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In a previous paper [J. L. McAfee and B. Poirier, J. Chem. Phys. 130, 064701 (2009)], using spin-polarized density functional theory (DFT), the authors reported a binding energy of 0.755 eV, for a single hydrogen atom adsorbed on a pristine (unrelaxed) (5,5) single-walled carbon nanotube (SWNT) substrate. A full three-dimensional (3D) potential energy surface (PES) for the SWNT-H system was also developed, and used in a quantum dynamics calculation to compute all rovibrational bound states, and associated equatorial and longitudinal adsorbate migration rates. A highly pronounced preference for the latter migration pathway at ambient temperatures was observed. In this work, we extend the aforementioned study to include multiple H-atom adsorbates. Extensive DFT calculations are performed, in order to ascertain the most relevant dynamical pathways. For two adsorbates, the SWNT-H-H system is found to exhibit highly site-specific binding, as well as long-range correlation and pronounced binding energy enhancement. The latter effect is even more pronounced in the full-hydrogenation limit, increasing the per-adsorbate binding energy to 2.6 eV. To study migration dynamics, a single-hole model is developed, for which the binding energy drops to 2.11 eV. A global 3D PES is developed for the hole migration model, using 40 radial × 18 cylindrical ab initio geometries, fit to a Fourier basis with radially dependent expansion coefficients (rms error 4.9 meV). As compared with the single-adsorbate case, the hole migration PES does not exhibit separate chemisorption and physisorption wells. The barrier to longitudinal migration is also found to be much lower. Quantum dynamics calculations for all rovibrational states are then performed (using a mixed spectral basis/phase-space optimized discrete variable representation), and used to compute longitudinal migration rates. Ramifications for the use of SWNTs as potential hydrogen storage materials are discussed. [ABSTRACT FROM AUTHOR]

In the quest towards coarse-grained potentials and new water models, we present an extension of the force matching technique to parameterize an all-atom force field for rigid water. The methodology presented here allows to improve the matching procedure by first optimizing the weighting exponents present in the objective function. A new gauge for unambiguously evaluating the quality of the fit has been introduced; it is based on the root mean square difference of the distributions of target properties between reference data and fitted potentials. Four rigid water models have been parameterized; the matching procedure has been used to assess the role of the ghost atom in TIP4P-like models and of electrostatic damping. In the former case, burying the negative charge inside the molecule allows to fit better the torques. In the latter, since short-range interactions are damped, a better fit of the forces is obtained. Overall, the best performing model is the one with a ghost atom and with electrostatic damping. The approach shown in this paper is of general validity and could be applied to any matching algorithm and to any level of coarse graining, also for non-rigid molecules. [ABSTRACT FROM AUTHOR]

Hybrid molecular dynamics (MD) simulations, which combine density functional theory (DFT) descriptions of a molecule with a molecular mechanics (MM) modeling of its solvent environment, have opened the way towards accurate computations of solvation effects in the vibrational spectra of molecules. Recently, Wheeler et al. [ChemPhysChem 4, 382 (2002)] have suggested to compute these spectra from DFT/MM-MD trajectories by diagonalizing the covariance matrix of atomic fluctuations. This so-called principal mode analysis (PMA) allegedly can replace the well-established approaches, which are based on Fourier transform methods or on conventional normal mode analyses. By scrutinizing and revising the PMA approach we identify five conditions, which must be guaranteed if PMA is supposed to render exact vibrational frequencies. Besides specific choices of (a) coordinates and (b) coordinate systems, these conditions cover (c) a harmonic intramolecular potential, (d) a complete thermal equilibrium within the molecule, and (e) a molecular Hamiltonian independent of time. However, the PMA conditions [(c)–(d)] and [(c)–(e)] are generally violated in gas phase DFT-MD and liquid phase DFT/MM-MD trajectories, respectively. Based on a series of simple analytical model calculations and on the analysis of MD trajectories calculated for the formaldehyde molecule in the gas phase (DFT) and in liquid water (DFT/MM) we show that in both phases the violation of condition (d) can cause huge errors in PMA frequency computations, whereas the inevitable violations of conditions (c) and (e), the latter being generic to the liquid phase, imply systematic and sizable underestimates of the vibrational frequencies by PMA. We demonstrate that the huge errors, which are caused by an incomplete thermal equilibrium violating (d), can be avoided if one introduces mode-specific temperatures Tj and calculates the frequencies from a “generalized virial” (GV) expression instead from PMA. Concerning ways to additionally remove the remaining errors, which GV still shares with PMA, we refer to Paper II of this work [M. Schmitz and P. Tavan, J. Chem. Phys. 121, 12247 (2004)]. © 2004 American Institute of Physics. [ABSTRACT FROM AUTHOR]

Combining simulation and model theories, this paper analyses the impact of pair dynamics on the intermolecular nuclear Overhauser effect (NOE) in liquids. For the first time, we give a distance resolved NOE. When applied to the ionic liquid 1-ethyl-3-methyl-imidazolium tetrafluoroborate the NOE turns out to be of long-range nature. This behaviour translates to the experimentally measured cross- and longitudinal relaxation rates.We were able to calculate the heteronuclear NOE from simulation data, despite the high computational effort.Model theories are computationally less demanding and cover the complete frequency range of the respective spectral density function, they are usually based on a very simple pair distribution function and the solution of the diffusion equation. In order to model the simulated data sufficiently, these simplifications in structure and dynamics have to be generalised considerably. [ABSTRACT FROM AUTHOR]

Recently, the use of polarizable force fields in Molecular Dynamics simulations has been gaining importance, since they allow a better description of heterogeneous systems compared to simple point charges force fields. Among the various techniques developed in the last years the one based on polarizable point dipoles represents one of the most used. In this paper, we review the basic technical issues of the method, illustrating the way to implement intramolecular and intermolecular damping of the electrostatic interactions, either with and without the Ewald summation method. We also show how to reduce the computational overhead for evaluating the dipoles, introducing to the state-of-the-art methods: the extended Lagrangian method and the always stable predictor corrector method. Finally we discuss the importance of screening the electrostatic interactions at short range, defending this technique against simpler approximations usually made. We compare results of density functional theory and classical force field-based Molecular Dynamics simulations of chloride in water. [ABSTRACT FROM AUTHOR]

The use of discrete variable representation (DVR) basis sets within ab initio molecular dynamics calculations allows the latter to be performed with converged energies and, more importantly, converged forces. In this paper, we show how to carry out ab initio molecular dynamics calculations in the isothermal-isobaric ensemble with fully flexible simulation boxes within the DVR basis set framework. In particular, we derive the appropriate DVR based expression for the pressure tensor when the electronic structure is represented using Kohn-Sham density functional theory, and we examine the convergence of this expression as a function of the basis set size. An illustrative example using 64 silicon atoms in a fully flexible box using a combination of the Martyna-Tobias-Klein [Martyna et al., J. Chem. Phys. 101, 4177 (1994)] and Car-Parrinello [Car and Parinello, Phys. Rev. Lett. 55, 2471 (1985)] algorithms is presented to demonstrate the efficacy of the approach. [ABSTRACT FROM AUTHOR]

