Volume 129, Issue 11, 21 September 2008
Index of content:
- Theoretical Methods and Algorithms
129(2008); http://dx.doi.org/10.1063/1.2976440View Description Hide Description
We present a simple method for utilizing experimental data to improve the efficiency of numerical calculations of free energy profiles from molecular dynamics simulations. The method involves umbrella sampling simulations with restraining potentials based on a known approximate estimate of the free energy profile derived solely from experimental data. The use of the experimental data results in optimal restraining potentials, guides the simulation along relevant pathways, and decreases overall computational time. In demonstration of the method, two systems are showcased. First, guided, unguided (regular) umbrella sampling simulations and exhaustive sampling simulations are compared to each other in the calculation of the free energy profile for the distance between the ends of a pentapeptide. The guided simulation use restraints based on a simulated “experimental” potential of mean force of the end-to-end distance that would be measured by fluorescence resonance energy transfer (obtained from exhaustive sampling). Statistical analysis shows a dramatic improvement in efficiency for a 5 window guided umbrella sampling over 5 and 17 window unguided umbrella sampling simulations. Moreover, the form of the potential of mean force for the guided simulations evolves, as one approaches convergence, along the same milestones as the extensive simulations, but exponentially faster. Second, the method is further validated by replicating the forced unfolding pathway of the titin I27 domain using guiding umbrella sampling potentials determined from actual single molecule pulling data. Comparison with unguided umbrella sampling reveals that the use of guided sampling encourages unfolding simulations to converge faster to a forced unfolding pathway that agrees with previous results and produces a more accurate potential of mean force.
129(2008); http://dx.doi.org/10.1063/1.2977735View Description Hide Description
We present a very efficient simultaneous optimization method for both molecular geometry and electronic wave function. We introduce a simultaneous least squares scheme to minimize errors in a full local quadratic space of both geometric and wave function vectors. Several self-consistent-field iterations are taken until a uniform search direction is achieved in every geometry optimization step. Not only does this new simultaneous optimization method significantly reduce the number of self-consistent-field iterations to reach convergence, it is able to overcome shallow potential wells to find a better stationary point. This new method exhibits up to savings in computational cost compared to conventional geometry optimization methods.
129(2008); http://dx.doi.org/10.1063/1.2976663View Description Hide Description
Coarse-grained (CG) modeling has emerged as a promising tool to bridge the gap between the temporal and spatial scales of all-atom (AA) simulations and those of many important biological processes. Resolution exchange, a variant of the replica exchange method, combines the efficiency of CG simulation and the accuracy of AA simulation by swapping configurations between AA and CG simulations. The crucial step in a resolution exchange move is to rigorously reconstruct the high-resolution system from models at coarser resolutions. In this paper, configurational-bias Monte Carlo is adopted as a general method to rebuild the missing degrees of freedom rigorously for CG models and for the first time combined with resolution exchange. The new approach is demonstrated on an alkane and a peptide system. It is found that the efficiency of resolution exchange depends significantly on the quality of the CG model.
129(2008); http://dx.doi.org/10.1063/1.2976010View Description Hide Description
The adaptive kinetic Monte Carlo method uses minimum-mode following saddle point searches and harmonic transition state theory to model rare-event, state-to-state dynamics in chemical and material systems. The dynamical events can be complex, involve many atoms, and are not constrained to a grid—relaxing many of the limitations of regular kinetic Monte Carlo. By focusing on low energy processes and asserting a minimum probability of finding any saddle, a confidence level is used to describe the completeness of the calculated event table for each state visited. This confidence level provides a dynamic criterion to decide when sufficient saddle point searches have been completed. The method has been made efficient enough to work with forces and energies from density functional theory calculations. Finding saddle points in parallel reduces the simulation time when many computers are available. Even more important is the recycling of calculated reaction mechanisms from previous states along the dynamics. For systems with localized reactions, the work required to update the event table from state to state does not increase with system size. When the reaction barriers are high with respect to the thermal energy, first-principles simulations over long time scales are possible.
129(2008); http://dx.doi.org/10.1063/1.2977789View Description Hide Description
The random phase approximation (RPA) to the density functionalcorrelationenergy systematically improves upon many limitations of present semilocal functionals, but was considered too computationally expensive for widespread use in the past. Here a physically appealing reformulation of the RPA correlation model is developed that substantially reduces its computational complexity. The density functional RPA correlationenergy is shown to equal one-half times the difference of all RPA electronic excitation energies computed at full and first order coupling. Thus, the RPA correlationenergy may be considered as a difference of electronic zero point vibrational energies, where each eigenmode corresponds to an electronic excitation. This surprisingly simple result is intimately related to plasma theories of electron correlation. Differences to electron pair correlation models underlying popular correlated wave function methods are discussed. The RPA correlationenergy is further transformed into an explicit functional of the Kohn–Sham orbitals. The only nontrivial ingredient to this functional is the sign function of the response operator. A stable iterative algorithm to evaluate this sign function based on the Newton–Schulz iteration is presented. Integral direct implementations scale as the fifth power of the system size, similar to second order Møller–Plesset calculations. With these improvements, RPA may become the long-sought robust and efficient zero order post-Kohn–Sham correlation model.
