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28 February 2008

Volume 128, Issue 8,  Articles (08xxxx)

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ARTICLES

Theoretical Methods and Algorithms

Accelerating the convergence of the total energy evaluation in density functional theory calculations

Baojing Zhou and Yan Alexander Wang

J. Chem. Phys. 128, 084101 (2008) (5 pages)

Online Publication Date: 25 February 2008

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A special feature of the Strutinsky shell correction method (SCM) [D. Ullmo et al., Phys. Rev. B 63, 125339 (2001)] and the recently proposed orbital-corrected orbital-free density functional theory (OO-DFT) [B. Zhou and Y. A. Wang, J. Chem. Phys. 124, 081107 (2006)] is that the second-order corrections are incorporated in the total energy evaluation. In the SCM, the series expansion of the total electronic energy is essentially the Harris functional with its second-order correction. Unfortunately, a serious technical problem for the SCM is the lack of the exact Kohn-Sham (KS) density rhoKS(r) required for the evaluation of the second-order correction. To overcome this obstacle, we design a scheme that utilizes the optimal density from a high-quality density mixing scheme to approximate rhoKS(r). Recently, we proposed two total energy density functionals, i.e., the Zhou-Wang-lambda (ZWlambda) and the Wang-Zhou-alpha (WZalpha) functionals, for use in the OO-DFT method. If the two interpolation parameters, lambda and alpha, are chosen to allow the second-order errors of the ZWlambda and the WZalpha functionals to vanish, these two functionals reduce to the Hohenberg-Kohn-Sham functional with its second-order correction. Again, the optimal density from a high-quality density mixing scheme is used to approximate rhoKS(r) in the evaluation of lambda and alpha. This approach is tested in iterative KS-DFT calculations on systems with different chemical environments and can also be generalized for use in other iterative first-principles quantum chemistry methods.
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31.15.eg

Systematically convergent basis sets for explicitly correlated wavefunctions: The atoms H, He, B–Ne, and Al–Ar

Kirk A. Peterson, Thomas B. Adler, and Hans-Joachim Werner

J. Chem. Phys. 128, 084102 (2008) (12 pages)

Online Publication Date: 25 February 2008

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Correlation consistent basis sets have been optimized for use with explicitly correlated F12 methods. The new sets, denoted cc-pVnZ-F12 (n=D,T,Q), are similar in size and construction to the standard aug-cc-pVnZ and aug-cc-pV(n+d)Z basis sets, but the new sets are shown in the present work to yield much improved convergence toward the complete basis set limit in MP2-F12/3C calculations on several small molecules involving elements of both the first and second row. For molecules containing only first row atoms, the smallest cc-pVDZ-F12 basis set consistently recovers nearly 99% of the MP2 valence correlation energy when combined with the MP2-F12/3C method. The convergence with basis set for molecules containing second row atoms is slower, but the new DZ basis set still recovers 97%–99% of the frozen core MP2 correlation energy. The accuracy of the new basis sets for relative energetics is demonstrated in benchmark calculations on a set of 15 chemical reactions.
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71.20.-b

Generalized approximation to the reaction path: The formic acid dimer case

Ivana Matanović, Nadja Došlić, and Bruce R. Johnson

J. Chem. Phys. 128, 084103 (2008) (10 pages)

Online Publication Date: 27 February 2008

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A set of mass-weighted internal coordinates was derived and applied to the double proton transfer reaction in the formic acid dimer (FAD). The coordinate set was obtained starting from the Hirschfelder “mobile” by an optimization procedure consisting of a sequence of kinematic rotations. In FAD, the optimization procedure leads to three coordinates that do change significantly along the reaction path. These coordinates span the reaction space, whereas the remaining modes are treated in a harmonic approximation. The effect that the dimer dissociative motion has on the ground and excited vibrational states dynamics was explored. In the frequency region corresponding to the symmetric OH-stretch vibration four doublets have been identified with splittings of 2.76, 0.07, 0.60, and 4.03  cm−1.
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82.37.Np, 82.30.Hk, 33.15.Mt

Stability of polycrystalline and wurtzite Si nanowires via symmetry-adapted tight-binding objective molecular dynamics

D.-B. Zhang, M. Hua, and T. Dumitrică

J. Chem. Phys. 128, 084104 (2008) (9 pages)

Online Publication Date: 27 February 2008

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The stability of the most promising ground state candidate Si nanowires with less than 10  nm in diameter is comparatively studied with objective molecular dynamics coupled with nonorthogonal tight-binding and classical potential models. The computationally expensive tight-binding treatment becomes tractable due to the substantial simplifications introduced by the presented symmetry-adapted scheme. It indicates that the achiral polycrystalline of fivefold symmetry and the wurtzite wires of threefold symmetry are the most favorable quasi-one-dimensional Si arrangements. Quantitative differences with the classical model description are noted over the whole diameter range. Using a Wulff energy decomposition approach it is revealed that these differences are caused by the inability of the classical potential to accurately describe the interaction of Si atoms on surfaces and strained morphologies.
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61.46.Km, 61.66.Bi

On the electron-electron counterbalance hole

Toshikatsu Koga and Masahiro Sekiya

J. Chem. Phys. 128, 084105 (2008) (4 pages)

Online Publication Date: 27 February 2008

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When a many-electron system has spatial inversion symmetry, the electron-electron counterbalance hole implies that two electrons with parallel spins cannot be at opposite positions with respect to the inversion center, and its presence was pointed out in the literature [T. Koga, J. Chem. Phys. 108, 2515 (1998)] for any pairs of Hartree-Fock orbitals with the same inversion parity. We report here a generalized result that in all two-electron systems with spatial inversion symmetry, the electron-electron counterbalance hole always exists for any approximate and exact wave functions with even inversion parity. The same is also true in momentum space. An extension of the hole to systems with three or more electrons is discussed.
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73.50.Gr, 71.15.Ap

Systematic optimization of long-range corrected hybrid density functionals

Jeng-Da Chai and Martin Head-Gordon

J. Chem. Phys. 128, 084106 (2008) (15 pages)

Online Publication Date: 27 February 2008

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A general scheme for systematically modeling long-range corrected (LC) hybrid density functionals is proposed. Our resulting two LC hybrid functionals are shown to be accurate in thermochemistry, kinetics, and noncovalent interactions, when compared with common hybrid density functionals. The qualitative failures of the commonly used hybrid density functionals in some “difficult problems,” such as dissociation of symmetric radical cations and long-range charge-transfer excitations, are significantly reduced by the present LC hybrid density functionals.
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71.15.Mb

Interpolating moving least-squares methods for fitting potential energy surfaces: A strategy for efficient automatic data point placement in high dimensions

Richard Dawes, Donald L. Thompson, Albert F. Wagner, and Michael Minkoff

J. Chem. Phys. 128, 084107 (2008) (10 pages)

Online Publication Date: 28 February 2008

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An accurate and efficient method for automated molecular global potential energy surface (PES) construction and fitting is demonstrated. An interpolating moving least-squares (IMLS) method is developed with the flexibility to fit various ab initio data: (1) energies, (2) energies and gradients, or (3) energies, gradients, and Hessian data. The method is automated and flexible so that a PES can be optimally generated for trajectories, spectroscopy, or other applications. High efficiency is achieved by employing local IMLS in which fitting coefficients are stored at a limited number of expansion points, thus eliminating the need to perform weighted least-squares fits each time the potential is evaluated. An automatic point selection scheme based on the difference in two successive orders of IMLS fits is used to determine where new ab initio data need to be calculated for the most efficient fitting of the PES. A simple scan of the coordinate is shown to work well to identify these maxima in one dimension, but this search strategy scales poorly with dimension. We demonstrate the efficacy of using conjugate gradient minimizations on the difference surface to locate optimal data point placement in high dimensions. Results that are indicative of the accuracy, efficiency, and scalability are presented for a one-dimensional model potential (Morse) as well as for three-dimensional (HCN), six-dimensional (HOOH), and nine-dimensional (CH4) molecular PESs.
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34.20.-b, 31.50.-x, 31.15.A-

Approximating correlation effects in multiconfigurational self-consistent field calculations of spin-spin coupling constants

J. San Fabián, E. Díez, J. M. García de la Vega, and R. Suardíaz

J. Chem. Phys. 128, 084108 (2008) (9 pages)

Online Publication Date: 28 February 2008

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The multiconfigurational self-consistent field (MCSCF) method in their approximations restricted and complete active spaces (RAS and CAS) provides a theoretically accurate description of the coupling constants of a wide range of molecules. To obtain accurate results, however, very large basis sets and large configuration spaces must be used. Nuclear magnetic resonance coupling constants for the equilibrium geometry have been calculated for a series of small molecules using approximated correlation contributions. The four contributions to the coupling constants (Fermi contact, spin dipolar, orbital paramagnetic, and orbital diamagnetic) have been calculated at the CAS and RAS MCSCF and second-order polarization propagator approximation levels using a large basis set. An additive model that considers the effect on the coupling constants from excitation of more than two electrons and from core-electron correlation is used to estimate the coupling constants. Compared with the experimental couplings, the best calculated values, which correspond to the MCSCF results, present a mean absolute error of 3.6  Hz and a maximum absolute deviation of 13.4  Hz. A detailed analysis of the different contributions and of the effects of the additive contributions on the coupling constants is carried out.
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33.25.+k, 33.15.Bh, 31.15.V-, 31.15.xr