We present an approach for the simulation of time resolved photoelectron spectra based on the combination of the ab initio nonadiabatic molecular dynamics ”on the fly” with the Stieltjes imaging method utilizing discrete neutral states above the ionization limit for the approximate description of the ionization continuum. Our approach has been implemented in the framework of the time-dependent density functional theory and has been applied to interrogate the ultrafast internal conversion between the S2 and S1 states in pyrazine. The simulations reveal that, parallel to the S2→S1 internal conversion, a change in the dominant ionization process (S2→D1 versus S1→D0) occurs on the time scale of 20 fs such that no significant change in the photoelectron kinetic energy distribution is observed. The presented results are in full agreement with the experimental results presented in the accompanying paper [Suzuki et al., J. Chem. Phys. 132, 174302 (2010)] and provide an insight into the interplay between the nonradiative relaxation and the photoionization process in pyrazine as reflected in the time resolved photoelectron spectrum. Our approach represents a general tool for the investigation of ultrafast photoionization processes in complex systems and thus can be used to investigate the ultrafast femtochemistry of complex molecular systems including all degrees of freedom. [ABSTRACT FROM AUTHOR]

Functionalizing nanoparticles with organic ligands, such as oligomers, polymers, DNA, and proteins, is an attractive way to manipulate the interfacial interactions between the nanoparticles and the medium the particles are placed in, and thus control the nanoparticle assembly. In this paper we have conducted a Monte Carlo simulation study on copolymer grafted spherical nanoparticles to show the tremendous potential of using monomer sequence on the copolymers to tune the grafted chain conformation, and thus the effective interactions between copolymer grafted nanoparticles. We have studied AB copolymers with alternating, multiblock, or diblock sequences, where either A monomers or B monomers have monomer-monomer attractive interactions. Our focus has been to show the nontrivial effect of monomer sequence on the conformations of the grafted copolymers at various particle diameters, grafting densities, copolymer chain lengths, and monomer-monomer interactions in an implicit small molecule solvent. We observe that the monomer sequence, particle diameter, and grafting density dictate whether (a) the grafted chains aggregate to bring attractive monomers from multiple grafted chains together (interchain and intrachain monomer aggregation) if the enthalpy gained by doing so offsets the entropic loss caused by stretching of chains, or (b) each grafted chain folds onto itself to bring its attractive monomers together (only intrachain monomer aggregation) if the entropic loss from interchain aggregation cannot be overcome by the enthalpic gain. For six copolymers of chain length N=24 grafted on a spherical particle of diameter D=4, interchain and intrachain monomer aggregation occurs, and the radius of gyration varies nonmonotonically with increasing blockiness of the monomer sequence. At larger particle diameters the grafted chains transition to purely intrachain monomer aggregation. The radius of gyration varies monotonically with monomer sequence for intrachain monomer aggregation because as the sequence becomes blockier (like monomers are grouped together), the copolymer chain has to fold less compactly to maximize the enthalpically favorable contacts while maintaining high conformational entropy. The radius of gyration of alternating and diblock copolymers scales with chain length N through a power law g2>1/2=αNν with the prefactor α and scaling exponent ν, varying with monomer sequence and monomer-monomer attraction strength. [ABSTRACT FROM AUTHOR]

In the recent density functional-based calculations, it was found that the conductivity of naphthalene molecular wires can be modulated by altering the linking position of the molecule to the electrode [D. Walter, D. Neuhauser, and R. Baer, Chem. Phys. 299, 139 (2004)]. A quantum interference model was proposed to interpret the observation. In this paper, we further studied the conductance of a series of conjugated molecules containing aromatic rings using density functional theory combined with nonequilibrium Green’s function method. For polyacene systems with different terminal connections, the conductivity is dependent on the substitution position of anchoring groups even with similar electron transport distance. The conductance of trans-substitution can be ten times or more as large as that of the cis-substitution. However, for the biphenyl system with different intramolecular connections, adding more connections between two benzene rings does not change the junction conductance. All these results indicate that the junction conductance is strongly dependent on the particular electron transport pathway. The alternating double-single linkage is the most probable one, since others are impeded by the single bonds. [ABSTRACT FROM AUTHOR]

A new method called adaptive force matching (AFM) has been developed that is capable of producing high quality force fields for condensed phase simulations. This procedure involves the parametrization of force fields to reproduce ab initio forces obtained from condensed phase quantum-mechanics/molecular-mechanics (QM/MM) calculations. During the procedure, the MM part of the QM/MM is iteratively improved so as to approach ab initio quality. In this work, the AFM method has been tested to parametrize force fields for liquid water so that the resulting force fields reproduce forces calculated using the ab initio MP2 and the Kohn–Sham density functional theory with the Becke–Lee–Yang–Parr (BLYP) and Becke three-parameter LYP (B3LYP) exchange correlation functionals. The AFM force fields generated in this work are very simple to evaluate and are supported by most molecular dynamics (MD) codes. At the same time, the quality of the forces predicted by the AFM force fields rivals that of very expensive ab initio calculations and are found to successfully reproduce many experimental properties. The site-site radial distribution functions (RDFs) obtained from MD simulations using the force field generated from the BLYP functional through AFM compare favorably with the previously published RDFs from Car–Parrinello MD simulations with the same functional. Technical aspects of AFM such as the optimal QM cluster size, optimal basis set, and optimal QM method to be used with the AFM procedure are discussed in this paper. [ABSTRACT FROM AUTHOR]

We present a method to compute the Fermi function of the Hamiltonian for a system of independent fermions based on an exact decomposition of the grand-canonical potential. This scheme does not rely on the localization of the orbitals and is insensitive to ill-conditioned Hamiltonians. It lends itself naturally to linear scaling as soon as the sparsity of the system’s density matrix is exploited. By using a combination of polynomial expansion and Newton-like iterative techniques, an arbitrarily large number of terms can be employed in the expansion, overcoming some of the difficulties encountered in previous papers. Moreover, this hybrid approach allows us to obtain a very favorable scaling of the computational cost with increasing inverse temperature, which makes the method competitive with other Fermi operator expansion techniques. After performing an in-depth theoretical analysis of computational cost and accuracy, we test our approach on the density functional theory Hamiltonian for the metallic phase of the LiAl alloy. [ABSTRACT FROM AUTHOR]

