Construction of Negatively Curved Cubic Carbon Crystals via Standard Realizations

We constructed physically stable sp2 negatively curved cubic carbon structures which reticulate a Schwarz P-like surface. The method for constructing such crystal structures is based on the notion of the standard realization of abstract crystal lattices. In this paper, we expound on the mathematical method to construct such crystal structures

Co-crystal structures of furosemide:urea and carbamazepine:indomethacin determined from powder x-ray diffraction data

Co-crystallization is a promising approach to improving both the solubility and the dissolution rate of active pharmaceutical ingredients. Crystal structure determination from powder diffraction data plays an important role in determining co-crystal structures, especially those generated by mechanochemical means. Here, two new structures of pharmaceutical interest are reported: a 1:1 co‑crystal of furosemide with urea formed by liquid-assisted grinding and a second polymorphic form of a 1:1 co‑crystal of carbamazepine with indomethacin, formed by solvent evaporation. Energy minimization using dispersion-corrected density functional theory was used in finalizing both structures. In the case of carbamazepine:indomethacin, this energy minimization step was essential in obtaining a satisfactory final Rietveld refinement

Predicting the Volumes of Crystals

New crystal structures are frequently derived by performing ionic substitutions on known crystal structures. These derived structures are then used in further experimental analysis, or as the initial guess for structural optimization in electronic structure calculations, both of which usually require a reasonable guess of the lattice parameters. In this work, we propose two lattice prediction schemes to improve the initial guess of a candidate crystal structure. The first scheme relies on a one-to-one mapping of species in the candidate crystal structure to a known crystal structure, while the second scheme relies on data-mined minimum atom pair distances to predict the crystal volume of the candidate crystal structure and does not require a reference structure. We demonstrate that the two schemes can effectively predict the volumes within mean absolute errors (MAE) as low as 3.8% and 8.2%. We also discuss the various factors that may impact the performance of the schemes. Implementations for both schemes are available in the open-source pymatgen software.Comment: 8 figures, 2 table

Photonic Crystal Laser Accelerator Structures

Photonic crystals have great potential for use as laser-driven accelerator structures. A photonic crystal is a dielectric structure arranged in a periodic geometry. Like a crystalline solid with its electronic band structure, the modes of a photonic crystal lie in a set of allowed photonic bands. Similarly, it is possible for a photonic crystal to exhibit one or more photonic band gaps, with frequencies in the gap unable to propagate in the crystal. Thus photonic crystals can confine an optical mode in an all-dielectric structure, eliminating the need for metals and their characteristic losses at optical frequencies. We discuss several geometries of photonic crystal accelerator structures. Photonic crystal fibers (PCFs) are optical fibers which can confine a speed-of-light optical mode in vacuum. Planar structures, both two- and three-dimensional, can also confine such a mode, and have the additional advantage that they can be manufactured using common microfabrication techniques such as those used for integrated circuits. This allows for a variety of possible materials, so that dielectrics with desirable optical and radiation-hardness properties can be chosen. We discuss examples of simulated photonic crystal structures to demonstrate the scaling laws and trade-offs involved, and touch on potential fabrication processes.Comment: 3 pages, 3 figures; Submitted to Particale Accelerator Conference (PAC 2003), May 12-16, 2003, Portland, Oregon (IEEE

Solution Structures of \u3cem\u3eMycobacterium tuberculosis\u3c/em\u3e Thioredoxin C and Models of Intact Thioredoxin System Suggest New Approaches to Inhibitor and Drug Design

Here, we report the NMR solution structures of Mycobacterium tuberculosis (M. tuberculosis) thioredoxin C in both oxidized and reduced states, with discussion of structural changes that occur in going between redox states. The NMR solution structure of the oxidized TrxC corresponds closely to that of the crystal structure, except in the C-terminal region. It appears that crystal packing effects have caused an artifactual shift in the α4 helix in the previously reported crystal structure, compared with the solution structure. On the basis of these TrxC structures, chemical shift mapping, a previously reported crystal structure of the M. tuberculosis thioredoxin reductase (not bound to a Trx) and structures for intermediates in the E. coli thioredoxin catalytic cycle, we have modeled the complete M. tuberculosis thioredoxin system for the various steps in the catalytic cycle. These structures and models reveal pockets at the TrxR/TrxC interface in various steps in the catalytic cycle, which can be targeted in the design of uncompetitive inhibitors as potential anti-mycobacterial agents, or as chemical genetic probes of function

Molecular crystal global phase diagrams. II. Reference lattices

In the first part of this series [Keith et al. (2004). Cryst. Growth Des. 4, 1009-1012; Mettes et al. (2004). Acta Cryst. A60, 621-636], a method was developed for constructing global phase diagrams (GPDs) for molecular crystals in which crystal structure is presented as a function of intermolecular potential parameters. In that work, a face-centered-cubic center-of-mass lattice was arbitrarily adopted as a reference state. In part two of the series, experimental crystal structures composed of tetrahedral point group molecules are classified to determine what fraction of structures are amenable to inclusion in the GPDs and the number of reference lattices necessary to span the observed structures. It is found that 60% of crystal structures composed of molecules with T_d point-group symmetry are amenable and that eight reference lattices are sufficient to span the observed structures. Similar results are expected for other cubic point groups

Applied Symmetry for Crystal Structure Prediction

This thesis presents an original open-source Python package called PyXtal (pronounced pi-crystal ) that generates random symmetric crystal structures for use in crystal structure prediction (CSP). The primary advantage of PyXtal over existing structure generation tools is its unique symmetrization method. For molecular structures, PyXtal uses an original algorithm to determine the compatibility of molecular point group symmetry with Wyckoff site symmetry. This allows the molecules in generated structures to occupy special Wyckoff positions without breaking the structure\u27s symmetry. This is a new feature which increases the space of search-able structures and in turn improves CSP performance. It is shown that using already-symmetric initial structures results in a higher probability of finding the lowest-energy structure. Ultimately, this lowers the computational time needed for CSP. Structures can be generated for any symmetry group of 0, 1, 2, or 3 dimensions of periodicity. Either atoms or rigid molecules may be used as building blocks. The generated structures can be optimized with VASP, LAMMPS, or other computational tools. Additional options are provided for the lattice and inter-atomic distance constraints. Results for carbon and silicon crystals, water ice crystals, and molybdenum clusters are presented as usage examples

Finite Element simulation of radiation losses in photonic crystal fibers

In our work we focus on the accurate computation of light propagation in finite size photonic crystal structures with the finite element method (FEM). We discuss how we utilize numerical concepts like high-order finite elements, transparent boundary conditions and goal-oriented error estimators for adaptive grid refinement in order to compute radiation leakage in photonic crystal fibers and waveguides. Due to the fast convergence of our method we can use it e.g. to optimize the design of photonic crystal structures with respect to geometrical parameters, to minimize radiation losses and to compute attenutation spectra for different geometries