Volume 124, Issue 11, 21 March 2006
 COMMUNICATIONS


Structural changes of an octanethiol monolayer via hyperthermal raregas collisions
View Description Hide DescriptionIn situscanning tunneling microscopy is used to measure the effect of hyperthermal raregas bombardment on octanethiol selfassembledmonolayers. Closepacked monolayers remain largely unchanged, even after repeated collisions with argon and xenon atoms. In contrast, gassurface collisions do induce structural changes in the octanethiol film near defects, domain boundaries, and disordered regions, with relatively larger changes observed for xenonatom bombardment.
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 ARTICLES

 Theoretical Methods and Algorithms

Highorder correlation effects on dynamic hyperpolarizabilities and their geometric derivatives: A comparison with density functional results
View Description Hide DescriptionSecond harmonic generation hyperpolarizabilities and their geometric derivatives have been calculated for HF, HCl, CO, and LiF, using the coupled cluster hierarchies, CCS, CC2, CCSD, CC3, and large correlationconsistentbasis sets. The full configuration interaction results have been used to test the accuracy of the coupled cluster results. The CCS and CC2 methods do not improve on the HartreeFock results while CCSD is robust and gives significant improvements compared to CCS and CC2. The effects of triples in CC3 are in some cases substantial. Higher order correlation effects are significant for LiF. Including corevalence correlation effects is required only if high accuracy is desired. The coupled cluster results have been used as benchmarks for the results obtained by means of density functional theory using various exchangecorrelation functionals. For the hyperpolarizability B3LYP was found to perform best, i.e., to give the results closest to the CC3 ones, while for the geometric derivatives none of the considered functionals was able to give a consistent description for all the considered molecules.

Improved density of states Monte Carlo method based on recycling of rejected states
View Description Hide DescriptionIn this paper a new algorithm is presented that improves the efficiency of Wang and Landau algorithm or density of states (DOS) Monte Carlo simulations by employing rejected states. The algorithm is shown to have a performance superior to that of the original WangLandau [F. Wang and D. P. Landau, Phys. Rev. Lett.86, 2050 (2001)] algorithm and the more recent configurational temperature DOS algorithm. The performance of the method is illustrated in the context of results for the LennardJones fluid.

Timedependent barrier passage of a nonOhmic damping system
View Description Hide DescriptionWe consider a particle passing over the saddle point of an inverse harmonic potential, which is described by a generalized Langevin equation with a nonOhmic damping of power exponent . The timedependent passing probability and transmission coefficient are obtained analytically by using the reaction flux method. It is shown that the overshooting phenomenon for the passing probability appears in the regime and the backflow recrossing over the saddle point is observed, where a nonmonotonous time dependence of the passage probability is detected. The long memory aspect of friction is at the origin of this behavior. Thus the steady transmission coefficient is also a nonmonotonous function of .

The correlation consistent composite approach (ccCA): An alternative to the Gaussian methods
View Description Hide DescriptionAn alternative to the Gaussian (G1, G2, and G3) composite methods of computing molecular energies is proposed and is named the “correlation consistent composite approach” (ccCA, ccCACBS1, ccCACBS2). This approach uses the correlation consistent polarized valence (ccpVZ) basis sets. The G21 test set of 48 enthalpies of formation, 38 adiabatic ionization potentials (IPs), 25 adiabatic electron affinities (EAs), and 8 adiabatic proton affinities (PAs) are computed using this approach, as well as the values of 30 more systems. Equilibrium molecular geometries and vibrational frequencies are obtained using B3LYP density functional theory. When applying the ccCACBS method with the ccpVZ series of basis sets augmented with diffuse functions, mean absolute deviations within the G21 test set compared to experiment are for for IPs, for EAs, and for PAs, without including the “highlevel correction” (HLC) contained in the original methods. Whereas the HLC originated in the Gaussian1 method as an isogyric correction, it evolved into a fitted parameter that minimized the error of the composite methods, eliminating its physical meaning. Recomputing the G1 and G3 enthalpies of formation without the HLC reveals a systematic trend where most values are significantly higher than experimental values. By extrapolating electronic energies to the complete basis set (CBS) limit and adding G3like corrections for the corevalence and infiniteorder electron correlationeffects, ccCACBS2 often underestimates the experimental , especially for larger systems. This is desired as inclusion of relativistic and atomic spinorbit effects subsequently improves theoretical values to give a mean absolute deviation with ccCACBS2. The ccCACBS method is a viable “black box” method that can be used on systems with at least 10–15 heavy atoms.

