Index of content:
Volume 130, Issue 10, 14 March 2009
- Theoretical Methods and Algorithms
130(2009); http://dx.doi.org/10.1063/1.3081144View Description Hide Description
Monte Carlo simulation and theory were used to study the potential of mean force (PMF) between a pair of big colloidal(solute) particles suspended in a sea of smaller particles (solvent) interacting via Baxter’s sticky hard sphere (SHS) potential. Simulation results were obtained by applying a special simulation technique developed for sampling the hard sphere collision force, while the theoretical predictions were calculated from the analytic solution of the Percus–Yevick/Ornstein–Zernike integral equation for spatial correlations in a two-component mixture at vanishing solute concentration. Both theory and simulation revealed oscillations of the solute-solute PMF with a period equal to the diameter of the solvent molecules. Further, the attractive PMF between solute particles in the SHS fluid decays slower than in a hard sphere solvent. Upon increasing the strength of attraction (stickiness) between the molecules of solvent, these oscillations gradually disappear, the PMF becoming long ranged and attractive at all separations.
Energy partitioning for generalized product functions: The interference contribution to the energy of generalized valence bond and spin coupled wave functions130(2009); http://dx.doi.org/10.1063/1.3085953View Description Hide Description
The main driving force for the formation of the covalent bond is the quantum-mechanical interference effect among one-electron states, as has been suggested in several works by the use of partition schemes to calculate the interference contributions to the energy. However, due to some difficulties associated with the original approaches, calculations were only carried out for a few, mostly diatomic molecules. In this work, we propose a general approach of partitioning based on generalized product functions with generalized valence bond at the perfect pairing approximation and spin-coupled groups, which should allow the investigation of a broader array of molecules, and hopefully, shed light on the nature of the chemical bond in molecules with unusual chemical features. Among other things, this approach lends itself naturally to the investigation of interference in individual bonds or groups of bonds in a molecule.
130(2009); http://dx.doi.org/10.1063/1.3081141View Description Hide Description
We describe a simulation method for the accurate study of the equilibrium freezing properties of polydisperse fluids under the experimentally relevant condition of fixed polydispersity. The approach is based on the phase switch Monte Carlo method of Wilding and Bruce [Phys. Rev. Lett.85, 5138 (2000)]. This we have generalized to deal with particle size polydispersity by incorporating updates which alter the diameter of a particle, under the control of a distribution of chemical potential differences . Within the resulting isobaric semi-grand-canonical ensemble, we detail how to adapt and the applied pressure such as to study coexistence, while ensuring that the ensemble averaged density distribution matches a fixed functional form. Results are presented for the effects of small degrees of polydispersity on the solid-liquidtransition of soft spheres.
A modified ansatz for explicitly correlated coupled-cluster wave functions that is suitable for response theory130(2009); http://dx.doi.org/10.1063/1.3079543View Description Hide Description
A modified ansatz for explicitly correlated coupled-clusterwave functions with a single correlation factor is set forward. It is based on the fixed amplitude ansatz of Ten-no [Chem. Phys. Lett.398, 56 (2004)] to which an extra term is added that allows for the explicitly correlated description of singly excited configurations. The new approach has been implemented for coupled-cluster singles and doubles with the aid of automated techniques. Numerical results are presented for vertical excitation energies, and ground and excited state equilibrium distances and harmonic frequencies of diatomics. The new approach is shown to provide a nearly unbiased description of ground and predominantly singly exited states, and the improvements seen for explicitly correlated treatments of ground states, as compared to conventional orbital expansions, carry over to excited states. In addition, a correction for contributions from one-electron terms—which are not improved by the correlation factor—is suggested, again with focus on applicability to a response formalism.
130(2009); http://dx.doi.org/10.1063/1.3079684View Description Hide Description
The nonlocal van der Waals density functional (vdW-DF) captures the essential physics of the dispersion interaction not only in the asymptotic regime but also for a general case of overlapping fragment densities. A balanced treatment of other energetic contributions, such as exchange, is crucial if we aim for accurate description of various properties of weakly bound systems. In this paper, the vdW-DF correlation functional is modified to make it better compatible with accurate exchange functionals. We suggest a slightly simplified construction of the nonlocal correlation, yielding more accurate asymptotic coefficients. We also derive a gradient correction, containing a parameter that can be adjusted to suit an exchange functional of choice. We devise a particularly apt combination of exchange and correlation terms, which satisfies many important constraints and performs well for our benchmark tests.
