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7 Jan 2012

Volume 136, Issue 1, Articles (01xxxx)

Issue Cover Spotlight Figure

J. Chem. Phys. 136, 014501 (2012); http://dx.doi.org/10.1063/1.3665140 (8 pages)

Minbiao Ji, Robert W. Hartsock, Zheng Sung, and Kelly J. Gaffney
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back to top Condensed Phase Dynamics, Structure, and Thermodynamics: Spectroscopy, Reactions, and Relaxation

Monte Carlo study of four dimensional binary hard hypersphere mixtures

Marvin Bishop and Paula A. Whitlock

J. Chem. Phys. 136, 014506 (2012); http://dx.doi.org/10.1063/1.3671651 (5 pages) | Cited 1 time

Online Publication Date: 4 January 2012

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A multithreaded Monte Carlo code was used to study the properties of binary mixtures of hard hyperspheres in four dimensions. The ratios of the diameters of the hyperspheres examined were 0.4, 0.5, 0.6, and 0.8. Many total densities of the binary mixtures were investigated. The pair correlation functions and the equations of state were determined and compared with other simulation results and theoretical predictions. At lower diameter ratios the pair correlation functions of the mixture agree with the pair correlation function of a one component fluid at an appropriately scaled density. The theoretical results for the equation of state compare well to the Monte Carlo calculations for all but the highest densities studied.
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61.20.Ja Computer simulation of liquid structure
64.30.-t Equations of state of specific substances

Structure and electronic properties of a benzene-water solution

Margarida P. S. Mateus, Nuno Galamba, and Benedito J. Costa Cabral

J. Chem. Phys. 136, 014507 (2012); http://dx.doi.org/10.1063/1.3671947 (12 pages) | Cited 6 times

Online Publication Date: 4 January 2012

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Electronic properties of benzene in water were investigated by a sequential quantum mechanical/molecular dynamics approach. Emphasis was placed on the analysis of the structure, polarization effects, and ionization spectrum. By adopting a polarizable model for both benzene and water the structure of the benzene-water solution is in good agreement with data from first principles molecular dynamics. Further, strong evidence that water molecules acquire enhanced orientational order near the benzene molecule is found. Upon hydration, the quadrupole moment of benzene is not significantly changed in comparison with the gas-phase value. We are also reporting results for the dynamic polarizability of benzene in water. Our results indicate that the low energy behaviour of the dynamic polarizability of gas-phase and hydrated benzene is quite similar. Outer valence Green's function calculations for benzene in liquid water show a splitting of the gas-phase energy levels associated with the 1e1g(π), 2e2g, and 2e1u orbitals upon hydration. Lifting of the orbitals degeneracy and redshift of the outer valence bands is related to symmetry breaking of the benzene structure in solution and polarization effects from the surrounding water molecules.
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61.20.Qg Structure of associated liquids: electrolytes, molten salts, etc.
71.15.Pd Molecular dynamics calculations (Car-Parrinello) and other numerical simulations
61.20.Ja Computer simulation of liquid structure

Rotational dynamics of solvated carbon dioxide studied by infrared, Raman, and time-resolved infrared spectroscopies and a molecular dynamics simulation

Kaori Watanabe, Hajime Okajima, Takuya Kato, and Hiro-o Hamaguchi

J. Chem. Phys. 136, 014508 (2012); http://dx.doi.org/10.1063/1.3671998 (7 pages) | Cited 1 time

Online Publication Date: 4 January 2012

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Rotational dynamics of solvated carbon dioxide (CO2) has been studied. The infrared absorption band of the antisymmetric stretch mode in acetonitrile is found to show a non-Lorentzian band shape, suggesting a non-exponential decay of the vibrational and/or rotational correlation functions. A combined method of a molecular dynamics (MD) simulation and a quantum chemical calculation well reproduces the observed band shape. The analysis suggests that the band broadening is almost purely rotational, while the contribution from the vibrational dephasing is negligibly small. The non-exponential rotational correlation decay can be explained by a simple rotor model simulation, which can treat large angle rotations of a relatively small molecule. A polarized Raman study of the symmetric stretch mode in acetonitrile gives a rotational bandwidth consistent with that obtained from the infrared analysis. A sub-picosecond time-resolved infrared absorption anisotropy measurement of the antisymmetric stretch mode in ethanol also gives a decay rate that is consistent with the observed rotational bandwidths.
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33.20.Sn Rotational analysis
33.20.Tp Vibrational analysis
33.20.Ea Infrared spectra
33.20.Fb Raman and Rayleigh spectra (including optical scattering)
33.70.Jg Line and band widths, shapes, and shifts
31.70.Dk Environmental and solvent effects

