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The absorption spectroscopy of calcium-doped argon clusters is described in terms of an effective diatomics molecule Ca-(Ar_n), in the framework of semiclassical vertical transitions. We show how, upon choosing a suitable reaction coordinate, the effective finite-temperature equilibrium properties can be obtained for the ground- and excited-surfaces from the potential of mean force (PMF). An extension of the recent multiple range random-walk method is used to calculate the PMF over continuous intervals of distances. The absorption spectra calculated using this single-coordinate description are found to be in good agreement with the spectra obtained from high-statistics Monte Carlo data, in various situations. For CaAr$_{13}$, we compare the performances of two different choices of the reaction coordinate. For CaAr_37, the method is seen to be accurate enough to distinguish between different low-energy structures. Finally, the idea of casting the initial many-body problem into a single degree of freedom problem is tested on the spectroscopy of calcium in bulk solid argon., Comment: 8 pages, 9 figures

An empirical potential with fluctuating charges is proposed for modeling $(\mathrm{MgO}{)}_{n}$ clusters in both the molecular (small $n)$ and the bulk $(\stackrel{\ensuremath{\rightarrow}}{n}\ensuremath{\infty})$ regimes. Vectorial polarization forces are explicitly taken into account in the self-consistent determination of charges. Our model predicts cuboid cluster structures, in agreement with previous experimental and theoretical results. The effective charge transferred between magnesium and oxygen smoothly increases from one to two, with an estimated crossover size above 300 MgO molecules.

Using approximate partition functions and a master equation approach, we investigate the statistical relaxation toward equilibrium in selected CaAr$_n$ clusters. The Gaussian theory of absorption (previous article) is employed to calculate the average photoabsorption intensity associated with the 4s^2-> 4s^14p^1 transition of calcium as a function of time during relaxation. In CaAr_6 and CaAr_10 simple relaxation is observed with a single time scale. CaAr_13 exhibits much slower dynamics and the relaxation occurs over two distinct time scales. CaAr_37 shows much slower relaxation with multiple transients, reminiscent of glassy behavior due to competition between different low-energy structures. We interpret these results in terms of the underlying potential energy surfaces for these clusters., 10 pages, 9 figures

We introduce a general Monte Carlo scheme for achieving atomistic simulations with monoelectronic Hamiltonians including the thermalization of both nuclear and electronic degrees of freedom. The kinetic Monte Carlo algorithm is used to obtain the exact occupation numbers of the electronic levels at canonical equilibrium, and comparison is made with Fermi-Dirac statistics in infinite and finite systems. The effects of a nonzero electronic temperature on the thermodynamic properties of liquid silver and sodium clusters are presented.

The inherent structure approach, or superposition approach is used to calculate some physical and chemical properties of clusters in thermodynamic equilibrium, for both the classical and quantum regimes. In the harmonic approximation some simple analytical estimates are obtained for the average polarizability of metal clusters, and for the photoabsorption intensity of chromophore-doped van der Waals clusters. Comparison with Monte Carlo simulations reveals good agreement, which could be further improved using systematic corrections for anharmonic perturbations. © 2002 Elsevier Science B.V. All rights reserved.

The collapse of Lennard-Jones homopolymers is investigated by means of Monte Carlo simulations and the inherent structure/superposition approach, with special emphasis on finite size effects. At thermal equilibrium, the polymers undergo a series of phase changes from the zero temperature folded state to a coexistence state, a molten globule state, the coil state, and finally to a high-temperature “soft” state where the bond lengths vary significantly from their equilibrium value. The correlation between the thermodynamic characteristics of the polymers and those of clusters is interpreted in terms of the energy landscapes of the two systems.

