Articles you may be interested inAdapting SAFT-γ perturbation theory to site-based molecular dynamics simulation. III. Molecules with partial charges at bulk phases, confined geometries and interfaces J. Chem. Phys. 141, 094708 (2014); 10.1063/1.4893966Study on the conformational equilibrium of the alanine dipeptide in water solution by using the averaged solvent electrostatic potential from molecular dynamics methodology J. Chem. Phys. 135, 194502 (2011); 10.1063/1.3658857 Combining ab initio quantum mechanics with a dipole-field model to describe acid dissociation reactions in water: First-principles free energy and entropy calculations J. Chem. Phys. 132, 074112 (2010); 10.1063/1.3317398
OD vibrations and hydration structure in an Al 3 + ( aq ) solution from a Car-Parrinello molecular-dynamics simulationStructure and dynamics of the silacyclobutane radical cation, studied by ab initio and density functional theory and electron spin resonance spectroscopy A variety of computational studies was undertaken to examine and establish the relative importance of open versus closed structures for unbranched secondary n-alkyl cations. First, the PW91 level of density functional theory was used to optimize over 20 minimum-energy structures of sec-pentyl, sec-hexyl, and sec-heptyl ions, demonstrating that closed structures are more stable than open ones on the potential energy surface ͑PES͒. Second, PW91 was used with a theoretical Andersen thermostat to perform a molecular dynamics simulation ͑150 ps͒ of C 9 H 19 + at a typical catalytic temperature of 800 K, demonstrating that the structure preference is inverted on the free-energy surface. Third, both quantum ͑rigid-rotor/harmonic oscillator͒ and classical partition functions were used to demonstrate that the simulated structure-opening at catalytic temperatures is due to the floppiness of the open forms, which improves its free energy by both lowering its zero-point vibrational energy and increasing its molecular entropy. The particular conformer of the preferred open form ͑at 800 K͒ is dependent on length of alkyl ion, with pentyl ions preferring syn/anti structures but longer ions preferring open-clinal ones. These results, plus an additional set of PES optimized structures from an alternative level of theory ͑MP2 / 6-31G͑d , p͒͒, are used to discuss the likely nature of secondary n-alkyl ions.