Volume 124, Issue 10, 14 March 2006
 COMMUNICATIONS


Hydration force between model hydrophilic surfaces: Computer simulations
View Description Hide DescriptionWe performed molecular dynamics simulations to study the interactions between model hydrophilic plates made of carbon atoms distributed on a hexagonal lattice. Although neutral, the plates carry equal amounts of positive and negative charges to represent physical dipoles. Using the thermodynamic perturbation theory we calculated the potential of mean force (PMF) acting between the plates as a function of the distance between these plates. We observed that, at distances when more than one water layer can be found between the plates, the contribution of water into the PMF can be either attractive or repulsive depending on the correlation between the charges situated on the plates.

Bonding and excitation in from a cluster model and density functional treatments
View Description Hide DescriptionThe bonding properties and charge distributions of the system have been studied within density functional theory(DFT) with several density functionals. A three layer cluster was found to give bond distances and energies in agreement with previous experimental and theoretical results for low coverage systems, provided the atomic basis set includes diffuse orbitals and orbitals at the Cu atoms. Charge distributions give insight on the nature of the localized adsorbate bonding. Timedependent DFT results on excitation energies and on transition and average electric dipoles, relevant to photodesorption, are also presented.
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 ARTICLES

 Theoretical Methods and Algorithms

Towards a force field based on density fitting
View Description Hide DescriptionTotal intermolecular interactionenergies are determined with a first version of the Gaussian electrostatic model (GEM0), a force field based on a density fitting approach using type Gaussian functions. The total interactionenergy is computed in the spirit of the sum of interacting fragment ab initio (SIBFA) force field by separately evaluating each one of its components: electrostatic (Coulomb), exchange repulsion, polarization, and charge transferintermolecular interactionenergies, in order to reproduce reference constrained space orbital variation (CSOV) energy decomposition calculations at the B3LYP/augccpVTZ level. The use of an auxiliary basis set restricted to spherical Gaussian functions facilitates the rotation of the fitted densities of rigid fragments and enables a fast and accurate density fitting evaluation of Coulomb and exchangerepulsion energy, the latter using the overlap model introduced by Wheatley and Price [Mol. Phys.69, 50718 (1990)]. The SIBFA energy scheme for polarization and charge transfer has been implemented using the electric fields and electrostatic potentials generated by the fitted densities. GEM0 has been tested on ten stationary points of the water dimer potential energy surface and on three waterclusters. The results show very good agreement with density functional theory calculations, reproducing the individual CSOV energy contributions for a given interaction as well as the B3LYP total interactionenergies with errors below at room temperature. Preliminary results for Coulomb and exchangerepulsion energies of metal cation complexes and coupled cluster singles doubles electron densities are discussed.

Configurational constant pressure molecular dynamics
View Description Hide DescriptionWe propose two new algorithms for generating isothermalisobaric molecular dynamics. The algorithms are based on an extended phase space dynamics where two extra degrees of freedom, representing the thermostat and the barostat, are included. These new methods adopt a totally different approach towards molecular dynamics simulation in the isothermalisobaric ensemble. They are fully configurational in the sense that only the particle positions are required in the control of the system temperature and pressure. Following on from the works of Delhommelle and Evans [Mol. Phys., 99, 1825 (2001)] and of Braga and Travis [J. Chem. Phys., 123, 134101 (2005)] concerning configurational canonical dynamics, these new algorithms can be seen as a natural extension to the isothermalisobaric ensemble. We have validated both of our new configurational isothermalisobaric schemes by conducting molecular dynamics simulations of a LennardJones fluid and comparing the static and dynamicproperties for a single state point. We find that both schemes generate similar results compared with schemes which use kinetic temperature and pressure control. We have also monitored the response of the system to a series of isothermal compressions and isobaric quenches. We find that the configurational schemes performed at least as well as the kinetic based scheme in bringing the system temperature and pressure into line with the set point values of these variables. These new methods will potentially play a significant role in simulations where the calculation of the kinetic temperature and pressure can be problematic. A well known example resides in the field of nonequilibrium simulations where the kinetic temperature and pressure require a knowledge of the streaming velocity of the fluid in order to calculate the true peculiar velocities (or momenta) that enter into their definitions. These are completely avoided by using our configurational thermostats and barostats, since these are independent of momenta. By extending the analysis of Kusnezov et al. [Ann. Phys., 204, 155 (1990)] in order to derive a set of generalized NoséHoover equations of motion which can generate isothermalisobaric dynamics in a number of different ways, we are able to show that both of our new configurational barostats and Hoover’s kinetic isothermalisobaric scheme are special cases of this more general set of equations. This generalization can be very powerful in generating constant pressure dynamics for a variety of systems.

