1,721,132 research outputs found
Porosity and crystal morphology of heterometallic coordination networks from β-diketonate ligands
Full text linkPorous coordination polymers (PCPs) or metal-organic-frameworks (MOFs) are considered very promising porous materials that can be exploited in many different technological fields such as gas storage, heterogeneous catalysis and separation of mixtures. In the field of MOF materials, many efforts are devoted to the search of rational synthetic procedures. Among others, a useful synthetic strategy is the so-called Metalloligand (MLs) approach. MLs are coordination complexes containing suitably oriented exo donor-groups that, used in place of organic linkers, can orient the formation of desired homo and heterometallic polymeric architectures [1]. Functionalized chelating ligands suited to obtain useful MLs are -diketonate molecules.[2]
We report the synthesis and the structural characterization of two families of coordination frameworks obtained through the use of different -diketonate ligands with copper salts of several counter-ions. The first family of polymers have a two-dimensional layered structure whereas the members of the second family adopt a three-dimensional flexible framework structure.
We have focused our attention to the correlations between the crystal structure, the dimensionality, the topology and porosity of the networks and the crystal morphologies, as well as to the investigation of the surface phenomena during the crystal growing process. Moreover, we have mapped a continuous set of crystal morphologies by controlling experimental variables such as the solvent system, the metal-ligand molar ratio and the nature of the counter-anion. The aim is to develop a method to tune the crystal habit according to the specific requirement of some important applications.[3]
[1] S. Kitagawa, R. Kitaura, S. Noro Angew. Chem., Int. Ed., 43 (2004) 2334.
[2] L. Carlucci, G. Ciani, S. Maggini, D.M. Proserpio, M. Visconti, Chem. Eur. J, 16 (2010) 12328.
[3] L. Carlucci, G. Ciani, J. M. Garcìa-Ruiz, M. Moret, D. M. Proserpio and S. Rizzato , Cryst. Growth Des., 2009, 9(12), 5024-5034
Crystal growth of coordination polymers by gel diffusion
Full text linkThe use of gels or viscous materials as growth media for a wide range of compounds, including proteins, inorganic and organic compounds has already been reported in the literature. In the presence of a gel, sedimentation and convection currents are greatly suppressed and the mass transport of the molecules occurs mainly by diffusion. As a result, a lower nucleation density and a better crystal quality are usually observed.[1a] We report, here, new interesting phenomena observed in crystallization experiments ofcoordination compounds by using gels as diffusion media.[1b].
We have tested a variety of gel and resin-like systems as dispersion matrixes to crystallize a special class of polymeric and porous inorganic compound: the “coordination polymers”. We have used the gel technique to increase the size and quality of the crystals and as a mean to modify the crystal habit and get new crystalline species. [1b] In our experiments, we have observed some new phenomena of gel inclusion and morphological alteration of crystal surfaces.
Diffraction, optical observations and interferometric measurements have been used for in situ monitoring the mass transport in the gelled/fluid phase during the crystallization process and for studying the crystallization kinetic.
Funding from the Cariplo Foundation grant ‘‘2012‐0921” is gratefully acknowledged.
[1] a) K.H. Henisch, Crystals in Gels and Liesegang Rings, Cambridge University Press, Cambridge, 1998; b) L.
Carlucci, G. Ciani, J. M. Garcìa-Ruiz, M. Moret, D. M. Proserpio and S. Rizzato Cryst. Growth Des., 2009, 9(12),
5024-5034.