Quantum modeling of transient infrared spectra reflecting photoinduced electrontransfer dynamics
View Description Hide DescriptionA theoretical description of transient vibrational spectra following the impulsive optical excitation of a molecular system is presented. The approach combines the nonsecular evaluation of the Redfield equations to describe the dissipative dynamics of the system with an efficient implementation of the doorwaywindow formalism to calculate optical pump/infrared probe (vis/IR) spectra. Both parts of the calculation scale with , thus facilitating the treatment of systems with a dimension up to . The formulation is applied to a simple model of photoinduced electron transfer, which takes into account two coupled electronic states and a single anharmonic vibrational mode. Despite its simplicity, the model is found to exhibit quite complex electronic and vibrational relaxation dynamics, which in turn give rise to rather complex time and frequencyresolved vis/IR spectra. Interestingly, the calculated IR spectra of the electrontransfer system predict the appearance of novel vibronically induced sidebands, which may even dominate the spectrum at early times.

Evaluation of lowscaling methods for calculation of phosphorescence parameters
View Description Hide DescriptionIn order to find a methodology that is a compromise between favorable computational scaling and tolerable errors, a series of nonrelativistic approaches for the calculation of radiative phosphorescence lifetimes are benchmarked against fully relativistic fourcomponent results. The study of the transition intensity in the series of molecules, where is a chalcogene atom, , indicates a general good agreement between fully relativistic fourcomponent and nonrelativistic perturbationtheoretical calculations. Among the nonrelativistic approaches, the scaledcharge spinorbit operator approach is recognized as to provide transition matrix elements that are in good agreement with those obtained with the more elaborate BreitPauli and atomic mean field spinorbit operators. This finding supports phosphorescence calculations using the available linear scaling technology for large complexes and, together with effectivecore potentials, large complexes including heavy elements.

Secondorder correction to perfect pairing: An inexpensive electronic structure method for the treatment of strong electronelectron correlations
View Description Hide DescriptionWe have formulated a secondorder perturbative correction for perfectpairing wave functions [PP(2)] based on similaritytransformed perturbation techniques in coupled clustertheory. The perfectpairing approximation is used to obtain a simple reference wave function which can qualitatively describe bond breaking, diradicals, and other highly correlated systems, and the perturbative correction accounts for the dynamical correlation. An efficient implementation of this correction using the resolution of the identity approximation enables PP(2) to be computed at a cost only a few times larger than that of canonical MP2 for systems with hundreds of active electrons and tens of heavy atoms. PP(2) significantly improves on MP2 predictions in various systems with a challenging electronic structure.

Twophoton absorption cross sections: An investigation of the accuracy of calculated absolute and relative values
View Description Hide DescriptionWe have studied the basis set and electron correlation effects on the ab initio calculations of twophoton absorption cross sections of water. Various series of correlation consistent basis sets up to triply augmented basis sets of valence pentuple level as well as the popular basis set have been employed in combination with several coupled cluster, configuration interaction, and density functional theory methods. We find that it is very difficult to obtain converged values of the cross sections for even a small molecule such as water. Acknowledging these difficulties in obtaining a fully converged cross section for a given state, we also investigated the possibility of determining relative cross sections for a series of organic molecules. However, we did not find consistency between the relative cross sections calculated at the HartreeFock level and several coupledcluster methods using the and augccpVDZ basis sets. However, we could reproduce the relative ordering of the twophoton absorption cross sections of the molecules studied at the HartreeFock level.