129(2008); http://dx.doi.org/10.1063/1.2976441View Description Hide Description
This paper presents a new approach to propagating the density matrix based on a time stepping procedure arising from a Trotter factorization and combining the forward and backward incremental propagators. The sums over intermediate states of the discrete quantum subsystem are implemented by a Monte Carlo surface hopping-like procedure, while the integrals over the continuous variables are performed using a linearization in the difference between the forward and backward paths of these variables leading to classical-like equations of motion with forces determined by the quantum subsystem states. The approach is tested on several models and numerical convergence is explored.
129(2008); http://dx.doi.org/10.1063/1.2977739View Description Hide Description
The potential energy surface of the low-lying excited state of is constructed by using the ionization potential equation-of-motion coupled-cluster method and also the RASPT2 method with a large active space of 21 electrons in 17 orbitals to improve the results. It is found by the multiconfiguration calculation that this state has a barrier of between two equivalent minima in which the linear molecule has a dipole moment. In our computations artifactual symmetry breaking is carefully avoided. Further refinement, including consideration of interaction between the two excited states, yields a somewhat higher barrier between 100 and . The mechanism of formation of the double-minimum potential is explained by the pseudo–Jahn–Teller effect theory. Computed spectroscopic constants are in good agreement with experimental ones.
129(2008); http://dx.doi.org/10.1063/1.2976011View Description Hide Description
Transition path sampling (TPS) was developed for studying activated processes in complex systems with unknown reaction coordinate. Transition interface sampling (TIS) allows efficient evaluation of the rate constants. However, when the transition can occur via more than one reaction channel separated by a high barrier, TPS and TIS are ineffective in sampling both channels. The combination of replica exchange with TIS can overcome this problem. This work shows how, by including both the backward and forward reactions, the corresponding rate constants, as well as the free energy barrier can be computed in a single simulation. The method is illustrated on a two dimensional potential using the Langevin dynamics. In addition, a simpler algorithm based on only forward shooting from the interfaces is shown to give equally accurate results, and forms a bridge between the transition interface and the forward flux sampling methods. The diffusive behavior of the replicas can be used to assess the quality of the choice of the order parameter used for the interfaces.
Higher-order processes of excitation energy transfer in supramolecular complexes: Liouville space analysis of bridge molecule mediated transfer and direct photon exchange129(2008); http://dx.doi.org/10.1063/1.2976150View Description Hide Description
Long-range electronic excitation energy transfer is studied in the framework of a generalized master equation approach, which offers a systematic account for higher-order processes. Bridge molecule mediated transfer is confronted with the direct excitation energy exchange via photon emission and absorption. It is the central aim of this paper to present a systematic study of fourth-order rates, which describe both types of transfer processes characterized by the presence of intermediate states. While such a Liouville space formulation of rates is known from bridge mediated transfer, it is new for the case of photon mediated processes. In the former case, however, a novel approach to account for intermediate state relaxation is introduced. Finally and for illustration, some estimates are offered for the length dependence of the various discussed transfer rates.
129(2008); http://dx.doi.org/10.1063/1.2978168View Description Hide Description
We have extended the constrained density functional theory(DFT) approach to explicitly control the magnitude of spin contamination. Unlike a restricted or restricted open-shell approach, the present method allows finer granularity, not only constraining the magnitude of the spin contamination but also allowing for the possibility of applying the constraint to a subsystem of a much larger system. This allows for the description of spin polarization where physically meaningful, while simultaneously enabling the reduction of spurious overpolarization that is present in many DFT functionals. We utilize this constraint in two particular model applications: The calculation of isotropic and anisotropic hyperfine couplings of a transition metal complex, , and the calculation of the diabatic dissociation curves of OF radical. In both cases, the spin contamination constraint is essential for obtaining physically meaningful, qualitatively correct, results.
