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7 November 2009

Volume 131, Issue 17,  Articles (17xxxx)

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Cover image from Alex W. Wilber, Jonathan P. K. Doye, and Ard A. Louis, J. Chem. Phys. 131, 175101 (2009).

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COMMUNICATIONS

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A least-constraint principle for population dynamics and reaction kinetics: Modeling entropy-controlled chemical hypercycles

Denis Horváth and Gerald R. Kneller

J. Chem. Phys. 131, 171101 (2009) (4 pages)

Online Publication Date: 2 November 2009

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In this paper, we investigate the treatment of constraints in rate equations describing the temporal evolution of biological populations or chemical reactions. We present a formulation for arbitrary holonomic and linear nonholonomic constraints which ensures the positivity of the dynamical variables and which is an analog of Gauss' principle of least constraint in classical mechanics. The approach is illustrated for the replication of molecular species in the Schuster–Eigen hypercycle model, imposing the conservation of the total number of molecules and the entropy production as constraints. The latter is used to model the behavior of an isolated system tending toward equilibrium and, for comparison, a stationary nonequilibrium state of an open system, which is characterized by undamped oscillations.
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82.20.-w, 82.39.-k, 82.60.Hc
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Nonequilibrium Fock space for the electron transport problem

D. S. Kosov

J. Chem. Phys. 131, 171102 (2009) (4 pages)

Online Publication Date: 3 November 2009

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Based on the formalism of thermofield dynamics we propose a concept of nonequilibrium Fock space and nonequilibrium quasiparticles for quantum many-body system in nonequilibrium steady state. We develop a general theory as well as demonstrate the utility of the approach on the example of electron transport through the interacting region. The proposed approach is compatible with advanced quantum chemical methods of electronic structure calculations such as coupled cluster theory and configuration interaction.
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31.15.bw, 03.65.Ta, 31.15.am
FREE

Universal perturbative explicitly correlated basis set incompleteness correction

Martin Torheyden and Edward F. Valeev

J. Chem. Phys. 131, 171103 (2009) (4 pages)

Online Publication Date: 4 November 2009

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Basis set incompleteness error for an arbitrary approximate electronic wave function is robustly reduced using a second-order perturbative correction into a basis of explicitly correlated, internally contracted geminal functions. The Hylleraas functional for the second-order energy correction is evaluated algebraically involving at most a four-electron reduced density matrix and four-electron integrals. By using the R12 technology in combination with screening approximations such a correction only requires a two-electron reduced density matrix and two-electron integrals. Preliminary investigations of potential energy surfaces of hydrogen fluoride and nitrogen molecules at the multireference configuration interaction singles and doubles indicate that with the perturbative correction only an aug-cc-pVDZ basis is necessary to compute correlation energies of an aug-cc-pVQZ quality, or better. The proposed correction, dubbed [2]R12, can in principle be combined with any single reference and multireference method in use today.
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31.15.vn, 31.50.-x, 02.60.Gf, 31.15.xp
FREE

Molecular rotor dynamics influenced by the elastic modulus of polyethylene nanocomposites

Ah-Young Jee, Haneul Kwon, and Minyung Lee

J. Chem. Phys. 131, 171104 (2009) (4 pages)

Online Publication Date: 5 November 2009

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We observed that the excited-state twisting motion of 3,3[prime]-diethyloxacarbocyanine in polymer nanocomposites (PNCs) depends strongly on the elastic modulus of medium. PNCs consist of low density polyethylene dispersed with surface-functionalized nanodiamonds with various alkyl groups. The mechanical properties of the PNCs were measured by a nanoindentation method, and the photoisomerization processes of the cyanine dye doped in the composites were investigated by time-resolved fluorescence spectroscopy. It was found that the molecular rotor dynamics in rigid media should be quantitatively describable by the elastic modulus of polymer.
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81.40.Jj, 62.20.de, 78.47.jd, 81.07.Bc
FREE

Vibrational spectroscopy of neutral silicon clusters via far-IR-VUV two color ionization

André Fielicke, Jonathan T. Lyon, Marko Haertelt, Gerard Meijer, Pieterjan Claes, Jorg de Haeck, and Peter Lievens

J. Chem. Phys. 131, 171105 (2009) (4 pages)

Online Publication Date: 5 November 2009

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Tunable far-infrared-vacuum-ultraviolet two color ionization is used to obtain vibrational spectra of neutral silicon clusters in the gas phase. Upon excitation with tunable infrared light prior to irradiation with UV photons we observe strong enhancements in the mass spectrometric signal of specific cluster sizes. This allowed the recording of the infrared absorption spectra of Si6, Si7, and Si10. Structural assignments were made by comparison with calculated linear absorption spectra from quantum chemical theory.
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36.40.Mr, 33.20.Tp, 33.20.Ni, 33.20.Ea, 33.80.Eh, 33.15.Mt
FREE

The role of the exchange in the embedding electrostatic potential for the fragment molecular orbital method

Dmitri G. Fedorov and Kazuo Kitaura (北浦和夫)

J. Chem. Phys. 131, 171106 (2009) (4 pages)

Online Publication Date: 6 November 2009

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We have examined the role of the exchange in describing the electrostatic potential in the fragment molecular orbital method and showed that it should be included in the total Fock matrix to obtain an accurate one-electron spectrum; however, adding it to the Fock matrices of individual fragments and pairs leads to very large errors. For the error analysis we have used the virial theorem; numerical tests have been performed for solvated phenol at the Hartree–Fock level with the 6-31G* and 6-311G** basis sets.
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31.15.-p
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ARTICLES

Theoretical Methods and Algorithms

Block correlated coupled cluster method with the complete active-space self-consistent-field reference function: Applications for low-lying electronic excited states

Jun Shen and Shuhua Li

J. Chem. Phys. 131, 174101 (2009) (10 pages)

Online Publication Date: 2 November 2009

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Block correlated coupled cluster (BCCC) method with the complete active-space (CAS) self-consistent-field reference function (CAS-BCCC) has been applied to investigate the vertical excitation energies of low-lying valence excited states in a number of medium-sized organic molecules, including unsaturated aliphatic hydrocarbons (ethene, E-butadiene, cyclopropene, and cyclopentadiene), aromatic heterocycles (furan and pyrrole), and carbonyl compounds (formaldehyde, acetone, and formamide). An approximate CAS-BCCC with the cluster operator truncated up to the four-block correlation level, CAS-BCCC4, is employed in the calculations. The results are compared with those from the multireference configuration interaction with singles and doubles (MR-CISD and its corrected version, MR-CISD+Q), the complete active space with second-order perturbation theory (CASPT2), and CC3. Our results show that the overall performance of CAS-BCCC4 is competitive with that of the multistate CASPT2 (slightly inferior to MR-CISD+Q), better than that of the single-state CASPT2 and MR-CISD approaches. For triplet excited states, various methods tend to give relatively consistent predictions. However, for singlet excited states, various methods lead to quite different excitation energies in some cases.
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31.15.bw, 31.15.xr, 31.15.xp

Geometry and stability of CunN (n=1–6) and Cu3nNn (n=1–5) clusters

Jian-Ning Ding, Ning-Yi Yuan, Feng Li, Gu-Qiao Ding, Zhi-Gang Chen, Xiao-Shuang Chen, and Wei Lu

J. Chem. Phys. 131, 174102 (2009) (6 pages)

Online Publication Date: 2 November 2009

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The gradient-corrected density functional calculation is applied to search the lowest-energy configurations of CunN (n=1–6) clusters and the calculation indicated that Cu3N cluster is the most stable one. Based on the result, we further investigate the equilibrium geometries and stabilities of the Cu3nNn (n=2–5) clusters. We found that in Cu6N2 cluster, N atoms formed a separate N2 molecule away from the other part of the cluster. Furthermore, it was shown that the lowest-energy configurations of Cu3nNn (n=3–5) are stable with the nitrogen atoms well separated by the copper atoms. Therefore, it can be concluded that the Cu3N cluster can be used as a building block for the construction of the cluster-assembled compounds.
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33.15.Bh, 31.15.bw, 31.15.es

Nonproduct quadrature grids for solving the vibrational Schrödinger equation

Gustavo Avila and Tucker Carrington, Jr.

J. Chem. Phys. 131, 174103 (2009) (15 pages)

Online Publication Date: 2 November 2009

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The size of the quadrature grid required to compute potential matrix elements impedes solution of the vibrational Schrödinger equation if the potential does not have a simple form. This quadrature grid-size problem can make computing (ro)vibrational spectra impossible even if the size of the basis used to construct the Hamiltonian matrix is itself manageable. Potential matrix elements are typically computed with a direct product Gauss quadrature whose grid size scales as ND, where N is the number of points per coordinate and D is the number of dimensions. In this article we demonstrate that this problem can be mitigated by using a pruned basis set and a nonproduct Smolyak grid. The constituent 1D quadratures are designed for the weight functions important for vibrational calculations. For the SF6 stretch problem (D=6) we obtain accurate results with a grid that is more than two orders of magnitude smaller than the direct product Gauss grid. If D>6 we expect an even bigger reduction.
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33.20.Tp

On the difference between the transition properties calculated with linear response- and equation of motion-CCSD approaches

Marco Caricato, Gary W. Trucks, and Michael J. Frisch

J. Chem. Phys. 131, 174104 (2009) (6 pages)

Online Publication Date: 2 November 2009

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In this work, we quantitatively investigate the difference between the linear response (LR) and the equation of motion (EOM) coupled cluster (CC) approaches in the calculation of transition properties, namely, dipole and oscillator strengths, for the most widely used truncated CC wave function, which includes single and double excitation operators. We compare systems of increasing size, where the size-extensivity may be important. Our results suggest that, for small molecules, the difference is small even with large basis sets. The difference increases with the size of the system, but it is numerically small until hundreds of electron pairs are correlated. Although these calculations may be possible in a few years, at present the EOM approach is more advantageous, albeit more approximate, because it is computationally less demanding.
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31.15.bw, 33.70.Ca

