MAGUS: machine learning and graph theory assisted universal structure searcher

Crystal structure predictions based on first-principles calculations have gained great success in materials science and solid state physics. However, the remaining challenges still limit their applications in systems with a large number of atoms, especially the complexity of conformational space and the cost of local optimizations for big systems. Here, we introduce a crystal structure prediction method, MAGUS, based on the evolutionary algorithm, which addresses the above challenges with machine learning and graph theory. Techniques used in the program are summarized in detail and benchmark tests are provided. With intensive tests, we demonstrate that on-the-fly machine-learning potentials can be used to significantly reduce the number of expensive first-principles calculations, and the crystal decomposition based on graph theory can efficiently decrease the required configurations in order to find the target structures. We also summarized the representative applications of this method on several research topics, including unexpected compounds in the interior of planets and their exotic states at high pressure and high temperature (superionic, plastic, partially diffusive state, etc.); new functional materials (superhard, high-energy-density, superconducting, photoelectric materials), etc. These successful applications demonstrated that MAGUS code can help to accelerate the discovery of interesting materials and phenomena, as well as the significant value of crystal structure predictions in general.

Design and Synthesis of Coordination Polymers with Cu(II) and Heterocyclic N-Oxides

The relations of coordination network connectivity with coordination properties of heterocyclic N-oxides, Cu(I,II), and co-ligands were discussed based on the comparative analysis of 623 structures extracted from the Cambridge Structural...

Topological Motifs in Dicyanamides of Transition Metals

Dicyanamides of d-metals provide a wide range of magnetic properties tuned by external cations, encapsulated ions and coordination modes of anions. Analysis of molecular, one-periodic (1D chain), two-periodic (2D layered)...

Depicting the DNA Binding and Cytotoxicity Studies against Human Colorectal Cancer of Aquabis (1-Formyl-2-Naphtholato-k2O,O′) Copper(II): A Biophysical and Molecular Docking Perspective

In this study, we attempted to examine the biological activity of the copper(II)–based small molecule aquabis (1-formyl-2-naphtholato-k2O,O′)copper(II) (1) against colon cancer. The characterization of complex 1 was established by analytical and spectral methods in accordance with the single-crystal X-ray results. A monomeric unit of complex 1 exists in an O4 (H2O) coordination environment with slightly distorted square pyramidal geometry (τ = ~0.1). The interaction of complex 1 with calf thymus DNA (ctDNA) was determined by employing various biophysical techniques, which revealed that complex 1 binds to ctDNA at the minor groove with a binding constant of 2.38 × 105 M–1. The cytotoxicity of complex 1 towards human colorectal cell line (HCT116) was evaluated by the MTT assay, which showed an IC50 value of 11.6 μM after treatment with complex 1 for 24 h. Furthermore, the apoptotic effect induced by complex 1 was validated by DNA fragmentation pattern, which clarified that apoptosis might be regulated through the mitochondrial-mediated production of reactive oxygen species (ROS) causing DNA damage pathway. Additionally, molecular docking was also carried out to confirm the recognition of complex 1 at the minor groove.

From the Ritter pile to the aluminum ion battery – Peter Paufler’s academic genealogy

This article highlights Peter Paufler’s academic genealogy on the occasion of his 80th birthday. We describe the academic background since 1776, which covers 11 generations of scientists: Ritter, Ørsted, Han-steen, Keilhau, Kjerulf, Brøgger, Goldschmidt, Schulze, Paufler, Meyer, and Leisegang. The biographies of these scientists are described in spotlight character and references to scientists such as Dehlinger, Ewald, Glocker, Röntgen, Vegard, Weiss, and Werner are given. A path is drawn that begins in the Romanticism with electrochemistry and the invention of what is probably the first accumulator. It leads through the industrialization and the modern geology, mineralogy, and crystallography to crystal chemistry, metal and crystal physics and eventually returns to electrochemistry and the aluminum-ion accumulator in the era of the energy transition. The academic genealogy exhibits one path of how crystallography develops and specializes over three centuries and how it contributes to the understanding of the genesis of the Earth and the Universe, the exploration of raw materials, and the development of modern materials and products during the industrialization and for the energy transition today. It is particularly characterized by the fields of physics and magnetism, X-ray analysis, and rare-earth compounds and has strong links to the scientific landscape of Germany (Freiberg) and Scandinavia, especially Norway (Oslo), as well as to Russia (Moscow, Samara, St. Petersburg). The article aims at contributing to the history of science, especially to the development of crystallography, which is the essential part of the structural science proposed by Peter Paufler.

A Genetic Algorithmic Approach to Determine the Structure of Li-Al Layered Double Hydroxides

Layered double hydroxides (LDH) demonstrate significant potential across a range of applications, including as catalysts, delivery vehicles for pharmaceuticals, environmental remediation, and supercapacitors. Explaining the mechanism of LDH action at the atomic scale in these and other applications is challenging, however, due to the difficulty in precisely defining the bulk and surface structure and chemical compositions. Here, we focus on the determination of the structure of lithium-aluminum (Li-Al) LDH, which has shown promise in the catalytic depolymerization of lignin, both directly as the catalyst and as a support for gold nanoparticles. While the relative positions of the Li and Al metals are generally well resolved by X-ray crystallography, it is the structures of the anionic layers, consisting of water and carbonate, that are less well established. Combinatorial analyses of all possible positions and rotations of the water and carbonate in the three-layered Li-AL LDH polytope reveals that the phase space is much too large to examine in any reasonable time frame in a one-by-one structure exploration. To overcome this limitation, we develop and deploy a genetic algorithm (GA) wherein fitness is determined by matching a calculated X-ray diffraction (XRD) pattern for a given structure to the known experimental XRD pattern. The GA approach results in structures of high fitness that portend the bulk Li-Al LDH structure. Importantly, the GA approach offers the potential to determine the structures of other LDH, and more generally layered materials, which are generally difficult to describe given the large chemical and structural space to be explored.