Temporal asymmetry of fluctuations in nonequilibrium steady states
View Description Hide DescriptionTemporal asymmetries of fluctuation paths in nonequilibrium microscopic shearing systems are observed for the first time. Inspired by theories that predict asymmetry of fluctuation paths in stochastic dynamics, we focus on deterministic reversible particle models, which represent a small part of a macroscopic system. We have monitored and measured the asymmetry of the fluctuation paths of various observables as they go away from and towards the mean. The understanding of such asymmetries may scatter light on how irreversibility emerges from the microscopic reversible dynamics and on the behavior of mesoscopic (nanoscale) systems.

Implementation of quantum gate operations in molecules with weak laser fields
View Description Hide DescriptionWe numerically propose a way to perform quantum computations by combining an ensemble of molecular states and weak laser pulses. A logical input state is expressed as a superposition state (a wave packet) of molecular states, which is initially prepared by a designed femtosecond laser pulse. The free propagation of the wave packet for a specified time interval leads to the specified change in the relative phases among the molecular basis states, which corresponds to a computational result. The computational results are retrieved by means of quantum interferometry. Numerical tests are implemented in the vibrational states of the state of employing controlledNOT gate, and 2 and Fourier transforms. All the steps involved in the computational scheme, i.e., the initial preparation, gate operation, and detection steps, are achieved with extremely high precision.

The invariant constrained equilibrium edge preimage curve method for the dimension reduction of chemical kinetics
View Description Hide DescriptionThis work addresses the construction and use of lowdimensional invariant manifolds to simplify complex chemical kinetics. Typically, chemical kinetic systems have a wide range of time scales. As a consequence, reaction trajectories rapidly approach a hierarchy of attracting manifolds of decreasing dimension in the full composition space. In previous research, several different methods have been proposed to identify these lowdimensional attracting manifolds. Here we propose a new method based on an invariant constrained equilibrium edge (ICE)manifold. This manifold (of dimension ) is generated by the reaction trajectories emanating from its dimensional edge, on which the composition is in a constrained equilibrium state. A reasonable choice of the represented variables (e.g., “major” species) ensures that there exists a unique point on the ICEmanifold corresponding to each realizable value of the represented variables. The process of identifying this point is referred to as species reconstruction. A second contribution of this work is a local method of species reconstruction, called ICEPIC, which is based on the ICEmanifold and uses preimage curves (PICs). The ICEPIC method is local in the sense that species reconstruction can be performed without generating the whole of the manifold (or a significant portion thereof). The ICEPIC method is the first approach that locally determines points on a lowdimensional invariant manifold, and its application to highdimensional chemical systems is straightforward. The “inputs” to the method are the detailed kinetic mechanism and the chosen reduced representation (e.g., some major species). The ICEPIC method is illustrated and demonstrated using an idealized system with six chemical species. It is then tested and compared to three other dimensionreduction methods for the test case of a onedimensional premixed laminar flame of stoichiometric hydrogen/air, which is described by a detailed mechanism containing nine species and 21 reactions. It is shown that the error incurred by the ICEPIC method with four represented species is small across the whole flame, even in the low temperature region.

Electrostatic fieldadapted molecular fractionation with conjugated caps for energy calculations of charged biomolecules
View Description Hide DescriptionAn electrostatic fieldadapted molecular fractionation with conjugated caps (EFAMFCC) approach is implemented for treating macromolecules with several charge centers. The molecular fragmentation is performed in an “electrostatic field,” which is described by putting point charges on charge centers, directly affecting the Hamiltonians of both fragments and conjugated caps. So the present method does not need truncation during the calculation of electrostatic interactions. Our test calculations on a series of charged model systems and biological macromolecules using the HF and B3LYP methods have demonstrated that this approach is capable of describing the electronic structure with accuracy comparable to other fragmentbased methods. The EFAMFCC approach is an alternative way for predicting the total energies of charged macromolecules with acyclic, loop, and intersectional loop structures and interaction energies between two molecules.

