Index of content:
Volume 128, Issue 2, 14 January 2008
- Theoretical Methods and Algorithms
128(2008); http://dx.doi.org/10.1063/1.2821102View Description Hide Description
The capability of using stabilization method with the asymptotic Coulomb potential for accurate resonance state parameter calculations is investigated for the one-dimensional model problem with a single open channel. It is shown that the replacement of the potential box conditions by the quantization with asymptotic Coulomb potential does not yield the significant errors in energy and width of resonances if the additional mathematical conditions are correctly taken into account. Analytical results are confirmed by the numerical calculations.
Development of the cyclic cluster model formalism for Kohn-Sham auxiliary density functional theory methods128(2008); http://dx.doi.org/10.1063/1.2817582View Description Hide Description
The development of the cyclic cluster model (CCM) formalism for Kohn-Sham auxiliary density functional theory (KS-ADFT) methods is presented. The CCM is a direct space approach for the calculation of perfect and defective systems under periodic boundary conditions. Translational symmetry is introduced in the CCM by integral weighting. A consistent weighting scheme for all two-center and three-center interactions appearing in the KS-ADFT method is presented. For the first time, an approach for the numerical integration of the exchange-correlation potential within the cyclic cluster formalism is derived. The presented KS-ADFT CCM implementation was applied to covalent periodic systems. The results of cyclic and molecular cluster model (MCM) calculations for trans-polyacetylene, graphene, and diamond are discussed as examples for systems periodic in one, two, and three dimensions, respectively. All structures were optimized. It is shown that the CCM results represent the results of MCM calculations in the limit of infinite molecular clusters. By analyzing the electronic structure, we demonstrate that the symmetry of the corresponding periodic systems is retained in CCM calculations. The obtained geometric and electronic structures are compared with available data from the literature.
128(2008); http://dx.doi.org/10.1063/1.2816560View Description Hide Description
The effect of the exchange-attempt frequency on sampling efficiency is studied in replica exchange molecular dynamics (REMD). We show that sampling efficiency increases with increasing exchange-attempt frequency. This conclusion is contrary to a commonly expressed view in REMD. Five peptides (1–21 residues long) are studied with a spectrum of exchange-attempt rates. Convergence rates are gauged by comparing ensemble properties between fixed length test REMD simulations and longer reference simulations. To show the fundamental correlation between exchange frequency and convergence time, a simple model is designed and studied, displaying the same basic behavior of much more complex systems.
128(2008); http://dx.doi.org/10.1063/1.2817332View Description Hide Description
We derive expressions for the equilibrium entropy and energy changes in the context of the Jarzynski equality relating nonequilibrium work to equilibrium free energy. The derivation is based on a stochastic path integral technique that reweights paths at different temperatures. Stochastic dynamics generated by either a Langevin equation or a Metropolis Monte Carlo scheme are treated. The approach enables the entropy-energy decomposition from trajectories evolving at a single-temperature and does not require simulations or measurements at two or more temperatures. Both finite difference and analytical formulae are derived. Testing is performed on a prototypical model system and the method is compared with existing thermodynamic integration and thermodynamic perturbation approaches for entropy-energy decomposition. The new formulae are also put in the context of more general, dynamics-independent expressions that derive from either a fluctuation theorem or the Feynman–Kac theorem.
128(2008); http://dx.doi.org/10.1063/1.2816709View Description Hide Description
A formulation and implementation of the quadratic response function in the adiabatic four-component Kohn-Sham approximation is presented. The noninteracting reference state is time-reversal symmetric and formed from Kramers pair spinors, and the energy density is gradient corrected. Example calculations are presented for the optical properties of disubstituted halobenzenes in their meta and ortho conformations. It is demonstrated that correlation and relativistic effects are not additive, and it is shown that relativity alone reduces the -response signal by 62% and 75% for meta- and ortho-bromobenzene, respectively, and enhances the same response by 17% and 21% for meta- and ortho-iodobenzene, respectively. Of the employed functionals, CAM-B3LYP shows the best performance and gives hyperpolarizabilities distinctly different from B3LYP.
