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

Suppressing diborane production during the hydrogen release of metal borohydrides: The example of alloyed Al(BH4_4)3_3

Aluminum borohydride (Al(BH$_4$)$_3$) is an example of a promising hydrogen storage material with exceptional hydrogen densities by weight and volume and a low hydrogen desorption temperature. But, unfortunately, its production of diborane (B$_2$H$_6$) gases upon heating to release the hydrogen restricts its practical use. To elucidate this issue, we investigate the properties of a number of metal borohydrides with the same problem and find that the electronegativity of the metal cation is not the best descriptor of diborane production. We show that, instead, the closely related formation enthalpy is a better descriptor and we find that diborane production is an exponential function thereof. We conclude that diborane production is sufficiently suppressed for formation enthalpies of $-$80 kJ/mol BH$_4$ or lower, providing specific design guidelines to tune existing metal borohydrides or synthesize new ones. We then use first-principles methods to study the effects of Sc alloying in Al(BH$_4$)$_3$. Our results for the thermodynamic properties of the Al$_{1-x}$Sc$_x$(BH$_4$)$_3$ alloy clearly show the stabilizing effect of Sc alloying and thus the suppression of diborane production. We conclude that stabilizing Al(BH$_4$)$_3$ and similar borohydrides via alloying or other means is a promising route to suppress diborane production and thus develop viable hydrogen storage materials.Comment: 16 pages, 2 figure

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

vdW-DF Study of energetic, structural, and vibrational properties of small water clusters and ice Ih

We present results for a density functional theory study of small water clusters and hexagonal ice Ih, using the van der Waals density functional (vdW-DF). In particular, we examine energetic, structural, and vibrational properties of these systems. Our results exhibit excellent agreement with both experiment and quantum-chemistry calculations and show a systematic and consistent improvement over standard exchange-correlation functionals---making vdW-DF a promising candidate for resolving longstanding difficulties with density functional theory in describing water. In addition, by comparing our vdW-DF results with quantum-chemistry calculations and other standard exchange-correlation functionals, we shed light on the question of why standard functionals often fail to describe these systems accurately.Comment: Supplementary material availabl

H4-Alkanes: A new class of hydrogen storage material?

The methane-based material (H$_2$)$_4$CH$_4$, also called H4M for short, is in essence a methane molecule with 4 physisorbed H$_2$ molecules. While H4M has exceptionally high hydrogen storage densities when it forms a molecular solid, unfortunately, this solid is only stable at impractically high pressures and/or low temperatures. To overcome this limitation, we show through simulations that longer alkanes (methane is the shortest alkane) also form stable structures that still physisorb 4 H$_2$ molecules per carbon atom; we call those structures H4-alkanes. We further show via molecular dynamics simulations that the stability field of molecular solids formed from H4-alkanes increases remarkably with chain length compared to H4M, just as it does for regular alkanes. From our simulations of H4-alkanes with lengths 1, 4, 10, and 20, we see that e.g. for the 20-carbon the stability field is doubled at higher pressures. While even longer chains show only insignificant improvements, we discuss various other options to stabilize H4-alkanes more. Our proof-of-principle results lay the groundwork to show that H4-alkanes can become viable hydrogen storage materials.Comment: 6 pages, 7 figure

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

Diffusion of Small Molecules in Metal Organic Framework Materials

Ab initio simulations are combined with in situ infrared spectroscopy to unveil the molecular transport of H$_2$, CO$_2$, and H$_2$O in the metal organic framework MOF-74-Mg. Our study uncovers---at the atomistic level---the major factors governing the transport mechanism of these small molecules. In particular, we identify four key diffusion mechanisms and calculate the corresponding diffusion barriers, which are nicely confirmed by time-resolved infrared experiments. We also answer a long-standing question about the existence of secondary adsorption sites for the guest molecules, and we show how those sites affect the macroscopic diffusion properties. Our findings are important to gain a fundamental understanding of the diffusion processes in these nano-porous materials, with direct implications for the usability of MOFs in gas sequestration and storage applications.Comment: 5 pages, 2 figures and supplementary material, Phys. Rev. Let

Wannier-based calculation of the orbital magnetization in crystals

We present a first-principles scheme that allows the orbital magnetization of a magnetic crystal to be evaluated accurately and efficiently even in the presence of complex Fermi surfaces. Starting from an initial electronic-structure calculation with a coarse ab initio k-point mesh, maximally localized Wannier functions are constructed and used to interpolate the necessary k-space quantities on a fine mesh, in parallel to a previously-developed formalism for the anomalous Hall conductivity [X.Wang, J. Yates, I. Souza, and D. Vanderbilt, Phys. Rev. B 74, 195118 (2006)]. We formulate our new approach in a manifestly gauge-invariant manner, expressing the orbital magnetization in terms of traces over matrices in Wannier space. Since only a few (e.g., of the order of 20) Wannier functions are typically needed to describe the occupied and partially occupied bands, these Wannier matrices are small, which makes the interpolation itself very efficient. The method has been used to calculate the orbital magnetization of bcc Fe, hcp Co, and fcc Ni. Unlike an approximate calculation based on integrating orbital currents inside atomic spheres, our results nicely reproduce the experimentally measured ordering of the orbital magnetization in these three materials.Comment: 13 pages, 3 figures, 4 table

Van der Waals interactions in the ground state of Mg(BH4)2 from density functional theory

In order to resolve an outstanding discrepancy between experiment and theory regarding the ground-state structure of Mg(BH4)2, we examine the importance of long-range dispersive interactions on the compound's thermodynamic stability. Careful treatment of the correlation effects within a recently developed nonlocal van der Waals density functional (vdW-DF) leads to a good agreement with experiment, favoring the {\alpha}-Mg(BH4)2 phase (P6122) and a closely related Mn(BH4)2-prototype phase (P3112) over a large set of polymorphs at low temperatures. Our study demonstrates the need to go beyond (semi)local density functional approximations for a reliable description of crystalline high-valent metal borohydrides.Comment: Phys. Rev. B, accepted, 7 pages, 4 figure

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