Removing systematic errors in interionic potentials of mean force computed in molecular simulations using reaction-field-based electrostatics130(2009); http://dx.doi.org/10.1063/1.3081138View Description Hide Description
The performance of reaction-field methods to treat electrostaticinteractions is tested in simulations of ions solvated in water. The potential of mean force between sodium chloride pair of ions and between side chains of lysine and aspartate are computed using umbrella sampling and molecular dynamics simulations. It is found that in comparison with lattice sum calculations, the charge-group-based approaches to reaction-field treatments produce a large error in the association energy of the ions that exhibits strong systematic dependence on the size of the simulation box. The atom-based implementation of the reaction field is seen to (i) improve the overall quality of the potential of mean force and (ii) remove the dependence on the size of the simulation box. It is suggested that the atom-based truncation be used in reaction-field simulations of mixed media.
Accuracies of the empirical theories of the escape probability based on Eigen model and Braun model compared with the exact extension of Onsager theory130(2009); http://dx.doi.org/10.1063/1.3082005View Description Hide Description
This paper deals with the exact extension of the original Onsager theory of the escape probability to the case of finite recombination rate at nonzero reaction radius. The empirical theories based on the Eigen model and the Braun model, which are applicable in the absence and presence of an external electric field, respectively, are based on a wrong assumption that both recombination and separation processes in geminate recombination follow exponential kinetics. The accuracies of the empirical theories are examined against the exact extension of the Onsager theory. The Eigen model gives the escape probability in the absence of an electric field, which is different by a factor of 3 from the exact one. We have shown that this difference can be removed by operationally redefining the volume occupied by the dissociating partner before dissociation, which appears in the Eigen model as a parameter. The Braun model gives the escape probability in the presence of an electric field, which is significantly different from the exact one over the whole range of electric fields. Appropriate modification of the original Braun model removes the discrepancy at zero or low electric fields, but it does not affect the discrepancy at high electric fields. In all the above theories it is assumed that recombination takes place only at the reaction radius. The escape probability in the case when recombination takes place over a range of distances is also calculated and compared with that in the case of recombination only at the reaction radius.
Bounding the electrostatic free energies associated with linear continuum models of molecular solvation130(2009); http://dx.doi.org/10.1063/1.3081148View Description Hide Description
The importance of electrostatic interactions in molecular biology has driven extensive research toward the development of accurate and efficient theoretical and computational models. Linear continuum electrostatic theory has been surprisingly successful, but the computational costs associated with solving the associated partial differential equations(PDEs) preclude the theory’s use in most dynamical simulations. Modern generalized-Born models for electrostatics can reproduce PDE-based calculations to within a few percent and are extremely computationally efficient but do not always faithfully reproduce interactions between chemical groups. Recent work has shown that a boundary-integral-equation formulation of the PDE problem leads naturally to a new approach called boundary-integral-based electrostatics estimation (BIBEE) to approximate electrostatic interactions. In the present paper, we prove that the BIBEE method can be used to rigorously bound the actual continuum-theory electrostaticfree energy. The bounds are validated using a set of more than 600 proteins. Detailed numerical results are presented for structures of the peptide met-enkephalin taken from a molecular-dynamics simulation. These bounds, in combination with our demonstration that the BIBEE methods accurately reproduce pairwise interactions, suggest a new approach toward building a highly accurate yet computationally tractable electrostatic model.
130(2009); http://dx.doi.org/10.1063/1.2981796View Description Hide Description
A broad class of quantum control problems entails optimizing the expectation value of an observable operator through tailored unitary propagation of the system density matrix. Such optimization processes can be viewed as a directed search over a quantum control landscape. The attainment of the global extrema of this landscape is the goal of quantum control. Local optima will generally exist, and their enumeration is shown to scale factorially with the system’s effective Hilbert space dimension. A Hessian analysis reveals that these local optima have saddlepoint topology and cannot behave as suboptimal extrema traps. The implications of the landscape topology for practical quantum control efforts are discussed, including in the context of nonideal operating conditions.
