Volume 134, Issue 8, 28 February 2011

We explore in detail the structural, mechanical, and thermodynamic properties of a coarsegrained model of DNA similar to that recently introduced in a study of DNA nanotweezers [T. E. Ouldridge, A. A. Louis, and J. P. K. Doye, Phys. Rev. Lett.134, 178101 (2010)]. Effective interactions are used to represent chain connectivity, excluded volume, base stacking, and hydrogen bonding, naturally reproducing a range of DNA behavior. The model incorporates the specificity of Watson–Crick base pairing, but otherwise neglects sequence dependence of interaction strengths, resulting in an “average base” description of DNA. We quantify the relation to experiment of the thermodynamics of singlestranded stacking, duplex hybridization, and hairpin formation, as well as structural properties such as the persistence length of single strands and duplexes, and the elastic torsional and stretching moduli of double helices. We also explore the model's representation of more complex motifs involving dangling ends, bulged bases and internal loops, and the effect of stacking and fraying on the thermodynamics of the duplex formation transition.
 COMMUNICATIONS


Communication: Generalizing Rosenfeld's excessentropy scaling to predict longtime diffusivity in dense fluids of Brownian particles: From hard to ultrasoft interactions
View Description Hide DescriptionComputer simulations are used to test whether a recently introduced generalization of Rosenfeld's excessentropy scaling method for estimating transport coefficients in systems obeying molecular dynamics can be extended to predict longtime diffusivities in fluids of particles undergoing Brownian dynamics in the absence of interparticle hydrodynamic forces. Model fluids with inversepowerlaw, Gaussiancore, and Hertzian pair interactions are considered. Within the generalized Rosenfeld scaling method, longtime diffusivities of ultrasoft Gaussiancore and Hertzian particle fluids, which display anomalous trends with increasing density, are predicted (to within 20%) based on knowledge of interparticle interactions, excess entropy, and scaling behavior of simpler inversepowerlaw fluids.

Communication: Shifted forces in molecular dynamics
View Description Hide DescriptionSimulations involving the LennardJones potential usually employ a cutoff at r = 2.5σ. This communication investigates the possibility of reducing the cutoff. Two different cutoff implementations are compared, the standard shifted potential cutoff and the less commonly used shifted forces cutoff. The first has correct forces below the cutoff, whereas the shifted forces cutoff modifies Newton's equations at all distances. The latter is nevertheless superior; we find that for most purposes realistic simulations may be obtained using a shifted forces cutoff at r = 1.5σ, even though the pair force is here 30 times larger than at r = 2.5σ.

Communication: A new approach to dualbasis secondorder Møller–Plesset calculations
View Description Hide DescriptionWe describe a hierarchy of approximations (MP2[x]) that allow one to estimate secondorder Møller–Plesset (MP2) energies in a large basis set from smallbasis calculations. The most costeffective approximation, MP2[K], is significantly cheaper than full MP2 but numerical tests on small atoms and molecules indicate that it is nonetheless accurate. We conclude that MP2[K] is an attractive level of theory for large systems.
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 ARTICLES

 Theoretical Methods and Algorithms

Modeling molecular effects on plasmon transport: Silver nanoparticles with tartrazine
View Description Hide DescriptionModulation of plasmon transport between silvernanoparticles by a yellow fluorophore, tartrazine, is studied theoretically. The system is studied by combining a finitedifference timedomainMaxwell treatment of the electric field and the plasmons with a timedependent parameterized method number 3 simulation of the tartrazine, resulting in an effective Maxwell/Schrödinger (i.e., classical/quantum) method. The modeled system has three linearly arranged small silvernanoparticles with a radius of 2 nm and a centertocenter separation of 4 nm; the molecule is centered between the second and third nanoparticles. We initiate an xpolarized current on the first nanoparticle and monitor the transmission through the system. The molecule rotates much of the xpolarized current into the ydirection and greatly reduces the overall transmission of xpolarized current.

