Resorcinol Crystallization from the Melt: A New Ambient Phase and New "Riddles".

Structures of the α and ß phases of resorcinol, a major commodity chemical in the pharmaceutical, agrichemical, and polymer industries, were the first polymorphic pair of molecular crystals solved by X-ray analysis. It was recently stated that "no additional phases can be found under atmospheric conditions" (Druzbicki, K. et al. J. Phys. Chem. B 2015, 119, 1681). Herein is described the growth and structure of a new ambient pressure phase, ε, through a combination of optical and X-ray crystallography and by computational crystal structure prediction algorithms. α-Resorcinol has long been a model for mechanistic crystal growth studies from both solution and vapor because prisms extended along the polar axis grow much faster in one direction than in the opposite direction. Research has focused on identifying the absolute sense of the fast direction-the so-called "resorcinol riddle"-with the aim of identifying how solvent controls crystal growth. Here, the growth velocity dissymmetry in the melt is analyzed for the ß phase. The ε phase only grows from the melt, concomitant with the ß phase, as polycrystalline, radially growing spherulites. If the radii are polar, then the sense of the polar axis is an essential feature of the form. Here, this determination is made for spherulites of ß resorcinol (ε, point symmetry 222, does not have a polar axis) with additives that stereoselectively modify growth velocities. Both ß and ε have the additional feature that individual radial lamellae may adopt helicoidal morphologies. We correlate the appearance of twisting in ß and ε with the symmetry of twist-inducing additives.

Carbon-14 decay as a source of non-canonical bases in DNA.

BACKGROUND: Significant experimental effort has been applied to study radioactive beta-decay in biological systems. Atomic-scale knowledge of this transmutation process is lacking due to the absence of computer simulations. Carbon-14 is an important beta-emitter, being ubiquitous in the environment and an intrinsic part of the genetic code. Over a lifetime, around 50 billion (14)C decays occur within human DNA. METHODS: We apply ab initio molecular dynamics to quantify (14)C-induced bond rupture in a variety of organic molecules, including DNA base pairs. RESULTS: We show that double bonds and ring structures confer radiation resistance. These features, present in the canonical bases of the DNA, enhance their resistance to (14)C-induced bond-breaking. In contrast, the sugar group of the DNA and RNA backbone is vulnerable to single-strand breaking. We also show that Carbon-14 decay provides a mechanism for creating mutagenic wobble-type mispairs. CONCLUSIONS: The observation that DNA has a resistance to natural radioactivity has not previously been recognized. We show that (14)C decay can be a source for generating non-canonical bases. GENERAL SIGNIFICANCE: Our findings raise questions such as how the genetic apparatus deals with the appearance of an extra nitrogen in the canonical bases. It is not obvious whether or not the DNA repair mechanism detects this modification nor how DNA replication is affected by a non-canonical nucleobase. Accordingly, (14)C may prove to be a source of genetic alteration that is impossible to avoid due to the universal presence of radiocarbon in the environment.

Valley splitting in a silicon quantum device platform.

By suppressing an undesirable surface Umklapp process, it is possible to resolve the two most occupied states (1Γ and 2Γ) in a buried two-dimensional electron gas (2DEG) in silicon. The 2DEG exists because of an atomically sharp profile of phosphorus dopants which have been formed beneath the Si(001) surface (a δ-layer). The energy separation, or valley splitting, of the two most occupied bands has critical implications for the properties of δ-layer derived devices, yet until now, has not been directly measurable. Density functional theory (DFT) allows the 2DEG band structure to be calculated, but without experimental verification the size of the valley splitting has been unclear. Using a combination of direct spectroscopic measurements and DFT we show that the measured band structure is in good qualitative agreement with calculations and reveal a valley splitting of 132 ± 5 meV. We also report the effective mass and occupation of the 2DEG states and compare the dispersions and Fermi surface with DFT.

Phosphorus δ-doped silicon: mixed-atom pseudopotentials and dopant disorder effects.

Within a full density functional theory framework we calculate the band structure and doping potential for phosphorus δ-doped silicon. We compare two different representations of the dopant plane; pseudo-atoms in which the nuclear charge is fractional between silicon and phosphorus, and explicit arrangements employing distinct silicon and phosphorus atoms. While the pseudo-atom approach offers several computational advantages, the explicit model calculations differ in a number of key points, including the valley splitting, the Fermi level and the width of the doping potential. These findings have implications for parameters used in device modelling.

