The geometry of periodic knots, polycatenanes and weaving from a chemical perspective: a library for reticular chemistry.

The geometry of simple knots and catenanes is described using the concept of linear line segments (sticks) joined at corners. This is extended to include woven linear threads as members of the extended family of knots. The concept of transitivity that can be used as a measure of regularity is explained. Then a review is given of the simplest, most 'regular' 2- and 3-periodic patterns of polycatenanes and weavings. Occurrences in crystal structures are noted but most structures are believed to be new and ripe targets for designed synthesis.

Interferometric Diffraction from Amorphous Double Films.

We explore the interference fringes that arise in diffraction patterns from double-layer amorphous samples where there is a substantial separation, up to about a micron, between two overlapping thin films. This interferometric diffraction geometry, where both waves have interacted with the specimen, reveals phase gradients within microdiffraction patterns. The rapid fading of the observed fringes as the magnitude of the diffraction vector increases confirms that displacement decoherence is strong in high-energy electron scattering from amorphous samples. The fading of fringes with increasing layer separation indicates an effective illumination coherence length of about 225 nm, which is consistent with the value of 270 nm expected for the heated Schottky field emitter source. A small reduction in measured coherence length is expected because of the additional energy spread induced in the beam after it passes through the first layer.

Speckle Suppression by Decoherence in Fluctuation Electron Microscopy.

We compare experimental fluctuation electron microscopy (FEM) speckle data with electron diffraction simulations for thin amorphous carbon and silicon samples. We find that the experimental speckle intensity variance is generally more than an order of magnitude lower than kinematical scattering theory predicts for spatially coherent illumination. We hypothesize that decoherence, which randomizes the phase relationship between scattered waves, is responsible for the anomaly. Specifically, displacement decoherence can contribute strongly to speckle suppression, particularly at higher beam energies. Displacement decoherence arises when the local structure is rearranged significantly by interactions with the beam during the exposure. Such motions cause diffraction speckle to twinkle, some of it at observable time scales. We also find that the continuous random network model of amorphous silicon can explain the experimental variance data if displacement decoherence and multiple scattering is included in the modeling. This may resolve the longstanding discrepancy between X-ray and electron diffraction studies of radial distribution functions, and conclusions reached from previous FEM studies. Decoherence likely affects all quantitative electron imaging and diffraction studies. It likely contributes to the so-called Stobbs factor, where high-resolution atomic-column image intensities are anomalously lower than predicted by a similar factor to that observed here.

The importance of averaging to interpret electron correlographs of disordered materials.

The development of effective new tools for structural characterization of disordered materials and systems is becoming increasingly important as such tools provide the key to understanding, and ultimately controlling, their properties. The relatively novel technique of correlograph analysis (i.e., the approach of calculating angular autocorrelations within diffraction patterns) promises unique advantages for probing the local symmetries of disordered structures. Because correlograph analysis examines a component of the high-order four-body correlation function, it is more sensitive to medium-range ordering than conventional diffraction methods. As a follow-up of our previous publication, where we studied thin samples of sputtered amorphous silicon, we describe here the practical experimental method and common systematic errors of electron correlograph analysis. Using both experimental data and numerical simulations, we demonstrate that reliable structural information about the sample can only be extracted from the mean correlograph averaged over a sufficient number of individual results.

Periodic Borromean rings, rods and chains.

This article describes periodic polycatenane structures built from interlocked rings in which no two are directly linked. The 2-periodic vertex-, edge- and ring-transitive families of hexagonal Borromean rings are described in detail, and it is shown how these give rise to 1- and 3-periodic ring-transitive (isonemal) families. A second isonemal 2-periodic family is identified, as is a unique 3-periodic Borromean assembly of equilateral triangles. Also reported is a notable 2-periodic structure comprising chains of linked rings in which the chains are locked in place but no two chains are directly interlinked, being held in place as a novel `quasi-Borromean' set of four repeating components.

Isogonal 2-periodic polycatenanes: chain mail.

For 2-periodic polycatenanes with isogonal (vertex-transitive) embeddings, the basic units linked are torus knots and links including the unknots (untangled polygons). Twenty-four infinite families have been identified, with hexagonal, tetragonal or rectangular symmetry. The simplest members of each family are described and illustrated. A method for determining the catenation number of a ring based on electromagnetic theory is described.

