Volume 131, Issue 22, 14 December 2009

Strain dependence of electronic structures and work functions of both pristine and potassium doped (5,5) (armchair) and (9,0) (zigzag) carbon nanotubes (CNTs) has been thoroughly studied using firstprinciples calculations based on density functional theory. We found that for pristine cases, the uniaxial strain has strong effects on work functions of CNTs, and the responses of work functions of CNT (5,5) and (9,0) to the strain are distinctly different. When the strain changes from −10% to 10%, the work function of the CNT (5,5) increases monotonically from 3.95 to 4.57 eV, and the work function of the (9,0) varies between 4.27 and 5.24 eV in a complicated manner. When coated with potassium, for both CNTs, work functions can be lowered down by more than 2.0 eV, and the strain dependence of work functions changes drastically. Our studies suggested that the combination of chemical coating and tuning of strain may be a powerful tool for controlling work functions of CNTs, which in turn will be useful in future design of CNTbased electronic and fieldemitting devices.
 COMMUNICATIONS


A robust approach to calculate entropy change based on density functional theory in the energy representation
View Description Hide DescriptionWe have developed a new approach to accurately calculate entropy change based on density functional theory in the energy representation. The entropy change was evaluated using the derived equation and energy distributions computed using molecular simulation and reweighting techniques. This approach was applied to a harmonic oscillator, an alanine dipeptide, and a small protein. We found that the results were accurate compared to conventional approaches, such as the quasiharmonic approximation.

Modeling the anisotropic selfassembly of spherical polymergrafted nanoparticles
View Description Hide DescriptionRecent experimental results demonstrated that polymer grafted nanoparticles in solvents display selfassembly behavior similar to the microphase separation of block copolymers and other amphiphiles. We present a meanfieldtheory and complementary computer simulations to shed light on the parametric underpinnings of the experimental observations. Our theory suggests that such selfassembledstructures occur most readily when the nanoparticle size is comparable to the radius of gyration of the polymer brush chains. Much smaller particle sizes are predicted to yield uniform particle dispersions, while larger particles are expected to agglomerate due to phase separation from the solvent. Selected aspects of our theoretical predictions are corroborated by computer simulations.

Controlling the composition of a confined fluid by an electric field
View Description Hide DescriptionStarting from a generic model of a pore/bulk mixture equilibrium, we propose a novel method for modulating the composition of the confined fluid without having to modify the bulk state. To achieve this, two basic mechanisms—sensitivity of the pore filling to the bulk thermodynamic state and electric field effect—are combined. We show by Monte Carlo simulation that the composition can be controlled both in a continuous and in a jumpwise way. Near the bulk demixing instability, we demonstrate a field induced population inversion in the pore. The conditions for the realization of this method should be best met with colloids, but being based on robust and generic mechanisms, it should also be applicable to some molecular fluids.

: A key reaction for interstellar chemistry. New theoretical results and comparison with experiment
View Description Hide DescriptionWe report extensive, fully quantum, timeindependent (TID) calculations of cross sections at low collision energies and rate constants at low temperatures for the reaction, of key importance in the production of molecular oxygen in cold, dark, interstellar clouds and in the chemistry of the Earth’s atmosphere. Our calculations are compared with TID calculations within the shifting approximation, with wavepacket calculations, and with quasiclassical trajectory calculations. The fully quantum TID calculations yield rate constants higher than those from the more approximate methods and are qualitatively consistent with a lowtemperature extrapolation of earlier experimental values but not with the most recent experiments at the lowest temperatures.

Stateselective spectroscopy of water up to its first dissociation limit
View Description Hide DescriptionA joint experimental and firstprinciples quantum chemical study of the vibrationrotation states of the water molecule up to its first dissociation limit is presented. Tripleresonance, quantum stateselective spectroscopy is used to probe the entire ladder of water’s stretching vibrations up to 19 quanta of OH stretch, the last stretching state below dissociation. A new ground statepotential energy surface of water is calculated using a large basis set and an allelectron, multireference configuration interaction procedure, which is augmented by relativistic corrections and fitted to a flexible functional form appropriate for a dissociating system. Variational nuclear motion calculations on this surface are used to give vibrational assignments. A total of 44 new vibrational states and 366 rotationvibration energy levels are characterized; these span the region from 35 508 to above the vibrational ground state.
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 ARTICLES

