Aurelia Falcicchio - Academia.edu (original) (raw)

Papers by Aurelia Falcicchio

Journal of Applied Crystallography, 2018

The Open Chemistry Database (OChemDb) is a new free online portal which uses an appropriately des... more 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 cr...

Proceedings of The 2nd International Online Conference on Crystals, 2020

European Journal of Organic Chemistry

Computational Materials Science

An entry from the Cambridge Structural Database, the world's repository for small molecule cr... more An entry from the Cambridge Structural Database, the world's repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.

Proceedings of The 2nd International Online Conference on Crystals, 2020

Inorganic Chemistry, 2021

Anionic complexes having vapochromic behavior are investigated: [K(H2O)][M(ppy)(CN)2], [K(H2O)][M... more Anionic complexes having vapochromic behavior are investigated: [K(H2O)][M(ppy)(CN)2], [K(H2O)][M(bzq)(CN)2], and [Li(H2O)n][Pt(bzq)(CN)2], where ppy = 2-phenylpyridinate, bzq = 7,8-benzoquinolate, and M = Pt(II) or Pd(II). These hydrated potassium/lithium salts exhibit a change in color upon being heated to 380 K, and they transform back into the original color upon absorption of water molecules from the environment. The challenging characterization of their structure in the vapochromic transition has been carried out by combining several experimental techniques, despite the availability of partially ordered and/or impure crystalline material. Room-temperature single-crystal and powder X-ray diffraction investigation revealed that [K(H2O)][Pt(ppy)(CN)2] crystallizes in the Pbca space group and is isostructural to [K(H2O)][Pd(ppy)(CN)2]. Variable-temperature powder X-ray diffraction allowed the color transition to be related to changes in the diffraction pattern and the decrease in sample crystallinity. Water loss, monitored by thermogravimetric analysis, occurs in two stages, well separated for potassium Pt compounds and strongly overlapped for potassium Pd compounds. The local structure of potassium compounds was monitored by in situ pair distribution function (PDF) measurements, which highlighted changes in the intermolecular distances due to a rearrangement of the crystal packing upon vapochromic transition. A reaction coordinate describing the structural changes was extracted for each compound by multivariate analysis applied to PDF data. It contributed to the study of the kinetics of the structural changes related to the vapochromic transition, revealing its dependence on the transition metal ion. Instead, the ligand influences the critical temperature, higher for ppy than for bzq, and the inclination of the molecular planes with respect to the unit cell planes, higher for bzq than for ppy. The first stage of water loss triggers a unit cell contraction, determined by the increase in the b axis length and the decrease in the a (for ppy) or c (for bzq) axis lengths. Consequent interplane distance variations and in-plane roto-translations weaken the π-stacking of the room-temperature structure and modify the distances and angles of Pt(II)/Pd(II) chains. The curve describing the intermolecular Pt(II)/Pd(II) distances as a function of temperature, validated by X-ray absorption spectroscopy, was found to reproduce the coordinate reaction determined by the model-free analysis.

Crystals, 2018

The Rietveld method is the most reliable and powerful tool for refining crystal structure when po... more The Rietveld method is the most reliable and powerful tool for refining crystal structure when powder diffraction data are available. It requires that the structure model to be adjusted is as close as possible to the true structure. The Rietveld method usually represents the final step of the powder solution process, in particular when a new structure is going to be determined and published. EXPO is a software able to execute all the steps of the solution process in a mostly automatic way, by starting from the chemical formula and the experimental diffraction pattern, passing through computational methods for locating the structure model and optimizing it, and ending to the Rietveld refinement. In this contribution, we present the most recent solution strategies in EXPO, both in reciprocal and direct space, aiming at obtaining models suitable to be refined by the Rietveld method. Examples of Rietveld refinements are described, whose results are related to different solution procedures and types of compounds (organic and inorganic).