Periodic diffraction from an aperiodic monohedral tiling.

The diffraction pattern from the recently reported aperiodic `einstein', or `hat', monohedral tiling [Smith et al. (2023). arXiv:2303.10798v1] has been analyzed. The structure is the hexagonal mta net, a kite tiling, with aperiodic vertex deletions. A large model's diffraction pattern displays a robust sixfold periodicity in plane group p6. A repeating, roughly triangular motif of `diffused intensity' arises between the strongest Bragg peaks. The motif contains high-density regions of discrete `satellite' peaks, rather than continuous `diffuse scattering', breaking mirror symmetry, consistent with the chiral hat tiling.

Borromean rings redux. A missing link found - a Borromean triplet of Borromean triplets.

This paper describes a nine-component Borromean structure - a Borromean triplet of Borromean triplets - that was missing from an earlier enumeration.

Isogonal embeddings of interwoven and self-entangled honeycomb (hcb) nets and related interpenetrating primitive cubic (pcu) nets.

Two- and three-periodic vertex-transitive (isogonal) piecewise-linear embeddings of self-entangled and interwoven honeycomb nets are described. The infinite families with trigonal symmetry and edge transitivity (isotoxal) are particularly interesting as they have the Borromean property that no two nets are directly linked. These also lead directly to infinite families of interpenetrating primitive cubic nets (pcu) that are also vertex- and edge-transitive and have embeddings with 90° angles between edges.

Three-periodic nets, tilings and surfaces. A short review and new results.

A brief introductory review is provided of the theory of tilings of 3-periodic nets and related periodic surfaces. Tilings have a transitivity [p q r s] indicating the vertex, edge, face and tile transitivity. Proper, natural and minimal-transitivity tilings of nets are described. Essential rings are used for finding the minimal-transitivity tiling for a given net. Tiling theory is used to find all edge- and face-transitive tilings (q = r = 1) and to find seven, one, one and 12 examples of tilings with transitivity [1 1 1 1], [1 1 1 2], [2 1 1 1] and [2 1 1 2], respectively. These are all minimal-transitivity tilings. This work identifies the 3-periodic surfaces defined by the nets of the tiling and its dual and indicates how 3-periodic nets arise from tilings of those surfaces.

Isogonal piecewise-linear embeddings of 1-periodic knots and links, and related 2-periodic chain-link and knitting patterns.

Families of 1- and 2-periodic knots and weavings that have isogonal (vertex-transitive) piecewise-linear embeddings are described. In these structures there is just one thread, or multiple threads with parallel or collinear axes. The principal structures are a large family of 1-periodic knots and related multi-thread infinite links, knitting patterns and chain-link weaving. The relevance to synthetic chemistry is described in terms of targets for designed synthesis such as mechanically interlocked polymers.

Tangled piecewise-linear embeddings of trivalent graphs.

A method is described for generating and exploring tangled piecewise-linear embeddings of trivalent graphs under the constraints of point-group symmetry. It is shown that the possible vertex-transitive tangles are either graphs of vertex-transitive polyhedra or bipartite vertex-transitive nonplanar graphs. One tangle is found for 6 vertices, three for 8 vertices (tangled cubes), seven for 10 vertices, and 21 for 12 vertices. Also described are four isogonal embeddings of pairs of cubes and 12 triplets of tangled cubes (16 and 24 vertices, respectively). Vertex 2-transitive embeddings are obtained for tangled trivalent graphs with 6 vertices (two found) and 8 vertices (45 found). Symmetrical tangles of the 10-vertex Petersen graph and the 20-vertex Desargues graph are also described. Extensions to periodic tangles are indicated. These are all interesting and viable targets for molecular synthesis.

Piecewise-linear embeddings of decussate extended θ graphs and tetrahedra.

An nθ graph is an n-valent graph with two vertices. From symmetry considerations, it has vertex-edge transitivity 1 1. Here, they are considered extended with divalent vertices added to the edges to explore the simplest piecewise-linear tangled embeddings with straight, non-intersecting edges (sticks). The simplest tangles found are those with 3n sticks, transitivity 2 2, and with 2⌊(n - 1)/2⌋ ambient-anisotopic tangles. The simplest finite and 1-, 2- and 3-periodic decussate structures (links and tangles) are described. These include finite cubic and icosahedral and 1- and 3-periodic links, all with minimal transitivity. The paper also presents the simplest tangles of extended tetrahedra and their linkages to form periodic polycatenanes. A vertex- and edge-transitive embedding of a tangled srs net with tangled and polycatenated θ graphs and vertex-transitive tangled diamond (dia) nets are described.

