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7 December 2007

Volume 127, Issue 21,  Articles (21xxxx)

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COMMUNICATIONS

Decoupling of exchange and persistence times in atomistic models of glass formers

Lester O. Hedges, Lutz Maibaum, David Chandler, and Juan P. Garrahan

J. Chem. Phys. 127, 211101 (2007) (4 pages)

Online Publication Date: 3 December 2007

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With molecular dynamics simulations of a fluid mixture of classical particles interacting with pairwise additive Weeks-Chandler-Andersen potentials, we consider the time series of particle displacements and thereby determine the distributions for local persistence times and local exchange times. These basic characterizations of glassy dynamics are studied over a range of supercooled conditions and were shown to have behaviors, most notably decoupling, similar to those found in kinetically constrained lattice models of structural glasses. Implications are noted.
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61.43.Fs, 61.20.Ja

Adsorption of gold on TiC(001): Au–C interactions and charge polarization

J. A. Rodriguez, F. Viñes, F. Illas, P. Liu, Y. Takahashi, and K. Nakamura

J. Chem. Phys. 127, 211102 (2007) (4 pages)

Online Publication Date: 5 December 2007

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High-resolution photoemission and first-principles density-functional slab calculations were used to study the adsorption of gold on a TiC(001) surface. A positive shift in the binding energy of the C 1s core level is observed after the deposition of Au on the metal carbide surface. The results of the density-functional calculations corroborate the formation of Au–C bonds. In general, the bond between Au and the TiC(001) surface exhibits very little ionic character, but there is a substantial polarization of electrons around Au that affects its chemical properties.
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68.43.Mn, 82.65.+r, 79.60.Dp, 71.15.Mb, 73.20.At

An automated integration-free path-integral method based on Kleinert's variational perturbation theory

Kin-Yiu Wong and Jiali Gao

J. Chem. Phys. 127, 211103 (2007) (4 pages)

Online Publication Date: 5 December 2007

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Based on Kleinert's variational perturbation (KP) theory [Path Integrals in Quantum Mechanics, Statistics, Polymer Physics, and Financial Markets, 3rd ed. (World Scientific, Singapore, 2004)], we present an analytic path-integral approach for computing the effective centroid potential. The approach enables the KP theory to be applied to any realistic systems beyond the first-order perturbation (i.e., the original Feynman-Kleinert [Phys. Rev. A 34, 5080 (1986)] variational method). Accurate values are obtained for several systems in which exact quantum results are known. Furthermore, the computed kinetic isotope effects for a series of proton transfer reactions, in which the potential energy surfaces are evaluated by density-functional theory, are in good accordance with experiments. We hope that our method could be used by non-path-integral experts or experimentalists as a “black box” for any given system.
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82.30.Hk, 82.20.Tr, 82.20.Kh
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ARTICLES

Theoretical Methods and Algorithms

Adiabatic approximation of time-dependent density matrix functional response theory

Katarzyna Pernal, Klaas Giesbertz, Oleg Gritsenko, and Evert Jan Baerends

J. Chem. Phys. 127, 214101 (2007) (11 pages)

Online Publication Date: 3 December 2007

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Time-dependent density matrix functional theory can be formulated in terms of coupled-perturbed response equations, in which a coupling matrix K(omega) features, analogous to the well-known time-dependent density functional theory (TDDFT) case. An adiabatic approximation is needed to solve these equations, but the adiabatic approximation is much more critical since there is not a good “zero order” as in TDDFT, in which the virtual-occupied Kohn-Sham orbital energy differences serve this purpose. We discuss a simple approximation proposed earlier which uses only results from static calculations, called the static approximation (SA), and show that it is deficient, since it leads to zero response of the natural orbital occupation numbers. This leads to wrong behavior in the omega-->0 limit. An improved adiabatic approximation (AA) is formulated. The two-electron system affords a derivation of exact coupled-perturbed equations for the density matrix response, permitting analytical comparison of the adiabatic approximation with the exact equations. For the two-electron system also, the exact density matrix functional (2-matrix in terms of 1-matrix) is known, enabling testing of the static and adiabatic approximations unobscured by approximations in the functional. The two-electron HeH+ molecule shows that at the equilibrium distance, SA consistently underestimates the frequency-dependent polarizability alpha(omega), the adiabatic TDDFT overestimates alpha(omega), while AA improves upon SA and, indeed, AA produces the correct alpha(0). For stretched HeH+, adiabatic density matrix functional theory corrects the too low first excitation energy and overpolarization of adiabatic TDDFT methods and exhibits excellent agreement with high-quality CCSD (“exact”) results over a large omega range.
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31.15.Ew, 34.80.Ht, 33.15.Kr

Linear and nonlinear optical properties of some organoxenon derivatives

Aggelos Avramopoulos, Luis Serrano-Andrés, Jiabo Li, Heribert Reis, and Manthos G. Papadopoulos

J. Chem. Phys. 127, 214102 (2007) (11 pages)

Online Publication Date: 4 December 2007

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We employ a series of state-of-the-art computational techniques to study the effect of inserting one or more Xe atoms in HC2H and HC4H, on the linear and nonlinear optical (L&NLO) properties of the resulting compounds. It has been found that the inserted Xe has a great effect on the L&NLO properties of the organoxenon derivatives. We analyze the bonding in HXeC2H, and the change of the electronic structure, which is induced by inserting Xe, in order to rationalize the observed extraordinary L&NLO properties. The derivatives, which are of interest in this work, have been synthesized in a Xe matrix. Thus the effect of the local field (LF), due to the Xe environment, on the properties of HXeC2H, has also been computed. It has been found that the LF effect on some properties is significant. The calculations have been performed by employing a hierarchy of basis sets and the techniques MP2 and CCSD(T) for taking into account correlation. For the interpretation of the results we have employed the complete active space valence bond and CASSCF/CASPT2 methods.
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31.15.Dv, 31.15.Ne, 31.15.Rh

Avoiding singularity problems associated with meta-GGA (generalized gradient approximation) exchange and correlation functionals containing the kinetic energy density

Jürgen Gräfenstein, Dmitry Izotov, and Dieter Cremer

J. Chem. Phys. 127, 214103 (2007) (6 pages)

Online Publication Date: 4 December 2007

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Convergence problems of meta-GGA (generalized gradient approximation) XC (exchange and correlation) functionals containing a self-interaction correction term are traced back to a singularity of the latter that occurs at critical points of the electron density. This is demonstrated for the bond critical point of equilibrium and stretched H2. A simple remedy is suggested that cures meta-XC functionals such as VSXC, TPSS, M05, M06, and their derivatives without extra cost.
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31.15.Ne, 31.25.-v, 31.15.Ew