 Theoretical Methods and Algorithms

Using wavepacket interferometry to monitor the external vibrational control of electronic excitation transfer
View Description Hide DescriptionWe investigate the control of electronic energy transfer in molecular dimers through the preparation of specific vibrational coherences prior to electronic excitation, and its observation by nonlinear wavepacket interferometry (nlWPI). Laserdriven coherent nuclear motion can affect the instantaneous resonance between siteexcited electronic states and thereby influence shorttime electronic excitation transfer (EET). We first illustrate this control mechanism with calculations on a dimer whose constituent monomers undergo harmonic vibrations. We then consider the use of nlWPI experiments to monitor the nuclear dynamics accompanying EET in general dimer complexes following impulsive vibrational excitation by a subresonant control pulse (or control pulse sequence). In measurements of this kind, two pairs of polarized phaserelated femtosecond pulses following the control pulse generate superpositions of coherent nuclear wave packets in optically accessible electronic states. Interference contributions to the time and frequencyintegrated fluorescence signals due to overlaps among the superposed wave packets provide amplitudelevel information on the nuclear and electronic dynamics. We derive the basic expression for a controlpulsedependent nlWPI signal. The electronic transition moments of the constituent monomers are assumed to have a fixed relative orientation, while the overall orientation of the complex is distributed isotropically. We include the limiting case of coincident arrival by pulses within each phaserelated pair in which controlinfluenced nlWPI reduces to a fluorescencedetected pumpprobe difference experiment. Numerical calculations of pumpprobe signals based on these theoretical expressions are presented in the following paper [J. D. Biggs and J. A. Cina, J. Chem. Phys.131, 224302 (2009)].

Quantum algorithm for molecular properties and geometry optimization
View Description Hide DescriptionQuantum computers, if available, could substantially accelerate quantum simulations. We extend this result to show that the computation of molecular properties (energy derivatives) could also be sped up using quantum computers. We provide a quantum algorithm for the numerical evaluation of molecular properties, whose time cost is a constant multiple of the time needed to compute the molecular energy, regardless of the size of the system. Molecular properties computed with the proposed approach could also be used for the optimization of molecular geometries or other properties. For that purpose, we discuss the benefits of quantum techniques for Newton’s method and Householder methods. Finally, global minima for the proposed optimizations can be found using the quantum basin hopper algorithm, which offers an additional quadratic reduction in cost over classical multistart techniques.

Accurate yet feasible postHartree–Fock computation of magnetic interactions in large biradicals through a combined variational/perturbative approach: Setup and validation
View Description Hide DescriptionWe present a scheme for the calculation of the spinspin coupling term J in diradicals which is quantitatively accurate and computationally cheap. The method exploits the use of modified virtual orbitals and perturbation theory, incorporated in a multireference configuration interaction approach. The results obtained for model diradical species which exhibit ferromagnetic and antiferromagnetic coupling are fully satisfactory and very promising for future applications of the method to larger molecular systems of technological interest in magneticbased devices.

Density functional method including weak interactions: Dispersion coefficients based on the local response approximation
View Description Hide DescriptionA new method to calculate the atomatom dispersion coefficients in a molecule is proposed for the use in density functional theory with dispersion (DFTD) correction. The method is based on the local response approximation due to Dobson and Dinte [Phys. Rev. Lett.76, 1780 (1996)], with modified dielectric model recently proposed by Vydrov and van Voorhis [J. Chem. Phys.130, 104105 (2009)]. The local response model is used to calculate the distributed multipole polarizabilities of atoms in a molecule, from which the dispersion coefficients are obtained by an explicit frequency integral of the Casimir–Polder type. Thus obtained atomic polarizabilities are also used in the damping function for the shortrange singularity. Unlike empirical DFTD methods, the local response dispersion (LRD) method is able to calculate the dispersion energy from the groundstate electron density only. It is applicable to any geometry, free from physical constants such as van der Waals radii or atomic polarizabilities, and computationally very efficient. The LRD method combined with the longrange corrected DFT functional (LCBOP) is applied to calculations of S22 weakly bound complex set [Phys. Chem. Chem. Phys.8, 1985 (2006)]. Binding energies obtained by the agree remarkably well with ab initio references.