A new dipole-free sum-over-states expression for the second hyperpolarizability

Javier Pérez-Moreno, Koen Clays, and Mark G. Kuzyk

J. Chem. Phys. 128, 084109 (2008) (11 pages)

Online Publication Date: 28 February 2008

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The generalized Thomas-Kuhn sum rules are used to eliminate the explicit dependence on dipolar terms in the traditional sum-over-states (SOS) expression for the second hyperpolarizability to derive a new, yet equivalent, SOS expression. This new dipole-free expression may be better suited to study the second hyperpolarizability of nondipolar systems such as quadrupolar, octupolar, and dodecapolar structures. The two expressions lead to the same fundamental limits of the off-resonance second hyperpolarizability; and when applied to a particle in a box and a clipped harmonic oscillator, have the same frequency dependence. We propose that the new dipole-free equation, when used in conjunction with the standard SOS expression, can be used to develop a three-state model of the dispersion of the third-order susceptibility that can be applied to molecules in cases where normally many more states would have been required. Furthermore, a comparison between the two expressions can be used as a convergence test of molecular orbital calculations when applied to the second hyperpolarizability.
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33.15.Kr, 31.15.ap

Performance of a nonempirical meta–generalized gradient approximation density functional for excitation energies

Jianmin Tao, Sergei Tretiak, and Jian-Xin Zhu

J. Chem. Phys. 128, 084110 (2008) (8 pages)

Online Publication Date: 28 February 2008

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It is known that the adiabatic approximation in time-dependent density functional theory usually provides a good description of low-lying excitations of molecules. In the present work, the capability of the adiabatic nonempirical meta–generalized gradient approximation (meta-GGA) of Tao, Perdew, Staroverov, and Scuseria (TPSS) to describe atomic and molecular excitations is tested. The adiabatic (one-parameter) hybrid version of the TPSS meta-GGA and the adiabatic GGA of Perdew, Burke, and Ernzerhof (PBE) are also included in the test. The results are compared to experiments and to those obtained with two well-established hybrid functionals PBE0 and B3LYP. Calculations show that both adiabatic TPSS and TPSSh functionals produce excitation energies in fairly good agreement with experiments, and improve upon the adiabatic local spin density approximation and, in particular, the adiabatic PBE GGA. This further confirms that TPSS is indeed a reliable nonhybrid universal functional which can serve as the starting point from which higher-level approximations can be constructed. The systematic underestimate of the low-lying vertical excitation energies of molecules with time-dependent density functionals within the adiabatic approximation suggests that further improvement can be made with nonadiabatic corrections.
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31.15.E-

Parameterized local hybrid functionals from density-matrix similarity metrics

Benjamin G. Janesko and Gustavo E. Scuseria

J. Chem. Phys. 128, 084111 (2008) (7 pages)

Online Publication Date: 28 February 2008

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We recently proposed a real-space similarity metric comparing the Kohn–Sham one-particle density matrix to the local spin-density approximation model density matrix [Janesko and Scuseria, J. Chem. Phys. 127, 164117 (2007)]. This metric provides a useful ingredient for constructing local hybrid density functionals that locally mix exact exchange and semilocal density functional theory exchange. Here we present two lines of inquiry: An approximate similarity metric comparing exact versus generalized gradient approximation (GGA), exchange and parameterized mixing functions using these similarity metrics. This approach yields significantly improved thermochemistry, including GGA local hybrids whose thermochemical performance approaches GGA global hybrids.
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71.15.Mb, 71.45.Gm

Density functional study of double ionization energies

D. P. Chong

J. Chem. Phys. 128, 084112 (2008) (5 pages)

Online Publication Date: 28 February 2008

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In this paper, double ionization energies (DIEs) of gas-phase atoms and molecules are calculated by energy difference method with density functional theory. To determine the best functional for double ionization energies, we first study 24 main group atoms in the second, third, and fourth periods. An approximation is used in which the electron density is first obtained from a density functional computation with the exchange-correlation potential Vxc known as statistical average of orbital potentials, after which the energy is computed from that density with 59 different exchange-correlation energy functionals Exc. For the 24 atoms, the two best Exc functional providing DIEs with average absolute deviation (AAD) of only 0.25  eV are the Perdew–Burke–Ernzerhof functional modified by Hammer et al. [Phys. Rev. B 59, 6413 (1999)] and one known as the Krieger–Chen–Iafrate–Savin functional modified by Krieger et al. (unpublished). Surprisingly, none of the 20 available hybrid functionals is among the top 15 functionals for the DIEs of the 24 atoms. A similar procedure is then applied to molecules, with opposite results: Only hybrid functionals are among the top 15 functionals for a selection of 29  molecules. The best Exc functional for the 29  molecules is found to be the Becke 1997 functional modified by Wilson et al. [J. Chem. Phys. 115, 9233 (2001)]. With that functional, the AAD from experiment for DIEs of 29  molecules is just under 0.5  eV. If the two suspected values for C2H2 and Fe(CO)5 are excluded, the AAD improves to 0.32  eV. Many other hybrid functionals perform almost as well.
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31.15.E-, 31.15.eg, 34.50.Fa, 34.50.Gb

Direct energy functional minimization under orthogonality constraints

Valéry Weber, Joost VandeVondele, Jürg Hutter, and Anders M. N. Niklasson

J. Chem. Phys. 128, 084113 (2008) (9 pages)

Online Publication Date: 29 February 2008

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The direct energy functional minimization problem in electronic structure theory, where the single-particle orbitals are optimized under the constraint of orthogonality, is explored. We present an orbital transformation based on an efficient expansion of the inverse factorization of the overlap matrix that keeps orbitals orthonormal. The orbital transformation maps the orthogonality constrained energy functional to an approximate unconstrained functional, which is correct to some order in a neighborhood of an orthogonal but approximate solution. A conjugate gradient scheme can then be used to find the ground state orbitals from the minimization of a sequence of transformed unconstrained electronic energy functionals. The technique provides an efficient, robust, and numerically stable approach to direct total energy minimization in first principles electronic structure theory based on tight-binding, Hartree–Fock, or density functional theory. For sparse problems, where both the orbitals and the effective single-particle Hamiltonians have sparse matrix representations, the effort scales linearly with the number of basis functions N in each iteration. For problems where only the overlap and Hamiltonian matrices are sparse the computational cost scales as [script O](M2N), where M is the number of occupied orbitals. We report a single point density functional energy calculation of a DNA decamer hydrated with 4003 water molecules under periodic boundary conditions. The DNA fragment containing a cis-syn thymine dimer is composed of 634 atoms and the whole system contains a total of 12 661 atoms and 103 333 spherical Gaussian basis functions.
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31.15.E-, 31.15.xr, 87.14.gk

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

Ab initio calculation of carbon clusters. II. Relative stabilities of fullerene and nonfullerene C24

Wei An, Nan Shao, Satya Bulusu, and X. C. Zeng

J. Chem. Phys. 128, 084301 (2008) (9 pages)

Online Publication Date: 25 February 2008

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Chemical stabilities of six low-energy isomers of C24 derived from global-minimum search are investigated. The six isomers include one classical fullerene (isomer 1) whose cage is composed of only five- and six-membered rings (5/6-MRs), three nonclassical fullerene structures whose cages contain at least one four-membered ring (4-MR), one plate, and one monocyclic ring. Chemical and electronic properties of the six C24 isomers are calculated based on a density-functional theory method (hybrid PBE1PBE functional and cc-pVTZ basis set). The properties include the nucleus-independent chemical shifts (NICS), singlet-triplet splitting, electron affinity, ionization potential, and gap between the highest occupied molecular orbital and the lowest unoccupied molecular orbital (HOMO-LUMO) gap. The calculation suggests that the neutral isomer 2, a nonclassical fullerene with two 4-MRs, may be more chemically stable than the classical fullerene (isomer 1). Analyses of molecular orbital NICS show that the incorporations of 4-MRs into the cage considerably reduce paratropic contributions from HOMO, HOMO-1, and HOMO-2, which are mainly responsible for the sign change in NICS from positive for isomer 1 (42) to negative (−19) for isomer 2, although C24 clusters satisfy neither 4N+2 nor 2(N+1)2 aromaticity rule. Anion photoelectron spectra of four cage isomers, one plate, one monocyclic ring, and one tadpole isomer, as well as three bicyclic ring isomers are calculated. The simulated photoelectron spectra of mono- and bicyclic rings (with C1 symmetry) appear to match the measured HOMO-LUMO gap (between the first and second band in the experimental spectra) [S. Yang et al., Chem. Phys. Lett. 144, 431 (1988)]. Nevertheless, the nonclassical fullerene isomers 3 and 4 apparently also match the measured vertical detachment energy (2.90  eV) reasonably well. These results suggest possible coexistence of nonclassical fullerene isomers with the mono- and bicyclic ring isomers of C<sub>24</sub><sup>-</sup> under the experimental conditions.
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31.15.A-, 31.15.E-, 33.25.+k, 33.15.Ry, 33.60.+q, 36.40.Mr

Acetylene-vinylidene isomerization in ultrashort intense laser fields studied by triple ion-coincidence momentum imaging

Akiyoshi Hishikawa, Akitaka Matsuda, Eiji J. Takahashi, and Mizuho Fushitani

J. Chem. Phys. 128, 084302 (2008) (5 pages)

Online Publication Date: 25 February 2008

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The isomerization of acetylene via hydrogen migration in intense laser fields (8×1014  W/cm2) has been investigated by coincidence momentum imaging of the three-body Coulomb explosion process, C2H<sub>2</sub><sup>3+</sup>-->H++C++CH+. When ultrashort (9  fs) laser pulses are used, the angle between the momenta of C+ and H+ fragments exhibits a sharp distribution peaked at a small angle (~20°), showing that the hydrogen atom remains near the original carbon site in the acetylene configuration. On the other hand, a significantly broad distribution extending to larger momentum angles (~120°) is observed when the pulse duration is increased to 35  fs, indicating that the ultrafast isomerization to vinylidene is induced in the longer laser pulse.
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82.30.Qt, 82.50.-m, 82.53.-k