Robust nonadiabatic molecular dynamics for metals and insulators

L. Stella, M. Meister, A. J. Fisher, and A. P. Horsfield

J. Chem. Phys. 127, 214104 (2007) (15 pages)

Online Publication Date: 4 December 2007

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We present a new formulation of the correlated electron-ion dynamics (CEID) scheme, which systematically improves Ehrenfest dynamics by including quantum fluctuations around the mean-field atomic trajectories. We show that the method can simulate models of nonadiabatic electronic transitions and test it against exact integration of the time-dependent Schrödinger equation. Unlike previous formulations of CEID, the accuracy of this scheme depends on a single tunable parameter which sets the level of atomic fluctuations included. The convergence to the exact dynamics by increasing the tunable parameter is demonstrated for a model two level system. This algorithm provides a smooth description of the nonadiabatic electronic transitions which satisfies the kinematic constraints (energy and momentum conservation) and preserves quantum coherence. The applicability of this algorithm to more complex atomic systems is discussed.
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31.15.Qg

The X1 method for accurate and efficient prediction of heats of formation

Jianming Wu and Xin Xu

J. Chem. Phys. 127, 214105 (2007) (8 pages)

Online Publication Date: 5 December 2007

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We propose the X1 method which combines the density functional theory method with a neural network (NN) correction for an accurate yet efficient prediction of heats of formation. It calculates the final energy by using B3LYP/6-311+G(3df,2p) at the B3LYP/6-311+G(d,p) optimized geometry to obtain the B3LYP standard heats of formation at 298  K with the unscaled zero-point energy and thermal corrections at the latter basis set. The NN parameters cover 15 elements of H, Li, Be, B, C, N, O, F, Na, Mg, Al, Si, P, S, and Cl. The performance of X1 is close to the Gn theories, giving a mean absolute deviation of 1.43  kcal/mol for the G3/99 set of 223  molecules up to 10 nonhydrogen atoms and 1.48  kcal/mol for the X1/07 set of 393  molecules up to 32 nonhydrogen atoms.
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82.60.Cx, 82.20.Wt

Interpolating moving least-squares methods for fitting potential energy surfaces: Improving efficiency via local approximants

Yin Guo, Igor Tokmakov, Donald L. Thompson, Albert F. Wagner, and Michael Minkoff

J. Chem. Phys. 127, 214106 (2007) (8 pages)

Online Publication Date: 5 December 2007

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The local interpolating moving least-squares (IMLS) method for constructing potential energy surfaces is investigated. The method retains the advantageous features of the IMLS approach in that the ab initio derivatives are not required and high degree polynomials can be used to provide accurate fits, while at the same time it is much more efficient than the standard IMLS approach because the least-squares solutions need to be calculated only once at the data points. Issues related to the implementation of the local IMLS method are investigated and the accuracy is assessed using HOOH as a test case. It is shown that the local IMLS method is at the same level of accuracy as the standard IMLS method. In addition, the scaling of the method is found to be a power law as a function of number of data points N, N−q. The results suggest that when fitting only to the energy values for a d-dimensional system by using a Qth degree polynomial the power law exponent q~Q/d when the energy range fitted is large (e.g., E<100  kcal/mol for HOOH), and q>Q/d when the energy range fitted is smaller (E<30  kcal/mol) and the density of data points is higher. This study demonstrates that the local IMLS method provides an efficient and accurate means for constructing potential energy surfaces.
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02.70.Rr, 31.50.-x, 02.10.De, 31.15.-p

A modified next reaction method for simulating chemical systems with time dependent propensities and delays

David F. Anderson

J. Chem. Phys. 127, 214107 (2007) (10 pages)

Online Publication Date: 6 December 2007

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Chemical reaction systems with a low to moderate number of molecules are typically modeled as discrete jump Markov processes. These systems are oftentimes simulated with methods that produce statistically exact sample paths such as the Gillespie algorithm or the next reaction method. In this paper we make explicit use of the fact that the initiation times of the reactions can be represented as the firing times of independent, unit rate Poisson processes with internal times given by integrated propensity functions. Using this representation we derive a modified next reaction method and, in a way that achieves efficiency over existing approaches for exact simulation, extend it to systems with time dependent propensities as well as to systems with delays.
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82.20.Uv, 82.20.Wt

Nonlinear scaling schemes for Lennard-Jones interactions in free energy calculations

Thomas Steinbrecher, David L. Mobley, and David A. Case

J. Chem. Phys. 127, 214108 (2007) (13 pages)

Online Publication Date: 7 December 2007

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Alchemical free energy calculations provide a means for the accurate determination of free energies from atomistic simulations and are increasingly used as a tool for computational studies of protein-ligand interactions. Much attention has been placed on efficient ways to deal with the “endpoint singularity” effect that can cause simulation instabilities when changing the number of atoms. In this study we compare the performance of linear and several nonlinear transformation methods, among them separation shifted “soft core” scaling, for a popular test system, the hydration free energy of an amino acid side chain. All the nonlinear methods yield similar results if extensive sampling is performed, but soft core scaling provides smooth lambda curves that are best suited for commonly used numerical integration schemes. Additionally, results from a more flexible solute, hexane, will also be discussed.
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87.15.Kg, 87.15.Rn, 87.15.Aa, 82.30.Nr, 82.60.-s, 34.20.Gj

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

Laser induced fluorescence of Mg-phthalocyanine in He droplets: Evidence for fluxionality of large H2 clusters at 0.38  K

Susumu Kuma, Haruka Goto, Mikhail N. Slipchenko, Andrey F. Vilesov, Alexander Khramov, and Takamasa Momose

J. Chem. Phys. 127, 214301 (2007) (7 pages)

Online Publication Date: 3 December 2007

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The formation of Ar and H2 clusters, having up to 900 particles in helium droplets, has been studied via laser induced fluorescence of attached Mg-phthalocyanine (Mg-Pc) molecules. In the experiments, one Mg-Pc molecule in average was added to each He droplet either before or after the cluster species, and the shift of the spectrum of the Mg-Pc molecules was studied as a function of the cluster size. For Ar clusters, about a factor of 2 smaller matrix shift was observed for the late pickup of the Mg-Pc molecules as compared with the prior pickup, indicating that in the former case, the Mg-Pc molecules reside on the surface of the preformed Ar clusters. On the other hand, the spectra of the Mg-Pc molecules attached to H2 clusters are independent of the pickup order, which is consistent with Mg-Pc molecules residing near the center of the H2 clusters in both cases. Therefore H2 clusters remain fluxional in helium droplets at T=0.38  K. No significant differences in the spectra were observed between the para-H2 and ortho-H2 clusters.
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33.70.Jg, 36.40.Mr, 33.50.Dq

Theoretical investigation of the energies and geometries of photoexcited uranyl(VI) ion: A comparison between wave-function theory and density functional theory