Exact Kohn–Sham potential of strongly correlated finite systems
View Description Hide DescriptionThe dissociation of molecules, even the most simple hydrogen molecule, cannot be described accurately within density functional theory because none of the currently available functionals accounts for strong onsite correlation. This problem led to a discussion of properties that the local Kohn–Sham potential has to satisfy in order to correctly describe strongly correlated systems. We derive an analytic expression for the nontrivial form of the Kohn–Sham potential in between the two fragments for the dissociation of a single bond. We show that the numerical calculations for a onedimensional twoelectron model system indeed approach and reach this limit. It is shown that the functional form of the potential is universal, i.e., independent of the details of the two fragments.

Calculations of rovibrational energies and dipole transition intensities for polyatomic molecules using MULTIMODE
View Description Hide DescriptionWe report rigorous calculations of rovibrational energies and dipole transition intensities for three molecules using a new version of the code MULTIMODE. The key features of this code which permit, for the first time, such calculations for moderately sized but otherwise general polyatomic molecules are briefly described. Calculations for the triatomic molecule are done to validate the code. New calculations for and are reported; these make use of semiempirical potentials but ab initiodipole momentsurfaces. The new dipole surface for is a fulldimensional fit to the dipole moment obtained with the coupledcluster with single and double excitations and a perturbative treatment of triple excitations method with the augmented correlation consistent triple zeta basis set. Detailed comparisons are made with experimental results from a fit to relative data for and absolute intensities from the HITRAN database for .

Gaussian approximation for the structure function in semiclassical forwardbackward initial value representations of time correlation functions
View Description Hide DescriptionInitial value representations (IVRs) of semiclassical (SC) theory provide a general approach for adding quantum mechanical effects to classical molecular dynamics simulations of large molecular systems. Of the various versions of SCIVR methodology for evaluating time correlation functions, the Fourier transform forwardbackward (FB) approach is the simplest one that is able to describe true quantum coherenceeffects, so it is of considerable importance to find efficient and systematic ways for implementing it. It is shown in this paper that a Gaussian approximation for the “structure function”—the dependence of the correlation function on the (typically) momentum jump parameter—provides an efficient and accurate way for doing so. The approach is illustrated by an application to the timedependent radial distribution function of (after photoexcitation) in a cluster of (up to 16) argon atoms.

Dispersion phenomena in helical flow in a concentric annulus
View Description Hide DescriptionWe examined dispersion phenomena of solutes in helical flow in a concentric annulus through a multiscale approach. The helical flow was developed by the combination of the Poiseuille flow and Couette flow. Here, we present an analytic model that can address the multidimensional Taylor dispersion in the helical flow under a lateral field of thermophoresis (or thermal diffusion) in the gapwise direction. Macroscopic parameters including the average solute velocity and dispersivity were analyzed using relevant microscopic physicochemical properties. The mathematically obtained results were validated by the numerical simulation carried out in this study. The findings show that macrotransport processes are robust and straightforward to handle multidimensional dispersion phenomena of solutes in helical flow. This study is expected to provide a theoretical platform for applications of helical flow such as tube exchangers, oil drilling, and multidimensional field flow fractionations (e.g., helical flow field flow fractionation).

Multiconfigurational timedependent Hartree calculations for tunneling splittings of vibrational states: Theoretical considerations and application to malonaldehyde
View Description Hide DescriptionFulldimensional multiconfigurational timedependent Hartree calculations on the tunneling splitting of the vibrational ground state and the low lying excited states of malonaldehyde are presented. Methodological developments utilizing the symmetry of double well systems for the efficient calculation of tunneling splittings are described and discussed. Important aspects of the theory underlying the previously communicated results for the ground statetunneling splitting [M. D. CoutinhoNeto et al., J. Chem. Phys.121, 9207 (2004)] are detailed and further developments facilitating the calculation of tunneling splittings for vibrationally excited states are introduced. Utilizing these developments, the 14 lowest vibrational states of malonaldehyde, i.e., seven tunneling splittings, have been computed. The tunneling splittings are found to vary significantly depending on the particular vibrational excitation. This results in a complex pattern of vibrational levels. Studying the dependence of the tunneling splittings on the vibrational excitation, good agreement with available experimental results is found and intuitive interpretations of the results can be given.