Vacuum ultraviolet excitation spectroscopy of the autoionizing Rydberg states of atomic sulfur in the 73  350–84  950  cm−1 frequency range

Xueliang Yang, Jingang Zhou, Brant Jones, C. Y. Ng, and William M. Jackson

J. Chem. Phys. 128, 084303 (2008) (9 pages)

Online Publication Date: 25 February 2008

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The photoionization efficiency (PIE) spectra of metastable sulfur (S) atoms in the 1D and 1S states have been recorded in the 73  350–84  950  cm−1 frequency range by using a velocity-mapped ion imaging apparatus that uses a tunable vacuum ultraviolet laser as the ionization source. The S(1D) and S(1S) atoms are produced by the 193  nm photodissociation of CS2. The observed PIE spectra of S(1D) and S(1S) shows 35 autoionizing resonances with little or no contribution from direct photoionization into the S+(4S3/2)+e− ionization continuum. Velocity-mapped ion images of the S+ at the individual autoionizing Rydberg resonances are used to distinguish whether the lower state of the resonance originates from the 1D, 1S, or 3P states. The analysis and assignment of the Rydberg peaks revealed 22 new Rydberg states that were not previously known. The autoionization lifetimes tau of the Rydberg states are derived from the linewidths by fitting the lines with the Fano formula. Deviations from the scaling law of tau(n*)[proportional]n*3, where n* is the effective quantum number of the Rydberg state, are observed. This observation is ascribed to perturbations by nearby triplet Rydberg states, which shorten the autoionization lifetimes of the singlet Rydberg levels.
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33.20.Ni, 32.70.Jz, 32.80.Fb, 32.80.Ee, 32.80.Zb

Spectroscopy of the UO<sub>2</sub><sup>+</sup> cation and the delayed ionization of UO2

Jeremy M. Merritt, Jiande Han, and Michael C. Heaven

J. Chem. Phys. 128, 084304 (2008) (8 pages)

Online Publication Date: 25 February 2008

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Vibronically resolved spectra for the UO<sub>2</sub><sup>+</sup> cation have been recorded using the pulsed field ionization zero electron kinetic energy (PFI-ZEKE) technique. For the ground state, long progressions in both the bending and symmetric stretch vibrations were observed. Bend and stretch progressions of the first electronically excited state were also observed, and the origin was found at an energy of 2678  cm−1 above the ground state zero-point level. This observation is consistent with a recent theoretical prediction [Infante et al., J. Chem. Phys. 127, 124308 (2007)]. The ionization energy for UO2, derived from the PFI-ZEKE spectrum, namely, 6.127(1)  eV, is in excellent agreement with the value obtained from an earlier photoionization efficiency measurement. Delayed ionization of UO2 in the gas phase has been reported previously [Han et al., J. Chem. Phys. 120, 5155 (2004)]. Here, we extend the characterization of the delayed ionization process by performing a quantitative study of the ionization rate as a function of the energy above the ionization threshold. The ionization rate was found to be 5×106  s−1 at threshold, and increased linearly with increasing energy in the range investigated (0–1200  cm−1).
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33.20.Wr, 33.15.Mt, 33.20.Tp, 33.15.Ta, 34.50.Gb

Vibrational action spectroscopy of the C–H and C–D stretches in partially deuterated formic acid dimer

Y. Heidi Yoon, Michael L. Hause, Amanda S. Case, and F. Fleming Crim

J. Chem. Phys. 128, 084305 (2008) (6 pages)

Online Publication Date: 27 February 2008

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Vibrational action spectroscopy of jet-cooled formic acid dimer measures the frequency of the C–H(D) stretching vibration and its coupling to nearby states. The action spectrum of (DCOOH)2 reveals a specific Fermi resonance between the C–D stretch and two antisymmetric combination states formed from the C–O stretch and DCO bend. A three-state deperturbation analysis shows that there is a relatively strong coupling between the fundamental vibration and each of the combination vibrations (|13  cm−1|) as well as between the combination states themselves (|7  cm−1|). This situation contrasts with that for the action spectrum of (HCOOD)2, where the C–H oscillator is isolated and not strongly coupled to other states.
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33.15.Mt, 33.20.Tp, 33.15.Bh, 33.70.Ca

Stability and magnetic properties of transition metal atoms endohedral BnNn (n=12–28) cages

Jianguang Wang, Li Ma, Jijun Zhao, Baolin Wang, and Guanghou Wang

J. Chem. Phys. 128, 084306 (2008) (7 pages)

Online Publication Date: 27 February 2008

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First-principles calculations have been conducted to systemically investigate the stability and magnetic properties of 3d and 4d transitional-metal (TM) atoms doped in the BnNn (n=12,16,20,24,28) cages. Among those cages, the B24N24 is the optimal one for encapsulating 3d and 4d TM atoms according to the computed heat of formation. Inside B24N24 cage, 3d and 4d TM dopants belonging to the same group in the Periodic Table exhibit similar magnetic behaviors. Most of the 3d and 4d TM atoms remain magnetic after doped in the B24N24 cage except for Ni, Zr, and Pd. The magnitudes of the remaining moments for 3d (except for Sc, Ti, and V) and 4d dopants are reduced from those of free atoms. The energy gaps are localized at the doped transition metal atoms. Encapsulations of two TM atoms inside the B24N24 cage were also considered.
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36.40.Cg, 36.40.Qv, 31.15.ap, 82.60.Cx, 32.10.Dk, 36.40.Mr

Many-body decomposition of the binding energies for OH·(H2O)2 and OH·(H2O)3 complexes

Shiyu Du, Joseph S. Francisco, Gregory K. Schenter, and Bruce C. Garrett

J. Chem. Phys. 128, 084307 (2008) (8 pages)

Online Publication Date: 27 February 2008

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We use ab initio electronic structure methods to calculate the many-body decomposition of the binding energies of the OH·(H2O)n (n=2,3) complexes. We employ MP2 and CCSD(T) levels of theory with aug-cc-pVDZ and aug-cc-pVTZ basis sets and analyze the significance of the nonpairwise interactions between OH radical and the surrounding water molecules. We also evaluate the accuracy of our newly developed potential function, the modified Thole-type model, for predicting the many-body terms in these complexes. Our analysis of the many-body contributions to the OH·(H2O)n binding energies clearly shows that they are just as important in the OH interactions with water as they are for interactions in pure water systems.
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82.30.Cf, 82.30.Lp, 82.20.-w

Reaction dynamics of Si(3PJ)+O2-->SiO(X  1Sigma+)+O studied by a crossed-beam laser-induced fluorescence technique

R. Yamashiro, Y. Matsumoto, and K. Honma

J. Chem. Phys. 128, 084308 (2008) (6 pages)

Online Publication Date: 28 February 2008

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Oxidation reaction of the ground state Si atom was studied by using a crossed molecular beam technique at 13.0  kJ/mol of collision energy. The Si atomic beam was generated by laser vaporization and crossed with the oxygen molecular beam at right angle. Products at the crossing region were detected by the laser-induced fluorescence (LIF). The LIF of SiO(A  1Pi-X  1Sigma+) was used to determine the vibrational state distribution of the electronic ground state, SiO(X  1Sigma+). The determined distribution was inverted with the maximum population at v[double-prime]=4, and in good agreement with the recent quasiclassical trajectory calculation on the singlet potential energy surface. The agreement suggested that an abstraction mechanism is dominant at the collision energy studied here. One of the counterproducts, O(3PJ), was also observed by the vacuum ultraviolet LIF and the distribution of the spin-orbit levels were determined. The formation of O(3PJ) was consistent with the significant population of v[double-prime]=7 and 8 states of SiO, which could be explained by the presence of the triplet product channel with higher exothermicity.
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82.40.-g, 82.20.Kh, 33.50.Dq

Theoretical radiative properties between states of the triplet manifold of NH radical

L. C. Owono Owono, D. Ben Abdallah, N. Jaidane, and Z. Ben Lakhdar

J. Chem. Phys. 128, 084309 (2008) (7 pages)

Online Publication Date: 28 February 2008

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Ab initio transition dipole moments between states of the triplet manifold of NH radical are determined at the complete active space self-consistent field, followed by the internally contracted multireference singles plus doubles configuration interaction level of theory with a modified aug-cc-pVTZ basis set that accounts for valence-Rydberg interactions. This enables the computation of various radiative characteristics such as Einstein coefficients, radiative lifetimes, and oscillator strengths. These properties concern as well valence and Rydberg states. For the valence states, only the (0, 0) band of the A  3Pi-X  3Sigma− transition has received some important amount of attention. Data for the other transitions are rather scarce and sometimes inexistent. The results obtained in this work show good agreement with the available experimental data in comparison to other theoretical numbers reported in the literature.
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32.80.Ee, 33.70.Ca, 31.15.xr, 31.15.ag

Computational investigation of the Jahn-Teller effect in the ground and excited electronic states of the tropyl radical. Part I. Theoretical calculation of spectroscopically observable parameters

Vadim L. Stakhursky, Ilias Sioutis, György Tarczay, and Terry A. Miller

J. Chem. Phys. 128, 084310 (2008) (13 pages)

Online Publication Date: 28 February 2008

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Theoretical calculations are performed for the X-tilde   2E<sub>2</sub><sup>[double-prime]</sup> and à 2E<sub>3</sub><sup>[double-prime]</sup> states of the cycloheptatrienyl (tropyl) radical C7H7. An important goal of these calculations is to predict and to guide the analysis of the experimentally observed à 2E<sub>3</sub><sup>[double-prime]</sup>-X-tilde   2E<sub>2</sub><sup>[double-prime]</sup> electronic spectrum. Vibrational frequencies of the tropyl radical at the conical intersection and stationary points of its X-tilde and à state Jahn-Teller distorted potential energy surfaces are given. Spectroscopically obtainable parameters describing the Jahn-Teller effect are calculated for the X-tilde and à electronic states. Additionally, the stabilization energies for the X-tilde and à states are computed at the CASSCF(7,7) and EOMEA-CCSD levels of theory using various basis sets.
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31.30.-i, 33.20.Tp, 31.50.Bc, 31.50.Df, 31.15.xr