Long-range corrected double-hybrid density functionals

Jeng-Da Chai and Martin Head-Gordon

J. Chem. Phys. 131, 174105 (2009) (13 pages)

Online Publication Date: 3 November 2009

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We extend the range of applicability of our previous long-range corrected (LC) hybrid functional, omegaB97X [J.-D. Chai and M. Head-Gordon, J. Chem. Phys. 128, 084106 (2008)], with a nonlocal description of electron correlation, inspired by second-order Møller–Plesset (many-body) perturbation theory. This LC “double-hybrid” density functional, denoted as omegaB97X-2, is fully optimized both at the complete basis set limit (using 2-point extrapolation from calculations using triple and quadruple zeta basis sets), and also separately using the somewhat less expensive 6-311++G(3df,3pd) basis. On independent test calculations (as well as training set results), omegaB97X-2 yields high accuracy for thermochemistry, kinetics, and noncovalent interactions. In addition, owing to its high fraction of exact Hartree–Fock exchange, omegaB97X-2 shows significant improvement for the systems where self-interaction errors are severe, such as symmetric homonuclear radical cations.
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31.15.eg, 31.15.V-, 31.15.xp, 31.15.xr

A separable shadow Hamiltonian hybrid Monte Carlo method

Christopher R. Sweet, Scott S. Hampton, Robert D. Skeel, and Jesús A. Izaguirre

J. Chem. Phys. 131, 174106 (2009) (7 pages)

Online Publication Date: 3 November 2009

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Hybrid Monte Carlo (HMC) is a rigorous sampling method that uses molecular dynamics (MD) as a global Monte Carlo move. The acceptance rate of HMC decays exponentially with system size. The shadow hybrid Monte Carlo (SHMC) was previously introduced to reduce this performance degradation by sampling instead from the shadow Hamiltonian defined for MD when using a symplectic integrator. SHMC's performance is limited by the need to generate momenta for the MD step from a nonseparable shadow Hamiltonian. We introduce the separable shadow Hamiltonian hybrid Monte Carlo (S2HMC) method based on a formulation of the leapfrog/Verlet integrator that corresponds to a separable shadow Hamiltonian, which allows efficient generation of momenta. S2HMC gives the acceptance rate of a fourth order integrator at the cost of a second-order integrator. Through numerical experiments we show that S2HMC consistently gives a speedup greater than two over HMC for systems with more than 4000 atoms for the same variance. By comparison, SHMC gave a maximum speedup of only 1.6 over HMC. S2HMC has the additional advantage of not requiring any user parameters beyond those of HMC. S2HMC is available in the program PROTOMOL 2.1. A Python version, adequate for didactic purposes, is also in MDL (http://mdlab.sourceforge.net/s2hmc).
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31.15.xv, 02.70.Uu

A soft-core Gay–Berne model for the simulation of liquid crystals by Hamiltonian replica exchange

Roberto Berardi, Claudio Zannoni, Juho S. Lintuvuori, and Mark R. Wilson

J. Chem. Phys. 131, 174107 (2009) (6 pages)

Online Publication Date: 3 November 2009

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The Gay–Berne (GB) potential has proved highly successful in the simulation of liquid crystal phases, although it is fairly demanding in terms of resources for simulations of large (e.g., N>105) systems, as increasingly required in applications. Here, we introduce a soft-core GB model, which exhibits both liquid crystal phase behavior and rapid equilibration. We show that the Hamiltonian replica exchange method, coupled with the newly introduced soft-core GB model, can effectively speed up the equilibration of a GB liquid crystal phase by frequent exchange of configurations between replicas, while still recovering the mesogenic properties of the standard GB potential.
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61.30.Cz

First-principles molecular dynamics simulations at solid-liquid interfaces with a continuum solvent

Verónica M. Sánchez, Mariela Sued, and Damián A. Scherlis

J. Chem. Phys. 131, 174108 (2009) (10 pages)

Online Publication Date: 4 November 2009

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Continuum solvent models have become a standard technique in the context of electronic structure calculations, yet no implementations have been reported capable to perform molecular dynamics at solid-liquid interfaces. We propose here such a continuum approach in a density functional theory framework using plane-wave basis sets and periodic boundary conditions. Our work stems from a recent model designed for Car–Parrinello simulations of quantum solutes in a dielectric medium [D. A. Scherlis et al., J. Chem. Phys. 124, 074103 (2006)], for which the permittivity of the solvent is defined as a function of the electronic density of the solute. This strategy turns out to be inadequate for systems extended in two dimensions: the dependence of the dielectric function on the electronic density introduces a new term in the Kohn–Sham potential, which becomes unphysically large at the interfacial region, seriously affecting the convergence of the self-consistent calculations. If the dielectric medium is properly redefined as a function of the atomic coordinates, a good convergence is obtained and the constant of motion is conserved during the molecular dynamics simulations. The Poisson problem is solved using a multigrid method, and in this way Car–Parrinello molecular dynamics simulations of solid-liquid interfaces can be performed at a very moderate computational cost. This scheme is employed to investigate the acid-base equilibrium at the TiO2-water interface. The aqueous behavior of titania surfaces has stimulated a large amount of experimental research, but many open questions remain concerning the molecular mechanisms determining the chemistry of the interface. Here we make an attempt to answer some of them, putting to the test our continuum model.
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68.08.De, 71.15.Pd, 77.22.Ch, 71.15.Mb, 82.65.+r, 71.45.Gm

Cumulant decomposition of reduced density matrices, multireference normal ordering, and Wicks theorem: A spin-free approach

K. R. Shamasundar

J. Chem. Phys. 131, 174109 (2009) (17 pages)

Online Publication Date: 4 November 2009

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We propose a spin-free approach to the cumulant decomposition of reduced density matrices of singlet and spin-rotation or SU(2) invariant ensemble of nonsinglet states as in [W. Kutzelnigg and D. Mukherjee, J. Chem. Phys. 110, 2800 (1999); 116, 4787 (2002)]. We provide a simple recursive procedure to obtain expressions which relate different spin components of spin-orbital reduced density matrices and cumulants of such states to the spin-free counterparts. These results are used to set up a spin-summation procedure to arrive at a definition of spin-free cumulants of any order. Alternatively, an analytic formula for the spin-free form resulting from a spin summation involving product of two spin-orbital cumulants is derived and its utility in spin-free cumulant decomposition of reduced density matrices is demonstrated. This leads to suitable definitions of spin-free analog of multireference normal ordering and the associated Wicks theorem. The results of this formulation are expected to be useful in investigations of spin-free multireference internally contracted coupled-cluster methods where cumulant approximations to the active reduced density matrices are employed.
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31.15.E-, 31.15.bw

Ca impurity in small mixed 4He–3He clusters

R. Guardiola, J. Navarro, D. Mateo, and M. Barranco

J. Chem. Phys. 131, 174110 (2009) (6 pages)

Online Publication Date: 4 November 2009

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The structure of small mixed helium clusters doped with one calcium atom has been determined within the diffusion Monte Carlo framework. The results show that the calcium atom sits at the 4He–3He interface. This is in agreement with previous studies, both experimental and theoretical, performed for large clusters. A comparison between the results obtained for the largest cluster we have considered for each isotope shows a clear tendency of the Ca atom to reside in a deep dimple at the surface of the cluster for 4He clusters, and to become fully solvated for 3He clusters. We have calculated the absorption spectrum of Ca around the 4s4p<--4s2 transition and have found that it is blueshifted from that of the free-atom transition by an amount that depends on the size and composition of the cluster.
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36.40.Cg, 36.40.Mr, 67.60.-g

The Landau free energy of a melt of graft copolymers

M. A. Aliev and S. I. Kuchanov

J. Chem. Phys. 131, 174111 (2009) (25 pages)

Online Publication Date: 5 November 2009

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New graphical algorithm is proposed to find vertex functions which are the coefficients of expansion of the Landau free energy of polydisperse multigraft copolymers whose macromolecules comprise an arbitrary number of types of side chains. This algorithm imposes no restriction on length distributions of side chains in copolymer macromolecules as well as on distribution of distances between two successive grafting points along the backbone. By way of example, with this algorithm the expressions for the second, third, and fourth order contributions into the free energy have been derived. The obtained results can be used for construction of the phase diagrams of polydisperse multigraft copolymers.
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61.25.hk, 65.20.Jk, 61.20.-p, 82.35.Jk

A relook at the compliance constants in redundant internal coordinates and some new insights

M. Vijay Madhav and S. Manogaran

J. Chem. Phys. 131, 174112 (2009) (6 pages)

Online Publication Date: 6 November 2009

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The compliance constants, the inverse of the force constant matrix elements offer the advantage that any one of them could be calculated directly without the need to calculate the full Hessian. Here we show that such a direct calculation produces accurate results. Since the diagonal G and the compliance matrix elements (Gii,Cii) give unique values that are independent of the other internal coordinates, an internal frequency ([overline nu ]) is defined which could be effectively used to study related molecules. The conventional coordinates used for benzene and cubane give some of the compliance constants, which differ from the values obtained by the direct method by 5%–40%, indicating that the coordinate systems used are deficient. We identify the source of this discrepancy and find a way to form the correct coordinate system in the sense that the Hessian method and the direct method will lead to the same compliance constants. This procedure takes away the simplicity of local coordinates at least in highly symmetric molecules and it is advantageous to have the potential energy distribution in redundant internal coordinates. A method is proposed for this purpose. All these imply that the most satisfactory way of describing the molecular force field is in terms of redundant internal compliance constants.
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33.20.Tp, 02.60.Dc, 31.15.X-, 33.15.Mt

