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 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

Positional disorder in ammonia borane at ambient conditions

We solve a long-standing experimental discrepancy of NH$_3$BH$_3$, which---as a molecule---has a threefold rotational axis, but in its crystallized form at room temperature shows a fourfold symmetry about the same axis, creating a geometric incompatibility. To explain this peculiar experimental result, we study the dynamics of this system with ab initio Car-Parrinello molecular dynamics and nudged-elastic-band simulations. We find that rotations, rather than spatial static disorder, at angular velocities of 2 rev/ps---a time scale too small to be resolved by standard experimental techniques---are responsible for the fourfold symmetry

An ab-initio converse NMR approach for pseudopotentials

We extend the recently developed converse NMR approach [T. Thonhauser, D. Ceresoli, A. Mostofi, N. Marzari, R. Resta, and D. Vanderbilt, J. Chem. Phys. \textbf{131}, 101101 (2009)] such that it can be used in conjunction with norm-conserving, non-local pseudopotentials. This extension permits the efficient ab-initio calculation of NMR chemical shifts for elements other than hydrogen within the convenience of a plane-wave pseudopotential approach. We have tested our approach on several finite and periodic systems, finding very good agreement with established methods and experimental results.Comment: 11 pages, 2 figures, 4 tables; references expande

Orbital magnetization in periodic insulators

Working in the Wannier representation, we derive an expression for the orbital magnetization of a periodic insulator. The magnetization is shown to be comprised of two contributions, an obvious one associated with the internal circulation of bulk-like Wannier functions in the interior, and an unexpected one arising from net currents carried by Wannier functions near the surface. Each contribution can be expressed as a bulk property in terms of Bloch functions in a gauge-invariant way. Our expression is verified by comparing numerical tight-binding calculations for finite and periodic samples.Comment: submitted to PRL; signs corrected in Eqs. (11), (12), (19), and (20