Florent Réal, Valérie Vallet, Christel Marian, and Ulf Wahlgren

J. Chem. Phys. 127, 214302 (2007) (11 pages)

Online Publication Date: 3 December 2007

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In order to assess the accuracy of wave-function and density functional theory (DFT) based methods for excited states of the uranyl(VI) UO<sub>2</sub><sup>2+</sup> molecule excitation energies and geometries of states originating from excitation from the sigmau, sigmag, piu, and pig orbitals to the nonbonding 5fdelta and 5fphi have been calculated with different methods. The investigation included linear-response CCSD (LR-CCSD), multiconfigurational perturbation theory (CASSCF/CASPT2), size-extensivity corrected multireference configuration interaction (MRCI) and AQCC, and the DFT based methods time-dependent density functional theory (TD-DFT) with different functionals and the hybrid DFT/MRCI method. Excellent agreement between all nonperturbative wave-function based methods was obtained. CASPT2 does not give energies in agreement with the nonperturbative wave-function based methods, and neither does TD-DFT, in particular, for the higher excitations. The CAM-B3LYP functional, which has a corrected asymptotic behavior, improves the accuracy especially in the higher region of the electronic spectrum. The hybrid DFT/MRCI method performs better than TD-DFT, again compared to the nonperturbative wave-function based results. However, TD-DFT, with common functionals such as B3LYP, yields acceptable geometries and relaxation energies for all excited states compared to LR-CCSD. The structure of excited states corresponding to excitation out of the highest occupied sigmau orbital are symmetric while that arising from excitations out of the piu orbitals have asymmetric structures. The distant oxygen atom acquires a radical character and likely becomes a strong proton acceptor. These electronic states may play an important role in photoinduced proton exchange with a water molecule of the aqueous environment.
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71.15.Mb, 82.50.-m, 82.30.Hk, 71.20.Ps

The d  3Pig-c  3Sigma<sub>u</sub><sup>+</sup> band system of C2

Jenna A. Joester, Masakazu Nakajima, Neil J. Reilly, Damien L. Kokkin, Klaas Nauta, Scott H. Kable, and Timothy W. Schmidt

J. Chem. Phys. 127, 214303 (2007) (6 pages)

Online Publication Date: 4 December 2007

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A two-dimensional fluorescence (excitation/emission) spectrum of C2 produced in an acetylene discharge was used to identify and separate emission bands from the d  3Pig<--c  3Sigma<sub>u</sub><sup>+</sup> and d  3Pig<--a  3Piu excitations. Rotationally resolved excitation spectra of the (4<--1), (5<--1), (5<--2), and (7<--3) bands in the d  3Pig<--c  3Sigma<sub>u</sub><sup>+</sup> system of C2 were observed by laser-induced fluorescence spectroscopy. The molecular constants of each vibrational level, determined from rotational analysis, were used to calculate the spectroscopic constants of the c  3Sigma<sub>u</sub><sup>+</sup> state. The principal molecular constants for the c  3Sigma<sub>u</sub><sup>+</sup> state are Be=1.9319(19)  cm−1, alphae=0.018  55(69)  cm−1, omegae=2061.9  cm−1, omegaexe=14.84  cm−1, and T0(c−a)=8662.925(3)  cm−1. We report also the first experimental observations of dispersed fluorescence from the d  3Pig state to the c  3Sigma<sub>u</sub><sup>+</sup> state, namely, d  3Pig(v=3)-->c  3Sigma<sub>u</sub><sup>+</sup>(v=0,1).
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33.50.Dq, 33.15.Mt, 33.20.Sn, 33.20.Tp

Vibrational inelastic and charge transfer processes in H++H2 system: An ab initio study

Saieswari Amaran and Sanjay Kumar

J. Chem. Phys. 127, 214304 (2007) (10 pages)

Online Publication Date: 5 December 2007

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State-resolved differential cross sections, total and integral cross sections, average vibrational energy transfer, and the relative probabilities are computed for the H++H2 system using the newly obtained ab initio potential energy surfaces at the full CI/cc-pVQZ level of accuracy which allow for both the direct vibrational inelastic and the charge transfer processes. The quantum dynamics is treated within the vibrational close-coupling infinite-order-sudden approximation approach using the two ab initio quasidiabatic potential energy surfaces. The computed collision attributes for both the processes are compared with the available state-to-state scattering experiments at Ec.m.=20  eV. The results are in overall good agreement with most of the observed scattering features such as rainbow positions, integral cross sections, and relative vibrational energy transfers. A comparison with the earlier theoretical study carried out on the semiempirical surfaces (diatomics in molecules) is also made to illustrate the reliability of the potential energy surfaces used in the present work.
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34.70.+e, 34.20.Mq, 34.50.Ez, 31.15.Ar

Ab initio calculations on the X-tilde   1A[prime] and à 1A[double-prime] states of HPO and Franck-Condon simulation of the single vibronic level emission spectra of HPO and DPO

Edmond P. F. Lee, Daniel K. W. Mok, Foo-Tim Chau, and John M. Dyke

J. Chem. Phys. 127, 214305 (2007) (12 pages)

Online Publication Date: 6 December 2007

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Minimum-energy geometries and relative electronic energies of the X-tilde   1A[prime] and à 1A[double-prime] states of HPO have been computed employing the coupled-cluster single-double plus perturbative triple excitations {RCCSD(T)} and/or complete-active-space self-consistent-field (CASSCF) multireference internally contracted configuration interaction (MRCI) methods with basis sets of up to the augmented correlation-consistent polarized-valence quintuple-zeta (aug-cc-pV5Z) quality. In addition, RCCSD(T)/aug-cc-pVQZ and CASSCF/MRCI/aug-cc-pVQZ potential energy functions, anharmonic vibrational wave functions, and energies involving all three vibrational modes for both electronic states of HPO and DPO, and Franck-Condon factors between the two electronic states, which allow for Duschinsky rotation and anharmonicity, were computed. Computed Franck-Condon factors were then used to simulate single vibronic level (SVL) emission spectra recently reported by Tackett and Clouthier [J. Chem. Phys. 117, 10604 (2002)]. Excellent agreement between the simulated and observed spectra was obtained for the à 1A[double-prime](1,0,0)-->X-tilde   1A[prime] SVL emission of HPO and DPO, when the best estimated ab initio geometries of the two states, which include contributions from core correlation and extrapolation to the complete basis set limit, were used in the simulation, suggesting that the best estimated ab initio geometry of the à 1A[double-prime] state of HPO, particularly the bond angle of 94.5°, is more reliable than the available experimentally derived geometry. A discussion on the geometrical parameters derived from rotational constants obtained from the rotational analysis of a high-resolution spectrum and from Franck-Condon simulation of the vibrational structure of an electronic spectrum is given.
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31.15.Ar, 33.20.Wr, 33.70.Ca, 33.15.Dj, 33.20.Sn, 33.50.Dq

Stabilization of flat aromatic Si6 rings analogous to benzene: Ab initio theoretical prediction