Design of effective kernels for spectroscopy and molecular transport: Timedependent current–densityfunctional theory
View Description Hide DescriptionTimedependent current–densityfunctional theory (TDCDFT) provides an, in principle, exact scheme to calculate efficiently response functions for a very broad range of applications. However, the lack of approximations valid for a range of parameters met in experimental conditions has so far delayed its extensive use in inhomogeneous systems. On the other side, in manybody perturbation theory accurate approximations are available, but at a price of a higher computational cost. In the present work, the possibility of combining the advantages of both approaches is exploited. In this way, an exact equation for the exchangecorrelation kernel of TDCDFT is obtained, which opens the way for a systematic improvement of the approximations adopted in practical applications. Finally, an approximate kernel for an efficient calculation of spectra of solids and molecular conductances is suggested and its validity is discussed.

Origin of anomeric effect: A density functional steric analysis
View Description Hide DescriptionThe anomeric effect (the tendency of heteroatomic substituents adjacent to a heteroatom within the cyclohexane ring to prefer the axial orientation instead of the sterically less hindered equatorial position) is traditionally explained through either the dipole moment repulsion or the hyperconjugation effect. In this work, by employing our recent work in density functional steric analysis, we provide a novel twocomponent explanation, which is consistent with the common belief in chemistry that the effect has a stereoelectronic origin. With αDglucopyranose as the prototype, we systematically explore its conformational space and generate 32 isomers, leading to a total of 80 axial–equatorial conformation pairs. The energy difference analysis of these pairs shows that while statistically speaking the tendency is valid, the anomeric effect is not always true and can be violated. Three energy components, exchange–correlation, classical electrostatic, and density functional steric, are found to be directly proportional to the total energy difference between axial and equatorial isomers. We also found that the total dipole moment change, not the hyperconjugation effect, is a reasonable indicator of the total energy difference. However, all these correlations alone are not strong enough to provide a compellingly convincing explanation for the general validity of the effect. With the help of strong correlations between energy components, an explanation with two energy components, steric and electrostatic, was proposed in this work. We show that the axial–equatorial energy difference in general, with the anomeric effect as a special case, is dictated by two factors of the stereoelectronic origin, steric hindrance and classical electrostaticinteractions, synchronously working together. Another explanation in terms of exchange–correlation and electrostaticinteractions has also been obtained in this work.

Accelerating the convergence of path integral dynamics with a generalized Langevin equation
View Description Hide DescriptionThe quantum nature of nuclei plays an important role in the accurate modelling of light atoms such as hydrogen, but it is often neglected in simulations due to the high computational overhead involved. It has recently been shown that zeropoint energyeffects can be included comparatively cheaply in simulations of harmonic and quasiharmonic systems by augmenting classical molecular dynamics with a generalized Langevin equation (GLE). Here we describe how a similar approach can be used to accelerate the convergence of path integral (PI) molecular dynamics to the exact quantum mechanical result in more strongly anharmonic systems exhibiting both zero point energy and tunnellingeffects. The resulting PIGLE method is illustrated with applications to a doublewell tunnelling problem and to liquid water.

Quantum Monte Carlo study of the firstrow atoms and ions
View Description Hide DescriptionQuantum Monte Carlo calculations of the firstrow atoms Li–Ne and their singly positively charged ions are reported. MultideterminantJastrowbackflow trial wave functions are used which recover more than 98% of the correlation energy at the variational Monte Carlo level and more than 99% of the correlation energy at the diffusion Monte Carlo level for both the atoms and ions. We obtain the first ionization potentials to chemical accuracy. We also report scalar relativistic corrections to the energies, masspolarization terms, and one and twoelectron expectation values.

Twophoton ionization of helium studied with the multiconfigurational timedependent Hartree–Fock method
View Description Hide DescriptionThe multiconfigurational timedependent Hartree–Fock method (MCTDHF) is applied for simulations of the twophotonionization of helium. We present results for the single and double ionizations from the ground state for photon energies in the nonsequential regime and compare them to direct solutions of the Schrödinger equation using the timedependent (full) configuration interaction (TDCI) method. We find that the single ionization is accurately reproduced by MCTDHF, whereas the double ionization results correctly capture the main trends of TDCI.

