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21 November 2009

Volume 131, Issue 19,  Articles (19xxxx)

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Cover image from Peter L. Cook, Xiaosong Liu, Wanli Yang, and F. J. Himpsel, J. Chem. Phys. 131, 194701 (2009).

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ARTICLES

Theoretical Methods and Algorithms

An optimized full-configuration-interaction nuclear orbital approach to a “hard-core” interaction problem: Application to (3He)N–Cl2(B) clusters (N<=4)

M. P. de Lara-Castells, P. Villarreal, G. Delgado-Barrio, and A. O. Mitrushchenkov

J. Chem. Phys. 131, 194101 (2009) (13 pages)

Online Publication Date: 16 November 2009

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An efficient full-configuration-interaction nuclear orbital treatment has been recently developed as a benchmark quantum-chemistry-like method to calculate ground and excited “solvent” energies and wave functions in small doped DeltaEest clusters (N<=4) [M. P. de Lara-Castells, G. Delgado-Barrio, P. Villarreal, and A. O. Mitrushchenkov, J. Chem. Phys. 125, 221101 (2006)]. Additional methodological and computational details of the implementation, which uses an iterative Jacobi–Davidson diagonalization algorithm to properly address the inherent “hard-core” He–He interaction problem, are described here. The convergence of total energies, average pair He–He interaction energies, and relevant one- and two-body properties upon increasing the angular part of the one-particle basis set (expanded in spherical harmonics) has been analyzed, considering Cl2 as the dopant and a semiempirical model (T-shaped) He–Cl2(B) potential. Converged results are used to analyze global energetic and structural aspects as well as the configuration makeup of the wave functions, associated with the ground and low-lying “solvent” excited states. Our study reveals that besides the fermionic nature of 3He atoms, key roles in determining total binding energies and wave-function structures are played by the strong repulsive core of the He–He potential as well as its very weak attractive region, the most stable arrangement somehow departing from the one of N He atoms equally spaced on equatorial “ring” around the dopant. The present results for N=4 fermions indicates the structural “pairing” of two 3He atoms at opposite sides on a broad “belt” around the dopant, executing a sort of asymmetric umbrella motion. This pairing is a compromise between maximizing the 3He–3He and the He-dopant attractions, and suppressing at the same time the “hard-core” repulsion. Although the He–He attractive interaction is rather weak, its contribution to the total energy is found to scale as a power of three and it thus increasingly affects the pair density distributions as the cluster grows in size.
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36.40.Mr, 31.15.V-, 33.15.Mt, 34.20.Gj

Stability of binary mixtures in electric field gradients

Sela Samin and Yoav Tsori

J. Chem. Phys. 131, 194102 (2009) (9 pages)

Online Publication Date: 17 November 2009

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We consider the influence of electric field gradients on the phase behavior of nonpolar binary mixtures. Small fields give rise to smooth composition profiles, whereas large enough fields lead to a phase-separation transition. The critical field for demixing as well as the equilibrium phase-separation interface are given as a function of the various system parameters. We show how the phase diagram in the temperature-composition plane is affected by electric fields, assuming a linear or nonlinear constitutive relations for the dielectric constant. Finally, we discuss the unusual case where the interface appears far from any bounding surface.
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64.75.Ef, 61.20.-p, 77.22.Ch, 64.75.Cd

Efficient calculation of the polarization induced by N coherent laser pulses

Maxim F. Gelin, Dassia Egorova, and Wolfgang Domcke

J. Chem. Phys. 131, 194103 (2009) (6 pages)

Online Publication Date: 18 November 2009

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We have developed a novel method, the equation-of-motion phase-matching approach (EOM-PMA), for the calculation of the response of a quantum system to N coherent laser fields. The N-pulse EOM-PMA is limited to weak fields (its domain of validity is equivalent to the traditional nonlinear response functions approach), but allows for arbitrary pulse durations and automatically accounts for pulse-overlap effects. The N-pulse EOM-PMA allows the evaluation of the time evolution of the N-pulse-induced polarization in any phase-matching direction by performing 2N−1 independent propagations of certain auxiliary density matrices. The N-pulse EOM-PMA can straightforwardly be incorporated into codes which provide the time evolution of the density matrix of material systems of interest and can efficiently be implemented on parallel computers.
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33.80.-b, 42.65.Hw, 33.15.Kr

Excited and ionized states of the ozone molecule with full triples coupled cluster methods

Monika Musial, Stanislaw A. Kucharski, Piotr Zerzucha, Tomasz Kuś, and Rodney J. Bartlett

J. Chem. Phys. 131, 194104 (2009) (10 pages)

Online Publication Date: 20 November 2009

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The role of connected triple excitations in coupled cluster (CC) calculations of vertical excitation energies, ionization potentials, and the electron affinity of the ozone molecule is evaluated. The equation of motion (EOM) and Fock space (FS) multireference CC approaches with full triples have been used in the calculations. The effect of the T3 and R3 operators significantly improve the EOM CCSD results for all considered quantities. A similar behavior is observed in the case of the FS-CC calculations. The FS-CC calculations with full triples have been obtained only for the intermediate Hamiltonian realization of the FS approach as the standard formulation diverges. The latter results are rigorously linked, and less expensive since smaller matrices are diagonalized.
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31.15.bw, 33.15.Ry

Extrapolating MP2 and CCSD explicitly correlated correlation energies to the complete basis set limit with first and second row correlation consistent basis sets

J. Grant Hill, Kirk A. Peterson, Gerald Knizia, and Hans-Joachim Werner

J. Chem. Phys. 131, 194105 (2009) (13 pages)

Online Publication Date: 20 November 2009

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Accurate extrapolation to the complete basis set (CBS) limit of valence correlation energies calculated with explicitly correlated MP2-F12 and CCSD(T)-F12b methods have been investigated using a Schwenke-style approach for molecules containing both first and second row atoms. Extrapolation coefficients that are optimal for molecular systems containing first row elements differ from those optimized for second row analogs, hence values optimized for a combined set of first and second row systems are also presented. The new coefficients are shown to produce excellent results in both Schwenke-style and equivalent power-law-based two-point CBS extrapolations, with the MP2-F12/cc-pV(D,T)Z-F12 extrapolations producing an average error of just 0.17  mEh with a maximum error of 0.49 for a collection of 23 small molecules. The use of larger basis sets, i.e., cc-pV(T,Q)Z-F12 and aug-cc-pV(Q,5)Z, in extrapolations of the MP2-F12 correlation energy leads to average errors that are smaller than the degree of confidence in the reference data (~0.1  mEh). The latter were obtained through use of very large basis sets in MP2-F12 calculations on small molecules containing both first and second row elements. CBS limits obtained from optimized coefficients for conventional MP2 are only comparable to the accuracy of the MP2-F12/cc-pV(D,T)Z-F12 extrapolation when the aug-cc-pV(5+d)Z and aug-cc-pV(6+d)Z basis sets are used. The CCSD(T)-F12b correlation energy is extrapolated as two distinct parts: CCSD-F12b and (T). While the CCSD-F12b extrapolations with smaller basis sets are statistically less accurate than those of the MP2-F12 correlation energies, this is presumably due to the slower basis set convergence of the CCSD-F12b method compared to MP2-F12. The use of larger basis sets in the CCSD-F12b extrapolations produces correlation energies with accuracies exceeding the confidence in the reference data (also obtained in large basis set F12 calculations). It is demonstrated that the use of the 3C(D) Ansatz is preferred for MP2-F12 CBS extrapolations. Optimal values of the geminal Slater exponent are presented for the diagonal, fixed amplitude Ansatz in MP2-F12 calculations, and these are also recommended for CCSD-F12b calculations.
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31.15.bw, 31.15.vn, 31.15.xp