Chemistry of Heterocyclic Compounds, 2017

Acta Crystallographica Section A Foundations of Crystallography, 2011

formula C 19 H 22 F N 3 O 3 , 6(H 2 O) which crystallizes in a triclinic crystal system with spac... more formula C 19 H 22 F N 3 O 3 , 6(H 2 O) which crystallizes in a triclinic crystal system with space group P-1. Water molecules of the network array of hydrogen bonding interactions of the type O-H…H with distances that are within the range of 1.93 a 2.23 Å and as a few examples, in this case shows that some water molecules have three hydrogen bonds at the same time, which favors a two-dimensional crystal growth with the motif R 6 6 (12), giving rise to the supramolecular arrangement in a laminar. In the dimeric complex of copper acetate (II) with molecular formula C 8 H 16 Cu 2 O 10 , have a monoclinic crystal system with space group C 2/c, in this compound the water molecules establish three hydrogen bonds in the range of 2.03 to 2.58 Å, giving rise to motif R 2 2 (8) mainly. While for crystals of [Fe(H 2 O) 6 ]SO 4 2(H 2 O) (II) with molecular formula Fe H 12 O 6 , 2(SO 4), 2(H 2 O) crystallizing in a monoclinic crystal system with space group P 21/n; the large number of water molecules present in this complex supports a large number of such interactions O-H…H with hydrogen bond lengths are in the range of 1.85 to 2.19 Å. In a global analysis of data from X-ray diffraction, is that the magnitude of the hydrogen bonds are present in the energy range of 4 to 15 Kcal, being strong bonds with weak covalence and dominant electrostatic contribution, these properties are required for the design and application engineering of crystals and / or molecular devices

Crystal Research and Technology, 2015

Innovative methodologies, introduced in the software EXPO and working both in the reciprocal and ... more Innovative methodologies, introduced in the software EXPO and working both in the reciprocal and in the direct space, can be successfully adopted for solving crystal structure by X-ray powder diffraction data. The principles underlying these methodologies are summarized. Three representative examples of crystal structure solution of the peptides Z-(Aib) 2-OH, Z-(Aib) 3-O-t-Bu and Z-(Aib) 4-OH are discussed in relation to their different degree of structure complexity.

Journal of Applied Crystallography, 2015

QUALX2.0is the new version ofQUALX, a computer program for qualitative phase analysis by powder d... more 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 ...

Chemical Science, 2014

C(2)-H(2B) 0.9800 C(2)-H(2C) 0.9800 C(3)-C(9) 1.377(2) C(3)-H(3) 0.9500 C(4)-C(6) 1.394(2) C(4)-C... more C(2)-H(2B) 0.9800 C(2)-H(2C) 0.9800 C(3)-C(9) 1.377(2) C(3)-H(3) 0.9500 C(4)-C(6) 1.394(2) C(4)-C(5) 1.487(2) C(6)-C(10) 1.376(2) C(6)-H(6) 0.9500 C(7)-C(20) 1.469(2) C(7)-Li(1) 2.167(3) C(8)-C(13) 1.514(2) C(8)-H(8A) 0.9900 C(8)-H(8B) 0.9900 C(9)-C(10) 1.384(2) C(9)-H(9) 0.9500 C(10)-H(10) 0.9500

Organic & Biomolecular Chemistry, 2012

Spectroscopic data of piperazines 2a-r. Determination of the enantiomeric purity. X-ray Structure... more Spectroscopic data of piperazines 2a-r. Determination of the enantiomeric purity. X-ray Structures Copy of 1H-NMR and 13C-NMR spectra of piperazines 2a-r.

Four-membered heterocycles (4-MH) with one or two heteroatoms are of great importance in medicina... more Four-membered heterocycles (4-MH) with one or two heteroatoms are of great importance in medicinal chemistry and synthetic organic chemistry. This kind of scaffolds show peculiar structural features, related to the ring “puckering”, and biological properties. Our recent research efforts have been focused on the stereoselective synthesis and functionalization of some 4-MH such as azetidines, thietanes and oxazetidines.

Journal of Applied Crystallography, 2013

EXPO2013, the heir of EXPO2009, has been enriched by a variety of new algorithms and graphical to... more 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.