Densityfunctional approaches to noncovalent interactions: A comparison of dispersion corrections (DFTD), exchangehole dipole moment (XDM) theory, and specialized functionals
View Description Hide DescriptionA systematic study of techniques for treating noncovalent interactions within the computationally efficient density functional theory(DFT) framework is presented through comparison to benchmarkquality evaluations of binding strength compiled for molecular complexes of diverse size and nature. In particular, the efficacy of functionals deliberately crafted to encompass longrange forces, a posteriori DFT+dispersion corrections (DFTD2 and DFTD3), and exchangehole dipole moment (XDM) theory is assessed against a large collection (469 energy points) of reference interaction energies at the CCSD(T) level of theory extrapolated to the estimated complete basis set limit. The established S22 [revised in J. Chem. Phys.132, 144104 (2010)] and JSCH test sets of minimumenergy structures, as well as collections of dispersionbound (NBC10) and hydrogenbonded (HBC6) dissociation curves and a pairwise decomposition of a protein–ligand reaction site (HSG), comprise the chemical systems for this work. From evaluations of accuracy, consistency, and efficiency for PBED, BP86D, B97D, PBE0D, B3LYPD, B970D, M052X, M062X, ωB97XD, B2PLYPD, XYG3, and B3LYPXDM methodologies, it is concluded that distinct, often contrasting, groups of these elicit the best performance within the accessible doubleζ or robust tripleζ basis set regimes and among hydrogenbonded or dispersiondominated complexes. For overall results, M052X, B97D3, and B970D2 yield superior values in conjunction with augccpVDZ, for a mean absolute deviation of 0.41 – 0.49 kcal/mol, and B3LYPD3, B97D3, ωB97XD, and B2PLYPD3 dominate with augccpVTZ, affording, together with XYG3/6311+G(3df,2p), a mean absolute deviation of 0.33 – 0.38 kcal/mol.

Quantum Monte Carlo with Jastrowvalencebond wave functions
View Description Hide DescriptionWe consider the use in quantum Monte Carlo calculations of two types of valence bondwave functions based on strictly localized active orbitals, namely valence bond selfconsistentfield and breathingorbital valence bondwave functions. Complemented by a Jastrow factor, these Jastrowvalencebond wave functions are tested by computing the equilibrium well depths of the four diatomic molecules C_{2}, N_{2}, O_{2}, and F_{2} in both variational Monte Carlo and diffusion Monte Carlo. We show that it is possible to design compact wave functions based on chemical grounds that are capable of describing both static and dynamic electron correlations. These wave functions can be systematically improved by inclusion of valence bond structures corresponding to additional bonding patterns.

Look before you leap: A confidencebased method for selecting species criticality while avoiding negative populations in τleaping
View Description Hide DescriptionThe stochastic simulation algorithm was introduced by Gillespie and in a different form by Kurtz. There have been many attempts at accelerating the algorithm without deviating from the behavior of the simulated system. The crux of the explicit τleaping procedure is the use of Poisson random variables to approximate the number of occurrences of each type of reaction event during a carefully selected time period, τ. This method is acceptable providing the leap condition, that no propensity function changes “significantly” during any timestep, is met. Using this method there is a possibility that species numbers can, artificially, become negative. Several recent papers have demonstrated methods that avoid this situation. One such method classifies, as critical, those reactions in danger of sending species populations negative. At most, one of these critical reactions is allowed to occur in the next timestep. We argue that the criticality of a reactant species and its dependent reaction channels should be related to the probability of the species number becoming negative. This way only reactions that, if fired, produce a high probability of driving a reactant population negative are labeled critical. The number of firings of more reaction channels can be approximated using Poisson random variables thus speeding up the simulation while maintaining the accuracy. In implementing this revised method of criticality selection we make use of the probability distribution from which the random variable describing the change in species number is drawn. We give several numerical examples to demonstrate the effectiveness of our new method.

