OChemDb: the free online Open Chemistry Database portal for searching and analysing crystal structure information

A generative artificial intelligence framework based on a molecular diffusion model for the design of metal-organic frameworks for carbon capture

Metal-organic frameworks (MOFs) exhibit great promise for CO2 capture. However, finding the best performing materials poses computational and experimental grand challenges in view of the vast chemical space of potential building blocks. Here, we introduce GHP-MOFassemble, a generative artificial intelligence (AI), high performance framework for the rational and accelerated design of MOFs with high CO2 adsorption capacity and synthesizable linkers. GHP-MOFassemble generates novel linkers, assembled with one of three pre-selected metal nodes (Cu paddlewheel, Zn paddlewheel, Zn tetramer) into MOFs in a primitive cubic topology. GHP-MOFassemble screens and validates AI-generated MOFs for uniqueness, synthesizability, structural validity, uses molecular dynamics simulations to study their stability and chemical consistency, and crystal graph neural networks and Grand Canonical Monte Carlo simulations to quantify their CO2 adsorption capacities. We present the top six AI-generated MOFs with CO2 capacities greater than 2m mol g-1, i.e., higher than 96.9% of structures in the hypothetical MOF dataset.

DypB peroxidase for aflatoxin removal: New insights into the toxin degradation process

Aflatoxin B1 (AFB1) is one of the most potent carcinogens and a widespread food and feed contaminant. As for other toxins, many efforts are devoted to find efficient and environmentally-friendly methods to degrade AFB1, such as enzymatic treatments, thus improving the safety of food and feed products. In this regard, the dye decolorizing peroxidase of type B (DypB) can efficiently degrade AFB1. The molecular mechanism, which is required to drive protein optimization in view of the usage of DypB as a mycotoxin reduction agent in large scale application, is unknown. Here, we focused on the role of four DypB residues in the degradation of AFB1 by alanine-scanning (residues 156, 215, 239 and 246), which were identified from biochemical assays to be kinetically relevant for the degradation. As a result of DypB degradation, AFB1 is converted into four products. Interestingly, the relative abundancy of these products depends on the replaced residues. Molecular dynamics simulations were used to investigate the role of these residues in the binding step between protein and manganese, a metal ion which is expected to be involved in the degradation process. We found that the size of the haem pocket as well as conformational changes in the protein structure could play a role in determining the kinetics of AFB1 removal and, consequently, guide the process towards specific degradation products.

Incommensurately Modulated Structure in AgCuSe-Based Thermoelectric Materials for Intriguing Electrical, Thermal, and Mechanical Properties

AgCuSe-based materials have attracted great attentions recently in thermoelectric (TE) field due to their extremely high electron mobility, ultralow lattice thermal conductivity, and abnormal "brittle-ductile" transition at room temperature. However, although the investigation on the crystal structure of AgCuSe low-temperature phase (named as β-AgCuSe) was started more than half a century before, it is still in controversy yet, which greatly limits the understanding of its intriguing electrical, thermal, and mechanical performance. In this work, via adopting the advanced three-dimensional electron diffraction technique, this study finds that the AgCuSe-based materials crystalize in an incommensurately modulated structure with an orthorhombic Pmmn(0β1/2)s00 superspace group. The local lattice distortion in the incommensurately modulated structure has weak effects on the conduction band minimum due to the delocalized and isotropic feature of Ag 5s states, leading to high carrier mobility. Likewise, the inhomogeneous, weak, and anisotropic Ag-Se bonds result in the high degree of anharmonicity and ultralow lattice thermal conductivity. Furthermore, alloying S in AgCuSe reinforces the interaction between the adjacent Ag-Se layers, yielding the "brittle-ductile" transition at room temperature. This work well interprets the structure-performance relationship of AgCuSe-based materials and sheds light on the future investigation of this class of promising TE materials.