Improving replica exchange using driven scaling

Alexis J. Lee and Steven W. Rick

J. Chem. Phys. 131, 174113 (2009) (8 pages)

Online Publication Date: 6 November 2009

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Replica exchange is a powerful simulation method in which simulations are run at a series of temperatures, with the highest temperature chosen so phase space can be sampled efficiently. In order for swaps to be accepted, the energy distributions of adjacent replicas must have some overlap. This can create the need for many replicas for large systems. In this paper, we present a new method in which the potential energy is scaled by a parameter, which has an explicit time dependence. Scaling the potential energy broadens the distribution of energy and reduces the number of replicas necessary to span a given temperature range. We demonstrate that if the system is driven by the time-dependent potential sufficiently slowly, then equilibrium is maintained and energetic and structural properties are identical to those of conventional replica exchange. The method is tested using two systems, the alanine dipeptide and the trpzip2 polypeptide, both in water.
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87.15.A-, 87.15.B-, 87.14.ef, 02.60.Pn

Phase diagram and structural properties of a simple model for one-patch particles

Achille Giacometti, Fred Lado, Julio Largo, Giorgio Pastore, and Francesco Sciortino

J. Chem. Phys. 131, 174114 (2009) (13 pages)

Online Publication Date: 6 November 2009

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We study the thermodynamic and structural properties of a simple, one-patch fluid model using the reference hypernetted-chain (RHNC) integral equation and specialized Monte Carlo simulations. In this model, the interacting particles are hard spheres, each of which carries a single identical, arbitrarily oriented and attractive circular patch on its surface; two spheres attract via a simple square-well potential only if the two patches on the spheres face each other within a specific angular range dictated by the size of the patch. For a ratio of attractive to repulsive surface of 0.8, we construct the RHNC fluid-fluid separation curve and compare with that obtained by Gibbs ensemble and grand canonical Monte Carlo simulations. We find that RHNC provides a quick and highly reliable estimate for the position of the fluid-fluid critical line. In addition, it gives a detailed (though approximate) description of all structural properties and their dependence on patch size.
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81.30.Dz, 61.20.Ja, 61.25.-f

Gas Phase Dynamics and Structure: Spectroscopy, Molecular Interactions, Scattering, and Photochemistry

Photodissociation cross sections of ClOOCl at 248.4 and 266 nm

Chien-Yu Lien, Wei-Yen Lin, Hsueh-Ying Chen, Wen-Tsung Huang, Bing Jin, I-Cheng Chen, and Jim J. Lin

J. Chem. Phys. 131, 174301 (2009) (6 pages)

Online Publication Date: 2 November 2009

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This study utilized a mass-resolved detection of ClOOCl to determine its photodissociation cross section, which is the product of the absorption cross section and dissociation quantum yield. An effusive molecular beam of ClOOCl was generated and its photodissociation probability was determined through measuring the decrease in the ClOOCl beam intensity upon laser irradiation. By comparing with a reference molecule, the absolute cross sections of ClOOCl were obtained without knowing its absolute concentration. The determined cross section of ClOOCl at 248.4 nm is (8.85±0.42)×10−18  cm2 at 200 K, significantly larger than previously reported values. The temperature dependence of the cross section was investigated at 248.4 nm in the range of 160–260 K; only a very small and negative temperature effect was observed. Because 248.4 nm is very close to the peak of the UV absorption band of ClOOCl, this work provides a new calibration point for normalizing relative absorption spectra of ClOOCl. In this work, the photodissociation cross section at 266 nm and 200 K was also reported to be (4.13±0.21)×10−18  cm2.
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82.50.Hp, 82.80.Gk

Structure and optical properties of core-shell bimetallic AgnNin clusters: Comparison with pure silver and nickel clusters

M. Harb, F. Rabilloud, and D. Simon

J. Chem. Phys. 131, 174302 (2009) (8 pages)

Online Publication Date: 2 November 2009

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We present the structural, electronic, and optical properties of bimetallic AgnNin (n<=7) clusters investigated in the framework of the density functional theory (DFT) (DFT and time-dependent DFT). The structure of AgnNin clusters is found to be governed essentially by the formation of a Ni-core surrounded by silver atoms. The cohesive energies and the ionization potentials are calculated. The UV-visible absorption spectra of bimetallic clusters are compared to those of pure silver and nickel clusters. An interpretation of spectroscopic patterns in terms of contribution from s- and d-type excitations is also given. In particular the d electrons of nickel atoms are found to play a crucial role in the optical transitions in Ni-rich systems.
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78.67.Bf, 78.40.Kc, 71.15.Mb, 61.46.Bc, 73.22.-f

Valence ionization spectra of group six metal hexacarbonyls studied by the symmetry-adapted cluster-configuration interaction method

Ryoichi Fukuda, Seigo Hayaki, and Hiroshi Nakatsuji

J. Chem. Phys. 131, 174303 (2009) (10 pages)

Online Publication Date: 2 November 2009

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The valence ionization spectra up to 20 eV of group six metal carbonyls, chromium hexacarbonyl, molybdenum hexacarbonyl, and tungsten hexacarbonyl were studied by the symmetry-adapted cluster-configuration interaction (SAC-CI) method. The assignments of the spectra are given based on reliable SAC-CI calculations. The relativistic effects including the spin-orbit effects are important for the ionization spectrum of W(CO)6. The relation between the metal-CO distance and ionization energies was examined. The lowest ionization energies of the three metal carbonyls are approximately the same because of the energy dependence of the metal-CO length and relativistic effects. In Cr(CO)6, the Cr–CO interaction significantly increases the lowest ionization energy in comparison with Mo(CO)6 and W(CO)6 because of the relatively short metal-CO bond length. The relativistic effect reduces the lowest ionization energy of W(CO)6 because the effective core potential of 5d electrons is more efficiently screened as a result of the relativistic contraction of the inner electrons.
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31.15.am, 33.15.Dj, 31.30.-i

On the kinetics of the Al13−+Cl2 reaction: Cluster degradation in consecutive steps

Matthias Olzmann, Ralf Burgert, and Hansgeorg Schnöckel

J. Chem. Phys. 131, 174304 (2009) (7 pages)

Online Publication Date: 2 November 2009

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The kinetics of the reaction system initiated by the Al13−+Cl2 reaction was experimentally studied in a Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometer. The Al13− clusters were produced by laser desorption/ionization of LiAlH4, then transferred into the ICR cell, cooled by collisions with Ar, and exposed to an excess of Cl2 with a concentration of ~108  cm−3. Relative concentration-time profiles of Aln− clusters with n=13, 11, 9, and 7 as well as profiles of Cl− ions have been recorded. Other ionic species, besides traces of Al12Cl−, were not found, which indicates a double-step degradation mechanism via the odd-numbered Aln− clusters. From a kinetic analysis of the experimental results, a rate coefficient of (5±2)×10−10  cm3 s−1 for the Al13−+Cl2 reaction was obtained. Furthermore, it is inferred from a simultaneous fit of all concentration-time profiles that the Aln−+Cl2 reactions for n=13, 11, 9, and 7 occur with rate coefficients near the Langevin limit in the range kbim~(5±4)×10−10  cm3 s−1. The branching ratios between the Aln−2−-producing and Cl−-producing channels of a given cluster AlnCl2− indicate an increasing contribution of the Cl−-producing channels with decreasing cluster size. Statistical rate theory calculations on the basis of molecular data from quantum chemical calculations show that the experimental Aln− profiles are compatible with a sequence of association-elimination reactions proceeding via the formation of highly excited AlnCl2− adducts followed by a sequential elimination of two AlCl molecules. Rate coefficients for these reactions were calculated, and the production of Cl− was shown probably not to proceed via these AlnCl2− intermediates.
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82.30.Cf, 82.30.Nr, 36.40.-c, 82.20.Pm, 82.20.Db

Comparison of the resonance-enhanced multiphoton ionization spectra of pyrrole and 2,5-dimethylpyrrole: Building toward an understanding of the electronic structure and photochemistry of porphyrins

Joseph M. Beames, Michael G. D. Nix, and Andrew J. Hudson

J. Chem. Phys. 131, 174305 (2009) (10 pages)

Online Publication Date: 3 November 2009

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The photophysical properties of porphyrins have relevance for their use as light-activated drugs in cancer treatment and sensitizers in solid-state solar cells. However, the appearance of their UV-visible spectra is usually explained inadequately by qualitative molecular-orbital theories. We intend to gain a better insight into the intense absorption bands, and excited-state dynamics, that make porphyrins appropriate for both of these applications by gradually building toward an understanding of the macrocyclic structure, starting with studies of smaller pyrrolic subunits. We have recorded the (1+1) and (2+1) resonance-enhanced multiphoton ionization (REMPI) spectra of pyrrole and 2,5-dimethylpyrrole between 25 600  cm−1 (390 nm) and 48 500  cm−1 (206 nm). We did not observe a (1+1) REMPI signal through the optically bright 1B2 (pipi*) and 1A1 (pipi*) states in pyrrole due to ultrafast deactivation via conical intersections with the dissociative 1A2 (pisigma*) and 1B1 (pisigma*) states. However, we did observe (2+1) REMPI through Rydberg states with a dominant feature at 27 432  cm−1 (two-photon energy, 54 864  cm−1) assigned to a 3d<--pi transition. In contrast, 2,5-dimethylpyrrole has a broad and structured (1+1) REMPI spectrum between 36 000 and 42 500  cm−1 as a result of vibronic transitions to the 1B2 (pipi*) state, and it does not show the 3d<--pi Rydberg transition via (2+1) REMPI. We have complemented the experimental studies by a theoretical treatment of the excited states of both molecules using time-dependent density functional theory (TD-DFT) and accounted for the contrasting features in the spectra. TD-DFT modeled the photochemical activity of both the optically dark 1pisigma* states (dissociative) and optically bright 1pipi* states well, predicting the barrierless deactivation of the 1B2 (pipi*) state of pyrrole and the bound minimum of the 1B2 (pipi*) state in 2,5-dimethylpyrrole. However, the quantitative agreement between vibronic transition energies and the excited-state frequencies calculated by TD-DFT was hampered by inaccurate modeling of Rydberg orbital mixing with the valence states, caused by the lack of an asymptotic correction to the exchange-correlation functionals used.
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82.50.Hp, 71.15.Mb, 78.40.Me