Aristides D. Zdetsis

J. Chem. Phys. 127, 214306 (2007) (4 pages)

Online Publication Date: 6 December 2007

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It is shown by ab initio calculations, based on density functional (DFT/B3LYP), and high level coupled-cluster [CCSD(T)] and quadratic CI [QCISD(T)] methods, that flat aromatic silicon structures analogous to benzene (C6H6) can be stabilized in the presence of lithium. The resulting planar Si6Li6 structure is both stable and aromatic, sharing many key characteristics with benzene. To facilitate possible synthesis and characterization of these species, routes of formation with high exothermicity are suggested and several spectral properties (including optical absorption, infrared, and Raman) are calculated.
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33.15.Bh

Fluorescence-detected two-dimensional electronic coherence spectroscopy by acousto-optic phase modulation

Patrick F. Tekavec, Geoffrey A. Lott, and Andrew H. Marcus

J. Chem. Phys. 127, 214307 (2007) (21 pages)

Online Publication Date: 7 December 2007

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Two-dimensional electronic coherence spectroscopy (ECS) is an important method to study the coupling between distinct optical modes of a material system. Such studies often involve excitation using a sequence of phased ultrashort laser pulses. In conventional approaches, the delays between pulse temporal envelopes must be precisely monitored or maintained. Here, we introduce a new experimental scheme for phase-selective nonlinear ECS, which combines acousto-optic phase modulation with ultrashort laser excitation to produce intensity modulated nonlinear fluorescence signals. We isolate specific nonlinear signal contributions by synchronous detection, with respect to appropriately constructed references. Our method effectively decouples the relative temporal phases from the pulse envelopes of a collinear train of four sequential pulses. We thus achieve a robust and high signal-to-noise scheme for phase-selective ECS to investigate the resonant nonlinear optical response of photoluminescent systems. We demonstrate the validity of our method using a model quantum three-level system—atomic Rb vapor. Moreover, we show how our measurements determine the resonant complex-valued third-order susceptibility.
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32.50.+d, 42.50.-p, 39.30.+w

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

Large attractive depletion interactions in soft repulsive–sphere binary mixtures

Giorgio Cinacchi, Yuri Martínez-Ratón, Luis Mederos, Guillermo Navascués, Alessandro Tani, and Enrique Velasco

J. Chem. Phys. 127, 214501 (2007) (11 pages)

Online Publication Date: 4 December 2007

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We consider binary mixtures of soft repulsive spherical particles and calculate the depletion interaction between two big spheres mediated by the fluid of small spheres, using different theoretical and simulation methods. The validity of the theoretical approach, a virial expansion in terms of the density of the small spheres, is checked against simulation results. Attention is given to the approach toward the hard-sphere limit and to the effect of density and temperature on the strength of the depletion potential. Our results indicate, surprisingly, that even a modest degree of softness in the pair potential governing the direct interactions between the particles may lead to a significantly more attractive total effective potential for the big spheres than in the hard-sphere case. This might lead to significant differences in phase behavior, structure, and dynamics of a binary mixture of soft repulsive spheres. In particular, a perturbative scheme is applied to predict the phase diagram of an effective system of big spheres interacting via depletion forces for a size ratio of small and big spheres of 0.2; this diagram includes the usual fluid-solid transition but, in the soft-sphere case, the metastable fluid-fluid transition, which is probably absent in hard-sphere mixtures, is close to being stable with respect to direct fluid-solid coexistence. From these results, the interesting possibility arises that, for sufficiently soft repulsive particles, this phase transition could become stable. Possible implications for the phase behavior of real colloidal dispersions are discussed.
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61.20.Gy, 82.70.Dd, 64.70.Ja, 64.60.My

The single-crystal, basal face of ice Ih investigated with sum frequency generation

Henning Groenzin, Irene Li, Victoria Buch, and Mary Jane Shultz

J. Chem. Phys. 127, 214502 (2007) (8 pages)

Online Publication Date: 4 December 2007

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Sum frequency generation spectroscopy has been used to investigate the hydrogen-bonded region of single-crystal, hexagonal ice in the temperature range of 113–178  K. The temperature and polarization dependences of the signal are used in conjunction with a recent theoretical model to suggest an interpretation of the bluest and reddest of the hydrogen-bonded peaks. The reddest feature is associated with strong hydrogen bonding; the dynamic polarizability of this feature is primarily parallel to the surface. It is assigned to a cooperative motion among the companion to the free-OH and four-coordinate oscillators hydrogen bonded to dangling lone-pair molecules on the surface. The bluest hydrogen-bonded feature is similarly assigned to a cooperative motion of the OH stretch of dangling lone-pair molecules and of four-coordinate molecules in the lower half bilayer that are hydrogen bonded to free-OH molecules. Reconstruction induced strain is present at as low as 113  K. These results provide a richer picture of the ice surface than has heretofore been possible.
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42.65.Ky, 68.35.Bs, 61.50.Lt, 78.20.-e, 61.66.Fn

A thermodynamically consistent kinetic framework for binary nucleation

Richard C. Flagan

J. Chem. Phys. 127, 214503 (2007) (7 pages)

Online Publication Date: 5 December 2007

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The traditional theory for binary homogeneous nucleation follows the classical derivation of the nucleation rate in the supposition of a hypothetical constrained-equilibrium distribution in the calculation of the cluster evaporation rate. This model enables calculation of the nucleation rate, but requires evaluation of the cluster distribution and cluster properties for an unstable equilibrium with supersaturated vapor. An alternate derivation of the classical homomolecular nucleation rate eliminated the need for this nonphysical approximation by calculating the evaporative flux at full thermodynamic equilibrium. The present paper develops that approach for binary nucleation; the framework is readily extended to ternary nucleation. In this analysis, the evaporative flux is evaluated by applying mass balance at full thermodynamic equilibrium of the system under study. This approach eliminates both the need for evaluating cluster properties in an unstable constrained-equilibrium state and ambiguity in the normalization constant required in the nucleation-rate expression. Moreover, it naturally spans the entire composition range between the two pure monomers. The cluster fluxes derived using this new model are similar in form to those of classical derivations, so previously developed methods for evaluation of the net nucleation rate can be applied directly to the new formulation.
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82.30.Nr, 82.60.Nh

Computing the melting point and thermodynamic stability of the orthorhombic and monoclinic crystalline polymorphs of the ionic liquid 1-n-butyl-3-methylimidazolium chloride

