1,721,145 research outputs found
Using X-ray derived charge densities to detect electron delocalization effects and non-covalent interactions
No full textBeing based on a quantum observable and measurable quantity, the Electron Density (ED) based descriptors retain the advantage of enabling a direct comparison of theoretical predictions with experimental results. We review here our most recent work aimed at evaluating whether two of such descriptors, the Source Function, SF, [1] and the Reduced Density Gradient (RDG), are able to unveil electron delocalization effects (EDEs) and non covalent interactions (NCI), respectively.
Making use of ab-initio EDs, we recently proved that the SF clearly detects EDEs in a series of supposedly electron-conjugated compounds [2]. That study is here extended to molecular crystals (benzene, a substituted binaphtyl-2-ol, citrinin), whose ED is derived from X-ray diffraction data. Regardless of the ED origin, the SF appears a useful tool to study fine details of EDEs, and independently from any symmetry constraint (e.g. / separation of the ED).
A novel NCI descriptor, based on the RDG and enabling an easy-to-catch image of either the supposedly attractive (dispersive, hydrogen bonding) or allegedly repulsive (steric) interactions, was recently proposed [3]. We have applied [4] this same tool to experimentally-derived ED’s of molecular solids (austdiol, benzene, famotidine), and discussed its performance in synergy with Bader’s analysis. We have also explored [5] the amount and type of information that is lost when the IAM replaces the “true” ED in evaluating the RDG.
References
[1] R.F.W. Bader, C. Gatti, Chem. Phys. Lett. 287 (1998) 233-238.
[2] E. Monza, C. Gatti, L. Lo Presti, E. Ortoleva, J. Phys. Chem. A 115 (2011) 12864-12878.
[3] E.R. Johnson, S. Keinan, P. Mori-Sanchez, J. Contreras-Garcia JACS 132 (2010), 6498.
[4] G. Saleh, C. Gatti, L. Lo Presti, J. Contreras-Garcia, submitted (2012)
[5] G. Saleh, C. Gatti, L. Lo Presti, submitted (2012
New descriptors for an “unbiased” and chemically insightful comparison of ab-initio and X-ray derived charge densities
No full textThe results of modelling always need to be compared and validated against the experiment. To be meaningful, the comparison should be as much as possible unbiased, and, hopefully, should use tools also able to provide chemical insight. Being based on a quantum observable and measurable quantity, the Electron Density (ED) based descriptors enable a direct comparison of ab-initio and X-ray derived EDs. They also provide a description of chemical paradigms which is, in principle, freed at the outset from any model preconception or arbitrariness. Furthermore, as for their nature rooted in physics, they are ideally suited to validate or reject the interpretive models of chemistry based on useful, but arbitrary objects. In this lecture, we will discuss the capability of two of such descriptors, the Source Function (SF) [1] and the Reduced Density Gradient (RDG), to unveil electron delocalization effects and to detect non covalent interactions, respectively. The SF enables one to view chemical bonding and other chemical paradigms under a new perspective [1,2]. We recently addressed the question of whether the SF is also capable to reveal electron delocalization effects (EDEs) in a series of supposedly electron-conjugated compounds, investigated through ab-initio methods [2]. The study is here extended to various molecular crystals (benzene, naphtalene and a substituted binaphtyl-2-ol), whose ED and SF results were obtained from X-ray diffraction data. Regardless of the derivation of the ED, the answer to the question above is convincingly positive. The capability of the SF to reveal EDEs is independent from a / separation and EDEs may be recovered even when such separation is unfeasible or when symmetry reasons would preclude it. Use of the SF to test the concept of hypervalency in the K2SO4 crystal [4] will also be discussed. A novel non covalent interaction (NCI) descriptor, based on the RDG and enabling an easy-to-catch pictorial visualization of either the supposedly attractive (dispersive, hydrogen bonding) or allegedly repulsive (steric) intermolecular interactions, was recently developed [5]. We apply for the first time [6] this same tool to experimentally-derived ED’s of molecular solids (austdiol, benzene, famotidine) discussing its performance in synergy with Bader’s analysis and using our software code, NCI-Milano [7], purposedly developed for such an extension.
[1] R.F.W. Bader, C. Gatti Chem Phys. Lett. 1998, 287, 233-238.
[2] C. Gatti Struct. Bond. 2012, 147, 193-286.
[3] E. Monza, C. Gatti, L. Lo Presti, E. Ortoleva J. Phys. Chem. A 2011, 115, 12864-12878.
[4] M.S. Schmøkel, S. Cenedese, J. Overgaard, M.R.V. Jørgensen, Y-S Chen, C. Gatti, D. Stalke, B.B. Iversen Inorg. Chem. 2012, 51, 8607-8616.
