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See detailMany-body dispersion effects in the binding of adsorbates on metal surfaces
Maurer, Reinhard J.; Ruiz, Victor G.; Tkatchenko, Alexandre UL

in JOURNAL OF CHEMICAL PHYSICS (2015), 143(10),

A correct description of electronic exchange and correlation effects for molecules in contact with extended (metal) surfaces is a challenging task for first-principles modeling. In this work, we ... [more ▼]

A correct description of electronic exchange and correlation effects for molecules in contact with extended (metal) surfaces is a challenging task for first-principles modeling. In this work, we demonstrate the importance of collective van der Waals dispersion effects beyond the pairwise approximation for organic-inorganic systems on the example of atoms, molecules, and nanostructures adsorbed on metals. We use the recently developed many-body dispersion (MBD) approach in the context of density-functional theory [Tkatchenko et al., Phys. Rev. Lett. 108 236402 (2012) and Ambrosetti et al., J. Chem. Phys. 140, 18A508 (2014)] and assess its ability to correctly describe the binding of adsorbates on metal surfaces. We briefly review the MBD method and highlight its similarities to quantum-chemical approaches to electron correlation in a quasiparticle picture. In particular, we study the binding properties of xenon, 3,4,9,10-perylene-tetracarboxylic acid, and a graphene sheet adsorbed on the Ag(111) surface. Accounting for MBD effects, we are able to describe changes in the anisotropic polarizability tensor, improve the description of adsorbate vibrations, and correctly capture the adsorbate-surface interaction screening. Comparison to other methods and experiment reveals that inclusion of MBD effects improves adsorption energies and geometries, by reducing the overbinding typically found in pairwise additive dispersion-correction approaches. (C) 2015 AIP Publishing LLC. [less ▲]

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See detailCrystal growth from a supersaturated melt: Relaxation of the solid-liquid dynamic stiffness
Turci, Francesco UL; Schilling, Tanja UL

in Journal of Chemical Physics (2014), 141

We discuss the growth process of a crystalline phase out of a metastable over-compressed liquid that is brought into contact with a crystalline substrate. The process is modeled by means of molecular ... [more ▼]

We discuss the growth process of a crystalline phase out of a metastable over-compressed liquid that is brought into contact with a crystalline substrate. The process is modeled by means of molecular dynamics. The particles interact via the Lennard-Jones potential and their motion is locally thermalized by Langevin dynamics. We characterize the relaxation process of the solid-liquid interface, showing that the growth speed is maximal for liquid densities above the solid coexistence density, and that the structural properties of the interface rapidly converge to equilibrium-like properties. In particular, we show that the off-equilibrium dynamic stiffness can be extracted using capillary wave theory arguments, even if the growth front moves fast compared to the typical diffusion time of the compressed liquid, and that the dynamic stiffness converges to the equilibrium stiffness in times much shorter than the diffusion time. [less ▲]

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See detailIrreversible thermodynamics of open chemical networks. I. Emergent cycles and broken conservation laws
Polettini, Matteo UL; Esposito, Massimiliano UL

in Journal of Chemical Physics (2014), 141

chemical reaction networks, with special regard to metabolic networks regulating cellular physiology and biochemical functions. We first introduce closed networks “in a box”, whose thermodynamics is ... [more ▼]

chemical reaction networks, with special regard to metabolic networks regulating cellular physiology and biochemical functions. We first introduce closed networks “in a box”, whose thermodynamics is subjected to strict physical constraints: the mass-action law, elementarity of processes, and detailed balance. We further digress on the role of solvents and on the seemingly unacknowledged property of network independence of free energy landscapes. We then open the system by assuming that the concentrations of certain substrate species (the chemostats) are fixed, whether because promptly regulated by the environment via contact with reservoirs, or because nearly constant in a time window. As a result, the system is driven out of equilibrium. A rich algebraic and topological structure ensues in the network of internal species: Emergent irreversible cycles are associated with nonvanishing affinities, whose symmetries are dictated by the breakage of conservation laws. These central results are resumed in the relation a + b = sY between the number of fundamental affinities a, that of broken conservation laws b and the number of chemostats sY. We decompose the steady state entropy production rate in terms of fundamental fluxes and affinities in the spirit of Schnakenberg’s theory of network thermodynamics, paving the way for the forthcoming treatment of the linear regime, of efficiency and tight coupling, of free energy transduction, and of thermodynamic constraints for network reconstruction. [less ▲]