Experimental investigation of the Jahn-Teller effect in the ground and excited electronic states of the tropyl radical. Part II. Vibrational analysis of the à 2E<sub>3</sub><sup>[double-prime]</sup>-X-tilde   2E<sub>2</sub><sup>[double-prime]</sup> electronic transition

Ilias Sioutis, Vadim L. Stakhursky, György Tarczay, and Terry A. Miller

J. Chem. Phys. 128, 084311 (2008) (18 pages)

Online Publication Date: 28 February 2008

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Laser-induced fluorescence (LIF) and laser-excited dispersed fluorescence (LEDF) spectra of the cycloheptatrienyl (tropyl) radical C7H7 have been observed under supersonic jet-cooling conditions. Assignment of the LIF excitation spectrum yields detailed information about the Ã-state vibronic structure. The LEDF emission was collected by pumping different vibronic bands of the à 2E<sub>3</sub><sup>[double-prime]</sup><--X-tilde   2E<sub>2</sub><sup>[double-prime]</sup> electronic spectrum. Analysis of the LEDF spectra yields valuable information about the vibronic levels of the X-tilde   2E<sub>2</sub><sup>[double-prime]</sup> state. The X-tilde- and Ã-state vibronic structures characterize the Jahn-Teller distortion of the respective potential energy surfaces. A thorough analysis reveals observable Jahn-Teller activity in three of the four e<sub>3</sub><sup>[prime]</sup> modes for the X-tilde   2E<sub>2</sub><sup>[double-prime]</sup> state and two of the three e<sub>1</sub><sup>[prime]</sup> modes for the à 2E<sub>3</sub><sup>[double-prime]</sup> state and provides values for their deperturbed vibrational frequencies as well as linear Jahn-Teller coupling constants. The molecular parameters characterizing the Jahn-Teller interaction in the X-tilde and à states of C7H7 are compared to theoretical results and to those previously obtained for C5H5 and C6H<sub>6</sub><sup>+</sup>.
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31.50.Df, 33.50.Dq, 33.15.Mt, 33.20.Tp, 33.80.-b, 31.30.-i

Nonadiabatic effects in the photodetachment of ClH<sub>2</sub><sup>-</sup>

Millard H. Alexander, Jacek Kłos, and David E. Manolopoulos

J. Chem. Phys. 128, 084312 (2008) (12 pages)

Online Publication Date: 28 February 2008

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The photoelectron spectra of the ClH<sub>2</sub><sup>-</sup> and ClD<sub>2</sub><sup>-</sup> anions have been simulated using a Franck–Condon model involving vertical excitation to the four coupled quasidiabatic potential energy surfaces that correlate with Cl(2P)+H2(1Sigma<sub>g</sub><sup>+</sup>). A careful analysis of the excitation process is presented. All electrostatic, spin-orbit, and Coriolis couplings in the photodetached ClH2 (ClD2) neutral are included. At a resolution of 1  meV, the resulting spectra are dominated by the bound and resonant states of the Cl[centered ellipsis]H2 and Cl[centered ellipsis]D2 van der Waals complexes, along with contributions from the associated continua. Only small differences occur between these spectra and those simulated under the assumption that each of the three electronically adiabatic Cl(2P)+H2 states can be treated separately. In particular, photodetachment to form the Cl*(2P1/2)H2 complex leads to very low intensity of spectral features associated with Cl(2P3/2)H2. This clearly implies that, while nonadiabatic effects do have some influence on the bound and resonance state energies of both complexes as shown recently by Garand et al. [Science 319, 72 (2008)], nonadiabatic transitions between the two complexes are extremely rare.
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34.50.Gb, 33.80.Eh, 33.60.+q, 33.70.Ca, 31.50.-x, 31.50.Df

Evidence for excited spin-orbit state reaction dynamics in F+H2: Theory and experiment

François Lique, Millard H. Alexander, Guoliang Li, Hans-Joachim Werner, Sergey A. Nizkorodov, Warren W. Harper, and David J. Nesbitt

J. Chem. Phys. 128, 084313 (2008) (9 pages)

Online Publication Date: 29 February 2008

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We describe fully quantum, time-independent scattering calculations of the F+H2-->HF+H reaction, concentrating on the HF product rotational distributions in v[prime]=3. The calculations involved two new sets of ab initio potential energy surfaces, based on large basis set, multireference configuration-interaction calculations, which are further scaled to reproduce the experimental exoergicity of the reaction. In addition, the spin-orbit, Coriolis, and electrostatic couplings between the three quasidiabatic F+H2 electronic states are included. The calculated integral cross sections are compared with the results of molecular beam experiments. At low collision energies, a significant fraction of the reaction is due to Born–Oppenheimer forbidden, but energetically allowed reaction of F in its excited (2P1/2) spin-orbit state. As the collision energy increases, the Born–Oppenheimer allowed reaction of F in its ground (2P3/2) spin-orbit state rapidly dominates. Overall, the calculations agree reasonably well with the experiment, although there remains some disagreement with respect to the degree of rotational excitation of the HF(v[prime]=3) products as well as with the energy dependence of the reactive cross sections at the lowest collision energies.
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82.30.Cf, 82.20.Kh, 82.20.Hf, 82.20.Pm

Resonant two-photon ionization spectroscopy of jet-cooled OsC

Olha Krechkivska and Michael D. Morse

J. Chem. Phys. 128, 084314 (2008) (9 pages)

Online Publication Date: 29 February 2008

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The optical spectrum of diatomic OsC has been investigated for the first time, with transitions recorded in the range from 17  390  to  22  990  cm−1. Six bands were rotationally resolved and analyzed to obtain ground and excited state rotational constants and bond lengths. Spectra for six OsC isotopomers, 192Os12C (40.3% natural abundance), 190Os12C(26.0%), 189Os12C(16.0%), 188Os12C(13.1%), 187Os12C(1.9%), and 186Os12C(1.6%), were recorded and rotationally analyzed. The ground state was found to be X  3Delta3, deriving from the 4delta316sigma1 electronic configuration. Four bands were found to originate from the X  3Delta3 ground state, giving B0[double-prime]=0.533  492(33)  cm−1 and r0[double-prime]=1.672  67(5)  Å for the 192Os12C isotopomer (1sigma error limits); two of these, the 0-0[19.1]2<--X  3Delta3 and 1-0[19.1]2<--X  3Delta3 bands, form a vibrational progression with DeltaG[prime]1/2=953.019  cm−1. The remaining two bands were identified as originating from an Omega[double-prime]=0 level that remains populated in the supersonic expansion. This level is assigned as the low-lying A  3Sigma<sub>0+</sub><sup>-</sup> state, which derives from the 4delta  216sigma2 electronic configuration. The OsC molecule differs from the isovalent RuC molecule in having an X  3Delta3 ground state, rather than the X  2delta  4, 1Sigma+ ground state found in RuC. This difference in electronic structure is due to the relativistic stabilization of the 6s orbital in Os, an effect which favors occupation of the 6s-like 16sigma orbital. The relativistic stabilization of the 16sigma orbital also lowers the energy of the 4delta  216sigma2, 3Sigma− term, allowing this term to remain populated in the supersonically cooled molecular beam.
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33.80.Rv, 33.80.Eh, 33.15.Mt, 33.20.Sn, 33.20.Tp, 33.15.Dj

Formation of the diphenyl molecule in the crossed beam reaction of phenyl radicals with benzene

Fangtong Zhang, Xibin Gu, and Ralf I. Kaiser

J. Chem. Phys. 128, 084315 (2008) (5 pages)

Online Publication Date: 29 February 2008

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The chemical dynamics to form the D5-diphenyl molecule, C6H5C6D5, via the neutral-neutral reaction of phenyl radicals (C6H5) with D6-benzene (C6D6), was investigated in a crossed molecular beams experiment at a collision energy of 185  kJ  mol−1. The laboratory angular distribution and time-of-flight spectra of the C6H5C6D5 product were recorded at mass to charge m/z of 159. Forward-convolution fitting of our data reveals that the reaction dynamics are governed by an initial addition of the phenyl radical to the pi electron density of the D6-benzene molecule yielding a short-lived C6H5C6D6 collision complex. The latter undergoes atomic deuterium elimination via a tight exit transition state located about 30  kJ  mol−1 above the separated reactants; the overall reaction to form D5-diphenyl from phenyl and D6-benzene was found to be weakly exoergic. The explicit identification of the D5-biphenyl molecules suggests that in high temperature combustion flames, a diphenyl molecule can be formed via a single collision event between a phenyl radical and a benzene molecule.
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82.50.Nd, 82.45.Wx

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

EPR and IR spectra of the FSO3 radical revisited: Strong vibronic interactions in the 2A2 electronic ground state

H. Beckers, H. Willner, D. Grote, and W. Sander

J. Chem. Phys. 128, 084501 (2008) (11 pages)

Online Publication Date: 25 February 2008

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The previous controversy about the ground-state symmetry and contradictory vibrational analyses of FSO3 has been solved by a reinvestigation of its EPR and IR matrix spectra. The anisotropic EPR spectrum of FSO3 isolated in an argon matrix at 5  K is in agreement with an axial symmetry and an 2A2 electronic ground state. While the obtained hyperfine-coupling constants agree quite well to previous measurements in different environments, the g values may be affected by the large motion of the low-lying (162  cm−1) rocking mode of FSO3. For the first time measurements of the IR matrix spectra were extended to the far infrared region and to all 16/18O isotopomers of FSO3. A new fundamental at 161.6  cm−1 in Ar matrix and, for the nine strongest bands of FSO3, the isotopic 16/18O pattern have been observed and analyzed. The four line pattern of the a1-type fundamental modes at 1052.7, 832.5, and 531.0  cm−1 confirmed the C3v symmetry of FSO3 in the electronic ground state. The e-type fundamental modes at 931.6, 426.2, and 161.6  cm−1 are unusually low in energy and in intensity due to vibronic interaction to the low-lying electronic excited 2E states. On the other hand, several combinations and overtones of e-type fundamentals are strongly enhanced due to vibronic interactions.
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33.35.+r, 33.20.Ea, 33.20.Wr, 31.50.Bc, 33.15.Hp, 31.50.Df, 33.80.Rv, 33.15.Pw