The crystal structure and thermal expansion of novel substitutionally disordered Ca10TM0.5(VO4)7 (TM = Co, Cu) orthovanadates

The whitlockite-related materials have attracted researchers' attention because of their potential application in various fields, especially in optoelectronics. In the present work, the structure of novel whitlockite-related oxides Ca₁₀TM_0.5(VO₄)₇ (TM = Co, Cu) is studied at room and high temperatures, using X-ray powder diffraction. These compounds form by fractional substitution of divalent transition metal atoms into the Ca₃(VO₄)₂ lattice. Rietveld refinements provided the structural details. The lattice parameters are a = 10.78074(6) Å, c = 37.8196(2) Å, and V = 3806.67(4) ų for Ca₁₀Co_0.5(VO₄)₇ and a = 10.78710(7) Å, c = 37.8997(3) Å, and V = 3819.23(4) ų for Ca₁₀Cu_0.5(VO₄)₇. Structure refinement results show that among the five available sites (M1-M5), the M²⁺ ions select the M5 site. This finding is confirmed by analysis of interatomic distances: due to the difference in size between TM and Ca ions sharing the M5 site, the M5-O distance shortens by about 5.0% for Ca₁₀Co_0.5(VO₄)₇ and 2.7% for Ca₁₀Cu_0.5(VO₄)₇ with respect to the unsubstituted parent compound, Ca₃(VO₄)₂. The observed trends in the crystallographic properties of the studied crystals are in line with those of previously reported structurally related phosphates, Ca_10.5-xM_x(PO₄)₇ (M = Mg or divalent transition metal). Moreover, the observed tendency for occupation of M5 by small divalent ions follows the earlier theoretical results. For cobalt and copper substituted orthovanadate and orthophosphate whitlockite related materials, a linear variation in the unit cell size is demonstrated. The common equation for evaluation of volume is applicable to the substitution of the two transition metals in orthovanadate and orthophosphate whitlockite related materials. Thermal expansion is investigated for both compounds. The variations of the lattice parameters and the thermal expansion coefficient with temperature are determined in the 300-810 K range. The lattice parameter, a, expands by 0.80% for Ca₁₀Co_0.5(VO₄)₇ and 0.74% for Ca₁₀Cu_0.5(VO₄)₇ in this range. The lattice parameter, c, enlarges by about 0.70% for both samples. In the studied temperature range, the volume thermal expansion coefficient of Ca₁₀Co_0.5(VO₄)₇ increases from 37.2 to 44.8 MK^-1 and for Ca₁₀Cu_0.5(VO₄)₇, it increases from 35.1 to 45.2 MK^-1; the observed expansion anisotropy is smaller than those of other related compounds.

New Ca2.90(Me2+)0.10(PO4)2 β-tricalcium Phosphates with Me2+ = Mn, Ni, Cu: Synthesis, Crystal-Chemistry, and Luminescence Properties

C a 2.90 M e 0.10 2 + ( P O 4 ) 2 (with Me = Mn, Ni, Cu) β-tricalcium phosphate (TCP) powders were synthesized by solid-state reaction at T = 1200 °C and investigated by means of a combination of scanning electron microscopy (SEM) equipped with energy dispersive X-ray spectroscopy (EDS), powder X-ray diffraction (PXRD), Fourier transform infrared (FTIR) spectroscopy, and luminescence spectroscopy. SEM morphological analysis showed the run products to consist of sub spherical microcrystalline aggregates, while EDS semi-quantitative analysis confirmed the nominal Ca/Me composition. The unit cell and the space group were determined by X-ray powder diffraction data showing that all the compounds crystallize in the rhombohedral R3c whitlockite-type structure, with the following unit cell constants: a = b = 10.41014(19) Å, c = 37.2984(13) Å, and cell volume V = 3500.53(15) Å3 (Mn); a = b = 10.39447(10) Å, c = 37.2901(8) Å; V = 3489.22(9) Å3 (Ni); a = b = 10.40764(8) Å, c = 37.3158(6) Å, V = 3500.48(7) Å3 (Cu). The investigation was completed with the structural refinement by the Rietveld method. The FTIR spectra are similar to those of the end-member Ca β-tricalcium phosphate (TCP), in agreement with the structure determination, and show minor band shifts of the (PO4) modes with the increasing size of the replacing Me2+ cation. Luminescence spectra and decay curves revealed significant luminescence properties for Mn and Cu phases.

StructureFinder

With the program StructureFinder it is possible to find single-crystal diffraction measurements stored in any location on a computer. StructureFinder collects the unit-cell information and other data from previous measurements and stores them in a database. Searching is performed via a graphical user interface, and both a stand-alone program and a web interface are available.