Fragmentation properties of three-membered heterocyclic molecules by partial ion yield spectroscopy: C2H4O and C2H4S

W. C. Stolte, I. Dumitriu, S.-W. Yu, G. Öhrwall, M. N. Piancastelli, and D. W. Lindle

J. Chem. Phys. 131, 174306 (2009) (10 pages)

Online Publication Date: 3 November 2009

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We investigated the photofragmentation properties of two three-membered ring heterocyclic molecules, C2H4O and C2H4S, by total and partial ion yield spectroscopy. Positive and negative ions have been collected as a function of photon energy around the C 1s and O 1s ionization thresholds in C2H4O, and around the S 2p and C 1s thresholds in C2H4S. We underline similarities and differences between these two analogous systems. We present a new assignment of the spectral features around the C K-edge and the sulfur L2,3 edges in C2H4S. In both systems, we observe high fragmentation efficiency leading to positive and negative ions when exciting these molecules at resonances involving core-to-Rydberg transitions. The system, with one electron in an orbital far from the ionic core, relaxes preferentially by spectator Auger decay, and the resulting singly charged ion with two valence holes and one electron in an outer diffuse orbital can remain in excited states more susceptible to dissociation. A state-selective fragmentation pattern is analyzed in C2H4S which leads to direct production of S2+ following the decay of virtual-orbital excitations to final states above the double-ionization threshold.
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33.80.Gj, 33.15.Ry

The interaction of Al atoms with water molecules: A theoretical study

S. Álvarez-Barcia and J. R. Flores

J. Chem. Phys. 131, 174307 (2009) (11 pages)

Online Publication Date: 4 November 2009

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The interaction of individual Al atoms with water molecules has been studied from the point of view of the energy by means of ab initio and DFT calculations in order to find the pathways for the generation of HAlOH·(H2O)n or AlOH·(H2O)n+H. The potential energy surface of the Al(H2O)n+1 (n=0–3) systems has been explored for local minima and the relevant saddle points. The interaction of Al and several water molecules tends to produce low-lying local minima in which (for n=2–3) Al is “inserted” into relatively compact structures of water molecules, so typically a ring is formed containing an Al·OH2 moiety. Isomerization of such moiety into HAlOH·(H2O)n may take place through saddle points of the “relay” type; however those saddle points lie very close to Al·OH2·(H2O)n−1+H2O, which means that such isomerization process has to compete with a water-elimination process. Larger systems Al(H2O)n+1 (n=4–7) have also been computed by means of a DFT method, as a first step to predict the behavior of isolated Al atoms in even larger clusters or in the bulk. Finally, an effective fragment potential method has been employed to simulate those large clusters together with a polarizable continuum model to take into account the effect of the bulk. Our results suggest that the reaction should take place in inert matrices and in the bulk. We also conclude that HAlOH·(H2O)n and AlOH·(H2O)n could be the intermediates involved in the generation of hydrogen by the interaction of Al atoms with water, so their production would be the critical step of such process.
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82.30.Cf, 82.20.Kh, 82.30.Qt, 82.20.Db

Isofulminic acid, HONC: Ab initio theory and microwave spectroscopy

Mirjana Mladenović, Marius Lewerenz, Michael C. McCarthy, and Patrick Thaddeus

J. Chem. Phys. 131, 174308 (2009) (10 pages)

Online Publication Date: 4 November 2009

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Isofulminic acid, HONC, the most energetic stable isomer of isocyanic acid HNCO, higher in energy by 84 kcal/mol, has been detected spectroscopically by rotational spectroscopy supported by coupled cluster electronic structure calculations. The fundamental rotational transitions of the normal, carbon-13, oxygen-18, and deuterium isotopic species have been detected in the centimeter band in a molecular beam by Fourier transform microwave spectroscopy, and rotational constants and nitrogen and deuterium quadrupole coupling constants have been derived. The measured constants agree well with those predicted by ab initio calculations. A number of other electronic and spectroscopic parameters of isofulminic acid, including the dipole moment, vibrational frequencies, infrared intensities, and centrifugal distortion constants have been calculated at a high level of theory. Isofulminic acid is a good candidate for astronomical detection with radio telescopes because it is highly polar and its more stable isomers (HNCO, HOCN, and HCNO) have all been identified in space.
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31.15.at, 33.15.Hp, 33.15.Mt, 33.20.Sn, 33.20.Bx, 31.15.bw

The photodissociation of CH3I in the red edge of the A-band: Comparison between slice imaging experiments and multisurface wave packet calculations

L. Rubio-Lago, A. García-Vela, A. Arregui, G. A. Amaral, and L. Bañares

J. Chem. Phys. 131, 174309 (2009) (17 pages)

Online Publication Date: 5 November 2009

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The photodissociation of methyl iodide at different wavelengths in the red edge of the A-band (286–333 nm) has been studied using a combination of slice imaging and resonance enhanced multiphoton ionization detection of the methyl fragment in the vibrational ground state (nu=0). The kinetic energy distributions (KED) of the produced CH3(nu=0) fragments show a vibrational structure, both in the I(2P3/2) and I*(2P1/2) channels, due to the contribution to the overall process of initial vibrational excitation in the nu3(C–I) mode of the parent CH3I. The structures observed in the KEDs shift toward upper vibrational excited levels of CH3I when the photolysis wavelength is increased. The I(2P3/2)/I*(2P1/2) branching ratios, photofragment anisotropies, and the contribution of vibrational excitation of the parent CH3I are explained in terms of the contribution of the three excited surfaces involved in the photodissociation process, 3Q0, 1Q1, and 3Q1, as well as the probability of nonadiabatic curve crossing 1Q1<--3Q0. The experimental results are compared with multisurface wave packet calculations carried out using the available ab initio potential energy surfaces, transition moments, and nonadiabatic couplings, employing a reduced dimensionality (pseudotriatomic) model. A general qualitative good agreement has been found between theory and experiment, the most important discrepancies being in the I(2P3/2)/[I(2P3/2)+I*(2P1/2)] branching ratios. Inaccuracies of the available potential energy surfaces are the main reason for the discrepancies.
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33.80.Gj, 31.15.A-, 33.15.Mt, 33.80.Rv, 33.80.Eh

Femtosecond time resolved coherent anti-Stokes Raman spectroscopy of H2–N2 mixtures in the Dicke regime: Experiments and modeling of velocity effects

H. Tran, F. Chaussard, N. Le Cong, B. Lavorel, O. Faucher, and P. Joubert

J. Chem. Phys. 131, 174310 (2009) (6 pages)

Online Publication Date: 5 November 2009

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In this paper, we present measurements and modeling of femtosecond time resolved coherent anti-Stokes Raman spectroscopy (CARS) signal in H2–N2 mixtures at low densities. Three approaches have been used to model the CARS response. The first is the usual sum of Voigt profiles. In the second approach, the speed dependent Voigt profile is used. In the last approach, a model of the temporal CARS signal is developed, which takes into account the velocity changes induced by collisions and the speed dependence of the collisional parameters. The velocity changes are modeled using the Keilson and Storer memory function; the radiator speed dependences of the collisional parameters are determined from their temperature dependences. The results obtained are consistent with previous studies in the frequency domain, showing that the changes of the velocity have important effects for the H2/N2 system in the Dicke narrowing density regime.
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33.20.Fb, 33.70.Jg, 06.60.Jn

Hydrogen bonding in acetone clusters probed by near-edge x-ray absorption fine structure spectroscopy in the carbon and oxygen K-edge regions

Y. Tamenori, O. Takahashi, K. Yamashita, T. Yamaguchi, K. Okada, K. Tabayashi, T. Gejo, and K. Honma

J. Chem. Phys. 131, 174311 (2009) (9 pages)

Online Publication Date: 5 November 2009

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Hydrogen bonding in acetone clusters was investigated using near-edge x-ray absorption fine structure (NEXAFS) spectroscopy and density functional theory calculations in the carbon and oxygen K-edge regions. The partial-ion-yield (PIY) curves of the cluster ions were measured as the NEXAFS spectra of acetone clusters. In the carbon K-edge region, the first resonance peak, which was assigned to the CCO 1s-->pi*(C=O) resonance transition, showed no substantial change in the PIY curves of the acetone clusters, while the CCH3 1s-->3ppi(CH3) excitation feature was found to be strongly suppressed. The selective suppression of the CCH3 1s-->3ppi(CH3) resonance transition can be explained by the change in the character of the 3ppi(CH3) orbital due to the C=O[centered ellipsis]H–C type of hydrogen-bonding interaction. On the other hand, the NEXAFS spectra of the acetone molecule and clusters were almost identical in the oxygen K-edge region, except for a small shift in the pi*(C=O) resonance of 0.13 eV, because the character of the pi*(C=O) orbital remained, regardless of the C=O[centered ellipsis]H–C hydrogen bonding interaction.
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78.70.Dm, 71.15.Mb, 73.22.-f, 61.46.Bc

Dynamics of multidissociation paths of acetaldehyde photoexcited at 157 nm: Branching ratios, distributions of kinetic energy, and angular anisotropies of products