Enhanced conformational sampling of nucleic acids by a new Hamiltonian replica exchange molecular dynamics approach130(2009); http://dx.doi.org/10.1063/1.3086832View Description Hide Description
Although molecular dynamics (MD) simulations have been applied frequently to study flexible molecules, the sampling of conformational states separated by barriers is limited due to currently possible simulation time scales. Replica-exchange (Rex)MD simulations that allow for exchanges between simulations performed at different temperatures (T-RexMD) can achieve improved conformational sampling. However, in the case of T-RexMD the computational demand grows rapidly with system size. A Hamiltonian RexMD method that specifically enhances coupled dihedral angle transitions has been developed. The method employs added biasing potentials as replica parameters that destabilize available dihedral substates and was applied to study coupled dihedral transitions in nucleic acid molecules. The biasing potentials can be either fixed at the beginning of the simulation or optimized during an equilibration phase. The method was extensively tested and compared to conventional MD simulations and T-RexMD simulations on an adenine dinucleotide system and on a DNA abasic site. The biasing potential RexMD method showed improved sampling of conformational substates compared to conventional MD simulations similar to T-RexMD simulations but at a fraction of the computational demand. It is well suited to study systematically the fine structure and dynamics of large nucleic acids under realistic conditions including explicit solvent and ions and can be easily extended to other types of molecules.
The calculation of adiabatic-connection curves from full configuration-interaction densities: Two-electron systems130(2009); http://dx.doi.org/10.1063/1.3082285View Description Hide Description
The Lieb formulation of density-functional theory is briefly reviewed and its straightforward generalization to arbitrary electron-electron interaction strengths discussed, leading to the introduction of density-fixed and potential-fixed adiabatic connections. An iterative scheme for the calculation of the Lieb functionals under the appropriate constraints is outlined following the direct optimization approach of Wu and Yang [J. Chem. Phys.118, 2498 (2003)]. First- and second-order optimization schemes for the calculation of accurate adiabatic-connection integrands are investigated and compared; the latter is preferred both in terms of computational efficiency and accuracy. The scheme is applicable to systems of any number of electrons. However, to determine the accuracy that may be achieved, the present work focuses on two-electron systems for which a number of simplifications may be exploited. The procedure is applied to the helium isoelectronic series and the molecule. The resulting adiabatic-connection curves yield the full configuration-interaction exchange-correlation energies extrapolated to the basis-set limit. The relationship between the Kohn–Sham and natural orbitals as functions of the electron-electron interaction strength is explored in detail for . The accuracy with which the exchange-correlation contributions to the modified local potential can be determined is discussed. The new accurate adiabatic-connection curves are then compared with some recently investigated approximate forms calculated using accurate full configuration-interaction input data. This study demonstrates that the adiabatic-connection integrand may be determined accurately and efficiently, providing important insights into the link between the Kohn–Sham and traditional quantum-chemical treatments of the exchange-correlation problem in electronic-structure theory.
- Gas Phase Dynamics and Structure: Spectroscopy, Molecular Interactions, Scattering, and Photochemistry
130(2009); http://dx.doi.org/10.1063/1.3072711View Description Hide Description
The electronic ground states of HSiN, HNSi, and the transition state connecting the two isomers were systematically studied using configuration interaction with single and double (CISD) excitations, coupled cluster with single and double (CCSD) excitations, CCSD with perturbative triple corrections [CCSD(T)], multireference complete active space self-consistent field (CASSCF), and internally contracted multireference configuration interaction (ICMRCI) methods. The correlation-consistent polarized valence , augmented correlation-consistent polarized valence , correlation-consistent polarized core-valence , and augmented correlation-consistent polarized core-valence basis sets were used. Via focal point analyses, we confirmed the HNSi isomer as the global minimum on the ground state zero-point vibrational energy corrected surface and is predicted to lie (, ) below the HSiN isomer. The barrier height for the forward isomerizationreaction is predicted to be , while the barrier height for the reverse process is determined to be . The dipole moments of the HSiN and HNSi isomers are predicted to be 4.36 and , respectively. The theoretical vibrational isotopic shifts for the HSiN/DSiN and HNSi/DNSi isotopomers are in strong agreement with the available experimental values. The dissociation energy for HSiN is predicted to be , whereas the dissociation energy for HNSi is predicted to be at the CCSD(T)/aug-cc-pCVQZ level of theory. Anharmonic vibrational frequencies computed using second order vibrational perturbation theory are in good agreement with available matrix isolation experimental data for both HSiN and HNSi isomers root mean squared derivation .