[2] S.Rizzato et al., unpublished results
Crystallization Behavior of Coordination Polymers. 2. Surface Micro-Morphology and Growth Mechanisms of [Cu(bpp)3Cl2] 3 2H2O by in Situ Atomic Force Microscopy
No full textCrystal growth of the one-dimensional coordination polymer [Cu(1,3-bis(4-pyridyl)propane)3Cl2]·2H2O was investigated in aqueous solutions by in situ atomic force microscopy. Details about the growth mechanisms of the {001} form at low supersaturation were obtained. In particular, growth hillocks due to simple and complex dislocation sources were observed as the only active mechanism. The thinnest steps observed on {001} faces and delimiting growth hillocks were d002 layers, in accordance with the elementary growth layer expected from the systematic extinction conditions of space group I2/a and hence from Bravais−Friedel−Donnay−Harker rules and Hartman and Perdok periodic bond chains theory. This feature of the {001} faces suggests that small oligomeric species can be involved in the crystal growth processes. The effects of unknown impurities in the organic ligand upon the growth of crystals of the title compound were also studied
Are racemic crystals favored over homochiral crystals by higher stability or by kinetics? Insights from comparative studies of crystalline stereoisomers
No full textThe crystal and molecular structures of 134 pairs of diastereoisomers and of 279 racemic-homochiral pairs were retrieved from the Cambridge Structural Database. Lattice and intramolecular energies are calculated. Density differences between crystals of stereoisomers of all kind are mostly within 5%, as observed also for crystal polymorphs. Racemic crystals are predominantly, but not exclusively, more stable and more dense. Denser crystals are predominantly more stable, but there is no quantitative correlation between density and energy differences between partners in the chosen pairs. Second-order symmetry operators are neither ubiquitous in the racemic nor patently superior to first-order operators in promoting crystal cohesion. Thermodynamic, energetic factors in the final crystalline products are not enough to explain the (largely) predominant occurrence of racemic crystallization from racemic solution. At least for homogeneous nucleation, a probabilistic factor, from kinetics or from statistical predominance of mixed versus enantiopure aggregates, must be in action during the early separation of liquid-like particles, which are thought to be the precursors of crystal nucleation
On the interplay among non-covalent interactions and activity of 4-aminoquinoline antimalarials: a crystallographic and spectroscopic study
Full text linkMalaria is due to protozoa of the genus Plasmodium, which infect human red blood cells and digest the host hemoglobin. Degradation of the latter in the acidic food vacuole (pH ~ 5) releases free hematin (hydroxylated Fe protoporphyrin-IX, FePPIX(OH)), which is toxic to the parasite [1]. Therefore, Plasmodium deactivates hematin by promoting its crystallization into harmless pale yellow P1bar crystals of beta-hematin. 4-aminoquinoline drugs (AQ), such as chloroquine (CQ) and piperaquine (PQ), interfere with this detoxification process, either by coordinating free heme in solution [2], or by poisoning fastest-growing crystal faces of beta-hematin [3]. However, there is no general consensus on the structure of the AQ/heme complex [4], which depends on various chemical variables (aqueous/lipidic environment, pH).
We here aim at quantitatively disclosing the chemical physics underlying the pharmacophoric features of CQ and PQ in the context of predicting which chemical modifications should be applied on the AQ scaffold to enhance the drug functionality against the biochemical resistance mechanism evolved by Plasmodium [5,6].
EXAFS spectroscopy in solution across the Fe Kalpha absorption edge (~ 7.1 keV) explored the first shell coordination geometry of iron in hematin, both in the presence and in the absence of AQ systems. Differences in the signal were related to the possible occurrence of a direct Fe–N coordinative bond involving the quinoline nitrogen atom, which might coexist with other possible (e.g. pi···pi stacked) adduct geometries [5] (Fig. 1). Quantum mechanical DFT calculations showed that an aliphatic tertiary NH+ amino group might also be a crucial part of the pharmacophore (Fig. 1), as it is able to set up strong charge-assisted hydrogen bonds with proprionate groups of hematin. This complies well with single-crystal X-ray diffraction outcomes on the CQ dihydrogen phosphate salt at 103 K[6], where H2PO4– ions form hydrogen-bonded pillars which strongly interact with positively charged chloroquine molecules. Comparison of the CQ crystal structure with those of various hydrated salts of PQ (NO3–, SO42–, H2PO4–), grown by advanced sol-gel methods, disclosed subtle analogies and differences in the non-covalent interaction networks of the two drugs, which are also related to their solubilities.
