1
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Milani G, Budriesi R, Tavazzani E, Cavalluzzi MM, Mattioli LB, Miniero DV, Delre P, Belviso BD, Denegri M, Cuocci C, Rotondo NP, De Palma A, Gualdani R, Caliandro R, Mangiatordi GF, Kumawat A, Camilloni C, Priori S, Lentini G. hERG stereoselective modulation by mexiletine-derived ureas: Molecular docking study, synthesis, and biological evaluation. Arch Pharm (Weinheim) 2023; 356:e2300116. [PMID: 37460390 DOI: 10.1002/ardp.202300116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 06/26/2023] [Accepted: 06/28/2023] [Indexed: 10/06/2023]
Abstract
Long QT syndrome (LQTS) is a disorder of cardiac electrophysiology resulting in life-threatening arrhythmias; nowadays, only a few drugs are available for the management of LQTS. Focusing our attention on LQT2, one of the most common subtypes of LQTS caused by mutations in the human ether-à-go-go-related gene (hERG), in the present work, the stereoselectivity of the recently discovered mexiletine-derived urea 8 was investigated on the hERG potassium channel. According to preliminary in silico predictions, in vitro studies revealed a stereoselective behavior, with the meso form showing the greatest hERG opening activity. In addition, functional studies on guinea pig isolated left atria, aorta, and ileum demonstrated that 8 does not present any cardiac or intestinal liability in our ex vivo studies. Due to its overall profile, (R,S)-8 paves the way for the design and development of a new series of compounds potentially useful in the treatment of both congenital and drug-induced forms of LQTS.
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Affiliation(s)
- Gualtiero Milani
- Department of Pharmacy-Pharmaceutical Sciences, University of Bari Aldo Moro, Bari, Italy
| | - Roberta Budriesi
- Department of Pharmacy and Biotechnology, Food Chemistry and Nutraceutical Lab, Alma Mater Studiorum-University of Bologna, Bologna, Italy
| | | | | | - Laura Beatrice Mattioli
- Department of Pharmacy and Biotechnology, Food Chemistry and Nutraceutical Lab, Alma Mater Studiorum-University of Bologna, Bologna, Italy
| | - Daniela Valeria Miniero
- Department of Biosciences, Biotechnologies, and Environment, University Aldo Moro of Bari, Bari, Italy
| | - Pietro Delre
- Chemistry Department, University of Bari Aldo Moro, Bari, Italy
- CNR-Institute of Crystallography, Bari, Italy
| | | | | | | | - Natalie Paola Rotondo
- Department of Pharmacy-Pharmaceutical Sciences, University of Bari Aldo Moro, Bari, Italy
| | - Annalisa De Palma
- Department of Biosciences, Biotechnologies, and Environment, University Aldo Moro of Bari, Bari, Italy
| | - Roberta Gualdani
- Institute of Neuroscience, Université Catholique de Louvain, Brussels, Belgium
| | | | | | - Amit Kumawat
- Department of Biosciences, University of Milan, Milano, Italy
| | - Carlo Camilloni
- Department of Biosciences, University of Milan, Milano, Italy
| | - Silvia Priori
- ICS-Maugeri IRCCS, Pavia, Italy
- Molecular Cardiology, Department of Molecular Medicine, University of Pavia, Pavia, Italy
- Centro Nacional de Investigaciones Cardiovasculares Carlos III, Madrid, Spain
| | - Giovanni Lentini
- Department of Pharmacy-Pharmaceutical Sciences, University of Bari Aldo Moro, Bari, Italy
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2
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Woods JF, Gallego L, Maisch A, Renggli D, Cuocci C, Blacque O, Steinfeld G, Kaech A, Spingler B, Vargas Jentzsch A, Rickhaus M. Saddles as rotational locks within shape-assisted self-assembled nanosheets. Nat Commun 2023; 14:4725. [PMID: 37550281 PMCID: PMC10406840 DOI: 10.1038/s41467-023-40475-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Accepted: 07/31/2023] [Indexed: 08/09/2023] Open
Abstract
Two-dimensional (2D) materials are a key target for many applications in the modern day. Self-assembly is one approach that can bring us closer to this goal, which usually relies upon strong, directional interactions instead of covalent bonds. Control over less directional forces is more challenging and usually does not result in as well-defined materials. Explicitly incorporating topography into the design as a guiding effect to enhance the interacting forces can help to form highly ordered structures. Herein, we show the process of shape-assisted self-assembly to be consistent across a range of derivatives that highlights the restriction of rotational motion and is verified using a diverse combination of solid state analyses. A molecular curvature governed angle distribution nurtures monomers into loose columns that then arrange to form 2D structures with long-range order observed in both crystalline and soft materials. These features strengthen the idea that shape becomes an important design principle leading towards precise molecular self-assembly and the inception of new materials.
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Affiliation(s)
- Joseph F Woods
- Department of Chemistry, University of Zurich, 8057, Zurich, Switzerland
| | - Lucía Gallego
- Department of Chemistry, University of Zurich, 8057, Zurich, Switzerland
| | - Amira Maisch
- Department of Chemistry, University of Zurich, 8057, Zurich, Switzerland
| | - Dominik Renggli
- Department of Chemistry, University of Zurich, 8057, Zurich, Switzerland
| | - Corrado Cuocci
- Institute of Crystallography, CNR, Via Amendola, 122/O, 70126, Bari, Italy
| | - Olivier Blacque
- Department of Chemistry, University of Zurich, 8057, Zurich, Switzerland
| | | | - Andres Kaech
- Center for Microscopy and Image Analysis, University of Zurich, 8057, Zurich, Switzerland
| | - Bernhard Spingler
- Department of Chemistry, University of Zurich, 8057, Zurich, Switzerland
| | - Andreas Vargas Jentzsch
- SAMS Research Group, University of Strasbourg, Institut Charles Sadron, CNRS, 67200, Strasbourg, France
| | - Michel Rickhaus
- Department of Chemistry, University of Zurich, 8057, Zurich, Switzerland.