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See detailInsight into the description of van der Waals forces for benzene adsorption on transition metal (111) surfaces
Tkatchenko, Alexandre UL; Carrasco, Javier; Liu, Wei et al

in Journal of Chemical Physics (2014), 140(8),

Exploring the role of van der Waals (vdW) forces on the adsorption of molecules on extended metal surfaces has become possible in recent years thanks to exciting developments in density functional theory ... [more ▼]

Exploring the role of van der Waals (vdW) forces on the adsorption of molecules on extended metal surfaces has become possible in recent years thanks to exciting developments in density functional theory (DFT). Among these newly developed vdW-inclusive methods, interatomic vdW approaches that account for the nonlocal screening within the bulk [V. G. Ruiz, W. Liu, E. Zojer, M. Scheffler, and A. Tkatchenko, Phys. Rev. Lett. 108, 146103 (2012)] and improved nonlocal functionals [J. Klimes, D. R. Bowler, and A. Michaelides, J. Phys.: Condens. Matter 22, 022201 (2010)] have emerged as promising candidates to account efficiently and accurately for the lack of long-range vdW forces in most popular DFT exchange-correlation functionals. Here we have used these two approaches to compute benzene adsorption on a range of close-packed (111) surfaces upon which it either physisorbs (Cu, Ag, and Au) or chemisorbs (Rh, Pd, Ir, and Pt). We have thoroughly compared the performance between the two classes of vdW-inclusive methods and when available compared the results obtained with experimental data. By examining the computed adsorption energies, equilibrium distances, and binding curves we conclude that both methods allow for an accurate treatment of adsorption at equilibrium adsorbate-substrate distances. To this end, explicit inclusion of electrodynamic screening in the interatomic vdW scheme and optimized exchange functionals in the case of nonlocal vdW density functionals is mandatory. Nevertheless, some discrepancies are found between these two classes of methods at large adsorbate-substrate separations. [less ▲]

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See detailLong-range correlation energy calculated from coupled atomic response functions
Ambrosetti, Alberto; Reilly, Anthony M.; DiStasio, Robert A. Jr et al

in JOURNAL OF CHEMICAL PHYSICS (2014), 140(18),

An accurate determination of the electron correlation energy is an essential prerequisite for describing the structure, stability, and function in a wide variety of systems. Therefore, the development of ... [more ▼]

An accurate determination of the electron correlation energy is an essential prerequisite for describing the structure, stability, and function in a wide variety of systems. Therefore, the development of efficient approaches for the calculation of the correlation energy (and hence the dispersion energy as well) is essential and such methods can be coupled with many density-functional approximations, local methods for the electron correlation energy, and even interatomic force fields. In this work, we build upon the previously developed many-body dispersion (MBD) framework, which is intimately linked to the random-phase approximation for the correlation energy. We separate the correlation energy into short-range contributions that are modeled by semi-local functionals and long-range contributions that are calculated by mapping the complex all-electron problem onto a set of atomic response functions coupled in the dipole approximation. We propose an effective range-separation of the coupling between the atomic response functions that extends the already broad applicability of the MBD method to non-metallic materials with highly anisotropic responses, such as layered nanostructures. Application to a variety of high-quality benchmark datasets illustrates the accuracy and applicability of the improved MBD approach, which offers the prospect of first-principles modeling of large structurally complex systems with an accurate description of the long-range correlation energy. (C) 2014 AIP Publishing LLC. [less ▲]

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See detailCrystal nucleation mechanism in melts of short polymer chains under quiescent conditions and under shear flow
Anwar, Muhammad UL; Berryman, Josh UL; Schilling, Tanja UL

in Journal of Chemical Physics (2014), (141), 124910

We present a molecular dynamics simulation study of crystal nucleation from undercooled melts of n-alkanes, and we identify the molecular mechanism of homogeneous crystal nucleation under quiescent ... [more ▼]