On the performance of two-component energy-consistent pseudopotentials in atomic Fock-space coupled cluster calculations128(2008); http://dx.doi.org/10.1063/1.2823053View Description Hide Description
The four-component atomic intermediate-Hamiltonian Fock-space coupled cluster (IHFSCC) code of Landau et al. [J. Chem. Phys.115, 6862 (2001)] has been adapted to two-component calculations with relativistic pseudopotentials of the energy-consistent variety. Recently adjusted energy-consistent pseudopotentials for group 11 and 12 transition elements as well as group 13 and 14 post- main group elements, which were fitted to atomic valence spectra from four-component multiconfiguration Dirac-Hartree-Fock calculations, are tested in IHFSCC calculations for ionization potentials,electron affinities, and excitation energies of a variety of atoms and ions. Where comparison is possible, the deviations from experimental data are in good agreement with those found in previously published IHFSCC all-electron calculations: experimental data are usually reproduced within a few hundred wavenumbers.
Symmetry breaking in benzene and larger aromatic molecules within generalized valence bond coupled cluster methods128(2008); http://dx.doi.org/10.1063/1.2817600View Description Hide Description
The origin of symmetry breaking (SB) in benzene in generalized valence bond methods is investigated within a coupled cluster formalism that correlates all valence electrons. Retention of a limited number of pair correlation amplitudes (as in the perfect- and imperfect-pairing models) that incompletely describes interpair correlations leads to symmetry breaking as the orbitals and amplitudes are optimized. Local correlationmodels that are exact for one, two, and three interacting pairs at the doubles excitation level are compared against the exact pair correlation treatment, which correlates four interacting pairs at once in the connected double substitution operator. For simplicity, this comparison is performed with a second-order model of electroncorrelation, which is reasonably faithful to the infinite-order result. The significant SB known for the one-pair model (perfect pairing) is not eliminated at the two-pair level, but is virtually eliminated at the three-pair level. Therefore, a tractable hybrid model is proposed, which combines three-pair correlations at the second-order level and infinite-order treatment for the strong imperfect-pairing correlations involving one and two-pair correlations. This model greatly reduces SB in benzene and larger delocalized systems such as naphthalene and the phenalenyl cation and anion. The resulting optimized orbitals are localized in the space but exhibit significant delocalization in the space. This means that correlation effects associated with different resonance structures are treated in a more balanced way than if the orbitals localize, leading to reduced SB.
- Gas Phase Dynamics and Structure: Spectroscopy, Molecular Interactions, Scattering, and Photochemistry
128(2008); http://dx.doi.org/10.1063/1.2821103View Description Hide Description
Potential energy curves (PECs) for the ground and low-lying excited states of the cesium iodide (CsI) molecule have been calculated using the internally contracted multireference configuration interaction calculation with single and double excitation method with the relativistic pseudopotentials. PECs for seven states, , , , , and are first calculated and then those for 13 states are obtained by diagonalizing the matrix of the electronic Hamiltonian plus the effective one-electron spin-orbit (SO) Hamiltonian . Spectroscopic constants for the calculated ground -state PEC with the Davidson correction are found to agree well with the experiment. Transition dipole moments (TDMs) between and the other states are also obtained and the TDM between and is predicted to be the largest and that between and is the second largest around the equilibrium internuclear distance. The TDMs between and the states are estimated to be nonzero, but they are notably small as compared with those between the states. Finally, vibrational levels of the PEC for the two isotopic analogs, and , are numerically obtained to investigate the isotope effect on the vibrational-level shift. It has been found that the maximized available isotope shift is around .
128(2008); http://dx.doi.org/10.1063/1.2821106View Description Hide Description
We have performed an unbiased global search for the geometries of low-lying clusters in the size range of using genetic algorithm incorporated with a tight-binding model. Density functional theory calculations were carried out to further optimize the isomer structures. clusters prefer the motif of superclusterstructures stacked by several stable subunits such as and , connecting via a few bridging atoms. Size-dependent cluster properties such as binding energy, HOMO-LUMO gaps, and ionization potentials were discussed and compared with experiments.