Exploring reaction pathways with transition path and umbrella sampling: Application to methyl maltoside
View Description Hide DescriptionThe transition path sampling (TPS) method is a powerful approach to study chemical reactions or transitional properties on complex potential energy landscapes. One of the main advantages of the method over potential of mean force methods is that reaction rates can be directly accessed without knowledge of the exact reaction coordinate. We have investigated the complementary nature of these two differing approaches, comparing transition path sampling with the weighted histogram analysis method to study a conformational change in a small model system. In this case study, the transition paths for a transition between two rotational conformers of a model disaccharide molecule, methyl Dmaltoside, were compared with a free energysurface constrained by the two commonly used glycosidic torsional angles. The TPS method revealed a reaction channel that was not apparent from the potential of mean force method, and the suitability of and as reaction coordinates to describe the isomerization in vacuo was confirmed by examination of the transition path ensemble. Using both transition state theory and transition path sampling methods, the transition rate was estimated. We have estimated a characteristic time between transitions of approximately 160 ns for this rare isomerization event between the two conformations of the carbohydrate. We conclude that transition path sampling can extract subtle information about the dynamics not apparent from the potential of mean force method. However, in calculating the reaction rate, the transition path sampling method required 27.5 times the computational effort than was needed by the potential of mean force method.

Rydberg states with quantum Monte Carlo
View Description Hide DescriptionCalculations on Rydberg states are performed using quantum Monte Carlo methods.Excitation energies and singlettriplet splittings are calculated for two model systems, the carbon atom ( and ) and carbon monoxide ( and ). KohnSham wave functions constructed from openshell localized HartreeFock orbitals are used as trial and guide functions. The fixednode diffusionquantum Monte Carlo (FNDMC) method depends strongly on the wave function’s nodal hypersurface. Nodal artefacts are investigated for the ground state of the carbon atom. Their effect on the FNDMC results can be analyzed quantitatively. FNDMC leads to accurate excitation energies but to less accurate singlettriplet splittings. Variational Monte Carlo calculations are able to reproduce the experimental results for both the excitation energies and the singlettriplet splittings.
 Gas Phase Dynamics and Structure: Spectroscopy, Molecular Interactions, Scattering, and Photochemistry

van der Waals interactions and dipole polarizabilities of lanthanides: –He and –He potentials
View Description Hide DescriptionAnisotropic dipole polarizabilities of , and are calculated using the finitefield multireference averaged quadratic coupled cluster (MRAQCC) (Tm and ) and RCCSD(T) (Yb) methods with smallcore relativistic pseudopotentials ECP28MWB combined with the augmented ANO basis sets. The lanthanide atoms are strongly polarizable with the scalar part originating from the electrons and the tensorial part from the open shells. The adiabatic interaction potentials , and of –He and –He were examined by the multireference approaches, multireference configuration interaction and MR, using the basis sets designed in the polarizability calculations. A closedshell lanthanide system –He was included for comparison. The Tm–He , and interaction potentials are very shallow and nearly degenerate (within ), with the well depths in the range of at . The basisset saturated well depths are expected to be larger by ca. 25%, as estimated using the bondfunction augmented basis set. The interactions of lanthanide atoms with He are one order of magnitude less anisotropic than those involving firstrow transition metal atoms. The suppression of anisotropy is chiefly attributed to the screening effected by the shell. When these electrons are removed as in the dication complex –He, the potentials deepen to a thousand wave number range and their anisotropy is enhanced 500fold.