We present a molecular dynamics simulation study of crystal nucleation from undercooled melts of n-alkanes, and we identify the molecular mechanism of homogeneous crystal nucleation under quiescent conditions and under shear flow. We compare results for n-eicosane (C20) and npentacontahectane (C150), i.e., one system below the entanglement length and one above, at 20%– 30% undercooling. Under quiescent conditions, we observe that entanglement does not have an effect on the nucleation mechanism. For both chain lengths, the chains first align and then straighten locally, then the local density increases and finally positional ordering sets in. At low shear rates the nucleation mechanism is the same as under quiescent conditions, while at high shear rates the chains align and straighten at the same time. We report on the effects of shear rate and temperature on the nucleation rates and estimate the critical shear rates, beyond which the nucleation rates increase with the shear rate. In agreement with previous experimental observation and theoretical work, we find that the critical shear rate corresponds to a Weissenberg number of order 1. Finally, we show that the viscosity of the system is not affected by the crystalline nuclei. [less ▲]

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See detailCrystallization mechanism in melts of short n-alkane chains
Anwar, Muhammad UL; Turci, Francesco UL; Schilling, Tanja UL

in Journal of Chemical Physics (2013), 139(21),

We study crystallization in a model system for eicosane (C20) by means of molecular dynamics simulation and identify the microscopic mechanisms of homogeneous crystal nucleation and growth. For the ... [more ▼]

We study crystallization in a model system for eicosane (C20) by means of molecular dynamics simulation and identify the microscopic mechanisms of homogeneous crystal nucleation and growth. For the nucleation process, we observe that chains first align and then straighten. Then the local density increases and finally the monomer units become ordered positionally. The subsequent crystal growth process is characterized by a sliding-in motion of the chains. Chains preferably attach to the crystalline cluster with one end and then move along the stems of already crystallized chains towards their final position. This process is cooperative, i.e., neighboring chains tend to get attached in clusters rather than independently. [less ▲]

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See detailCrystallization in glassy suspensions of hard ellipsoids
Dorosz, Sven UL; Schilling, Tanja UL

in Journal of Chemical Physics (2013), 139(12),

We have carried out computer simulations of overcompressed suspensions of hard monodisperse ellipsoids and observed their crystallization dynamics. The system was compressed very rapidly in order to reach ... [more ▼]

We have carried out computer simulations of overcompressed suspensions of hard monodisperse ellipsoids and observed their crystallization dynamics. The system was compressed very rapidly in order to reach the regime of slow, glass-like dynamics. We find that, although particle dynamics become sub-diffusive and the intermediate scattering function clearly develops a shoulder, crystallization proceeds via the usual scenario: nucleation and growth for small supersaturations, spinodal decomposition for large supersaturations. In particular, we compared the mobility of the particles in the regions where crystallization set in with the mobility in the rest of the system. We did not find any signature in the dynamics of the melt that pointed towards the imminent crystallization events. [less ▲]

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See detailOn the accuracy of van der Waals inclusive density-functional theory exchange-correlation functionals for ice at ambient and high pressures
Santra, Biswajit; Klimes, Jiri; Tkatchenko, Alexandre UL et al

in JOURNAL OF CHEMICAL PHYSICS (2013), 139(15),

Density-functional theory (DFT) has been widely used to study water and ice for at least 20 years. However, the reliability of different DFT exchange-correlation (xc) functionals for water remains a ... [more ▼]

Density-functional theory (DFT) has been widely used to study water and ice for at least 20 years. However, the reliability of different DFT exchange-correlation (xc) functionals for water remains a matter of considerable debate. This is particularly true in light of the recent development of DFT based methods that account for van der Waals (vdW) dispersion forces. Here, we report a detailed study with several xc functionals (semi-local, hybrid, and vdW inclusive approaches) on ice Ih and six proton ordered phases of ice. Consistent with our previous study [B. Santra, J. Klimes, D. Alfe, A. Tkatchenko, B. Slater, A. Michaelides, R. Car, and M. Scheffler, Phys. Rev. Lett. 107, 185701 (2011)] which showed that vdW forces become increasingly important at high pressures, we find here that all vdW inclusive methods considered improve the relative energies and transition pressures of the high-pressure ice phases compared to those obtained with semi-local or hybrid xc functionals. However, we also find that significant discrepancies between experiment and the vdW inclusive approaches remain in the cohesive properties of the various phases, causing certain phases to be absent from the phase diagram. Therefore, room for improvement in the description of water at ambient and high pressures remains and we suggest that because of the stern test the high pressure ice phases pose they should be used in future benchmark studies of simulation methods for water. (C) 2013 AIP Publishing LLC. [less ▲]