In this paper, double ionization energies (DIEs) of gas-phase atoms and molecules are calculated by energy difference method with density functional theory. To determine the best functional for double ionization energies, we first study 24 main group atoms in the second, third, and fourth periods. An approximation is used in which the electron density is first obtained from a density functional computation with the exchange-correlation potential Vxc known as statistical average of orbital potentials, after which the energy is computed from that density with 59 different exchange-correlation energy functionals Exc. For the 24 atoms, the two best Exc functional providing DIEs with average absolute deviation (AAD) of only 0.25 eV are the Perdew–Burke–Ernzerhof functional modified by Hammer et al. [Phys. Rev. B 59, 6413 (1999)] and one known as the Krieger–Chen–Iafrate–Savin functional modified by Krieger et al. (unpublished). Surprisingly, none of the 20 available hybrid functionals is among the top 15 functionals for the DIEs of the 24 atoms. A similar procedure is then applied to molecules, with opposite results: Only hybrid functionals are among the top 15 functionals for a selection of 29 molecules. The best Exc functional for the 29 molecules is found to be the Becke 1997 functional modified by Wilson et al. [J. Chem. Phys. 115, 9233 (2001)]. With that functional, the AAD from experiment for DIEs of 29 molecules is just under 0.5 eV. If the two suspected values for C2H2 and Fe(CO)5 are excluded, the AAD improves to 0.32 eV. Many other hybrid functionals perform almost as well. [ABSTRACT FROM AUTHOR]

Morphology control is important for practical applications of composite materials that consist of functional polymers and nanoparticles. Toward that end, block copolymers provide useful templates to arrange nanoparticles in the scaffold of self-organized polymer microdomains. This paper reports theoretical predictions for the distribution of nanoparticles in the lamellar structures of symmetric diblock copolymers on the basis of a polymer density functional theory (DFT) and the potential distribution theorem (PDT). The DFT predicts periodic spacing of lamellar structures in good agreement with molecular dynamics simulations. With the polymer structure from DFT as the input, the PDT is used to examine the effects of particle size, surface energy, polymer chain length, and compressibility on the distribution of nanoparticles in the limit of low particle density. It is found that the nanoparticle distribution depends not only on the particle size and surface energy but also on the local structure of the microdomain interface, polymer chain length, and compressibility. The theoretical predictions are compared well with experiments and simulations. [ABSTRACT FROM AUTHOR]

Structural properties of liquid water at ambient temperature were studied using Car-Parrinello [Phys. Rev. Lett. 55, 2471 (1985)] ab initio molecular dynamics (CPAIMD) simulations combined with the Kohn-Sham (KS) density functional theory and the BLYP exchange-correlation functional for the electronic structure. Unlike other recent work on the same subject, where plane-wave (PW) or hybrid Gaussian/plane-wave basis sets were employed, in the present paper, a discrete variable representation (DVR) basis set is used to expand the KS orbitals, so that with the real-space grid adapted in the present work, the properties of liquid water could be obtained very near the complete basis set limit. Structural properties of liquid water were extracted from a 30 ps CPAIMD-BLYP/DVR trajectory at 300 K. The radial distribution functions (RDFs), spatial distribution functions, and hydrogen bond geometry obtained from the CPAIMD-BLYP/DVR simulation are generally in good agreement with the most up to date experimental measurements. Compared to recent ab initio MD simulations based on PW basis sets, less significant overstructuring was found in the RDFs and the distributions of hydrogen bond angles, suggesting that previous plane-wave and Gaussian basis set calculations have exaggerated the tendency toward overstructuring. [ABSTRACT FROM AUTHOR]

We propose a general method of thermodynamic integration to find the free energy of a surface, where our integration parameter is taken to be the strain on the unit cell of the system (which in the example presented in this paper is simply the extension of the unit cell along the normal to the surface), and the integration is performed over the thermal average stress from a molecular dynamics run. In order to open up a vacuum gap in a continuous and reversible manner, an additional control interaction has been introduced. We also use temperature integration to find a linear relation for the temperature dependence of the free surface energy. These methods have been applied to the titanium dioxide (110) surface, using first principles density functional theory. A proof of principle calculation for zero temperature shows excellent agreement between the integral calculation and the difference in energy calculated by the DFT program. Calculations that have been performed at 295 and 1000 K give excellent agreement between the two integration methods. [ABSTRACT FROM AUTHOR]

In this paper the structures of 4-aminophenol(H2O)1+ and 3-aminophenol(H2O)1+ clusters are investigated in molecular beam experiments by different IR/UV-double resonance techniques as well as the mass analyzed threshold ionization spectroscopy yielding both inter- and intramolecular vibrations of the ionic and neutral species. Possible structures are extensively calculated at the level of density functional theory (DFT) or at the ab initio level of theory. From the experimental and theoretical investigations it can be concluded that in the case of 4-aminophenol(H2O)1 one O[Single_Bond]H...O hydrogen-bonded structure exists in the neutral cluster but two structures containing either an O[Single_Bond]H...O or a N[Single_Bond]H...O hydrogen-bonded arrangement are observed in the spectra of the ionic species. This observation is a result of an intramolecular rearrangement reaction within the ion which can only take place if high excess energies are used. A reaction path via the CH bonds is calculated and explains the experimental observations. In the case of 3-aminophenol(H2O)1+ only one O[Single_Bond]H...O bound structure is observed both in the neutral and ionic species. Ab initio and DFT calculations show that due to geometrical and energetical reasons a rearrangement cannot be observed in the 3-aminophenol(H2O)1+ cluster ion. [ABSTRACT FROM AUTHOR]

The midinfrared (MIR) spectra of molecules in polar solvents exhibit inhomogeneously broadened bands whose spectral positions are shifted as compared to the gas phase. The shifts are caused by interactions with structured solvation shells and the broadenings by fluctuations of these interactions. The MIR spectra can be calculated from hybrid molecular dynamics (MD) simulations, which treat the solute molecule by density functional theory and the solvent by molecular mechanics by the so-called instantaneous normal mode analysis (INMA) or by Fourier transforming the time correlation function (FTTCF) of the molecular dipole moment. In Paper I of this work [M. Schmitz and P. Tavan, J. Chem. Phys. 121, 12233 (2004)] we explored an alternative method based on generalized virial (GV) frequencies noting, however, that GV systematically underestimates frequencies. As shown by us these artifacts are caused by solvent-induced fluctuations of the (i) equilibrium geometry, (ii) force constants, and (iii) normal mode directions as well as by (iv) diagonal and (v) off-diagonal anharmonicities. Here we now show, by analyzing the time scales of fluctuations and sample MD trajectories of formaldehyde in the gas phase and in water, that all these sources of computational artifacts can be made visible by a Fourier analysis of the normal coordinates. Correspondingly, the error sources (i) and (iii)–(v) can be removed by bandpass filtering, as long as the spectral signatures of the respective effects are well separated from the fundamental band. Furthermore, the artifacts arising from effect (ii) can be strongly diminished by a time-resolved version of the GV approach (TF-GV). The TF-GV method then yields for each mode j a trajectory of the vibrational frequency ωj(t|τ) at a time resolution τ>τj, which is only limited by the corresponding oscillation time τj=2π/ωj and, thus, is in the femtosecond range. A correlation analysis of these trajectories clearly separates the librational motions from the conformational dynamics of the solvation shells and yields the inhomogeneously broadened MIR spectra, if the theory of motional narrowing is properly included. The MIR spectrum of formaldehyde in solution obtained by TF-GV agrees very well with the FTTCF result, if one applies the so-called “harmonic approximation” quantum correction factor and a temperature scaling to the FTTCF intensities. Also for INMA an excellent agreement is achieved if one disregards a slight INMA overestimate of linewidths.© 2004 American Institute of Physics. [ABSTRACT FROM AUTHOR]