[5] E.R. Johnson, S. Keinan, P. Mori-Sanchez, J. Contreras-Garcia, A.J. Cohen, W. Yang J. Am. Chem. Soc 2010, 132, 6498-6506.
[6] G. Saleh, C. Gatti, L. Lo Presti, J. Contreras-Garcia Chem. Eur. J. 2012,18,15523-15536.
[7] G. Saleh, L. Lo Presti, C. Gatti, D. Ceresoli J. Appl. Cryst. 2013, 46, 1513-1517
Progettazione di nuovi materiali per l'abbattimento di inquinanti : Come proteggere i nostri monumenti
No full textSi illustra una parte dei risultati del progetto LISA 2013 di cui M. Ceotto è il PI. Co-PI L. Lo Presti e D. Tamascelli
Can electron delocalization be revealed through the Source Function?
No full textThe Source Function (SF) [1,2] enables one to view chemical bonding and other chemical paradigms under a new perspective and using only information from the electron density observable, rho, and its derivatives. Being completely independent from the tools used to get rho, the SF represents a very useful descriptor, able in many cases to bridge the gap between the rich information ine gains from an ab-initio wavefunction of an ideal system and that, quite often more limited, but referred to a real system, obtained from an experimental rho derived from X-ray diffraction data.
The potential uses of SF are, however, not fully explored. In this lecture we discuss our recent work where the question of wheter the SF is or not capable to reveal electron delocalization has been addressed [3,4].
[1] R. F. W. Bader, C. Gatti, Chem. Phys. Lett. 1998, 287, 233-238. [2] C. Gatti, C. Cargnoni et al., J. Comput. Chem. 2003, 24, 422-436. [3] C. Gatti, Struct. Bond. 2011, 1, DOI: 10.1007/430_2010_31 [4] E. Monza, C. Gatti, L. Lo Presti, E. Ortoleva, J. Phys. Chem. Article ASAP DOI: 10.1021/jp204000d, Richard Bader's Festchrifte issu
Experimental and theoretical charge density study of an antimalarial drug
No full textMalaria, an infection caused by the Plasmodium Falciparum protozoa, is nowadays one of the most lethal parasitic disease. As the Plasmodium protozoon is becoming resistant to quinoline-based molecules, the development of new drugs and the understanding of the key chemical features for their activity and of their mechanism of action is of great importance. In this context, we carried out a thorough analysis on the antimalarial drug dihydroartemisinin (DHA, Figure 1), through the study of its experimental and theoretical charge density (CD) distributions.[1]
The experimental CD has been obtained by a single-crystal X-ray diffraction experiment at T = 100 K on a Bruker SMART APEX II diffractometer equipped with a CCD area detector, while the corresponding theoretical CD has been derived through fully periodic single point DFT calculations at the experimental geometry.
We have identified nucleophilic as well as electrophilic regions of the molecule by analyzing its electrostatic potential and investigated the crystal packing and the change in the CD distribution moving from the isolated molecule to the crystal. Several CD analysis tools, with special emphasis on the Quantum Theory of Atoms in Molecules (QTAIM) [2], have been adopted, with the aim of fully characterize the chemical nature of specific functional groups, such as the peroxide group and the polyether chain.
We have also performed geometry optimizations on deprotonated and radical anion of DHA, the latter being the intermediate species in most of the proposed antimalarial modes of action of the drug.
[1] G. Saleh, R. Soave, L. Lo Presti, R. Destro Chem. Eur. J. 2013, 19, 3490.
[2] R. F. W. Bader Atoms in Molecules: A Quantum Theory Oxford University Press, Oxford, 1990
Simulation of aggregation phenomena in solution
Full text linkHow does crystallization begin? An answer to this apparently simple question is out of reach for current experimental techniques, which are blind to transient supramolecular aggregates that may occur in the no man’s land between a homogeneous liquid state and a suspension of crystal nuclei. Despite an increasing understanding of the thermodynamics of crystallization in the framework of Classical and Multi-Step nucleation theories, a predictive theory of nucleation has never been developed so far.
