Dispersion Corrected Atom-Centered Potentials for Phosphorus

Exfoliation Energy of Black Phosphorus Revisited: A Coupled Cluster Benchmark

Black phosphorus (black-P) consists of phosphorene sheets, stacked by van der Waals dispersion. In a recent study based on periodic local second-order Møller-Plesset perturbation theory (LMP2) with higher-order corrections evaluated on finite clusters, we obtained a value of -151 meV/atom for the exfoliation energy. This is almost twice as large as another recent theoretical result (around -80 meV/atom) obtained with quantum Monte Carlo (QMC). Here, we revisit this system on the basis of the recently implemented, periodically embedded ring coupled cluster (rCCD) model instead of LMP2. Higher-order coupled cluster corrections on top of rCCD are obtained from finite clusters by utilizing our new "unit-cell-in-cluster" scheme. Our new value of -92 meV/atom is noticeably lower than that based on LMP2 and in reasonably close agreement with the QMC result. However, in contrast to QMC, no strong effect from the second-neighbor and farther layers in black-P are observed in our calculations.

Toward an Accurate Estimate of the Exfoliation Energy of Black Phosphorus: A Periodic Quantum Chemical Approach

The black phosphorus (black-P) crystal is formed of covalently bound layers of phosphorene stacked together by weak van der Waals interactions. An experimental measurement of the exfoliation energy of black-P is not available presently, making theoretical studies the most important source of information for the optimization of phosphorene production. Here, we provide an accurate estimate of the exfoliation energy of black-P on the basis of multilevel quantum chemical calculations, which include the periodic local Møller-Plesset perturbation theory of second order, augmented by higher-order corrections, which are evaluated with finite clusters mimicking the crystal. Very similar results are also obtained by density functional theory with the D3-version of Grimme's empirical dispersion correction. Our estimate of the exfoliation energy for black-P of -151 meV/atom is substantially larger than that of graphite, suggesting the need for different strategies to generate isolated layers for these two systems.

Generalized QM/MM Force Matching Approach Applied to the 11-cis Protonated Schiff Base Chromophore of Rhodopsin

We extended a previously developed force matching approach to systems with covalent QM/MM boundaries and describe its user-friendly implementation in the publicly available software package CPMD. We applied this approach to the challenging case of the retinal protonated Schiff base in dark state bovine rhodopsin. We were able to develop a highly accurate force field that is able to capture subtle structural changes within the chromophore that have a pronounced influence on the optical properties. The optical absorption spectrum calculated from configurations extracted from a MD trajectory using the new force field is in excellent agreement with QM/MM and experimental references.

Intricacies of Describing Weak Interactions Involving Halogen Atoms within Density Functional Theory

In this work we assess the performance of different dispersion-corrected density functional theory (DFT) approaches (M06, M06-2X, DFT-D3, and DCACP) in reproducing high-level wave function based benchmark calculations on the weakly bound halogen dimers X2···X2 and X2···Ar (for X = F, Cl, Br, and I), as well as the prototype halogen bonded complexes H3CX···OCH2 (X = Cl, Br, I). In spite of the generally good performance of all tested methods for weakly bound systems, their performance for halogen-containing compounds varies largely. We find maximum errors in the energies with respect to the CCSD(T) reference values of 0.13 kcal/mol for DCACP, 0.22 kcal/mol for M06-2X, 0.47 kcal/mol for BLYP-D3, and 0.77 kcal/mol for M06. The root-mean-square deviations are 0.13 kcal/mol for DCACP and M06-2X, 0.44 kcal/mol for M06, and 0.51 kcal/mol for BLYP-D3.

MOLECULAR BIOLOGY AT THE QUANTUM LEVEL: CAN MODERN DENSITY FUNCTIONAL THEORY FORGE THE PATH?

Recent years have seen vast improvements in the ability of rigorous quantum-mechanical methods to treat systems of interest to molecular biology. In this review article, we survey common computational methods used to study such large, weakly bound systems, starting from classical simulations and reaching to quantum chemistry and density functional theory. We sketch their underlying frameworks and investigate their strengths and weaknesses when applied to potentially large biomolecules. In particular, density functional theory — a framework that can treat thousands of atoms on firm theoretical ground — can now accurately describe systems dominated by weak van der Waals interactions. This newfound ability has rekindled interest in using this tried-and-true approach to investigate biological systems of real importance. In this review, we focus on some new methods within the density functional theory that allow for accurate inclusion of the weak interactions that dominate binding in biological macromolecules. Recent work utilizing these methods to study biologically relevant systems will be highlighted, and a vision for the future of density functional theory within molecular biology will be discussed.