The photoabsorption spectra of calcium-doped argon clusters CaAr_n are investigated at thermal equilibrium using a variety of theoretical and numerical tools. The influence of temperature on the absorption spectra is estimated using the quantum superposition method for a variety of cluster sizes in the range 6, 17 pages, 9 figures

In this article we present the first measurement of the electric dipole susceptibility of one excess electron NanFn–1 clusters. The static electronic polarizability and the permanent electric dipole of these clusters have been calculated with a one-electron model. Experimental values for the susceptibility are clearly related to the calculated values of the permanent dipole. The size evolution of the dipole moments is interpreted in terms of the interplay between the lattice and electron properties. This study outlines that the response of the cluster to the electric field cannot be fully understood with only equilibrium structure calculations and that the coupling between the permanent dipole and the vibrational motion of the cluster has to be taken into account

We examine in detail the causes of the structural transitions that occur for those small Lennard-Jones clusters that have a non-icosahedral global minima. Based on the principles learned from these examples we develop a method to construct structural phase diagrams that show in a coarse-grained manner how the equilibrium structure of large clusters depends on both size and temperature. The method can be augmented to account for anharmonicity and quantum effects. Our results illustrate that the vibrational entropy can play a crucial role in determining the equilibrium structure of a cluster., Comment: 13 pages, 9 figures

We have systematically investigated the effect of anharmonicity on the equilibrium properties of systems with a complex potential energy surface. Anharmonicities are modeled by the temperature dependence of the harmonic frequencies {νi} near a stationary point of the PES. The low-temperature behavior is described by a simple thermal expansion ν(i)(β)=ν0(i)[1−α1(i)/β+α2(i)/2β2+⋯], where the coefficients {αj(i)} are obtained from perturbation theory. Using a simple diagrammatic representation, we give the complete expressions for the first two coefficients α1 and α2 in terms of derivatives of the potential. This approach is illustrated for the example of a bulk Lennard-Jones system of 32 particles, in both the solid and the liquid states. We also determine the anharmonic frequencies from reversible-scaling Monte Carlo simulations, which appear particularly well suited to this problem. As an example, we have studied a model biopolymer that exhibits significant first and second order anharmonicities. To show ...

We investigate the thermodynamic behavior of quantum many-body systems using several methods based on classical calculations. These approaches are compared for the melting of Lennard-Jones (LJ) clusters, where path-integral Monte Carlo (PIMC) results are also available. First, we examine two quasiclassical approaches where the classical potential is replaced by effective potentials accounting for quantum corrections of low order in ℏ. Of the Wigner–Kirkwood and Feynman–Hibbs effective potentials, only the latter is found to be in quantitative agreement with quantum simulations. However, both potentials fail to describe even qualitatively the low-temperature regime, where quantum effects are strong. Our second approach is based on the harmonic superposition approximation, but with explicit quantum oscillators. In its basic form, this approach is in good qualitative agreement with PIMC results, and becomes more accurate at low temperatures. By including anharmonic corrections in the form of temperature-depe...

Physical Review Letters

We show that the vibrational entropy can play a crucial role in determining the equilibrium structure of clusters by constructing structural phase diagrams showing how the structure depends upon both size and temperature. These phase diagrams are obtained for example rare gas and metal clusters.

Using a potential recently proposed by Baskes [Phys. Rev. Lett. 83, 2592 (1999)], we study the influence of the many-body interactions on the thermodynamics and chaotic dynamics of small atomic clusters. With standard molecular dynamics simulations as well as parallel tempering Monte Carlo, we calculate the complete heat capacity curves and the variations of the largest Lyapunov exponent with total energy. We observe that increasing the magnitude or decreasing the range of the many-body forces leads to an increase of chaos and a decrease in the melting temperature. Decreasing the range of the many-body interactions also results in a significantly lower latent heat of melting., NA