Theoretical studies of transition states by the multioverlap molecular dynamics methods
View Description Hide DescriptionThe multioverlap molecular dynamics method gives a flat probability distribution in the multidimensional dihedralangledistance space, where the dihedralangle distance of a configuration with respect to a reference state gives a measure for structural similarity. Hence, this method realizes a random walk among specific configurations in the multidimensional dihedralangledistance space at a constant temperature and explores widely in the configurational space. We applied the multioverlap molecular dynamics method to a pentapeptide, Metenkephalin, in gas phase as a test system. Comparing the results of this method with those of the conventional canonical and multicanonical algorithms, we demonstrate its effectiveness. Furthermore, from the detailed freeenergy landscape obtained from the results of the multioverlap molecular dynamics simulation, we obtain the transition state between two specific reference configurations of Metenkephalin. We also deduce the transition pathway between the two specific reference configurations.

Kohn’s theory of the insulating state: A quantumchemistry viewpoint
View Description Hide DescriptionThe qualitative difference between insulators and conductors not only manifests itself in the excitation spectra but also—according to Kohn's theory [Phys. Rev.133, A171 (1964)]—in a different organization of the electrons in their ground state: the wave function is localized in insulators and delocalized in conductors. Such localization, however, is hidden in a rather subtle way in the manybody wave function. The theory has been substantially revisited and extended in modern times, invariably within a periodicboundarycondition framework, i.e., ideally addressing an infinite condensed system. Here we show how the localization/delocalization of the manybody wave function shows up when considering either threedimensional clusters of increasing size or quasionedimensional systems (linear polymers, nanotubes, and nanowires) of increasing length, within the ordinary “open” boundary conditions adopted for finite systems. We also show that the theory, when specialized to uncorrelated wave functions, has a very close relationship with Boy's theory of localization [Rev. Mod. Phys.32, 296 (1960)]: the Boys orbitals in the bulk of the sample behave in a qualitatively different way in insulating versus conducting cases.

Simple estimation of absolute free energies for biomolecules
View Description Hide DescriptionOne reason that free energy difference calculations are notoriously difficult in molecular systems is due to insufficient conformational overlap, or similarity, between the two states or systems of interest. The degree of overlap is irrelevant, however, if the absolute free energy of each state can be computed. We present a method for calculating the absolute free energy that employs a simple construction of an exactly computable reference system which possesses high overlap with the state of interest. The approach requires only a physical ensemble of conformations generated via simulation and an auxiliary calculation of approximately equal centralprocessingunit cost. Moreover, the calculations can converge to the correct free energy value even when the physical ensemble is incomplete or improperly distributed. As a “proof of principle,” we use the approach to correctly predict free energies for test systems where the absolute values can be calculated exactly and also to predict the conformational equilibrium for leucine dipeptide in implicit solvent.

The generalized active space concept for the relativistic treatment of electron correlation. III. Largescale configuration interaction and multiconfiguration selfconsistentfield fourcomponent methods with application to
View Description Hide DescriptionWe present an implementation for largescale relativistic electronic structure calculations including spindependent contributions and electron correlation in a fully variational procedure. The modular implementation of the double group configuration interaction (CI) program into a multiconfiguration selfconsistentfield (MCSCF) code allows for the treatment of large CI expansions in both the spinor optimization step and the postMCSCF dynamic electron correlation step. As an illustration of the potential of the new code, we calculate the spectroscopic properties of the molecule where we study the ground state and a few excited states in vertical and adiabatic calculations.