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3
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Klitou P, Parisi E, Bordignon S, Bravetti F, Rosbottom I, Dell’Aera M, Cuocci C, Chierotti MR, Altomare A, Simone E. Navigating the Complex Solid Form Landscape of the Quercetin Flavonoid Molecule. Cryst Growth Des 2023; 23:6034-6045. [PMID: 37547879 PMCID: PMC10401642 DOI: 10.1021/acs.cgd.3c00584] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/14/2023] [Revised: 07/01/2023] [Indexed: 08/08/2023]
Abstract
Quercetin, a naturally occurring bioflavonoid substance widely used in the nutraceutical and food industries, exists in various solid forms that can have different physicochemical properties, thus impacting this compound's performance in various applications. In this work, we will clarify the complex solid-form landscape of this molecule. Two elusive isostructural solvates of quercetin were obtained from ethanol and methanol. The obtained crystals were characterized experimentally, but the crystallographic structure could not be solved due to their high instability. Nevertheless, the desolvated structure resulting from a high-temperature treatment (or prolonged storage at ambient conditions) of both these two labile crystals was characterized and solved via powder X-ray diffraction and solid-state nuclear magnetic resonance (SSNMR). This anhydrous crystal structure was compared with another anhydrous quercetin form obtained in our previous work, indicating that, at least, two different anhydrous polymorphs of quercetin exist. Navigating the solid-form landscape of quercetin is essential to ensure accurate control of the functional properties of food, nutraceutical, or pharmaceutical products containing crystal forms of this substance.
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Affiliation(s)
- Panayiotis Klitou
- School
of Food Science and Nutrition, Food Colloids and Bioprocessing Group, University of Leeds, Leeds LS2 9JT, UK
| | - Emmanuele Parisi
- Department
of Applied Science and Technology (DISAT), Politecnico di Torino, Torino I-10129, Italy
| | - Simone Bordignon
- Dipartimento
di Chimica I.F.M, Università degli
Studi di Torino, Via P. Giuria 7, Torino I-10125, Italy
| | - Federica Bravetti
- Dipartimento
di Chimica I.F.M, Università degli
Studi di Torino, Via P. Giuria 7, Torino I-10125, Italy
| | - Ian Rosbottom
- School
of Chemical and Process Engineering, University
of Leeds, Woodhouse
Lane Leeds LS2 9JT, UK
| | - Marzia Dell’Aera
- Institute
of Crystallography IC − CNR, via Amendola 122/O, Bari I-70126, Italy
| | - Corrado Cuocci
- Institute
of Crystallography IC − CNR, via Amendola 122/O, Bari I-70126, Italy
| | - Michele R. Chierotti
- Dipartimento
di Chimica I.F.M, Università degli
Studi di Torino, Via P. Giuria 7, Torino I-10125, Italy
| | - Angela Altomare
- Institute
of Crystallography IC − CNR, via Amendola 122/O, Bari I-70126, Italy
| | - Elena Simone
- School
of Food Science and Nutrition, Food Colloids and Bioprocessing Group, University of Leeds, Leeds LS2 9JT, UK
- Department
of Applied Science and Technology (DISAT), Politecnico di Torino, Torino I-10129, Italy
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4
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Mancuso R, Russo P, Lettieri M, Santandrea D, Cuocci C, Gabriele B. Disclosing Polycyclic Heterocycles: Synthesis of Furothienopyran and Pyranothienopyran Derivatives by Palladium Iodide Catalyzed Carbonylative Double Cyclization. Adv Synth Catal 2022. [DOI: 10.1002/adsc.202200958] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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5
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Cuocci C, Corriero N, Baldassarre F, Dell'Aera M, Falcicchio A, Rizzi R, Altomare A. Advanced perspectives in the EXPO software for solving crystal structures from powder diffraction data. J Appl Crystallogr 2022. [DOI: 10.1107/s160057672200245x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Innovative computational and graphical tools have been implemented for advancing the crystal structure solution process from powder diffraction data using the EXPO software. These improve the capacity of EXPO to tackle challenging solution cases and make the structural study of microcrystalline materials more user friendly. The novel features concern the structure solution both in reciprocal space and in direct space. For reciprocal-space solution, the new capability to solve an unknown structure from a mixture composed of one unknown structure and one or more phases with known structures is particularly valuable. For direct-space structure solution, EXPO has been enhanced by parallelized simulated annealing with the aim of both reducing the execution time of the solution process and providing a successful result when several degrees of freedom must be varied. Many other new tools, functional for overcoming practical difficulties usually encountered during the solution process, have also been completed. In particular, a new tool for searching and importing structures from the Crystallography Open Database is effective for supporting the solution process in direct space. The advances in EXPO aim to provide software with improved reliability, expanded operation and greater speed.
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Mancuso R, Ziccarelli I, Novello M, Cuocci C, Centore R, Della Ca' N, Olivieri D, Carfagna C, Gabriele B. A palladium iodide catalyzed regioselective carbonylative route to isocoumarin and thienopyranone carboxylic esters. J Catal 2022. [DOI: 10.1016/j.jcat.2021.11.028] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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7
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Veltri L, Amuso R, Petrilli M, Cuocci C, Chiacchio MA, Vitale P, Gabriele B. A Zinc-Mediated Deprotective Annulation Approach to New Polycyclic Heterocycles. Molecules 2021; 26:molecules26082318. [PMID: 33923572 PMCID: PMC8072660 DOI: 10.3390/molecules26082318] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 04/12/2021] [Accepted: 04/15/2021] [Indexed: 11/25/2022] Open
Abstract
A straightforward approach to new polycyclic heterocycles, 1H-benzo[4,5]imidazo[1,2-c][1,3]oxazin-1-ones, is presented. It is based on the ZnCl2-promoted deprotective 6-endo-dig heterocyclization of N-Boc-2-alkynylbenzimidazoles under mild conditions (CH2Cl2, 40 °C for 3 h). The zinc center plays a dual role, as it promotes Boc deprotection (with formation of the tert-butyl carbocation, which can be trapped by substrates bearing a nucleophilic group) and activates the triple bond toward intramolecular nucleophilic attack by the carbamate group. The structure of representative products has been confirmed by X-ray diffraction analysis.
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Affiliation(s)
- Lucia Veltri
- Laboratory of Industrial and Synthetic Organic Chemistry (LISOC), Department of Chemistry and Chemical Technologies, University of Calabria, Via Pietro Bucci 12/C, 87036 Arcavacata di Rende, Italy; (R.A.); (M.P.)
- Correspondence: (L.V.); (B.G.); Tel.: +39-0984-492817 (L.V.); +39-0984-492815 (B.G.)
| | - Roberta Amuso
- Laboratory of Industrial and Synthetic Organic Chemistry (LISOC), Department of Chemistry and Chemical Technologies, University of Calabria, Via Pietro Bucci 12/C, 87036 Arcavacata di Rende, Italy; (R.A.); (M.P.)
| | - Marzia Petrilli
- Laboratory of Industrial and Synthetic Organic Chemistry (LISOC), Department of Chemistry and Chemical Technologies, University of Calabria, Via Pietro Bucci 12/C, 87036 Arcavacata di Rende, Italy; (R.A.); (M.P.)
| | - Corrado Cuocci
- Institute of Crystallography, National Research Council, Via Amendola, 122/O, 70126 Bari, Italy;
| | - Maria A. Chiacchio
- Department of Drug Sciences, University of Catania, Viale A. Doria 6, 95125 Catania, Italy;
| | - Paola Vitale
- Department of Pharmacy—Pharmaceutical Sciences, University of Bari “Aldo Moro”, Via E. Orabona 4, 70125 Bari, Italy;
| | - Bartolo Gabriele
- Laboratory of Industrial and Synthetic Organic Chemistry (LISOC), Department of Chemistry and Chemical Technologies, University of Calabria, Via Pietro Bucci 12/C, 87036 Arcavacata di Rende, Italy; (R.A.); (M.P.)
