Improved performance of crystal structure solution from powder diffraction data through parameter tuning of a simulated annealing algorithm

Ammonium Polyuranates: Old Dog, New Structural Tricks

The crystal structure of ammonium polyuranates xUO3·yNH3·zH2O has been investigated. Powder X-ray diffraction (PXRD) has been employed to define single-phase samples within a series of synthesized compounds, which are further characterized by elemental analysis to ascertain the stoichiometry, revealing compositions of 3UO3·NH3·5H2O and 2UO3·NH3·3H2O. Analysis using extended X-ray absorption fine structure and vibrational spectroscopy has elucidated that both 3UO3·NH3·5H2O and 2UO3·NH3·3H2O possess a local structure similar to the metaschoepite─layered U(VI) oxohydroxide UO3·2H2O, but with H2O and NH4+ groups in the interlayers. The structures of ammonium polyuranates are solved from PXRD data, revealing their relationship to the U(VI) oxohydroxide with the established composition of NH4[(UO2)3O2(OH)3]·3H2O and NH4[(UO2)2O2(OH)]·2H2O for 3UO3·NH3·5H2O and 2UO3·NH3·H2O, respectively. These structures maintain the arrangement of U-O polyhedra as pentagonal bipyramids. However, disparities in lattice parameters, space group, and layer topology from UO3·2H2O emphasize significant structural modifications resulting from the substitution of water by ammonium. Moreover, the anion topology of the NH4[(UO2)2O2(OH)]·2H2O has no analogues among uranium oxohydroxide minerals. Notably, ammonium polyuranates, when compared, have minimal alterations in lattice parameters regardless of the presence of ammonia within the structure. The revealed results contribute valuable insights into the UO3-NH3-H2O system and hold potential applications in the field of nuclear power as ammonium polyuranates form during actinide precipitation in back-end of the nuclear fuel cycle and also serve as precursors in the fabrication of nuclear fuel.

Indomethacin-omeprazole as therapeutic hybrids? Salt and co-amorphous systems enhancing physicochemical and pharmacological properties

Multidrug therapeutic hybrids constitute a promising proposal to overcome problems associated with traditional formulations containing physical mixtures of drugs, potentially improving pharmacological and pharmaceutical performance. Indomethacin (IND) is a non-selective non-steroidal anti-inflammatory drug (NSAIDs) that acts by inhibiting normal processes of homeostasis, causing a series of side effects, such as gastrointestinal symptoms. Proton pump inhibitors, such as omeprazole (OME), have been used to treat such gastrointestinal tract symptoms. In this work, two new multidrug therapeutic hybrids were prepared (an IND:OME salt and an IND:OME co-amorphous system) by ball mill grinding crystalline IND and OME under different conditions, i.e., liquid assisted grinding (LAG) with ethanol and dry grinding, respectively. The crystalline salt returned to a neutral state co-amorphous system when submitted to ball mill grinding in the absence of solvent (dry grinding), but the reverse process (LAG of the IND:OME co-amorphous system) showed partial decomposition of OME. The IND:OME co-amorphous system showed a higher physical stability than the neat IND and OME amorphous materials (with an amorphous stability longer than 100 days, compared to 4 and 16 h for the neat amorphous drugs, respectively, when stored at dry conditions at room temperature). Furthermore, OME presented a higher chemical stability in solution when dissolved from a salt form than from the pure crystalline form. The dissolution studies showed a dissolution enhancement for IND in both salt (1.8-fold after 8 h of dissolution) and co-amorphous (2.5-fold after 8 h of dissolution) forms. Anti-inflammatory activity using a mice paw oedema model showed an increase of the pharmacological response to IND at a lower dose (∼5mg/kg) for both IND:OME salt (2.8-fold) and IND:OME co-amorphous system (3.2-fold) after 6 h, when compared to the positive control group (IND, administered at 10 mg/kg). Additionally, the anti-inflammatory activity of both salt and co-amorphous form was faster than for the crystalline IND. Finally, an indomethacin-induced gastric ulceration assay in mice resulted in a higher mucosal protection at the same dose (40 mg/kg) for both IND:OME salt and IND:OME co-amorphous system when compared with crystalline OME.