[1] L. Kořený, M. Oborník, J. Lukeš, PLoS Pathog. 2013, 9(1), e1003088.
[2] D.C. Warhurst J.C. Craig, K.S. Raheem, Biochem. Pharmacol. 2007, 73, 1910.
[3] M.S.Walczak, K. Lawniczak-Jablonska, A. Wolska, A. Sienkiewicz, L. Suarez, A.J. Kosar, D.S. Bohle J. Phys. Chem. B 2011, 115, 1145.
[4] J. Gildenhuys, T. Roex, T.J. Egan, K.A. De Villiers, J. Am. Chem. Soc. 2013, 135, 1037.
[5] G. Macetti, S. Rizzato, F. Beghi, L. Silvestrini, L. Lo Presti, Physica Scripta 2016, 91, 023001.
[6] G. Macetti, L. Loconte, S. Rizzato, C. Gatti, L. Lo Presti, Crystal Growth Des. 2016. 16, 6043
Neutrons in chemistry : contributions of single crystal neutron diffraction to coordination chemistry
No full text1. Introduction
Single crystal neutron diffraction is the technique of choice for unambiguously and accurately locating hydrogen atoms even in the presence of nearby “heavy atoms”. Recent advances in instrumentation and neutron sources are opening up new possibilities: in particular the use of fairly small crystals and short data collection times.
2. Results and Discussion
We will report three examples to illustrate the power of this technique in inorganic chemistry:
1) the first unambiguous structural evidence for non-conventional hydrogen bonding between a water molecule and a metal center in trans-[PtCl2(NH3)(N-glycine)]∙H2O.[1]
2) The coordination geometries of the binary platinum hydrides [Pt2(P-P)2(H)3]+ (P-P = dppb: 1,4–Bis(diphenylphosphino)butane and dpe: 1,2–Bis(diphenylphosphino)ethane).
3) The unambiguous location of deuterium atoms in the deuterated form of RuH2(η2-H2)2(PCyp3)2 (Cyp = cyclopentyl) complex as a proof of the metal-mediated C-H activation.[2]
3. References
[1] Silvia Rizzato, Jacqueline Bergès, Sax A. Mason, Alberto Albinati and Jiří Kozelka, Angew. Chem. Int. Ed., in press.
[2] M. Grellier, L. Vendier, B. Chaudret, A. Albinati, S. Rizzato, S. A. Mason and S. Sabo-Etienne J. Am. Chem. Soc., 2005,127 (50), 17593
"Coulombic Compression", a pervasive force in ionic solids. A study of anion stacking in croconate salts
No full textWe describe coulombic compression as the driving factor in the tight packing of crystals formed under ionic interactions. In the crystal structures of croconic acid salts, the disk-shaped dianions form stacks with interlayer distances as short as 3.1-3.4 Å. Crystal packing energies have been estimated using atom-atom potentials (AA-CLP) and semi-classical density sums (PIXEL) with evaluation of coulombic, polarization, dispersion, and repulsion terms; the simpler model yields reliable energy estimates even for the multiatomic molecular anions. The structure of the potassium salt is discussed in detail. Calculations show that although the repulsion energy between adjacent anionic disks is enormous, as result of coulombic compression, the overall structure is stable because the cation-anion interaction energy exceeds the combined cation-cation and anion-anion interaction energies. Ion-water coulombic terms are much smaller, and dispersion energies are even smaller but not negligible. Even for crystals with packing energies of several hundred kilojoules per mole, energy differences of a few kilojoules per mole determine structural details, such as the preference of neighboring stacked anions to be staggered rather than eclipsed or the relative stability of two polymorphs of calcium croconate trihydrate. © 2013 American Chemical Society
Stechiometria : dal testo di M. Freni e A. Sacco
