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J Chem Inf Model ; 2020 Jun 18.
Artigo em Inglês | MEDLINE | ID: mdl-32470296


Solute-solvent systems are an important topic of study, as the effects of the solvent on the solute can drastically change its properties. Theoretical studies of these systems are done with ab initio methods, molecular simulations, or a combination of both. The simulations of molecular systems are usually performed with either molecular dynamics (MD) or Monte Carlo (MC) methods. Classical MD has evolved much in the last decades, both in algorithms and implementations, having several stable and efficient codes developed and available. Similarly, MC methods have also evolved, focusing mainly in creating and improving methods and implementations in available codes. In this paper, we provide some enhancements to a configurational bias Monte Carlo (CBMC) methodology to simulate flexible molecules using the molecular fragments concept. In our implementation the acceptance criterion of the CBMC method was simplified and a generalization was proposed to allow the simulation of molecules with any kind of fragments. We also introduce the new version of DICE, an MC code for molecular simulation (available at This code was mainly developed to simulate solute-solvent systems in liquid and gas phases and in interfaces (gas-liquid and solid-liquid) that has been mostly used to generate configurations for a sequential quantum mechanics/molecular mechanics method (S-QM/MM). This new version introduces several improvements over the previous ones, with the ability of simulating flexible molecules with CBMC as one of them. Simulations of well-known molecules, such as n-octane and 1,2-dichloroethane in vacuum and in solution, are presented to validate the new implementations compared with MD simulations, experimental data, and other theoretical results. The efficiency of the conformational sampling was analyzed using the acceptance rates of different alkanes: n-octane, neopentane, and 4-ethylheptane. Furthermore, a very complex molecule, boron subphtalocyanine, was simulated in vacuum and in aqueous solution showing the versatility of the new implementation. We show that the CBMC is a very good method to perform conformation sampling of complex moderately sized molecules (up to 150 atoms) in solution following the Boltzmann thermodynamic equilibrium distribution.

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.