We investigate the thermodynamical stability of the interaction between two clusters at thermal equilibrium using classical molecular-dynamics (MD) and Monte Carlo (MC) simulations. The intercluster distance {ital Z} is fixed as a parameter in the microcanonical and canonical ensembles. We use and develop several techniques to calculate the fundamental quantities of interest in these ensembles, namely, the density of states {Omega}({ital E},{ital Z}) and the partition function {ital Q}({ital T},{ital Z}), yielding respectively, the microcanonical entropy {ital S}({ital E},{ital Z}) and the Helmholtz free energy {ital F}({ital T},{ital Z}). The multiple histogram method is used to estimate the variations of {ital S} with {ital E} and of {ital F} with {ital T}, both extracted from either constant energy MD or constant-temperature MC simulations. The thermodynamic perturbation and the displacement-vector methods are used to provide the variations of the free energy along the {ital Z} coordinate. These methods are applied to the interaction of Ar{sub 13}+Ar{sub 13} and Na{sub 8}+Na{sub 8} clusters. The Lennard-Jones (Ar{sub 13}){sub 2} cluster dimer has a locally mechanically stable structure at {ital Z}=8.6 A, which appears to remain thermodynamically stable until {ital T}{approx_equal}25 K. The temperature effects also stabilize two intermediate compact configurations, near {ital Z}=5more » and 6.6 A. On the other hand, the interaction between Na{sub 8}+Na{sub 8}, modeled by a distance-dependent tight-binding Hamiltonian, does not exhibit a stable structure except in its compact shape Na{sub 16}. The entropic effects, favored by the thermal phenomena, do not occur to induce any thermodynamical local stability for a dimerized (Na{sub 8}){sub 2}. In other terms, the stability of Na{sub 16} does not seem to be governed by the underlying two Na{sub 8} magic-number units. {copyright} {ital 1996 The American Physical Society.}« less

The anharmonic infrared emission spectrum following an optical excitation has been calculated for a variety of polycyclic aromatic hydrocarbon molecules in their ground singlet electronic state or in their triplet state. The computational protocol relies on second-order perturbation theory and involves a quartic vibrational Hamiltonian, the vibrational quantum numbers being sampled according to a Monte Carlo procedure. In the case of neutral naphthalene, the IR spectrum obtained in the (ground) singlet state differs significantly from the spectrum in the triplet state, especially for out-of-plane CH bending modes. Although not as prominent, spectral differences in larger molecules are still observable.

C(60) molecules highly excited in the nanosecond regime decay following ionization and dissociation by emitting a series of carbon dimers, as well as other small fragments if excitation is strong enough. The fragmentation mass spectrum and kinetic energy release of all charged fragments obtained in these experiments are interpreted within the framework of the Weisskopf theory, using a realistic Monte Carlo procedure in which the rates of all relevant decay channels are modeled using Arrhenius expressions. Comparison between the measurements and the simulated spectra allows the distribution of deposited energy to be accurately estimated. The dependence of the fragment kinetic energies on the laser fluence, found in the simulation but not observed in the experimental results, indicates that the small fragments are not necessarily emitted from small fullerenes resulting from C(60) by sequential decay. Rather, direct multifragmentation of C(60) is invoked to interpret the observed patterns. The possible role of post-ionization of neutral emitted fragments is discussed.

We assess the performance of colored-noise thermostats to generate quantum mechanical initial conditions for molecular dynamics simulations, in the context of infrared spectra of large polyatomic molecules. Comparison with centroid molecular dynamics simulations taken as reference shows that the method is accurate in predicting line shifts and band widths in the ionic cluster (NaCl)(32) and in the naphthalene molecule. As illustrated on much larger polycyclic aromatic hydrocarbons, the method also allows fundamental spectra to be evaluated in the limit of T = 0, taking into account anharmonicities and vibrational delocalization.

The stable structures and low temperature thermodynamics of cationic helium clusters are investigated theoretically using a diatomics-in-molecules model for the potential energy surfaces and a computational framework in which both electronic and nuclear degrees of freedom are treated on a quantum mechanical footing. While the charge is generally carried by two atoms, vibrational delocalization significantly spreads out the charge over multiple isomers for clusters containing five or more helium atoms. Our calculations indicate that large clusters are essentially fluid with a well-defined solvation shell around the charged core.