128(2008); http://dx.doi.org/10.1063/1.2817592View Description Hide Description
Diatomic has been proposed as a good candidate for precision measurement of possible time variation of fundamental constants. Precise knowledge of its vibrational structure and Stark shift of its levels in an optical lattice is required for realization of this proposal. Motivated by these ideas we have performed a numerical calculation of interatomic potentials and transitiondipole moments of the molecule using an ab initio relativistic configuration interaction valence bond self-consistent-field method.
Spectral tuning by switching C–H⋯O hydrogen bonds: Rotation-induced spectral shifts of 7-hydroxyquinoline∙HCOOH isomers128(2008); http://dx.doi.org/10.1063/1.2816710View Description Hide Description
Spectral tuning effects on visible chromophores by hydrogen bonds are central to the chemistry of vision and of photosynthesis. A model for large spectral tuning effects by hydrogen bond switching is provided by the 7-hydroxyquinoline∙HCOOH complex, which forms two isomers, CTN1 and CTN2, both with an HCOOH⋯N hydrogen bond but with different hydrogen bonds. A 180° rotation of the HCOOH moiety around the O–H⋯N hydrogen bond exchanges the C–H⋯O hydrogen bonds, rotates the dipole moment of HCOOH, and leads to an shift of the electronic spectrum. Mass-selected resonant two-photon ionization, UV-UV holeburning, fluorescence spectra, and photoionization efficiency curves of the two 7-hydroxyquinoline∙HCOOH isomers were measured in supersonic expansions. Comparison to ab initio calculations allow us to determine the H-bond connectivity and structure of the two isomers and to assign their inter- and intramolecular vibrations. The Franck-Condon factors of the intermolecular shear vibration in the spectra indicate that the weak C–H⋯O hydrogen bond contracts markedly in the CTN1 isomer but expands in the CTN2 isomer. These changes of H-bond lengths agree with the spectral shifts. In contrast, the strong O–H⋯N hydrogen bond undergoes little change upon excitation.
128(2008); http://dx.doi.org/10.1063/1.2805386View Description Hide Description
Photoelectron spectroscopy (PES) is combined with theoretical calculations to investigate the electronic and atomic structures of three dopedaluminum clusters, (, Cu, and Au). Well-resolved PES spectra have been obtained at two detachment photon energies, and . Basin-hopping global optimization method in combination with density-functional theory calculations has been used for the structural searches. Good agreement between the measured PES spectra and theoretical simulations helps to identify the global minimum structures. It is found that can be viewed as replacing a surface Al atom by Li on an icosahedral , whereas Cu prefers the central site to form the encapsulated . For , Au also prefers the central site, but severely distorts the cage due to its large size.
Study of the dissociation of nitrous oxide following resonant excitation of the nitrogen and oxygen -shells128(2008); http://dx.doi.org/10.1063/1.2812926View Description Hide Description
A photochemistry study on nitrous oxide making use of site-selective excitation of terminal nitrogen, central nitrogen, and oxygen excitations is presented. The resonant Auger decay which takes place following excitation can lead to dissociation of the ion. To elucidate the nuclear dynamics, energy-resolved Auger electrons were detected in coincidence with the ionic dissociation products, and a strong dependence of the fragmentation pathways on the core-hole site was observed in the binding energy region of the first satellite states. A description based on the molecular orbitals as well as the correlation between the thermodynamical thresholds of ion formation and the first electronic states of has been used to qualitatively explain the observed fragmentation patterns.