Mediation of resonance energy transfer by a third molecule

A. Salam

J. Chem. Phys. 136, 014509 (2012); http://dx.doi.org/10.1063/1.3673779 (5 pages)

Online Publication Date: 5 January 2012

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The influence of a third molecule on the rate of resonance energy transfer is studied using diagrammatic perturbation theory within the framework of molecular quantum electrodynamics. Two distinct mechanisms are identified. One corresponds to direct transfer between donor and acceptor while the other involves relay of energy by the third species. Fermi Golden rule transition rates valid for all separation distances beyond wave function overlap are evaluated for these two processes as well as for the interference term between direct and indirect exchange, thereby extending previous work which was limited to the near-zone only. Short- and long-range limits are also obtained in each case. It is found that in the near-zone the indirect rate contribution exhibits inverse sixth power dependence on relative distances of emitter and absorber relative to the third body, in contrast to its far-zone counterpart, which exhibits inverse square behavior. The interference term, however, displays inverse cubic dependence on all three distance vectors at short-range and inverse behavior in the far-zone. Interestingly, for a collinear arrangement of the three molecules in the near-zone, the interference term is negative, reducing the overall rate of energy transfer. The results obtained are interpreted in terms of microscopic and macroscopic pictures of transfer occurring within a surrounding medium.
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31.30.J- Relativistic and quantum electrodynamic (QED) effects in atoms, molecules, and ions
31.15.xp Perturbation theory
31.15.am Relativistic configuration interaction (CI) and many-body perturbation calculations
33.20.Tp Vibrational analysis

Nuclear magnetic resonance investigation of dynamics in poly(ethylene oxide)-based lithium polyether-ester-sulfonate ionomers

David J. Roach, Shichen Dou, Ralph H. Colby, and Karl T. Mueller

J. Chem. Phys. 136, 014510 (2012); http://dx.doi.org/10.1063/1.3669449 (9 pages) | Cited 3 times

Online Publication Date: 6 January 2012

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Nuclear magnetic resonance spectroscopy has been utilized to investigate the dynamics of poly(ethylene oxide)-based lithium sulfonate ionomer samples that have low glass transition temperatures. 1H and 7Li spin-lattice relaxation times (T1) of the bulk polymer and lithium ions, respectively, were measured and analyzed in samples with a range of ion contents. The temperature dependence of T1 values along with the presence of minima in T1 as a function of temperature enabled correlation times and activation energies to be obtained for both the segmental motion of the polymer backbone and the hopping motion of lithium cations. Similar activation energies for motion of both the polymer and lithium ions in the samples with lower ion content indicate that the polymer segmental motion and lithium ion hopping motion are correlated in these samples, even though lithium hopping is about ten times slower than the segmental motion. A divergent trend is observed for correlation times and activation energies of the highest ion content sample with 100% lithium sulfonation due to the presence of ionic aggregation. Details of the polymer and cation dynamics on the nanosecond timescale are discussed and complement the findings of X-ray scattering and quasi-elastic neutron scattering experiments.
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33.25.+k Nuclear resonance and relaxation
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Free energy profiles for penetration of methane and water molecules into spherical sodium dodecyl sulfate micelles obtained using the thermodynamic integration method combined with molecular dynamics calculations