Journal of Applied Crystallography, 2018

The Open Chemistry Database (OChemDb) is a new free online portal which uses an appropriately des... more 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 cr...

Proceedings of The 2nd International Online Conference on Crystals, 2020

European Journal of Organic Chemistry

Computational Materials Science

An entry from the Cambridge Structural Database, the world's repository for small molecule cr... more An entry from the Cambridge Structural Database, the world's repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.

Proceedings of The 2nd International Online Conference on Crystals, 2020

Inorganic Chemistry, 2021

Anionic complexes having vapochromic behavior are investigated: [K(H2O)][M(ppy)(CN)2], [K(H2O)][M... more Anionic complexes having vapochromic behavior are investigated: [K(H2O)][M(ppy)(CN)2], [K(H2O)][M(bzq)(CN)2], and [Li(H2O)n][Pt(bzq)(CN)2], where ppy = 2-phenylpyridinate, bzq = 7,8-benzoquinolate, and M = Pt(II) or Pd(II). These hydrated potassium/lithium salts exhibit a change in color upon being heated to 380 K, and they transform back into the original color upon absorption of water molecules from the environment. The challenging characterization of their structure in the vapochromic transition has been carried out by combining several experimental techniques, despite the availability of partially ordered and/or impure crystalline material. Room-temperature single-crystal and powder X-ray diffraction investigation revealed that [K(H2O)][Pt(ppy)(CN)2] crystallizes in the Pbca space group and is isostructural to [K(H2O)][Pd(ppy)(CN)2]. Variable-temperature powder X-ray diffraction allowed the color transition to be related to changes in the diffraction pattern and the decrease in sample crystallinity. Water loss, monitored by thermogravimetric analysis, occurs in two stages, well separated for potassium Pt compounds and strongly overlapped for potassium Pd compounds. The local structure of potassium compounds was monitored by in situ pair distribution function (PDF) measurements, which highlighted changes in the intermolecular distances due to a rearrangement of the crystal packing upon vapochromic transition. A reaction coordinate describing the structural changes was extracted for each compound by multivariate analysis applied to PDF data. It contributed to the study of the kinetics of the structural changes related to the vapochromic transition, revealing its dependence on the transition metal ion. Instead, the ligand influences the critical temperature, higher for ppy than for bzq, and the inclination of the molecular planes with respect to the unit cell planes, higher for bzq than for ppy. The first stage of water loss triggers a unit cell contraction, determined by the increase in the b axis length and the decrease in the a (for ppy) or c (for bzq) axis lengths. Consequent interplane distance variations and in-plane roto-translations weaken the π-stacking of the room-temperature structure and modify the distances and angles of Pt(II)/Pd(II) chains. The curve describing the intermolecular Pt(II)/Pd(II) distances as a function of temperature, validated by X-ray absorption spectroscopy, was found to reproduce the coordinate reaction determined by the model-free analysis.

Crystals, 2018

The Rietveld method is the most reliable and powerful tool for refining crystal structure when po... more The Rietveld method is the most reliable and powerful tool for refining crystal structure when powder diffraction data are available. It requires that the structure model to be adjusted is as close as possible to the true structure. The Rietveld method usually represents the final step of the powder solution process, in particular when a new structure is going to be determined and published. EXPO is a software able to execute all the steps of the solution process in a mostly automatic way, by starting from the chemical formula and the experimental diffraction pattern, passing through computational methods for locating the structure model and optimizing it, and ending to the Rietveld refinement. In this contribution, we present the most recent solution strategies in EXPO, both in reciprocal and direct space, aiming at obtaining models suitable to be refined by the Rietveld method. Examples of Rietveld refinements are described, whose results are related to different solution procedures and types of compounds (organic and inorganic).