Saivenkataraman Jayaraman and Edward J. Maginn

J. Chem. Phys. 127, 214504 (2007) (14 pages)

Online Publication Date: 5 December 2007

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The melting point, enthalpy of fusion, and thermodynamic stability of two crystal polymorphs of the ionic liquid 1-n-butyl-3-methylimidazolium chloride are calculated using a thermodynamic integration-based atomistic simulation method. The computed melting point of the orthorhombic phase ranges from 365 to 369 K, depending on the classical force field used. This compares reasonably well with the experimental values, which range from 337 to 339 K. The computed enthalpy of fusion ranges from 19 to 29  kJ/mol, compared to the experimental values of 18.5−21.5  kJ/mol. Only one of the two force fields evaluated in this work yielded a stable monoclinic phase, despite the fact that both give accurate liquid state densities. The computed melting point of the monoclinic polymorph was found to be 373 K, which is somewhat higher than the experimental range of 318–340 K. The computed enthalpy of fusion was 23  kJ/mol, which is also higher than the experimental value of 9.3−14.5  kJ/mol. The simulations predict that the monoclinic form is more stable than the orthorhombic form at low temperature, in agreement with one set of experiments but in conflict with another. The difference in free energy between the two polymorphs is very small, due to the fact that a single trans-gauche conformational difference in an alkyl sidechain distinguishes the two structures. As a result, it is very difficult to construct simple classical force fields that are accurate enough to definitively predict which polymorph is most stable. A liquid phase analysis of the probability distribution of the dihedral angles in the alkyl chain indicates that less than half of the dihedral angles are in the gauche-trans configuration that is adopted in the orthorhombic crystal. The low melting point and glass forming tendency of this ionic liquid is likely due to the energy barrier for conversion of the remaining dihedral angles into the gauche-trans state. The simulation procedure used to perform the melting point calculations is an extension of the so-called pseudosupercritical path sampling procedure. This study demonstrates that the method can be effectively applied to quite complex systems such as ionic liquids and that the appropriate choice of tethering potentials for a key step in the thermodynamic path can enable first order phase transitions to be avoided.
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61.66.Hq, 64.70.Dv, 65.40.Gr, 82.60.Fa

Interaction of water with LiCl, LiBr, and LiI in the deeply supercooled region

Ryutaro Souda

J. Chem. Phys. 127, 214505 (2007) (7 pages)

Online Publication Date: 5 December 2007

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The hydration mechanism of lithium halides was studied using time-of-flight secondary ion mass spectrometry as a function of temperature. The lithium halides embedded in thin films of amorphous solid water segregate to the surface at temperatures higher than 135–140  K, with efficiency increasing in the order of LiCl, LiBr, and LiI. A monolayer of LiCl and LiI adsorbed on the surface of amorphous solid water tends to diffuse into the bulk at 160  K. The infrared absorption band revealed that the aqueous lithium-halide solutions and crystals are formed simultaneously at 160  K; these phenomena are explicable as a consequence of the evolution of supercooled liquid water. The strong surfactant effect is inferred to arise from hydration of a contact ion pair having hydrophilic (lithium) and hydrophobic (halide) moieties. Furthermore, bulk diffusion of lithium halides might result from the formation of a solvent-separated ion pair in supercooled liquid water. The presence of two liquid phases of water with different local structures is probably responsible for the formation of these two hydrates, consistent with the calculated result reported by Jungwirth and Tobias[J. Phys. Chem. B 106, 6361 (2002)].
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68.55.-a, 68.43.Mn, 78.30.Hv, 61.25.Em

Analysis of band broadening in vibrational high-resolution electron-energy-loss spectra of condensed methane

P. Swiderek and E. Burean

J. Chem. Phys. 127, 214506 (2007) (9 pages)

Online Publication Date: 6 December 2007

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High-resolution vibrational electron-energy-loss spectra of multilayer condensed films of methane recorded at 20  K show a strong tailing of the vibrational bands that clearly exceeds the instrumental resolution. At low incident electron energy, this tailing is remarkably less important for the dipole-allowed bending vibration (nu4) than for other bands. Also, the tailing becomes less pronounced with increasing size of the molecule as demonstrated by spectra of ethane and heptane recorded under the same conditions. Dipole coupling, rotational broadening, and multiple inelastic scattering have been considered as origins of this band broadening. While the first two effects can be excluded, multiple scattering involving a low-frequency phonon band provides a reasonable explanation as demonstrated by simulations of the spectrum of methane using a classical two-stream model. A lower phonon frequency in the cases of the larger molecules is held responsible for the better resolved vibrational signals in the spectra of ethane and heptane.
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79.20.Uv, 68.65.Ac, 63.22.+m

Extended study of molecular dynamics simulation of homogeneous vapor-liquid nucleation of water

Hiroki Matsubara, Takahiro Koishi, Toshikazu Ebisuzaki, and Kenji Yasuoka

J. Chem. Phys. 127, 214507 (2007) (11 pages)

Online Publication Date: 6 December 2007

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Using the simple point charge/extended water model, we performed molecular dynamics simulations of homogeneous vapor-liquid nucleation at various values of temperature T and supersaturation S, from which the nucleation rate J, critical nucleus size n*, and the cluster formation free energy DeltaG were derived. As well as providing lots of simulation data, the results were compared with theories on homogeneous nucleation, including the classical, semiphenomenological, and scaled models, but none of these gave a satisfactory explanation for our results. It was found that two main factors made the theories fail: (1) The average cluster structure including the nonspherical shape and the core structure that is not like the bulk liquid and (2) the forward rate which is larger than assumed by the theories by about one order of magnitude. The quantitative evaluation of these factors is left for future investigations.
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65.20.+w, 61.25.Em, 61.20.Ja, 64.60.Qb, 64.70.Fx

Photoionization of isooctane and n-octane in intense laser fields. I. Effect of irradiance on ionization rates

Andrew T. Healy, Sanford Lipsky, and David A. Blank

J. Chem. Phys. 127, 214508 (2007) (8 pages)

Online Publication Date: 7 December 2007

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The population of ejected electrons following multiphoton ionization of neat liquids isooctane and n-octane is investigated over a large range of ionizing irradiance Iex. Transient absorption (TA) at 1200  nm in both neat liquids is measured in a 60  µm path at time delays of 0.7 and 2.5  ps following an intense 400  nm (3.1  eV) ionizing pulse. As the irradiance of this pulse is varied over the range from 4  to  410  TW/cm2, the dependence of TA on Iex exhibits the periodic structure theoretically predicted for multiphoton channel openings and closings. At low Iex (<9  TW/cm2), TA in isooctane is proportional to I<sub>ex</sub><sup>n</sup> where n=3, consistent with nonresonant, near threshold ionization (liquid phase ionization potential=8.6  eV). At Iex>9  TW/cm2, n declines with increasing Iex up to Iex=13  TW/cm2, at which point n abruptly increases to 4. The pattern is repeated at Iex>13  TW/cm2, albeit with n declining from 4 and then abruptly increasing to 5 as Iex becomes greater than 100  TW/cm2. A similar trend is observed in n-octane. The dependence of the TA on Iex in the regions of channel openings and closings is compared to the nonperturbative, strong field approximation developed by Reiss [Phys. Rev. A 22, 1786 (1980)].
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79.60.-i, 61.80.Ba

Inelastic neutron scattering study of methyl groups rotation in some methylxanthines