- Correspondence: (L.V.); (B.G.); Tel.: +39-0984-492817 (L.V.); +39-0984-492815 (B.G.)
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8
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Burazer S, Popović J, Jagličić Z, Jagodič M, Šantić A, Altomare A, Cuocci C, Corriero N, Vrankić M. Magnetoelectric Coupling Springing Up in Molecular Ferroelectric: [N(C 2H 5) 3CH 3][FeCl 4]. Inorg Chem 2020; 59:6876-6883. [PMID: 32330029 DOI: 10.1021/acs.inorgchem.0c00288] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A molecule-based ferroelectric triethylmethylammonium tetrachloroferrate(III) ([N(C2H5)3CH3][FeCl4]) powder was designed as a multifunctional material exhibiting excellent multiple bistability. Prepared by the slow evaporation method at room temperature, the compound crystallizes in the non-centrosymmetric assembly of hexagonal symmetry (P63mc space group) which undergoes a reversible temperature-triggered phase transition pinpointed at 363 K to the centrosymmetric packing within the P63/mmc space group. Aside from the inseparable role of the symmetry-breaking process smoothly unveiled from the X-ray powder diffraction data, a striking change in the dielectric permittivity observed during the paraelectric-to-ferroelectric phase transition directly discloses the bistable dielectric behavior-an exceptionally high increase in the dielectric permittivity of about 360% at 100 kHz across the heating and cooling cycles is direct proof showing the highly desirable stimuli-responsive electric ordering in this improper ferroelectric architecture. Due to the magnetically modulated physical properties resulting in the coupling of magnetic and electric orderings, the flexible assembly of [N(C2H5)3CH3][FeCl4] could be used to boost the design and development of novel magnetoelectric devices.
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Affiliation(s)
- Sanja Burazer
- Division of Materials Physics, Ruđer Bošković Institute, Bijenička 54, 10000 Zagreb, Croatia
| | - Jasminka Popović
- Division of Materials Physics, Ruđer Bošković Institute, Bijenička 54, 10000 Zagreb, Croatia.,Center of Excellence for Advanced Materials and Sensing Devices, Ruđer Bošković Institute, Bijenička 54, 10000 Zagreb, Croatia
| | - Zvonko Jagličić
- Institute of Mathematics, Physics and Mechanics, Jadranska 19, 1000 Ljubljana, Slovenia.,Faculty of Civil and Geodetic Engineering, University of Ljubljana, Jamova cesta 2, 1000 Ljubljana, Slovenia
| | - Marko Jagodič
- Institute of Mathematics, Physics and Mechanics, Jadranska 19, 1000 Ljubljana, Slovenia
| | - Ana Šantić
- Division of Materials Chemistry, Ruđer Bošković Institute, Bijenička 54, 10000 Zagreb, Croatia
| | - Angela Altomare
- Institute of Crystallography-CNR, via Amendola 122/o, 70126 Bari, Italy
| | - Corrado Cuocci
- Institute of Crystallography-CNR, via Amendola 122/o, 70126 Bari, Italy
| | - Nicola Corriero
- Institute of Crystallography-CNR, via Amendola 122/o, 70126 Bari, Italy
| | - Martina Vrankić
- Division of Materials Physics, Ruđer Bošković Institute, Bijenička 54, 10000 Zagreb, Croatia.,Center of Excellence for Advanced Materials and Sensing Devices, Ruđer Bošković Institute, Bijenička 54, 10000 Zagreb, Croatia
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9
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Veltri L, Amuso R, Cuocci C, Vitale P, Gabriele B. Palladium-Catalyzed Cyclocarbonylation Approach to Thiadiazafluorenones: A Correction. J Org Chem 2019; 84:8743-8749. [DOI: 10.1021/acs.joc.9b01043] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Lucia Veltri
- Laboratory of Industrial and Synthetic Organic Chemistry (LISOC), Department of Chemistry and Chemical Technologies, University of Calabria, Via Pietro Bucci 12/C, 87036 Arcavacata di Rende (CS), Italy
| | - Roberta Amuso
- Laboratory of Industrial and Synthetic Organic Chemistry (LISOC), Department of Chemistry and Chemical Technologies, University of Calabria, Via Pietro Bucci 12/C, 87036 Arcavacata di Rende (CS), Italy
| | - Corrado Cuocci
- Institute of Crystallography (CNR), Via Amendola 122/O, 70124 Bari, Italy
| | - Paola Vitale
- Department of Pharmacy−Pharmaceutical Sciences, University of Bari “Aldo Moro”, Via E. Orabona 4, 70125 Bari, Italy
| | - Bartolo Gabriele
- Laboratory of Industrial and Synthetic Organic Chemistry (LISOC), Department of Chemistry and Chemical Technologies, University of Calabria, Via Pietro Bucci 12/C, 87036 Arcavacata di Rende (CS), Italy
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10
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Altomare A, Corriero N, Cuocci C, Falcicchio A, Moliterni A, Rizzi R. OChemDb: the free online Open Chemistry Database portal for searching and analysing crystal structure information. J Appl Crystallogr 2018. [DOI: 10.1107/s1600576718008166] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
The Open Chemistry Database (OChemDb) is a new free online portal which uses an appropriately designed database of already solved crystal structures. It makes freely available computational and graphical tools for searching and analysing crystal-chemical information of organic, metal–organic and inorganic structures, and providing statistics on desired bond distances, bond angles, torsion angles and space groups. Atom types have been classified by an identifier code containing information about the chemical topology and local environment. The crystallographic data used by OChemDb are acquired from the CIFs contained in the free small-molecule Crystallography Open Database (COD). OChemDb offers easy-to-use and intuitive options for searching. It is updated by following the continuous growth of information stored in the COD. It can be of great utility for structural chemistry, in particular in the process of determination of a new crystal structure, and for any discipline involving crystalline structure knowledge. The use of OChemDb requires only a web browser and an internet connection. Every device (mobile or desktop) and every operating system is able to use OChemDb by accessing its web page. Examples of application of OChemDb are reported.