Chemistry of Heterocyclic Compounds, 2017

Acta Crystallographica Section A Foundations of Crystallography, 2011

formula C 19 H 22 F N 3 O 3 , 6(H 2 O) which crystallizes in a triclinic crystal system with spac... more formula C 19 H 22 F N 3 O 3 , 6(H 2 O) which crystallizes in a triclinic crystal system with space group P-1. Water molecules of the network array of hydrogen bonding interactions of the type O-H…H with distances that are within the range of 1.93 a 2.23 Å and as a few examples, in this case shows that some water molecules have three hydrogen bonds at the same time, which favors a two-dimensional crystal growth with the motif R 6 6 (12), giving rise to the supramolecular arrangement in a laminar. In the dimeric complex of copper acetate (II) with molecular formula C 8 H 16 Cu 2 O 10 , have a monoclinic crystal system with space group C 2/c, in this compound the water molecules establish three hydrogen bonds in the range of 2.03 to 2.58 Å, giving rise to motif R 2 2 (8) mainly. While for crystals of [Fe(H 2 O) 6 ]SO 4 2(H 2 O) (II) with molecular formula Fe H 12 O 6 , 2(SO 4), 2(H 2 O) crystallizing in a monoclinic crystal system with space group P 21/n; the large number of water molecules present in this complex supports a large number of such interactions O-H…H with hydrogen bond lengths are in the range of 1.85 to 2.19 Å. In a global analysis of data from X-ray diffraction, is that the magnitude of the hydrogen bonds are present in the energy range of 4 to 15 Kcal, being strong bonds with weak covalence and dominant electrostatic contribution, these properties are required for the design and application engineering of crystals and / or molecular devices

Crystal Research and Technology, 2015

Innovative methodologies, introduced in the software EXPO and working both in the reciprocal and ... more Innovative methodologies, introduced in the software EXPO and working both in the reciprocal and in the direct space, can be successfully adopted for solving crystal structure by X-ray powder diffraction data. The principles underlying these methodologies are summarized. Three representative examples of crystal structure solution of the peptides Z-(Aib) 2-OH, Z-(Aib) 3-O-t-Bu and Z-(Aib) 4-OH are discussed in relation to their different degree of structure complexity.

Journal of Applied Crystallography, 2015

QUALX2.0is the new version ofQUALX, a computer program for qualitative phase analysis by powder d... more 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 ...

Chemical Science, 2014

C(2)-H(2B) 0.9800 C(2)-H(2C) 0.9800 C(3)-C(9) 1.377(2) C(3)-H(3) 0.9500 C(4)-C(6) 1.394(2) C(4)-C... more C(2)-H(2B) 0.9800 C(2)-H(2C) 0.9800 C(3)-C(9) 1.377(2) C(3)-H(3) 0.9500 C(4)-C(6) 1.394(2) C(4)-C(5) 1.487(2) C(6)-C(10) 1.376(2) C(6)-H(6) 0.9500 C(7)-C(20) 1.469(2) C(7)-Li(1) 2.167(3) C(8)-C(13) 1.514(2) C(8)-H(8A) 0.9900 C(8)-H(8B) 0.9900 C(9)-C(10) 1.384(2) C(9)-H(9) 0.9500 C(10)-H(10) 0.9500

Organic & Biomolecular Chemistry, 2012

Spectroscopic data of piperazines 2a-r. Determination of the enantiomeric purity. X-ray Structure... more Spectroscopic data of piperazines 2a-r. Determination of the enantiomeric purity. X-ray Structures Copy of 1H-NMR and 13C-NMR spectra of piperazines 2a-r.

Four-membered heterocycles (4-MH) with one or two heteroatoms are of great importance in medicina... more Four-membered heterocycles (4-MH) with one or two heteroatoms are of great importance in medicinal chemistry and synthetic organic chemistry. This kind of scaffolds show peculiar structural features, related to the ring “puckering”, and biological properties. Our recent research efforts have been focused on the stereoselective synthesis and functionalization of some 4-MH such as azetidines, thietanes and oxazetidines.

Journal of Applied Crystallography, 2013

EXPO2013, the heir of EXPO2009, has been enriched by a variety of new algorithms and graphical to... more 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.