Characterization of the <i>t</i>‑Butyl Radical and Its Elusive Anion

The <i>t</i>-butyl radical and its anion are studied theoretically using state-of-the-art quantum mechanical methods including coupled cluster theory with full single, double, and triple excitations (CCSDT) and CCSDT with perturbative quadruple excitations [CCSDT­(Q)], in concert with large correlation-consistent cc-pVXZ and aug-cc-pVXZ (X = D, T, Q, 5) basis sets. The relative energies are extrapolated to the complete basis set limit (CBS). The lowest energy structure of the <i>t</i>-butyl radical has a nonplanar carbon backbone with overall <i>C</i>_3<i>v</i> symmetry. Low-lying <i>C</i>_3<i>h</i> and <i>C</i>_<i>s</i> symmetry transition states, for pyramidal inversion and methyl group rotation, respectively, between equivalent <i>C</i>_3<i>v</i> minima are investigated. The barriers for these interconversions are both less than 1 kcal mol^–1, but the corresponding barriers on the anion potential energy surface are more pronounced. Using the focal point analysis technique, we obtain a value of −0.48 kcal mol^–1 for the <i>t</i>-butyl radical adiabatic electron affinity at the CCSDT­(Q)/CBS level of theory, where the negative sign indicates that the formation of the <i>t</i>-butyl anion is adiabatically unfavorable. We show that the electron affinity, whose sign has been the subject of debate, is very sensitive to both the basis set and the correlation treatment, and previous experimental and theoretical estimates of its value bracket the value computed herein. Our results indicate that the <i>t</i>-butyl anion is classically metastable with a vertical detachment energy of over 10 kcal mol^–1 to reach the neutral potential energy surface. However, the inclusion of the zero-point vibrational effects seems to favor its nonexistence

Numerical Study on the Partitioning of the Molecular Polarizability into Fluctuating Charge and Induced Atomic Dipole Contributions

In order to carry out a detailed analysis of the molecular static polarizability, which is the response of the molecule to a uniform external electric field, the molecular polarizability was computed using the finite-difference method for 21 small molecules, using density functional theory. Within nine charge population schemes (Löwdin, Mulliken, Becke, Hirshfeld, CM5, Hirshfeld-I, NPA, CHELPG, MK-ESP) in common use, the charge fluctuation contribution is found to dominate the molecular polarizability, with its ratio ranging from 59.9% with the Hirshfeld or CM5 scheme to 96.2% with the Mulliken scheme. The Hirshfeld-I scheme is also used to compute the other contribution to the molecular polarizability coming from the induced atomic dipoles, and the atomic polarizabilities in eight small molecules and water pentamer are found to be highly anisotropic for most atoms. Overall, the results suggest that (a) more emphasis probably should be placed on the charge fluctuation terms in future polarizable force field development and (b) an anisotropic polarizability might be more suitable than an isotropic one in polarizable force fields based entirely or partially on the induced atomic dipoles

Comparison of Additive and Polarizable Models with Explicit Treatment of Long-Range Lennard-Jones Interactions Using Alkane Simulations

Long-range Lennard-Jones (LJ) interactions have a significant impact on the structural and thermodynamic properties of nonpolar systems. While several methods have been introduced for the treatment of long-range LJ interactions in molecular dynamics (MD) simulations, increased accuracy and extended applicability is required for anisotropic systems such as lipid bilayers. The recently refined Lennard-Jones particle-mesh Ewald (LJ-PME) method extends the particle-mesh Ewald (PME) method to long-range LJ interactions and is suitable for use with anisotropic systems. Implementation of LJ-PME with the CHARMM36 (C36) additive and CHARMM Drude polarizable force fields improves agreement with experiment for density, isothermal compressibility, surface tension, viscosity, translational diffusion, and ¹³C <i>T</i>₁ relaxation times of pure alkanes. Trends in the temperature dependence of the density and isothermal compressibility of hexadecane are also improved. While the C36 additive force field with LJ-PME remains a useful model for liquid alkanes, the Drude polarizable force field with LJ-PME is more accurate for nearly all quantities considered. LJ-PME is also preferable to the isotropic long-range correction for hexadecane because the molecular order extends to nearly 20 Å, well beyond the usual 10–12 Å cutoffs used in most simulations

Computation of Hydration Free Energies Using the Multiple Environment Single System Quantum Mechanical/Molecular Mechanical Method

A recently developed MESS-E-QM/MM method (multiple-environment single-system quantum mechanical molecular/mechanical calculations with a Roothaan-step extrapolation) is applied to the computation of hydration free energies for the blind SAMPL4 test set and for 12 small molecules. First, free energy simulations are performed with a classical molecular mechanics force field using fixed-geometry solute molecules and explicit TIP3P solvent, and then the non-Boltzmann-Bennett method is employed to compute the QM/MM correction (QM/MM-NBB) to the molecular mechanical hydration free energies. For the SAMPL4 set, MESS-E-QM/MM-NBB corrections to the hydration free energy can be obtained 2 or 3 orders of magnitude faster than fully converged QM/MM-NBB corrections, and, on average, the hydration free energies predicted with MESS-E-QM/MM-NBB fall within 0.10–0.20 kcal/mol of full-converged QM/MM-NBB results. Out of five density functionals (BLYP, B3LYP, PBE0, M06-2X, and ωB97X-D), the BLYP functional is found to be most compatible with the TIP3P solvent model and yields the most accurate hydration free energies against experimental values for solute molecules included in this study

Comparison of energy components, as calculated by Gromacs and OpenMM.

<p>Comparison of energy components, as calculated by Gromacs and OpenMM.</p

Comparison of forces as computed by Amber and OpenMM.

<p>Comparison of forces as computed by Amber and OpenMM.</p

Custom forces supported by OpenMM 7.0.

<p>Custom forces supported by OpenMM 7.0.</p

OpenMM 7: Rapid development of high performance algorithms for molecular dynamics

<div><p>OpenMM is a molecular dynamics simulation toolkit with a unique focus on extensibility. It allows users to easily add new features, including forces with novel functional forms, new integration algorithms, and new simulation protocols. Those features automatically work on all supported hardware types (including both CPUs and GPUs) and perform well on all of them. In many cases they require minimal coding, just a mathematical description of the desired function. They also require no modification to OpenMM itself and can be distributed independently of OpenMM. This makes it an ideal tool for researchers developing new simulation methods, and also allows those new methods to be immediately available to the larger community.</p></div

Architecture of OpenMM.

<p>Architecture of OpenMM.</p

Comparison of energy components, as calculated by Amber and OpenMM.

<p>Comparison of energy components, as calculated by Amber and OpenMM.</p