Shih-Huang Lee

J. Chem. Phys. 131, 174312 (2009) (10 pages)

Online Publication Date: 6 November 2009

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After the photolysis of acetaldehyde (CH3CHO) at 157.6 nm in a molecular-beam apparatus using photofragment translational spectroscopy and vacuum-ultraviolet photoionization to detect products, we observed 13 photofragments associated with six primary dissociation channels and secondary dissociation of products CH3CO and HCO. We measured time-of-flight spectra and spatial angular anisotropies of products and evaluated the branching ratios of products. All photoproducts have nearly isotropic angular distributions with an average |beta| value less than 0.05. Primary dissociations to CH3CO+H and CH3+HCO are two major paths; most CH3CO subsequently decomposes spontaneously to CH3+CO and CH2CO+H and most HCO decomposes to H+CO. The ternary dissociation to CH3+CO+H thus accounts for approximately half of the total branching. Dissociations to CH2CO+H2 and CH2+CH2O are observable, but the production of CH4+CO is ambiguous. The productions of C2H3+OH and C2H2+H2O indicate that isomerization from acetaldehyde to ethenol occurs before fragmentation. After photoexcitation to the n-3p state, most acetaldehyde converts into states T1 and S0 but a little isomerizes to ethenol followed by multichannel decomposition.
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82.50.Hp, 82.80.Gk, 82.30.Qt, 82.30.Lp

Ab initio study of the excited singlet states of all-trans alpha,omega-diphenylpolyenes with one to seven polyene double bonds: Simulation of the spectral data within Franck–Condon approximation

Wataru Mizukami, Yuki Kurashige, Masahiro Ehara, Takeshi Yanai, and Takao Itoh

J. Chem. Phys. 131, 174313 (2009) (10 pages)

Online Publication Date: 6 November 2009

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Computational simulations of the electronic spectra with ab initio electronic structure calculations are presented for all-trans alpha,omega-diphenylpolyenes with the polyene double bond number (N) from 1 to 7. A direct comparison of the fluorescence spectra of diphenylpolyenes was made between the results of highly accurate calculations and the experimental data for the systems with various chain lengths. For the realistic simulation of the emission, the total vibrational wave function was described approximately as a direct product of one-dimensional (1D) vibrational wave functions along the normal coordinates that are determined from the vibrational analysis of the ground state. The observed spectra can be reproduced in a computationally efficient way by selecting effective C–C and C=C stretching modes for the constructions of the 1D vibrational Hamiltonians. The electronic structure calculations were performed using the multireference Møller–Plesset perturbation theory with complete active space configuration interaction reference functions. Based on the vertical excitation energies computed, the lowest singlet excited state of diphenylbutadiene is shown to be the optically forbidden 2 1Ag state. The simulations of fluorescence spectra involving vibronic coupling effects reveal that the observed strong single C=C band consists of two major degenerate vibrational C=C modes for the shorter diphenylpolyenes with N=3 and 5. Further, the relative intensities of the C–C stretching modes in the fluorescence spectra tend to be larger than those of the C=C stretching modes for the systems with N over 5. This indicates that the geometric differences of the energy minima between the ground (1 1Ag) and 2 1Ag states grow larger towards the direction of the C–C stretching mode with increasing N.
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71.15.Qe, 61.50.Lt, 78.55.Kz, 63.50.-x, 71.20.Rv

Condensed Phase Dynamics, Structure, and Thermodynamics: Spectroscopy, Reactions, and Relaxation

Optimal excitation of 23Na nuclear spins in the presence of residual quadrupolar coupling and quadrupolar relaxation

Jae-Seung Lee, Ravinder R. Regatte, and Alexej Jerschow

J. Chem. Phys. 131, 174501 (2009) (8 pages)

Online Publication Date: 2 November 2009

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Optimal control theory is applied for designing pulse sequences to optimally excite a spin-3/2 system with residual quadrupolar coupling in the presence of quadrupolar relaxation. A homogeneous form of the master equation is constructed to simulate the dynamics of the spin system, and a general optimization procedure with a homogeneous form of the equation of motion is described. The optimized pulses are tested with 23Na NMR, and their performance is compared with that of pulses optimized in the absence of relaxation.
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33.25.+k

Bulk viscosity universality and scaling function near the binary liquid consolute point

Jayanta K. Bhattacharjee, Ireneusz Iwanowski, and Udo Kaatze

J. Chem. Phys. 131, 174502 (2009) (5 pages)

Online Publication Date: 2 November 2009

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The hydrodynamical equations and the notion of a frequency dependent complex specific heat near the critical point of binary liquids are used to obtain an expression for the low-frequency bulk viscosity. In this way the interrelations between different theoretical models, treating the critical sound attenuation from either a specific heat or a bulk viscosity approach, are made evident. The general structure of the bulk viscosity relation agrees with that of Onuki [Phys. Rev. E 55, 403 (1997)] but a universal number emerges only if a normalization to the critical point value is done.
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66.20.-d, 65.20.-w, 61.20.-p

Coadsorption of CO and NO on the Cu2O(111) surface: A periodic density functional theory study

Bao-Zhen Sun, Wen-Kai Chen, and Yi-Jun Xu

J. Chem. Phys. 131, 174503 (2009) (8 pages)

Online Publication Date: 2 November 2009

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Coadsorption of carbon monoxide (CO) and nitric oxide (NO) on the Cu2O(111) surface was studied using periodic density functional theory calculations. It is interesting to find that CO+NO on Cu2O(111) could react to form adsorbed NCO surface species. Coadsorption of CO and NO could give rise to the formation of a O–C[centered ellipsis]N–O complex well bound to the Cu2O(111) surface, in which both the C–O and N–O bonds are greatly activated and the C–N bond is formed. Consequently, the reaction of CO with NO to form adsorbed NCO and CNO species may occur, for which it is disclosed that NCO formation is more possible than CNO formation both thermodynamically and kinetically. In addition, our calculations of searching transition states reveal that it is facile for NCO formation both kinetically and thermodynamically when CO+NO reaction takes place at CuCUS site, and is impossible when this reaction takes places at Ovac site. Moreover, CO2 species cannot form when CO+NO reaction occurs at Ovac site. Therefore, oxygen vacancy on Cu2O(111) does not play a positive role on CO+NO reaction to forming NCO, CNO, or CO2 species.
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82.65.+r, 68.43.Mn, 82.20.Db, 82.20.Hf

Solid-liquid equilibria and triple points of n-6 Lennard-Jones fluids

Alauddin Ahmed and Richard J. Sadus

J. Chem. Phys. 131, 174504 (2009) (8 pages)

Online Publication Date: 2 November 2009

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Molecular dynamics simulations are reported for the solid-liquid coexistence properties of n-6 Lennard-Jones fluids, where n=12, 11, 10, 9, 8, and 7. The complete phase behavior for these systems has been obtained by combining these data with vapor-liquid simulations. The influence of n on the solid-liquid coexistence region is compared using relative density difference and miscibility gap calculations. Analytical expressions for the coexistence pressure, liquid, and solid densities as a function of temperature have been determined, which accurately reproduce the molecular simulation data. The triple point temperature, pressure, and liquid and solid densities are estimated. The triple point temperature and pressure scale with respect to 1/n, resulting in simple linear relationships that can be used to determine the pressure and temperature for the limiting [infinity]-6 Lennard-Jones potential. The simulation data are used to obtain parameters for the Raveché, Mountain, and Streett and Lindemann melting rules, which indicate that they are obeyed by the n-6 Lennard Jones potentials. In contrast, it is demonstrated that the Hansen–Verlet freezing rule is not valid for n-6 Lennard-Jones potentials.
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64.70.dj, 64.75.Bc, 61.20.Ja

Failure of the constrained equilibrium hypothesis in nucleation

Lawrence S. Bartell

J. Chem. Phys. 131, 174505 (2009) (6 pages)

Online Publication Date: 3 November 2009

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The purpose of this investigation is to find whether solutions of the Becker–Döring–Tunitskii coupled differential equations can yield results closely paralleling those found in molecular dynamics (MD) simulations of freezing. What is investigated, in particular, is the validity of the constrained equilibrium hypothesis (CEH). It is shown that the MD results cannot be reproduced unless the CEH is violated. A physically plausible reason for the violation is proposed. In addition, methods for determining the size of critical nuclei are examined. It is found that a new criterion for identifying that size, a criterion incorporating the CEH, can be significantly in error. Methods for avoiding the use of the CEH are briefly discussed.
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64.60.Q-

In situ high-pressure study of diborane by infrared spectroscopy

Yang Song, Chitra Murli, and Zhenxian Liu

J. Chem. Phys. 131, 174506 (2009) (5 pages)

Online Publication Date: 3 November 2009

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As the simplest stable boron hydride in its condensed phase, diborane exhibits an interesting structural chemistry with uniquely bridged hydrogen bonds. Here we report the first room-temperature infrared (IR) absorption spectra of solid diborane compressed to pressures as high as 50 GPa using a diamond anvil cell. At room temperature and 3.5 GPa, the IR spectrum of diborane displays rich sharply resolved fundamentals and overtones of the IR active bands, consistent with the previous low-temperature IR measurements of condensed diborane at ambient pressure. When compressed stepwise to 50 GPa, several structural transformations can be identified at pressures of ~3.5 GPa, ~6.9 GPa and ~14.7 GPa, as indicated by the changes in the band profile as well as the pressure dependence of the characteristic IR modes and bandwidths. These transformations can be interpreted as being enhanced intermolecular interactions resulting from compression. The geometry of the four-member ring of B2H6, however, does not seem to be altered significantly during the transformations and the B2H6 molecule remains chemically stable up to 50 GPa.
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62.50.-p, 64.70.K-, 78.30.Hv

Vibrational circular dichroism signal enhancement using self-heterodyning with elliptically polarized laser pulses

Jan Helbing and Mathias Bonmarin

J. Chem. Phys. 131, 174507 (2009) (9 pages)

Online Publication Date: 3 November 2009

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Vibrational circular dichroism (VCD) spectra were recorded using elliptically polarized ultrashort laser pulses, produced with the help of a photoelastic modulator. The short polarization axis of the elliptical light acts as a phase-locked local oscillator field, heterodyning the chiral signal generated by the field along the long polarization axis. This leads to VCD signals that increase linearly with the ellipticity of the probe pulses and enhanced signal to noise, which is expected to improve recently reported transient VCD scans. An analogous scheme allows for vibrational optical rotary dispersion measurements. The techniques are compared with similar approaches using both a linear response picture and the Jones matrix calculus.
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33.55.+b, 33.20.Tp, 33.15.Mt, 33.15.Bh