Towards benchmark secondorder correlation energies for large atoms. II. Angular extrapolation problems
View Description Hide DescriptionWe have studied the use of the asymptotic expansions (AEs) for the angular momentum extrapolation (to ) of atomic secondorder MøllerPlesset (MP2) correlation energies of symmetryadapted pairs (SAPs). The AEs have been defined in terms of partial wave (PW) increments to the SAP correlation energies obtained with the finite element MP2 method (FEMMP2), as well as with the variational perturbation method in a Slatertype orbital basis. The method employed to obtain AEs from PW increments is general in the sense that it can be applied to methods other than MP2 and, if modified, to molecular systems. Optimal AEs have been determined for all types of SAPs possible in large atoms using very accurate FEM PW increments up to . The impact of the error of the PW increments on the coefficients of the AEs is computed and taken into account in our procedure. The first AE coefficient is determined to a very high accuracy, whereas the second involves much larger errors. The optimum values for starting the extrapolation procedures are determined and their properties, interesting from the practical point of view, are discussed. It is found that the values of the first AE coefficients obey expressions of the type derived by Kutzelnigg and Morgan [J. Chem. Phys.96, 4484 (1992); 97, 8821(E) (1992)] for Hetype systems in the barenucleus case provided they are modified by fractional factors in the case of triplet and unnatural singlet SAPs. These expressions give extremely accurate values for the first AE coefficient both for the STO and the FEM HartreeFock orbitals. We have compared the performance of our angular momentum extrapolations with those of some of the principal expansion extrapolations performed with correlation consistent basis sets employed in the literature and indicated the main sources of inaccuracy.

Activespace coupledcluster methods through connected quadruple excitations
View Description Hide DescriptionCoupledcluster methods that include just a subset of all connected triple, quadruple, or both excitation amplitudes, according to the ansatz of and Adamowicz coworkers [Int. Rev. Phys. Chem.12, 339 (1993);J. Chem. Phys.99, 1875 (1993);100, 5792 (1994)] and Piecuch et al. [J. Chem. Phys.110, 6103 (1999)], have been implemented into parallel execution programs. They are applicable to closed and openshell species and they take advantage of real Abelian pointgroup symmetry. A symbol manipulation program has been invoked to automate the implementation. These methods have been applied to the singlettriplet separations of five triatomic hydrides (, , , , and ) with consideration of scalar relativistic effects. They have been shown to be remarkably effective with errors arising from the use of a very small subset of higherorder excitations being no more than a few tenths of .

System size and control parameter effects in reverse perturbation nonequilibrium molecular dynamics
View Description Hide DescriptionThe issue of system size effects in the reverse perturbation nonequilibrium molecular dynamics method for determining transport coefficients of fluids is examined for the case of the LennardJones model. It is found that when adequate precautions are observed in obtaining linear temperature or momentum profiles, a 250 atom system is adequate for determining the thermal conductivity and the shear viscosity. Also, a means of determining the uncertainties in the transport coefficients is described. The conclusion is that this method is computationally competitive with other simulation methods for estimating transport coefficients.

On the use of transition matrix methods with extended ensembles
View Description Hide DescriptionDifferent extended ensemble schemes for nonBoltzmann sampling (NBS) of a selected reaction coordinate were formulated so that they employ (i) “variable” sampling window schemes (that include the “successive umbrella sampling” method) to comprehensibly explore the domain and (ii) transitionmatrix methods to iteratively obtain the underlying freeenergy landscape (or “importance” weights) associated with . The connection between “acceptance ratio” and transitionmatrix methods was first established to form the basis of the approach for estimating . The validity and performance of the different NBS schemes were then assessed using as coordinate the configurational energy of the LennardJones fluid. For the cases studied, it was found that the convergence rate in the estimation of is little affected by the use of data from highorder transitions, while it is noticeably improved by the use of a broader window of sampling in the variable window methods. Finally, it is shown how an “elastic” window of sampling can be used to effectively enact (nonuniform) preferential sampling over the domain, and how to stitch the weights from separate onedimensional NBS runs to produce a surface over a twodimensional domain.
 Gas Phase Dynamics and Structure: Spectroscopy, Molecular Interactions, Scattering, and Photochemistry