130(2009); http://dx.doi.org/10.1063/1.3075561View Description Hide Description
Photodissociation of the 1:1 linear van der Waals complex is studied over the 490–520 nm region using the velocity-map imaging technique. Molecular iodine, and both the T-shaped and linear ground-state complexes absorb strongly in this range, and these transitions access both the bound and dissociative regions of the state. We measure the angle-speed distribution of vibrationally excited state products by resonant ionization via the and ion-pair states, forming , which is imaged under velocity-mapping conditions. The images show a strong angular anisotropy, which is the same for all excitation energies, spanning from the bound region to above the molecular dissociation limit. The observed angular anisotropy of the fragments is consistent with a direct dissociation of linear complexes promoted to the inner repulsive potential wall of the potential energy surface.
130(2009); http://dx.doi.org/10.1063/1.3079541View Description Hide Description
The two lowest energy intermolecular potential-energysurfaces (IPESs) of the water-nitric oxide complex are evaluated using the spin-restricted coupled-cluster R-CCSD(T) model and the augmented correlation-consistent polarized-valence triple-zeta basis set extended with a set of the midbond functions. A detailed characterization of the IPESs for both the and electronic states in the -symmetry configurations of the complex is performed. The global minimum for the state represented by the lowest energy of is deeper than the global minimum in the state with an energy of . To explore the physics of the interaction an open-shell implementation of the symmetry-adapted perturbation theory is employed and the results are analyzed as a function of the intermolecular parameters. The electrostatic term shows the strongest geometric anisotropy, while the exchange, induction, and dispersion contributions mostly depend on the intermolecular distance. The energy separation between the and states is largely dominated by electrostatic contribution for long intermolecular distances. In the region of short intermolecular distances the exchange part is as important as the electrostatic one and the induction and dispersion effects are also substantial.
Intra- and intermolecular electrostatic interactions and their significance for the structure, acidity, and tautomerization behavior of trinitromethane130(2009); http://dx.doi.org/10.1063/1.3082406View Description Hide Description
We have addressed several interesting issues related to trinitromethane: the propellerlike arrangement of its nitro groups, its lower-than-predicted (although still high) acidity, its aci tautomerization, and the absence of expected very short intermolecular bridges in the crystal. A combination of crystallographic and computed data was used in our analysis. The structural features mentioned and the anomalous acidity can be attributed to intra- and/or intermolecular electrostaticinteractions. Decomposition via bond scission may occur before aci tautomerization can take place.
Effects of -stacking interactions on the near carbon -edge x-ray absorption fine structure: A theoretical study of the ethylene pentamer and the phthalocyanine dimer130(2009); http://dx.doi.org/10.1063/1.3079820View Description Hide Description
X-ray absorption spectra have been determined for ethylene and free base phthalocyanine at the carbon-edge with use of the complex polarization propagator method combined with Kohn–Sham density functional theory and the Coulomb attenuated method B3LYP exchange-correlation functional. Apart from isolated molecules, the study includes -stacked systems of the phthalocyanine dimer and the ethylene dimer, trimer, tetramer, and pentamer. For ethylene, -stacking involves a reduction in transition energy of the valence -band by some 70 meV and large spectral changes (regarding also shape and intensity) of the Rydberg bands. For phthalocyanine, there are large spectral changes in the entire valence -part of the spectrum.
130(2009); http://dx.doi.org/10.1063/1.3081454View Description Hide Description
Kinetic studies were carried out to explore the role of the excited species , , and in the dissociation of by singlet oxygen. A flow tube apparatus that utilized a chemical singlet oxygen generator was used to measure the dissociation rate in mixtures. Vibrationally excited is thought to be a significant intermediate in the dissociation process. Excitation probabilities for population of the vibrational level in the reaction were estimated based on a comparison of calculated populations with experimentally determined values. Satisfactory agreement with the experimental data [Barnault et al., J. Phys. IV1, C7–647 (1991)] was achieved for total excitation probabilities partitioned in two ranges, such that and . A multipathway dissociation model was developed in which the intermediates are and . It was shown that the iodine dissociation process passes predominantly through the intermediate. These states are populated by collisions of with vibrationally excited at the initiation and the chain stages, when the mole fraction of is small . For higher concentrations the excited states are populated in the chain stage by collisions of with .