The ab initio molecular-dynamics formalism of Car and Parrinello is extended to preserve the locality of the orbitals. The supplementary term in the Lagrangian does not affect the nuclear dynamics, but ensures “on the fly” localization of the electronic orbitals within a periodic supercell in the Γ-point approximation. The relationship between the resulting equations of motion and the formation of a gauge-invariant Lagrangian combined with a gauge-fixing procedure is briefly discussed. The equations of motion can be used to generate a very stable and easy to implement numerical integration algorithm. It is demonstrated that this algorithm can be used to compute the trajectory of the maximally localized orbitals, known as Wannier orbitals, in ab initio molecular dynamics with only a modest increase in the overall computer time. In the present paper, the new method is implemented within the generalized gradient approximation to Kohn–Sham density-functional theory employing plane wave basis sets and atomic pseudopotentials. In the course of the presentation, we briefly discuss how the present approach can be combined with localized basis sets to design fast linear scaling ab initio molecular-dynamics methods. © 2004 American Institute of Physics. [ABSTRACT FROM AUTHOR]

Here, extensions to quantum chemical nanoreactor molecular dynamics simulations for discovering complex reactive events are presented. The species-selective algorithm, where the nanoreactor effectively works for the selected desired reactants, was introduced to the original scheme. Moreover, for efficient simulations of large model systems with the modified approach, the divide-and-conquer linear-scaling density functional tight-binding method was exploited. Two illustrative applications of the polymerization of propylene and cyclopropane mixtures and the aggregation of sodium chloride from aqueous solutions indicate that species-selective quantum chemical nanoreactor molecular dynamics is a promising method to accelerate the sampling of multicomponent chemical processes proceeding under relatively mild conditions. [ABSTRACT FROM AUTHOR]

Glutaredoxins are small enzymes that catalyze the oxidation and reduction of protein disulfide bonds by the thiol–disulfide exchange mechanism. They have either one or two cysteines in their active site, resulting in different catalytic reaction cycles that have been investigated in many experimental studies. However, the exact mechanisms are not yet fully known, and to our knowledge, no theoretical studies have been performed to elucidate the underlying mechanism. In this study, we investigated a proposed mechanism for the reduction of the disulfide bond in the protein HMA4n by a mutated monothiol Homo sapiens glutaredoxin and the co-substrate glutathione. The catalytic cycle involves three successive thiol–disulfide exchanges that occur between the molecules. To estimate the regioselectivity of the different attacks, classical molecular dynamics simulations were performed and the trajectories analyzed regarding the sulfur–sulfur distances and the attack angles between the sulfurs. The free energy profile of each reaction was obtained with hybrid quantum mechanical/molecular mechanical metadynamics simulations. Since this required extensive phase space sampling, the semi-empirical density functional tight-binding method was used to describe the reactive cysteines. For an accurate description, we used specific reaction parameters fitted to B3LYP energies of the thiol–disulfide exchange and a machine learned energy correction that was trained on coupled-cluster single double perturbative triple [CCSD(T)] energies of thiol–disulfide exchanges. Our calculations show the same regiospecificity as observed in the experiment, and the obtained barrier heights are about 12 and 20 kcal/mol for the different reaction steps, which confirms the proposed pathway. [ABSTRACT FROM AUTHOR]

Nonadiabatic excited state molecular dynamics underpin many photophysical and photochemical phenomena, such as exciton dynamics, and charge separation and transport. In this work, we present an efficient nonadiabatic molecular dynamics (NAMD) simulation method based on time-dependent density functional tight-binding (TDDFTB) theory. Specifically, the adiabatic electronic structure, an essential NAMD input, is described at the TDDFTB level. The nonadiabatic effects originating from the coupled motions of electrons and nuclei are treated by the trajectory surface hopping algorithm. To improve the computational efficiency, nonadiabatic couplings between excited states within the TDDFTB method are derived and implemented using an analytical approach. Furthermore, the time-dependent nonadiabatic coupling scalars are calculated based on the overlap between molecular orbitals rather than the Slater determinants to speed up the simulations. In addition, the electronic decoherence scheme and a state reassigned unavoided crossings algorithm, which has been implemented in the NEXMD software, are used to improve the accuracy of the simulated dynamics and handle trivial unavoided crossings. Finally, the photoinduced nonadiabatic dynamics of a benzene molecule are simulated to demonstrate our implementation. The results for excited state NAMD simulations of benzene molecule based on TDDFTB method compare well to those obtained with numerically expensive time-dependent density functional theory. The proposed methodology provides an attractive theoretical simulation tool for predicting the photophysical and photochemical properties of complex materials. [ABSTRACT FROM AUTHOR]

The clustering, collision, and relaxation dynamics of pristine and doped helium nanodroplets is theoretically investigated in cases of pickup and clustering of heliophilic argon, collision of heliophobic cesium atoms, and coalescence of two droplets brought into contact by their mutual long-range van der Waals interaction. Three approaches are used and compared with each other. The He time-dependent density functional theory method considers the droplet as a continuous medium and accounts for its superfluid character. The ring-polymer molecular dynamics method uses a path-integral description of nuclear motion and incorporates zero-point delocalization while bosonic exchange effects are ignored. Finally, the zero-point averaged dynamics approach is a mixed quantum–classical method in which quantum delocalization is described by attaching a frozen wavefunction to each He atom, equivalent to classical dynamics with effective interaction potentials. All three methods predict that the growth of argon clusters is significantly hindered by the helium host droplet due to the impeding shell structure around the dopants and kinematic effects freezing the growing cluster in metastable configurations. The effects of superfluidity are qualitatively manifested by different collision dynamics of the heliophilic atom at high velocities, as well as quadrupole oscillations that are not seen with particle-based methods, for droplets experiencing a collision with cesium atoms or merging with each other. [ABSTRACT FROM AUTHOR]

The structure of the double-layer formed at the surface of carbon electrodes is governed by the interactions between the electrode and the electrolyte species. However, carbon is notoriously difficult to simulate accurately, even with well-established methods such as electronic density functional theory and molecular dynamics. Here, we focus on the important case of a lithium ion in contact with the surface of graphite, and we perform a series of reference quantum Monte Carlo calculations that allow us to benchmark various electronic density functional theory functionals. We then fit an accurate carbon–lithium pair potential, which is used in molecular density functional theory calculations to determine the free energy of the adsorption of the ion on the surface in the presence of water. The adsorption profile in aqueous solution differs markedly from the gas phase results, which emphasize the role of the solvent on the properties of the double-layer. [ABSTRACT FROM AUTHOR]