- Gas Phase Dynamics and Structure: Spectroscopy, Molecular Interactions, Scattering, and Photochemistry
129(2008); http://dx.doi.org/10.1063/1.2977730View Description Hide Description
Laser-induced fluorescence, resonant two-photon ionization, UV-UV hole burning, UV depletion, and single vibronic level fluorescence (SVLF) spectra of jet-cooled diphenylmethane (DPM) have been recorded over the region that encompasses the and transitions. All transitions in the laser-induced fluorescence excitation spectrum are due to a single conformational isomer of DPM with symmetry. The origin transition occurs at , supporting a short progression in the symmetric torsion with spacing of . The origin transition occurs above the origin and possesses very weak torsional structure, observable only under saturating laser power conditions. A combination of SVLF spectroscopy and hot band studies is used to assign the frequencies of the symmetric torsion , antisymmetric torsion , and butterfly vibrations in the , , and states. The emission from the origin is composed of two components, a set of sharp transitions ascribable to the state and a dense “clump” of transitions ending in ground-state levels 81, 88, and above the zero-point level ascribable to emission. Assignment of the transitions in the clump leads to the conclusion that the single vibronic level responsible for the emission has mixed character. The mixing involves several torsional vibronic levels in the manifold close in energy to the origin, with the correct symmetry to couple the two states. These levels involve significant torsional excitation. The close energetic proximity of these levels leads to a breakdown of typical vibronic coupling selection rules.
129(2008); http://dx.doi.org/10.1063/1.2976152View Description Hide Description
Four types of possible structural motifs of the medium-sized clusters i.e., fcc like, decahedron based, icosahedron based, and prolate ellipsoid based, have been generated from an empirical genetic algorithm search and further investigated using spin-polarized density functional theory calculations. fcc-like structures based on octahedron dominate the growth pathway of clusters. For larger clusters such as and , a prolate ellipsoid-based geometry and a structure consisting of three interpenetrating decahedra are energetically favorable, respectively. The size-dependent cluster properties as well as the correlation between electronic properties and clustergeometry are also discussed, suggesting a particular stabilitycluster at with a fcc-like octahedron structure.
Low energy hydrogenation products of extended systems : A density functional theory search strategy, benchmarked against CCSD(T), and applied to129(2008); http://dx.doi.org/10.1063/1.2973636View Description Hide Description
An approach for the systematic determination of particularly stable hydride compositions of a fullerene is presented. The study is divided into three parts. First, a CCSD(T) benchmark study on benzene and naphthalene hydrogenation is carried out. We show that the TPSS and BP86 functionals give more reliable relative isomer energies and reactionenergies than B3LYP, when compared to CCSD(T) calculations. We therefore recommend BP86 for use on fullerenes. In the second part, a scheme for reduction in the immense number of possible fullerene hydride isomers is proposed. The scheme is based on thermodynamic sampling and involves density functional based tight binding as fast preselection method. The testing of the approach for constitutes the last part of the study. A low energy pathway for production is determined. Particularly stable structures are identified through analysis of the reactionenergies along this pathway. These are with , 30, and 36. The good agreement of these results with the experimental and previous theoretical data suggests that our method is reliable and can be used to study fullerene hydrogenation.
Tungsten carbide revisited: New anion photoelectron spectrum and density functional theory calculations129(2008); http://dx.doi.org/10.1063/1.2976342View Description Hide Description
A new anion photoelectron (PE) spectrum of is presented and analyzed using existing and new calculations. This spectrum is different from the PE spectrum previously published [X. Li et al., J. Chem. Phys.111, 2464 (1999)], which we suggest was actually the PE spectrum of . The ground anion state is determined by calculations and comparison with spectral features to be the state. The transition is observed at an electron binding energy of , which corresponds to the adiabatic electron affinity of WC. The bond length of the anion is determined to be . A number of spectral assignments corresponding to both excited anion and neutral states are made based on previously obtained fluorescence spectra [S. M. Sickafoose et al., J. Chem. Phys.116, 993 (2002)] and density functional theory calculations.
Vacuum ultraviolet pulsed field ionization-photoelectron and infrared-photoinduced Rydberg ionization study of trans-1,3-butadiene129(2008); http://dx.doi.org/10.1063/1.2973635View Description Hide Description
The vacuum ultraviolet (VUV) laser pulsed field ionization-photoelectron (PFI-PE) spectrum of trans-1,3-butadiene (trans-) has been measured in the region of above its ionization energy (IE) to probe the vibrational modes of trans-. The high-frequency vibrational modes (, 22, and 23) of trans- have also been probed by the VUV-infrared-photoinduced Rydbergionization (VUV-IR-PIRI) measurement. On the basis of the semiempirical simulation of the origin VUV-PFI-PE band, the IE(trans-) is determined to be . This value has been used to benchmark the state-of-the-art theoretical IE prediction based on the CCSD(T,Full)/CBS procedures, the calculation of which is reported in the present study. The vibrational bands observed in the VUV-PFI-PE and VUV-IR-PIRI spectra were assigned based on ab initio anharmonic vibrational frequencies and Franck–Condon factor calculations for the photoionization transitions. Combining the VUV-PFI-PE and VUV-IR-PIRI measurements, 17 fundamental vibrational frequencies of trans- have been determined, including , , , , , , , , , , , , , , , , and .