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

Laser spectroscopy of NiI: New electronic states and hyperfine structure

A. S.-C. Cheung, H. F. Pang, W. S. Tam, and J. W.-H. Leung

J. Chem. Phys. 131, 194301 (2009) (7 pages)

Online Publication Date: 16 November 2009

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Two new electronic transition systems, namely, the [14.0]2Phi7/2-X 2Delta5/2 and the [15.7]2Phi5/2-X 2Delta5/2 transitions were observed and analyzed using laser vaporization/reaction supersonic free jet expansion and high resolution laser induced fluorescence spectroscopy. In addition, the (v, 0) bands with v=6–10 of the [14.6]2Delta5/2-X 2Delta5/2 transition were found to be perturbed by the [15.7]2Phi5/2 state. The interaction between the [14.6]2Delta5/2 and the [15.7]2Phi5/2 states is evident in the progressive increase in hyperfine width of rotational lines of the [14.6]2Delta5/2-X 2Delta5/2 transition as the vibrational quantum number increases. Deperturbation procedures were successfully applied to analyze the interaction between these two states. All observed spectra show partially resolved hyperfine structure, and the hyperfine width decreases rapidly as J increases suggested that the hyperfine structure conforms to the Hund's case abeta coupling scheme. Accurate molecular and hyperfine constants for the [14.0]2Phi7/2, the [14.6]2Delta5/2 and the [15.7]2Phi5/2 states were obtained and analyzed.
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33.15.Pw, 33.50.Dq, 33.15.Mt, 33.20.Tp, 33.80.-b, 31.50.Df

Electronic relaxation dynamics in large anionic water clusters: (H2O)n− and (D2O)n− (n=25–200)

Graham B. Griffin, Ryan M. Young, Oli T. Ehrler, and Daniel M. Neumark

J. Chem. Phys. 131, 194302 (2009) (9 pages)

Online Publication Date: 16 November 2009

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Electronic relaxation dynamics subsequent to s-->p excitation of the excess electron in large anionic water clusters, (H2O)n− and (D2O)n− with 25<=n<=200, were investigated using time-resolved photoelectron imaging. Experimental improvements have enabled considerably larger clusters to be probed than in previous work, and the temporal resolution of the instrument has been improved. New trends are seen in the size-dependent p-state lifetimes for clusters with n>=70, suggesting a significant change in the electron-water interaction for clusters in this size range. Extrapolating the results for these larger clusters to the infinite-size limit yields internal conversion lifetimes tauIC of 60 and 160 fs for electrons dissolved in H2O and D2O, respectively. In addition, the time-evolving spectra show evidence for solvent relaxation in the excited electronic state prior to internal conversion and in the ground state subsequent to internal conversion. Relaxation in the excited state appears to occur on a time scale similar to that of internal conversion, while ground state solvent dynamics occur on a ~1  ps time scale, in reasonable agreement with previous measurements on water cluster anions and electrons solvated in liquid water.
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36.40.Mr, 36.40.Sx, 33.60.+q, 33.50.Hv, 33.70.Ca, 31.70.Dk

Multiconfiguration time-dependent Hartree and classical dynamics studies of the photodissociation of HF and HCl molecules adsorbed on ice: Extension to three dimensions

S. Woittequand, C. Toubin, M. Monnerville, S. Briquez, B. Pouilly, and H.-D. Meyer

J. Chem. Phys. 131, 194303 (2009) (8 pages)

Online Publication Date: 17 November 2009

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The 3D photodissociation dynamics of HCl and HF molecules adsorbed on ice is studied by quantum and classical simulations. The quantum calculations are carried out with the multiconfiguration time-dependent Hartree (MCTDH) approach. Dynamical observables like angular distributions in the momentum space of the H fragments, absorption cross sections are computed. The results are compared with our previous 2D studies. As expected, less encapsulation of the H atom between the ice surface and the halogen atom is obtained in the 3D study, resulting in less pronounced interference structures in the photoabsorption cross sections and in a decrease of the classical rainbow peaks observed in the 2D scheme. Although the amplitudes of the oscillations corresponding to quantum interferences in the asymptotic angular distribution of the H fragment are different between the 2D and 3D results, the qualitative pattern of the oscillations is similar in the 2D and 3D approaches. In addition, a good agreement is observed for the angular distribution between the classical and the quantum calculations.
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33.80.Gj, 31.15.xr

Unimolecular decomposition of tetrazine-N-oxide based high nitrogen content energetic materials from excited electronic states

A. Bhattacharya, Y. Q. Guo, and E. R. Bernstein

J. Chem. Phys. 131, 194304 (2009) (8 pages)

Online Publication Date: 18 November 2009

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Unimolecular excited electronic state decomposition of novel high nitrogen content energetic molecules, such as 3,3[prime]-azobis(6-amino-1,2,4,5-tetrazine)-mixed N-oxides (DAATO3.5), 3-amino-6-chloro-1,2,4,5-tetrazine-2,4-dioxide (ACTO), and 3,6-diamino-1,2,4,5-tetrazine-1,4-dioxde (DATO), is investigated. Although these molecules are based on N-oxides of a tetrazine aromatic heterocyclic ring, their decomposition behavior distinctly differs from that of bare tetrazine, in which N2 and HCN are produced as decomposition products through a concerted dissociation mechanism. NO is observed to be an initial decomposition product from all tetrazine-N-oxide based molecules from their low lying excited electronic states. The NO product from DAATO3.5 and ACTO is rotationally cold (20 K) and vibrationally hot (1200 K), while the NO product from DATO is rotationally hot (50 K) and vibrationally cold [only the (0–0) vibronic transition of NO is observed]. DAATO3.5 and ACTO primarily differ from DATO with regard to molecular structure, by the relative position of oxygen atom attachment to the tetrazine ring. Therefore, the relative position of oxygen in tetrazine-N-oxides is proposed to play an important role in their energetic behavior. N2O is ruled out as an intermediate precursor of the NO product observed from all three molecules. Theoretical calculations at CASMP2/CASSCF level of theory predict a ring contraction mechanism for generation of the initial NO product from these molecules. The ring contraction occurs through an (S1/S0)CI conical intersection.
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82.30.Lp, 82.20.Hf