A simple, efficient polarizable coarsegrained water model for molecular dynamics simulations
View Description Hide DescriptionThe development of coarsegrained (CG) models that correctly represent the important features of compounds is essential to overcome the limitations in time scale and system size currently encountered in atomistic molecular dynamics simulations. Most approaches reported in the literature model one or several molecules into a single uncharged CG bead. For water, this implicit treatment of the electrostaticinteractions, however, fails to mimic important properties, e.g., the dielectric screening. Therefore, a coarsegrained model for water is proposed which treats the electrostaticinteractions between clusters of water molecules explicitly. Five water molecules are embedded in a spherical CG bead consisting of two oppositely charged particles which represent a dipole. The bond connecting the two particles in a bead is unconstrained, which makes the model polarizable. Experimental and allatom simulated data of liquid water at room temperature are used for parametrization of the model. The experimental density and the relative static dielectricpermittivity were chosen as primary target properties. The modelproperties are compared with those obtained from experiment, from clusters of simplepointcharge water molecules of appropriate size in the liquid phase, and for other CG watermodels if available. The comparison shows that not all atomistic properties can be reproduced by a CG model, so properties of key importance have to be selected when coarse graining is applied. Yet, the CG model reproduces the key characteristics of liquid water while being computationally 1–2 orders of magnitude more efficient than standard finegrained atomistic watermodels.

Molecular cluster building algorithm: Electrostatic guidelines and molecular tailoring approach
View Description Hide DescriptionNanosized clusters of various materials are recent experimental targets, since they exhibit sizedependent physicochemical properties. A vast amount of literature is available on the study of molecular clusters but general methods for systematic evolution of their growth are rather scarce. The present work reports a molecular cluster building algorithm based on the electrostatic guidelines, followed by ab initio investigations, enabled by the application of molecular tailoring approach. Applications of the algorithm for generating geometries and interactionenergies of large molecular clusters of zinc sulfide, benzene, and water are presented.

Reformulated spacechargelimited current model and its application to disordered organic systems
View Description Hide DescriptionWe have reformulated a traditional model used to describe the current–voltage dependence of low mobilitymaterials sandwiched between planar electrodes by using the quasielectrochemical potential as the fundamental variable instead of the local electric field or the local charge carrier density. This allows the material densityofstates to enter explicitly in the equations and dispenses with the need to assume a particular type of contact. The diffusioncurrent is included and as a consequence the current–voltage dependence obtained covers, with increasing bias, the diffusion limited current, the spacecharge limited current, and the injection limited current regimes. The generalized Einstein relation and the field and density dependent mobility are naturally incorporated into the formalism; these two points being of particular relevance for disordered organic semiconductors. The reformulated model can be applied to any material where the carrier density and the mobility may be written as a function of the quasielectrochemical potential. We applied it to the textbook example of a nondegenerate, constant mobilitymaterial and showed how a single dimensionless parameter determines the form of the I(V) curve. We obtained integral expressions for the carrier density and for the mobility as a function of the quasielectrochemical potential for a Gaussianly disordered organic material and found the general form of the I(V) curve for such materials over the full range of bias, showing how the energetic disorder alone can give rise, in the spacecharge limited current regime, to an I∝V ^{ n } dependence with an exponent n larger than 2.
 Gas Phase Dynamics and Structure: Spectroscopy, Molecular Interactions, Scattering, and Photochemistry

Intensity analysis of overlapped discrete and continuous absorption by spectral simulation: The electronic transition moment for the B–X system in I_{2}
View Description Hide DescriptionThe spectrum of I_{2} is examined anew in the wavelength region 520–640 nm, where discrete absorption in the B–X transition is prominent. The spectrum is recorded with high quantitative precision at moderate resolution (0.1 nm) and is analyzed by leastsquares spectral simulation, yielding the B–X electronic transition strength μ _{ e }^{2} with unprecedented precision (<2% relative standard error) over most of the studied region. The analysis also yields directly new estimates of the continuous absorption in this region, which support previous assessments of the A ← X transition but lower the C(^{1}Π_{ u }) ← X transition strength by 25%. The new analysis method is applicable to any situation where the discrete spectrum can be simulated reliably.