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11
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Altomare A, Corriero N, Cuocci C, Falcicchio A, Moliterni A, Rizzi R. Direct-space solution in theEXPOpackage: the combination of the HBB–BC algorithm with GRASP. J Appl Crystallogr 2018. [DOI: 10.1107/s1600576718002984] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
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.
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12
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Altomare A, Cuocci C, Moliterni A, Rizzi R, Corriero N, Falcicchio A. The Shift_and_Fix procedure inEXPO: advances for solvingab initiocrystal structures by powder diffraction data. J Appl Crystallogr 2017. [DOI: 10.1107/s1600576717015400] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
The Shift_and_Fix procedure is a new method which has been developed for improving the quality of a structure model obtained by theab initiosolution process from powder diffraction data. The main features of the new approach, which is fully automatic, are as follows: (a) the structure model usually attained at the end of the phasing process by direct methods is shifted partly and randomly; (b) a combination of Fourier map calculation and least-squares cycles has been designed for relocating the shifted atoms onto positions which can finally be moved onto the true ones by the standard model optimization approaches; (c) the Fourier map is calculated using coefficients which depend on the chemical content of the compound under study. When the figure of merit for selecting the best set of phases derived by direct methods does not work well, the ALLTRIALS strategy can be applied: it aims to investigate, automatically and sequentially, all the stored direct methods phasing sets and pick up the correct solution. The Shift_and_Fix method has been applied for improving the structure model calculated by each one of the phasing sets processed by ALLTRIALS. It has been implemented in the computer programEXPOand proved to be effective in providing a better ALLTRIALS outcome and increasing the probability of succeeding in theab initiopowder solution.
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13
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Veltri L, Gabriele B, Mancuso R, Russo P, Grasso G, Cuocci C, Romeo R. Palladium-Catalyzed Carbonylative Synthesis of Functionalized Benzimidazopyrimidinones. SYNTHESIS-STUTTGART 2017. [DOI: 10.1055/s-0036-1591835] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
A new and convenient approach to functionalized benzimidazopyrimidinones is reported. It is based on a two-step procedure starting from readily available 1-(prop-2-yn-1-yl)-1H-benzo[d]imidazol-2-amines, consisting of a multicomponent palladium-catalyzed oxidative cyclocarbonylation–alkoxycarbonylation process, followed by base-promoted isomerization of the initially formed mixture of isomeric carbonylated products. Fair to good overall yields of the final alkyl 2-(2-oxo-1,2-dihydrobenzo[4,5]imidazo[1,2-a]pyrimidin-3-yl)acetates are obtained, using different alcohols as solvent and nucleophile in the carbonylation step (carried out in the presence of 0.33–1 mol% PdI2 in conjunction with 17–50 mol% KI, at 100 °C and under 20 atm of a 4:1 mixture of CO–air) and the corresponding sodium alkoxide as base in the subsequent isomerization step (carried out in the alcoholic solvent at room temperature). The structures of a representative substrate [N-benzyl-1-(prop-2-yn-1-yl)-1H-benzo[d]imidazol-2-amine] and a representative product [methyl 2-(1-isopentyl-2-oxo-1,2-dihydrobenzo-[4,5]imidazo[1,2-a]pyrimidin-3-yl)acetate] were confirmed by X-ray diffraction analysis.
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Affiliation(s)
- Lucia Veltri
- Laboratory of Industrial and Synthetic Organic Chemistry (LISOC), Department of Chemistry and Chemical Technologies, University of Calabria
| | - Bartolo Gabriele
- Laboratory of Industrial and Synthetic Organic Chemistry (LISOC), Department of Chemistry and Chemical Technologies, University of Calabria
| | - Raffaella Mancuso
- Laboratory of Industrial and Synthetic Organic Chemistry (LISOC), Department of Chemistry and Chemical Technologies, University of Calabria
| | - Patrizio Russo
- Laboratory of Industrial and Synthetic Organic Chemistry (LISOC), Department of Chemistry and Chemical Technologies, University of Calabria
| | - Giuseppe Grasso
- Laboratory of Industrial and Synthetic Organic Chemistry (LISOC), Department of Chemistry and Chemical Technologies, University of Calabria
| | | | - Roberto Romeo
- Dipartimento di Scienze Chimiche, Biologiche, Farmaceutiche e Ambientali
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14
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Volpe A, Pagano M, Pastore C, Cuocci C, Milella A. Sorption properties of an amorphous hydroxo titanate towards Pb(2+), Ni(2+), and Cu(2+) ions in aqueous solution. J Environ Sci Health A Tox Hazard Subst Environ Eng 2016; 51:1121-1130. [PMID: 27419851 DOI: 10.1080/10934529.2016.1199885] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Titanates may be selectively used as inorganic adsorbents for heavy metal ions owing to their stability and fast adsorption kinetics. Nevertheless, the synthesis of such materials usually requires extreme reaction conditions. In this work, a new titanium-based material was rapidly synthesized under mild laboratory conditions. The obtained amorphous hydroxo titanate was tested for heavy metal sorption through kinetic and equilibrium batch tests, which indicated that the new material had high adsorption rates and adsorption capacities towards Cu(2+), Ni(2+) and Pb(2) ions. Adsorption kinetics were pseudo-second order, and equilibrium data fitted the Langmuir isotherm model. The calculated maximum adsorption capacities of Cu(2+), Ni(2+) and Pb(2+) in deionized water were around 1 mmol g(-1), and they decreased for Cu(2+) and Ni(2+) in the presence of Na(+), Ca(2+) and Mg(2+) ions, whereas the alkali metal ions did not influence Pb(2+) uptake. The efficiency of adsorption and recovery of lead ions were evaluated through column dynamic tests, by feeding the column with groundwater and tap water spiked with Pb(2+). The high performance of the hydroxo titanate over several cycles of retention and elution suggested that the product is potentially useful for the solid phase extraction of lead at trace levels in natural water samples, with potential use in metal pre-concentration for analytical applications.