K. Fujimoto, N. Yoshii, and S. Okazaki

J. Chem. Phys. 136, 014511 (2012); http://dx.doi.org/10.1063/1.3671997 (9 pages) | Cited 2 times

Online Publication Date: 6 January 2012

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The free energy profiles, ΔG(r), for penetration of methane and water molecules into sodium dodecyl sulfate (SDS) micelles have been calculated as a function of distance r from the SDS micelle to the methane and water molecules, using the thermodynamic integration method combined with molecular dynamics calculations. The calculations showed that methane is about 6–12 kJ mol−1 more stable in the SDS micelle than in the water phase, and no ΔG(r) barrier is observed in the vicinity of the sulfate ions of the SDS micelle, implying that methane is easily drawn into the SDS micelle. Based on analysis of the contributions from hydrophobic groups, sulfate ions, sodium ions, and solvent water to ΔG(r), it is clear that methane in the SDS micelle is about 25 kJ mol−1 more stable than it is in the water phase because of the contribution from the solvent water itself. This can be understood by the hydrophobic effect. In contrast, methane is destabilized by 5–15 kJ mol−1 by the contribution from the hydrophobic groups of the SDS micelle because of the repulsive interactions between the methane and the crowded hydrophobic groups of the SDS. The large stabilizing effect of the solvent water is higher than the repulsion by the hydrophobic groups, driving methane to become solubilized into the SDS micelle. A good correlation was found between the distribution of cavities and the distribution of methane molecules in the micelle. The methane may move about in the SDS micelle by diffusing between cavities. In contrast, with respect to the water, ΔG(r) has a large positive value of 24–35 kJ mol−1, so water is not stabilized in the micelle. Analysis showed that the contributions change in complex ways as a function of r and cancel each other out. Reference calculations of the mean forces on a penetrating water molecule into a dodecane droplet clearly showed the same free energy behavior. The common feature is that water is less stable in the hydrophobic core than in the water phase because of the energetic disadvantage of breaking hydrogen bonds formed in the water phase. The difference between the behaviors of the SDS micelles and the dodecane droplets is found just at the interface; this is caused by the strong surface dipole moment formed by sulfate ions and sodium ions in the SDS micelles.
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31.70.Dk Environmental and solvent effects
31.15.xv Molecular dynamics and other numerical methods
33.15.Kr Electric and magnetic moments (and derivatives), polarizability, and magnetic susceptibility
33.15.Fm Bond strengths, dissociation energies
82.70.Dd Colloids
82.70.Uv Surfactants, micellar solutions, vesicles, lamellae, amphiphilic systems, (hydrophilic and hydrophobic interactions)
back to top Surfaces, Interfaces, and Materials

Incorporating C2 into C60 films

Seyithan Ulas, Dmitry Strelnikov, Patrick Weis, Artur Böttcher, and Manfred M. Kappes

J. Chem. Phys. 136, 014701 (2012); http://dx.doi.org/10.1063/1.3673887 (12 pages) | Cited 1 time

Online Publication Date: 5 January 2012

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The material formed by depositing C2− anions onto/into thin C60 films (on graphite) at room temperature has been studied by means of thermal desorption mass spectroscopy, ultraviolet photoionization spectroscopy, atomic force microscopy (AFM), and surface enhanced Raman spectroscopy. As-prepared, C2/C60 films manifest thermal desorption behaviour which differs significantly from pure C60 films. Whereas the latter can be fully sublimed, we observe decomposition of C2/C60 films to a high-temperature-stable material while predominantly C60, C62, and C64 are desorbed in parallel. Deposition of C2− also leads to significantly modified electronic and vibrational properties. Based on DFT model calculations of the Raman spectra, we suggest that as-prepared C2/C60 films contain appreciable amounts of polymeric networks comprising –C2–C60–C2–C60– chains. Detection of sublimed C62 and C64 upon heating implies that thermal decomposition of C2/C60 films involves addition/uptake of C2 units into individual fullerene cages. Correspondingly, annealing films up to various intermediate temperatures results in significant modifications to valence-band UP spectra as well as to surface topographies as imaged by AFM. The novel carbonaceous material obtained by heating to T > 950 K has a finite density of states at the Fermi level in contrast to as-prepared C2/C60. It comprises fused fullerene cages.
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78.40.Ri Fullerenes and related materials
61.48.-c Structure of fullerenes and related hollow and planar molecular structures
71.20.Tx Fullerenes and related materials; intercalation compounds
71.15.Mb Density functional theory, local density approximation, gradient and other corrections
78.30.Na Fullerenes and related materials
68.43.Nr Desorption kinetics