128(2008); http://dx.doi.org/10.1063/1.2818564View Description Hide Description
The electrostatic complex has a vibrationally resolved photodissociationspectrum in the visible. Photodissociation produces (nonreactive pathway) and (reactive pathway). Production of is energetically favored, but spin forbidden. One-photon dissociation studies confirm mode selectivity observed by Lessen et al. [J. Chem. Phys.95, 1414 (1991)]: excitation of one quantum of rocking motion enhances production by . Branching ratio measurements in one-photon dissociation are extended to higher energy. The effect of OCO antisymmetric stretch vibrations on reactivity is investigated using vibrationally mediated photodissociation, in which the OCO antisymmetric stretch is excited at . Vibrationally excited molecules are then dissociated in the visible. Seven vibronic bands are investigated, involving the antisymmetric stretch alone and in combination with the bend, the stretch and rock. Exciting the antisymmetric stretch leads to a increase in the reactive channel, compared to other states at similar energy. Combination bands involving the antisymmetric stretch all show slightly higher reactivity. Electronic structure calculations were performed to characterize the dissociation pathways and excited electronic states of . The geometries of reactants, products, and transition states and relative energies of quintet and triplet states were determined using hybrid density functional theory; energies were also calculated using the coupled cluster with single, double and perturbative triple excitations method. In addition, time-dependent density functional theory calculations were performed to predict the excited electronic states of quintet and triplet . Spin-orbit coupling of quintet states to triplet states was calculated and used to compute intersystem crossing rates, which reproduce many of the observed mode selective trends. The stretch and OCO antisymmetric stretch appear to enhance reactivity by increasing the intersystem crossing rate.
Structure and electronic properties of (, Al, In, Mg, Sr, Ba, and Pb; , 10, 12, and 14) clusters: Theoretical investigations based on first principles calculations128(2008); http://dx.doi.org/10.1063/1.2814166View Description Hide Description
A systematic theoretical study of the (, Al, In, Mg, Sr, Ba, and Pb;, 10, 12, and 14) clusters have been investigated to explore the effect of impurity atoms on the structure and electronic properties of lead clusters. The calculations were carried out using the density functional theory with generalized gradient approximation for exchange-correlation potential. Extensive search based on large numbers of initial configurations has been carried out to locate the stable isomers of clusters. The results revealed that the location of the impurity atom depends on the nature of interaction between the impurity atom and the host cluster and the size of the impurity atom. Whereas, the impurity atoms smaller than Pb favor to occupy the endohedral position, the larger atoms form exohedral capping of the host cluster. The stability of these clusters has been analyzed based on the average binding energy, interaction energy of the impurity atoms, and the energy gap between the highest occupied and lowest unoccupied energy levels (HLG). Based on the energetics, it is found that interaction dominates over the interaction and smaller size atoms interact more strongly. The stabilityanalysis of these clusters suggests that, while the substitution of Pb by C or Al enhances the stability of the clusters, Mg lowers the stability. Further investigations of the stability of clusters reveal that the interplay between the atomic and electronic structure is crucial to understand the stability of these clusters. The energy gapanalysis reveals that, while the substitution of Mg atom widens the HLG, all other elements reduce the gap of the clusters.
128(2008); http://dx.doi.org/10.1063/1.2819105View Description Hide Description
Butadiene monoxide (BMO) undergoes the transition, involving the excitation of both and electrons to orbital, at . After relaxing to the ground electronic state via internal conversion, BMO molecules undergo intramolecular rearrangement and subsequently dissociate to form unexpected OH radicals, which were detected state selectively by laser-induced fluorescence technique, and the energy state distribution was measured. OH is produced vibrationally cold, , with the rotational population characterized by a rotational temperature of . The major portion of the available energy is partitioned into internal degrees of the photofragments, namely, vibration and rotation. A considerable portion (25%–35%) also goes to the relative translation of the products. The doublet and spin-orbit ratios of OH were measured to be nearly unity, implying statistical distribution of these states and, hence, no preference for any of the doublet ( and ) and spin-orbit ( and ) states. Formation time of the nascent OH radical was measured to be . Different products, such as crotonaldehyde and methyl vinyl ketone, were detected by gas chromatography as stable products of photodissociation. A reaction mechanism for the formation of all these photoproducts, transient and stable, is proposed. The multiple pathways by which these products can be formed have been theoretically optimized, and energies have been calculated. Absorption cross section of BMO at was measured, and quantum yield of OH generation channel was also determined.