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.

Construction of (3,8)-connected three-dimensional cobalt(II) and copper(II) coordination polymers with 1,3-bis[(1,2,4-triazol-4-yl)methyl]benzene and benzene-1,3,5-tricarboxylate ligands

Coordination polymers (CPs) have been widely studied because of their diverse and adjustable topologies and wide-ranging applications in luminescence, chemical sensors, magnetism, photocatalysis, gas adsorption and separation. In the present work, two coordination polymers, namely poly[(μ5-benzene-1,3,5-tricarboxylato-κ6 O 1:O 1′:O 3:O 3:O 5,O 5′){μ3-1,3-bis[(1,2,4-triazol-4-yl)methyl]benzene-κ3 N:N′:N′′}di-μ3-hydroxido-dicobalt(II)], [Co2(C9H3O6)(OH)(C12H12N6)] n or [Co2(btc)(OH)(mtrb)] n , (1), and poly[[diaquabis(μ3-benzene-1,3,5-tricarboxylato-κ3 O 1:O 3:O 5)bis{μ3-1,3-bis[(1,2,4-triazol-4-yl)methyl]benzene-κ3 N:N′:N′′}tetra-μ3-hydroxido-tetracopper(II)] monohydrate], {[Cu4(C9H3O6)2(OH)2(C12H12N6)2(H2O)2]·H2O} n or {[Cu4(btc)2(OH)2(mtrb)2(H2O)2]·H2O} n , (2), were synthesized by the hydrothermal method using 1,3-bis[(1,2,4-triazol-4-yl)methyl]benzene (mtrb) and benzene-1,3,5-tricarboxylate (btc3−). CP (1) exhibits a (3,8)-coordinated three-dimensional (3D) network of the 3,8T38 topological type, with a point symbol of {4,5,6}2{42·56·616·72·82}, based on the tetranuclear hydroxide cobalt(II) cluster [Co4(μ3-OH)2]. CP (2) shows a (3,8)-coordinated tfz-d topology, with a point symbol of {43}2{46·618·84}, based on the tetranuclear hydroxide copper(II) cluster [Cu4(μ3-OH)2]. The different (3,8)-coordinated 3D networks based on tetranuclear hydroxide–metal clusters of (1) and (2) are controlled by the different central metal ions [CoII for (1) and CuII for (2)]. The thermal stabilities and solid-state optical diffuse-reflection spectra were measured. The energy band gaps (E g) obtained for (1) and (2) were 2.72 and 2.29 eV, respectively. CPs (1) and (2) exhibit good photocatalytic degradation of the organic dyes methylene blue (MB) and rhodamine B (RhB) under visible-light irradiation.

Exploitation of knowledge databases in the synthesis of zinc(II) malonates with photo-sensitive and photo-insensitive N,N'-containing linkers

Photoinitiated solid-state reactions are known to affect the physical properties of coordination polymers, such as fluorescence and sorption behaviour, and also afford extraordinary architectures (e.g. three-periodic structures with polyorganic ligands). However, the construction of novel photo-sensitive coordination polymers requires an understanding of the factors which govern the mutual disposition of reactive fragments. A series of zinc(II) malonate complexes with 1,2-bis(pyridin-4-yl)ethylene and its photo-insensitive analogues has been synthesized for the purpose of systematic analysis of their underlying nets and mutual disposition of N-donor ligands. The application of a big data-set analysis for the prediction of a variety of possible complex compositions, coordination environments and networks for a four-component system has been demonstrated for the first time. Seven of the nine compounds possess one of the highly probable topologies for their underlying nets; in addition, two novel closely related four-coordinated networks were obtained. Complexes containing 1,2-bis(pyridin-4-yl)ethylene and 1,2-bis(pyridin-4-yl)ethane form isoreticular compounds more readily than those with 4,4'-bipyridine and 1,2-bis(pyridin-4-yl)ethylene. The effects of the precursor, either zinc(II) nitrate or zinc(II) acetate, on the composition and dimensionality of the resulting architecture are discussed. For three of the four novel complexes containing 1,2-bis(pyridin-4-yl)ethylene, the single-crystal-to-single-crystal [2 + 2] cycloaddition reactions were carried out. UV irradiation of these crystals afforded either the 0D→1D or the 3D→3D transformations, with and without network changes. One of the two 3D→3D transformations was accompanied by solvent (H₂O) cleavage.

Cobalt(ii/iii), nickel(ii) and copper(ii) coordination clusters employing a monoanionic Schiff base ligand: synthetic, topological and computational mechanistic aspects

Nine coordination clusters (M = Co^II/III, Ni^II, Cu^II) using a monoanionic Schiff base ligand were synthesized and characterized. A series of transformations occur in the ligand in certain compounds.