Theory of nitrogen doping of carbon nanoribbons: Edge effects

Jie Jiang, Joseph Turnbull, Wenchang Lu, Piotr Boguslawski, and J. Bernholc

J. Chem. Phys. 136, 014702 (2012); http://dx.doi.org/10.1063/1.3673441 (6 pages) | Cited 2 times

Online Publication Date: 5 January 2012

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Nitrogen doping of a carbon nanoribbon is profoundly affected by its one-dimensional character, symmetry, and interaction with edge states. Using state-of-the-art ab initio calculations, including hybrid exact-exchange density functional theory, we find that, for N-doped zigzag ribbons, the electronic properties are strongly dependent upon sublattice effects due to the non-equivalence of the two sublattices. For armchair ribbons, N-doping effects are different depending upon the ribbon family: for families 2 and 0, the N-induced levels are in the conduction band, while for family 1 the N levels are in the gap. In zigzag nanoribbons, nitrogen close to the edge is a deep center, while in armchair nanoribbons its behavior is close to an effective-mass-like donor with the ionization energy dependent on the value of the band gap. In chiral nanoribbons, we find strong dependence of the impurity level and formation energy upon the edge position of the dopant, while such site-specificity is not manifested in the magnitude of the magnetization.
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71.55.Ht Other nonmetals
73.20.Hb Impurity and defect levels; energy states of adsorbed species
71.15.Mb Density functional theory, local density approximation, gradient and other corrections
71.18.+y Fermi surface: calculations and measurements; effective mass, g factor

Identification of the atomic scale structures of the gold-thiol interfaces of molecular nanowires by inelastic tunneling spectroscopy

Firuz Demir and George Kirczenow

J. Chem. Phys. 136, 014703 (2012); http://dx.doi.org/10.1063/1.3671455 (12 pages) | Cited 3 times

Online Publication Date: 5 January 2012

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We examine theoretically the effects of the bonding geometries at the gold-thiol interfaces on the inelastic tunneling spectra of propanedithiolate (PDT) molecules bridging gold electrodes and show that inelastic tunneling spectroscopy combined with theory can be used to determine these bonding geometries experimentally. With the help of density functional theory, we calculate the relaxed geometries and vibrational modes of extended molecules each consisting of one or two PDT molecules connecting two gold nanoclusters. We formulate a perturbative theory of inelastic tunneling through molecules bridging metal contacts in terms of elastic transmission amplitudes, and use this theory to calculate the inelastic tunneling spectra of the gold-PDT-gold extended molecules. We consider PDT molecules with both trans and gauche conformations bound to the gold clusters at top, bridge, and hollow bonding sites. Comparing our results with the experimental data of Hihath et al. [Nano Lett. 8, 1673 (2008)]10.1021/nl080580e, we identify the most frequently realized conformation in the experiment as that of trans molecules top-site bonded to both electrodes. We find the switching from the 42 meV vibrational mode to the 46 meV mode observed in the experiment to be due to the transition of trans molecules from mixed top-bridge to pure top-site bonding geometries. Our results also indicate that gauche molecular conformations and hollow site bonding did not contribute significantly to the experimental inelastic tunneling spectra. For pairs of PDT molecules connecting the gold electrodes in parallel we find total elastic conductances close to twice those of single molecules bridging the contacts with similar bonding conformations and small splittings of the vibrational mode energies for the modes that are the most sensitive to the molecule-electrode bonding geometries.
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68.35.Ct Interface structure and roughness
68.35.Ja Surface and interface dynamics and vibrations
73.40.Rw Metal-insulator-metal structures
61.46.Km Structure of nanowires and nanorods (long, free or loosely attached, quantum wires and quantum rods, but not gate-isolated embedded quantum wires)
63.22.Gh Nanotubes and nanowires
61.46.Bc Structure of clusters (e.g., metcars; not fragments of crystals; free or loosely aggregated or loosely attached to a substrate)

Structure factors in granular experiments with homogeneous fluidization

Andrea Puglisi, Andrea Gnoli, Giacomo Gradenigo, Alessandro Sarracino, and Dario Villamaina