Femtosecond electronic relaxation of excited metalloporphyrins in the gas phase
View Description Hide DescriptionA systematic study of the ultrafast decay of metalloporphyrins containing various transition metals with partially filled shells and zinc ( filled) is reported here after excitation in the second excited state of the system (Soret band). Both timeofflight mass spectrometry and velocity map imaging have been used for detection. A general biexponential decay with a short time constant is observed for the transition metalporphyrins, followed by a time decay. This evolution is interpreted as a porphyrintometal charge transfer,, followed by a back transfer, , which leads to an excited state localized on the metal. These conclusions stem from the different behaviors of zinc and the transition metalporphyrins. A porphyrintometal charge transfer model is chosen to describe the relaxation mechanism, based upon the fact that transition metalloporphyrins can accept electrons on the metal site, in contrast to zincporphyrins.

Ab initio study of the structure, bonding, vibrational spectra, and energetics of (where , F, and Cl)
View Description Hide DescriptionHigh level ab initio electronic structure calculations at the CCSD(T) level with augmented correlationconsistent basis set extrapolated to complete basis set limit have been performed on and for , F, and Cl. The geometries have been optimized up through the augccpV5Z level and the vibrational frequencies have been calculated with the augccpVQZ basis sets. Analysis of the bonding in and using natural bond orbital analysis shows that the BS bond in is a triple bond, while in it is a double bond. The energetic properties of cation and its first excited state are reported. The calculated adiabatic ionization potential is as compared to the experimental value of for HBS. The adiabatic ionization potentials for FBS and CIBS are and , respectively.

Estimated MP2 and CCSD(T) interaction energies of alkane dimers at the basis set limit: Comparison of the methods of Helgaker et al. and Feller
View Description Hide DescriptionThe MP2 (the secondorder MøllerPlesset calculation) and CCSD(T) (coupled cluster calculation with single and double substitutions with noniterative triple excitations) interaction energies of alltrans alkane dimers were calculated using Dunning's [J. Chem. Phys.90, 1007 (1989)] correlation consistent basis sets. The estimated MP2 interaction energies of methane, ethane, and propane dimers at the basis set limit by the method of Helgaker et al. [J. Chem. Phys.106, 9639 (1997)] from the ( and T) level interaction energies are very close to those estimated from the ( and Q) level interaction energies. The estimated values of butane to heptane dimers from the ( and T) level interaction energies are very close to those from the ( and T) ones. The values estimated by Feller's [J. Chem. Phys.96, 6104 (1992)] method from the (, T, and Q) level interaction energies are close to those estimated by the method of Helgaker et al. from the ( and Q) ones. The estimated values by the method of Helgaker et al. using the ( and T) are close to these values. The estimated of the methane, ethane, propane,butane, pentane, hexane, heptane, octane, nonane, and decane dimers by the method of Helgaker et al. are , , , , , , , , , and , respectively. Effects of electron correlation beyond MP2 are not large. The estimated CCSD(T) interaction energies of the methane, ethane, propane, and butane dimers at the basis set limit by the method of Helgaker et al. (, , , and , respectively) from the ( and T) level interaction energies are close to the obtained using the same basis sets. The estimated values of the ten dimers were fitted to the form ( is 1 for methane, 2 for ethane, etc.). The obtained and (0.595 and ) show that the interactions between long alkane chains are significant. Analysis of basis set effects shows that (, Q, or 5), (, T, Q, or 5) basis set, or basis set augmented with diffuse polarization function is necessary for quantitative evaluation of the interaction energies between alkane chains.

Vibronic spectroscopy of the peroxyacetyl radical in the near IR
View Description Hide DescriptionThe electronic transition of the peroxyacetyl radical (PA) is observed employing NIR/VUV ion enhancement, supersonic jet spectroscopy. Rotational envelope simulations yield a rotational temperature for ground state PA of ca. . Ab initio calculations of transition energies and vibrational frequencies for the transition assist in the assignment of the observed spectrum. A number of the vibrational modes of the state are assigned to observed transitions (the O–O stretch , the COO bend , and the CCOO backbone bend ). The calculations and mass spectra suggest that the ground state of the PA ion is repulsive. An increase in rotational linewidth of the overtone of the O–O stretch is observed and discussed in terms of state dynamics. The O–O stretch anharmonicity is estimated to be .