Large Ramanscattering activities for the lowfrequency modes of substituted benzenes: Induced polarizability and stereospecific ringsubstituent interactions
View Description Hide DescriptionThe large nonresonant Ramanscattering activities of the outofplane bending and torsional modes of monosubstituted benzene analogs are studied by lowfrequency Raman experiments and calculations. Electronic interactions between the orbitals of the substituent and the orbitals of the ring are found to enhance the Raman activities, depending on the substituent and its conformation. In the case of tertbutylbenzene and trimethylphenylsilane , three single bonds which are linked to the atom of the substituent have low rotational barriers around the joint bond. Nearly free rotation of the substituents leads to a significant probability for one of the single bonds to occupy a conformation close to the vertical configuration with respect to the ring at room temperature. The resultant electronic interaction gives rise to the large Raman activities. In contrast, those possessing a single bond in a coplanar (or nearly coplanar) configuration at the most stable equilibrium state, i.e., anisole , thioanisole , and methylaniline , display no prominent Raman bands for the lowfrequency vibrational modes. In these molecules, the conjugation does not take place due to the orthogonal orientation of the orbitals. Strong conformational dependence of the Raman enhancement is clearly obtained for the metastable vertical conformer of thioanisole, for which Raman activities are oneorder magnitude greater than those of the coplanar conformer.

Efficient calculation of low energy statistical rates for gas phase dissociation using umbrella sampling
View Description Hide DescriptionMonte Carlo(MC) simulations can be used to compute microcanonical statistical rates of gas phase dissociationreactions. Unfortunately, the MC approach may suffer from a slow convergence and large statistical errors for energies just above the dissociation threshold. In this work, umbrella sampling is proposed as a device to reduce the statistical error of MCrate constants. The method is tested by computing the classical dissociation rate for the reaction over the range of internal energy. Comparing with other literature methods, it is found that umbrella sampling reduces the computational effort by up to two orders of magnitude when used in conjunction with a careful choice of sampling distributions. The comparison between MCrate constants and classical RiceRamsperbergKassel harmonic theory shows that anharmonicity plays an important role in the dissociation process of the Zundel cation at all energies.

Recombination of ozone via the chaperon mechanism
View Description Hide DescriptionThe recombination of ozone via the chaperon mechanism, i.e., and , is studied by means of classical trajectories and a pairwise additive potential energy surface. The recombination rate coefficient has a strong temperature dependence, which approximately can be described by with . It is negligible for temperatures above 700 K or so, but it becomes important for low temperatures. The calculations unambiguously affirm the conclusions of Hippler et al. [J. Chem. Phys.93, 6560 (1990)] and Luther et al. [Phys. Chem. Chem. Phys.7, 2764 (2005)] that the chaperon mechanism makes a sizable contribution to the recombination of at room temperature and below. The dependence of the chaperon recombination rate coefficient on the isotopomer, studied for two different isotope combinations, is only in rough qualitative agreement with the experimental data. The oxygen atom isotopeexchange reaction involving ArO and van der Waals complexes is also investigated; the weak binding of O or to Ar has only a small effect.

Quenching of rotationally excited CO by collisions with
View Description Hide DescriptionQuantum closecoupling and coupledstates approximation scattering calculations of rotational energy transfer in CO due to collisions with are presented for collisionenergies between and using the interaction potentials of Jankowski and Szalewicz [J. Chem. Phys.123, 104301 (2005); 108, 3554 (1998)]. Statetostate cross sections and rate coefficients are reported for the quenching of CO initially in rotational levels by collisions with both para and ortho. Comparison with the available theoretical and experimental results shows good agreement, but some discrepancies with previous calculations using the earlier potential remain. Interestingly, elastic and inelastic cross sections for the quenching of CO by para reveal significant differences at low collisionenergies. The differences in the well depths of the van der Waals interactions of the two potential surfaces lead to different resonance structures in the cross sections. In particular, the presence of a nearzeroenergy resonance for the earlier potential which has a deeper van der Waals well yields elastic and inelastic cross sections that are about a factor of 5 larger than that for the newer potential at collisionenergies lower than .