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See detailUnderstanding the role of vibrations, exact exchange, and many-body van der Waals interactions in the cohesive properties of molecular crystals
Reilly, Anthony M.; Tkatchenko, Alexandre UL

in Journal of Chemical Physics (2013), 139(2),

The development and application of computational methods for studying molecular crystals, particularly density-functional theory (DFT), is a large and ever-growing field, driven by their numerous ... [more ▼]

The development and application of computational methods for studying molecular crystals, particularly density-functional theory (DFT), is a large and ever-growing field, driven by their numerous applications. Here we expand on our recent study of the importance of many-body van der Waals interactions in molecular crystals [A. M. Reilly and A. Tkatchenko, J. Phys. Chem. Lett. 4, 1028 (2013)], with a larger database of 23 molecular crystals. Particular attention has been paid to the role of the vibrational contributions that are required to compare experiment sublimation enthalpies with calculated lattice energies, employing both phonon calculations and experimental heat-capacity data to provide harmonic and anharmonic estimates of the vibrational contributions. Exact exchange, which is rarely considered in DFT studies of molecular crystals, is shown to have a significant contribution to lattice energies, systematically improving agreement between theory and experiment. When the vibrational and exact-exchange contributions are coupled with a many-body approach to dispersion, DFT yields a mean absolute error (3.92 kJ/mol) within the coveted "chemical accuracy" target (4.2 kJ/mol). The role of many-body dispersion for structures has also been investigated for a subset of the database, showing good performance compared to X-ray and neutron diffraction crystal structures. The results show that the approach employed here can reach the demanding accuracy of crystal-structure prediction and organic material design with minimal empiricism. © 2013 AIP Publishing LLC. [less ▲]

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See detailInteratomic methods for the dispersion energy derived from the adiabatic connection fluctuation-dissipation theorem
Tkatchenko, Alexandre UL; Ambrosetti, Alberto; DiStasio, Jr

in JOURNAL OF CHEMICAL PHYSICS (2013), 138(7),

Interatomic pairwise methods are currently among the most popular and accurate ways to include dispersion energy in density functional theory calculations. However, when applied to more than two atoms ... [more ▼]

Interatomic pairwise methods are currently among the most popular and accurate ways to include dispersion energy in density functional theory calculations. However, when applied to more than two atoms, these methods are still frequently perceived to be based on ad hoc assumptions, rather than a rigorous derivation from quantum mechanics. Starting from the adiabatic connection fluctuation-dissipation (ACFD) theorem, an exact expression for the electronic exchange-correlation energy, we demonstrate that the pairwise interatomic dispersion energy for an arbitrary collection of isotropic polarizable dipoles emerges from the second-order expansion of the ACFD formula upon invoking the random-phase approximation (RPA) or the full-potential approximation. Moreover, for a system of quantum harmonic oscillators coupled through a dipole-dipole potential, we prove the equivalence between the full interaction energy obtained from the Hamiltonian diagonalization and the ACFD-RPA correlation energy. This property makes the Hamiltonian diagonalization an efficient method for the calculation of the many-body dispersion energy. In addition, we show that the switching function used to damp the dispersion interaction at short distances arises from a short-range screened Coulomb potential, whose role is to account for the spatial spread of the individual atomic dipole moments. By using the ACFD formula, we gain a deeper understanding of the approximations made in the interatomic pairwise approaches, providing a powerful formalism for further development of accurate and efficient methods for the calculation of the dispersion energy. (C) 2013 American Institute of Physics. [http://dx.doi.org/10.1063/1.4789814] [less ▲]

