Development and Implementation of Atomically Anisotropic First-Principles Force Fields: A Benzene Case Study.

π-interactions are an important motif in chemical and biochemical systems. However, due to their anisotropic electron densities and complex balance of intermolecular interactions, aromatic molecules represent an ongoing challenge for accurate and transferable force field development. Historically, ab initio force fields for aromatics have not exhibited good accuracy with respect to bulk properties or have only been used to study gas-phase dimers. Using benzene as a proof of concept, herein we show how our own ab initio MASTIFF force field incorporates an atomically anisotropic description of intermolecular interactions to yield an accurate and robust model for aromatic interactions irrespective of phase. Compared to existing models, the MASTIFF benzene force field not only is accurate for liquid phase properties but also offers transferability to the gas and solid phases. Additionally, we introduce a computationally efficient OpenMM plugin which enables customizable anisotropic intermolecular functional forms and which can be generically used in any MD simulation where a model for nonspherical atomic features is required. Overall, our results demonstrate the importance of atomic-level anisotropy in enabling next-generation ab initio force field development.

Phase Selection and Structure of Low-Defect-Density γ-Al2O3 Created by Epitaxial Crystallization of Amorphous Al2O3.

A multistep phase sequence following the crystallization of amorphous Al2O3 via solid-phase epitaxy (SPE) points to methods to create low-defect-density thin films of the metastable cubic γ-Al2O3 polymorph. An amorphous Al2O3 thin film on a (0001) α-Al2O3 sapphire substrate initially transforms upon heating to form epitaxial γ-Al2O3, followed by a transformation to monoclinic θ-Al2O3, and eventually to α-Al2O3. Epitaxial γ-Al2O3 layers with low mosaic widths in X-ray rocking curves can be formed via SPE by crystallizing the γ-Al2O3 phase from amorphous Al2O3 and avoiding the microstructural inhomogeneity arising from the spatially inhomogeneous transformation to θ-Al2O3. A complementary molecular dynamics (MD) simulation indicates that the amorphous layer and γ-Al2O3 have similar Al coordination geometry, suggesting that γ-Al2O3 forms in part because it involves the minimum rearrangement of the initially amorphous configuration. The lattice parameters of γ-Al2O3 are consistent with a structure in which the majority of the Al vacancies in the spinel structure occupy sites with tetrahedral coordination, consistent with the MD results. The formation of Al vacancies at tetrahedral spinel sites in epitaxial γ-Al2O3 can minimize the epitaxial elastic deformation of γ-Al2O3 during crystallization.

Evidence of an unusual N-H···N hydrogen bond in proteins.

Many residues within proteins adopt conformations that appear to be stabilized by interactions between an amide N-H and the amide N of the previous residue. To explore whether these interactions constitute hydrogen bonds, we characterized the IR stretching frequencies of deuterated variants of proline and the corresponding carbamate, as well as the four proline residues of an Src homology 3 domain protein. The CδD2 stretching frequencies are shifted to lower energies due to hyperconjugation with Ni electron density, and engaging this density via protonation or the formation of the Ni+1-H···Ni interaction ablates this hyperconjugation and thus induces an otherwise difficult to explain blue shift in the C-D absorptions. Along with density functional theory calculations, the data reveal that the Ni+1-H···Ni interactions constitute H-bonds and suggest that they may play an important and previously underappreciated role in protein folding, structure, and function.