Infrared laser spectroscopy of the radical complex stabilized in helium nanodroplets
View Description Hide DescriptionThe and radical complexes have been formed in helium nanodroplets by sequential pickup of a radical and a molecule and have been studied by highresolution infrared laser spectroscopy. The complexes have a hydrogenbonded structure with symmetry, as inferred from the analysis of their rotationally resolved vibrational bands. The rotational constants of the complexes are found to change significantly upon vibrational excitation of the stretch of within the complex, (for ), whereas the rotational constants are found to be 2.9 times smaller than that predicted by theory. The reduction in can be attributed to the effects of helium solvation, whereas the large is found to be a sensitive probe of the vibrational averaging dynamics of such weakly bound systems. The complex has a permanent electric dipole moment of , as measured by Stark spectroscopy. A vibrationvibration resonance is observed to couple the excited stretching vibration of within the complex to the lowerfrequency stretches of the methyl radical. Deuteration of the methyl radical was used to detune these levels from resonance, increasing the lifetime of the complex by a factor of 2. Ab initio calculations for the energies and molecular parameters of the stationary points on the potentialenergy surface are also presented.

Interaction of the early transition metals Sc, Ti, V, and Cr with : An ab initio study
View Description Hide DescriptionThe interaction of the early transition elements , Ti, V, and Cr with has been studied by coupledcluster and multiconfigurational techniques in conjunction with quantitative basis sets. We investigated both triatomic and tetratomic species but focused mainly on highspin linear and Tshaped triatomics. The lowest bound states of , and correlate to the first excited state of the atom, with binding energies of 24, 14, and , respectively. In , the first bound state correlates to the sixth excited state of the Cr atom with . The bond strength of highspin linear tetratomics is twice as large the binding energy of the corresponding linear triatomics, , Ti, V, and Cr.

A study of the radicalradical reaction dynamics of
View Description Hide DescriptionThe radicalradical reaction dynamics of groundstate atomic oxygen with butyl radicals in the gas phase were investigated using highresolution laser spectroscopy in a crossedbeam configuration, together with ab initio theoretical calculations. The radical reactants, and , were produced by the photodissociation of and the supersonic flash pyrolysis of the precursor, azobutane, respectively. A new exothermic channel, , was identified and the nascent rovibrational distributions of the OH products were examined. The population analyses for the two spinorbit states of and showed that the level is described by a bimodal feature composed of low and high rotational components, whereas the and 2 levels exhibit unimodal distributions. No noticeable spinorbit or doublet propensities were observed in any vibrational state. The partitioning ratio of the vibrational populations with respect to the low components of the level was estimated to be , indicating that the nascent internal distributions are highly excited. On the basis of the comparison of the experimental results with the statistical theory, the reaction mechanism at the molecular level can be described in terms of two competing dynamic pathways: the major, direct abstraction process leading to the inversion of the vibrational populations, and the minor, shortlived additioncomplex process responsible for the hot rotational distributions. After considering the reaction exothermicity, the barrier height, and the number of intermediates along the addition reaction pathways on the lowest doublet potential energy surface, the formation of was predicted to be dominant in the addition mechanism.

Probing anisotropic interaction potentials of unsaturated hydrocarbons with metastable atom: Attractivesite preference of direction in and direction in
View Description Hide DescriptionStateresolved collision energy dependence of Penning ionization cross sections of acetylene and ethylene with metastable atoms was observed in a wide collision energy range from . A recently developed discharge nozzle source with a liquid circulator was employed for the measurements in the lowenergy range from . Based on classical trajectory calculations for the energy dependence of the partial ionization cross sections, anisotropic potential energy surfaces for the present systems were obtained by optimizing ab initio model potentials for the chemically related systems and . In the case of , the global minimum was found to be located around the H atom along the molecular axis with a well depth of (ca. ). On the other hand, a dominant attractive well with a depth of (ca. ) was found in the electron region of . These findings were discussed in connection with orbital interactions between molecular orbitals of the target molecules and atomic orbitals of the metastable atom. It is concluded that type unoccupied molecular orbitals of and a type highest occupied molecular orbital of play a significant role for the attractivesite preference of direction in and direction in , respectively.