- Condensed Phase Dynamics, Structure, and Thermodynamics: Spectroscopy, Reactions, and Relaxation
On the interpretation of continuous wave electron spin resonance spectra of tempo-palmitate in 5-cyanobiphenyl128(2008); http://dx.doi.org/10.1063/1.2812280View Description Hide Description
Electron spin resonance(ESR) measurements are highly informative on the dynamic behavior of molecules, which is of fundamental importance to understand their stability, biological functions and activities, and catalytic action. The wealth of dynamic information which can be extracted from a continuous wave electron spin resonance (cw-ESR) spectrum can be inferred by a basic theoretical approach defined within the stochastic Liouville equation formalism, i.e., the direct inclusion of motional dynamics in the form of stochastic (Fokker-Planck/diffusive) operators in the super Hamiltonian governing the time evolution of the system. Modeling requires the characterization of magnetic parameters (e.g., hyperfine and Zeeman tensors) and the calculation of ESR observables in terms of spectral densities. The magnetic observables can be pursued by the employment of density functional theory which is apt, provided that hybrid functionals are employed, for the accurate computation of structural properties of molecular systems. Recently, an ab initio integrated computational approach to the in silico interpretation of cw-ESR spectra of multilabeled systems in isotropic fluids has been discussed. In this work we present the extension to the case of nematic liquid crystalline environments by performing simulations of the ESR spectra of the prototypical nitroxide probe 4-(hexadecanoyloxy)-2,2,6,6-tetramethylpiperidine-1-oxy in isotropic and nematic phases of 5-cyanobiphenyl. We first discuss the basic ingredients of the integrated approach, i.e., (1) determination of geometric and local magnetic parameters by quantum-mechanical calculations, taking into account the solvent and, when needed, the vibrational averaging contributions; (2) numerical solution of a stochastic Liouville equation in the presence of diffusive rotational dynamics, based on (3) parameterization of diffusion rotational tensor provided by a hydrodynamic model. Next we present simulated spectra with minimal resorting to fitting procedures, proving that the combination of sensitive ESRspectroscopy and sophisticated modeling can be highly helpful in providing three-dimensional structural and dynamic information on molecular systems in anisotropic environments.
128(2008); http://dx.doi.org/10.1063/1.2820765View Description Hide Description
The ultrafast dynamics of ice at is studied by midinfrared ultrafast pump-probe spectroscopy. The vibrational relaxation of ice is observed to proceed via an intermediate state, which has a blueshifted absorptionspectrum. Polarization resolved measurements reveal that the intermediate state is part of the intramolecular relaxation pathway of the HDO molecule. In addition, slow dynamics on a time scale of the order of is observed, related to thermally induced collective reorganizations of the ice lattice. The transient absorption line shape is analyzed within a Lippincott-Schroeder model for the OH-stretch potential. This analysis identifies the main mechanism behind the strong spectral broadening of the transition.
128(2008); http://dx.doi.org/10.1063/1.2819486View Description Hide Description
We present a dual-resolution molecular dynamics (MD) simulation of liquid water employing a recently introduced Adaptive Resolution Scheme (AdResS). The spatially adaptive molecular resolution procedure allows for changing from a coarse-grained to an all-atom representation and vice versa on-the-fly. In order to find the most appropriate coarse-grained watermodel to be employed with AdResS, we first study the accuracy of different coarse-grained watermodels in reproducing the structural properties of the all-atom system. Typically, coarse-grained molecular models have a higher diffusion constant than the corresponding all-atom models due to the reduction in degrees of freedom (DOFs) upon coarse-graining that eliminates the fluctuating forces associated with those integrated-out molecular DOFs. Here, we introduce the methodology to obtain the same diffusionaldynamics across different resolutions. We show that this approach leads to the correct description of the here relevant structural, thermodynamical, and dynamical properties, i.e., radial distribution functions, pressure, temperature, and diffusion, of liquid water at ambient conditions.
128(2008); http://dx.doi.org/10.1063/1.2813416View Description Hide Description
A new “mesoscopic” stochastic model has been developed to describe the diffusive behavior of a system of particles at equilibrium. The model is based on discretizing space into slabs by drawing equispaced parallel planes along a coordinate direction. A central role is played by the probability that a particle exits a slab via the face opposite to the one through which it entered (transmission probability), as opposed to exiting via the same face through which it entered (reflection probability). A simple second-order Markov process invoking this probability is developed, leading to an expression for the self-diffusivity, applicable for large slab widths, consistent with a continuous formulation of diffusional motion. This model is validated via molecular dynamics simulations in a bulk system of soft spheres across a wide range of densities.