Reactions of simple aromatic heterocycles with niobium cluster ions (n<=30)

Britta Pfeffer, Stephanie Jaberg, and Gereon Niedner-Schatteburg

J. Chem. Phys. 131, 194305 (2009) (12 pages)

Online Publication Date: 19 November 2009

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Prior work on benzene activation by size selected niobium cluster cations and anions of up to 30 atoms is extended systematically through studying aromatic poly- and heterocyclic molecules such as naphthalene, pyridine, thiophene, pyrrole, furan, and benzofuran. Naphthalene is found to act much like benzene when reacting under single collision conditions with individual clusters. The most likely process is carbidization through complete dehydrogenation. Some clusters of particular sizes (most notably n=19) fail to activate both homocyclic molecules. Instead seemingly intact adsorption is observed which proves that activation is kinetically hindered at some point. All of the five studied heterocyclic aromatic molecules react unconditionally and by complete dehydrogenation with cationic niobium clusters, while they only attach to or react with anionic clusters larger than a minimum size of n=19–21. These findings are taken as strong evidence for initial coordination to the metal clusters of the heterocycles through their lone pair orbitals. The paper comprehends the observations in terms of cluster surface structure and reactivity.
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82.30.Cf, 82.65.+r, 68.35.B-

Ab initio molecular dynamics simulation of photoisomerization in azobenzene in the npi* state

Yusuke Ootani, Kiminori Satoh, Akira Nakayama, Takeshi Noro, and Tetsuya Taketsugu

J. Chem. Phys. 131, 194306 (2009) (10 pages)

Online Publication Date: 19 November 2009

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Photoisomerization mechanism of azobenzene in the lowest excited state S1(npi*) is investigated by ab initio molecular dynamics (AIMD) simulation with the RATTLE algorithm, based on the state-averaged complete active space self-consistent field method. AIMD simulations show that cis to trans isomerization occurs via two-step rotation mechanism, accompanying rotations of the central NN part and two phenyl rings, and this process can be classified into two types, namely, clockwise and counterclockwise rotation pathways. On the other hand, trans to cis isomerization occurs via conventional rotation pathway where two phenyl rings rotate around the NN bond. The quantum yields are calculated to be 0.45 and 0.28±0.14 for cis to trans and trans to cis photoisomerizations, respectively, which are in very good agreement with the corresponding experimental results.
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31.15.A-, 31.15.xv, 31.15.xr, 82.50.-m, 82.30.Qt

Photochemistry of 3-hydroxyflavone inside superfluid helium nanodroplets

R. Lehnig, D. Pentlehner, A. Vdovin, B. Dick, and A. Slenczka

J. Chem. Phys. 131, 194307 (2009) (8 pages)

Online Publication Date: 20 November 2009

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3-hydroxyflavone is a prototype system for excited state intramolecular proton transfer which is one step of a closed loop photocycle. It was intensively studied for the bare molecule and for the influence of solvents. In the present paper this photocycle is investigated for 3-hydroxyflavone and some hydrated complexes when doped into superfluid helium droplets by the combined measurement of fluorescence excitation spectra and dispersed emission spectra. Significant discrepancies in the proton transfer behavior to gas phase experiments provide evidence for the presence of different complex configurations of the hydrated complexes in helium droplets. Moreover, for bare 3-hydroxyflavone and its hydrated complexes the proton transfer appears to be promoted by the helium environment.
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82.50.-m, 33.80.Rv, 33.80.Gj, 82.80.-d, 82.30.Hk, 33.50.Dq

Oscillator strengths and line widths of dipole-allowed transitions in 14N2 between 86.0 and 89.7 nm

A. N. Heays, B. R. Lewis, G. Stark, K. Yoshino, Peter L. Smith, K. P. Huber, and K. Ito

J. Chem. Phys. 131, 194308 (2009) (9 pages)

Online Publication Date: 20 November 2009

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Oscillator strengths of 23 electric-dipole-allowed bands of 14N2 in the 86.0–89.7 nm (111 480–116 280  cm−1) region are reported from synchrotron-based photoabsorption measurements at an instrumental resolution of 6.5×10−4  nm  (0.7  cm−1) full width at half maximum. The absorption spectrum comprises transitions to vibrational levels of the cn 1Piu  (n=3,4), o3 1Piu, and c<sub>n + 1</sub><sup>[prime]</sup> 1Sigma<sub>u</sub><sup>+</sup>(n=3,4) Rydberg states as well as the b 1Piu and b[prime] 1Sigma<sub>u</sub><sup>+</sup> valence states. The J dependences of band f-values derived from the experimental line f-values are reported as polynomials in J(J+1) and are extrapolated to zero nuclear rotation in order to facilitate comparisons with the results of coupled Schrödinger equation calculations. Many bands in this study are characterized by a strong J dependence of the band f-values and display anomalous P-, Q-, and R-branch intensity patterns. Predissociation line widths are reported for six bands. The experimental f-value and line-width patterns inform current efforts to develop comprehensive spectroscopic models for N2 that incorporate rotational effects and predissociation mechanisms, and are critical for the construction of realistic atmospheric radiative-transfer models.
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33.70.Ca, 33.70.Jg, 33.80.Gj, 33.80.Rv, 33.15.Mt

Electronic photodissociation spectra and decay pathways of gas-phase IrBr62−

Jesse C. Marcum and J. Mathias Weber

J. Chem. Phys. 131, 194309 (2009) (8 pages)

Online Publication Date: 20 November 2009

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We report photodissociation action spectra for the dianion IrBr62− in the range of 1.08–5.6 eV. The photoproducts observed are IrBr6−, IrBr5−, IrBr4− and Br−. Comparison of the action spectra to the aqueous absorption spectrum of K2IrBr6 leads to the determination of solvatochromic shifts of between 0.02 and 0.16 eV in the visible region and approximately 0.3 eV in the ultraviolet. The fragmentation branching ratios vary greatly as a function of photon energy. This behavior can be attributed to differences in the fragmentation mechanisms as well as differences in the excited states that are accessed at different energies. Absorption in the visible region favors fragmentation into IrBr5− and Br−, whereas a number of fragmentation channels and mechanisms are active in the ultraviolet region. These mechanisms include fragmentation as well as electron detachment and dissociative electron detachment.
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33.80.Gj, 82.50.Hp, 33.20.Kf, 82.80.Dx

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

Improvement of the ab initio embedded cluster method for luminescence properties of doped materials by taking into account impurity induced distortions: The example of Y2O3:Bi3+

Florent Réal, Belén Ordejón, Valérie Vallet, Jean-Pierre Flament, and Joël Schamps

