of a solid dotriacontane film that has a phase closest to the SiO2 surface in which the long-axis of the molecules is oriented parallel to the interface. Above this “parallel film” phase, a solid monolayer adsorbs in which the molecules are oriented perpendicular to the interface. At still higher coverages and at temperatures below the bulk melting point at Tb=341 K, solid bulk particles coexist on top of the “perpendicular film.” For higher temperatures in the range Tb Ts, a uniformly thick fluid film wets to the parallel film phase. This struc...

Molecular dynamics studies of the melting of butane and hexane monolayers adsorbed on the basal‐plane surface of graphite

The effect of molecular steric properties on the melting of quasi‐two‐dimensional solids is investigated by comparing results of molecular dynamics simulations of the melting of butane and hexane monolayers adsorbed on the basal‐plane surface of graphite. These molecules differ only in their length, being members of the n‐alkane series [CH3(CH2)n−2CH3] where n=4 for butane and n=6 for hexane. The simulations employ a skeletal model, which does not include the hydrogen atoms explicitly, to represent the intermolecular and molecule–substrate interactions. Nearest‐neighbor intramolecular bonds are fixed in length, but the molecular flexibility is preserved by allowing the bend and dihedral torsion angles to vary. The simulations show a qualitatively different melting behavior for the butane and hexane monolayers consistent with neutron and x‐ray scattering experiments. The melting of the low‐temperature herringbone (HB) phase of the butane monolayer is abrupt and characterized by a simultaneous breakdown of ...

Dissociative chemisorption of N2 on rhenium: Dynamics at high impact energies

The dissociative chemisorption of N 2 on the (0001) rhenium crystal surface is studied theoretically at high impact energies. The dynamics of the molecule is accordingly treated classically excluding tunneling processes. This study extends previous low energy studies in three important ways: (1) all six degrees of freedom of the N 2 molecule are considered; (2) lateral variations (corrugation) are included in the molecule-crystal interaction potential; (3) energy exchange between the molecule and the surface is allowed for by treating the dynamics of the crystal atoms within a linear phonon forcing model. It is found that the energy transfer from the molecule to the phonons of the crystal is very significant. The smaller than unity dissociative sticking probability found experimentally even at the highest impact energies well above the barrier energy can be accounted for by the Landau-Zener probability of a transition from the dissociative potential energy surface (PES) to a non-dissociative PES.

A novel growth mode of alkane films on a SiO2 surface

Abstract Synchrotron X-ray specular scattering measurements confirm microscopically a structural model recently inferred by very-high-resolution ellipsometry of a solid dotriacontane ( n -C 32 H 66 or C32) film formed by adsorption from solution onto a SiO 2 surface. Sequentially, one or two layers adsorb on the SiO 2 surface with the long-axis of the C32 molecules oriented parallel to the interface followed by a C32 monolayer with the long-axis perpendicular to it. Finally, preferentially oriented bulk particles nucleate having two different crystal structures. This growth model differs from that found previously for shorter alkanes deposited from the vapor phase onto solid surfaces.

Dissociative chemisorption of N2 on rhenium: Dynamics at low impact energies

Abstract The dissociative chemisorption of nitrogen on the (0001) rhenium surface is studied at low impact energies, where tunnelling processes are important. A quantum-classical model is used in which two coordinates, the distance from the surface and the vibrational coordinate, are treated quantum mechanically using the FFT (fast Fourier transform) technique. Also normal modes of the solid are quantized using a quantum boson approach and the remaining degrees of freedom are treated classically. Full corrugation of the surface and phonon coupling to infinite order as well as rotational motion of the diatom are included in the model.

Equilibrium partitioning of macromolecules in confining geometries: Improved universality with a new molecular size parameter

We present a new framework for the description of macromolecules subject to confining geometries. The two main ingredients are a new computational method and the definition of a new molecular size parameter. The computational method, hereafter referred to the confinement analysis from bulk structures (CABS), allows the computation of equilibrium partition coefficients as a function of confinement size solely based on a single sampling of the configuration space of a macromolecule in bulk. Superior in computational speed to previous computational methods, CABS is capable of handling slits, channels, and box confining geometries for all molecular architectures. The new molecular size parameter, hereafter referred to the steric exclusion radius R(s), is explicitly defined and computed for a number of rigid objects and flexible polymers. We suggest that R(s) is the relevant molecular size parameter for characterization of spatial confinement effects on macromolecules. Results for the equilibrium partition coefficient in the weak confinement regime depend only on the ratio of R(s) to the confinement size regardless of molecular details.

New insight in the microscopic mechanism of the catalytic synthesis of ammonia

Abstract Theoretical quantum calculations and molecular beam experiments of the dissociative chemisorption of N 2 molecules on catalytic active metal surfaces have given new insight in the fundamental process of the ammonia synthesis. This new approach to the study of catalytic process supplements the conclusions based on a traditional kinetic analysis and may resolve some existing ambiguities in the analysis of the kinetic data. In this paper we address two controversial questions concerning the dissociative chemisorption of N 2 , namely: The existence of a precursor state, and the existence of a barrier to dissociation. Our analysis of the dissociation process suggests that it is not possible to define, in some well specified way, a precursor state at typical temperatures in the technical ammonia synthesis. The kinetic scheme for the complete ammonia synthesis without the precursor state can still account for the observed conversion to ammonia. We have constructed an empirical potential energy surface for N 2 Fe (111) which has barriers to dissociation even larger than for the previously studied N 2 Re system. It is shown that the presence of barriers is consistent with the observation that the activation energy, determined from an Arrhenius plot of the rate constant, is close to zero. This is due to tunneling through the barrier and energy exchange between the molecule and metal.

The accuracy of the time-dependent self-consistent-field approximation for inelastic collisions

Abstract We study the accuracy of the time-dependent self-consistent-field approximation for colliner inelastic collisions between an atom and a diatomic molecule. Individual state-to-state transition probabilities, total energy transfer, and the global description of the wavefunction is considered. It is shown that errors in these properties may be very considerable and they depend strongly on the initial form of the wave packet. For the individual state-to-state transition probabilities we show, however, that the errors can be minimized dramatically by a proper choice of the initial average momentum of the wave packet.