Following previous work [F. Calvo et al. J. Chem. Phys. 132, 124308 (2010)], infrared spectra of several polycyclic aromatic hydrocarbon molecules are simulated with classical and quantum molecular dynamics trajectories. The interactions are modeled using a tight-binding potential energy surface and quantum delocalization is accounted for using the partially adiabatic centroid and ring-polymer molecular dynamics frameworks, both built upon the path-integral representation. The spectra obtained directly by Fourier transformation of the dipole moment autocorrelation function are here compared with several quasiharmonic approximations that provide additional information about the vibrational modes. A principal mode analysis (PMA) is carried out from the covariance matrix of atomic displacements in classical and quantum trajectories. The method systematically overestimates the line shifts due to anharmonicities, except in the power spectra of atomic displacements, and is not robust in predicting IR intensities for such large molecules. Alternatively, effective normal modes have also been determined by adapting the self-consistent phonon (SCP) theory of condensed matter physics to the present tight-binding model, in both classical and quantum mechanical descriptions. The SCP approximation turns out as semiquantitative in estimating the redshift of tight stretching modes, and performs better for classical systems. More problematic, it predicts that many low- or medium-frequency modes should be blueshifted, in contradiction with the molecular dynamics results. The sets of anharmonic normal modes extracted from the PMA and SCP approaches reveal important mixings within the tightest C-H and C-C stretching modes, which are also manifested on the corresponding power spectra.

The vibrational spectra of the naphthalene, pyrene, and coronene molecules have been computed in the 0-3500 cm(-1) infrared range using classical and quantum molecular dynamics simulations based on a dedicated tight-binding potential energy surface. The ring-polymer molecular dynamics (RPMD) and partially adiabatic centroid molecular dynamics (CMD) methods have been employed to account for quantum nuclear effects. The contributions of quantum delocalization to the line shift and broadening are significant in the entire spectral range and of comparable magnitude as pure thermal effects. While the two methods generally produce similar results, the CMD method may converge slower at low temperature with increasing Trotter discretization number. However, and contrary to the CMD method, the RPMD approach suffers from serious resonance problems at high frequencies and low temperatures.

The superposition method is used to calculate quantum densities of states of polyatomic systems with multiple isomeric structures. For each isomer, anharmonicities are included rigorously using a Dunham expansion of the vibrational energy levels and short exchange Monte Carlo simulations are used to compute the individual quantum densities of states. The method is applied to the computation of thermodynamical properties of the Ar(13) and Ne(13) clusters. The canonical heat capacities are found in very satisfactory agreement with the predictions of quantum or semiclassical sampling methods.

The sequential thermal dissociation of up to five carbon dimers from neutral, singly and doubly charged C(60) molecules is theoretically investigated in the framework of phase space theory. Using a semiclassical treatment of vibrations and rotations, we quantify the amount of kinetic energies released in the form of translation, rotation, and vibration under realistic experimental conditions. Our results reveal that translational and vibrational energies of the dimers are nearly equilibrated after a few emissions, whereas the rotational contribution lies far below equipartition. An approximate treatment in which dimers are rotationally and vibrationally frozen essentially leads to the same conclusions.

The Wang-Landau sampling method is adapted to the calculation of quantum densities of states for fully coupled anharmonic systems. The accuracy of the method is illustrated against exact counting for two molecules with separable oscillators, namely, the Zundel complex H(5)O(2) (+) and the Na(11) cluster. Application to the fully coupled naphthalene molecule (C(10)H(8)) reveals significant deviations in the finite temperature thermodynamical properties that are not captured by simple perturbation theory. There are no limitations in the size of the molecules that can be treated with this method.

Experimental kinetic energy release distributions obtained for the thermionic emission from C(n) (-) clusters, 10or =nor =20, exhibit significant non-Boltzmann variations. Using phase space theory, these different features are analyzed and interpreted as the consequence of contrasting shapes in the daughter clusters; linear and nonlinear isomers have clearly distinct signatures. These results provide a novel indirect structural probe for atomic clusters associated with their thermionic emission spectra.

The temperature-dependent conformations of alanine-rich polypeptides are investi- gated using generalized ensemble Monte Carlo simulations. Pure polyalanines form α helices at low temperature, but exhibit an intermediate β-sheet structure below the coil transition. For the substituted peptide WA13 , the simulation predicts the β conformation to be more stable than helices already at low temperatures, and the β motif is further favored by entropy. Measure- ments of the electric dipole of this peptide do not provide evidence for helical structures even at room temperature. These experimental observations are thus compatible with our suggestion of β conformations, even though random-coil structures cannot be ruled out. Finally, we show how to stabilize α helices by an intense electric field, possibly leading to electrofreezing behavior.

