1,721,450 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
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
Insights on spin polarization through the spin density source function
No full textUnderstanding how spin information is transmitted from paramagnetic to non-magnetic centers is crucial in advanced materials research and calls for novel interpretive tools. Herein, we show that the spin density at a point may be seen as determined by a local Source Function for such density, operating at all other points of space [1],[2]. Integration of the local Source over Bader’s quantum atoms measures their contribution in determining the spin polarization at any system’s location. Each contribution may be then conveniently decomposed in a magnetic term due to the magnetic natural orbital(s) density and in a reaction or relaxation term due to the remaining orbitals density [2]. A simple test case, 3B1 water, is chosen to exemplify whether an atom or group of atoms concur or oppose the paramagnetic center in determining a given local spin polarization. Discriminating magnetic from reaction or relaxation contributions to such behaviour strongly enhances chemical insight, though care need to be paid to the large sensitivity of the latter contributions to the level of the computational approach [2]. Comparison of Source Function atomic contributions to the spin density with those reconstructing the electron density at a system’s position, enlightens how the mechanisms which determine the two densities may in general differ and how diverse may be the role played by each system’s atom in determining each of the two densities. These mechanisms reflect the quite diverse portraits of the electron density and electron spin density Laplacians, hence the different local concentration/dilution of the total and (α-β) electron densities throughout the system. Being defined in term of an observable, the Source Function for the spin density is also potentially amenable to experimental determination, as customarily performed for its electron density analogue [3].
[1] C. Gatti et al. Acta Crystallogr. 2014, A70, C281
[2] C. Gatti et al. Chem. Sci. 2015 accepted, DOI: 10.1039/c4sc03988b
[3] C. Gatti, Struct. Bond. 2012, 147, 19
Revealing electron conjugation through an observable
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, ρ, and
its derivatives. Being completely independent from the tools used to
get ρ, the SF represents a very useful descriptor, able in some cases to
bridge the gap between the rich information one 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 ρ derived from
X-ray diffraction data.
The potential uses of the SF are, however, yet not fully explored. In
a preliminary work, we addressed the question of whether the SF is or is
not capable to reveal electron conjugation [3]. Question arose because
of a recent claim [4] according to which “π-electron delocalization in
the benzene ring is not manifest in the SF when the reference point (rp)
- the point at which the atomic sources for its density are calculated
- is taken at the C-C bond critical point (bcp)”. Reasoning behind this
statement is the null contribution from π molecular orbitals (MOs)
to ρ in their nodal plane. However, since σ- and π-distributions are
not independent, but self-consistently interrelated, we conjectured
that some, albeit small, effect of electron conjugation could also be
manifest when the rp lies in the π-nodal plane, even though π-orbitals
do not obviously yield direct contributions to ρ in that plane. Results
on a series of increasingly π-conjugated systems demonstrate that this
is actually the case. By looking at the C-C bcp electron density for
the shortest bond(s) in cyclohexene, cyclohexadiene, benzene, i.e.
those bonds with largest double-bond character, one observes that
both the SF and the SF% contributions of the C atoms other than those
directly involved in such a bond increase with decreasing double bond
character and electron localization of the bond. The enhanced S%
value then becomes largely more evident when analysed using rps for
which the effect of π-electron conjugation takes place directly through
π-electron distribution rather than, indirectly, through σ-π electron
interdependency. In this work, the analysis is extended to more complex systems,
formed by more than one ring, with fully conjugated or partially
interrupted sequence of formal double-bonds and with planar or non
planar geometry. In the case of benzene, the analysis is also performed
on a ρ derived through multipole refinement of a set of X-ray diffraction
data taken on a benzene molecular crystal. In the inspected cases and
regardless of the theoretical or experimental origin of ρ, the SF reveals
capable to detect electron conjugation. Such an ability is independent
from a σ and π separation of ρ, since the SF tool was applied to the total
ρ. This observation is important in view of the possibility to recover
electron conjugation effects using both ρ’s derived experimentally
(hence without σ and π separation being allowed) and ρ’s where
the departure from symmetry inhibits a proper separation of σ and π
contributions. Using a MO approach, the σ and π contributions to the
SF values can also be revealed and quantified. [1] R.F.W. Bader, C. Gatti, Chem Phys Lett 1998, 287, 233-238. [2] C. Gatti,
F. Cargnoni et al., J Comput Chem 2003 24, 422-436. [3] C. Gatti, Struct Bond
2011 [4] L.J. Farrugia, P. Macchi, J. Phys. Chem. 2009, A113, 10058-10067
Immediate loading of dental implants placed in revascularized fibula free flaps: a clinical report on 2 consecutive patients
No full textThe objective of this study was to report the clinical outcome of dental implants placed in revascularized fibula flaps for the reconstruction of severely atrophied edentulous maxillae and immediately loaded with full-arch implant-supported prostheses
Immediate loading of Brånemark implants: a 24-month follow-up of a comparative prospective pilot study between mandibular overdentures supported by Conical transmucosal and standard MK II implants
No full textThe purpose of this prospective study is to compare the long-term outcome of immediately loaded implant-retained mandibular overdentures supported by four screw-type one-piece transmucosal implants with that of four screw-type two-piece implants inserted in the interforaminal area of the mandible and rigidly connected by a U-shaped curve
Implant-retained mandibular overdentures with immediate loading: a 3- to 8-year prospective study on 328 implants
No full textThe purpose of this study is to evaluate prospectively survival and success rates of implants placed in the interforaminal area of edentulous mandibles and immediately loaded with an implant-supported overdenture
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
- …
