Index of content:
Volume 127, Issue 9, 07 September 2007
- Theoretical Methods and Algorithms
Essential energy space random walk via energy space metadynamics method to accelerate molecular dynamics simulations127(2007); http://dx.doi.org/10.1063/1.2769356View Description Hide Description
To overcome the possible pseudoergodicity problem, molecular dynamic simulation can be accelerated via the realization of an energy space random walk. To achieve this, a biased free energy function (BFEF) needs to be priori obtained. Although the quality of BFEF is essential for sampling efficiency, its generation is usually tedious and nontrivial. In this work, we present an energy space metadynamics algorithm to efficiently and robustly obtain BFEFs. Moreover, in order to deal with the associated diffusion sampling problem caused by the random walk in the total energy space, the idea in the original umbrella sampling method is generalized to be the random walk in the essential energy space, which only includes the energy terms determining the conformation of a region of interest. This essential energy space generalization allows the realization of efficient localized enhanced sampling and also offers the possibility of further sampling efficiency improvement when high frequency energy terms irrelevant to the target events are free of activation. The energy space metadynamics method and its generalization in the essential energy space for the molecular dynamics acceleration are demonstrated in the simulation of a pentanelike system, the blocked alanine dipeptide model, and the leucine model.
127(2007); http://dx.doi.org/10.1063/1.2770700View Description Hide Description
The first transitions of 18 nitroso and 16 thiocarbonyl dyes have been computed by time-dependent density functional theory (TD-DFT) using pure as well as global and range-separated hybrid functionals. It turns out that the accuracy of all hybrids is relatively similar, i.e., the inclusion of a growing fraction of exact exchange does neither worsen nor improve significantly the raw TD-DFT estimations. However, after a simple linear regression, it appears that the range-separated hybrids provide a better accuracy than global hybrids.
127(2007); http://dx.doi.org/10.1063/1.2757170View Description Hide Description
Within the adiabatic approximation, it is trivial to generalize existing imaginary time path-integral techniques to the case of multiple electronic surfaces. However, there are many times where nonadiabatic effects can play an important role. To this end, we reformulate the well-known path-integral expressions to incorporate multiple potential surfaces, without necessitating the adiabatic approximation. We show that the resulting expression, like its adiabatic counterpart, can be interpreted in terms of a simple classical isomorphic system and thus is amenable to simulation through Monte Carlo techniques. We derive simple expressions to compute expectation values of a general operator in both the nuclear coordinate and electronic state, and demonstrate the existence of a simple internal diagnostic that can be used to evaluate the magnitude of equilibrium nonadiabatic effects.
On the vibronic coupling approximation: A generally applicable approach for determining fully quadratic quasidiabatic coupled electronic state Hamiltonians127(2007); http://dx.doi.org/10.1063/1.2756540View Description Hide Description
In this report we introduce an iterative procedure for constructing a quasidiabatic Hamiltonian representing -coupled electronic states in the vicinity of an arbitrary point in -dimensional nuclear coordinate space. The Hamiltonian, which is designed to compute vibronic spectra employing the multimode vibronic coupling approximation, includes all linear terms which are determined exactly using analytic gradient techniques. In addition, all quadratic terms, where , are determined from energy gradient and derivative coupling information obtained from reliable multireference configuration interactionwave functions. The use of energy gradient and derivative coupling information enables the large number of second order parameters to be determined employing ab initio data computed at a limited number of points ( being minimal) and assures a maximal degree of quasidiabaticity. Numerical examples are given in which quasidiabatic Hamiltonians centered around three points on the potential energy surface (the minimum energy point on the ground statesurface and the minimum energy points on the two- and three-state seams of conical intersection) were computed and compared. A method to modify the conical intersection based Hamiltonians to better describe the region of the ground state minimum is introduced, yielding improved agreement with ab initio results, particularly in the case of the Hamiltonian defined at the two-state minimum energy crossing.
Line shape studies of a state coupled to a random background including large fluctuations of the couplings127(2007); http://dx.doi.org/10.1063/1.2771174View Description Hide Description
Line shape functions of a model system are analyzed, describing an oscillator carrying state coupled to background states randomly distributed in energy and with random coupling constants. Depending on the energydistribution functions or the nature of the coupling distribution, different line shape functions, such as the Lorentzian, the Fano, or that related to the nonexponential decay of the Förster type are recovered as limiting cases. Conditions for the range of applicability of a specially introduced mean square coupling approximation are derived. It is shown that the appearance of a Lorentzian line shape does not imply directly a homogeneous decay mechanism and that, on the other hand, commonly accepted conditions for the so-called statistical limit, expressed in terms of an average density and an average coupling, do not necessarily lead to a Lorentzian line shape. This is illustrated analytically through a model with randomly distributed transition dipolar couplings. Other applications relate to spectral diffusion in proteins and to bridged charge transfer.