Onedimensional description of diffusion in a tube of abruptly changing diameter: Boundary homogenization based approach
View Description Hide DescriptionReduction of threedimensional (3D) description of diffusion in a tube of variable cross section to an approximate onedimensional (1D) description has been studied in detail previously only in tubes of slowly varying diameter. Here we discuss an effective 1D description in the opposite limiting case when the tube diameter changes abruptly, i.e., in a tube composed of any number of cylindrical sections of different diameters. The key step of our approach is an approximate description of the particle transitions between the wide and narrow parts of the tube as trapping by partially absorbing boundaries with appropriately chosen trapping rates. Boundary homogenization is used to determine the trapping rate for transitions from the wide part of the tube to the narrow one. This trapping rate is then used in combination with the condition of detailed balance to find the trapping rate for transitions in the opposite direction, from the narrow part of the tube to the wide one. Comparison with numerical solution of the 3D diffusionequation allows us to test the approximate 1D description and to establish the conditions of its applicability. We find that suggested 1D description works quite well when the wide part of the tube is not too short, whereas the length of the narrow part can be arbitrary. Taking advantage of this description in the problem of escape of diffusing particle from a cylindrical cavity through a cylindrical tunnel we can lift restricting assumptions accepted in earlier theories: We can consider the particle motion in the tunnel and in the cavity on an equal footing, i.e., we can relax the assumption of fast intracavity relaxation used in all earlier theories. As a consequence, the dependence of the escape kinetics on the particle initial position in the system can be analyzed. Moreover, using the 1D description we can analyze the escape kinetics at an arbitrary tunnel radius, whereas all earlier theories are based on the assumption that the tunnel is narrow.

Approximate inclusion of quantum effects in transition path sampling
View Description Hide DescriptionWe propose a method for incorporating nuclear quantum effects in transition path sampling studies of systems that consist of a few degrees of freedom that must be treated quantum mechanically, while the rest are classicallike. We used the normal mode centroid method to describe the quantum subsystem, which is a method that is not CPU intensive but still reasonably accurate. We applied this mixed centroid/classical transition path sampling method to a model system that has nontrivial quantum behavior, and showed that it can capture the correct quantum dynamical features.

Estimating diffusivity along a reaction coordinate in the high friction limit: Insights on pulse times in laserinduced nucleation
View Description Hide DescriptionIn the high friction limit of Kramers’ theory, the diffusion coefficient for motion along the reaction coordinate is a crucial parameter in determining reaction rates from mean first passage times. The Einstein relation between mean squared displacement, time, and diffusivity is inaccurate at short times because of ballistic motion and inaccurate at long times because trajectories drift away from maxima in the potential of mean force. Starting from the Smoluchowski equation for a downward parabolic barrier, we show how drift induced by the potential of mean force can be included in estimating the diffusivity. A modified relation between mean squared displacement, time, and diffusivity now also includes a dependence on the barrier curvature. The new relation provides the diffusivity at the top of the barrier from a linear regression that is analogous to the procedure commonly used with Einstein's relation. The new approach has particular advantages over previous approaches when evaluations of the reaction coordinate are costly or when the reaction coordinate cannot be differentiated to compute restraining forces or velocities. We use the new method to study the dynamics of barrier crossing in a Potts lattice gas model of nucleation from solution. Our analysis shows that some current hypotheses about laserinduced nucleation mechanisms lead to a nonzero threshold laser pulse duration below which a laser pulse will not affect nucleation. We therefore propose experiments that might be used to test these hypotheses.
 Gas Phase Dynamics and Structure: Spectroscopy, Molecular Interactions, Scattering, and Photochemistry

How long are the ends of polyene chains?
View Description Hide DescriptionIn this work we study conjugation in alltrans polyene chains with a view to establishing the length scale for the interaction between conjugated double bonds. As a polyene oligomer is made longer, bond length alternation between formal carboncarbon single and double bonds diminishes toward the middle of the chain, eventually reaching a constant value characteristic of an “infinite” chain. However those bonds near the end of the chain continue to be influenced by the end, even in the longchain limit. We have determined optimized geometries for polyene oligomers with up to repeat units at the MP2/ccpVTZ level. At this length the centralmost bonds are almost converged to the long chain limit, for which we estimate and . In contrast, the endmost double bond has a length of and the endmost single bond has a length of . We find that a given bond is significantly influenced by conjugation paths through up to six neighboring conjugated double bonds. End effects can also be monitored by examining the energy increment per added monomer as the oligomer length is increased. This analysis also indicates that significant conjugation effects extend out through approximately six neighboring double bonds. From the energy per monomer of the longest chains we extract a value of about 8 kcal/mol for the extra stabilization energy per monomer due to conjugation in long chains.

