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J Chem Theory Comput ; 16(3): 1431-1447, 2020 Mar 10.
Artigo em Inglês | MEDLINE | ID: mdl-32031377


We cast the acceleration of the dynamics of coarse-grained polymer models, or, conversely, the decrease in monomer friction in terms of excess entropy differences between different coarse-grained resolutions. From a simple bead-spring model of unentangled polymers in a melt, we systematically derive two coarse-grained models of different resolutions, for which exact excess entropies are obtained through a carefully carried out two-step thermodynamic integration. We found that the excess entropy differences between the coarser and finer models correlated well with the logarithm of the ratio of dynamical properties quantifying the acceleration upon changing the model resolution. Moreover, we have considered how well the two-body approximation to the excess entropy is correlated and also the scaling of the excess entropy in the analysis. Our results indicate that the acceleration brought about by coarse-graining can be understood in terms of excess entropy differences for unentangled polymers also. The correlations presented in this work may open new possibilities to a posteriori correct the coarse-graining dynamics by a simple route.

J Chem Phys ; 151(20): 204301, 2019 Nov 28.
Artigo em Inglês | MEDLINE | ID: mdl-31779323


Atomistic understanding of thermodynamic processes such as phase transitions in nanoalloys is crucial to improve real-life applications of Pt-based nanocatalysts. In this work, we investigate the thermodynamic properties of 55-atom PtCo and PtNi nanoalloys and compare them to reference unary systems, Pt55, Co55, and Ni55. Our results are based on the combination of the parallel tempering Monte Carlo and the revised basin-hopping Monte Carlo algorithms with many-body Gupta potentials, and furthermore, density functional theory calculations were employed to validate the adopted Gupta parameters and to analyze electronic effects induced by structural changes derived from temperature effects. We identified first-order phase transitions for Pt55, Co55, Pt30Co25, Ni55, and Pt40Ni15 at 727, 1027, 1003, 914, and 1051 K, respectively. Thus, alloying unary Pt nanoclusters with Ni and Co leads to an increase in the melting temperature, indicating that the nanoalloys are able to sustain higher temperatures while maintaining their structure. A low-temperature solid-solid transition was also identified for Pt55, which is characterized by a change from a face-centered cubic like structure (putative global minimum configuration) to the icosahedron structure. The structural transformations led by the temperature increase induce small changes on the total density of states, namely, a slight shift of the d-band center toward the highest occupied molecular orbital with increasing temperature, which was found for all considered nanoclusters.

J Chem Phys ; 146(6): 064114, 2017 Feb 14.
Artigo em Inglês | MEDLINE | ID: mdl-28201917


A basic requirement for an atom-level understanding of nanoclusters is the knowledge of their atomic structure. This understanding is incomplete if it does not take into account temperature effects, which play a crucial role in phase transitions and changes in the overall stability of the particles. Finite size particles present intricate potential energy surfaces, and rigorous descriptions of temperature effects are best achieved by exploiting extended ensemble algorithms, such as the Parallel Tempering Monte Carlo (PTMC). In this study, we employed the PTMC algorithm, implemented from scratch, to sample configurations of LJn (n=38, 55, 98, 147) particles at a wide range of temperatures. The heat capacities and phase transitions obtained with our PTMC implementation are consistent with all the expected features for the LJ nanoclusters, e.g., solid to solid and solid to liquid. To identify the known phase transitions and assess the prevalence of various structural motifs available at different temperatures, we propose a combination of a Leader-like clustering algorithm based on a Euclidean metric with the PTMC sampling. This combined approach is further compared with the more computationally demanding bond order analysis, typically employed for this kind of problem. We show that the clustering technique yields the same results in most cases, with the advantage that it requires no previous knowledge of the parameters defining each geometry. Being simple to implement, we believe that this straightforward clustering approach is a valuable data analysis tool that can provide insights into the physics of finite size particles with few to thousand atoms at a relatively low cost.