129(2008); http://dx.doi.org/10.1063/1.2978172View Description Hide Description
Using variational Monte Carlo and simple explicitly correlated fully nonadiabaticwavefunctions we have computed the energy and 29 properties of the lowest rovibrational state of all the isotopomers. Our results are in very good agreement with previous calculations on these systems.
129(2008); http://dx.doi.org/10.1063/1.2976772View Description Hide Description
We have measured the IR spectrum of the acetylene-furan complex in ultracold heliumnanodroplets in the region of the -stretch vibration of the acetylene (between 3240 and ). We have observed eight bands that can be attributed to acetylene-furan complexes. Two of these bands are assigned to two different isomers of the 1:1 acetylene-furan complex. The vibrational band at is assigned to the -stretch vibration of the dimer structure with the C–H of the acetylene being attached to the -system of the furan. The peak at is assigned to the -stretch vibration of the dimer structure with the C–H of the acetylene being attached to the oxygen atom of the furan. These assignments are confirmed by additional measurements of the spectrum of the -acetylene-furan complex.
129(2008); http://dx.doi.org/10.1063/1.2973637View Description Hide Description
The reaction (2) is of crucial importance for sulfuric acid formation in the atmosphere, and reliable thermochemical data are required for an adequate modeling. The currently least well known thermochemical quantity of reaction (2) is the enthalpy of formation of the hydroxysulfonyl radical . We report on high-level quantum chemical calculations to predict the binding energy of the bond and deduce a value for the enthalpy of formation of using the most reliable thermodynamic data of OH and . On the basis of anharmonic vibrational frequencies from calculations at the level of theory, the enthalpy of reaction at 0 K for the reaction(1) was computed to be and the thermal corrections result in . From these values, we obtain and , respectively. Accordingly, and .
Dynamics and mechanism of the , , , , and nonadiabatic transitions induced in molecular iodine by collisions with and molecules129(2008); http://dx.doi.org/10.1063/1.2978170View Description Hide Description
Nonadiabatictransitions among the first-tier ion-pair states of the iodine molecule in collisions with and partners are investigated by detecting the luminescence following the optical-optical double resonance excitation of the -state to the vibrational levels , 13, and 19. Total and partial rate constants, as well as vibrational product state distributions, are determined. It is found that electronic energy transfer in all channels is predominantly assisted by excitation of the dipole-allowed and modes of the partner. The measurements are accompanied by quantum scattering calculations that implement a close coupling treatment for the electronic and vibrational degrees of freedom and combine diatomics-in-molecule and long-range models for diabatic potential energy surfaces and coupling matrix elements. The analysis of experimental and theoretical data shows that the transitions without excitation of the partner are due to short-range couplings, whereas the vibrational excitation of the partner in the channel originates from the long-range coupling of two transitiondipole moments: electronic of the iodine molecule and vibrational of the partner. Unexpectedly efficient excitations of the partner in the other ion-pair states, which are not coupled to the initial -state by the transition dipole, are interpreted within the postcollision mechanism. Qualitatively, this implies that during a single collision the long-range nonadiabatictransitions to , and , channels are followed by secondary short-range transitions without changing the state of the partner.
- Condensed Phase Dynamics, Structure, and Thermodynamics: Spectroscopy, Reactions, and Relaxation
129(2008); http://dx.doi.org/10.1063/1.2976765View Description Hide Description
Spectroscopy of alkali-metal complexes on helium droplets (, ) provides the unique opportunity to observe high-spin species, which exhibit prominent spin-orbit (SO) effects. In this work we present laser-induced-fluorescence and magnetic-circular-dichroism (MCD)spectra of the band of and on . For we find a progression of four SO split bands, weakly perturbed by linear vibronic [Jahn–Teller (JT)] coupling. The transition was previously observed and interpreted in terms of linear and quadratic JT effects in the state [J. H. Reho et al., J. Chem. Phys.115, 10265 (2001)]. The structure of the MCDspectrum, however, clearly reveals the importance of SO coupling also for the transition and suggests a different assignment with weak linear JT and nonsignificant quadratic JT coupling. The observed strong -type MCDspectra arise from different populations of the ground-stateZeeman sublevels. Thus a quantitative analysis allows a determination of the spin temperature, and since alkali-metal complexes are situated on the surface of the helium droplet this corresponds to a determination of the surface temperature. Our results from the trimer spectra are consistent with the value of , which is found in the interior of a droplet and which we already confirmed for the surface from the spectra of triplet-state alkali-metal dimers in a previous work.