Emergence of hidden phases of methylammonium lead iodide (CH3NH3PbI3) upon compression

We perform a thorough structural search with the minima hopping method (MHM) to explore low-energy structures of methylammonium lead iodide. By combining the MHM with a forcefield, we efficiently screen vast portions of the configurational space with large simulation cells containing up to 96 atoms. Our search reveals two structures of methylammonium iodide perovskite (MAPI) that are substantially lower in energy than the well-studied experimentally observed low-temperature Pnma orthorhombic phase according to density functional calculations. Both structures have not yet been reported in the literature for MAPI, but our results show that they could emerge as thermodynamically stable phases via compression at low temperatures. In terms of the electronic properties, the two phases exhibit larger band gaps than the standard perovskite-type structures. Hence, the pressure-induced phase selection at technologically achievable pressures (i.e., via thin-film strain) is a viable route towards the synthesis of several MAPI polymorph with variable band gaps

Vibrational signatures for low-energy intermediate-sized Si clusters

We report low-energy locally stable structures for the clusters Si20 and Si21. The structures were obtained by performing geometry optimizations within the local density approximation. Our calculated binding energies for these clusters are larger than any previously reported for this size regime. To aid in the experimental identification of the structures, we have computed the full vibrational spectra of the clusters, along with the Raman and IR activities of the various modes using a recently developed first-principles technique. These represent, to our knowledge, the first calculations of Raman and IR spectra for Si clusters of this size

Ab initio molecular dynamics using density based energy functionals: application to ground state geometries of some small clusters

The ground state geometries of some small clusters have been obtained via ab initio molecular dynamical simulations by employing density based energy functionals. The approximate kinetic energy functionals that have been employed are the standard Thomas-Fermi $(T_{TF})$ along with the Weizsacker correction $T_W$ and a combination $F(N_e)T_{TF} + T_W$. It is shown that the functional involving $F(N_e)$ gives superior charge densities and bondlengths over the standard functional. Apart from dimers and trimers of Na, Mg, Al, Li, Si, equilibrium geometries for $Li_nAl, n=1,8$ and $Al_{13}$ clusters have also been reported. For all the clusters investigated, the method yields the ground state geometries with the correct symmetries with bondlengths within 5\% when compared with the corresponding results obtained via full orbital based Kohn-Sham method. The method is fast and a promising one to study the ground state geometries of large clusters.Comment: 15 pages, 3 PS figure

A 50-year record of NOx and SO2 sources in precipitation in the Northern Rocky Mountains, USA

Ice-core samples from Upper Fremont Glacier (UFG), Wyoming, were used as proxy records for the chemical composition of atmospheric deposition. Results of analysis of the ice-core samples for stable isotopes of nitrogen (δ15N, ) and sulfur (δ34S, ), as well as and deposition rates from the late-1940s thru the early-1990s, were used to enhance and extend existing National Atmospheric Deposition Program/National Trends Network (NADP/NTN) data in western Wyoming. The most enriched δ34S value in the UFG ice-core samples coincided with snow deposited during the 1980 eruption of Mt. St. Helens, Washington. The remaining δ34S values were similar to the isotopic composition of coal from southern Wyoming. The δ15N values in ice-core samples representing a similar period of snow deposition were negative, ranging from -5.9 to -3.2 ‰ and all fall within the δ15N values expected from vehicle emissions. Ice-core nitrate and sulfate deposition data reflect the sharply increasing U.S. emissions data from 1950 to the mid-1970s

Enzyme Promiscuity in Enolase Superfamily. Theoretical Study of o-Succinylbenzoate Synthase Using QM/MM Methods

The promiscuous activity of the enzyme o-succinylbenzoate synthase (OSBS) from the actinobacteria Amycolatopsis is investigated by means of QM/MM methods, using both density functional theory and semiempirical Hamiltonians. This enzyme catalyzes not only the dehydration of 2-succinyl-6R-hydroxy-2,4-cyclohexadiene-1R-carboxylate but also catalyzes racemization of different acylamino acids, with N-succinyl-R-phenylglycine being the best substrate. We investigated the molecular mechanisms for both reactions exploring the potential energy surface. Then, molecular dynamics simulations were performed to obtain the free energy profiles and the averaged interaction energies of enzymatic residues with the reacting system. Our results confirm the plausibility of the reaction mechanisms proposed in the literature, with a good agreement between theoretical and experimentally derived activation free energies. Our simulations unravel the role played by the different residues in each of the two possible reactions. The presence of flexible loops in the active site and the selection of structural modifications in the substrate seem to be key elements to promote the promiscuity of this enzyme.This work was supported by the Spanish Ministerio de Economia y Competitividad project CTQ2012-36253-C03-03 ́ and FEDER funds. K.S. thanks the Polish National Science Center (NCN) for Grant 2011/02/A/ST4/00246. The authors acknowledge computational facilities of the Servei d’Informatica ̀ de la Universitat de Valencia in the ̀ “Tirant” supercomputer, which is part of the Spanish Supercomputing Network