Application of Artificial Intelligence in the Unit Commitment System in the Application of Energy Sustainability

This article approaches the optimal solution of energy sustainability based on the use of artificial intelligence (AI). The application of renewable energy sources (RES) and unit commitment (UC) is the basic idea of this concept. Therefore, a new approach to solving the UC problem is introduced. The proposed method has a simple procedure to obtain the popular solutions in an acceptable time interval, by creating a basic model of the schedule of the state of energy units RES. It is obvious that individual consumer units, of an operational nature, take hourly performance values by performing economic evaluations on them in the sense of cost optimization. This is conducted through an artificial intelligence (AI) algorithm by optimizing the dedicated cost function, simulated by annealing. Despite the acceptable solution obtained from these two steps, another shift is proposed, called the TDD process in a given consumer area. This process in the application of AI in the system of selection of universal load TDD from hundreds of possible ones is based on the use of artificial neural networks and cluster analysis, which is represented by the application of the Kohonen map. This logical process to achieve a modified solution is a self-organizing map (SOM). It is a software tool for visualizing high-dimensional data. Converts complex, nonlinear statistical relationships (functions) between high-dimensional data to simple geometric relationships, low-dimensional representation. The output of SOM is an optimized load TDD on the basis of which the process of automatic control of UC in the local urban area is built. The results of the AI application in the case of sustainable energy solutions confirm that this UC method provides a robust solution to an almost optimal solution.

SDPD-SX: Combining a single crystal X-ray diffraction setup with advanced powder data structure determination for use in early stage drug discovery

We report a method for routine crystal structure determination on very small (typically 0.1 mg or less) amounts of crystalline material using powder X-ray diffraction data from a laboratory-based single-crystal...

An efficient treatment of ring conformations during molecular crystal structure determination from powder diffraction data

An effective and efficient method for dealing with ring systems during global optimisation-based crystal structure determination from powder diffraction data.

Structure determination of organic compounds by a fit to the pair distribution function from scratch without prior indexing

A method for the ab initio crystal structure determination of organic compounds by a fit to the pair distribution function (PDF), without prior knowledge of lattice parameters and space group, has been developed. The method is called 'PDF-Global-Fit' and is implemented by extension of the program FIDEL (fit with deviating lattice parameters). The structure solution is based on a global optimization approach starting from random structural models in selected space groups. No prior indexing of the powder data is needed. The new method requires only the molecular geometry and a carefully determined PDF. The generated random structures are compared with the experimental PDF and ranked by a similarity measure based on cross-correlation functions. The most promising structure candidates are fitted to the experimental PDF data using a restricted simulated annealing structure solution approach within the program TOPAS, followed by a structure refinement against the PDF to identify the correct crystal structure. With the PDF-Global-Fit it is possible to determine the local structure of crystalline and disordered organic materials, as well as to determine the local structure of unindexable powder patterns, such as nanocrystalline samples, by a fit to the PDF. The success of the method is demonstrated using barbituric acid as an example. The crystal structure of barbituric acid form IV solved and refined by the PDF-Global-Fit is in excellent agreement with the published crystal structure data.

Structure and spectroscopy of methionyl-methionine for aquaculture

The amino acid L-methionine is an essential amino acid and is commonly used as a feed supplement in terrestrial animals. It is less suitable for marine organisms because it is readily excreted. It is also highly water soluble and this results in loss of the feed and eutrophication of the water. To address these problems, the dipeptide DL-methionyl-DL-methionine (trade name: AQUAVI Met-Met) has been developed as a dedicated methionine source for aquaculture. The commercial product is a mixture of a racemic crystal form of D-methionyl-D-methionine/L-methionyl-L-methionine and a racemic crystal form of D-methionyl-L-methionine/L-methionyl-D-methionine. In this work, we have computationally, structurally, spectroscopically and by electron microscopy characterised these materials. The microscopy and spectroscopy demonstrate that there is no interaction between the DD-LL and DL-LD racemates on any length scale from the macroscopic to the nanoscale.

GALLOP: accelerated molecular crystal structure determination from powder diffraction data

A new GPU-accelerated algorithm delivers state-of-the-art performance for molecular crystal structure determination from powder diffraction data.