J. Chem. Phys. 131, 194501 (2009) (17 pages)

Online Publication Date: 16 November 2009

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New ab initio embedded-cluster calculations devoted to simulating the electronic spectroscopy of Bi3+ impurities in Y2O3 sesquioxide for substitutions in either S6 or C2 cationic sites have been carried out taking special care of the quality of the environment. A considerable quantitative improvement with respect to previous studies [F. Réal et al. J. Chem. Phys. 125, 174709 (2006); F. Réal et al. J. Chem. Phys. 127, 104705 (2007)] is brought by using environments of the impurities obtained via supercell techniques that allow the whole (pseudo) crystal to relax (WCR geometries) instead of environments obtained from local relaxation of the first coordination shell only (FSR geometries) within the embedded cluster approach, as was done previously. In particular the uniform 0.4 eV discrepancy of absorption energies found previously with FSR environments disappears completely when the new WCR environments of the impurities are employed. Moreover emission energies and hence Stokes shifts are in much better agreement with experiment. These decisive improvements are mainly due to a lowering of the local point-group symmetry (S6-->C3 and C2-->C1) when relaxing the geometry of the emitting (lowest) triplet state. This symmetry lowering was not observed in FSR embedded cluster relaxations because the crystal field of the embedding frozen at the genuine pure crystal positions seems to be a more important driving force than the interactions within the cluster, thus constraining the overall symmetry of the system. Variations of the doping rate are found to have negligible influence on the spectra. In conclusion, the use of WCR environments may be crucial to render the structural distortions occurring in a doped crystal and it may help to significantly improve the embedded-cluster methodology to reach the quantitative accuracy necessary to interpret and predict luminescence properties of doped materials of this type.
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78.55.Hx, 61.72.up, 61.72.S-, 61.50.Ah, 71.70.Ch, 61.66.Fn

Pressure dependence of the large-scale structure of water

A. Cunsolo, F. Formisano, C. Ferrero, F. Bencivenga, and S. Finet

J. Chem. Phys. 131, 194502 (2009) (5 pages)

Online Publication Date: 16 November 2009

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We report on small-angle x-ray scattering measurements on liquid water aimed at characterizing the pressure evolution of its large-scale structure. Diffraction profiles have been fitted assuming a Lorentzian dependence on the exchanged momentum. As a result, we observe an anomalous behavior of the diffracted intensity that tends to disappear, increasing either the pressure or the temperature. This effect is discussed in detail and imputed to the ability of hydrostatic pressure to weaken hydrogen bonds.
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61.25.Em

Multiplet splittings and intensities of fine structure components of the Q1(0)H2+S0(0)N2 transition in a solid parahydrogen matrix

Adya P. Mishra and Param Jeet Singh

J. Chem. Phys. 131, 194503 (2009) (6 pages)

Online Publication Date: 16 November 2009

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A comprehensive analysis of theoretical multiplet splittings and intensities of the fine structure components of the Q1(0)H2+S0(0)N2 transition in a solid parahydrogen crystal is presented. The consideration of higher order anisotropic term responsible for splittings is essential to explain the observed splitting of the three components. The pair interaction parameters DeltaB and DeltaC have been determined by comparing the theoretical splittings with the experimental values. The information about the small splittings (~0.1  cm−1) due to crystal-field interaction is completely obscured due to fast hopping of v[prime]=1, J[prime]=0 H2 vibron. Also, the theoretical expressions are derived for the intensities of the fine structure components of the QvH2(0)+SvN2(0) transition and the theoretical results are compared with the experimental findings.
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34.20.Gj, 33.15.Pw, 71.70.Ch
FREE

Theory for the three-dimensional Mercedes-Benz model of water

Alan Bizjak, Tomaz Urbic, Vojko Vlachy, and Ken A. Dill

J. Chem. Phys. 131, 194504 (2009) (7 pages)

Online Publication Date: 16 November 2009

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The two-dimensional Mercedes-Benz (MB) model of water has been widely studied, both by Monte Carlo simulations and by integral equation methods. Here, we study the three-dimensional (3D) MB model. We treat water as spheres that interact through Lennard-Jones potentials and through a tetrahedral Gaussian hydrogen bonding function. As the “right answer,” we perform isothermal-isobaric Monte Carlo simulations on the 3D MB model for different pressures and temperatures. The purpose of this work is to develop and test Wertheim's Ornstein–Zernike integral equation and thermodynamic perturbation theories. The two analytical approaches are orders of magnitude more efficient than the Monte Carlo simulations. The ultimate goal is to find statistical mechanical theories that can efficiently predict the properties of orientationally complex molecules, such as water. Also, here, the 3D MB model simply serves as a useful workbench for testing such analytical approaches. For hot water, the analytical theories give accurate agreement with the computer simulations. For cold water, the agreement is not as good. Nevertheless, these approaches are qualitatively consistent with energies, volumes, heat capacities, compressibilities, and thermal expansion coefficients versus temperature and pressure. Such analytical approaches offer a promising route to a better understanding of water and also the aqueous solvation.
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61.20.Ja, 65.20.-w, 62.10.+s

A theoretical basis for spontaneous polarization transfer in non-hydrogenative parahydrogen-induced polarization

Ralph W. Adams, Simon B. Duckett, Richard A. Green, David C. Williamson, and Gary G. R. Green

J. Chem. Phys. 131, 194505 (2009) (15 pages)

Online Publication Date: 16 November 2009

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When parahydrogen adds to a metal template containing a substrate of interest, the substrate and parahydrogen become coupled, and polarization is shared between the two without the incorporation of the parahydrogen into the substrate. A mechanism for this polarization transfer is presented in which the transfer is propagated through the scalar couplings. At zero field, polarization is transferred between two-, three-, and four-spin zero quantum states, but no single spin magnetization is created. The interplay between the chemical shift evolution and the evolution under scalar coupling at non-zero field generates additional longitudinal spin order and now includes single spin longitudinal z-magnetization. The additional chemical shift interaction introduces a field dependency to the nuclear spin states of the polarized substrate. The net effect of the polarization field strength on the resultant nuclear spin states is shown to be predictable but complex.
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33.25.+k

A new generic model potential for mesogenic systems: Square well line potential of variable range

Szabolcs Varga and Franz J. Vesely

J. Chem. Phys. 131, 194506 (2009) (8 pages)

Online Publication Date: 18 November 2009

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A single-site pair potential is derived to approximate the linear n-site square well interaction. The resulting square well line (SWL) potential is analytical, fairly smooth, and reproduces the distance and orientation dependence of the multisite pair energy. It contains only three control parameters n, L, and s2, in addition to the units of length s1 and energy epsilon. The advantages of the new model over the traditional potentials such as Gay–Berne and Kihara are that n, L, and s2 are physically meaningful quantities and that no additional adjustable parameters are introduced. With the SWL potential even very long square well chain molecules may be treated in Monte Carlo (MC) simulations; moreover the model is well suited for perturbation theory. Using Onsager-like theories we test the effect of molecular elongation, temperature, and the range of the square well potential on the vapor-liquid and nematic-smectic A (NS) phase transitions. We find that the vapor-liquid binodal of the SWL fluid is in good agreement with MC results for square well dumbbells. For repulsive SWL particles, varying the interaction range s2 results in a similar effect on the NS transition as the change in the ionic strength in a real suspension of fd viruses.
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34.20.Gj, 31.15.xp

