The solvent effect on the syn/anti population ratio of the mesityl oxide (MOx) was investigated using a new implementation of conformational bias Monte Carlo (CBMC) and molecular dynamics (MD) methods. It was observed by a previous theoretical work (Theor. Chem. Acc. (2012) 131:1214) that in gas-phase the MOx exists dominantly in syn-form and in aqueous solution in anti-form. The syn/anti free energy difference in the gas phase was used in the intramolecular parametrization and a rotational barrier of approximately 10 kcal mol −1 was found. Molecular systems with barriers of this order of magnitude have been studied by experimental techniques. However, they have not been discussed yet comparing CBMC and MD simulations. In this work, we show that the intramolecular geometrical information such as bond lengths, angles and torsional angles sampled with CBMC and MD methods are equivalent. Nonetheless, only the CBMC simulations sample appropriately the syn/anti population ratio. With the CBMC configurations in gas phase, it was obtained 95% in syn-form and 5% in anti-form regardless the initial conformation. An inversion of the population was found in water, 25% in syn-form and 75% in anti-form. Comparing the gas phase and in-water CBMC sampling, it was observed that the MOx spends typically approximately 110 successive MC cycles in anti-form and approximately 2300 in syn-form in gas phase. While it was much larger with explicit water, approximately 400 times more for anti-form and approximately 6 times more for syn-form. We argue that this strong stabilization of the anti-form in aqueous solution, does not come from the MOx-water hydrogen bonds interactions, because they are the same for both conformations. Instead, the stabilization comes from the dipole-dipole interaction caused by a larger dipole moment of the MOx in the anti-form, 7.2 D, than in the syn-form, 5.2 D. With the MD sampled configurations in both conditions, we observe that the syn/anti conformational change is a very rare event due to the rotational barrier, which is approximately 17 times larger than the thermal energy. Therefore, the MD sampling of the MOx is not appropriated because it is strongly dependent on the initial conformation even for large simulations with 150 ns up to 400 ns for the isolated solute and for solute-solvent systems.

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.

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.

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