M. Prager, A. Pawlukojc, A. Wischnewski, and J. Wuttke

J. Chem. Phys. 127, 214509 (2007) (10 pages)

Online Publication Date: 7 December 2007

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The three isomeric dimethylxanthines and trimethylxanthine are studied by neutron spectroscopy up to energy transfers of 100  meV at energy resolutions ranging from 0.7  µeV to some meV. The loss of elastic intensity with increasing temperature can be modeled by quasielastic methyl rotation. The number of inequivalent methyl groups is in agreement with those of the room temperature crystal structures. Activation energies are obtained. In the case of theophylline, a doublet tunneling band is observed at 15.1 and 17.5  µeV. In theobromine, a single tunneling band at 0.3  µeV is found. Orientational disorder in caffeine leads to a 2.7  µeV broad distribution of tunneling bands around the elastic line. At the same time, broad low energy phonon spectra characterize an orientational glassy state with weak methyl rotational potentials. Librational energies of the dimethylxanthines are clearly seen in the phonon densities of states. Rotational potentials can be derived which explain consistently all observables. While their symmetry in general is threefold, theophylline shows a close to sixfold potential reflecting a mirror symmetry.
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61.66.Hq, 63.20.Pw, 61.50.Ah

Spin selective multiple quantum NMR for spectral simplification, determination of relative signs, and magnitudes of scalar couplings by spin state selection

Bikash Baishya and N. Suryaprakash

J. Chem. Phys. 127, 214510 (2007) (11 pages)

Online Publication Date: 7 December 2007

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In the present work we demonstrate a novel method for spectral simplification and determination of the relative signs of the scalar couplings using a spin selective multiple quantum NMR experiment. A spin selective excitation of double quantum coherence of A and M spins in a weakly coupled three spin system of the type AMX, results in a doublet in the double quantum dimension whose separation corresponds to the sum of couplings of the active spins to the passive spin X. One component of the doublet has the passive spin X in |alpha⟩ state while the other component has the passive spin X in |beta⟩ state. The spin selective conversion of double quantum coherence to single quantum coherence does not disturb the spin states of the passive spin thereby providing the spin state selection. There will be two domains of single quantum transitions in single quantum dimension at the chemical shift positions of A and M spins. The |alpha⟩ domain of A spin is a doublet because of |alpha⟩ and |beta⟩ states of M spin only, while that of |beta⟩ domain is another doublet in a different cross section of the spectra. The scalar coupling JAM can be extracted from any of the |alpha⟩ and |beta⟩ domain transitions while the relative displacements of the two doublets between the two domains at the two chemical shifts provides the magnitude and sign of the scalar coupling JAX relative to the coupling JMX. Similar result is obtained for zero quantum studies on AMX spin system. The proposed technique is discussed theoretically using product operator approach. The new spin state selective double quantum J-resolved sequence has also been developed. The methodology is confirmed experimentally on a homonuclear weakly coupled three spin system and applied to two different heteronuclear five spin systems.
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33.25.+k, 07.57.Pt, 76.60.Cq

Vibronic dynamics of I2 trapped in amorphous ice: Coherent following of cage relaxation

V. Senekerimyan, I. Goldschleger, and V. A. Apkarian

J. Chem. Phys. 127, 214511 (2007) (8 pages)

Online Publication Date: 7 December 2007

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Four-wave mixing measurements are carried out on I2-doped ice, prepared by quench condensing the premixed vapor at 128  K. Coherent vibrational dynamics is observed in two distinct ensembles. The first is ascribed to trapping in asymmetric polar cages in which, as in water, the valence absorption of the molecule is blueshifted by 3500  cm−1, predissociation of the B state is complete upon the first extension of the molecular bond, and the vibrational frequency in the ground state (observed through coherent anti-Stokes Raman scattering) is reduced by 6.5%. The effect is ascribed to polarization of the molecule. The implied local field and the ionicity of the molecule are extracted, to conclude that the molecule is oxygen bonded to one water molecule on one side and hydrogen bonded on the other side. The second ensemble is characterized by the transient grating signal, which shows coherent vibrational dynamics on the B state. The small predissociation rate in this site suggests a symmetric cage in which the local electric field undergoes effective cancellation; and consistent with this, the extracted blueshift of the valence transition in this site (~1500  cm−1) coincides with that observed in clathrate hydrates of iodine. Remarkably, in this site, the vibrational period of the B state packet coherently stretches from an initial value of 245  fs  to  325  fs in the course of five oscillations (1.3  ps), indicative of vibrationally adiabatic following of the cage expansion. The dynamics is characteristic of a molecule trapped in a tight symmetric cage, with a soft cage coordinate that relaxes without eliciting elastic response. Enclathration in low-density amorphous ice is concluded.
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33.20.Wr, 33.70.Jg, 33.80.Gj, 33.20.Fb

Surfaces, Interfaces, and Materials

A density functional theory study on the binding of NO onto FePc films

Ngoc L. Tran and Andrew C. Kummel

J. Chem. Phys. 127, 214701 (2007) (7 pages)

Online Publication Date: 4 December 2007

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To develop an atomistic understanding of the binding of NO with iron phthalocyanine (FePc), the interaction between NO (an electron withdrawing gas) and NH3 (an electron donating gas) with an isolated FePc molecule (monomer) was compared with density functional theory. The simulations show that NO strongly chemisorbs to the Fe metal and physisorbs to all the nonmetal sites. Additionally, when NO physisorbs to the inner ring nitrogens, NO subsequently undergoes a barrierless migration to the deep chemisorption well on the Fe metal. Conversely, NH3 only weakly chemisorbs to the Fe metal and does not bind to any other sites. Projected density of states simulations and analysis of the atomic charges show that the binding of NO to the FePc metal results in a charge transfer from the Fe metal to the NO chemisorbate; the opposite effect is observed for the binding of NH3 to the Fe metal. Simulations of NO binding to the Fe metal of a monolayer FePc film and FePc trimer were also performed to show that intermolecular FePc-FePc interactions have a negligible effect on the FePc electronic structure and NO binding.
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68.43.Fg, 73.20.At, 73.20.Hb, 71.15.Mb, 34.70.+e

Dynamics of analyte binding onto a metallophthalocyanine: NO/FePc

Sarah R. Bishop, Ngoc L. Tran, Gary C. Poon, and Andrew C. Kummel

J. Chem. Phys. 127, 214702 (2007) (8 pages)

Online Publication Date: 4 December 2007

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The gas-surface reaction dynamics of NO impinging on an iron(II) phthalocyanine (FePc) monolayer were investigated using King and Wells sticking measurements. The initial sticking probability was measured as a function of both incident molecular beam energy (0.09–0.4  eV) and surface temperature (100–300  K). NO adsorption onto FePc saturates at 3% of a monolayer for all incident beam energies and surface temperatures, suggesting that the final chemisorption site is confined to the Fe metal centers. At low surface temperature and low incident beam energy, the initial sticking probability is 40% and decreases linearly with increasing beam energy and surface temperature. The results are consistent with the NO molecule sticking onto the FePc molecules via physisorption to the aromatics followed by diffusion to the Fe metal center, or precursor-mediated chemisorption. The adsorption mechanism of NO onto FePc was confirmed by control studies of NO sticking onto metal-free H2Pc, inert Au(111), and reactive Al(111).
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82.65.+r, 68.43.Mn