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Affiliation(s)
- Angela Volpe
- a National Research Council , Water Research Institute (CNR IRSA) , Bari , Italy
| | - Michele Pagano
- a National Research Council , Water Research Institute (CNR IRSA) , Bari , Italy
| | - Carlo Pastore
- a National Research Council , Water Research Institute (CNR IRSA) , Bari , Italy
| | - Corrado Cuocci
- b National Research Council , Institute of Crystallography (CNR IC) , Bari , Italy
| | - Antonella Milella
- c Department of Chemistry , University of Bari Aldo Moro , Bari , Italy
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Altomare A, Corriero N, Cuocci C, Falcicchio A, Moliterni A, Rizzi R. EXPO software for solving crystal structures by powder diffraction data: methods and application. Crystal Research and Technology 2015. [DOI: 10.1002/crat.201500024] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Angela Altomare
- Institute of Crystallography-CNR; via Amendola 122/o 70126 Bari Italy
| | - Nicola Corriero
- Institute of Crystallography-CNR; via Amendola 122/o 70126 Bari Italy
| | - Corrado Cuocci
- Institute of Crystallography-CNR; via Amendola 122/o 70126 Bari Italy
| | | | - Anna Moliterni
- Institute of Crystallography-CNR; via Amendola 122/o 70126 Bari Italy
| | - Rosanna Rizzi
- Institute of Crystallography-CNR; via Amendola 122/o 70126 Bari Italy
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Altomare A, Corriero N, Cuocci C, Falcicchio A, Moliterni A, Rizzi R. QUALX2.0: a qualitative phase analysis software using the freely available database POW_COD. J Appl Crystallogr 2015. [DOI: 10.1107/s1600576715002319] [Citation(s) in RCA: 152] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
QUALX2.0is the new version ofQUALX, a computer program for qualitative phase analysis by powder diffraction data. The previous version ofQUALXwas able to carry out phase identification by querying the PDF-2 commercial database. The main novelty ofQUALX2.0is the possibility of querying also a freely available database, POW_COD. POW_COD has been built up by starting from the structure information contained in the Crystallography Open Database (COD). The latter is a growing collection of diffraction data, freely downloadable from the web, corresponding to inorganic, metal–organic, organic and mineral structures.QUALX2.0retains the main capabilities of the previous version: (a) automatically estimating and subtracting the background; (b) locating the experimental diffraction peaks; (c) searching the database for single-phase pattern(s) best matching to the experimental powder diffraction data; (d) taking into account suitable restraints in the search; (e) performing a semi-quantitative analysis; (f) enabling the change of default choices and strategiesviaa user-friendly graphic interface. The advances ofQUALX2.0with respect toQUALXinclude (i) a wider variety of types of importable ASCII file containing the experimental diffraction pattern and (ii) new search–match options. The program, written in Fortran and C++, runs on PCs under the Windows operating system. The POW_COD database is exported in SQLite3 format.
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Burla MC, Caliandro R, Carrozzini B, Cascarano GL, Cuocci C, Giacovazzo C, Mallamo M, Mazzone A, Polidori G. Crystal structure determination and refinementviaSIR2014. J Appl Crystallogr 2015. [DOI: 10.1107/s1600576715001132] [Citation(s) in RCA: 596] [Impact Index Per Article: 66.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
SIR2014is the latest program of theSIRsuite for crystal structure solution of small, medium and large structures. A variety of phasing algorithms have been implemented, bothab initio(standard or modern direct methods, Patterson techniques,Vive la Différence) and non-ab initio(simulated annealing, molecular replacement). The program contains tools for crystal structure refinement and for the study of three-dimensional electron-density mapsviasuitable viewers.
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Falcicchio A, Nilsson Lill SO, Perna FM, Salomone A, Coppi DI, Cuocci C, Stalke D, Capriati V. Organotrifluoroborates as attractive self-assembling systems: the case of bifunctional dipotassium phenylene-1,4-bis(trifluoroborate). Dalton Trans 2015; 44:19447-50. [DOI: 10.1039/c5dt02020d] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A multitude of non-covalent interactions, investigated by X-ray crystallography and computational chemistry techniques, proved to be responsible of the spontaneous self-assembly of a bis(trifluoroborate) dipotassium salt.
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Affiliation(s)
| | - Sten O. Nilsson Lill
- Pharmaceutical Innovation
- Pharmaceutical Development
- AstraZeneca
- SE-431 83, Mölndal
- Sweden
| | - Filippo M. Perna
- Dipartimento di Farmacia-Scienze del Farmaco
- Università di Bari “Aldo Moro”
- I-70125, Bari
- Italy
| | - Antonio Salomone
- Dipartimento di Farmacia-Scienze del Farmaco
- Università di Bari “Aldo Moro”
- I-70125, Bari
- Italy
| | - Donato I. Coppi
- Dipartimento di Farmacia-Scienze del Farmaco
- Università di Bari “Aldo Moro”
- I-70125, Bari
- Italy
| | | | - Dietmar Stalke
- Institut für Anorganische Chemie
- Universität Göttingen
- D-37077, Göttingen
- Germany
| | - Vito Capriati
- Dipartimento di Farmacia-Scienze del Farmaco
- Università di Bari “Aldo Moro”
- I-70125, Bari
- Italy
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Carroccia L, Degennaro L, Romanazzi G, Cuocci C, Pisano L, Luisi R. Straightforward access to 4-membered sulfurated heterocycles: introducing a strategy for the single and double functionalization of thietane 1-oxide. Org Biomol Chem 2014; 12:2180-4. [DOI: 10.1039/c4ob00173g] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A strategy for the stereoselective functionalization of thietane 1-oxide has been developed by using the corresponding organometallic intermediates that reacted with electrophiles leaving intact the 4-membered ring.
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Affiliation(s)
- Laura Carroccia
- Department of Pharmacy – Drug Sciences
- University of Bari “A. Moro”
- Bari 70125 – I, Italy
| | - Leonardo Degennaro
- Department of Pharmacy – Drug Sciences
- University of Bari “A. Moro”
- Bari 70125 – I, Italy
| | | | - Corrado Cuocci
- Istituto di Cristallografia (IC-CNR)
- 70125 Bari – I, Italy
| | - Luisa Pisano
- Department of Chemistry and Pharmacy
- University of Sassari
- 07100 Sassari – I, Italy
| | - Renzo Luisi
- Department of Pharmacy – Drug Sciences
- University of Bari “A. Moro”
- Bari 70125 – I, Italy
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Altomare A, Cuocci C, Giacovazzo C, Moliterni A, Rizzi R, Corriero N, Falcicchio A. EXPO2013: a kit of tools for phasing crystal structures from powder data. J Appl Crystallogr 2013. [DOI: 10.1107/s0021889813013113] [Citation(s) in RCA: 540] [Impact Index Per Article: 49.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
EXPO2013, the heir of EXPO2009, has been enriched by a variety of new algorithms and graphical tools aiming at strengthening the individual steps of the powder structure solution pathway. Particular attention has been addressed to the procedures devoted to improving structural models provided by direct methods in ab initio approaches. In addition, a new procedure has been implemented, working in direct space, which may be chosen by the user as an alternative to the traditional simulated annealing algorithm.