We present a "basin-sampling" approach for calculation of the potential energy density of states for classical statistical models. It combines a Wang-Landau-type uniform sampling of local minima and a novel approach for approximating the relative contributions from local minima in terms of the volumes of basins of attraction. We have employed basin-sampling to study phase changes in atomic clusters modeled by the Lennard-Jones potential and for ionic clusters. The approach proves to be efficient for systems involving broken ergodicity and has allowed us to calculate converged heat capacity curves for systems that could previously only be treated using the harmonic superposition approximation. Benchmarks are also provided by comparison with parallel tempering and Wang-Landau simulations, where these proved feasible.

An alternative exchange strategy for parallel tempering simulations is introduced. Instead of attempting to swap configurations between two randomly chosen but adjacent replicas, the acceptance probabilities of all possible swap moves are calculated a priori. One specific swap move is then selected according to its probability and enforced. The efficiency of the method is illustrated first on the case of two Lennard-Jones (LJ) clusters containing 13 and 31 atoms, respectively. The convergence of the caloric curve is seen to be at least twice as fast as in conventional parallel tempering simulations, especially for the difficult case of LJ31. Further evidence for an improved efficiency is reported on the ergodic measure introduced by Mountain and Thirumalai [J. Phys. Chem. 93, 6975 (1989)], calculated here for LJ13 close to the melting point. Finally, tests on two simple spin systems indicate that the method should be particularly useful when a limited number of replicas are available.

International audience; The structure of the sodiated peptide GGGGGGGG-Na(+) or G(8)-Na(+) was investigated by infrared multiple photon dissociation (IRMPD) spectroscopy and a combination of theoretical methods. IRMPD was carried out in both the fingerprint and N-H/O-H stretching regions. Modeling used the polarizable force field AMOEBA in conjunction with the replica-exchange molecular dynamics (REMD) method, allowing an efficient exploration of the potential energy surface. Geometries and energetics were further refined at B3LYP-D and MP2 quantum chemical levels. The IRMPD spectra indicate that there is no free C-terminus OH and that several N-Hs are free of hydrogen bonding, while several others are bound, however not very strongly. The structure must then be either of the charge solvation (CS) type with a hydrogen-bound acidic OH, or a salt bridge (SB). Extensive REMD searches generated several low-energy structures of both types. The most stable structures of each type are computed to be very close in energy. The computed energy barrier separating these structures is small enough that G(8)-Na(+) is likely fluxional with easy proton transfer between the two peptide termini. There is, however, good agreement between experiment and computations in the entire spectral range for the CS isomer only, which thus appears to be the most likely structure of G(8)-Na(+) at room temperature.

Applications of metal nanoparticles require monodisperse and stable assemblies on a substrate such as graphene or graphite. Epitaxial graphene on metal (GOM) has attracted research interest because it contributes to the self-organisation of adsorbates. The difference in the lattice constants of graphene and metal leads to a moiré that contains certain regions that are favorable for adsorption. This work is mainly concerned with the Ru-C and Pt-C systems where we were interested in the bare substrate of GOM, adsorbates deposited thereon and metal clusters on graphite. Bond order potentials allow to carry out molecular dynamics studies for systems of realistic size and at finite temperature. In the case of the Pt-C, a parametrization is available in the literature. However, for Ru-C systems a custom parametrization effort based on data from electronic structure calculations was necessary. This atomistic model neglects long ranged dispersion forces that are important for adsorption phenomena on extended substrates. Based on the Grimme models, we developed an implicit description that takes the layered structure and the semi-infinite extension of the substrate into account. Also, screening effects that are important for metal materials are taken into account. Based on this force field, we show results concerning the properties of adsorbates on carbon substrates while evaluating the dispersion model. With the help of molecular dynamics simulations, the stability of adsorbates and graphene has been studied in the context of vibrational and diffusion dynamics. In agreement with experiments, the mobility of the adsorbates on graphite is high in comparison with adsorbates on GOM; Les applications des nanoparticules métalliques nécessitent des assemblées monodisperses et stables sur un substrat tel que le graphène ou le graphite. Le graphène épitaxié sur métal (GEM) est étudié, car il facilite l'auto-organisation des adsorbats. La différence entre les mailles du graphène et du métal conduit à un effet de moiré contenant certaines régions favorables de l'adsorption. Ce travail est consacré surtout aux systèmes Ru-C et Pt-C où nous nous sommes intéressé au substrat du GEM nu, des agrégats y etant deposés et des agrégats métalliques sur graphite. Les potentiels d'ordre de liason permettent de mener des études en dynamique moléculaire sur des systèmes de taille réaliste à température finie. Dans le cas du système Pt-C une paramétrisation est disponible dans la littérature. Cependant, pour le système du Ru-C une paramétrisation sur la base de données DFT était nécessaire. Ce modèle atomistique néglige les forces de dispersion importantes pour des milieux étendus. Basé sur les modèles de Grimme, nous avons développé une description implicite tenant compte de la structure du substrat et son extension semi-infinie. De plus les effets d'écrantage importants pour des milieux métalliques sont pris en compte. Basé sur ce champ de force nous montrons des propriétés des adsorbats sur des substrats carbonés où nous évaluons le modèle de forces de dispersion. Grâce à des simulations de dynamique moléculaire, la stabilité des adsorbats et du graphène a été étudié dans le contexte de la dynamique vibrationnelle et de diffusion. En accord avec les expériences, la mobilité des adsorbats sur graphite s'avère élevée en comparaison avec des adsorbats sur GEM

