Layer groups: Brillouin-zone and crystallographic databases on the Bilbao Crystallographic Server

The section of the Bilbao Crystallographic Server (https://www.cryst.ehu.es/) dedicated to subperiodic groups contains crystallographic and Brillouin-zone databases for the layer groups. The crystallographic databases include the generators/general positions (GENPOS), Wyckoff positions (WYCKPOS) and maximal subgroups (MAXSUB). The Brillouin-zone database (LKVEC) offers k-vector tables and Brillouin-zone figures of all 80 layer groups which form the background of the classification of their irreducible representations. The symmetry properties of the wavevectors are described applying the so-called reciprocal-space-group approach and this classification scheme is compared with that of Litvin & Wike [(1991), Character Tables and Compatibility Relations of the Eighty Layer Groups and Seventeen Plane Groups. New York: Plenum Press]. The specification of independent parameter ranges of k vectors in the representation domains of the Brillouin zones provides a solution to the problems of uniqueness and completeness of layer-group representations. The Brillouin-zone figures and k-vector tables are described in detail and illustrated by several examples.

AFLOW-XtalFinder: a reliable choice to identify crystalline prototypes

The accelerated growth rate of repository entries in crystallographic databases makes it arduous to identify and classify their prototype structures. The open-source AFLOW-XtalFinder package was developed to solve this problem. It symbolically maps structures into standard designations following the AFLOW Prototype Encyclopedia and calculates the internal degrees of freedom consistent with the International Tables for Crystallography. To ensure uniqueness, structures are analyzed and compared via symmetry, local atomic geometries, and crystal mapping techniques, simultaneously grouping them by similarity. The software (i) distinguishes distinct crystal prototypes and atom decorations, (ii) determines equivalent spin configurations, (iii) reveals compounds with similar properties, and (iv) guides the discovery of unexplored materials. The operations are accessible through a Python module ready for workflows, and through command line syntax. All the 4+ million compounds in the AFLOW.org repositories are mapped to their ideal prototype, allowing users to search database entries via symbolic structure-type. Furthermore, 15,000 unique structures — sorted by prevalence — are extracted from the AFLOW-ICSD catalog to serve as future prototypes in the Encyclopedia.

The CSD and knowledge databases: from answers to questions

We develop tools for extracting new information on crystal structures from crystallographic databases and show how to use these tools in the design of coordination compounds.

Fast, Efficient Fragment-Based Coordinate Generation for Open Babel

<div>Rapidly predicting an accurate three dimensional geometry of a molecule is a crucial task in cheminformatics and a range of molecular modeling. Fast, accurate, and open implementation of structure prediction is necessary for reproducible cheminformatics research. We introduce fragment-based coordinate generation for Open Babel, a widely accepted open source toolkit for cheminformatics. The new implementation significant improves speed and stereochemical accuracy, while retaining or improving accuracy of bond lengths, bond angles, and dihedral torsions. We first separate an input molecule into fragments by cutting at rotatable bonds. Coordinates of fragments are set according to the fragment library, which is prepared from open crystallographic databases. Since coordinates of multiple atoms are decided at once, coordinate prediction is accelerated over the previous rules-based implementation or the widely-used distance geometry methods in RDKit. This new implementation will be beneficial for a wide range of applications, including computational property prediction in polymers, molecular materials and drug design.</div>

Fast, Efficient Fragment-Based Coordinate Generation for Open Babel

<div>Rapidly predicting an accurate three dimensional geometry of a molecule is a crucial task in cheminformatics and a range of molecular modeling. Fast, accurate, and open implementation of structure prediction is necessary for reproducible cheminformatics research. We introduce fragment-based coordinate generation for Open Babel, a widely accepted open source toolkit for cheminformatics. The new implementation significant improves speed and stereochemical accuracy, while retaining or improving accuracy of bond lengths, bond angles, and dihedral torsions. We first separate an input molecule into fragments by cutting at rotatable bonds. Coordinates of fragments are set according to the fragment library, which is prepared from open crystallographic databases. Since coordinates of multiple atoms are decided at once, coordinate prediction is accelerated over the previous rules-based implementation or the widely-used distance geometry methods in RDKit. This new implementation will be beneficial for a wide range of applications, including computational property prediction in polymers, molecular materials and drug design.</div>

Screening topological materials with a CsCl-type structure in crystallographic databases

CsCl-type materials have many outstanding characteristics, i.e. simple in structure, ease of synthesis and good stability at room temperature, thus are an excellent choice for designing functional materials. Using high-throughput first-principles calculations, a large number of topological semimetals/metals (TMs) were designed from CsCl-type materials found in crystallographic databases and their crystal and electronic structures have been studied. The CsCl-type TMs in this work show rich topological character, ranging from triple nodal points, type-I nodal lines and critical-type nodal lines, to hybrid nodal lines. The TMs identified show clean topological band structures near the Fermi level, which are suitable for experimental investigations and future applications. This work provides a rich data set of TMs with a CsCl-type structure.

Chiral Peculiar Properties of Self-Organization of Diphenylalanine Peptide Nanotubes: Modeling Of Structure and Properties

The structure and properties of diphenylalanine peptide nanotubes based on phenylalanine were investigated by various molecular modeling methods. The main approaches were semi-empirical quantum-chemical methods (PM3 and AM1), and molecular mechanical ones. Both the model structures and the structures extracted from their experimental crystallographic databases obtained by X-ray methods were examined. A comparison of optimized model structures and structures obtained by naturally-occurring self-assembly showed their important differences depending on D- and L-chirality. In both the cases, the effect of chirality on the results of self-assembly of diphenylalanine peptide nanotubes was established: peptide nanotubes based on the D-diphenylalanine (D-FF) has high condensation energy E0 in transverse direction and forms thicker and shorter peptide nanotubes bundles, than that based on L-diphenylalanine (L-FF). A topological difference was established: model peptide nanotubes were optimized into structures consisting of rings, while naturally self-assembled peptide nanotubes consisted of helical coils. The latter were different for the original L-FF and D-FF. They formed helix structures in which the chirality sign changes as the level of the macromolecule hierarchy raises. Total energy of the optimal distances between two units are deeper for L-FF (–1.014 eV) then for D-FF (–0.607 eV) for ring models, while for helix coil are approximately the same and have for L-FF (–6.18 eV) and for D-FF (–6.22 eV) by PM3 method; for molecular mechanical methods energy changes are of the order of 2–3 eV for both the cases. A topological transition between a ring and a helix coil of peptide nanotube structures is discussed: self-assembled natural helix structures are more stable and favourable, they have lower energy in optimal configuration as compared with ring models by a value of the order of 1 eV for molecular mechanical methods and 5 eV for PM3 method.

Fast, Efficient Fragment-Based Coordinate Generation for Open Babel

<div>Rapidly predicting an accurate three dimensional geometry of a molecule is a crucial task in cheminformatics and a range of molecular modeling. Fast, accurate, and open implementation of structure prediction is necessary for reproducible cheminformatics research. We introduce fragment-based coordinate generation for Open Babel, a widely accepted open source toolkit for cheminformatics. The new implementation significant improves speed and stereochemical accuracy, while retaining or improving accuracy of bond lengths, bond angles, and dihedral torsions. We first separate an input molecule into fragments by cutting at rotatable bonds. Coordinates of fragments are set according to the fragment library, which is prepared from open crystallographic databases. Since coordinates of multiple atoms are decided at once, coordinate prediction is accelerated over the previous rules-based implementation or the widely-used distance geometry methods in RDKit. This new implementation will be beneficial for a wide range of applications, including computational property prediction in polymers, molecular materials and drug design.</div>