Integrated experimental and theoretical approach for the structural characterization of Hg2+ aqueous solutions

Paola D'Angelo, Valentina Migliorati, Giordano Mancini, Vincenzo Barone, and Giovanni Chillemi

J. Chem. Phys. 128, 084502 (2008) (6 pages)

Online Publication Date: 25 February 2008

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The structural and dynamic properties of the solvated Hg2+ ion in aqueous solution have been investigated by a combined experimental-theoretical approach employing x-ray absorption spectroscopy and molecular dynamics (MD) simulations. This method allows one to perform a quantitative analysis of the x-ray absorption near-edge structure (XANES) spectra of ionic solutions using a proper description of the thermal and structural fluctuations. XANES spectra have been computed starting from the MD trajectory, without carrying out any minimization in the structural parameter space. The XANES experimental data are accurately reproduced by a first-shell heptacoordinated cluster only if the second hydration shell is included in the calculations. These results confirm at the same time the existence of a sevenfold first hydration shell for the Hg2+ ion in aqueous solution and the reliability of the potentials used in the MD simulations. The combination of MD and XANES is found to be very helpful to get important new insights into the quantitative estimation of structural properties of disordered systems.
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61.20.Ja, 61.25.Mv, 82.30.Nr, 78.70.Dm

Calorimetric versus kinetic glass transitions in viscous monohydroxy alcohols

Li-Min Wang, Yongjun Tian, Riping Liu, and Ranko Richert

J. Chem. Phys. 128, 084503 (2008) (8 pages)

Online Publication Date: 25 February 2008

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An extensive comparison of calorimetric and dielectric measurements is carried out for generic molecular liquids and monohydroxy alcohols with focus on the identification of the dielectric modes which are associated with the glass transition. For generic liquids, the calorimetric glass transition temperatures (Tg-cal) are always greater than their kinetic counterparts (Tg-kin), but the difference remains below 3  K. Also, the nonexponentiality parameters of the Tool-Narayanaswamy-Moynihan-Hodge model applied to the calorimetric data and the stretching exponents of the dielectric measurements show remarkable agreement. The same behavior is found for glass-forming monohydroxy alcohols, provided that the faster and smaller non-Debye relaxation rather than the large dielectric Debye process is assigned to the structural relaxation. The study emphasizes that the dielectric signature of the glass transition in monohydroxy alcohols is a dispersive loss peak that is faster and significantly smaller than the prominent Debye feature.
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64.70.pm, 61.25.Em, 77.22.Gm

Direct numerical simulation of homogeneous nucleation and growth in a phase-field model using cell dynamics method

Masao Iwamatsu

J. Chem. Phys. 128, 084504 (2008) (8 pages)

Online Publication Date: 25 February 2008

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The homogeneous nucleation and growth in a simplest two-dimensional phase field model is numerically studied using the cell dynamics method. The whole process from nucleation to growth is simulated and is shown to follow closely the Kolmogorov-Johnson-Mehl-Avrami (KJMA) scenario of phase transformation. Specifically the time evolution of the volume fraction of new stable phase is found to follow closely the KJMA formula. By fitting the KJMA formula directly to the simulation data, not only the Avrami exponent but the magnitude of nucleation rate and, in particular, of incubation time are quantitatively studied. The modified Avrami plot is also used to verify the derived KJMA parameters. It is found that the Avrami exponent is close to the ideal theoretical value m=3. The temperature dependence of nucleation rate follows the activation-type behavior expected from the classical nucleation theory. On the other hand, the temperature dependence of incubation time does not follow the exponential activation-type behavior. Rather the incubation time is inversely proportional to the temperature predicted from the theory of Shneidman and Weinberg [J. Non-Cryst. Solids 160, 89 (1993)]. A need to restrict thermal noise in simulation to deduce correct Avrami exponent is also discussed.
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64.60.qe, 64.60.My

Molecular dynamics simulations of beta-SiC using both fixed charge and variable charge models

Ying Ma and S. H. Garofalini

J. Chem. Phys. 128, 084505 (2008) (5 pages)

Online Publication Date: 26 February 2008

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In this paper, molecular dynamics simulations have been performed using both fixed charge and variable charge models. In the fixed charge model, partial charges are introduced to Si and C atoms to model the charge transfer observed in first principles studies. The calculated phonon dispersions, elastic constants, and lattice constants are in good accuracy. Variable charge model is also used to obtain geometry and connectivity dependent atomic charges. Our results show that although the variable charge model may not be advantageous in the study of ordered structures, it is important in describing structural disorders such as vacancies.
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63.20.dk, 81.40.Jj, 62.20.dq, 61.66.Fn, 61.72.jd

Shear viscosity of liquid copper at experimentally accessible shear rates: Application of the transient-time correlation function formalism

Caroline Desgranges and Jerome Delhommelle

J. Chem. Phys. 128, 084506 (2008) (6 pages)

Online Publication Date: 26 February 2008

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We report on nonequilibrium molecular dynamics (NEMD) simulations results on the shear viscosity of liquid copper, modeled by a many-body embedded-atoms model potential. Because conventional NEMD methods are restricted to very high shear rates (at least of the order of 1010  s−1, that is several orders of magnitude larger than those accessible by experiment), previous work only provided access to the response of the fluid in the shear-thinning regime. Using the transient-time correlation function formalism, we show how NEMD simulations can be extended to study the rheological properties of liquid copper subjected to low, experimentally accessible, shear rates. Our results provide a full picture of the rheology of the system, in the Newtonian regime as well as in the shear-thinning regime.
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61.25.Mv, 66.20.Cy, 66.20.Ej, 61.20.Ja, 47.57.Qk

Quasielastic neutron scattering study of pyridinium cation reorientation in thiourea pyridinium nitrate inclusion compound

A. Pajzderska, M. A. Gonzalez, and J. Wąsicki

J. Chem. Phys. 128, 084507 (2008) (9 pages)

Online Publication Date: 26 February 2008

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The dynamics of the pyridinium cation in thiourea pyridinium nitrate inclusion compound has been studied using quasielastic neutron scattering in a wide temperature range (10–350  K). The elastic incoherent structure factor was determined from neutron backscattering and time-of-flight measurements and its analysis allows to describe in detail the geometry of the motions of the pyridinium cation. Our study reveals two types of motion having two different correlation times. The pyridinium cation reorients about the axis perpendicular to its molecular plane over inequivalent threefold potential energy barriers and also executes a faster out-of-plane motion about the axis passing through two opposite atoms of the ring.
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61.66.Hq, 61.72.Qq

Charge redistribution and photoacidity: Neutral versus cationic photoacids

D. B. Spry and M. D. Fayer

J. Chem. Phys. 128, 084508 (2008) (9 pages)

Online Publication Date: 27 February 2008

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A series of pyrene photoacids is used to investigate excited-state proton transfer with time-dependent pump-probe spectroscopy. The deprotonation dynamics of a cationic photoacid, 8-aminopyrene-1,3,6-trisulfonic acid trisodium salt (APTS), shows single exponential dynamics(~30  ps) in water. This is in contrast to what is observed for the neutral photoacids 8-hydroxypyrene-1,3,6-trisulfonic acid trisodium salt (HPTS) and 8-hydroxy-N,N,N[prime],N[prime],N[double-prime],N[double-prime]-hexamethylpyrene-1,3,6-trisulfonamide, which display biexponential dynamics. For the cationic photoacid, the vast majority of the intramolecular charge redistribution does not occur in the protonated state. Instead, the charge redistribution, which is responsible for the photoacidity and the observed spectroscopic changes, occurs primarily following the excited-state proton transfer. The lack of charge redistribution prior to proton transfer causes APTS to display single exponential kinetics. In contrast, the dynamics for the neutral photoacids are multiexponential because major charge redistribution precedes proton transfer followed by additional charge redistribution that accompanies proton transfer. Previous studies of HPTS in water are discussed in terms of the results presented here.
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82.30.Hk, 82.80.-d, 82.30.Lp, 82.50.-m

Theory of gelation, vitrification, and activated barrier hopping in mixtures of hard and sticky spheres

Douglas C. Viehman and Kenneth S. Schweizer

J. Chem. Phys. 128, 084509 (2008) (13 pages)

Online Publication Date: 28 February 2008

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Naive mode coupling theory (NMCT) and the nonlinear stochastic Langevin equation theory of activated dynamics have been generalized to mixtures of spherical particles. Two types of ideal nonergodicity transitions are predicted corresponding to localization of both, or only one, species. The NMCT transition signals a dynamical crossover to activated barrier hopping dynamics. For binary mixtures of equal diameter hard and attractive spheres, a mixture composition sensitive “glass-melting” type of phenomenon is predicted at high total packing fractions and weak attractions. As the total packing fraction decreases, a transition to partial localization occurs corresponding to the coexistence of a tightly localized sticky species in a gel-like state with a fluid of hard spheres. Complex behavior of the localization lengths and shear moduli exist because of the competition between excluded volume caging forces and attraction-induced physical bond formation between sticky particles. Beyond the NMCT transition, a two-dimensional nonequilibrium free energy surface emerges, which quantifies cooperative activated motions. The barrier locations and heights are sensitive to the relative amplitude of the cooperative displacements of the different species.
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82.70.Gg, 62.10.+s, 65.20.-w, 68.03.Cd, 64.70.dj

