On the structure and dynamics of secondary n-alkyl cations

Abstract

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.

Performance of CuII‐, PbII‐, and HgII‐Exchanged Mordenite in the Adsorption of I2, ICH3, H2O, CO, ClCH3, and Cl2: A Density Functional Study

“…To analyze how the bonding between the cation (M:C u 2 + ,P b 2 + and Hg 2 + )a nd the oxygen atoms in the five-and six-membered rings (5MR and 6MR) of mordenite evolve on adsorption, we computed ac oordination number (CN). [41][42][43][44][45] The CN is as um of terms over the number of oxygen atoms in the ring (N = 5f or 5MR, N = 6 for 6MR) depending on the MÀOdistance [Eq. (3)]:…”

Spin crossover transition of Fe(phen)2(NCS)2: periodic dispersion-corrected density-functional study

“…For similar purposes, a function measuring the coordination number of atoms is often used in the literature. [41][42][43][44] In this work we define a function cn as…”

The Carbocation Rearrangement Mechanism, Clarified

“…Although such hypothetical structures were used in the earliest semiempirical and ab initio computations on C 3 H 7 + , once geometry optimization became available it was discovered in 1971 by Radom, Pople, Buss, and Schleyer that the PCP + isomer of C 3 H 7 + is neither of these (Figure ) but instead is what they termed a “methyl-eclipsed 1-propyl cation” or a “distorted corner-protonated cyclopropane.” In 1939, Wilson suggested that a carbocation intermediate could be “mesomeric” between two classical structures; this “methyl-eclipsed” structure is in a sense even further mesomeric, between the corner-PCP + and edge-PCP + ideas of the 1960s. We have referred to these meso-PCP + alkyl-eclipsed cations as “closed” versions of “open” classical ions for dynamical reasons based on molecular dynamics (MD) simulations …”

“…A perusal of modern texts reveals that confusion still abounds 40 years later and that the outdated terms corner-PCP + and edge-PCP + are still in use, albeit cautiously . Since meso-PCP + structures continued to be found computationally for larger alkyl ions , we anticipated that mechanisms like those of Radom et al might generally apply. We thus set upon the tasks of updating the Brouwer–Hogeveen mechanism for hexyl ion rearrangement with the meso-PCP + ideas of Radom et al and testing the result with simulations and transition-state computations .…”