A molecular dynamics study of the influence of ionic charge distribution on the dynamics of a molten salt

Hualin Li and Mark N. Kobrak

J. Chem. Phys. 131, 194507 (2009) (7 pages)

Online Publication Date: 19 November 2009

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The distribution of charge in an ion of a fused salt is known to be an important determinant of liquid dynamics. However, the details of this relationship remain poorly understood. We present the results of molecular dynamics simulations on a model molten salt system and show that changes in the distribution of ionic charge can have a profound effect on liquid dynamics. In particular, we observe complex relationships between the distribution of charge, the rate of ionic rotation, and the translational diffusion of ions in the liquid.
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61.25.-f, 66.10.C-, 61.20.Ja

Localized soft modes and the supercooled liquid's irreversible passage through its configuration space

Asaph Widmer-Cooper, Heidi Perry, Peter Harrowell, and David R. Reichman

J. Chem. Phys. 131, 194508 (2009) (12 pages)

Online Publication Date: 19 November 2009

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Using computer simulations, we show that the localized low frequency normal modes of a configuration in a supercooled liquid are strongly correlated with the irreversible structural reorganization of the particles within that configuration. Establishing this correlation constitutes the identification of the aspect of a configuration that determines the heterogeneity of the subsequent motion. We demonstrate that the spatial distribution of the summation over the soft local modes can persist in spite of particle reorganization that produces significant changes in individual modes. Along with spatial localization, the persistent influence of soft modes in particle relaxation results in anisotropy in the displacements of mobile particles over the time scale referred to as beta-relaxation.
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61.20.Ja, 61.25.-f, 64.70.pm

Spin-locking of half-integer quadrupolar nuclei in nuclear magnetic resonance of solids: Second-order quadrupolar and resonance offset effects

Sharon E. Ashbrook and Stephen Wimperis

J. Chem. Phys. 131, 194509 (2009) (15 pages)

Online Publication Date: 19 November 2009

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Spin-locking of spin I=3/2 and I=5/2 nuclei in the presence of small resonance offset and second-order quadrupolar interactions has been investigated using both exact and approximate theoretical and experimental nuclear magnetic resonance (NMR) approaches. In the presence of second-order quadrupolar interactions, we show that the initial rapid dephasing that arises from the noncommutation of the state prepared by the first pulse and the spin-locking Hamiltonian gives rise to tensor components of the spin density matrix that are antisymmetric with respect to inversion, in addition to those symmetric with respect to inversion that are found when only a first-order quadrupolar interaction is considered. We also find that spin-locking of multiple-quantum coherence in a static solid is much more sensitive to resonance offset than that of single-quantum coherence and show that good spin-locking of multiple-quantum coherence can still be achieved if the resonance offset matches the second-order shift of the multiple-quantum coherence in the appropriate reference frame. Under magic angle spinning (MAS) conditions, and in the "adiabatic" limit, we demonstrate that rotor-driven interconversion of central-transition single- and three-quantum coherences for a spin I=3/2 nucleus can be best achieved by performing the spin-locking on resonance with the three-quantum coherence in the three-quantum frame. Finally, in the "sudden" MAS limit, we show that spin I=3/2 spin-locking behavior is generally similar to that found in static solids, except when the central-transition nutation rate matches a multiple of the MAS rate and a variety of rotary resonance phenomena are observed depending on the internal spin interactions present. This investigation should aid in the application of spin-locking techniques to multiple-quantum NMR of quadrupolar nuclei and of cross-polarization and homonuclear dipolar recoupling experiments to quadrupolar nuclei such as 7Li, 11B, 17O, 23Na, and 27Al.
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76.60.-k

Manipulating stimulated coherent anti-Stokes Raman spectroscopy signals by broad-band and narrow-band pulses

Saar Rahav, Oleksiy Roslyak, and Shaul Mukamel

J. Chem. Phys. 131, 194510 (2009) (11 pages)

Online Publication Date: 20 November 2009

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A transition-amplitude based representation of heterodyne detected coherent anti-Stokes Raman signals is used to separate them into a parametric component that involves no change in the material and dissipative processes associated with various transitions between states. Qualitatively different contributions from the two processes are predicted for the signal generated by an overlapping narrow (picosecond) and broad-band (femtosecond) pulse.
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42.65.Dr, 42.70.Nq, 42.65.Hw, 42.65.Re

Molecular cooperativity in the dynamics of glass-forming systems: A new insight

L. Hong, P. D. Gujrati, V. N. Novikov, and A. P. Sokolov

J. Chem. Phys. 131, 194511 (2009) (7 pages)

Online Publication Date: 20 November 2009

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The mechanism behind the steep slowing down of molecular motions upon approaching the glass transition remains a great puzzle. Most of the theories relate this mechanism to the cooperativity in molecular motion. In this work, we estimate the length scale of molecular cooperativity xi for many glass-forming systems from the collective vibrations (the so-called boson peak). The obtained values agree well with the dynamic heterogeneity length scale estimated using four-dimensional NMR. We demonstrate that xi directly correlates to the dependence of the structural relaxation on volume. This dependence presents only one part of the mechanism of slowing down the structural relaxation. Our analysis reveals that another part, the purely thermal variation in the structural relaxation (at constant volume), does not have a direct correlation with molecular cooperativity. These results call for a conceptually new approach to the analysis of the mechanism of the glass transition and to the role of molecular cooperativity.
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64.70.qj, 76.60.-k, 61.43.Fs, 63.50.Lm

Surfaces, Interfaces, and Materials

FREE

X-ray absorption spectroscopy of biomimetic dye molecules for solar cells

Peter L. Cook, Xiaosong Liu, Wanli Yang, and F. J. Himpsel

J. Chem. Phys. 131, 194701 (2009) (10 pages)

Online Publication Date: 16 November 2009

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Dye-sensitized solar cells are potentially inexpensive alternatives to traditional semiconductor solar cells. In order to optimize dyes for solar cells we systematically investigate the electronic structure of a variety of porphyrins and phthalocyanines. As a biological model system we use the heme group in cytochrome c which plays a role in biological charge transfer processes. X-ray absorption spectroscopy of the N 1s and C 1s edges reveals the unoccupied molecular orbitals and the orientation of the molecules in thin films. The transition metal 2p edges reflect the oxidation state of the central metal atom, its spin state, and the ligand field of the surrounding N atoms. The latter allows tuning of the energy position of the lowest unoccupied orbital by several tenths of an eV by tailoring the molecules and their deposition. Fe and Mn containing phthalocyanines oxidize easily from +2 to +3 in air and require vacuum deposition for obtaining a reproducible oxidation state. Chlorinated porphyrins, on the other hand, are reduced from +3 to +2 during vacuum deposition at elevated temperatures. These findings stress the importance of controlled thin film deposition for obtaining photovoltaic devices with an optimum match between the energy levels of the dye and those of the donor and acceptor electrodes, together with a molecular orientation for optimal overlap between the pi orbitals in the direction of the carrier transport.
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85.65.+h, 33.20.Rm