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Altomare A, Corriero N, Cuocci C, Moliterni A, Rizzi R. The hybrid big bang–big crunch method for solving crystal structure from powder diffraction data. J Appl Crystallogr 2013. [DOI: 10.1107/s0021889813010571] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
The big bang–big crunch method is a global optimization approach developed upon the analogy of one of the cosmological theories of the evolution of the universe. It has been suitably combined with a simulated annealing algorithm and used for solving crystal structure from powder diffraction data in direct space. When compared with the traditional simulated annealing method, it provides a significant advance: good solutions are attained in a shorter time. The new method has been implemented in theEXPOpackage. Its successful application is demonstrated with examples of already known structures.
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Altomare A, Cuocci C, Moliterni A, Rizzi R. RAMM: a new random-model-based method for solvingab initiocrystal structure using theEXPOpackage. J Appl Crystallogr 2013. [DOI: 10.1107/s0021889813002227] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
The new method RAMM (random-model-based method) has been developed and implemented in theEXPOcomputing program for improving theab initiocrystal structure solution process. When the available information consists of only the experimental powder diffraction pattern and the chemical formula of the compound under study, the classical structure solution approach follows two main steps: (1) phasing by direct methods (or by Patterson methods) in order to obtain a structure model (this last is usually incomplete and/or approximate); (2) improving the model by structure optimization techniques. This article proposes the alternative procedure RAMM, which skips step (1) and supplies a fully random model to step (2). This model is then submitted to effective structure optimization tools present inEXPO– wLSQ (weighted least squares), RBM (resolution bias minimization) and COVMAP (a procedure of electron density modification based on the concept of covariance between points of the map) – which are able to lead to the correct structure. RAMM is based on a cyclic process, generating several random models which are then optimized. The process stops automatically when it recognizes the correct structure.
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Mugnaioli E, Kolb U, Cascarano GL, Cuocci C. Structure investigation of nanocrystalline small-molecule organics and MOF by ADT and simulated annealing. Acta Crystallogr A 2012. [DOI: 10.1107/s0108767312098042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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Altomare A, Cuocci C, Giacovazzo C, Moliterni A, Rizzi R. COVMAP: a new algorithm for structure model optimization in theEXPOpackage. J Appl Crystallogr 2012. [DOI: 10.1107/s002188981201953x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
A new procedure (COVMAP) has been developed with the aim of recovering the full structure from very poor models, such as those provided by direct methods in unfavorable conditions. The procedure is based on the concept of covariance between points of an electron density map, mathematically set out by the authors in a recent paper:i.e.the density at one point depends on the density at another point of the map if their covariance is not vanishing. This concept suggested a procedure of electron density modification that uses pairs of model peaks to restrict the region where the density modification should be applied. Such modified densities lead to additional peaks, which in turn are submitted to two other important phasing tools present inEXPO2011, the resolution bias minimization and weighted least-squares procedures, which relocate, refine or reject these peaks. The procedure is cyclic and often leads to the correct structure even if the starting model is very poor.
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Altomare A, Cuocci C, Giacovazzo C, Moliterni A, Rizzi R. Covariance and correlation estimation in electron-density maps. Acta Crystallogr A 2012; 68:244-55. [PMID: 22338659 DOI: 10.1107/s0108767311053281] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2011] [Accepted: 12/11/2011] [Indexed: 11/10/2022] Open
Abstract
Quite recently two papers have been published [Giacovazzo & Mazzone (2011). Acta Cryst. A67, 210-218; Giacovazzo et al. (2011). Acta Cryst. A67, 368-382] which calculate the variance in any point of an electron-density map at any stage of the phasing process. The main aim of the papers was to associate a standard deviation to each pixel of the map, in order to obtain a better estimate of the map reliability. This paper deals with the covariance estimate between points of an electron-density map in any space group, centrosymmetric or non-centrosymmetric, no matter the correlation between the model and target structures. The aim is as follows: to verify if the electron density in one point of the map is amplified or depressed as an effect of the electron density in one or more other points of the map. High values of the covariances are usually connected with undesired features of the map. The phases are the primitive random variables of our probabilistic model; the covariance changes with the quality of the model and therefore with the quality of the phases. The conclusive formulas show that the covariance is also influenced by the Patterson map. Uncertainty on measurements may influence the covariance, particularly in the final stages of the structure refinement; a general formula is obtained taking into account both phase and measurement uncertainty, valid at any stage of the crystal structure solution.
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Braga D, Grepioni F, Maini L, Lampronti GI, Capucci D, Cuocci C. Structure determination of novel ionic co-crystals from powder data: the use of rigid fragments in simulated annealing algorithms. CrystEngComm 2012. [DOI: 10.1039/c2ce25057h] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Altomare A, Cuocci C, Giacovazzo C, Moliterni A, Rizzi R. Automation and efficiency in the powder structure solution by EXPOpackage. Acta Crystallogr A 2011. [DOI: 10.1107/s0108767311094888] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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Falcicchio A, Altomare A, Cuocci C, Luisi R, Moliterni A, Rizzi R. Structural analysis of aziridine-2-methanol derivatives. Acta Crystallogr A 2011. [DOI: 10.1107/s0108767311083140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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Lampronti GI, Maini L, Turrina A, Capucci D, Grepioni F, Braga D, Cuocci C, Chierotti MR, Gobetto R, Griesser UJ. Ionic co-crystals of active pharmaceutical ingredients and their applications in the pharmaceutical industry. Acta Crystallogr A 2011. [DOI: 10.1107/s0108767311090854] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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Altomare A, Cuocci C, Giacovazzo C, Moliterni A, Rizzi R. Advances in theEXPO2009systematic decomposition procedure: an atom-matching-based figure of merit. J Appl Crystallogr 2011. [DOI: 10.1107/s0021889811010727] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Ab initiocrystal structure determination from powder diffraction data is not yet a straightforward process: it is strongly disrupted by the low quality of the estimated Bragg reflection intensities. In a two-stage method the integrated intensities calculated from a powder pattern are immediately submitted to direct methods to obtain phases. The larger the accuracy of the integrated intensities, the more efficient the phasing process. A systematic decomposition procedure was introduced in theEXPO2004program to improve the efficiency of the phasing process. The disadvantage of this approach is that a large number of feasible trial structures are generated, among which the correct solution must be recognized. A new procedure is described aiming at introducing strategies to reduce the total number of trials to explore by defining an appropriate figure of merit able to regroup trial structures into different batches, each element of a batch sharing a high percentage of atoms with the other elements of the same batch. The new figure of merit, implemented in an updated version ofEXPO2009, is able to discriminate non-solutions from promising trials, corresponding to incomplete or rough models which evolve, after refinement, into the correct solution.