Local and global properties of mixtures in one-dimensional systems. Part I. Mixtures of two simple components

Arieh Ben-Naim

J. Chem. Phys. 128, 084510 (2008) (13 pages)

Online Publication Date: 28 February 2008

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Two sets of quantities are calculated for two-component mixtures in one dimension. One consists of the traditional excess thermodynamic quantities which provide global information on the mixtures. The second, referred to as local properties, consists of the Kirkwood–Buff integrals, local composition, solvation, and preferential solvation quantities. In this part, we discuss simple particles interacting via either square-well potential or hard rod potential. It is shown that a host of new information can be obtained from the local properties of the mixtures which supplements the information conveyed by the global properties.
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65.20.Jk, 82.30.-b, 61.20.Gy

The inflection point in the pressure dependence of viscosity under high pressure: A comprehensive study of the temperature and pressure dependence of the viscosity of propylene carbonate

R. Casalini and S. Bair

J. Chem. Phys. 128, 084511 (2008) (7 pages)

Online Publication Date: 28 February 2008

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The pressure dependence of the prototypical glass-former propylene carbonate has been investigated over a broad range of temperature and pressure that were inaccessible in previous investigations using dielectric spectroscopy. We find that the viscosity measurements validate the scaling relation, eta(T,V)=[fraktur I](TVgamma), with a scaling parameter gamma close to that found from dielectric relaxation measurements. In the pressure dependence of the viscosity, we observe an inflection point in the log(eta) versus P response, similar to that found previously for other materials. However, this inflection has never been observed in dielectric relaxation measurements. Using the scaling property above, it is possible to determine the behavior of the dielectric relaxation time in this otherwise inaccessible experimental range and compare it with the viscosity measurements. We find that the behaviors of eta and tau are very similar, and a very good agreement between the function phiP calculated for these two quantities is found. Starting from the validity of the scaling properties, we show that the inflection point in the pressure dependence of the viscosity can be attributed to the convolution of the pressure dependences of the compressibility kappaT and the apparent activation energy at constant volume EV.
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77.22.Gm, 82.20.Pm

Surfaces, Interfaces, and Materials

Mean field kinetic theory for a lattice gas model of fluids confined in porous materials

Peter A. Monson

J. Chem. Phys. 128, 084701 (2008) (10 pages)

Online Publication Date: 25 February 2008

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We consider the mean field kinetic equations describing the relaxation dynamics of a lattice model of a fluid confined in a porous material. The dynamical theory embodied in these equations can be viewed as a mean field approximation to a Kawasaki dynamics Monte Carlo simulation of the system, as a theory of diffusion, or as a dynamical density functional theory. The solutions of the kinetic equations for long times coincide with the solutions of the static mean field equations for the inhomogeneous lattice gas. The approach is applied to a lattice gas model of a fluid confined in a finite length slit pore open at both ends and is in contact with the bulk fluid at a temperature where capillary condensation and hysteresis occur. The states emerging dynamically during irreversible changes in the chemical potential are compared with those obtained from the static mean field equations for states associated with a quasistatic progression up and down the adsorption/desorption isotherm. In the capillary transition region, the dynamics involves the appearance of undulates (adsorption) and liquid bridges (adsorption and desorption) which are unstable in the static mean field theory in the grand ensemble for the open pore but which are stable in the static mean field theory in the canonical ensemble for an infinite pore.
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61.43.Gt, 61.20.Ja, 65.20.-w, 66.10.C-, 68.43.Mn, 68.43.Nr

The sticking of H and D atoms on a graphite (0001) surface: The effects of coverage and energy dissipation

Jay Kerwin and Bret Jackson

J. Chem. Phys. 128, 084702 (2008) (7 pages)

Online Publication Date: 25 February 2008

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Classical trajectory methods are used to examine the trapping and sticking of H and D atoms on the graphite (0001) surface. Total energy calculations based on density functional theory are used to construct the model potential energy surface, and graphite clusters of up to 121 atoms are considered. For hydrogen to chemisorb, the bonding carbon must pucker out of the surface plane by roughly 0.4  Å. For incident energies above the 0.2  eV barrier, any trapped H atoms must rapidly dissipate their excess energy into the surrounding lattice within a few vibrations of the C–H stretch in order to remain bound. For sufficiently large clusters, the C–H bond stabilizes within about 0.1  ps. The sticking probability for D at 150  K is in the range of 5%–10%, more-or-less consistent with the most recent measurements in the limit of zero coverge. Variation with isotope and substrate temperature is weak. We estimate that the sticking cross section for adsorption at the para site, directly across the sixfold carbon ring from an already adsorbed H atom, can be four or more times larger that the zero coverage sticking cross section.
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68.43.Mn, 71.15.Nc

Reaction of molecular and atomic deuterium with methanol on Pd(111)

E. Demirci and A. Winkler

J. Chem. Phys. 128, 084703 (2008) (7 pages)

Online Publication Date: 26 February 2008

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Multiplexed thermal desorption spectroscopy was used to study the influence of preadsorbed and postadsorbed deuterium on a methanol monolayer on Pd(111). In particular, the effect of atomic deuterium exposure on the reaction products was examined in detail. Preadsorbed deuterium hinders the formation of chemisorbed methanol and favors physisorption of methanol. This leads to a strong reduction of methanol dehydrogenation during sample heating. Postadsorption of molecular deuterium also changes partially chemisorbed to physisorbed methanol. No deuteration of methanol is found under these conditions. With atomic deuterium exposure, however, significant amounts of deuterated methanol, from methanol-D1 through methanol-D4, can be produced. In addition, D exposure also causes an increased dehydrogenation probability during sample heating. The probabilities for methanol deuteration, for methanol dehydrogenation, and for D-atom bulk absorption have been determined quantitatively.
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82.30.Cf, 68.43.Nr, 82.20.Hf, 82.80.Dx

Structural transition of nematic liquid crystal in cylindrical capillary as a result of the annihilation of two point defects

Milan Svetec and Mitja Slavinec

J. Chem. Phys. 128, 084704 (2008) (6 pages)

Online Publication Date: 26 February 2008

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We study the annihilation of hedgehog-antihedgehog defects in confined nematic liquid crystals using Brownian molecular dynamics simulations. After the collision, merging of defects, and building a loop disclination structure, system can experience a structural transition into another nematic structure, triggered by a nucleation of loop disclination structure. In our rough theoretical approach we calculate the size of the emerged loop structure as the function of the typical size of the confining cavity. Attention is paid also to the dynamics of the loop structure after collision.
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64.70.mf, 61.30.Jf, 61.30.Cz, 64.70.Ja

First-principles local density approximation+U and generalized gradient approximation+U study of plutonium oxides

Bo Sun, Ping Zhang, and Xian-Geng Zhao

J. Chem. Phys. 128, 084705 (2008) (7 pages)

Online Publication Date: 27 February 2008

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The electronic structure and properties of PuO2 and Pu2O3 have been studied from first principles by the all-electron projector-augmented-wave method. The local density approximation+U and the generalized gradient approximation+U formalisms have been used to account for the strong on-site Coulomb repulsion among the localized Pu 5f electrons. We discuss how the properties of PuO2 and Pu2O3 are affected by the choice of U as well as the choice of exchange-correlation potential. Also, oxidation reaction of Pu2O3, leading to formation of PuO2, and its dependence on U and exchange-correlation potential have been studied. Our results show that by choosing an appropriate U, it is promising to correctly and consistently describe structural, electronic, and thermodynamic properties of PuO2 and Pu2O3, which enable the modeling of redox process involving Pu-based materials possible.
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71.15.-m, 73.20.Hb

Intrinsic optical bistability of thin films of linear molecular aggregates: The two-exciton approximation

Joost A. Klugkist, Victor A. Malyshev, and Jasper Knoester

J. Chem. Phys. 128, 084706 (2008) (9 pages)

Online Publication Date: 27 February 2008

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We generalize our recent work on the optical bistability of thin films of molecular aggregates [J. A. Klugkist et al., J. Chem. Phys. 127, 164705 (2007)] by accounting for the optical transitions from the one-exciton manifold to the two-exciton manifold as well as the exciton-exciton annihilation of the two-exciton states via a high-lying molecular vibronic term. We also include the relaxation from the vibronic level back to both the one-exciton manifold and the ground state. By selecting the dominant optical transitions between the ground state, the one-exciton manifold, and the two-exciton manifold, we reduce the problem to four levels, enabling us to describe the nonlinear optical response of the film. The one- and two-exciton states are obtained by diagonalizing a Frenkel Hamiltonian with an uncorrelated on-site (diagonal) disorder. The optical dynamics is described by means of the density matrix equations coupled to the electromagnetic field in the film. We show that the one- to two-exciton transitions followed by a fast exciton-exciton annihilation promote the occurrence of bistability and reduce the switching intensity. We provide estimates of pertinent parameters for actual materials and conclude that the effect can be realized.
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78.66.-w, 71.35.-y, 42.65.Pc

Energy gaps, electronic structures, and x-ray spectroscopies of finite semiconductor single-walled carbon nanotubes