Applications of metal nanoparticles require monodisperse and stable assemblies on a substrate such as graphene or graphite. Epitaxial graphene on metal (GOM) has attracted research interest because it contributes to the self-organisation of adsorbates. The difference in the lattice constants of graphene and metal leads to a moiré that contains certain regions that are favorable for adsorption. This work is mainly concerned with the Ru-C and Pt-C systems where we were interested in the bare substrate of GOM, adsorbates deposited thereon and metal clusters on graphite. Bond order potentials allow to carry out molecular dynamics studies for systems of realistic size and at finite temperature. In the case of the Pt-C, a parametrization is available in the literature. However, for Ru-C systems a custom parametrization effort based on data from electronic structure calculations was necessary. This atomistic model neglects long ranged dispersion forces that are important for adsorption phenomena on extended substrates. Based on the Grimme models, we developed an implicit description that takes the layered structure and the semi-infinite extension of the substrate into account. Also, screening effects that are important for metal materials are taken into account. Based on this force field, we show results concerning the properties of adsorbates on carbon substrates while evaluating the dispersion model. With the help of molecular dynamics simulations, the stability of adsorbates and graphene has been studied in the context of vibrational and diffusion dynamics. In agreement with experiments, the mobility of the adsorbates on graphite is high in comparison with adsorbates on GOM, Les applications des nanoparticules métalliques nécessitent des assemblées monodisperses et stables sur un substrat tel que le graphène ou le graphite. Le graphène épitaxié sur métal (GEM) est étudié, car il facilite l'auto-organisation des adsorbats. La différence entre les mailles du graphène et du métal conduit à un effet de moiré contenant certaines régions favorables de l'adsorption. Ce travail est consacré surtout aux systèmes Ru-C et Pt-C où nous nous sommes intéressé au substrat du GEM nu, des agrégats y etant deposés et des agrégats métalliques sur graphite. Les potentiels d'ordre de liason permettent de mener des études en dynamique moléculaire sur des systèmes de taille réaliste à température finie. Dans le cas du système Pt-C une paramétrisation est disponible dans la littérature. Cependant, pour le système du Ru-C une paramétrisation sur la base de données DFT était nécessaire. Ce modèle atomistique néglige les forces de dispersion importantes pour des milieux étendus. Basé sur les modèles de Grimme, nous avons développé une description implicite tenant compte de la structure du substrat et son extension semi-infinie. De plus les effets d'écrantage importants pour des milieux métalliques sont pris en compte. Basé sur ce champ de force nous montrons des propriétés des adsorbats sur des substrats carbonés où nous évaluons le modèle de forces de dispersion. Grâce à des simulations de dynamique moléculaire, la stabilité des adsorbats et du graphène a été étudié dans le contexte de la dynamique vibrationnelle et de diffusion. En accord avec les expériences, la mobilité des adsorbats sur graphite s'avère élevée en comparaison avec des adsorbats sur GEM