127(2007); http://dx.doi.org/10.1063/1.2764480View Description Hide Description
The quasi-steady-state approximation (QSSA) is a model reduction technique used to remove highly reactive species from deterministic models of reaction mechanisms. In many reaction networks the highly reactive intermediates (QSSA species) have populations small enough to require a stochastic representation. In this work we apply singular perturbation analysis to remove the QSSA species from the chemical master equation for two classes of problems. The first class occurs in reaction networks where all the species have small populations and the QSSA species sample zero the majority of the time. The perturbation analysis provides a reduced master equation in which the highly reactive species can sample only zero, and are effectively removed from the model. The reduced master equation can be sampled with the Gillespie algorithm. This first stochastic QSSA reduction is applied to several example reaction mechanisms (including Michaelis-Menten kinetics) [Biochem. Z.49, 333 (1913)]. A general framework for applying the first QSSA reduction technique to new reaction mechanisms is derived. The second class of QSSA model reductions is derived for reaction networks where non-QSSA species have large populations and QSSA species numbers are small and stochastic. We derive this second QSSA reduction from a combination of singular perturbation analysis and the expansion. In some cases the reduced mechanisms and reaction rates from these two stochastic QSSA models and the classical deterministic QSSA reduction are equivalent; however, this is not usually the case.
127(2007); http://dx.doi.org/10.1063/1.2753472View Description Hide Description
A two-pulse degenerate four-wave mixingexperiment is analyzed in the case where the medium under investigation can be modeled by two-level systems having unequal permanent dipole moments. By modeling the light pulses by double exponentials , we give an analytical expression of the third-order nonlinear polarization of the medium. We apply this result to simulate the measured signal in such experiment. We show that in the case of a two-photon transition, a signal can be detected if the pump pulse interacts with the medium before the probe pulse contrary to what is observed for excitations in the resonance region. An attempt to explain this behavior is made and the detected signal is analyzed in terms of pure coherent processes. This effect appears as a signature of the presence of permanent dipole moments. To test this property on a more realistic system, we then have considered a one-dimensional frequency-selected infrared degenerate four-wave mixingexperiment on a molecular anharmonic vibrational mode modeled by a Morse potential and coupled to a dissipative bath of harmonic oscillators. We show that the two-photon transitions allowed by the presence of permanent dipole moments enable to analyze the multilevel system dynamics as if they were the one of a two-level system. Our results can also be extended to the case of inhomogeneous broadening and are of interest to study the infrared photon-echo response of anharmonic vibrational modes.
- Gas Phase Dynamics and Structure: Spectroscopy, Molecular Interactions, Scattering, and Photochemistry
Dimensional scaling treatment of stability of atomic anions induced by superintense, high-frequency laser fields127(2007); http://dx.doi.org/10.1063/1.2768037View Description Hide Description
We show that dimensional scaling, combined with the high-frequency Floquet theory, provides useful means to evaluate the stability of gas phase atomic anions in a superintense laser field. At the large-dimension limit , in a suitably scaled space, electrons become localized along the polarization direction of the laser field. We find that calculations at large are much simpler than , yet yield similar results for the field strengths needed to bind an “extra” one or two electrons to H and He atoms. For both linearly and circularly polarized laser fields, the amplitude of quiver motion of the electrons correlates with the detachment energy. Despite large differences in scale, this correlation is qualitatively like that found between internuclear distances and dissociation energies of chemical bonds.
127(2007); http://dx.doi.org/10.1063/1.2770463View Description Hide Description
The reaction of HOCO with O atoms has been studied using a direct ab initiodynamics approach based on the scaling all correlation method. Ab initio calculations point to two possible reaction mechanisms for the reaction. They are a direct hydrogen abstraction and an oxygen addition reaction through a short-lived HOC(O)O intermediate. The dynamics results show that only the addition mechanism is important under the conditions considered here. The lifetime of the HOC(O)O complex is predicted to be . This is typical of a direct and fast radical-radical reaction. At room temperature, the calculated thermal rate coefficient is and its temperature dependence is rather weak. The two kinds of reactive trajectories are illustrated in detail.