Bin Gao, Jun Jiang, ZiYu Wu, and Yi Luo

J. Chem. Phys. 128, 084707 (2008) (8 pages)

Online Publication Date: 27 February 2008

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We report hybrid density functional theory calculations for electronic structures of hydrogen-terminated finite single-walled carbon nanotubes (6,5) and (8,3) up to 100  nm in length. Gap states that are mainly arisen from the hydrogen-terminated edges have been found in (8,3) tubes, but their contributions to the density of states become invisible when the tube is longer than 10  nm. The electronic structures of (6,5) and (8,3) tubes are found to be converged around 20  nm. The calculated band-gap energies of 100  nm long nanotubes are in good agreement with experimental results. The valence band structures of (6,5), (8,3), as well as (5,5) tubes are also investigated by means of ultraviolet photoelectron spectra (UPS), x-ray emission spectroscopy (XES), and the resonant inelastic x-ray scattering (RIXS) spectra theoretically. The UPS, XES and RIXS spectra become converged already at 10  nm. The length-dependent oscillation behavior is found in the RIXS spectra of (5,5) tubes, indicating that the RIXS spectra may be used to determine the size and length of metallic nanotubes. Furthermore, the chiral dependence observed in the simulated RIXS spectra suggests that RIXS spectra could be a useful technique for the determination of chirality of carbon nanotubes.
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73.22.-f, 71.15.Mb, 79.60.Jv, 78.70.En

Forced dissociation of a biomolecular complex under periodic and correlated random forcing

Han-Jou Lin, Yu-Jane Sheng, Hsuan-Yi Chen, and Heng-Kwong Tsao

J. Chem. Phys. 128, 084708 (2008) (8 pages)

Online Publication Date: 27 February 2008

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The dissociation of a biomolecular complex under the action of periodic and correlated random forcing is studied theoretically. The former is characterized by the period taup and the latter by the correlation time taur. The rupture rates are calculated by overdamped Langevin dynamics and three distinct regimes are identified for both cases by comparison to local relaxation time tauR and bond lifetime <T>. For periodic forcing, the adiabatic approximation cannot be applied in the regime taup<<tauR and the bond lifetime is determined by the average pulling. As tauR<<taup<<<T>, the rupture rate is enhanced by periodic forcing but is taup independent. Analytical expressions are obtained for small and large force amplitudes. As <T><<taup, the rupture rate depends on the phase lag and the process behaves like it is under constant force or loading rate. The result of correlated random forcing is similar to that of periodic forcing. Since the fluctuating forces greater than the average force <F> contribute more than the fluctuating forces less than <F>, the force fluctuations enhance the rupture rate. As <T><taur, the pulling felt by the bond before rupture cannot follow the random forcing protocol and, thus, force fluctuations decline with increasing taur.
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87.15.Ya, 87.15.Fh, 87.15.hg, 87.15.K-, 87.15.rs

From clusters to fibers: Parameters for discontinuous para-hexaphenylene thin film growth

Laxman Kankate, Frank Balzer, Horst Niehus, and Horst-Günter Rubahn

J. Chem. Phys. 128, 084709 (2008) (12 pages)

Online Publication Date: 27 February 2008

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All relevant steps of discontinuous thin film growth of para-hexaphenylene on muscovite mica (0 0 1) from wetting layer over small and large clusters to nanofibers are observed and investigated in detail by a combined polarized fluorescence and atomic force microscopy study. From a variation of film thickness and surface temperature, we determine effective activation energies for cluster growth of 0.17  eV, for nanofiber length growth of 0.46  eV, for width growth of 0.19  eV, and for height growth of 0.07  eV. The corresponding exponential prefactors for the nanofiber growth are 1×109, 6×104, and 3×102  nm. Polarized fluorescence studies reveal that nanofibers grow along the grooves of the mica surface and that they do not change direction if they cross an even number of mica surface steps, while they change direction by 120° for an odd number of steps. These results are taken as an input for a model of the unidirectional growth process on mica. Absolute parameters allowing one to grow nanofibers of predetermined morphology via organic molecular beam epitaxy are also given.
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68.55.am, 81.15.Hi

Dynamic evolution of light-induced orientation of dye-doped liquid crystals in liquid phase studied by time-resolved optically heterodyned optical Kerr effect technique

Pei Yang, Liying Liu, and Lei Xu

J. Chem. Phys. 128, 084710 (2008) (7 pages)

Online Publication Date: 27 February 2008

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Transient evolution of light-induced molecular reorientation both in 1-amino-anthraquinone (1AAQ) dye and azobenzene doped isotropic liquid crystals (LCs) were studied by time-resolved optically heterodyned optical Kerr effect method. The results give clear direct experimental proof that under short pulse (30  ps) excitation, LC molecules orientate toward the excitation light polarization direction in the 1AAQ/LC system. However, LC molecular orientation becomes orthogonal to the light polarization in azobenzene/LC system. Time-resolved excited-state absorption of 1AAQ and wavelength dependent excited-state absorption of azobenzene were also observed and their contributions to the early dynamics of the third order optical responses of the two systems were confirmed. A simplified two-level mean-field theory was derived to reveal the intensity dependence of orientation enhancement factor in azobenzene/LC system considering the photoisomerization process.
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61.30.Gd, 78.47.jc

Growth behavior of La@Sin (n=1–21) metal-encapsulated clusters

Qi Peng and Jiang Shen

J. Chem. Phys. 128, 084711 (2008) (11 pages)

Online Publication Date: 28 February 2008

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Density functional theory involving generalized gradient approximation correlation functional is used to investigate the cluster series La@Sin (n=1–21). We find that the growth process of La@Sin (n=1–21) could be divided into three stages: First, La atom adheres to other Si atoms in the size range of 1<=n<=10; then, La atom is surrounded by Si atoms with basketlike structures in the size range of 11<=n<=15; finally, La atom is completely encapsulated into the fullerene cage structures in the size range of 16<=n<=21. The growth of fullerene cage starts from La@Si16 and stops at La@Si20. By studying La@Sin+ cations and La@Sin− anions, we find that the La atom charge curves of neutral clusters, cations, and anions have a cross point at La@Si12. Adiabatic ionization potential and electron affinity are studied too. Lastly, based on the ground state geometries of La@Sin clusters, we simulate the chemical reaction in which La@SinH2n+ cation has been produced and explain why Hiura et al. [Phys. Rev. Lett. 86, 1733 (2001)] only observed La@SinH2n+ (n=1–4) cations in their experiment.
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36.40.Qv, 31.15.eg, 33.15.Ry

Atomistic and electronic structure of bimetallic cobalt/rhenium clusters from density functional theory calculations

Vebjørn Bakken and Ole Swang

J. Chem. Phys. 128, 084712 (2008) (8 pages)

Online Publication Date: 28 February 2008

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We have carried out computational density functional investigations of CoIReJ (J=0,1,2; I+J=14) metal atom clusters. Through thorough optimization of geometry, spin polarization, and electronic configuration, the most stable structures for each cluster have been identified. While the global minima are found to be well defined and energetically well separated from other local minima, the study reveals a plethora of different structures and symmetries only moderately higher in energy. A key point of interest is the effect of doping the cobalt clusters with rhenium. Aside from significant structural reorganizations, rhenium is found to stabilize the clusters and couple down the spin. Furthermore, the most stable clusters comprise highly coordinated rhenium and, in the case of Co12Re2, Re–Re bonding. Our results are compared to earlier experimental and computational data.
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61.46.Bc, 71.20.Be, 71.15.Mb

Effects of surface passivation on the exciton dynamics of CdSe nanocrystals as observed by ultrafast fluorescence upconversion spectroscopy

Tadd C. Kippeny, Michael J. Bowers, II, Albert D. Dukes, III, James R. McBride, Rebecca L. Orndorff, Maria Danielle Garrett, and Sandra J. Rosenthal

J. Chem. Phys. 128, 084713 (2008) (7 pages)

Online Publication Date: 28 February 2008

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The exciton dynamics of CdSe nanocrystals are intimately linked to the surface morphology. Photo-oxidation of the selenium surfaces of the nanocrystal leads to an increase in radiative decay efficiency from both the band edge and deep trap emission states. The addition of the primary amine hexadecylamine curtails nonradiative excitonic decay attributed to the dangling surface selenium orbitals by passivation of those trap sites by the methylene protons on the amine, leading to enhanced band edge emission and the absence of deep trap emission. Furthermore, CdSe/ZnSe core/shell nanocrystals are not immune from contributions from surface states because of the alignment of the band structures of the core and shell materials.
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78.67.Bf, 71.35.-y, 73.20.At, 81.65.Rv, 78.55.Et, 82.50.-m, 82.65.+r

The AM05 density functional applied to solids

Ann E. Mattsson, Rickard Armiento, Joachim Paier, Georg Kresse, John M. Wills, and Thomas R. Mattsson

J. Chem. Phys. 128, 084714 (2008) (11 pages)

Online Publication Date: 29 February 2008

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We show that the AM05 functional [Armiento and Mattsson, Phys. Rev. B 72, 085108 (2005)] has the same excellent performance for solids as the hybrid density functionals tested in Paier et al. [J. Chem. Phys. 124, 154709 (2006); 125, 249901 (2006)]. This confirms the original finding that AM05 performs exceptionally well for solids and surfaces. Hartree–Fock hybrid calculations are typically an order of magnitude slower than local or semilocal density functionals such as AM05, which is of a regular semilocal generalized gradient approximation form. The performance of AM05 is on average found to be superior to selecting the best of local density approximation and PBE for each solid. By comparing data from several different electronic-structure codes, we have determined that the numerical errors in this study are equal to or smaller than the corresponding experimental uncertainties.
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71.15.Mb, 71.15.Ap

Density, distribution, and orientation of water molecules inside and outside carbon nanotubes