Stacking of polycyclic aromatic hydrocarbons as prototype for graphene multilayers, studied using density functional theory augmented with a dispersion term

C. Feng, C. S. Lin, W. Fan, R. Q. Zhang, and M. A. Van Hove

J. Chem. Phys. 131, 194702 (2009) (8 pages)

Online Publication Date: 16 November 2009

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The interlayer pi-pi interaction between finite-size models of graphene sheets was investigated by using a density functional theory method, augmented with an empirical R−6 term for the description of long-range dispersive interaction; these were calibrated by studying the pi-pi interaction between various benzene dimer configurations and comparing the results with previous calculations. For stacked bilayers (dimers) and multilayers of polyaromatic hydrocarbons, which serve as molecular models of graphene sheets, we found that binding energies and energy gaps are strongly dependent on their sizes, while the stacking order and the number of stacked layers have a minor influence. The remarkably broad variation of the energy gap, ranging from 1.0 to 2.5 eV, due mainly to variation of the model size, suggests the potential of broadband luminescence in the visible range for carbon-based nanomaterials that have pi-pi interacting.
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73.21.Ac, 71.20.Tx, 71.15.Nc, 78.67.Pt, 78.55.Hx, 71.15.Mb

Effects of methanol on nanoparticle self-assembly at liquid-liquid interfaces: A molecular dynamics approach

Mingxiang Luo, Yanmei Song, and Lenore L. Dai

J. Chem. Phys. 131, 194703 (2009) (6 pages)

Online Publication Date: 18 November 2009

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Molecular dynamics simulations have been performed to study the influence of methanol on the self-assembly of nanoparticles at liquid-liquid interfaces. The simulation shows that the methanol molecules, at low volume fraction, stay in the aqueous phase but with a preference of the water-trichloroethylene (TCE) interfaces. However, at higher methanol volume fraction, methanol dominates the aqueous phase and no preferable location of methanol molecules is observed. The simulations also suggest that the interfacial tension decreases and the interfacial thickness increases with increasing methanol concentration. The presence of the nanoparticles at water-TCE interfaces has minor effect on the interfacial properties compared to those of methanol, and the presence of methanol drives the noncharged nanoparticle clusters closer to the interfaces. Although the methanol molecules do not affect the monolayer distribution of the negatively charged nanoparticles at the water-TCE interfaces, they increase the three-phase contact angles of these nanoparticles.
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68.03.Cd, 61.20.Ja, 81.16.Dn

Interfering pathways in benzene: An analytical treatment

Thorsten Hansen, Gemma C. Solomon, David Q. Andrews, and Mark A. Ratner

J. Chem. Phys. 131, 194704 (2009) (12 pages)

Online Publication Date: 18 November 2009

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The mechanism for off-resonant electron transport through small organic molecules in metallic junctions is predominantly coherent tunneling. Thus, new device functionalities based on quantum interference could be developed in the field of molecular electronics. We invoke a partitioning technique to give an analytical treatment of quantum interference in a benzene ring. We interpret the antiresonances in the transmission as either multipath zeroes resulting from interfering spatial pathways or resonance zeroes analogous to zeroes induced by sidechains.
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85.65.+h, 73.40.Gk, 73.23.-b

Deliquescence and efflorescence of small particles

Robert McGraw and Ernie R. Lewis

J. Chem. Phys. 131, 194705 (2009) (14 pages)

Online Publication Date: 20 November 2009

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We examine size-dependent deliquescence/efflorescence phase transformation for particles down to several nanometers in size. Thermodynamic properties of inorganic salt particles, coated with aqueous solution layers of varying thickness and surrounded by vapor, are analyzed. A thin layer criterion (TLC) is introduced to define a limiting deliquescence relative humidity (RHD) for small particles. This requires: (1) equality of chemical potentials between salt in an undissolved core, and thin adsorbed solution layer, and (2) equality of chemical potentials between water in the thin layer and vapor phase. The usual bulk deliquescence conditions are recovered in the limit of large dry particle size. Nanosize particles are found to deliquesce at relative humidity just below the RHD on crossing a nucleation barrier, located at a critical solution layer thickness. This barrier vanishes precisely at the RHD defined by the TLC. Concepts and methods from nucleation theory including the kinetic potential, self-consistent nucleation theory, nucleation theorems, and the Gibbs dividing surface provide theoretical foundation and point to unifying features of small particle deliquescence/efflorescence processes. These include common thermodynamic area constructions, useful for interpretation of small particle water uptake measurements, and a common free-energy surface, with constant RH cross sections describing deliquescence and efflorescence related through the nucleation theorem.
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82.60.Qr, 68.35.Md, 68.43.-h, 82.60.Nh

Polymers and Complex Systems

Numerical determination of the exponents controlling the relationship between time, length, and temperature in glass-forming liquids

Chiara Cammarota, Andrea Cavagna, Giacomo Gradenigo, Tomas S. Grigera, and Paolo Verrocchio

J. Chem. Phys. 131, 194901 (2009) (8 pages)

Online Publication Date: 16 November 2009

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There is a certain consensus that the very fast growth of the relaxation time tau occurring in glass-forming liquids on lowering the temperature must be due to the thermally activated rearrangement of correlated regions of growing size. Even though measuring the size of these regions has defied scientists for a while, there is indeed recent evidence of a growing correlation length xi in glass formers. If we use Arrhenius law and make the mild assumption that the free-energy barrier to rearrangement scales as some power psi of the size of the correlated regions, we obtain a relationship between time and length, T log tau~xipsi. According to both the Adam–Gibbs and the random first order theory the correlation length grows as xi~(T−Tk)−1/(d−theta), even though the two theories disagree on the value of theta. Therefore, the super-Arrhenius growth of the relaxation time with the temperature is regulated by the two exponents psi and theta through the relationship T log tau~(T−Tk)−psi/(d−theta). Despite a few theoretical speculations, up to now there has been no experimental determination of these two exponents. Here we measure them numerically in a model glass former, finding psi=1 and theta=2. Surprisingly, even though the values we found disagree with most previous theoretical suggestions, they give back the well-known VFT law for the relaxation time, T log tau~(T−Tk)−1.
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64.70.Q-, 65.20.-w