Thermal properties and Brillouin-scattering study of glass, crystal, and “glacial” states in n-butanol

Merzak Hassaine, Rafael J. Jiménez-Riobóo, Irina V. Sharapova, Oxana A. Korolyuk, Alexander I. Krivchikov, and Miguel A. Ramos

J. Chem. Phys. 131, 174508 (2009) (8 pages)

Online Publication Date: 6 November 2009

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We investigated through noncommercial calorimetry and elastoacoustic Brillouin experiments the phase diagram of n-butanol and measured the specific heat and the thermal conductivity in a wide low-temperature range for its three different states, namely, glass, crystal, and the so-called “glacial” states. The main aim of the work was to shed light on the controversial issue of these allegedly polyamorphic transitions found in some molecular glass-forming liquids, first reported to occur in triphenyl phosphite and later in n-butanol. Our experimental results show that the obtained glacial state in n-butanol is not a homogenous, amorphous state, but rather a mixture of two different coexisting phases, very likely the (frustrated) crystal phase embedded in a disordered, glassy phase.
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78.35.+c, 81.30.Dz, 66.70.Hk, 65.60.+a, 65.40.Ba, 64.70.pm

Relaxation of Voronoi shells in hydrated molecular ionic liquids

G. Neumayr, C. Schröder, and O. Steinhauser

J. Chem. Phys. 131, 174509 (2009) (14 pages)

Online Publication Date: 6 November 2009

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The relaxation of solvation shells is studied following a twofold strategy based on a direct analysis of simulated data as well as on a solution of a Markovian master equation. In both cases solvation shells are constructed by Voronoi decomposition or equivalent Delaunay tessellation. The theoretical framework is applied to two types of hydrated molecular ionic liquids, 1-butyl-3-methyl-imidazolium tetrafluoroborate and 1-ethyl-3-methyl-imidazolium trifluoromethylsulfonate, both mixed with water. Molecular dynamics simulations of both systems were performed at various mole fractions of water. A linear relationship between the mean residence time and the system's viscosity is found from the direct analysis independent of the system's type. The complex time behavior of shell relaxation can be modeled by a Kohlrausch–Williams–Watts function with an almost universal stretching parameter of 1/2 indicative of a square root time law. The probabilistic model enables an intuitive interpretation of essential motional parameters otherwise not accessible by direct analysis. Even more, incorporating the square root time law into the probabilistic model enables a quantitative prediction of shell relaxation from very short simulation studies. In particular, the viscosity of the respective systems can be predicted.
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61.20.Ja, 64.75.Cd, 61.25.Em, 66.20.Ej, 66.20.Cy

Comprehensive study of sodium, copper, and silver clusters over a wide range of sizes 2<=N<=75

Masahiro Itoh, Vijay Kumar, Tadafumi Adschiri, and Yoshiyuki Kawazoe

J. Chem. Phys. 131, 174510 (2009) (19 pages)

Online Publication Date: 6 November 2009

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The geometric and electronic structures of NaN, CuN, and AgN metal clusters are systematically studied based on the density functional theory over a wide range of cluster sizes 2<=N<=75. A remarkable similarity is observed between the optimized geometric structures of alkali and noble metal clusters over all of the calculated cluster sizes N. The most stable structures are the same for the three different metal clusters for approximately half the cluster sizes N considered in this study. Even if the most stable structures are different, the same types of structures are obtained when the metastable structures are also considered. For all of the three different metal clusters, the cluster shapes change in the order of linear, planar, opened, and closed structures with increasing N. This structural-type transition leads to a deviation from the monotonic increase in the specific volume with N. A remarkable similarity is also observed for the N dependence of the cluster energy E(N) for the most stable geometric structures. The amplitude of this energy difference is larger in the two noble metal clusters than in the alkali metal cluster. This is attributed to the contribution of d electrons to the bonds. The magic number is explicitly defined with a new criterion in the framework of total energy calculations. In the case of NaN, a semiquantitative comparison between the experimental abundance spectra [Knight et al., Phys. Rev. Lett. 52, 2141 (1984)] and the total energy calculations is carried out. The changing aspect of the Kohn–Sham eigenvalues from N=2 to N=75 is presented for the three different metal clusters. The feature of the bulk density of states already appears at N=75 for all of three clusters. With increasing N, the highest occupied molecular orbital (HOMO)-lowest unoccupied molecular orbital (LUMO) gap clearly exhibits an odd-even alternation and converges to 0. Although there is a similarity in the N dependence of the HOMO-LUMO gap between the three metal clusters, it is much stronger between the two noble metal clusters. The growth aspect of the d band below the Fermi level of the noble metal clusters with increasing N is presented. A good correspondence is observed in the d characteristic of the electronic states between the cluster composed of 75 atoms and the bulk metal. The similarities observed in the N dependence of the geometric structures and E(N)s originate from the similarity in that of the electronic structures.
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71.15.Mb, 61.46.Bc, 71.15.Nc, 71.20.Dg

Surfaces, Interfaces, and Materials

The isotropic-nematic interface with an oblique anchoring condition

S. M. Kamil, A. K. Bhattacharjee, R. Adhikari, and Gautam I. Menon

J. Chem. Phys. 131, 174701 (2009) (9 pages)

Online Publication Date: 2 November 2009

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We present numerical and analytic results for uniaxial and biaxial orders at the isotropic-nematic interface within Ginzburg–Landau–de Gennes theory. We study the case where an oblique anchoring condition is imposed asymptotically on the nematic side of the interface, reproducing results of previous work when this condition reduces to planar or homeotropic anchoring. We construct physically motivated and computationally flexible variational profiles for uniaxial and biaxial orders, comparing our variational results to numerical results obtained from a minimization of the Ginzburg–Landau–de Gennes free energy. While spatial variations of the scalar uniaxial and biaxial order parameters are confined to the neighborhood of the interface, nematic elasticity requires that the director orientation interpolate linearly between either planar or homeotropic anchoring at the location of the interface and the imposed boundary condition at infinity. The selection of planar or homeotropic anchoring at the interface is governed by the sign of the Ginzburg–Landau–de Gennes elastic coefficient L2. Our variational calculations are in close agreement with our numerics and agree qualitatively with results from density functional theory and molecular simulations.
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61.30.Hn, 65.20.Jk, 61.30.Cz

First-principles study of methane dehydrogenation on a bimetallic Cu/Ni(111) surface

Wei An, X. C. Zeng, and C. Heath Turner

J. Chem. Phys. 131, 174702 (2009) (11 pages)

Online Publication Date: 2 November 2009

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We present density-functional theory calculations of the dehydrogenation of methane and CHx (x=1–3) on a Cu/Ni(111) surface, where Cu atoms are substituted on the Ni surface at a coverage of (1/4) monolayer. As compared to the results on other metal surfaces, including Ni(111), a similar activation mechanism with different energetics is found for the successive dehydrogenation of CH4 on the Cu/Ni(111) surface. In particular, the activation energy barrier (Eact) for CH-->C+H is found to be 1.8 times larger than that on Ni(111), while Eact for CH4-->CH3+H is 1.3 times larger. Considering the proven beneficial effect of Cu observed in the experimental systems, our findings reveal that the relative Eact in the successive dehydrogenation of CH4 plays a key role in impeding carbon formation during the industrial steam reforming of methane. Our calculations also indicate that previous scaling relationships of the adsorption energy (Eads) for CHx (x=1–3) and carbon on pure metals also hold for several Ni(111)-based alloy systems.
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68.43.Bc, 82.65.+r, 68.43.Mn

Calculation of hydrogen storage capacity of metal-organic and covalent-organic frameworks by spillover

Mayur Suri, Matthew Dornfeld, and Eric Ganz

J. Chem. Phys. 131, 174703 (2009) (4 pages)

Online Publication Date: 2 November 2009

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We have used accurate ab initio quantum chemistry calculations together with a simple model to study the hydrogen storage capacity of metal-organic and covalent-organic frameworks by spillover. Recent experiments by Tsao et al. [J. Am. Chem. Soc. 131, 1404 (2009)] {based on an earlier work by Li and Yang [J. Am. Chem. Soc. 128, 8136 (2006)]} have found that IRMOF-8 with bridged Pt catalysts can reversibly store up to 4.7 wt % of hydrogen at room temperature and 100 bar. We have calculated the binding energy for multiple H atoms on model molecules. By counting active storage sites, we predict a saturation excess storage density at room temperature of 5.0 wt % for IRMOF-8. We also predict storage densities of 4.5 wt % for IRMOF-1, 5.4 wt % for MOF-177, 4.5 wt % for COF-1, and 5.7 wt % for IRMOF-15 and IRMOF-16. This suggests that the current experimental H storage results for IRMOF-8 are well optimized. However, for other materials such as MOF-177 and COF-1, the experimental results are not yet optimized, and significantly more H can be stored on these materials. We also find that significant strain will result from shrinkage of the linker molecules as H atoms are loaded onto the crystals.
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84.60.-h, 82.65.+r

Dielectric discontinuity effects on the adsorption of a linear polyelectrolyte at the surface of a neutral nanoparticle