J. Chem. Phys. 136, 014704 (2012); http://dx.doi.org/10.1063/1.3673876 (14 pages) | Cited 6 times

Online Publication Date: 6 January 2012

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Velocity and density structure factors are measured over a hydrodynamic range of scales in a horizontal quasi-2D fluidized granular experiment, with packing fractions ϕ ∈ [10%, 40%]. The fluidization is realized by vertically vibrating a rough plate, on top of which particles perform a Brownian-like horizontal motion in addition to inelastic collisions. On one hand, the density structure factor is equal to that of elastic hard spheres, except in the limit of large length-scales, as it occurs in the presence of an effective interaction. On the other hand, the velocity field shows a more complex structure which is a genuine expression of a non-equilibrium steady state and which can be compared to a recent fluctuating hydrodynamic theory with non-equilibrium noise. The temporal decay of velocity modes autocorrelations is compatible with linear hydrodynamic equations with rates dictated by viscous momentum diffusion, corrected by a typical interaction time with the thermostat. Equal-time velocity structure factors display a peculiar shape with a plateau at large length-scales and another one at small scales, marking two different temperatures: the “bath” temperature Tb, depending on shaking parameters, and the “granular” temperature Tg < Tb, which is affected by collisions. The two ranges of scales are separated by a correlation length which grows with ϕ, after proper rescaling with the mean free path.
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45.70.-n Granular systems
05.40.Jc Brownian motion

Self-metalation of 2H-tetraphenylporphyrin on Cu(111): An x-ray spectroscopy study

K. Diller, F. Klappenberger, M. Marschall, K. Hermann, A. Nefedov, Ch. Wöll, and J. V. Barth

J. Chem. Phys. 136, 014705 (2012); http://dx.doi.org/10.1063/1.3674165 (13 pages) | Cited 13 times

Online Publication Date: 6 January 2012

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The bonding and the temperature-driven metalation of 2H-tetraphenylporphyrin (2H-TPP) on the Cu(111) surface under ultrahigh vacuum conditions were investigated by a combination of x-ray photoelectron spectroscopy (XPS) and near-edge x-ray absorption fine structure (NEXAFS) spectroscopy with density functional theory calculations. Thin films were prepared by organic molecular beam epitaxy and subsequent annealing. Our systematic study provides an understanding of the changes of the spectroscopic signature during adsorption and metalation. Specifically, we achieved a detailed peak assignment of the 2H-TPP multilayer data of the C1s and the N1s region. After annealing to 420 K both XPS and NEXAFS show the signatures of a metalloporphyrin, which indicates self-metalation at the porphyrin-substrate interface, resulting in Cu-TPP. Furthermore, for 2H-TPP monolayer samples we show how the strong influence of the copper surface is reflected in the spectroscopic signatures. Adsorption results in a strongly deformed macrocycle and a quenching of the first NEXAFS resonance in the nitrogen edge suggesting electron transfer into the LUMO. For Cu-TPP the spectroscopic data indicate a reduced interaction of first-layer molecules with the substrate as demonstrated by the relaxed macrocycle geometry.
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78.70.Dm X-ray absorption spectra
68.37.-d Microscopy of surfaces, interfaces, and thin films
71.15.Mb Density functional theory, local density approximation, gradient and other corrections
68.35.B- Structure of clean surfaces (and surface reconstruction)
back to top Polymers and Complex Systems

An immersed boundary method for Brownian dynamics simulation of polymers in complex geometries: Application to DNA flowing through a nanoslit with embedded nanopits