130(2009); http://dx.doi.org/10.1063/1.3077027View Description Hide Description
The nascent OH product state distribution arising from collisional quenching of electronically excited OH by has been determined using a pump-probe technique. The majority of OH products are observed in their lowest vibrational level, , with significantly less population in . The OH products are generated with a substantial degree of rotational excitation, peaking around , with an average rotational energy of . A preference is found for the OH -doublet, indicating some degree of orbital alignment. The branching fraction into OH product states demonstrates that nonreactive quenching is the dominant decay pathway for quenching of OH by . The topography of the conical intersection region that couples the electronically excited and ground statepotential energy surfaces is also examined theoretically. The rotational excitation of the OH products and branching fraction are found to be dynamical signatures of nonadiabatic passage through the conical intersection region.
- Condensed Phase Dynamics, Structure, and Thermodynamics: Spectroscopy, Reactions, and Relaxation
Building a polarizable pair interaction potential for lanthanoids(III) in liquid water: A molecular dynamics study of structure and dynamics of the whole series130(2009); http://dx.doi.org/10.1063/1.3081143View Description Hide Description
In this work we have extended our previously presented polarizable pair interaction potential for -water [Duvail et al., J. Chem. Phys.127, 034503 (2007)] to the whole lanthanoid(III) series interacting with water. This was performed taking into account known modification of ionic radius and atomic polarizability across the series and thus changing potential parameters according to that. Our procedure avoids the hard task of doing expensive high level ab initio calculations for all the atoms in the series and provides results in good agreement with experimental data and with ab initio calculations performed on the last atom in the series (, the atom for which the extrapolation should be in principle much crude). Thus we have studied the hydration properties of the whole series by performing classical molecular dynamics in liquid phase. This systematic study allows us to rationalize from a microscopic point of view the different experimental results on -water distances, first shell coordination numbers and first shell water self-exchange reactivity. In particular, we found that across the series the coordination number decreases from 9 for light lanthanoids to 8 for heavy lanthanoids in a continuous shape. This is due to the continuous changing in relative stability of the two forms that can be both populated at finite temperature with different probabilities as a function of the atomic number. The changeover of the ionic radius across the series resulted to be the main driving physical properties governing not always the -water distance changing across the series but also the observed coordination number and consequently ligand dynamics.
Experimental correlation of nitroxide recollision spin exchange with free volume and compressibility in alkane and aromatic compounds130(2009); http://dx.doi.org/10.1063/1.3082510View Description Hide Description
Diffusion of perdeuterated tempone (PDT) in various nonpolar hydrocarbon solvents on both the large and microscopic scales is examined through electron paramagnetic resonance spectroscopy.Spectral line broadening and hyperfine spacing are measured in order to extract both the Heisenberg spin-exchange rate as well as the average recollision times between spin-probe pairs. Probe recollision is responsible for a linear component to the dependence of the line shift on spectral broadening which has been identified in recent years. The present study extends the work of a previous paper by Kurban et al. [J. Chem. Phys.129, 064501 (2008)], in which it was reported that recollision rates for PDT formed a common curve across -alkanes when plotted with respect to free volume and to isothermal compressibility. It is now found that such common curves occur within distinct chemical families, in particular, the alkane and aromatic groups. Within each chemical family, the spin probe recollision rate correlates with free volume and compressibility independently of the geometry of the particular solvent. All solvents show significantly enhanced recollisional diffusion over the Stokes–Einstein (SE) prediction at high temperatures. The spin-exchange rate forms a common curve with respect to for all alkanes except cyclohexane and another common curve in all three aromatic compounds. It is reasoned that although all spin-exchange rates are near to the SE prediction, the semblance of hydrodynamic behavior is superficial and arises incidentally from mathematical cancellation of terms in a generalized diffusion coefficient. As a collision pair coexists for a time within a solvation shell, the recollision time places a lower limit on the lifetime of the solvent cage. Although molecular dynamics simulations conducted thus far have yielded cage lifetimes lower than the measured recollision times, this is attributable to the fact that such simulations have mostly examined cage configurations too small to harbor a spin-exchange encounter, and is also likely due to restrictive mathematical definitions of cage lifetimes that are employed in such simulations.