Marianne Seijo, Martin Pohl, Serge Ulrich, and Serge Stoll

J. Chem. Phys. 131, 174704 (2009) (6 pages)

Online Publication Date: 3 November 2009

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The formation of complexes between nanoparticles and polyelectrolytes is a key process for the control of the reactivity of manufactured nanoparticles and rational design of core shell nanostructures. In this work, we investigate the influence of the nanoparticle dielectric constant on the adsorption of a linear charged polymer (polyelectrolyte) at the surface of a neutral nanoparticle. The polyelectrolyte linear charge density, as well as the image charges in the nanoparticle due to the dielectric discontinuity, is taken into account. Monte Carlo simulations are used to predict the adsorption/desorption limits and system properties. Effects of the nanoparticle size and polyelectrolyte length are also investigated. The polyelectrolyte is found adsorbed on the nanoparticle when the dielectric constant of the nanoparticle is greater than the dielectric constant of the medium. Attractive interactions induced by the presence of opposite sign image charges are found strong enough to adsorb the polyelectrolyte showing that the reaction field contribution has to be considered. The affinity between the polyelectrolyte and the nanoparticle is found to increase in magnitude by increasing the nanoparticle size and dielectric constant. The reaction field magnitude is also found to depend in a nonlinear way from the polyelectrolyte length.
Show PACS
68.43.Mn, 82.65.+r, 68.43.Nr, 77.22.Ch, 61.46.Df

Adsorbate-induced absorption redshift in an organic-inorganic cluster conjugate: Electronic effects of surfactants and organic adsorbates on the lowest excited states of a methanethiol-CdSe conjugate

Christopher Liu, Sang-Yoon Chung, Sungyul Lee, Shimon Weiss, and Daniel Neuhauser

J. Chem. Phys. 131, 174705 (2009) (8 pages)

Online Publication Date: 5 November 2009

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Bioconjugated CdSe quantum dots are promising reagents for bioimaging applications. Experimentally, the binding of a short peptide has been found to redshift the optical absorption of nanoclusters [J. Tsay et al., J. Phys. Chem. B 109, 1669 (2005)]. This study examines this issue by performing density functional theory (DFT) and time-dependent-DFT calculations to study the ground state and low-lying excited states of (CdSe)6[SCH3]−, a transition metal complex built by binding methanethiolate to a CdSe molecular cluster. Natural bond orbital results show that the redshift is caused by ligand-inorganic cluster orbital interaction. The highest occupied molecular orbital (HOMO) of (CdSe)6 is dominated by selenium 4p orbitals; in contrast, the HOMO of (CdSe)6[SCH3]− is dominated by sulfur 3p orbitals. This difference shows that [SCH3]− binding effectively introduces filled sulfur orbitals above the selenium 4p orbitals of (CdSe)6. The resulting smaller HOMO-LUMO gap of (CdSe)6[SCH3]− indeed leads to redshifts in its excitation energies compared to (CdSe)6. In contrast, binding of multiple NH3 destabilizes cadmium 5p orbitals, which contribute significantly to the lowest unoccupied molecular orbital (LUMO) of (CdSe)6, while leaving the selenium 4p orbitals near the HOMO relatively unaffected. This has the effect of widening the HOMO-LUMO gap of (CdSe)6·6NH3 compared to (CdSe)6. As expected, the excitation energies of the passivated (CdSe)6·6NH3 are also blueshifted compared to (CdSe)6. As far as NH3 is a faithful representation of a surfactant, the results clearly illustrate the differences between the electronic effects of an alkylthiolate versus those of surfactant molecules. Surface passivation of (CdSe)6[SCH3]− is then simulated by coating it with multiple NH3 molecules. The results suggest that the [SCH3]− adsorption induces a redshift in the excitation energies in a surfactant environment.
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31.15.E-, 82.70.Dd, 33.70.Jg, 82.70.Uv, 31.15.vj, 31.15.ve

Experimental and theoretical investigations on the epitaxial growth of 4,4[prime] stilbenedicarboxylic acid molecules on Au(111)

Yan Feng Zhang, Yong Yang, Yoshiyuki Kawazoe, and Tadahiro Komeda

J. Chem. Phys. 131, 174706 (2009) (5 pages)

Online Publication Date: 5 November 2009

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We report on scanning tunneling microscope observations of the epitaxial growth of 4,4[prime] stilbenedicarboxylic acid (SDA) molecules on Au(111), with the coverage ranges from submonolayer to one monolayer. The surface assembly evolves from one-dimensional molecular chains to striped islands and finally monolayer films. For two-dimensional assembly, the head-to-tail hydrogen bonding is found to dominate the molecule-molecule interactions. Each linking region of the SDA molecular chains consists of two hydrogen bonds. This is confirmed by our first-principles calculations where the hydrogen bond length, hydrogen bond energy, and SDA-Au interaction energy are deduced theoretically. Moreover, the configurations with interchain hydrogen bonds are energetically unstable. The roles of the herringbone reconstruction of Au(111) and the compression effect of a complete film on the formation of molecular ribbons are discussed.
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68.55.am, 68.37.Ef

Diffusion behavior in a liquid-liquid interfacial crystallization by molecular dynamics simulations

Akira Kitayama, Shinya Yamanaka, Kazunori Kadota, Atsuko Shimosaka, Yoshiyuki Shirakawa, and Jusuke Hidaka

J. Chem. Phys. 131, 174707 (2009) (7 pages)

Online Publication Date: 5 November 2009

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Interfacial crystallization, such as surface crystallization in solution (solid-liquid) and liquid-liquid crystallization, gives us an asymmetric reaction field and is a technique for morphology control of crystals. In the liquid-liquid crystallization, the concentration distribution of solute ions and solvent molecules at the liquid-liquid interface directly relates to nucleation, crystal growth, and crystal morphology. Nonequilibrium molecular dynamics (MD) simulations have been performed at interfaces in NaCl solution/1-butanol and KCl solution/1-butanol system in order to clarify diffusion behavior of solute ions and solvent molecules. As simulation results, the hydrated solute ions were dehydrated with the diffusion of water from solution phase into 1-butanol phase. The different dehydration behaviors between NaCl and KCl solution can be also obtained from MD simulation results. Aggregated ions or clusters were formed by the dehydration near the solution/1-butanol interface. By comparison on the normalized number of total solute ions, the size and number of generated cluster in KCl solution/1-butanol interface are larger than those in the NaCl system. This originates in the difference hydration structures in the each solute ion.
Show PACS
61.20.Ja, 64.75.Cd, 82.30.-b

Do the interfacial fluidities of cationic reverse micelles enhance with an increase in the water content?

K. S. Mali and G. B. Dutt

J. Chem. Phys. 131, 174708 (2009) (8 pages)

Online Publication Date: 6 November 2009

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The role of cosurfactant and water on the interfacial fluidities of reverse micelles formed with the cationic surfactant, cetyltrimethylammonium bromide (CTAB) has been examined by measuring the fluorescence anisotropies of two structurally similar ionic solutes, rhodamine 110 and fluorescein. For this purpose, reverse micellar systems with (CTAB/1-pentanol/cyclohexane/water) and without a cosurfactant (CTAB/chloroform–isooctane/water) have been chosen. In this study, the mole ratio of water to surfactant W has been varied in the region of 4–25. Experimental results indicate that the average reorientation time of the probe, which is a measure of the fluidity near the interfacial region, decreases by a factor of 1.5 and 1.4 for rhodamine 110 and fluorescein, respectively, as W goes up from 5 to 25 in CTAB/1-pentanol/cyclohexane/water reverse micellar system. In contrast, the average reorientation time, remains invariant for both the probe molecules in CTAB/chloroform–isooctane/water reverse micellar system despite an increase in W from 4 to 24. In case of CTAB/1-pentanol/cyclohexane/water reverse micellar system, the added water binds to bromide counter ions and also the hydroxyl groups of the cosurfactant, 1-pentanol, which results in an increase in the effective head group area. Such an increase in the effective head group area leads to a decrease in the packing parameter, and hence an increase in the interfacial fluidity. On the other hand, in CTAB/chloroform–isooctane/water system, the added water merely hydrates the bromide ions, thereby leaving the effective head group area unchanged. Thus, the interfacial fluidities remain invariant upon the addition of water in the absence of a cosurfactant.
Show PACS
82.70.Dd, 68.05.-n, 78.55.Bq

Hard repulsive barrier in hot adatom motion during dissociative adsorption of oxygen on Ag(100)

Ming-Feng Hsieh, Deng-Sung Lin, Heiko Gawronski, and Karina Morgenstern

J. Chem. Phys. 131, 174709 (2009) (6 pages)

Online Publication Date: 6 November 2009

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Random pairing simulation and low temperature scanning tunneling microscopy (STM) are used to investigate the detailed O2 dissociative adsorption processes at 200 K for various coverages. The distribution of oxygen adatoms shows a strong repulsion between the adsorbates with a radius of ~0.8  nm. The comparison between STM results and simulation reveals two prominent pairing distances of 2 and 4 nm and their branching ratio is about 2:1. These findings shed new light on the origin of the large intrapair distances found and on the process behind the empirical “eight-site rule.”
Show PACS
68.43.Mn, 82.30.Lp

Electronic states of CuPc chains on the Au(110) surface

F. Evangelista, A. Ruocco, R. Gotter, A. Cossaro, L. Floreano, A. Morgante, F. Crispoldi, M. G. Betti, and C. Mariani

J. Chem. Phys. 131, 174710 (2009) (8 pages)

Online Publication Date: 6 November 2009

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The electronic properties of Cu-phthalocyanine (CuPc) molecules flat lying along the channels of the Au(110) reconstructed surface have been investigated by means of ultraviolet and x-ray photoelectron spectroscopy. The ordered chains give rise to a highly ordered single-layer structure with a (5×3) symmetry. Although from the core-level analysis not any significant charge transfer between the molecules and the underlying Au surface is observed, the valence band photoemission data bring to light CuPc-induced features localized at the interface. In particular, energy versus momentum dispersion of an interface state reveals a bandwidth of about 90 meV along the enlarged Au channels, where the CuPc chains are formed, with a defined fivefold symmetry well fitting the CuPc intermolecular distance.
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73.40.Qv, 68.35.bd, 79.60.Jv, 73.20.At

Tribology of the lubricant quantized sliding state

Ivano Eligio Castelli, Rosario Capozza, Andrea Vanossi, Giuseppe E. Santoro, Nicola Manini, and Erio Tosatti