A novel method for evaluating the critical nucleus and the surface tension in systems with first order phase transition

Chiara Cammarota and Andrea Cavagna

J. Chem. Phys. 127, 214703 (2007) (10 pages)

Online Publication Date: 5 December 2007

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We introduce a novel method for calculating the size of the critical nucleus and the value of the surface tension in systems with first order phase transition. The method is based on classical nucleation theory, and it consists in studying the thermodynamics of a sphere of given radius embedded in a frozen metastable surrounding. The frozen configuration creates a pinning field on the surface of the free sphere. The pinning field forces the sphere to stay in the metastable phase as long as its size is smaller than the critical nucleus. We test our method in two first order systems, both on a two-dimensional lattice: a system where the parameter tuning the transition is the magnetic field, and a second system where the tuning parameter is the temperature. In both cases the results are satisfying. Unlike previous techniques, our method does not require an infinite volume limit to compute the surface tension, and it therefore gives reliable estimates even by using relatively small systems. However, our method cannot be used at, or close to, the critical point, i.e., at coexistence, where the critical nucleus becomes infinitely large.
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68.03.Cd, 64.70.-p

Hydrogen absorption in bulk BC3: A first-principles study

Changjun Zhang and Ali Alavi

J. Chem. Phys. 127, 214704 (2007) (7 pages)

Online Publication Date: 6 December 2007

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We have performed first-principles calculations for H absorption, H2 dissociation, and H diffusion in bulk BC3, a graphitelike layered structure. We show that in bulk BC3, H2 can dissociatively (and exothermically) absorb at low coverages. Several low-energy pathways have been computed for the dissociation process. The dissociation barriers are on the order of 0.2  eV or less. This presents a striking contrast to the situation in pure graphite and also on monolayer BC3(0001), where H2 dissociative absorption is considerably more difficult. Hydrogen absorption at high coverages has also been investigated; we find that the absorption enthalpy becomes moderately more exothermic at higher coverages. The calculated range of H binding energies is close to the desired value for reversible hydrogen storage.
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82.37.Np, 68.43.Jk, 71.15.Mb

Electronic and vibrational properties of nickel sulfides from first principles

Jeng-Han Wang, Zhe Cheng, Jean-Luc Brédas, and Meilin Liu

J. Chem. Phys. 127, 214705 (2007) (8 pages)

Online Publication Date: 6 December 2007

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We report the results of first-principles calculations (generalized gradient approximation–Perdew Wang 1991) on the electronic and vibrational properties of several nickel sulfides that are observed on Ni-based anodes in solid oxide fuel cells (SOFCs) upon exposure to H2S contaminated fuels: heazlewoodite Ni3S2, millerite NiS, polydymite Ni3S4, and pyrite NiS2. The optimized lattice parameters of these sulfides are within 1% of the values determined from x-ray diffraction. The electronic structure analysis indicates that all Ni–S bonds are strongly covalent. Furthermore, it is found that the nickel d orbitals shift downward in energy, whereas the sulfur p orbitals shift upward with increasing sulfur content; this is consistent with the decrease in conductivity and catalytic activity of sulfur-contaminated Ni-based electrodes (or degradation in SOFC performance). In addition, we systematically analyze the classifications of the vibrational modes at the Gamma point from the crystal symmetry and calculate the corresponding vibrational frequencies from the optimized lattice constants. This information is vital to the identification with in situ vibrational spectroscopy of the nickel sulfides formed on Ni-based electrodes under the conditions for SOFC operation. Finally, the effect of thermal expansion on frequency calculations for the Ni3S2 system is also briefly examined.
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71.20.Ps, 78.30.Hv, 71.15.-m, 82.45.Fk, 82.47.Ed, 72.80.Jc

Structure of SiAu16: Can a silicon atom be stabilized in a gold cage?

Qiang Sun, Qian Wang, Gang Chen, and Puru Jena

J. Chem. Phys. 127, 214706 (2007) (4 pages)

Online Publication Date: 7 December 2007

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Nanostructures of Au and Si as well as Au–Si hybrid structures are topics of great current interest from both scientific and technological points of view. Recent discovery of Au clusters having fullerenelike geometries and the possibility of endohedral complexes with Si atoms inside the Au cage opens new possibilities for designing Au–Si nanostructures. Using ab initio simulated annealing method we have examined the stability of Si–Au16 endohedral complex. Contrary to what we believed, we find that the endohedral configuration is metastable and the structure where Si atom binds to the exterior surface of the Au16 cage is the lowest energy structure. The bonding of Si to Au cluster mimics its behavior of that in bulk and liquid phase of Au. In addition, doping of Si in high concentration would cause fracture and embrittlement in gold nanostructures just as it does in the bulk phase. Covalent bonding between Au–Au and Au–Si is found to be a dominant feature in the stability of the Au–Si nanostructures. Our study provides insight that may be useful in fabricating hybrid Au–Si nanostructures for applications microelectronics, catalysis, biomedine, and jewelry industry.
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61.46.Bc, 61.50.Lt, 71.15.-m

Polymers and Complex Systems

Macroion adsorption: The crucial role of excluded volume and coions

René Messina

J. Chem. Phys. 127, 214901 (2007) (4 pages)

Online Publication Date: 5 December 2007

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The adsorption of charged colloids (macroions) onto an oppositely charged planar substrate is investigated theoretically. Taking properly into account the finite size of the macroions, unusual behaviors are reported. It is found that the role of the coions (the little salt-ions carrying the same sign of charge as that of the substrate) is crucial in understanding the mechanisms involved in the process of macroion adsorption. In particular, the coions can accumulate near the substrate's surface and lead to a counterintuitive surface charge amplification.
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82.70.Dd, 68.43.-h

Rotational relaxation in simple chain models

Julieanne V. Heffernan, Joanne Budzien, Francisco Avila, Taylor C. Dotson, Victoria J. Aston, John D. McCoy, and Douglas B. Adolf

J. Chem. Phys. 127, 214902 (2007) (10 pages)

Online Publication Date: 5 December 2007

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The rotational dynamics of chemically similar systems based on freely jointed and freely rotating chains are studied. The second Legendre polynomial of vectors along chain backbones is used to investigate the rotational dynamics at different length scales. In a previous study, it was demonstrated that the additional bond-angle constraint in the freely rotating case noticeably perturbs the character of the translational relaxation away from that of the freely jointed system. Here, it is shown that differences are also apparent in the two systems' rotational dynamics. The relaxation of the end-to-end vector is found to display a long time, single-exponential tail and a stretched exponential region at intermediate times. The stretching exponents beta are found to be 0.75±0.02 for the freely jointed case and 0.68±0.02 for the freely rotating case. For both system types, time-packing-fraction superposition is seen to hold on the end-to-end length scale. In addition, for both systems, the rotational relaxation times are shown to be proportional to the translational relaxation times, demonstrating that the Debye-Stokes-Einstein law holds. The second Legendre polynomial of the bond vector is used to probe relaxation behavior at short length scales. For the freely rotating case, the end-to-end relaxation times scale differently than the bond relaxation times, implying that the behavior is non-Stokes-Einstein, and that time-packing-fraction superposition does not hold across length scales for this system. For the freely jointed case, end-to-endrelaxation times do scale with bond relaxation times, and both Stokes-Einstein and time-packing-fraction-across-length-scales superposition are obeyed.
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33.15.Dj, 33.15.Mt, 33.20.Sn, 36.20.Ng, 36.20.Fz, 36.20.Hb