Quantum confinement effects in gallium nitride nanostructures: ab initio investigations.

We present ab initio density functional investigations of the atomic and electronic structure of gallium nitride nanodots and nanowires. With increasing diameter, the average Ga-N bond length in the nanostructures increases, as does the relative stability (heat of formation), approaching the values for bulk GaN. As the diameter decreases, the band gap increases, with the variation for the nanodots greater than that for the nanowires, in qualitative accordance with expectations based on simple geometrical quantum confinement considerations. Interestingly, in contrast to nanowires, the lowest unoccupied states of the nanodots exhibit an extended delocalized (Ga-derived) character, weighted in the centre of the nanodot.

Powder diffraction and crystal structure prediction identify four new coumarin polymorphs.

Coumarin, a simple, commodity chemical isolated from beans in 1820, has, to date, only yielded one solid state structure. Here, we report a rich polymorphism of coumarin grown from the melt. Four new metastable forms were identified and their crystal structures were solved using a combination of computational crystal structure prediction algorithms and X-ray powder diffraction. With five crystal structures, coumarin has become one of the few rigid molecules showing extensive polymorphism at ambient conditions. We demonstrate the crucial role of advanced electronic structure calculations including many-body dispersion effects for accurate ranking of the stability of coumarin polymorphs and the need to account for anharmonic vibrational contributions to their free energy. As such, coumarin is a model system for studying weak intermolecular interactions, crystallization mechanisms, and kinetic effects.

Silver(I), gold(I) and palladium(II) complexes of a NHC-pincer ligand with an aminotriazine core: a comparison with pyridyl analogues.

Dinuclear silver, di- and tetra-nuclear gold, and mononuclear palladium complexes with chelating C,N,C diethylaminotriazinyl-bridged bis(NHC) pincer ligands were prepared and characterised. The silver and gold complexes exist in a twisted, helical conformation in both the solution- and the solid state. In contrast, an analogous dinuclear gold complex with pyridyl-bridged NHCs exists in a linear conformation. Computational studies have been performed to rationalise the formation of twisted/helical vs. linear forms.

Bottom-up assembly of metallic germanium.

Extending chip performance beyond current limits of miniaturisation requires new materials and functionalities that integrate well with the silicon platform. Germanium fits these requirements and has been proposed as a high-mobility channel material, a light emitting medium in silicon-integrated lasers, and a plasmonic conductor for bio-sensing. Common to these diverse applications is the need for homogeneous, high electron densities in three-dimensions (3D). Here we use a bottom-up approach to demonstrate the 3D assembly of atomically sharp doping profiles in germanium by a repeated stacking of two-dimensional (2D) high-density phosphorus layers. This produces high-density (10(19) to 10(20) cm(-3)) low-resistivity (10(-4)Ω · cm) metallic germanium of precisely defined thickness, beyond the capabilities of diffusion-based doping technologies. We demonstrate that free electrons from distinct 2D dopant layers coalesce into a homogeneous 3D conductor using anisotropic quantum interference measurements, atom probe tomography, and density functional theory.

Benchmarking Calculated Lattice Parameters and Energies of Molecular Crystals Using van der Waals Density Functionals.

The development of new functionals and methods to accurately describe van der Waals forces in density functional theory (DFT) has become popular in recent years, with the vast majority of studies assessing the accuracy of the energetics of collections of molecules, and to a lesser extent molecular crystalline systems. As the energies are a function of the atom positions, we assess the accuracy of DFT calculations from both a geometric and energetics point of view for the C21 reference data set of Otero-de-la-Roza and Johnson for molecular crystals, and a set of monosaccharide molecular crystals. In particular, we examine the performance of exchange-correlation functionals designed to handle van der Waals forces, including the vdW-DF, vdW-DF2, and XDM methods. We also assess the effect of using small and large basis sets, the choice of basis functions (local atomic orbitals using the SIESTA code versus planewaves using the Quantum ESPRESSO code), and the effect of corrections for basis set superposition errors. Finally, we examine the geometries and energies of the S22 reference set of molecular complexes. Overall, the most accurate geometries for both choices of basis functions are obtained with the vdW-DF2 functional, while the most accurate lattice energies are obtained using vdW-DF2 with local atomic orbitals and XDM with planewaves with mean absolute errors of less than 4 kJ/mol.