J Phys Condens Matter ; 28(17): 175302, 2016 May 05.
Artigo em Inglês | MEDLINE | ID: mdl-27045947


We report a basin-hopping Monte Carlo investigation within the embedded-atom method of the structural and energetic properties of bimetallic ZrCu, ZrAl, and CuAl nanoclusters with 55 and 561 atoms. We found that unary Zr55, Zr561, Cu55, Cu561, Al55, and Al561 systems adopt the well known compact icosahedron (ICO) structure. The excess energy is negative for all systems and compositions, which indicates an energetic preference for the mixing of both chemical species. The ICO structure is preserved if a few atoms of the host system are replaced by different species, however, the composition limit in which the ICO structure is preserved depends on both the host and new chemical species. Using several structural analyses, three classes of structures, namely ideal ICO, nearly ICO, and distorted ICO structures, were identified. As the amounts of both chemical species change towards a more balanced composition, configurations far from the ICO structure arise and the dominant structures are nearly spherical, which indicates a strong minimization of the surface energy by decreasing the number of atoms with lower coordination on the surface. The average bond lengths follow Vegard's law almost exactly for ZrCu and ZrAl, however, this is not the case for CuAl. Furthermore, the radial distribution allowed us to identify the presence of an onion-like behavior in the surface of the 561-atom CuAl nanocluster with the Al atoms located in the outermost surface shell, which can be explained by the lower surface energies of the Al surfaces compared with the Cu surfaces. In ZrCu and ZrAl the radial distribution indicates a nearly homogeneous distribution for the chemical species, however, with a slightly higher concentration of Al atoms on the ZrAl surface, which can also be explained by the lower surface energy.

J Phys Chem A ; 118(45): 10813-21, 2014 Nov 13.
Artigo em Inglês | MEDLINE | ID: mdl-25329243


In general, because of the high computational demand, most theoretical studies addressing cationic and anionic clusters assume structural relaxation from the ground state neutral geometries. Such approach has its limits as some clusters could undergo a drastic structural deformation upon gaining or losing one electron. By engaging symmetry-unrestricted density functional calculations with an extensive search among various structures for each size and state of charge, we addressed the investigation of the technologically relevant Cu(n) and Pt(n) clusters for n = 2-14 atoms in the cationic, neutral, and anionic states to analyze the behavior of the structural, electronic, and energetic properties as a function of size and charge state. Moreover, we considered potentially high-energy isomers allowing foresight comparison with experimental results. Considering fixed cluster sizes, we found that distinct charge states lead to different structural geometries, revealing a clear tendency of decreasing average coordination as the electron density is increased. This behavior prompts significant changes in all considered properties, namely, energy gaps between occupied and unoccupied states, magnetic moment, detachment energy, ionization potential, center of gravity and "bandwidth" of occupied d-states, stability function, binding energy, electric dipole moment and sd hybridization. Furthermore, we identified a strong correlation between magic Pt clusters with peaks in sd hybridization index, allowing us to conclude that sd hybridization is one of the mechanisms for stabilization for Pt(n) clusters. Our results form a well-established basis upon which a deeper understanding of the stability and reactivity of metal clusters can be built, as well as the possibility to tune and exploit cluster properties as a function of size and charge.

J Chem Inf Model ; 53(9): 2282-98, 2013 Sep 23.
Artigo em Inglês | MEDLINE | ID: mdl-23957311


Suggestions for improving the Basin-Hopping Monte Carlo (BHMC) algorithm for unbiased global optimization of clusters and nanoparticles are presented. The traditional basin-hopping exploration scheme with Monte Carlo sampling is improved by bringing together novel strategies and techniques employed in different global optimization methods, however, with the care of keeping the underlying algorithm of BHMC unchanged. The improvements include a total of eleven local and nonlocal trial operators tailored for clusters and nanoparticles that allow an efficient exploration of the potential energy surface, two different strategies (static and dynamic) of operator selection, and a filter operator to handle unphysical solutions. In order to assess the efficiency of our strategies, we applied our implementation to several classes of systems, including Lennard-Jones and Sutton-Chen clusters with up to 147 and 148 atoms, respectively, a set of Lennard-Jones nanoparticles with sizes ranging from 200 to 1500 atoms, binary Lennard-Jones clusters with up to 100 atoms, (AgPd)55 alloy clusters described by the Sutton-Chen potential, and aluminum clusters with up to 30 atoms described within the density functional theory framework. Using unbiased global search our implementation was able to reproduce successfully the great majority of all published results for the systems considered and in many cases with more efficiency than the standard BHMC. We were also able to locate previously unknown global minimum structures for some of the systems considered. This revised BHMC method is a valuable tool for aiding theoretical investigations leading to a better understanding of atomic structures of clusters and nanoparticles.

Algoritmos , Método de Monte Carlo , Nanopartículas/química , Modelos Moleculares , Conformação Molecular , Termodinâmica