Effects of topology and size on statics and dynamics of complexes of hyperbranched polymers with linear polyelectrolytes

G. K. Dalakoglou, K. Karatasos, S. V. Lyulin, and A. V. Lyulin

J. Chem. Phys. 127, 214903 (2007) (11 pages)

Online Publication Date: 7 December 2007

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Brownian dynamics simulations with explicit hydrodynamic interactions have been employed to study generic effects of size and topology in noncovalent (Coulombic-driven) complexes formed by irregular-shaped hyperbranched polymers and linear polyelectrolytes. The behavior of the complexes was explored in detail in terms of static and dynamic properties, both in local and in the entire complex scale. The results were compared to previous studies on perfect dendrimers and other hyperbranched molecules where available. It was found that both molecular weight and structure may impart significant changes to key factors known to be associated with the ability of these systems to take part in relevant nanoscale applications.
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82.35.Rs

Biological Molecules, Biopolymers, and Biological Systems

Stern-Volmer modeling of steady-state Förster energy transfer between dilute, freely diffusing membrane-bound fluorophores

Jeffrey T. Buboltz, Charles Bwalya, Santiago Reyes, and Dobromir Kamburov

J. Chem. Phys. 127, 215101 (2007) (7 pages)

Online Publication Date: 3 December 2007

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Two different metrics are used to assess Förster resonance energy transfer (FRET) between fluorophores in the steady state: (i) acceptor-quenching of donor fluorescence E (also known as transfer efficiency) and (ii) donor-excited acceptor fluorescence F<sub>A</sub><sup>Dex</sup>. While E is still more widely used, F<sub>A</sub><sup>Dex</sup> has been gaining in popularity for practical reasons among experimentalists who study biomembranes. Here, for the special case of membrane-bound fluorophores, we present a substantial body of experimental evidence that justifies the use of simple Stern-Volmer expressions when modeling either FRET metric under dilute-probe conditions. We have also discovered a dilute-regime correspondence between our Stern-Volmer expression for E and Wolber and Hudson's series approximation for steady-state Förster quenching in two dimensions (2D). This novel correspondence allows us to interpret each of our 2D quenching constants in terms of both (i) an effective Förster distance and (ii) two maximum acceptor-concentration limits, each of which defines its own useful experimental regime. Taken together, our results suggest a three-step strategy toward designing more effective steady-state FRET experiments for the study of biomembranes.
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87.16.Dg, 87.16.Ac

Coherent oscillations in ultrafast fluorescence of photoactive yellow protein

Ryosuke Nakamura, Norio Hamada, Hideki Ichida, Fumio Tokunaga, and Yasuo Kanematsu

J. Chem. Phys. 127, 215102 (2007) (7 pages)

Online Publication Date: 6 December 2007

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The ultrafast photoinduced dynamics of photoactive yellow protein in aqueous solution were studied at room temperature by femtosecond fluorescence spectroscopy using an optical Kerr-gate technique. Coherent oscillations of the wave packet were directly observed in the two-dimensional time-energy map of ultrafast fluorescence with 180  fs time resolution and 5  nm spectral resolution. The two-dimensional map revealed that four or more oscillatory components exist within the broad bandwidth of the fluorescence spectrum, each of which is restricted in the respective narrow spectral region. Typical frequencies of the oscillatory modes are 50 and 120  cm−1. In the landscape on the map, the oscillatory components were recognized as the ridges which were winding and descending with time. The amplitude of the oscillatory and winding behaviors is a few hundred cm−1, which is the same order as the frequencies of the oscillations. The mean spectral positions of the oscillatory components in the two-dimensional map are well explained by considering the vibrational energies of intramolecular modes in the electronic ground state of the chromophore. The entire view of the wave packet oscillations and broadening in the electronic excited state, accompanied by fluorescence transitions to the vibrational sublevels belonging to the electronic ground state, was obtained.
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33.50.Dq, 36.20.Ng, 87.14.Ee, 87.15.Mi, 42.65.Hw

Diffusion-controlled reaction on a sink with two active sites

S. D. Traytak and A. V. Barzykin

J. Chem. Phys. 127, 215103 (2007) (4 pages)

Online Publication Date: 7 December 2007

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We have presented an exact solution for the problem of diffusive binding to a spherical macromolecule with two axially symmetric active patches. A highly accurate approximate formula for an effective steric factor has been suggested. This model solution may serve as a benchmark for further studies of diffusive interaction in more realistic models of anisotropic reactivity.
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05.60.-k, 82.39.-k, 87.15.Vv

The influence of zwitterionic lipids on the electrostatic adsorption of macroions onto mixed lipid membranes

Andrew Haugen and Sylvio May

J. Chem. Phys. 127, 215104 (2007) (8 pages)

Online Publication Date: 7 December 2007

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Charged lipid membranes commonly consist of a mixture of charged and zwitterionic lipids. We suggest a model that characterizes the influence of the dipolar nature of the zwitterionic lipid species on the electrostatic adsorption of macroions onto mixed membranes in the fluid state. The model is based on Poisson-Boltzmann theory which we have modified so as to account for the dipolar character of the zwitterionic lipids. In addition the membrane lipids are allowed to adjust their lateral distribution upon macroion adsorption. We consider and compare two experimentally relevant scenarios: cationic macroions adsorbed onto anionic membranes and anionic macroions adsorbed onto cationic membranes. We show that in the former case the adsorption strength is slightly weakened by the presence of the headgroup dipoles of the zwitterionic lipids. Here, macroion-induced lipid demixing is more pronounced and the lipid headgroups tilt away from a cationic macroion upon adsorption. In contrast, for the adsorption of anionic macroions onto a cationic membrane the zwitterionic lipids strongly participate in the electrostatic interaction between membrane and macroion, thus enhancing the adsorption strength significantly (we predict up to 20%). Consistent with that we find less lateral demixing of the charged lipids and a reorientation of the dipoles of the zwitterionic headgroups towards the anionic macroions. Our results may be of importance to understand the differences in the electrostatic adsorption of proteins/peptides onto cellular membranes versus complex formation between cationic membranes and DNA.
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82.39.Wj, 82.39.Pj, 68.43.-h

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