Calculations of nonlinear wavepacket interferometry signals in the pumpprobe limit as tests for vibrational control over electronic excitation transfer
View Description Hide DescriptionThe preceding paper [J. D. Biggs and J. A. Cina, J. Chem. Phys.131, 224101 (2009)] (referred to here as Paper 1), describes a strategy for externally influencing the course of shorttime electronic excitation transfer (EET) in molecular dimers and observing the process by nonlinear wavepacket interferometry (nlWPI). External influence can, for example, be exerted by inducing coherent intramolecular vibration in one of the chromophores prior to shortpulse electronic excitation of the other. Within a sample of isotropically oriented dimers having a specified internal geometry, a vibrational mode internal to the acceptor chromophore can be preferentially driven by electronically nonresonant impulsive stimulated Raman (or resonant infrared) excitation with a short polarized “control” pulse. A subsequent electronically resonant polarized pump then preferentially excites the donor, and EET ensues. Paper 1 investigates controlpulseinfluenced nlWPI as a tool for the spectroscopic evaluation of the effect of coherent molecular vibration on excitation transfer, presenting general expressions for the nlWPI difference signal from a dimer following the action of a control pulse of arbitrary polarization and shape. Electronic excitation is to be effected and its interchromophore transfer monitored by resonant pump and probe “pulses,” respectively, each consisting of an opticalphasecontrolled ultrashort pulsepair having arbitrary polarization, duration, center frequency, and other characteristics. Here we test both the control strategy and its spectroscopic investigation—with some sacrifice of amplitudelevel detail—by calculating the pumpprobe difference signal. That signal is the limiting case of the controlinfluenced nlWPI signal in which the two pulses in the pump pulsepair coincide, as do the two pulses in the probe pulsepair. We present calculated pumpprobe difference signals for (1) a model excitationtransfer complex in which two equalenergy monomers each support one moderately Franck–Condon active intramolecular vibration; (2) a simplified model of the covalent dimer dithiaanthracenophane, representing its EET dynamics following selective impulsive excitation of the weakly Franck–Condon active anthracene vibration at ; and (3) a model complex featuring moderate electronicvibrational coupling in which the site energy of the acceptor chromophore is lower than that of the donor.

Rotational effects in complexforming bimolecular substitution reactions: A quantummechanical approach
View Description Hide DescriptionThe quantum dynamics of the complexforming reaction is studied with emphasis on rotational effects. The pseudotriatomic system ClMeBr is treated with a corresponding threedimensional (3D) potential energy surface as a function of the two scattering coordinates and the enclosed angle where the geometry of the methyl group Me is optimized at each point. The 3D space is divided into three different parts, the interaction region, an intermediate region, and the asymptotic region. In line with simple classicalmechanical arguments and previous classical trajectory calculations, initial rotational motion of seemingly decreases the reaction probability. However, the dynamical inclusion of the rotational degree of freedom and the presence of the many rovibrational product states overall lead to a large increase in reactivity compared to our previous collinear study on this reaction. If the reactant is rotationally excited, the higher vibrational product states are depleted in favor of lowerlying levels. Starting the reaction with rotationless reactants may end up in significant rotational excitation in the product molecules (translationtorotation energy transfer). On the other hand, initial rotational energy in rotationally highly excited reactants is to a large amount converted into translational and vibrational energy. The average amount of rotational energy in the products shows a twofold vibrational excitationindependent saturation (i.e., memorylessness), with respect to both initial rotational excitation and translational energy. Since only about onehalf of all reactant states end in rotationless products, the reaction probability should be increased by a factor of 2; the actually larger reactivity points to other dynamical effects that play an important role in the reaction.