The influence of a water solvent on the optical absorption properties of alizarin is investigated using time-dependent density functional theory (TDDFT). The solvent is modeled at two different levels of theory: a structureless dielectric medium, using a polarizable continuum model, and the explicit inclusion of water molecules which are treated at the same level of theory as the solute. Thermal effects on the photoabsorption spectra are included by combining TDDFT with first principle molecular dynamics. The effect of molecular distortions on the excitation energies and oscillator strengths is analyzed, and a strong correlation between particular structural and optical properties is found. [ABSTRACT FROM AUTHOR]

The performance of single-determinant methods for finding geometries and energies of excited states is tested on the ozone molecule. Geometries for low-lying singlet and triplet states of ozone were optimized by CCSD(T) and density functional theory (DFT) (with BPW91 functional) methods. DFT geometries were found to lie close to CCSD(T) values. Most CCSD(T) and DFT geometries and energies are in good agreement with available experimental and recent high-level theoretical values, with deviations lying within 0.02 Å, 2°, and 0.3 eV. An exception is the 1 1B2 state, having a larger deviation of bond distance and energy. A multiconfigurational treatment is required for this state. DFT geometry optimizations and calculations of vibrational frequencies were extended to higher states, covering over 30 excited states of ozone, with adiabatic excitation energies up to about 6 eV. Calculated harmonic frequencies showed several states, including 1 1B2, to be saddle points. Multireference configuration interaction (MRCI) bending potentials for first and second singlet and triplet states were used in verifying the CCSD(T) and DFT geometries and for locating additional minima. For first states, DFT bending potentials are compared with MRCI potentials. As a criterion for the quality of single-determinant geometries and energies of excited states, comparison of their vertical excitation energies with MRCI or time-dependent DFT values is recommended. [ABSTRACT FROM AUTHOR]

This paper describes an empirical localized orbital correction model which improves the accuracy of density functional theory (DFT) methods for the prediction of thermochemical properties for molecules of first and second row elements. The B3LYP localized orbital correction version of the model improves B3LYP DFT atomization energy calculations on the G3 data set of 222 molecules from a mean absolute deviation (MAD) from experiment of 4.8 to 0.8 kcal/mol. The almost complete elimination of large outliers and the substantial reduction in MAD yield overall results comparable to the G3 wave-function-based method; furthermore, the new model has zero additional computational cost beyond standard DFT calculations. The following four classes of correction parameters are applied to a molecule based on standard valence bond assignments: corrections to atoms, corrections to individual bonds, corrections for neighboring bonds of a given bond, and radical environmental corrections. Although the model is heuristic and is based on a 22 parameter multiple linear regression to experimental errors, each of the parameters is justified on physical grounds, and each provides insight into the fundamental limitations of DFT, most importantly the failure of current DFT methods to accurately account for nondynamical electron correlation. [ABSTRACT FROM AUTHOR]

A theoretical description of the vibrational excitons in DNA is presented by using the vibrational basis mode theory developed in Papers I and II. The parameters obtained from the density functional theory calculations, such as vibrational coupling constants and basis mode frequencies, are used to numerically simulate two-dimensional (2D) IR spectra of dGn:dCn and dAn:dTn double helices with n varying from 1 to 10. From the molecular dynamics simulations of dG5C5 and dA5T5 double helices in D2O solution, it is found that the thermally driven internal motions of these systems in an aqueous solution do not induce strong fluctuations of basis mode frequencies nor vibrational couplings. In order to construct the two-exciton Hamiltonian, the vibrational anharmonicities of eight basis modes are obtained by carrying out B3LYP/6-31G* calculations for the nine basis modes. The simulated 2D IR spectra of dGn:dCn double helix in D2O solution are directly compared with closely related experimental results. The 2D IR spectra of dGn:dCn and dAn:dTn are found to be weakly dependent on the number of base pairs. The present work demonstrates that the computational procedure combining quantum chemistry calculation and molecular dynamics simulation methods can be of use to predict 2D IR spectra of nucleic acids in solutions. [ABSTRACT FROM AUTHOR]

Within the scope of studying the molecular implications of the Pb2+ cation in environmental and polluting processes, this paper reports Hartree-Fock and density functional theory (B3LYP) four-component relativistic calculations using an all-electron basis set applied to [Pb(H2O)]2+ and [Pb(OH)]+, two complexes expected to be found in the terrestrial atmosphere. It is shown that full-relativistic calculations validate the use of scalar relativistic approaches within the framework of density functional theory. [Pb(H2O)]2+ is found C2v at any level of calculations whereas [Pb(OH)]+ can be found bent or linear depending of the computational methodology used. When Cs is found the barrier to inversion through the C∞v structure is very low, and can be overcome at high enough temperature, making the molecule floppy. In order to get a better understanding of the bonding occurring between the Pb2+ cation and the H2O and OH- ligands, natural bond orbital and atoms-in-molecule calculations have been performed. These approaches are supplemented by a topological analysis of the electron localization function. Finally, the description of these complexes is refined using constrained-space orbital variation complexation energy decompositions. [ABSTRACT FROM AUTHOR]

Density functional theory (DFT) was used to study polymer chains, tethered to a surface and in the presence of a solvent. For reasons of computational practicality, it is common practice to remove the explicit solvent molecules from the problem. Contact was made with two such models, which we call the "implicit-solvent" and "continuum-solvent" approximations. First, DFT was applied to tethered chains in an implicit solvent. Using the equation of state of bead-spring chains as input, we found excellent agreement of the theory with density profiles obtained in molecular dynamics simulations on the same model as a function of temperature. Next, DFT was applied to tethered chains in an incompressible, continuum solvent. Using the Flory-Huggins theory as input, our DFT equations reduced to conventional self-consistent field theory. From our DFT formalism, we demonstrated that the implicit-solvent problem, at a given temperature, is equivalent to the continuum-solvent problem, provided the x parameter and total density are interpreted appropriately. [ABSTRACT FROM AUTHOR]

The HNC (hypemetted-chain) equation is generalized at a three-body level based on the three-body density functional theory and the Percus' idea. Supplementing with the generalized OrnsteinZemike relations, we derive the three-body HNC theory for two- and three-body correlation functions. We solved the three-body HNC theory numerically for the case of a one-dimensional fluid and obtained the solution self-consistently. Our results are compared with the (two-body) HNC theory and molecular dynamics simulations. It is found that the three-body HNC theory improves the HNC one from the viewpoint of the radial distribution function. [ABSTRACT FROM AUTHOR]