Spectroscopy of the transition of jet-cooled fluorobenzene: Laser-induced fluorescence, dispersed fluorescence, and pathological Fermi resonances127(2007); http://dx.doi.org/10.1063/1.2759931View Description Hide Description
A detailed study of the electronic transition of jet-cooled fluorobenzene has been carried out using laser-induced fluorescence and dispersed fluorescence (DF) spectroscopies. Analysis of over 40 single vibronic level DF spectra resulted in the assignment of 16 fundamental frequencies in the excited electronic state. Progressions in totally symmetric modes, particularly in the ring-breathing mode , feature in both types of fluorescencespectrum. There is also significant activity in non-totally-symmetric modes, with activity in Franck-Condon (FC)-allowed overtones, FC-forbidden combinations induced by Duschinsky mixing, and symmetry-forbidden transitions induced by the same Herzberg-Teller vibronic coupling mechanism that induces the benzene transition. Fermi resonances (FRs) are extensive throughout the spectrum, especially in the important FC-active modes. A consequence of these extensive FRs is that several important previous assignments are shown to be incorrect and have been reassigned here. Ab initio and density functional theory calculations have also been performed to support the experimental assignments.
127(2007); http://dx.doi.org/10.1063/1.2767260View Description Hide Description
Population transfers in degenerate (or almost degenerate) two-level systems interacting with the few-cycle laser pulse are investigated. A simple and analytical formula of nonadiabatic transition probability is derived with completely degenerate condition, demonstrating the sensitive dependence of the transition probability on the phase of the few-cycle pulses. As one of the applications of this formula, a new way of controlling the nuclear wave packet dynamics at a potential curve crossing by laser pulse is proposed.
127(2007); http://dx.doi.org/10.1063/1.2764074View Description Hide Description
The vibrational spectroscopy of is studied by theoretical calculations for , and the results are compared with experiments for . The calculations use both ab initio MP2 and DFT/B3LYP potential energy surfaces. Both harmonic and anharmonic calculations are reported, the latter with the CC-VSCF method. The main findings are the following: (1) With one exception ( bending mode), the anharmonicity of the observed transitions, all in the experimental window of , is negligible. The computed anharmonic coupling suggests that intramolecular vibrational redistribution does not play any role for the observed linewidths. (2) Comparison with experiment at the harmonic level of computed fundamental frequencies indicates that MP2 is significantly more accurate than DFT/B3LYP for these systems. (3) Strong anharmonic effects are, however, calculated for numerous transitions of these systems, which are outside the present observation window. These include fundamentals as well as combination modes. (4) Combination modes for the and clusters are computed. Several relatively strong combination transitions are predicted. These show strong anharmonic effects. (5) An interesting effect of the zero point energy (ZPE) on structure is found for : The global minimum of the potential energy corresponds to a structure, but with incorporation of ZPE the lowest energy structure is , in accordance with experiment. (6) No stable structures were found for , for .
Ab initio calculations on low-lying electronic states of and Franck-Condon simulation of its photodetachment spectrum127(2007); http://dx.doi.org/10.1063/1.2768355View Description Hide Description
Geometry optimization and harmonic vibrational frequency calculations have been carried out on the low-lying singlet and triplet electronic states of the antimony dioxide anion employing a variety of ab initio methods. Both large-core and small-core relativistic effective core potentials were used for Sb in these calculations, together with valence basis sets of up to augmented correlation-consistent polarized-valence quintuple-zeta (aug-cc-pV5Z) quality. The ground electronic state of is determined to be the state, with the state, calculated to be higher in energy. Further calculations were performed on the , , and states of with the aim to simulating the photodetachment spectrum of . Potential energy functions (PEFs) of the state of and the , , and states of were computed at the complete-active-space self-consistent-field multireference internally contracted configuration interaction level with basis sets of augmented correlation-consistent polarized valence quadruple-zeta quality. Anharmonic vibrational wave functions obtained from these PEFs were used to compute Franck-Condon factors between the state of and the , , and states of , which were then used to simulate the photodetachment spectrum of , which is yet to be recorded experimentally.
127(2007); http://dx.doi.org/10.1063/1.2768347View Description Hide Description
Detailed simulation study is reported for the excited-statedynamics of photoisomerization of cis-tetraphenylethylene (TPE) following excitation by a femtosecond laser pulse. The technique for this investigation is semiclassical dynamics simulation, which is described briefly in the paper. Upon photoexcitation by a femtosecond laser pulse, the stretching motion of the ethylenic bond of TPE is initially excited, leading to a significant lengthening of ethylenic bond in . Twisting motion about the ethylenic bond is activated by the energy released from the relaxation of the stretching mode. The 90° twisting about the ethylenic bond from an approximately planar geometry to nearly a perpendicular conformation in the electronically excited state is completed in . The torsional dynamics of phenyl rings which is temporally lagging behind occurs at about . Finally, the twisted TPE reverts to the initial conformation along the twisting coordinate through nonadiabatic transitions. The simulation results provide a basis for understanding several spectroscopic observations at molecular levels, including ultrafast dynamic Stokes shift, multicomponent fluorescence,viscosity dependence of the fluorescence lifetime, and radiationless decay from electronically excited state to the ground state along the isomerization coordinate.