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See detailTunneling Conductivity in Composites of Attractive Colloids
Nigro, Biagio; Grimaldi, Claudio; Miller, M.A. et al

in Journal of Chemical Physics (2012), 136(164903), 1-5

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See detailOn the influence of a patterned substrate on crystallization in suspensions of hard spheres
Dorosz, Sven UL; Schilling, Tanja UL

in Journal of Chemical Physics (2012), 136(issue 4), 1-5

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See detailHow Close to Two Dimensions Does a Lennard-Jones System Need to Be to Produce a Hexatic Phase?
Gribova, Nadezhda; Arnold, A.; Schilling, Tanja UL et al

in Journal of Chemical Physics (2011), 054514(135), 1-10

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See detailA general algorithm for sampling rare events in non-equilibrium and non-stationary systems
Berryman, Josh UL; Schilling, Tanja UL

in Journal of Chemical Physics (2010), 133

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See detailTwo- and three-body interatomic dispersion energy contributions to binding in molecules and solids
Anatole Von Lilienfeld, O.; Tkatchenko, Alexandre UL

in Journal of Chemical Physics (2010), 132(23),

We present numerical estimates of the leading two- and three-body dispersion energy terms in van der Waals interactions for a broad variety of molecules and solids. The calculations are based on London ... [more ▼]

We present numerical estimates of the leading two- and three-body dispersion energy terms in van der Waals interactions for a broad variety of molecules and solids. The calculations are based on London and Axilrod-Teller-Muto expressions where the required interatomic dispersion energy coefficients, C6 and C9, are computed "on the fly" from the electron density. Inter- and intramolecular energy contributions are obtained using the Tang-Toennies (TT) damping function for short interatomic distances. The TT range parameters are equally extracted on the fly from the electron density using their linear relationship to van der Waals radii. This relationship is empiricially determined for all the combinations of He-Xe rare gas dimers, as well as for the He and Ar trimers. The investigated systems include the S22 database of noncovalent interactions, Ar, benzene and ice crystals, bilayer graphene, C60 dimer, a peptide (Ala10), an intercalated drug-DNA model [ellipticine- d (CG) 2], 42 DNA base pairs, a protein (DHFR, 2616 atoms), double stranded DNA (1905 atoms), and 12 molecular crystal polymorphs from crystal structure prediction blind test studies. The two- and three-body interatomic dispersion energies are found to contribute significantly to binding and cohesive energies, for bilayer graphene the latter reaches 50% of experimentally derived binding energy. These results suggest that interatomic three-body dispersion potentials should be accounted for in atomistic simulations when modeling bulky molecules or condensed phase systems. © 2010 American Institute of Physics. [less ▲]

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See detailSolid-solid phase transition in hard ellipsoids
Radu, Marc UL; Pfleiderer, P.; Schilling, Tanja UL

in Journal of Chemical Physics (2009), 131(16),

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See detailOsmotic compression of droplets of hard rods: A computer simulation study
Trukhina, Yu; Jungblut, S.; van der Schoot, Paul et al

in Journal of Chemical Physics (2009), 130(16),

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See detailDispersion-corrected Moller-Plesset second-order perturbation theory
Tkatchenko, Alexandre UL; Distasio, Robert A. Jr.; Head-Gordon, Martin et al

in Journal of Chemical Physics (2009), 131

We show that the often unsatisfactory performance of Møller-Plesset second-order perturbation theory (MP2) for the dispersion interaction between closed-shell molecules can be rectified by adding a ... [more ▼]

We show that the often unsatisfactory performance of Møller-Plesset second-order perturbation theory (MP2) for the dispersion interaction between closed-shell molecules can be rectified by adding a correction Δ C n / Rn, to its long-range behavior. The dispersion-corrected MP2 (MP2+ΔvdW) results are in excellent agreement with the quantum chemistry "gold standard" [coupled cluster theory with single, double and perturbative triple excitations, CCSD(T)] for a range of systems bounded by hydrogen bonding, electrostatics and dispersion forces. The MP2+ΔvdW method is only mildly dependent on the short-range damping function and consistently outperforms state-of-the-art dispersion-corrected density-functional theory. © 2009 American Institute of Physics. [less ▲]

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See detailComputing absolute free energies of disordered structures by molecular simulation
Schilling, Tanja UL; Schmid, Friederike

in Journal of Chemical Physics (2009), 131(23),

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