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Moliterni A, Altomare A, Cuocci C, Giacovazzo C, Rizzi R. Ab initiostructure determination by powders: recent developments in EXPO2010. Acta Crystallogr A 2010. [DOI: 10.1107/s010876731009762x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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Altomare A, Cuocci C, Giacovazzo C, Moliterni A, Rizzi R. The dual-space resolution bias correction algorithm: applications to powder data. J Appl Crystallogr 2010. [DOI: 10.1107/s0021889810015499] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
A reciprocal-space resolution bias correction algorithm has been recently suggested, providing suitable corrections for the classical atomic scattering factors. The Fourier maps calculated by using as coefficients the structure factors obtained by the modified scattering factors proved to be less resolution biased. In this paper the correction has been generalized in order to apply it to the experimental structure factor moduli; in this way more useful electron density maps may be calculated. In a less recent paper a direct-space resolution bias correction algorithm was devised and tested on a large set of powder patterns; the algorithm implies the modification of the electron density maps to reduce the truncation errors in the Fourier syntheses. In the present paper direct and reciprocal resolution bias correction algorithms are combined into the dual-space resolution bias correction algorithm. The usefulness of the new algorithm is checked on a set of powder patterns.
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Altomare A, Camalli M, Cuocci C, Giacovazzo C, Moliterni A, Rizzi R. EXPO2009: structure solution by powder data in direct and reciprocal space. J Appl Crystallogr 2009. [DOI: 10.1107/s0021889809042915] [Citation(s) in RCA: 246] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
The programEXPO2009is the evolution ofEXPO2004[Altomare, Caliandro, Camalli, Cuocci, Giacovazzo, Moliterni & Rizzi (2004).J. Appl. Cryst.37, 1025–1028].EXPO2009performs all the steps ofab initiostructure solution by powder data: indexing, space-group determination, estimation of the reflection integrated intensities, structure solution by direct/Patterson methods and/or by a direct-space/hybrid approach, and model refinement by the Rietveld technique. New procedures have been introduced inEXPO2009for enhancing the structure solution process, particularly in the case of low-resolution data and/or organic compounds, when traditional approaches like direct methods may fail. TheEXPO2009graphical interface has been optimized and made very user friendly.
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Altomare A, Campi G, Cuocci C, Eriksson L, Giacovazzo C, Moliterni A, Rizzi R, Werner PE. Advances in powder diffraction pattern indexing:N-TREOR09. J Appl Crystallogr 2009. [DOI: 10.1107/s0021889809025503] [Citation(s) in RCA: 92] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Powder pattern indexing can still be a challenge, despite the great recent advances in theoretical approaches, computer speed and experimental devices. More plausible unit cells, belonging to different crystal systems, are frequently found by the indexing programs, and recognition of the correct one may not be trivial. The task is, however, of extreme importance: in case of failure a lot of effort and computing time may be wasted. The classical figures of merit for estimating the unit-cell reliability {i.e.M20[de Wolff (1968).J. Appl. Cryst.1, 108–113] andFN[Smith & Snyder (1979).J. Appl. Cryst.12, 60–65]} sometimes fail. For this reason, a new figure of merit has been introduced inN-TREOR09, the updated version of the indexing packageN-TREOR[Altomare, Giacovazzo, Guagliardi, Moliterni, Rizzi & Werner (2000).J. Appl. Cryst.33, 1180–1186], combining the information supplied byM20with additional parameters such as the number of unindexed lines, the degree of overlap in the pattern (the so-called number of statistically independent observations), the symmetry deriving from the automatic evaluation of the extinction group, and the agreement between the calculated and observed profiles. The use of the new parameters requires a dramatic modification of the procedures used worldwide: in the approach presented here, extinction symbol and unit-cell determination are simultaneously estimated.N-TREOR09benefits also from an improved indexing procedure in the triclinic system and has been integrated intoEXPO2009, the updated version ofEXPO2004[Altomare, Caliandro, Camalli, Cuocci, Giacovazzo, Moliterni & Rizzi (2004).J. Appl. Cryst.37, 1025–1028]. The application of the new procedure to a large set of test structures is described.
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Burla MC, Altomare A, Cuocci C, Giacovazzo C, Gozzo F, Moliterni A, Polidori G, Rizzi R. MAD techniques applied to the structure solution from powder data: a new probabilistic approach. Acta Crystallogr A 2009. [DOI: 10.1107/s0108767309097761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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Moliterni A, Altomare A, Campi G, Cuocci C, Eriksson L, Giacovazzo C, Rizzi R, Werner PE. New frontiers in powder diffraction pattern indexing: the program N-TREOR09. Acta Crystallogr A 2009. [DOI: 10.1107/s0108767309097815] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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Altomare A, Cuocci C, Giacovazzo C, Maggi S, Moliterni A, Rizzi R. Resolution bias correction in EXPO2009. Acta Crystallogr A 2009. [DOI: 10.1107/s0108767309097827] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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Rizzi R, Altomare A, Cuocci C, Giacovazzo C, Moliterni A. New strategies in EXPO2009: applications to pharmaceutical compounds. Acta Crystallogr A 2009. [DOI: 10.1107/s0108767309098006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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Altomare A, Burla MC, Cuocci C, Giacovazzo C, Gozzo F, Moliterni A, Polidori G, Rizzi R. MAD techniques applied to powder data: finding the structure given the substructure. Acta Crystallogr A 2009; 65:291-9. [PMID: 19535850 DOI: 10.1107/s0108767309016304] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2009] [Accepted: 04/30/2009] [Indexed: 11/11/2022] Open
Abstract
The joint probability distribution function method is applied to multiple-wavelength anomalous dispersion (MAD) powder data. The distributions are calculated by assuming prior knowledge of the scattering intensities at two wavelengths and of the anomalous-scatterer substructure. The method leads to formulas estimating the full structure phases and their reliability. The procedure has been applied to two structures, one unknown and one known; the second was used as a control for the phasing procedure. In spite of the unavoidable peak overlapping in the diffraction pattern, the formulas proved to be very effective. Combined with a new algorithm for phase extension, they enabled the solution of both crystal structures.