127(2007); http://dx.doi.org/10.1063/1.2761915View Description Hide Description
We present an analytical expression for the observed signal in time- and phase-resolved pump-probe studies, with particular emphasis on terahertz time-domain spectroscopy. Maxwell’sequations are solved for the response of damped, harmonic oscillators to a driving probe field in the perturbative regime. Our analytical expressions agree with the one previously reported in the literature [Nemec et al., J. Chem. Phys.122, 104503 (2005)] in the Drude limit; however, they differ in the case of a vibrational resonance.
127(2007); http://dx.doi.org/10.1063/1.2753489View Description Hide Description
This paper reports a series of electronic structure calculations performed on the dissociation pathways of the vinoxy radical . We use coupled-cluster with single, double, and perturbative triple excitations (CCSD(T)), complete active space self-consistent field (CASSCF), multireference configuration interaction (MRCI), and MRCI with the Davidson correction to calculate the barrier heights of the two unimolecular dissociation pathways of this radical. The effect of state averaging on the barrier heights is investigated at the CASSCF, MRCI, and levels. The change in mixing angle along the reaction path is calculated as a measure of derivative coupling and found to be insufficient to suggest nonadiabatic recrossing. We also present a new analysis of previous experimental data on the unimolecular dissociation of ground state vinoxy. In particular, an error in the internal energy distribution of vinoxy radicals reported in a previous paper is corrected and a new analysis of the experimental sensitivity to the onset energy (barrier height) for the isomerizationreaction is given. Combining these studies, a final “worst case” analysis of the product branching ratio is given and a statistical model using each of the calculated transition states is found to be unable to correctly reproduce the experimental data.
- Condensed Phase Dynamics, Structure, and Thermodynamics: Spectroscopy, Reactions, and Relaxation
127(2007); http://dx.doi.org/10.1063/1.2770457View Description Hide Description
We have measured resonant and off-resonant Auger-electron spectra of liquid water. Continuumlike transitions near and above the vertical ionizationenergy are identified by the characteristic normal Auger-electron spectra. On the contrary, well-resolved spectator shifts of the main Auger-electron peak are observed at the liquid-water absorption main edge and near the absorption pre-edge. The shifts of 1.4 and arise from the localized nature of the excitation. Excited-state localization/delocalization is also discussed for the analogous vacuum ultraviolet (VUV) transitions, and we point out the similarities between x-ray and VUV absorption spectra of liquid water.
127(2007); http://dx.doi.org/10.1063/1.2769357View Description Hide Description
Using powderx-ray diffraction and first-principles calculations, we provide evidence for a structural transition of PETN-I below to an orthorhombic phase of space group . The transition can be rationalized as shear-stress induced and ferroelastic, which involves a slight static displacement of the molecules that breaks the fourfold symmetry of PETN-I. Previously reported changes in the optical spectra reflect a lifting of the twofold degeneracy of modes in tetragonal PETN-I. The observed transition is expected to induce soft shear compliances along specific directions in PETN crystallites that may relate to the observed dependence of detonation pressure on crystal orientation.
Non-Debye response for the structural relaxation in glass-forming liquids: Test of the Avramov model127(2007); http://dx.doi.org/10.1063/1.2768962View Description Hide Description
The experimentally observed characteristic features of the -relaxation process in glass-forming liquids are the non-Arrhenius behavior of the structural relaxation times and the non-Debye character of the macroscopic relaxation function. The Avramov model in which relaxation is considered as an energy activation process of surmounting random barriers in liquidenergy landscape was successfully applied to describe the temperature and pressure dependences of the macroscopic relaxation times or viscosity. In this paper, we consider the dielectric spectrum associated with Avramov model. The asymmetrical broadening of the loss spectra was found to be related directly to dispersion of the energy barrier distribution. However, it turns out that temperature dependence of the spectrum broadening as predicted by the Avromov model is at odds to experimental observation in glass-forming liquids.
Quasielastic neutron scattering experiments including activation energies and mathematical modeling of methyl halide dynamics127(2007); http://dx.doi.org/10.1063/1.2760205View Description Hide Description
Quasielastic neutron scatteringexperiments were carried out using the multichopper time-of-flight spectrometer V3 at the Hahn-Meitner Institut, Germany and the backscattering spectrometer at Forschungszentrum Jülich, Germany. Activation energies for , , Cl, Br, and I, were obtained. In combination with results from previous inelastic neutron scatteringexperiments the data were taken to describe the dynamics of the halides in terms of two different models, the single particle model and the coupling model. Coupled motions of methyl groups seem to explain the dynamics of the methyl fluoride and chloride; however, the coupling vanishes with the increase of the mass of the halide atom in and .