J. Chem. Phys. 131, 174711 (2009) (10 pages)

Online Publication Date: 6 November 2009

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In the framework of Langevin dynamics, we demonstrate clear evidence of the peculiar quantized sliding state, previously found in a simple one-dimensional boundary lubricated model [A. Vanossi et al., Phys. Rev. Lett. 97, 056101 (2006)], for a substantially less idealized two-dimensional description of a confined multilayer solid lubricant under shear. This dynamical state, marked by a nontrivial “quantized” ratio of the averaged lubricant center-of-mass velocity to the externally imposed sliding speed, is recovered, and shown to be robust against the effects of thermal fluctuations, quenched disorder in the confining substrates, and over a wide range of loading forces. The lubricant softness, setting the width of the propagating solitonic structures, is found to play a major role in promoting in-registry commensurate regions beneficial to this quantized sliding. By evaluating the force instantaneously exerted on the top plate, we find that this quantized sliding represents a dynamical “pinned” state, characterized by significantly low values of the kinetic friction. While the quantized sliding occurs due to solitons being driven gently, the transition to ordinary unpinned sliding regimes can involve lubricant melting due to large shear-induced Joule heating, for example at large speed.
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81.40.Pq, 64.70.dj, 62.20.Qp

Polymers and Complex Systems

Neutron scattering study of the dynamics of a polymer melt under nanoscopic confinement

Margarita Krutyeva, Jaime Martin, Arantxa Arbe, Juan Colmenero, Carmen Mijangos, Gerald J. Schneider, Tobias Unruh, Yixi Su, and Dieter Richter

J. Chem. Phys. 131, 174901 (2009) (11 pages)

Online Publication Date: 4 November 2009

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Poly(ethylene oxide) confined in an anodic aluminum oxide solid matrix has been studied by different neutron scattering techniques in the momentum transfer (Q-vector) range 0.2<=Q=|Q-vector |<=1.9  Å−1. The cylindrical pores of the matrix present a diameter (40 nm) much smaller than their length (150  µm) and are parallel and hexagonally ordered. In particular, we investigated the neutron intensity scattered for two orientations of the sample with respect to the incident beam, for which the Q-vector direction was either parallel or perpendicular to the pores for a scattering angle of 90°. Diffuse neutron scattering at room temperature has shown that the aluminum oxide has amorphous structure and the polymer in the nanoporous matrix is partially crystallized. Concerning the dynamical behavior, for Q<1  Å−1, the spectra show Rouse-like motions indistinguishable from those in the bulk within the uncertainties. In the high-Q limit we observe a slowing down of the dynamics with respect to the bulk behavior that evidences an effect of confinement. This effect is more pronounced for molecular displacements perpendicular to the pore axis than for parallel displacements. Our results clearly rule out the strong corset effect proposed for this polymer from nuclear magnetic resonance (NMR) studies and can be rationalized by assuming that the interactions with the pore walls affect one to two adjacent monomer monolayers.
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61.25.hk, 82.45.Fk, 82.45.Mp, 76.60.Es

Connectivity effects in the segmental self- and cross-reorientation of unentangled polymer melts

A. Ottochian, D. Molin, A. Barbieri, and D. Leporini

J. Chem. Phys. 131, 174902 (2009) (10 pages)

Online Publication Date: 6 November 2009

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The segmental (bond) rotational dynamics in a polymer melt of unentangled, linear bead-spring chains is studied by molecular dynamics simulations. To single out the connectivity effects, states with limited deviations from the Gaussian behavior of the linear displacement are considered. Both the self and the cross bond-bond correlations with rank [script-l]=1,2 are studied in detail. For [script-l]=1 the correlation functions are precisely described by expressions involving the correlation functions of the chain modes. Several approximations concerning both the self- and the cross-correlations with [script-l]=1,2 are developed and assessed. It is found that the simplified description of the excluded volume static effects derived elsewhere [D. Molin et al., J. Phys.: Condens. Matter 18, 7543 (2006)] well accounts for the short time cross-correlations. It also allows a proper modification of the Rouse theory which provides quantitative account of the intermediate and the long time decay of the rotational correlations with [script-l]=1.
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61.25.hk, 61.20.Ja

Biological Molecules, Biopolymers, and Biological Systems

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Self-assembly of monodisperse clusters: Dependence on target geometry

Alex W. Wilber, Jonathan P. K. Doye, and Ard A. Louis

J. Chem. Phys. 131, 175101 (2009) (13 pages)

Online Publication Date: 2 November 2009

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We apply a simple model system of patchy particles to study monodisperse self-assembly using the Platonic solids as target structures. We find marked differences between the assembly behaviors of the different systems. Tetrahedra, octahedral, and icosahedra assemble easily, while cubes are more challenging and dodecahedra do not assemble. We relate these differences to the kinetics and thermodynamics of assembly, with the formation of large disordered aggregates a particular important competitor to correct assembly. In particular, the free energy landscapes of those targets that are easy to assemble are funnel-like, whereas for the dodecahedral system the landscape is relatively flat with little driving force to facilitate escape from disordered aggregates.
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81.16.Dn, 61.46.Bc

Monodisperse self-assembly in a model with protein-like interactions

Alex W. Wilber, Jonathan P. K. Doye, Ard A. Louis, and Anna C. F. Lewis

J. Chem. Phys. 131, 175102 (2009) (10 pages)

Online Publication Date: 2 November 2009

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We study the self-assembly behavior of patchy particles with “proteinlike” interactions that can be considered as a minimal model for the assembly of viral capsids and other shell-like protein complexes. We thoroughly explore the thermodynamics and dynamics of self-assembly as a function of the parameters of the model and find robust assembly of all target structures considered. Optimal assembly occurs in the region of parameter space where a free energy barrier regulates the rate of nucleation, thus preventing the premature exhaustion of the supply of monomers that can lead to the formation of incomplete shells. The interactions also need to be specific enough to prevent the assembly of malformed shells, but while maintaining kinetic accessibility. Free energy landscapes computed for our model have a funnel-like topography guiding the system to form the target structure and show that the torsional component of the interparticle interactions prevents the formation of disordered aggregates that would otherwise act as kinetic traps.
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87.15.km, 87.14.E-, 87.15.ak

Phase equilibria in DOPC/DPPC: Conversion from gel to subgel in two component mixtures

Miranda L. Schmidt, Latifa Ziani, Michelle Boudreau, and James H. Davis

J. Chem. Phys. 131, 175103 (2009) (11 pages)

Online Publication Date: 5 November 2009

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Biological membranes contain a mixture of phospholipids with varying degrees of hydrocarbon chain unsaturation. Mixtures of long chain saturated and unsaturated lipids with cholesterol have attracted a lot of attention because of the formation of two coexisting fluid bilayer phases in such systems over a broad range of temperature and composition. Interpretation of the phase behavior of such ternary mixtures must be based on a thorough understanding of the phase behavior of the binary mixtures formed with the same components. This article describes the phase behavior of mixtures of 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC) with 1,2-di-d31-palmitoyl-sn-glycero-3-phosphocholine (DPPC) between −20 and 50 °C. Particular attention has been paid to the phase coexistence below about 16 °C where the subgel phase appears. The changes in the shape of the spectrum (and its spectral moments) during the slow transformation process leads to the conclusion that below 16 °C the gel phase is metastable and the gel component of the two-phase mixture slowly transforms to the subgel phase with a slightly different composition. This results in a line of three-phase coexistence near 16 °C. Analysis of the transformation of the metastable gel domains into the subgel phase using the nucleation and growth model shows that the subgel domain growth is a two dimensional process.
Show PACS
64.75.-g, 81.30.Dz, 64.60.Q-, 64.75.Ef, 82.70.Gg

Density imbalances and free energy of lipid transfer in supported lipid bilayers

Chenyue Xing and Roland Faller

J. Chem. Phys. 131, 175104 (2009) (7 pages)

Online Publication Date: 6 November 2009

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Supported lipid bilayers are an abundant research platform for understanding the behavior of real cell membranes as they allow for additional mechanical stability and at the same time have a fundamental structure approximating cell membranes. However, in computer simulations these systems have been studied only rarely up to now. An important property, which cannot be easily determined by molecular dynamics or experiments, is the unsymmetrical density profiles of bilayer leaflets (density imbalance) inflicted on the membrane by the support. This imbalance in the leaflets composition has consequences for membrane structure and phase behavior, and therefore we need to understand it in detail. The free energy can be used to determine the equilibrium structure of a given system. We employ an umbrella sampling approach to obtain the free energy of a lipid crossing the membrane (i.e., lipid flip-flop) as a function of bilayer composition and hence the equilibrium composition of the supported bilayers. In this paper, we use a variant of the coarse-grained Martini model. The results of the free energy calculation lead to a 5% higher density in the proximal leaflet. Recent data obtained by large scale modeling using a water free model suggested that the proximal leaflet had 3.2% more lipids than the distal leaflet [Hoopes et al., J. Chem. Phys. 129, 175102 (2008)]. Our findings are in line with these results. We compare results of the free energy of transport obtained by pulling the lipid across the membrane in different ways. There are small quantitative differences, but the overall picture is consistent. We additionally characterize the intermediate states, which determine the barrier height and therefore the rate of translocation. Calculations on unsupported bilayers are used to validate the approach and to determine the barrier to flip-flop in a free membrane.
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87.16.dp, 02.50.-r, 87.16.dt, 87.14.Cc
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Errata

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Erratum: “Interaction between silver nanowires and CO on a stepped platinum surface” [J. Chem. Phys. 131, 064702 (2009)]

R. Streber, B. Tränkenschuh, J. Schöck, C. Papp, H.-P. Steinrück, J.-S. McEwen, P. Gaspard, and R. Denecke

J. Chem. Phys. 131, 179901 (2009) (1 page)

Online Publication Date: 4 November 2009

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99.10.Cd, 61.46.Km

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