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Affiliation(s)
- Angela Altomare
- Istituto di Cristallografia, Sede di Bari, Via G. Amendola 122/o, 70126 Bari, Italy
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Altomare A, Cuocci C, Giacovazzo C, Maggi S, Moliterni A, Rizzi R. Correcting electron-density resolution bias in reciprocal space. Acta Crystallogr A 2009; 65:183-9. [DOI: 10.1107/s0108767309003687] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2008] [Accepted: 01/29/2009] [Indexed: 11/11/2022] Open
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Altomare A, Belviso BD, Burla MC, Campi G, Cuocci C, Giacovazzo C, Gozzo F, Moliterni A, Polidori G, Rizzi R. Multiple-wavelength anomalous dispersion techniques applied to powder data: a probabilistic method for finding the substructureviajoint probability distribution functions. J Appl Crystallogr 2008. [DOI: 10.1107/s0021889808039538] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
A new joint probability distribution function method is described to find the anomalous scatterer substructure from powder data. The method requires two wavelengths; the conclusive formulas provide estimates of the substructure structure factor moduli, from which the anomalous scatterer positions can be found by Patterson or direct methods. The theory has been preliminarily applied to two compounds, the first having Pt and the second having Fe as anomalous scatterer. Both substructures were correctly identified.
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Burla M, Altomare A, Cuocci C, Belviso B, Giacovazzo C, Gozzo F, Moliterni A, Polidori G, Rizzi R. MAD techniques applied to powder data: the method of the joint probability distribution functions. Acta Crystallogr A 2008. [DOI: 10.1107/s0108767308096980] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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Giacovazzo C, Altomare A, Campi G, Cuocci C, Moliterni A, Rizzi R. Advances in methods and algorithms in EXPO2008. Acta Crystallogr A 2008. [DOI: 10.1107/s0108767308099443] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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Altomare A, Cuocci C, Giacovazzo C, Moliterni A, Rizzi R. QUALX: a computer program for qualitative analysis using powder diffraction data. J Appl Crystallogr 2008. [DOI: 10.1107/s0021889808016956] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
QUALXis a new computer program for phase identification using powder diffraction data. It uses the Powder Diffraction File database, where a search for the phase best matching the experimental powder diffraction pattern is carried out. The program is characterized by a high level of automation: the traditional steps aimed at interpreting the experimental pattern before the search (background estimation, peak search, peak intensity evaluation) are executed automatically. The search may be carried outviaconstraints on compound name and/or chemical elements. In addition, several graphical options requested interactively enable the user to perform zero point correction evaluation,Kα2stripping and smoothing. The program, written in Fortran95 and C++, runs on PCs under the Windows XP operating system. It is supported by a very effective graphical interface.
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Altomare A, Cuocci C, Giacovazzo C, Moliterni A, Rizzi R. Correcting resolution bias in electron density maps of organic molecules derived by direct methods from powder data. J Appl Crystallogr 2008. [DOI: 10.1107/s0021889808011527] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Fourier syntheses providing electron density maps are usually affected by truncation effects due to the limited data resolution. A recent theoretical approach [Altomare, Cuocci, Giacovazzo, Kamel, Moliterni & Rizzi (2008).Acta Cryst.A64, 326–336] suggests that the resolution bias may be reduced by correcting the current electron density maps in accordance with the physics of the diffraction experiment. We have implemented the approach inEXPO2004[Altomare, Caliandro, Camalli, Cuocci, Giacovazzo, Moliterni & Rizzi (2004).J. Appl. Cryst.37, 1025–1028], a program devoted to the solution of crystal structures from powder data. The new algorithm was applied at the end of the direct methods modulus, to verify if the reduction of the resolution bias is able to improve the electron density maps and to provide additional power to direct methods. Application of this method to a large set of test structures indicates that resolution-bias correction often makes the difference between success and failure, and thus constitutes a new tool for reducing the dependence of modern crystallography on resolution effects. The chances of failure are expected to depend on the quality of the experimental data (e.g.the accuracy of the full-pattern decomposition procedure and the data resolution), on the size of the structure and on its chemical composition.
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Altomare A, Cuocci C, Giacovazzo C, Kamel GS, Moliterni A, Rizzi R. Minimally resolution biased electron-density maps. Acta Crystallogr A 2008; 64:326-36. [PMID: 18285628 DOI: 10.1107/s0108767308004303] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2007] [Accepted: 01/10/2008] [Indexed: 11/11/2022] Open
Abstract
Electron-density maps are calculated by Fourier syntheses with coefficients based on structure factors. Diffraction experiments provide intensities up to a limited resolution; as a consequence, the Fourier syntheses always show series-termination errors. The worse the resolution, the less accurate is the Fourier representation of the electron density. In general, each atomic peak is shifted from the correct position, shows a deformed (with respect to the true distribution of the electrons in the atomic domain) profile, and is surrounded by a series of negative and positive ripples of gradually decreasing amplitude. An algorithm is described which is able to reduce the resolution bias by relocating the peaks in more correct positions and by modifying the peak profile to better fit the real atomic electron densities. Some experimental tests are performed showing the usefulness of the procedure.
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Altomare A, Caliandro R, Cuocci C, Giacovazzo C, Moliterni AGG, Rizzi R, Platteau C. Direct methods and simulated annealing: a hybrid approach for powder diffraction data. J Appl Crystallogr 2008. [DOI: 10.1107/s0021889807054192] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
The solution of crystal structures from powder data using direct methods can be very difficult if the quality of the diffraction pattern is low and if no heavy atoms are present in the molecule. On the contrary, the use of direct-space methods does not require good quality diffraction data, but if a molecular model is available, the structure solution is limited principally by the number of degrees of freedom used to describe the model. The combination of the information contained in the electron density map (direct methods) with the Monte Carlo method, which uses simulated annealing as a global minimization algorithm (direct-space techniques), can be a useful tool for crystal structure solution, especially for organic structures. A modified and improved version of this approach [Altomareet al.(2003),J. Appl. Cryst.36, 230–238] has been implemented in theEXPO2004program and is described here.
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Capriati V, Degennaro L, Florio S, Luisi R, Cuocci C. Asymmetric synthesis of α,β-substituted β-aminoalkanamides and stereochemical determination. Tetrahedron Lett 2007. [DOI: 10.1016/j.tetlet.2007.10.035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Altomare A, Camalli M, Cuocci C, Giacovazzo C, Moliterni AGG, Rizzi R. Advances in space-group determination from powder diffraction data. J Appl Crystallogr 2007. [DOI: 10.1107/s0021889807027501] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
The space-group determination process by powder diffraction data is not straightforward. The low accuracy of the reflection intensities may invalidate the calculation of the probability associated to each extinction group that is compatible with the crystal system determined in the indexation step. Here the combination of thezstatistics with two new algorithms is reported: the first checks the quality of each 2θ interval in order to omit doubtfulzestimates from the calculations; the second creates a list of reflections with peaks that weakly overlap with any other peak, in order to check if any of them violates the extinction rules of the extinction symbol. The new approach has been applied to a large set of test structures and proved to be much more efficient than the procedure based only on thezstatistics.
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