We study nonideal mixing effects in the regime of warm dense matter (WDM) by computing the shock Hugoniot curves of BN, MgO, and MgSiO3. First, we derive these curves from the equations of state (EOS) of the fully interacting systems, which were obtained using a combination of path integral Monte Carlo calculations at high temperature and density functional molecular dynamics simulations at lower temperatures. We then use the ideal mixing approximation at constant pressure and temperature to rederive these Hugoniot curves from the EOS tables of the individual elements. We find that the linear mixing approximation works remarkably well at temperatures above ∼2 × 105 K, where the shock compression ratio exceeds ∼3.2. The shape of the Hugoniot curve of each compound is well reproduced. Regions of increased shock compression, which emerge because of the ionization of L and K shell electrons, are well represented, and the maximum compression ratio of the Hugoniot curves is reproduced with high precision. Some deviations are seen near the onset of the L shell ionization regime, where ionization equilibrium in the fully interacting system cannot be well reproduced by the ideal mixing approximation. This approximation also breaks down at lower temperatures, where chemical bonds play an increasingly important role. However, the results imply that the equilibrium properties of binary and ternary mixtures in the regime of WDM can be derived from the EOS tables of the individual elements. This significantly simplifies the characterization of binary and ternary mixtures in the WDM and plasma phases, which otherwise requires large numbers of more computationally expensive first-principles computer simulations. [ABSTRACT FROM AUTHOR]

This paper explores the possibility of combining projected Hartree-Fock and density functional theories for treating static and dynamic correlations in molecular systems with mean-field computational cost. The combination of spin-projected unrestricted Hartree-Fock (SUHF) with the TPSS correlation functional (SUHF+TPSS) yields excellent results for non-metallic molecular dissociations and singlet-triplet splittings. However, SUHF+TPSS fails to provide the qualitatively correct dissociation curve for the notoriously difficult case of the chromium dimer. By tuning the TPSS correlation parameters and adding complex conjugation symmetry breaking and restoration to SUHF, the right curve shape for Cr2 can be obtained; unfortunately, such a combination is found to lead to overcorrelation in the general case. [ABSTRACT FROM AUTHOR]

It is a well recognized difficult task to simulate the vibrational dynamics of ices using the density functional theory (DFT), and there has thus been rather limited success in modelling the inelastic neutron scattering (INS) spectra for even the simplest structure of ice, ice Ih, particularly in the translational region below 400 cm-1. The reason is partly due to the complex nature of hydrogen bonding (H-bond) among water-water molecules which require considerable improvement of the quantum mechanical simulation methods, and partly owing to the randomness of protons in ice structures which often requires simulation of large super-lattices. In this report, we present the first series of successful simulation results for ice Ih using DFT methods. On the basis of the recent advancement in the DFT programs, we have achieved for the first time theoretical outcomes that not only reproduce the rotational frequencies between 500 to 1200 cm-1 for ice Ih, but also the two optic peaks at ∼240 and 320 cm-1 in the translational region of the INS spectra [J. C. Li, J. Chem. Phys 105, 6733 (1996)]. Besides, we have also investigated the impact of pairwise configurations of H2O molecules on the H-bond and found that different proton arrangements of pairwise H2O in the ice Ih crystal lattice could not alter the nature of H-bond as significantly as suggested in an early paper [J. C. Li and D. K. Ross, Nature (London) 365, 327 (1993)], i.e., reproducing the two experimental optic peaks do not need to invoke the two H-bonds as proposed in the previous model which led to considerable debates. The results of this work suggest that the observed optic peaks may be attributed to the coupling between the two bands of H-O stretching modes in H2O. The current computational work is expected to shed new light on the nature of the H-bonds in water, and in addition to offer a new approach towards probing the interaction between water and biomaterials for which H-bond is essential. [ABSTRACT FROM AUTHOR]

Plane wave basis sets offer many advantages in ab initio molecular dynamics due to their efficiency and simplicity. In combination with hybrid density functionals, they become computationally expensive due to the evaluation of the Hartree-Fock exchange energy. The computational cost can be significantly reduced by screening the Kohn-Sham orbital products after localizing the orbitals in real space. However, such a procedure introduces apparent errors in the wavefunctions and nuclear forces resulting in unstable dynamics. It is shown here that a noise-stabilized dynamics approach can overcome this problem and at the same time permits using insufficiently converged wavefunctions for evaluating atomic forces. In this way, we achieve significant speed up even for a small system containing about 100 atoms. After benchmarking the accuracy and efficiency of this approach, we use it in combination with well-sliced metadynamics to compute the free energy barrier of formamide hydrolysis in alkaline aqueous medium. These results provide insight into the error of the Perdew-Burke-Ernzerhof functional in predicting the free energy barrier for hydrolysis reactions in water. [ABSTRACT FROM AUTHOR]

In this paper the ab initio potential of mean force for the formic acid-water system is calculated in a Monte Carlo simulation using a classical fluctuating charge molecular mechanics potential to guide Monte Carlo updates. The ab initio energies in the simulation are calculated using density-functional theory (DFT) methods recently developed by Salahub et al. [J. Chem. Phys. 107, 6770 (1997)] to describe hydrogen-bonded systems. Importance sampling methods are used to investigate structural changes and it is demonstrated that using a molecular mechanics importance function can improve the efficiency of a DFT simulation by several orders of magnitude. Monte Carlo simulation of the system in a canonical ensemble at T=300 K reveals two chemical processes at intermediate time scales: The rotation of the H[sub 2]O bonded to HCOOH, which takes place on a time scale of 3 ps, and the dissociation of the complex which occurs in 24 ps. It is shown that these are the only important structural "reactions" in the formic acid-water cluster which take place on a time scale shorter than the double transfer of the proton. © 2000 American Institute of Physics. [ABSTRACT FROM AUTHOR]

Recently, we introduced a new density-functional theory (DFT) approach for the calculation of NMR shielding constants. First, a hybrid DFT calculation (using 5% exact exchange) is performed on the molecule to determine Kohn-Sham orbitals and their energies; second, the constants are determined as in nonhybrid DFT theory, that is, the paramagnetic contribution to the constants is calculated from a noniterative, uncoupled sum-over-states expression. The initial results suggested that this semiempirical DFT approach gives shielding constants in good agreement with the best ab initio and experimental data; in this paper, we further validate this procedure, using London orbitals in the theory, having implemented DFT into the ab initio code DALTON. Calculations on a number of small and medium-sized molecules confirm that our approach produces shieldings in excellent agreement with experiment and the best ab initio results available, demonstrating its potential for the study of shielding constants of large systems. © 2000 American Institute of Physics. [ABSTRACT FROM AUTHOR]