No full textIl testo è stato completamente rinnovato e ampliato per renderlo più adatto alle esigenze di studio degli odierni corsi universitari. Gli Autori hanno cercato di apportare delle modifiche che, nel rispetto dello spirito del testo originario, consentissero di rinnovare parte dei capitoli, alleggerendo la trattazione di qualche argomento, ormai considerato “accessorio”. In ogni capitolo sono richiamate le conoscenze fondamentali e necessarie per affrontare la risoluzione dei problemi ed è stato aggiunto un capitolo sulle formule di Lewis che, nonostante sia una tematica non appartenente in senso stretto alla stechiometria “classica”, rappresenta comunque un bagaglio di conoscenza fondamentale per lo studente che voglia affacciarsi al mondo della chimica. Sono presenti un cospicuo numero di esercizi risolti e problemi con risoluzione e dei problemi di argomento biologico. Alla fine di ciascun capitolo, inoltre, sono stati inseriti dei problemi da risolvere per verificare l'apprendimento dei concetti chiave discussi. Il volume è completato da un capitolo di esercizi di ricapitolazione per fissare i concetti studiati in precedenza
Experimental and theoretical study of the mechanism of action of the antimalarial drug chloroquine
Full text linkMalaria is due to the Plasmodium protozoon. The parasite infects human red blood cells, where it digests hemoglobin, in the end releasing free heme (Fe-protoporphyrin IX, FePPIX) in the cytosol. There, FePPIX could produce reactive oxygen species which are toxic to the parasite.
As a defense mechanism, the protozoon deactivates FePPIX by promoting its biocrystallization into hemozoin, a triclinic harmless solid. It is largely accepted that 4-aminoquinoline (AQ) drugs, and in particular the low-cost compound chloroquine (CQ), interfere with this detoxification process [1], but no unequivocal evidences on their mechanism of action still exist [2,3]. Moreover, emerging parasite resistance made CQ ineffective in the last decades. In this context, understanding the mechanism of action of chloroquine is a key point to develop novel cheap CQ-based compounds, exploitable in large-scale health campaigns, able to thwart the parasite resistance.
In our very recent work [4], evidences of the existence of a direct Fe – N coordinative bond between CQ and heme in solution have been obtained. DFT calculations highlighted that charge-assisted hydrogen bonds (CAHBs) among the hydrocarbon chain of CQ and the propionate groups of heme play a crucial role in the molecular recognition, particularly in the presence of lipidic micelles.
In this contribution we report on a high-resolution low-temperature single crystal X-ray diffraction study on the chloroquine diphosphate dihydrate salt. CQ crystallizes as P21/c, with dihydrogenphosphate ions (H2PO4–) forming infinite chains parallel to the monoclinic axis. Doubly protonated CQ molecules, CQH22+, and H2PO4– are connected through strong N-H•••O CAHBs. A π-π stacking interaction could be also set up between the quinoline rings, which lie parallel to the (a,c) plane to occupy as much as possible the free space between phosphate chains.
From the molecular recognition viewpoint, π-π stacking in the CQ crystal could be taken as a model for the π-π CQ:heme interaction in solution, described in the literature as a possible way of interaction between the drug and its substrate, while negatively charged the phosphate ions behave as propionate groups in heme.
The study of the CQ self-recognition energies through the analysis of the primary charge density confirm the hypothesis that the coulombic interactions between CQ and the phosphate are the real dominant ones, while the stacking between the quinoline moieties has just an ancillary role. These evidences further confirm that the protonated tertiary amine of CQ is an essential component of the drug pharmacophore.
[1] A. F. G. Slater, W. J. Swiggard, B. R. Orton, W. D. Flitter, D. E. Goldberg. A. Cerami, G. B. Henderson Proc. Natl. Acad. Sci. USA 1991, 88, 325-329.
[2] M. S. Walckzak, K. Lawniczak-Jablonska, A. Wolska, A. Sienkiewicz, L. Suarez, A. J. Kosar, D. S. Bohle J. Phys. Chem. B, 2011, 115, 1145-1150.