Dynamic rheology of sphere- and rod-based magnetorheological fluids

J. de Vicente, J. P. Segovia-Gutiérrez, E. Andablo-Reyes, F. Vereda, and R. Hidalgo-Álvarez

J. Chem. Phys. 131, 194902 (2009) (10 pages)

Online Publication Date: 16 November 2009

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The effect of particle shape in the small amplitude oscillatory shear behavior of magnetorheological (MR) fluids is investigated from zero magnetic field strengths up to 800 kA/m. Two types of MR fluids are studied: the first system is prepared with spherical particles and a second system is prepared with rodlike particles. Both types of particles are fabricated following practically the same precipitation technique and have the same intrinsic magnetic and crystallographic properties. Furthermore, the distribution of sphere diameters is very similar to that of rod thicknesses. Rod-based MR fluids show an enhanced MR performance under oscillatory shear in the viscoelastic linear regime. A lower magnetic field strength is needed for the structuration of the colloid and, once saturation is fully achieved, a larger storage modulus is observed. Existing sphere- and rod-based models usually underestimate experimental results regarding the magnetic field strength and particle volume fraction dependences of both storage modulus and yield stress. A simple model is proposed here to explain the behavior of microrod-based MR fluids at low, medium and saturating magnetic fields in the viscoelastic linear regime in terms of magnetic interaction forces between particles. These results are further completed with rheomicroscopic and dynamic yield stress observations.
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83.80.Gv, 62.10.+s, 83.80.Hj

Origin of translocation barriers for polyelectrolyte chains

Rajeev Kumar and M. Muthukumar

J. Chem. Phys. 131, 194903 (2009) (18 pages)

Online Publication Date: 17 November 2009

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For single-file translocations of a charged macromolecule through a narrow pore, the crucial step of arrival of an end at the pore suffers from free energy barriers, arising from changes in intrachain electrostatic interaction, distribution of ionic clouds and solvent molecules, and conformational entropy of the chain. All contributing factors to the barrier in the initial stage of translocation are evaluated by using the self-consistent field theory for the polyelectrolyte and the coupled Poisson–Boltzmann description for ions without radial symmetry. The barrier is found to be essentially entropic due to conformational changes. For moderate and high salt concentrations, the barriers for the polyelectrolyte chain are quantitatively equivalent to that of uncharged self-avoiding walks. Electrostatic effects are shown to increase the free energy barriers, but only slightly. The degree of ionization, electrostatic interaction strength, decreasing salt concentration, and the solvent quality all result in increases in the barrier.
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61.25.H-, 82.45.Wx, 82.35.Rs, 65.20.Jk, 82.45.Mp

Free energy landscape for the translocation of polymer through an interacting pore

Li-Zhen Sun, Wei-Ping Cao, and Meng-Bo Luo

J. Chem. Phys. 131, 194904 (2009) (5 pages)

Online Publication Date: 17 November 2009

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Free energy landscapes for polymer chain translocating through an interacting pore are calculated by using exact enumeration method. A potential barrier exists at weak attractive or repulsive polymer-pore interaction and it changes to a potential well with the increase in the attraction. The result reveals that there is a free translocation point where polymer is free of energy barrier. Using the free energy landscape, the translocation time tau for polymer worming through the pore and the migration time taum for polymer migrating from cis side to trans side are calculated with the Fokker–Plank equation. It shows that a moderate attractive polymer-pore interaction accelerates the migration of polymer from cis side to trans side.
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65.60.+a, 61.41.+e

Fluorescence depolarization in poly[2-methoxy-5-((2-ethylhexyl)oxy)-1,4-phenylenevinylene]: Sites versus eigenstates hopping

Jaykrishna Singh, Eric R. Bittner, David Beljonne, and Gregory D. Scholes

J. Chem. Phys. 131, 194905 (2009) (10 pages)

Online Publication Date: 17 November 2009

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We report upon a theoretical study of singlet exciton migration and relaxation within a model conjugated polymer chain. Starting from poly[2-methoxy-5-((2-ethylhexyl)oxy)-1,4-phenylenevinylene] polymer chains, we assume that the pi-conjugation is disrupted by conformational disorder of the chain itself, giving rise to a localized Frenkel exciton basis. Electronic coupling between segments as determined by the coupling between the transition densities of the localized excitons gives rise to delocalized exciton states. Using a kinetic Monte Carlo approach to compute the exciton transfer kinetics within the manifold of either the dressed chromophore site basis or dressed eigenstate basis, we find that the decay of the polarization anisotropy of the exciton is profoundly affected by the delocalization of the exciton over multiple basis segments. Two time scales emerge from the exciton migration simulations: a short, roughly 10 ps, time scale corresponding to rapid hopping about the initial excitation site followed by a slower, 180 ps, component corresponding to long range hopping. We also find that excitations can become trapped at long times when the hopping rate to lower-energy states is longer than the radiative lifetime of the exciton.
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78.55.Kz, 71.35.-y, 71.15.Dx

Emergence of complex behavior in gelling systems starting from simple behavior of single clusters

A. Fierro, T. Abete, and A. Coniglio

J. Chem. Phys. 131, 194906 (2009) (9 pages)

Online Publication Date: 18 November 2009

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A theoretical and numerically study of dynamical properties in the sol-gel transition is presented. In particular, the complex phenomenology observed experimentally and numerically in gelling systems is reproduced in the framework of percolation theory, under simple assumptions on the relaxation of single clusters. By neglecting the correlation between particles belonging to different clusters, the quantities of interest (such as the self intermediate scattering function, the dynamical susceptibility, the Van-Hove function, and the non-Gaussian parameter) are written as superposition of those due to single clusters. Connection between these behaviors and the critical exponents of percolation are given. The theoretical predictions are checked in a model for permanent gels, where bonds between monomers are described by a finitely extendable nonlinear elastic potential. The data obtained in the numerical simulations are in good agreement with the analytical predictions.
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82.70.Gg, 64.70.dm, 64.60.ah, 61.43.Bn, 61.25.H-, 61.20.Ja

Swelling and collapse of polyelectrolyte gels in equilibrium with monovalent and divalent electrolyte solutions

De-Wei Yin, Monica Olvera de la Cruz, and Juan J. de Pablo

J. Chem. Phys. 131, 194907 (2009) (6 pages)

Online Publication Date: 19 November 2009

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The swelling of polyelectrolyte (PE) gels by 1:1 and 2:1 salts is studied via osmotic ensemble Monte Carlo simulations at constant osmotic pressure and electrolyte chemical potential of a reservoir phase in equilibrium with a model PE network. Large molecular weight gels exhibit a remarkable swelling response to small changes in 2:1 salt concentration. Gel collapse is accompanied by the formation of a previously unknown heterogeneous nanostructure, predicted by theory and observed in simulations, consisting of regions dense in monomers coexisting with regions rich in mono- and divalent ions.
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61.25.hp, 61.25.he, 82.70.Gg, 82.45.Wx, 82.45.Gj, 82.35.Rs

Kinetics and morphology of cluster growth in a model of short-range attractive colloids