Infrared spectroscopy of small protonated water clusters at room temperature: An effective modes analysis
View Description Hide DescriptionWe perform infrared vibrational analysis on small protonated water clusters , with n = 2, …, 6, at room temperature. The absorption spectra are calculated based on classical trajectories obtained by the multistate empirical valence bond method. The analysis is carried out based on the effective modes analysis, which has been recently developed [Martinez et al., J. Chem. Phys.125, 144106 (2006)] as generalization of the normal modes analysis. This technique enables us to decompose the full spectrum in maximally localized bands which are obtained by accounting for temperature and anharmonic effects. These effects are especially considered in the determination of the modes coupling. The spectra of the small clusters are interpreted by identifying the behavior of the excess charge, by understanding the role of hydrogen bonds, and by considering the effect of (micro)solvation. Our results are presented by showing comparisons with other numerical methods and experimental measurements which are available in the literature.

Infrared spectroscopy and effective modes analysis of the protonated water dimer H^{+}(H_{2}O)_{2} at room temperature under H/D substitution
View Description Hide DescriptionWe study the vibrational properties of the protonated water dimer and its deuterated forms at room temperature. Molecular dynamics simulations within the empirical valence bond (EVB) model are used to generate the vibrational spectra that are interpreted using the effective modes analysis (EMA). Quantum effects are taken into account through an effective parametrization of the EVB model. EMA allows for the assignment of the bands in the 1000 − 2000 cm^{−1} region of the protonated water dimer from the molecular dynamics trajectory. It is then found that although this system is very anharmonic the two main bands in this spectral region arise from a linear coupling between the asymmetric stretch and asymmetric bend of the two water molecules. This mixing explains the simulated band shifts upon isotopic substitution of the central proton or of the hydrogens of the two water molecules.

Phase space geometry of dynamics passing through saddle coupled with spatial rotation
View Description Hide DescriptionNonlinear reaction dynamics through a rankone saddle is investigated for manyparticle system with spatial rotation. Based on the recently developed theories of the phase space geometry in the saddle region, we present a theoretical framework to incorporate the spatial rotation which is dynamically coupled with the internal vibrational motions through centrifugal and Coriolis interactions. As an illustrative simple example, we apply it to isomerizationreaction of HCN with some nonzero total angular momenta. It is found that noreturn transition state (TS) and a set of impenetrable reaction boundaries to separate the “past” and “future” of trajectories can be identified analytically under rovibrational couplings. The three components of the angular momentum are found to have distinct effects on the migration of the “anchor” of the TS and the reaction boundaries through rovibrational couplings and anharmonicities in vibrational degrees of freedom. This method provides new insights in understanding the origin of a wide class of reactions with nonzero angular momentum.

Vibrational spectrum of Ar_{3} ^{+} and relative importance of linear and perpendicular isomers in its photodissociation
View Description Hide DescriptionThe photodissociation dynamics of the argon ionized trimer is revisited in the light of recent experimental results of Lepère et al. [J. Chem. Phys.134, 194301 (2009)], which show that the fragment with little kinetic energy is always a neutral one, thus the available energy is shared by a neutral and ionic fragments as in . We show that these results can be interpreted as the photodissociation of the linear isomer of the system. We perform a 3D quantum computation of the vibrational spectrum of the system and study the relative populations of the linear (trimercore) and perpendicular (dimercore) isomers. We then show that the charge initially located on the central atom in the ground electronic state of the linear isomer migrates toward the extreme ones in the photoexcitation process such that photodissociation of the linear isomer produces a neutral central atom at rest in agreement with measured product state distributions.