Hydrogen bond disruption in DNA base pairs from (14)C transmutation.

Recent ab initio molecular dynamics simulations have shown that radioactive carbon does not normally fragment DNA bases when it decays. Motivated by this finding, density functional theory and Bader analysis have been used to quantify the effect of C → N transmutation on hydrogen bonding in DNA base pairs. We find that (14)C decay has the potential to significantly alter hydrogen bonds in a variety of ways including direct proton shuttling (thymine and cytosine), thermally activated proton shuttling (guanine), and hydrogen bond breaking (cytosine). Transmutation substantially modifies both the absolute and relative strengths of the hydrogen bonding pattern, and in two instances (adenine and cytosine), the density at the critical point indicates development of mild covalent character. Since hydrogen bonding is an important component of Watson-Crick pairing, these (14)C-induced modifications, while infrequent, may trigger errors in DNA transcription and replication.

Noncovalent Interactions in SIESTA Using the vdW-DF Functional: S22 Benchmark and Macrocyclic Structures.

We investigate the performance of the vdW-DF functional of Dion et al. implemented in the SIESTA code. In particular, the S22 data set and several calixarene-based host-guest structures are examined to assess the performance of the functional. The binding energy error statistics for the S22 data set reveal that the vdW-DF functional performs very well when compared to a range of other methods of treating dispersion in density functional theory, and to vdW-DF implementations in other codes. For the calixarene host-guest structures, the structural properties and binding energies are compared to previous experimental and computational studies, and in most cases we find that vdW-DF provides superior results to other computational studies.

Vacancies in GaN bulk and nanowires: effect of self-interaction corrections.

We investigate gallium and nitrogen vacancies in gallium nitride (GaN) bulk and nanowires using self-interaction corrected pseudopotentials (SIC). In particular, we examine the band structures to compare and contrast differences between the SIC results and standard density functional theory (DFT) results using a generalized gradient approximation (GGA) (Perdew et al 1996 Phys. Rev. Lett. 77 3865) functional. For pure nanowires, we observed similar trends in the bandgap behaviour, with the gap decreasing for increasing nanowire diameters (with larger bandgaps using SIC pseudopotentials). For gallium vacancies in bulk GaN and GaN nanowires, SIC results are similar to DFT-GGA results, albeit with larger bandgaps. Nitrogen vacancies in bulk GaN show similar defect-induced states near the conduction band, whilst a lower lying defect state is observed below the valence band for the DFT-GGA calculations and above the valence band for the SIC results. For nitrogen vacancies in GaN nanowires, similar defect states are observed near the conduction band, however, while the SIC calculations also show a defect state/s above the valence band, we were unable to locate this state for the DFT-GGA calculations (possibly because it is hybridized with edge states and buried below the valence band).

Ab Initio Molecular Dynamics Simulations of (101) Surfaces of Potassium Dihydrogenphosphate.

We present an ab initio molecular dynamics study of bare and hydrated (101) surfaces of KDP. We examine the dynamical nature of the hydrogen bonding in the high and low temperature phases of bulk KDP and find evidence to support the theory that hydrogen atoms oscillate between two off-center positions in the high-temperature phase. We report the translational relaxation of the surface species on the (101) surface and find good agreement with experimental results, particularly with reference to the direction of the relaxation. We find a strongly hydrogen bound water layer close to the KDP surface, comparing closely to a highly ordered water layer observed experimentally. Overall, there is good agreement with the results of nanoscale experimental studies, demonstrating the effectiveness of ab initio molecular dynamics calculations at simulating bulk and surface properties.

Ab Initio Simulations of the (101) Surfaces of Potassium Dihydrogenphosphate (KDP).

We have used density functional calculations to examine the (101) surfaces of KDP, under vacuum, nitrogen, and aqueous conditions, and these simulations are found to agree well with nanoscale experimental studies demonstrating that the density functional calculations are providing a good description of the surfaces of this complex inorganic salt.