Yu Zhang, Juan J. de Pablo, and Michael D. Graham

J. Chem. Phys. 136, 014901 (2012); http://dx.doi.org/10.1063/1.3672103 (14 pages) | Cited 9 times

Online Publication Date: 4 January 2012

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This work presents an immersed boundary method that allows fast Brownian dynamics simulation of solutions of polymer chains and other Brownian objects in complex geometries with fluctuating hydrodynamics. The approach is based on the general geometry Ewald-like method, which solves the Stokes equation with distributed regularized point forces in O(N) or O(NlogN) operations, where N is the number of point forces in the system. Time-integration is performed using a midpoint algorithm and Chebyshev polynomial approximation proposed by Fixman. This approach is applied to the dynamics of a genomic DNA molecule driven by flow through a nanofluidic slit with an array of nanopits on one wall of the slit. The dynamics of the DNA molecule was studied as a function of the Péclet number and chain length (the base case being λ-DNA). The transport characteristics of the hopping dynamics in this device differ at low and high Péclet number, and for long DNA, relative to the pit size, the dynamics is governed by the segments residing in the pit. By comparing with results that neglect them, hydrodynamic interactions are shown to play an important quantitative role in the hopping dynamics.
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87.15.hj Transport dynamics
87.15.B- Structure of biomolecules
87.15.A- Theory, modeling, and computer simulation
05.40.Jc Brownian motion
87.85.Rs Nanotechnologies-applications
87.18.Wd Genomics

Multi-scale modeling of diffusion-controlled reactions in polymers: Renormalisation of reactivity parameters

Ralf Everaers and Angelo Rosa

J. Chem. Phys. 136, 014902 (2012); http://dx.doi.org/10.1063/1.3673444 (13 pages) | Cited 3 times

Online Publication Date: 4 January 2012

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The quantitative description of polymeric systems requires hierarchical modeling schemes, which bridge the gap between the atomic scale, relevant to chemical or biomolecular reactions, and the macromolecular scale, where the longest relaxation modes occur. Here, we use the formalism for diffusion-controlled reactions in polymers developed by Wilemski, Fixman, and Doi to discuss the renormalisation of the reactivity parameters in polymer models with varying spatial resolution. In particular, we show that the adjustments are independent of chain length. As a consequence, it is possible to match reactions times between descriptions with different resolution for relatively short reference chains and to use the coarse-grained model to make quantitative predictions for longer chains. We illustrate our results by a detailed discussion of the classical problem of chain cyclization in the Rouse model, which offers the simplest example of a multi-scale descriptions, if we consider differently discretized Rouse models for the same physical system. Moreover, we are able to explore different combinations of compact and non-compact diffusion in the local and large-scale dynamics by varying the embedding dimension.
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82.20.Wt Computational modeling; simulation
82.35.-x Polymers: properties; reactions; polymerization
36.20.Fz Constitution (chains and sequences)
back to top Biological Molecules, Biopolymers, and Biological Systems

Solid effect dynamic nuclear polarization and polarization pathways

Albert A. Smith, Björn Corzilius, Alexander B. Barnes, Thorsten Maly, and Robert G. Griffin

J. Chem. Phys. 136, 015101 (2012); http://dx.doi.org/10.1063/1.3670019 (16 pages) | Cited 10 times

Online Publication Date: 4 January 2012

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Using dynamic nuclear polarization (DNP)/nuclear magnetic resonance instrumentation that utilizes a microwave cavity and a balanced rf circuit, we observe a solid effect DNP enhancement of 94 at 5 T and 80 K using trityl radical as the polarizing agent. Because the buildup rate of the solid effect increases with microwave field strength, we obtain a sensitivity gain of 128. The data suggest that higher microwave field strengths would lead to further improvements in sensitivity. In addition, the observation of microwave field dependent enhancements permits us to draw conclusions about the path that polarization takes during the DNP process. By measuring the time constant for the polarization buildup and enhancement as a function of the microwave field strength, we are able to compare models of polarization transfer, and show that the major contribution to the bulk polarization arises via direct transfer from electrons, rather than transferring first to nearby nuclei and then transferring to bulk nuclei in a slow diffusion step. In addition, the model predicts that nuclei near the electron receive polarization that can relax, decrease the electron polarization, and attenuate the DNP enhancement. The magnitude of this effect depends on the number of near nuclei participating in the polarization transfer, hence the size of the diffusion barrier, their T1, and the transfer rate. Approaches to optimizing the DNP enhancement are discussed.
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76.70.Fz Double nuclear magnetic resonance (DNMR), dynamical nuclear polarization
07.57.Pt Submillimeter wave, microwave and radiowave spectrometers; magnetic resonance spectrometers, auxiliary equipment, and techniques

Effect of glycerol and dimethyl sulfoxide on the phase behavior of lysozyme: Theory and experiments