Z dependence of electron scattering by single atoms into annular dark-field detectors.

A simple parameterization is presented for the elastic electron scattering cross sections from single atoms into the annular dark-field (ADF) detector of a scanning transmission electron microscope (STEM). The dependence on atomic number, Z, and inner reciprocal radius of the annular detector, q(0), of the cross section σ(Z,q(0)) is expressed by the empirical relation [see formula in text] where A(q(0)) is the cross section for hydrogen (Z = 1), and the detector is assumed to have a large outer reciprocal radius. Using electron elastic scattering factors determined from relativistic Hartree-Fock simulations of the atomic electron charge density, values of the exponent n(Z,q(0)) are tabulated as a function of Z and q(0), for STEM probe sizes of 1.0 and 2.0 Å. Comparison with recently published experimental data for single-atom scattering [Krivanek et al. (2010). Nature 464, 571-574] suggests that experimentally measured exponent values are systematically lower than the values predicted for elastic scattering from low-Z atoms. It is proposed that this discrepancy arises from the inelastic scattering contribution to the ADF signal. A simple expression is proposed that corrects the exponent n(Z,q(0)) for inelastic scattering into the annular detector.

On Borromean links and related structures.

The creation of knotted, woven and linked molecular structures is an exciting and growing field in synthetic chemistry. Presented here is a description of an extended family of structures related to the classical `Borromean rings', in which no two rings are directly linked. These structures may serve as templates for the designed synthesis of Borromean polycatenanes. Links of n components in which no two are directly linked are termed `n-Borromean' [Liang & Mislow (1994). J. Math. Chem. 16, 27-35]. In the classic Borromean rings the components are three rings (closed loops). More generally, they may be a finite number of periodic objects such as graphs (nets), or sets of strings related by translations as in periodic chain mail. It has been shown [Chamberland & Herman (2015). Math. Intelligencer, 37, 20-25] that the linking patterns can be described by complete directed graphs (known as tournaments) and those up to 13 vertices that are vertex-transitive are enumerated. In turn, these lead to ring-transitive (isonemal) n-Borromean rings. Optimal piecewise-linear embeddings of such structures are given in their highest-symmetry point groups. In particular, isonemal embeddings with rotoinversion symmetry are described for three, five, six, seven, nine, ten, 11, 13 and 14 rings. Piecewise-linear embeddings are also given of isonemal 1- and 2-periodic polycatenanes (chains and chain mail) in their highest-symmetry setting. Also the linking of n-Borromean sets of interleaved honeycomb nets is described.

Piecewise-linear embeddings of knots and links with rotoinversion symmetry.

This article describes the simplest members of an infinite family of knots and links that have achiral piecewise-linear embeddings in which linear segments (sticks) meet at corners. The structures described are all corner- and stick-2-transitive - the smallest possible for achiral knots.

Isogonal piecewise linear embeddings of 1-periodic weaves and some related structures.

Crystallographic descriptions of isogonal piecewise linear embeddings of 1-periodic weaves and links (chains) are presented. These are composed of straight segments (sticks) that meet at corners (2-valent vertices). Descriptions are also given of some plaits - woven periodic bands, three simple periodic knots and isogonal interwoven rods.

Isogonal weavings on the sphere: knots, links, polycatenanes.

Mathematical knots and links are described as piecewise linear - straight, non-intersecting sticks meeting at corners. Isogonal structures have all corners related by symmetry (`vertex'-transitive). Corner- and stick-transitive structures are termed regular. No regular knots are found. Regular links are cubic or icosahedral and a complete account of these (36 in number) is given, including optimal (thickest-stick) embeddings. Stick 2-transitive isogonal structures are again cubic and icosahedral and also encompass the infinite family of torus knots and links. The major types of these structures are identified and reported with optimal embeddings. The relevance of this work to materials chemistry and biochemistry is noted.