In this work, a range of van der Waals type density functionals are applied to the H2O/NaCl(001) and H2O/MgO(001) interface systems to explore the effect of an explicit dispersion treatment. The functionals we use are the self-consistent vdW functionalsvdW-DF,vdW-DF2, optPBE-vdW, optB88- vdW, optB86b-vdW, and vdW-DF-cx, as well as the dispersion-corrected PBE-TS and PBE-D2 methods; they are all compared with the standard PBE functional. For both NaCl(001) and MgO(001), we find that the dispersion-flavoured functionals stabilize thewater-surface interface by approximately 20%-40% compared to the PBE results. For NaCl(001), where the water molecules remain intact for all overlayers, the dominant contribution to the adsorption energy from "density functional theory dispersion" stems from the water-surface interactions rather than the water-water interactions. The optPBE-vdW and vdW-DF-cx functionals yield adsorption energies in good agreement with available experimental values for both NaCl and MgO. To probe the strengths of the perturbations of the adsorbed water molecules, we also calculated water dipole moments and found an increase up to 85% for water at the MgO(001) surface and 70% at the NaCl(001) surface, compared to the gas-phase dipole moment. [ABSTRACT FROM AUTHOR]

Accounting for electrons and nuclei simultaneously is a powerful capability of ab initio molecular dynamics (AIMD). However, AIMD is often unable to accurately reproduce properties of systems such as water due to inaccuracies in the underlying electronic density functionals. This shortcoming is often addressed by added empirical corrections and/or increasing the simulation temperature. We present here a maximum-entropy approach to directly incorporate limited experimental data via a minimal bias. Biased AIMD simulations of water and an excess proton in water are shown to give significantly improved properties both for observables which were biased to match experimental data and for unbiased observables. This approach also yields new physical insight into inaccuracies in the underlying density functional theory as utilized in the unbiased AIMD. [ABSTRACT FROM AUTHOR]

The structural properties of a-HfO2/Ge(2 × 1)-(001) and a-ZrO2/Ge(2 × 1)-(001) interfaces were investigated with and without a GeOx interface interlayer using density-functional theory (DFT) molecular dynamics (MD) simulations. Realistic a-HfO2 and a-ZrO2 samples were generated using a hybrid classical-DFT MD "melt-and-quench" approach and tested against experimental properties. The oxide/Ge stacks were annealed at 700 K, cooled to 0 K, and relaxed providing the system withenough freedom toform realistic interfaces. For each high-K/Ge stack type, two systems with single and double interfaces were investigated. All stacks were free of midgap states; however, stacks with a GeOx interlayer had band-edge states which decreased the band gaps by 0%-30%. These band-edge states were mainly produced by under-coordinated Ge atoms in GeOx layer or its vicinity due to deformation, intermixing, and bond-breaking. The DFT-MD simulations show that electronically passive interfaces can be formed either directly between high-K dielectrics and Ge or with a monolayer of GeO2 if the processing does not create or properly passivate under-coordinated Ge atoms and Ge's with significantly distorted bonding angles. Comparison to the charge states of the interfacial atoms from DFT to experimental x-ray photoelectron spectroscopy results shows that while most studies of gate oxide on Ge(001) have a GeOx interfacial layer, it is possible toform an oxide/Ge interface without a GeOx interfacial layer. Comparison to experiments is consistent with the dangling bonds in the suboxide being responsible for midgap state formation. [ABSTRACT FROM AUTHOR]

We investigate the adsorption behavior of four different amino acids (glutamine, glutamate, serine, cysteine) on the zinc oxide (10110) surface, comparing the geometry and energy associated with a number of different adsorption configurations. In doing this, we highlight the benefits and limits of using density-functional tight-binding (DFTB) with respect to standard density functional theory (DFT). The DFTB method is found to reliably reproduce the DFT adsorption geometries. Analysis of the adsorption configurations emphasizes the fundamental role of the first hydration layer in mediating the interactions between the amino acids and the surface. Direct surface-molecule bonds are found to form predominantly via the carboxylate groups of the studied amino acids. No surfacemediated chemical reactions are observed, with the notable exception of a proton transfer from the thiol group of cysteine to a hydroxyl group of the surface hydration layer. The adsorption energies are found to be dominated both by the formation of direct or indirect surface-molecule hydrogen bonds, but also by the rearrangement of the hydrogen-bond network in surface proximity in a non-intuitive way. Energetic comparisons between DFTB and DFT are made difficult on one side by the long time necessary to achieve convergence of potential energy values in MD simulations and on the other side by the necessity of including higher-order corrections to DFTB to obtain a good description of the hydrogen bond energetics. Overall, our results suggest that DFTB is a good reference method to set the correct chemical states and the initial geometries of hybrid biomolecule/ZnO systems to be simulated with non-reactive force fields. [ABSTRACT FROM AUTHOR]

How do lipid molecules in membranes perform a flip-flop? The flip-flops of lipid molecules play a crucial role in the formation and flexibility of membranes. However, little has been determined about the behavior of flip-flops, either experimentally, or in molecular dynamics simulations. Here, we provide numerical results of the flip-flops of model lipid molecules in a model membrane and investigate the statistical properties, using millisecond-order coarse-grained molecular simulations (dissipative particle dynamics). We find that there are three different ways of flip-flops, which can be clearly characterized by their paths on the free energy surface. Furthermore, we found that the probability of the number of the flip-flops is well fitted by the Poisson distribution, and the probability density function for the inter-occurrence times of flip-flops coincides with that of the forward recurrence times. These results indicate that the occurrence of flip-flops is a Poisson process, which will play an important role in the flexibilities of membranes. [ABSTRACT FROM AUTHOR]

Asymmetric binary mixtures of hard-spheres exhibit several interesting thermodynamic phenomena, such as multiple kinds of glassy states. When the degrees of freedom of the small spheres are integrated out from the description, their effects are incorporated into an effective pair interaction between large spheres known as the depletion potential. The latter has been widely used to study both the phase behavior and dynamic arrest of the big particles. Depletion forces can be accounted for by a contraction of the description in the multicomponent Ornstein-Zernike equation [R. Castañeda-Priego, A. Rodríguez-López, and J. M. Méndez-Alcaraz, Phys. Rev. E 73, 051404 (2006)]. Within this theoretical scheme, an approximation for the difference between the effective and bare bridge functions is needed. In the limit of infinite dilution, this difference is irrelevant and the typical Asakura-Osawa depletion potential is recovered. At higher particle concentrations, however, this difference becomes important, especially where the shell of first neighbors is formed, and, as shown here, cannot be simply neglected. In this work, we use a variant of the Verlet expression for the bridge functions to highlight their importance in the calculation of the depletion potential at high densities and close to the spinodal decomposition. We demonstrate that the modified Verlet closure predicts demixing in binary mixtures of hard spheres for different size ratios and compare its predictions with both liquid state and density functional theories, computer simulations, and experiments. We also show that it provides accurate correlation functions even near the thermodynamic instability; this is explicitly corroborated with results of molecular dynamics simulations of the whole mixture. Particularly, our findings point toward a possible universal behavior of the depletion potential around the spinodal line. [ABSTRACT FROM AUTHOR]