Classical Molecular Dynamics can shed light on the events that initiate aggregation phenomena, as in principle it can simulate the very elementary acts that lead to nucleation. The recently developed MiCMoS platform , provides several flexible and cheap tools to investigate small organic molecules in condensed phase. MiCMoS relies on accurately calibrated intermolecular force fields and was successfully applied to investigate several systems, including liquids, crystals, nanodroplets and nanoparticles . In this contribution, the implementation of a biased Molecular Dynamics algorithm to speed up the self-recognition process is reported. The procedure is employed to probe pre-nucleation aggregation phenomena in solutions of benzoic acid, selected as a suitable test case. The algorithm is already available in the most recent release MiCMoS v2.0, which can be downloaded for free at https://sites.unimi.it/xtal_chem_group/index.php/research/5-micmos
Segnali dall'invisibile : una breve storia della diffrazione
No full textLa diffrazione di raggi X è oggi uno strumento preziosissimo per studiare l'intima struttura della materia. Nel seminario 'Segnali dall'invisibile: una breve storia della diffrazione' ripercorreremo insieme la storia, affascinante e a tratti avventurosa, che ha portato questa tecnologia dalle prime, pioneristiche scoperte del '600 fino all'avvento dei moderni sincrotroni. Come vedremo, si è trattato di un percorso non sempre lineare, ma che ha dato un importante contributo nel risolvere problemi antichissimi, quali la natura della luce e la struttura atomica della materia
CLPdyn: a cheap and reliable tool for molecular dynamics studies of organic molecules in condensed phase
Full text linkWe present CLPdyn, a freely available code intended to perform Molecular Dynamics simulations of organic molecules in condensed phase.[1–3] CLPdyn can handle both continuous phases (liquids, crystals) and finite-size clusters (liquid droplets, nanoparticles), and exploits the thoroughly tested Coulomb-London-Pauli atom-atom intermolecular potential[4,5]. The implementation relies on standard MD algebra, but also includes new algorithms, specifically designed to deal with isolated clusters, to (i) suppress net overall translational and rotational momenta, (ii) handle the evaporation of molecules from the cluster surface, and (iii) measure the amount of residual symmetry from the number and kind of isometries present in the cluster. Application to organic solvents (benzene, chloroform, methanol and pyridine) [2] and crystals spanning very different intermolecular recognition patterns (maleic/succinic anhydrides, alanine/glutamic acid, methylurea, 1,4-cyclohexadiene and methyl-2-amino-5-hydroxybenzoate) [3], shows that CLPdyn reliably reproduces macroscopic thermodynamic quantities, and highlights the effect of the relative strengths of intermolecular forces on rotational correlation times, self-diffusion coefficients and pair distribution functions. Possible applications of CLPdyn to the molecular–level study of non–equilibrium solution chemistry, including the early stages of crystal nuclei formation, are also discussed.
[1] A. Gavezzotti, CLPdyn, Monte Carlo and Molecular Dynamics modules, Description and user manual, www.angelogavezzotti.it (2018).
[2] A. Gavezzotti, L. Lo Presti, New J. Chem., 2019,43, 2077-2084.
[3] A. Gavezzotti, L. Lo Presti, in preparation
[4] A. Gavezzotti, New J. Chem. 2011, 35, 1360–1368.
[5] A. Gavezzotti and L. Lo Presti, Crystal Growth Des. 2016, 16, 2952–2962
Using the Source Function descriptor to dampen the multipole model bias in charge density studies from X-ray structure factors refinements
No full textThe Source Function (SF) atomic contributions were evaluated at bond critical points (bcps) for three test
systems, using theoretical electron densities and multipole modelled densities derived from the former projected into structure factors. In general, the SF percentage atomic contributions obtained from the multipole modelled density agree well with those calculated from the corresponding primary density, despite large discrepancies in the electron density and, particularly, in the density Laplacian values occur at bcps. The SF percentage contributions represent a more robust chemical bond descriptor than are other
commonly used bond topological indices which are too sensitive to the multipole model bias
The multipolar model bias on primary densities as revealed by the source function descriptor
No full textThe Source Function (SF), which enables one to equate the value of the electron density rho(r) at any point within a molecule to a sum of atomic contributions, is nowadays being employed by an increasing number of groups as a powerful tool to gain insight into the chemical bond.
As the SF is defined in terms of the Laplacian of rho(r), L(r), one does not need to know the wavefunction to apply it and computation of the SF through the multipole model (MM) electron density obtained from X-ray structure factors appears to be straightforward. However, since the MM is known to bias the primary density8, and the more so its Laplacian L(r), the SF contributions should also be affected to some extent.
The aim of the present work is to critically examine the results obtained by applying the SF to the MM electron density. Three test cases have been considered: exafluorocyclobutene, C4F6, carbon monoxyde, CO, and bis(pentacarbonylmanganese), Mn2(CO)10. The SF contributions at representative bond critical points (bcp's) have been evaluated from both the primary and the MM density, the latter having been computed from a set of theoretical structure factors for ideal crystals of non-interacting molecules. In the case of Mn2(CO)10, the SF contributions have been also compared to those obtained from a set of experimental structure factors9 to reconstruct the MM density (r). We show that the MM results are in general consistent with the theoretical ones, as they should be, with the SF being a quite interesting tool to provide chemical insight, whilst minimizing the MM bias on the primary density. Conversely, significant differences emerge for the SF contributions at the Mn–Mn bcp in Mn2(CO)10, where we demonstrate that the discrepancies between the theoretical and the experimental SF contributions arises from the MM inadequacies. The SF could be a valuable tool to check and improve the quality of the MM currently adopted in experimental studies of organometallic compounds
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