Siddique J. Khan, C. M. Sorensen, and A. Chakrabarti

J. Chem. Phys. 131, 194908 (2009) (9 pages)

Online Publication Date: 19 November 2009

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We present results from detailed three-dimensional Brownian dynamics simulations of the self-assembly process in quenched short-range attractive colloids. Clusters obtained in the simulations range from dense faceted crystals to fractal aggregates which show ramified morphology on large length scales but close-packed crystalline morphology on short length scales. For low volume fractions of the colloids, the morphology and crystal structure of a nucleating cluster are studied at various times after the quench. As the volume fraction of the colloids is increased, growth of clusters is controlled by cluster diffusion and cluster-cluster interactions. For shallower quenches and low volume fractions, clusters are compact and the growth-law exponent agrees well with Binder–Stauffer predictions and with recent experimental results. As the volume fraction is increased, clusters do not completely coalesce when they meet each other and the kinetics crosses over to diffusion-limited cluster-cluster aggregation (DLCA) limit. For deeper quenches, clusters are fractals even at low volume fractions and the growth kinetics asymptotically reaches the irreversible DLCA case.
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82.70.Dd, 64.75.Yz, 64.75.Xc, 83.10.Mj

Biological Molecules, Biopolymers, and Biological Systems

The transition state transit time of WW domain folding is controlled by energy landscape roughness

Feng Liu, Marcelo Nakaema, and Martin Gruebele

J. Chem. Phys. 131, 195101 (2009) (9 pages)

Online Publication Date: 16 November 2009

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Protein folding barriers can be so low that a substantial protein population diffusing in the transition state region can be detected. The very fast kinetic phase contributed by transition state transit is the molecular phase. We detect the molecular phase of the beta-sheet protein FiP35 from 60 to 83 °C by T-jump relaxation experiments. The molecular phase actually slows down slightly with increasing temperature. Thus the friction that controls the prefactor in Kramers' transition state model does not scale with solvent viscosity. Instead, we postulate that an increase in the energy landscape roughness as the hydrophobic effect strengthens with increasing temperature explains the slowing of the molecular phase. We measured that the duration taum of the molecular phase depends slightly on the size of the T-jump, in agreement with this explanation. The taum measured here provides the best current estimate for the transit time from folded to unfolded state of a single protein molecule. We confirm this by directly comparing relaxation and single molecule signals computed by using Langevin trajectory models on a realistic FiP35 free energy surface.
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87.15.-v, 87.14.E-, 87.80.-y

All-atom ab initio native structure prediction of a mixed fold (1FME): A comparison of structural and folding characteristics of various betabetaalpha miniproteins

Eunae Kim, Soonmin Jang, and Youngshang Pak

J. Chem. Phys. 131, 195102 (2009) (8 pages)

Online Publication Date: 19 November 2009

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We performed an all-atom ab initio native structure prediction of 1FME, which is one of the computationally challenging mixed fold betabetaalpha miniproteins, by combining a novel conformational search algorithm (multiplexed Q-replica exchange molecular dynamics scheme) with a well-balanced all-atom force field employing a generalized Born implicit solvation model (param99MOD5/GBSA). The nativelike structure of 1FME was identified from the lowest free energy minimum state and in excellent agreement with the NMR structure. Based on the interpretation of the free energy landscape, the structural properties as well as the folding behaviors of 1FME were compared with other betabetaalpha miniproteins (1FSD, 1PSV, and BBA5) that we have previously studied with the same force field. Our simulation showed that the 28-residue betabetaalpha miniproteins (1FME, 1FSD, and 1PSV) share a common feature of the free energy topography and exhibit the three local minimum states on each computed free energy map, but the 23-residue miniprotein (BBA5) follows a downhill folding with a single minimum state. Also, the structure and stability changes resulting from the two point mutation (Gln1-->Glu1 and Ile7-->Tyr7) of 1FSD were investigated in details for direct comparison with the experiment. The comparison shows that upon mutation, the experimentally observed turn type switch from an irregular turn (1FSD) to type I[prime] turn (1FME) was well reproduced with the present simulation.
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87.15.B-, 87.15.ap, 87.15.Cc, 87.15.hp, 36.20.Ey, 87.14.E-

Stochastic bimodalities in deterministically monostable reversible chemical networks due to network topology reduction

Maxim N. Artyomov, Manikandan Mathur, Michael S. Samoilov, and Arup K. Chakraborty

J. Chem. Phys. 131, 195103 (2009) (6 pages)

Online Publication Date: 19 November 2009

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Recently, stochastic simulations of networks of chemical reactions have shown distributions of steady states that are inconsistent with the steady state solutions of the corresponding deterministic ordinary differential equations. One such class of systems is comprised of networks that have irreversible reactions, and the origin of the anomalous behavior in these cases is understood to be due to the existence of absorbing states. More puzzling is the report of such anomalies in reaction networks without irreversible reactions. One such biologically important example is the futile cycle. Here we show that, in these systems, nonclassical behavior can originate from a stochastic elimination of all the molecules of a key species. This leads to a reduction in the topology of the network and the sampling of steady states corresponding to a truncated network. Surprisingly, we find that, in spite of the purely discrete character of the topology reduction mechanism revealed by “exact” numerical solutions of the master equations, this phenomenon is reproduced by the corresponding Fokker–Planck equations.
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82.20.Uv, 05.40.-a
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LETTERS TO THE EDITOR

Notes

On nonadiabatic coupling vectors in time-dependent density functional theory

Ivano Tavernelli, Basile F. E. Curchod, and Ursula Rothlisberger

J. Chem. Phys. 131, 196101 (2009) (2 pages)

Online Publication Date: 20 November 2009

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In this note, we show that the development for the calculation of nonadiabatic coupling vectors in the framework of TDDFT introduced by the authors in the series of recent publications [E. Tapavicza et al., Phys. Rev. Lett.98, 023001 (2007); I. Tavernelli et al., J. Chem. Phys.130, 124107 (2009)] is rigorous and fully equivalent to the one proposed by Sugino and co-workers [C. P. Hu et al., J. Chem. Phys.127, 064103 (2007)]. Specific applications of our formulation are also discussed.
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31.15.ee

Errata

FREE

Publisher's Note: “Transition state analysis of solid-solid transformations in nanocrystals” [J. Chem. Phys. 131, 164116 (2009)]

Michael Grünwald and Christoph Dellago

J. Chem. Phys. 131, 199901 (2009) (1 page)

Online Publication Date: 19 November 2009

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+
 Abstract Unavailable
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64.70.kg, 61.46.Df, 81.05.Dz, 61.66.Fn, 65.80.+n, 99.10.Fg
FREE

Publisher's Note: “On the kinetics of the Al13−+Cl2 reaction: Cluster degradation in consecutive steps” [J. Chem. Phys. 131, 174304 (2009)]

Matthias Olzmann, Ralf Burgert, and Hansgeorg Schnöckel

J. Chem. Phys. 131, 199902 (2009) (1 page)

Online Publication Date: 19 November 2009

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+
 Abstract Unavailable
Show PACS
82.30.Cf, 82.30.Nr, 36.40.-c, 82.20.Pm, 82.20.Db, 99.10.Fg

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