Mercury 4.0: from visualization to analysis, design and prediction

The program Mercury, developed at the Cambridge Crystallographic Data Centre, was originally designed primarily as a crystal structure visualization tool. Over the years the fields and scientific communities of chemical crystallography and crystal engineering have developed to require more advanced structural analysis software. Mercury has evolved alongside these scientific communities and is now a powerful analysis, design and prediction platform which goes a lot further than simple structure visualization.

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.

Challenging structure determination from powder diffraction data: two pharmaceutical salts and one cocrystal with Z′ = 2

Structure solution of molecular crystals from powder diffraction data by real-space methods becomes challenging when the total number of degrees of freedom (DoF) for molecular position, orientation and intramolecular torsions exceeds a value of 20. Here we describe the structure determination from powder diffraction data of three pharmaceutical salts or cocrystals, each with four molecules per asymmetric unit on general position: Lamivudine camphorsulfonate (1, P 21, Z=4, Z′=2; 31 DoF), Theophylline benzamide (2, P 41, Z=8, Z′=2; 23 DoF) and Aminoglutethimide camphorsulfonate hemihydrate [3, P 21, Z=4, Z′=2; 31 DoF (if the H2O molecule is ignored)]. In the salts 1 and 3 the cations and anions have two intramolecular DoF each. The molecules in the cocrystal 2 are rigid. The structures of 1 and 2 could be solved without major problems by DASH using simulated annealing. For compound 3, indexing, space group determination and Pawley fit proceeded without problems, but the structure could not be solved by the real-space method, despite extensive trials. By chance, a single crystal of 3 was obtained and the structure was determined by single-crystal X-ray diffraction. A post-analysis revealed that the failure of the real-space method could neither be explained by common sources of error such as incorrect indexing, wrong space group, phase impurities, preferred orientation, spottiness or wrong assumptions on the molecular geometry or other user errors, nor by the real-space method itself. Finally, is turned out that the structure solution failed because of problems in the extraction of the integrated reflection intensities in the Pawley fit. With suitable extracted reflection intensities the structure of 3 could be determined in a routine way.

Hybrid Approach with Improved Genetic Algorithm and Simulated Annealing for Thesis Sampling

Sampling inspection uses the sample characteristics to estimate that of the population, and it is an important method to describe the population, which has the features of low cost, strong applicability and high scientificity. This paper aims at the sampling inspection of the master’s degree thesis to ensure their quality, which is commonly estimated by random sampling. Since there are disadvantages in random sampling, a hybrid algorithm combined with an improved genetic algorithm and a simulated annealing algorithm is proposed in this paper. Furthermore, a novel mutation strategy is introduced according to the specialty of Shanghai’s thesis sampling to improve the efficiency of sampling inspection; the acceleration of convergence of the algorithm can also take advantage of this. The new algorithm features the traditional genetic algorithm, and it can obtain the global optimum in the optimization process and provide the fairest sampling plan under the constraint of multiple sampling indexes. The experimental results on the master’s thesis dataset of Shanghai show that the proposed algorithm well meets the requirements of the sampling inspection in Shanghai with a lower time-complexity.

Direct-space solution in theEXPOpackage: the combination of the HBB–BC algorithm with GRASP

The hybrid big bang–big crunch algorithm is a combination of a global optimization algorithm inspired by one of the theories of the evolution of the universe, named the big bang and big crunch theory, and the simulated annealing method. The procedure was implemented in the latest version of the programEXPOand applied to crystal-structure solution from powder diffraction data. Several aspects of the hybrid big bang–big crunch algorithm can be further optimized with the aim of obtaining good quality solutions in a shorter computation time. In the present study, the hybrid big bang–big crunch procedure has been combined with the greedy randomized adaptive search procedure (GRASP) and some steps of the algorithm have been improved. The new approach, implemented in theEXPOpackage, has been successfully tested on numerous known crystal structures.

Improved crystal structure solution from powder diffraction data by the use of conformational information

The effect of introducing conformational information to theDASHimplementation of crystal structure determination from powder diffraction data is investigated using 51 crystal structures, with the aim of allowing increasingly complex crystal structures to be solved more easily. The findings confirm that conformational information derived from the Cambridge Structural Database is indeed of value, considerably increasing the chances of obtaining a successful structure determination. Its routine use is therefore encouraged.