Christoph Gögelein, Dana Wagner, Frédéric Cardinaux, Gerhard Nägele, and Stefan U. Egelhaaf

J. Chem. Phys. 136, 015102 (2012); http://dx.doi.org/10.1063/1.3673442 (12 pages) | Cited 3 times

Online Publication Date: 4 January 2012

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Salt, glycerol, and dimethyl sulfoxide (DMSO) are used to modify the properties of protein solutions. We experimentally determined the effect of these additives on the phase behavior of lysozyme solutions. Upon the addition of glycerol and DMSO, the fluid–solid transition and the gas–liquid coexistence curve (binodal) shift to lower temperatures and the gap between them increases. The experimentally observed trends are consistent with our theoretical predictions based on the thermodynamic perturbation theory and the Derjaguin-Landau-Verwey-Overbeek model for the lysozyme-lysozyme pair interactions. The values of the parameters describing the interactions, namely the refractive indices, dielectric constants, Hamaker constant and cut-off length, are extracted from literature or are experimentally determined by independent experiments, including static light scattering, to determine the second virial coefficient. We observe that both, glycerol and DMSO, render the potential more repulsive, while sodium chloride reduces the repulsion.
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87.15.km Protein-protein interactions
87.15.R- Reactions and kinetics
87.15.Zg Phase transitions
05.70.Ce Thermodynamic functions and equations of state
87.14.ej Enzymes
87.15.B- Structure of biomolecules

Structure and dynamics of nano-sized raft-like domains on the plasma membrane

Fernando E. Herrera and Sergio Pantano

J. Chem. Phys. 136, 015103 (2012); http://dx.doi.org/10.1063/1.3672704 (11 pages) | Cited 2 times

Online Publication Date: 5 January 2012

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Cell membranes are constitutively composed of thousands of different lipidic species, whose specific organization leads to functional heterogeneities. In particular, sphingolipids, cholesterol and some proteins associate among them to form stable nanoscale domains involved in recognition, signaling, membrane trafficking, etc. Atomic-detail information in the nanometer/second scale is still elusive to experimental techniques. In this context, molecular simulations on membrane systems have provided useful insights contributing to bridge this gap. Here we present the results of a series of simulations of biomembranes representing non-raft and raft-like nano-sized domains in order to analyze the particular structural and dynamical properties of these domains. Our results indicate that the smallest (5 nm) raft domains are able to preserve their distinctive structural and dynamical features, such as an increased thickness, higher ordering, lower lateral diffusion, and specific lipid-ion interactions. The insertion of a transmembrane protein helix into non-raft, extended raft-like, and raft-like nanodomain environments result in markedly different protein orientations, highlighting the interplay between the lipid-lipid and lipid-protein interactions.
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87.16.dt Structure, static correlations, domains, and rafts
87.16.dj Dynamics and fluctuations
87.14.Cc Lipids
87.14.E- Proteins
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Erratum: “Generalized Langevin dynamics of a nanoparticle using a finite element approach: Thermostating with correlated noise” [J. Chem. Phys. 135, 114104 (2011)]

B. Uma, T. N. Swaminathan, P. S. Ayyaswamy, D. M. Eckmann, and R. Radhakrishnan

J. Chem. Phys. 136, 019901 (2012); http://dx.doi.org/10.1063/1.3674980 (1 page)

Online Publication Date: 4 January 2012

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Abstract Unavailable
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99.10.Cd Errata
02.70.Dh Finite-element and Galerkin methods
02.50.Cw Probability theory
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Erratum: “QM:QM embedding using electronic densities within an ONIOM framework: Energies and analytic gradients” [J. Chem. Phys. 135, 014105 (2011)]

Hrant P. Hratchian, Aliaksandr V. Krukau, Priya V. Parandekar, Michael J. Frisch, and Krishnan Raghavachari

J. Chem. Phys. 136, 019902 (2012); http://dx.doi.org/10.1063/1.3673819 (2 pages)

Online Publication Date: 6 January 2012

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Abstract Unavailable
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99.10.Cd Errata
31.10.+z Theory of electronic structure, electronic transitions, and chemical binding
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