[3] A. C. De Dios, R. Tycko, L. M. B. Ursos, P. D. Roepe J. Phys. Chem. A, 2003, 107, 5821-5825.
[4] G. Macetti, S. Rizzato, F. Beghi, L. Silvestrini, L. Lo Presti Physica Scripta 2016, 91, 023001, 1-13
Study of the key interactions in the self-recognition of the antimalarial drug chloroquine
Full text linkMalaria is a parasitic disease that causes thousands of deaths every year, especially in undeveloped countries. The Plasmodium protozoa, responsible of the infection, kill human red blood cells by digesting hemoglobin. Many compounds have been employed in the last century against malaria, but nowadays the increasing resistance of Plasmodium is becoming a very serious problem. New drugs are required and to this end it is desirable to quantitatively understand the role of different functional groups in determining effective pharmacophores.
This work focuses on chloroquine (CQ), a 4-aminoquinoline antiplasmodial whose effectiveness is now hampered by evolved parasite resistance. It is accepted that CQ interferes with a crucial detoxification process of the parasite [1], namely the inhibition of heme bio-crystallization, but several details of this process still remain rather obscure. In the acidic digestive vacuole of Plasmodium, CQ is supposed to interact in its diprotonated form directly with the monomeric heme in two possible ways: 1) π-π stacking interactions between quinoline ring and heme proto-porphyrin [2] or 2) a direct Fe-N quinoline coordinative bond, supported by strong charge-assisted hydrogen bonds (CAHBs) between the tertiary amine of CQ and the propionate groups of heme [3-4].
In this work, the self-recognition of chloroquine diphosphate dihydrate salt was studied both theoretically and experimentally. High-resolution single crystal X-ray data were collected at low temperature (103 K) and complemented by quantum simulations with CRYSTAL14 [5] at the B3LYP/6-31G(p,d) theory level. The salt crystalizes in a P21/c structure, with phosphate ions forming infinite chains parallel to the b axis. CQ molecules and phosphates are connected through strong N-H•••O CAHBs, while a π-π interaction is present between the quinoline rings (see figure).
The topological analysis of the primary charge density, performed according with the Quantum Theory of Atoms in Molecules [6], along with the ab-initio energy decomposition, show that the coulombic interactions between the charged hydrocarbon chain of CQ and the phosphate ions seem to provide the dominant features in the molecular self-recognition, while the π-π stacking between the quinoline moieties has just an ancillary role. These evidences suggest that, in agreement with our previous DFT/EXAFS results [3], the protonated tertiary amine of CQ is an essential component of the drug pharmacophore.
[1] A. F. G. Slater, W. J. Swiggard, B. R. Orton, W. D. Flitter, D. E. Goldberg. A. Cerami and G. B. Henderson, Proc. Natl. Acad. Sci. USA 1991, 88, 325
[2] M. S. Walckzak, K. Lawniczak-Jablonska, A. Wolska, A. Sienkiewicz, L. Suarez, A. J. Kosar and D. S. Bohle, J. Phys. Chem. B 2011, 115, 1145
[3] G. Macetti, S. Rizzato, F. Beghi, L. Silvestrini and L. Lo Presti, Physica Scripta 2016, 91, 023001
[4] A. C. De Dios, R. Tycko, L. M. B. Ursos and P. D. Roepe, J. Phys. Chem. A 2003, 107, 5821
[5] R. Dovesi, V. R. Saunders, C. Roetti, R. Orlando, C. M. Zicovich-Wilson, F. Pascale, B. Civalleri, K. Doll, N. M. Harrison, I. J. Bush, P. D’Arco, M. Llunell, M. Causà and Y. Noël, CRYSTAL14 2014 CRYSTAL14 User's Manual. University of Torino, Torino
[6] R. F. W. Bader, Atoms in molecules. A quantum theory 1990, Oxford University Press. Oxford, U.K
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