We present first principles molecular dynamics simulations of the chloride anion in liquid water performed using gradient-corrected and hybrid density functionals. We show that it is necessary to use hybrid functionals both for the generation of molecular dynamics trajectories and for the calculation of electronic states in order to obtain a qualitatively correct description of the electronic properties of the solution. In particular, it is only with hybrid functionals that the highest occupied molecular orbital of the anion is found above the valence band maximum of water, consistent with photoelectron detachment measurements. Similar results were obtained using many body perturbation theory within the G0W0 approximation. [ABSTRACT FROM AUTHOR]

In biological and synthetic materials, many important processes involve charges that are present in a medium with spatially varying dielectric permittivity. To accurately understand the role of electrostatic interactions in such systems, it is important to take into account the spatial dependence of the permittivity of the medium. However, due to the ensuing theoretical and computational challenges, this inhomogeneous dielectric response of the medium is often ignored or excessively simplified. We develop a variational formulation of electrostatics to accurately investigate systems that exhibit this inhomogeneous dielectric response. Our formulation is based on a true energy functional of the polarization charge density. The defining characteristic of a true energy functional is that at its minimum it evaluates to the actual value of the energy; this is a feature not found in many commonly used electrostatic functionals. We explore in detail the charged systems that exhibit sharp discontinuous change in dielectric permittivity, and we show that for this case our functional reduces to a functional of only the surface polarization charge density. We apply this reduced functional to study model problems for which analytical solutions are well known. We demonstrate, in addition, that the functional has many properties that make it ideal for use in molecular dynamics simulations. [ABSTRACT FROM AUTHOR]

Hydrogen bond interactions strongly affect vibrational properties and frequencies, the most common consequence being a redshift of the stretching vibration involved; there are, however, few exceptions to this general trend. In previous works, we have proved the effectiveness of ab initio simulations combined with wavelet analysis to investigate these effects and put them into relation to structural environment. In this work, we investigate the hydrogen bond effects on the structural and vibrational properties of 1,3-propanediol in acetonitrile by a combined experimental and computational approach. We explain the appearance of two spectral components in the O-H stretching band on the basis of intra- and intermolecular hydrogen bond interactions. We also elucidate the blueshift of the C≡N stretching band as due to a hydrogen bond interaction between the glycol and acetonitrile that modify the electron density distribution inside the CN group. This effect is well reproduced by ab initio molecular dynamics simulations and density functional calculations reported in this work. [ABSTRACT FROM AUTHOR]

Molecular structures that permit intramolecular rotational motion have the potential to function as molecular rotors. We have employed density functional theory and vibrational frequency analysis to study the characteristic structure and vibrational behavior of the molecule (4′,4″″-(bicyclo[2,2,2]octane-1,4-diyldi-4,1-phenylene)-bis-2,2′:6′,2″-terpyridine. IR active vibrational modes were found that favor intramolecular rotation. To demonstrate the rotor behavior of the isolated single molecule, ab initio molecular dynamics simulations at various temperatures were carried out. This molecular rotor is expected to be thermally triggered via excitation of specific vibrational modes, which implies randomness in its direction of rotation. [ABSTRACT FROM AUTHOR]

There is a growing need to understand the stability of quasi-one-dimensional one-layer-thick graphene nanoribbons. Objective molecular dynamics based on density-functional tight-binding models are used to investigate the stability against torsional deformations of nanoribbons with bare, F-, and OH-decorated armchair edges. The prevalence of chiral nanoribbons, including homochiral ones, prompted the construction of a simple phenomenological model inspired from the Landau phase transition theory. Our model is based on atomistic data and gives the structural parameters of the nanoribbon as a function of its edge chemistry and axial strain. [ABSTRACT FROM AUTHOR]

We show that classical molecular density functional theory, here in the homogeneous reference fluid approximation in which the functional is inferred from the properties of the bulk solvent, is a powerful new tool to study, at a fully molecular level, the solvation of complex surfaces and interfaces by polar solvents. This implicit solvent method allows for the determination of structural, orientational, and energetic solvation properties that are on a par with all-atom molecular simulations performed for the same system, while reducing the computer time by two orders of magnitude. This is illustrated by the study of an atomistically-resolved clay surface composed of over a thousand atoms wetted by a molecular dipolar solvent. The high numerical efficiency of the method is exploited to carry a systematic analysis of the electrostatic and non-electrostatic components of the surface-solvent interaction within the popular Clay Force Field (CLAYFF). Solvent energetics and structure are found to depend weakly upon the atomic charges distribution of the clay surface, even for a rather polar solvent. We conclude on the consequences of such findings for force-field development. [ABSTRACT FROM AUTHOR]

We use the weighted histogram analysis method [S. Kumar, D. Bouzida, R. H. Swendsen, P. A. Kollman, and J. M. Rosenberg, J. Comput. Chem. 13, 1011 (1992)] to calculate the free energy surface of the ST2 model of water as a function of density and bond-orientational order. We perform our calculations at deeply supercooled conditions (T = 228.6 K, P = 2.2 kbar; T = 235 K, P = 2.2 kbar) and focus our attention on the region of bond-orientational order that is relevant to disordered phases. We find a first-order transition between a low-density liquid (LDL, ρ ≈ 0.9 g/cc) and a high-density liquid (HDL, ρ ≈ 1.15 g/cc), confirming our earlier sampling of the free energy surface of this model as a function of density [Y. Liu, A. Z. Panagiotopoulos, and P. G. Debenedetti, J. Chem. Phys. 131, 104508 (2009)]. We demonstrate the disappearance of the LDL basin at high pressure and of the HDL basin at low pressure, in agreement with independent simulations of the system's equation of state. Consistency between directly computed and reweighted free energies, as well as between free energy surfaces computed using different thermodynamic starting conditions, confirms proper equilibrium sampling. Diffusion and structural relaxation calculations demonstrate that equilibration of the LDL phase, which exhibits slow dynamics, is attained in the course of the simulations. Repeated flipping between the LDL and HDL phases in the course of long molecular dynamics runs provides further evidence of a phase transition. We use the Ewald summation with vacuum boundary conditions to calculate long-ranged Coulombic interactions and show that conducting boundary conditions lead to unphysical behavior at low temperatures. [ABSTRACT FROM AUTHOR]

Using quantum mechanics (QM) and classical force-field based molecular dynamics (FF), we have calculated the principle shock Hugoniot curves for numerous amorphous polymers including poly[methyl methacrylate] (PMMA), poly[styrene], polycarbonate, as well as both the amorphous and crystalline forms of poly[ethylene]. In the FF calculations, we considered a non-reactive force field (i.e., polymer consistent FF). The QM calculations were performed with density functional theory (DFT) using dispersion corrected atom centered pseudopotentials. Overall, results obtained by DFT show much better agreement with available experimental data than classical force fields. In particular, DFT calculated Hugoniot curves for PMMA up to 74 GPa are in very good agreement with experimental data, where a preliminary study of chain fracture and association was also performed. Structure analysis calculations of the radius of gyration and carbon-carbon radial distribution function were also carried out to elucidate contraction of the polymer chains with increasing pressure. [ABSTRACT FROM AUTHOR]