J. A. Thomas and A. J. H. McGaughey

J. Chem. Phys. 128, 084715 (2008) (6 pages)

Online Publication Date: 29 February 2008

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The behavior of water molecules inside and outside 1.1, 2.8, 6.9, and 10.4  nm diameter armchair carbon nanotubes (CNTs) is predicted using molecular dynamics simulations. The effects of CNT diameter on mass density, molecular distribution, and molecular orientation are identified for both the confined and unconfined fluids. Within 1  nm of the CNT surface, unconfined water molecules assume a spatially varying density profile. The molecules distribute nonuniformly around the carbon surface and have preferred orientations. The behavior of the unconfined water molecules is invariant with CNT diameter. The behavior of the confined water, however, can be correlated to tube diameter. Inside the 10.4  nm CNT, the molecular behavior is indistinguishable from that of the unconfined fluid. Within the smaller CNTs, surface curvature effects reduce the equilibrium water density and force water molecules away from the surface. This effect changes both the molecular distribution and preferred molecular orientations.
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61.46.Fg, 61.20.Ja, 61.25.Em

Polymers and Complex Systems

Block copolymers confined in a nanopore: Pathfinding in a curving and frustrating flatland

G. J. A. Sevink and A. V. Zvelindovsky

J. Chem. Phys. 128, 084901 (2008) (16 pages)

Online Publication Date: 25 February 2008

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We have studied structure formation in a confined block copolymer melt by means of dynamic density functional theory. The confinement is two dimensional, and the confined geometry is that of a cylindrical nanopore. Although the results of this study are general, our coarse-grained molecular model is inspired by an experimental lamella-forming polysterene-polybutadiene diblock copolymer system [K. Shin et al., Science 306, 76 (2004)], in which an exotic toroidal structure was observed upon confinement in alumina nanopores. Our computational study shows that a zoo of exotic structures can be formed, although the majority, including the catenoid, helix, and double helix that were also found in Monte Carlo nanopore studies, are metastable states. We introduce a general classification scheme and consider the role of kinetics and elongational pressure on stability and formation pathway of both equilibrium and metastable structures in detail. We find that helicity and threefold connections mediate structural transitions on a larger scale. Moreover, by matching the remaining parameter in our mesoscopic method, the Flory-Huggins parameter chi, to the experimental system, we obtain a structure that resembles the experimental toroidal structure in great detail. Here, the most important factor seems to be the roughness of the pore, i.e., small variations of the pore radius on a scale that is larger than the characteristic size in the system.
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61.25.he, 61.20.Gy, 61.25.hk

Effects due to molecular shape and flexibility on the permeability ratio of binary fluid mixtures in a model polymer network via computer simulation

Henning Hörstermann and Reinhard Hentschke

J. Chem. Phys. 128, 084902 (2008) (6 pages)

Online Publication Date: 27 February 2008

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Sorption and diffusion of binary mixtures of small molecules in model polymer networks is studied via computer simulation. Three types of molecules identical in volume but different in shape and flexibility (compact, linear stiff, and linear flexible) are combined into binary mixtures (compact/linear stiff) and (linear stiff/linear flexible). The relative effects of shape and flexibility on separation factor and diffusion coefficient inside random polymer networks are studied using a molecular dynamics/Gibbs-ensemble Monte Carlo hybrid technique. In addition the effects of temperature, pressure, and network strand length are considered. We find that the compact molecules are preferentially absorbed into the network at all strand lengths and temperatures considered here. Flexibility only leads to minor preferential sorption under most conditions. Diffusion coefficients of the competing species inside the network are found to agree within the error bars.
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66.10.C-, 68.43.-h

Statistical geometry of lattice chain polymers with voids of defined shapes: Sampling with strong constraints

Ming Lin, Rong Chen, and Jie Liang

J. Chem. Phys. 128, 084903 (2008) (12 pages)

Online Publication Date: 28 February 2008

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Proteins contain many voids, which are unfilled spaces enclosed in the interior. A few of them have shapes compatible to ligands and substrates and are important for protein functions. An important general question is how the need for maintaining functional voids is influenced by, and affects other aspects of proteins structures and properties (e.g., protein folding stability, kinetic accessibility, and evolution selection pressure). In this paper, we examine in detail the effects of maintaining voids of different shapes and sizes using two-dimensional lattice models. We study the propensity for conformations to form a void of specific shape, which is related to the entropic cost of void maintenance. We also study the location that voids of a specific shape and size tend to form, and the influence of compactness on the formation of such voids. As enumeration is infeasible for long chain polymer, a key development in this work is the design of a novel sequential Monte Carlo strategy for generating large number of sample conformations under very constraining restrictions. Our method is validated by comparing results obtained from sampling and from enumeration for short polymer chains. We succeeded in accurate estimation of entropic cost of void maintenance, with and without an increasing number of restrictive conditions, such as loops forming the wall of void with fixed length, with additionally fixed starting position in the sequence. Additionally, we have identified the key structural properties of voids that are important in determining the entropic cost of void formation. We have further developed a parametric model to predict quantitatively void entropy. Our model is highly effective, and these results indicate that voids representing functional sites can be used as an improved model for studying the evolution of protein functions and how protein function relates to protein stability.
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36.20.Ey, 36.20.Fz

Biological Molecules, Biopolymers, and Biological Systems

Effect of interactions on molecular fluxes and fluctuations in the transport across membrane channels

Anatoly B. Kolomeisky and Stanislav Kotsev

J. Chem. Phys. 128, 085101 (2008) (6 pages)

Online Publication Date: 25 February 2008

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Transport of molecules across membrane channels is investigated theoretically using exactly solvable one-dimensional discrete-state stochastic models. An interaction between molecules and membrane pores is modeled via a set of binding sites with different energies. It is shown that the interaction potential strongly influences the particle currents as well as fluctuations in the number of translocated molecules. For small concentration gradients, the attractive sites lead to largest currents and fluctuations, while the repulsive interactions yield the largest fluxes and dispersions for large concentration gradients. Interaction energies that lead to maximal currents and maximal fluctuations are the same only for locally symmetric potentials, where transition states are equally distant from the neighboring binding sites, while they differ for the locally asymmetric potentials. The conditions for the most optimal translocation transport with maximal current and minimal dispersion are discussed. It is argued that, in this case, the interaction strength is independent of local symmetry of the potential of mean forces. In addition, the effect of the global asymmetry of the interaction potential is investigated, and it is shown that it also strongly affects the particle translocation dynamics. These phenomena can be explained by analyzing the details of the particle entering and leaving the binding sites in the channel.
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87.15.A-, 87.15.hg, 87.15.hj, 87.15.K-, 87.15.R-, 87.15.Ya

The effect of hydrodynamic interactions on the dynamics of DNA translocation through pores

Aslin Izmitli, David C. Schwartz, Michael D. Graham, and Juan J. de Pablo

J. Chem. Phys. 128, 085102 (2008) (7 pages)

Online Publication Date: 25 February 2008

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In this work, we investigate the effect of hydrodynamic interactions on the dynamics of DNA translocation through micropores. We simulate DNA as a bead-spring chain and use a lattice Boltzmann method to simulate the flow field that arises from the motion of the molecule. We investigate the free-draining entrance of DNA to the pore by diffusion and find that, consistent with experiments, molecules have a higher probability of entering the pore from one end. We then consider the electric-field driven translocation of 21–210  µm DNA with and without hydrodynamic interactions. Consistent with experiments, we study translocation events that are much shorter than the relaxation time of DNA. We find that the effect of hydrodynamic interactions on this process is to cause different regions of a molecule, other than the ones pulled by voltage or chain connectivity into the pore, to move toward the pore. We quantify this effect and show that it is smaller than the difference in the translocation dynamics of chains that arises from different initial configurations of the molecules. A power-law scaling of translocation time with chain length is observed, with exponents of 1.28±0.03 and 1.31±0.03 in simulations with and without hydrodynamic interactions, respectively. Our results are in good agreement with recent translocation experiments conducted in small pores and show that, for the regime considered in this work, hydrodynamic interactions play a minor role in the relation of the translocation time to chain length. For fast translocation processes, the effect of hydrodynamic interactions is local and the main factor determining the dynamics of DNA is the initial configuration of the molecules.
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87.15.Vv, 87.15.hg, 87.10.-e

Thermodynamics of peptide aggregation processes: An analysis from perspectives of three statistical ensembles

Christoph Junghans, Michael Bachmann, and Wolfhard Janke

J. Chem. Phys. 128, 085103 (2008) (9 pages)

Online Publication Date: 28 February 2008

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We employ a mesoscopic model for studying aggregation processes of proteinlike hydrophobic-polar heteropolymers. By means of multicanonical Monte Carlo computer simulations, we find strong indications that peptide aggregation is a phase separation process, in which the microcanonical entropy exhibits a convex intruder due to non-negligible surface effects of the small systems. We analyze thermodynamic properties of the conformational transitions accompanying the aggregation process from the multicanonical, canonical, and microcanonical perspective. It turns out that the microcanonical description is particularly advantageous as it allows for unraveling details of the phase-separation transition in the thermodynamic region, where the temperature is not a suitable external control parameter anymore.
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87.14.ef, 87.15.Cc, 87.15.ak, 87.15.hp, 87.15.nr
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LETTERS TO THE EDITOR

Notes

Estimation of bulk liquid properties from Monte Carlo simulations of Lennard-Jones clusters

Jonathan C. Barrett and Andrew P. Knight

J. Chem. Phys. 128, 086101 (2008) (2 pages)

Online Publication Date: 28 February 2008

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Monte Carlo simulations are performed to determine the free energies of clusters containing between i=20 and i=100 atoms interacting via the Lennard-Jones potential at dimensionless temperatures T* between 0.25 and 0.875. A cluster is defined by the condition that all atoms are within a specified distance of their mutual center of mass. A function of the form [b−alpha(i−1)−theta(i2/3−1)] is found to provide a good fit to the Monte Carlo data and the fitted values of the temperature-dependent parameters alpha and theta agree reasonably well with the predictions of bulk simulations (extrapolated as necessary) for the vapor pressure and surface energy per atom in the range T*=0.375–0.7.
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61.20.Ja, 62.10.+s

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