RosettaScripts: A Scripting Language Interface to the Rosetta Macromolecular Modeling Suite

Macromolecular modeling and design are increasingly useful in basic research, biotechnology, and teaching. However, the absence of a user-friendly modeling framework that provides access to a wide range of modeling capabilities is hampering the wider adoption of computational methods by non-experts. RosettaScripts is an XML-like language for specifying modeling tasks in the Rosetta framework. RosettaScripts provides access to protocol-level functionalities, such as rigid-body docking and sequence redesign, and allows fast testing and deployment of complex protocols without need for modifying or recompiling the underlying C++ code. We illustrate these capabilities with RosettaScripts protocols for the stabilization of proteins, the generation of computationally constrained libraries for experimental selection of higher-affinity binding proteins, loop remodeling, small-molecule ligand docking, design of ligand-binding proteins, and specificity redesign in DNA-binding proteins

Installing hydrolytic activity into a completely <i>de novo </i>protein framework

The design of enzyme-like catalysts tests our understanding of sequence-to-structure/function relationships in proteins. Here we install hydrolytic activity predictably into a completely de novo and thermostable α-helical barrel, which comprises seven helices arranged around an accessible channel. We show that the lumen of the barrel accepts 21 mutations to functional polar residues. The resulting variant, which has cysteine–histidine–glutamic acid triads on each helix, hydrolyses p-nitrophenyl acetate with catalytic efficiencies that match the most-efficient redesigned hydrolases based on natural protein scaffolds. This is the first report of a functional catalytic triad engineered into a de novo protein framework. The flexibility of our system also allows the facile incorporation of unnatural side chains to improve activity and probe the catalytic mechanism. Such a predictable and robust construction of truly de novo biocatalysts holds promise for applications in chemical and biochemical synthesis

Ab initio studies of structures and properties of small potassium clusters

We have studied the structure and properties of potassium clusters containing even number of atoms ranging from 2 to 20 at the ab initio level. The geometry optimization calculations are performed using all-electron density functional theory with gradient corrected exchange-correlation functional. Using these optimized geometries we investigate the evolution of binding energy, ionization potential, and static polarizability with the increasing size of the clusters. The polarizabilities are calculated by employing Moller-Plesset perturbation theory and time dependent density functional theory. The polarizabilities of dimer and tetramer are also calculated by employing large basis set coupled cluster theory with single and double excitations and perturbative triple excitations. The time dependent density functional theory calculations of polarizabilities are carried out with two different exchange-correlation potentials: (i) an asymptotically correct model potential and (ii) within the local density approximation. A systematic comparison with the other available theoretical and experimental data for various properties of small potassium clusters mentioned above has been performed. These comparisons reveal that both the binding energy and the ionization potential obtained with gradient corrected potential match quite well with the already published data. Similarly, the polarizabilities obtained with Moller-Plesset perturbation theory and with model potential are quite close to each other and also close to experimental data.Comment: 33 pages including 10 figure

A Generic Program for Multistate Protein Design

Some protein design tasks cannot be modeled by the traditional single state design strategy of finding a sequence that is optimal for a single fixed backbone. Such cases require multistate design, where a single sequence is threaded onto multiple backbones (states) and evaluated for its strengths and weaknesses on each backbone. For example, to design a protein that can switch between two specific conformations, it is necessary to to find a sequence that is compatible with both backbone conformations. We present in this paper a generic implementation of multistate design that is suited for a wide range of protein design tasks and demonstrate in silico its capabilities at two design tasks: one of redesigning an obligate homodimer into an obligate heterodimer such that the new monomers would not homodimerize, and one of redesigning a promiscuous interface to bind to only a single partner and to no longer bind the rest of its partners. Both tasks contained negative design in that multistate design was asked to find sequences that would produce high energies for several of the states being modeled. Success at negative design was assessed by computationally redocking the undesired protein-pair interactions; we found that multistate design's accuracy improved as the diversity of conformations for the undesired protein-pair interactions increased. The paper concludes with a discussion of the pitfalls of negative design, which has proven considerably more challenging than positive design