Mercedes Alonso

Understanding the Fundamental Role of π/π, σ/σ, and σ/π Dispersion Interactions in Shaping Carbon‐Based Materials

Noncovalent interactions involving aromatic rings, such as π-stacking and CH/π interactions, are central to many areas of modern chemistry. However, recent studies proved that aromaticity is not required for stacking interactions, since similar interaction energies were computed for several aromatic and aliphatic dimers. Herein, the nature and origin of π/π, σ/σ, and σ/π dispersion interactions has been investigated by using dispersion-corrected density functional theory, energy decomposition analysis, and the recently developed noncovalent interaction (NCI) method. Our analysis shows that π/π and σ/σ stacking interactions are equally important for the benzene and cyclohexane dimers, explaining why both compounds have similar boiling points. Also, similar dispersion forces are found in the benzene⋅⋅⋅methane and cyclohexane⋅⋅⋅methane complexes. However, for systems larger than naphthalene, there are enhanced stacking interactions in the aromatic dimers adopting a parallel-displaced configuration compared to the analogous saturated systems. Although dispersion plays a decisive role in stabilizing all the complexes, the origin of the π/π, σ/σ, and σ/π interactions is different. The NCI method reveals that the dispersion interactions between the hydrogen atoms are responsible for the surprisingly strong aliphatic interactions. Moreover, whereas σ/σ and σ/π interactions are local, the π/π stacking are inherently delocalized, which give rise to a non-additive effect. These new types of dispersion interactions between saturated groups can be exploited in the rational design of novel carbon materials.

A universal scale of aromaticity for π‐organic compounds

Aromaticity is an essential concept in chemistry, invented to account for the stability, reactivity, molecular structure, and properties of many organic and inorganic compounds. In recent years, numerous methods to quantify aromaticity based on the energetic, magnetic, structural, and electronic properties of molecules have been proposed but none of them is universal. The inability of establishing a universal scale of aromaticity based on a single parameter is due to the multidimensional character of this phenomenon. Consequently, aromaticity analyses should be carried out by employing a set of aromaticity descriptors on the basis of different physical manifestations of aromaticity. Here, we report a universal scale of aromaticity for π‐organic compounds based on the Euclidean distance between neurons in a self‐organizing map. The most widely used aromaticity indicators have been used as molecular descriptors, and so our approach provides the first scale of aromaticity which contains the energetic, magnetic, and structural aspects of this property. The method is applicable to a wide variety of unsaturated organic compounds and allows quantification of both aromaticity and antiaromaticity. Additionally, the position of a compound on the bidimensional map determinates immediately the following: (a) the group (aromatic, nonaromatic, or antiaromatic) to which the system belongs, (b) their degree of π‐electronic delocalization, and (c) the similarity in aromaticity/antiaromaticity between different compounds. This new scale of aromaticity is able to indicate the expected order of aromaticity of analogues of fulvene and heptafulvene, heteroaromatic species, substituted benzenes, and functionalized cyclopentadienyl compounds.

Viability of Möbius Topologies in [26]‐ and [28]Hexaphyrins

Recently, hexaphyrins have emerged as a promising class of π-conjugated molecules that display a range of interesting electronic, optical, and conformational properties, including the formation of stable Möbius aromatic systems. Besides the Möbius topology, hexaphyrins can adopt a variety of conformations with Hückel and twisted Hückel topologies, which can be interconverted under certain conditions. To determine the optimum conditions for viable Möbius topologies, the conformational preferences of [26]- and [28]hexaphyrins and the dynamic interconversion between the Möbius and Hückel topologies were investigated by density functional calculations. In the absence of meso substituents, [26]hexaphyrin prefers a planar dumbbell conformation, strongly aromatic and relatively strain free. The Möbius topology is highly improbable: the most stable tautomer is 33 kcal mol(-1) higher in energy than the global minimum. On the other hand, the Möbius conformer of [28]hexaphyrin is only 6.5 kcal mol(-1) higher in energy than the most stable dumbbell conformation. This marked difference is due to aromatic stabilization in the Möbius 4n electron macrocycle as opposed to antiaromatic destabilization in the 4n+2 electron system, as revealed by several energetic, magnetic, structural, and reactivity indices of aromaticity. For [28]hexaphyrins, the computed activation barrier for interconversion between the Möbius aromatic and Hückel antiaromatic conformers ranges from 7.2 to 10.2 kcal mol(-1), in very good agreement with the available experimental data. The conformation of the hexaphyrin macrocycle is strongly dependent on oxidation state and solvent, and this feature creates a promising platform for the development of molecular switches.

Activation of the aryl hydrocarbon receptor by carbaryl: Computational evidence of the ability of carbaryl to assume a planar conformation

It has been accepted that aryl hydrocarbon receptor (AhR) ligands are compounds with two or more aromatic rings in a coplanar conformation. Although general agreement exists that carbaryl is able to activate the AhR, it has been proposed that such activation could occur through alternative pathways without ligand binding. This idea was supported by studies showing a planar conformation of carbaryl as unlikely. The objective of the present work was to clarify the process of AhR activation by carbaryl. In rat H4IIE cells permanently transfected with a luciferase gene under the indirect control of AhR, incubation with carbaryl led to an increase of luminescence. Ligand binding to the AhR was studied by means of a cell-free in vitro system in which the activation of AhR can occur only by ligand binding. In this system, exposure to carbaryl also led to activation of AhR. These results were similar to those obtained with the AhR model ligand beta-naphthoflavone, although this compound exhibited higher potency than carbaryl in both assays. By means of computational modeling (molecular mechanics and quantum chemical calculations), the structural characteristics and electrostatic properties of carbaryl were described in detail, and it was observed that the substituent at C-1 and the naphthyl ring were not coplanar. Assuming that carbaryl would interact with the AhR through a hydrogen bond, this interaction was studied computationally using hydrogen fluoride as a model H-bond donor. Under this situation, the stabilization energy of the carbaryl molecule would permit it to adopt a planar conformation. These results are in accordance with the mechanism traditionally accepted for AhR activation: Binding of ligands in a planar conformation.

A benchmark for the non-covalent interaction (NCI) index or… is it really all in the geometry?

Describing non-covalent interactions (NCIs) has shown to be of paramount importance in many areas of theoretical chemistry and related disciplines, such as biochemistry and material science. However, non-covalent interactions are subtle effects, very difficult to reproduce from most common computational approaches. Electron density studies have shown to provide a good semiquantitative visual approach to such interactions, which are much less prone to method dependency. But to which extent? This is the question addressed in this contribution. The NCI approach based on the reduced density gradient is given the third degree so as to provide the user with a benchmark on how it is affected by the computational method and the basis set of choice. We have assessed the dependence of the NCI results on the geometry. This last question is addressed in detail to dissect how, why and when the NCI method can be used to understand dispersion interactions. Along various examples, we will show that the NCI index is very little dependent on the method and basis set used in the calculation of the electron density as long as the geometry is kept fixed. Indeed, the biggest variations in NCI come from changes in the geometry. Thus, methods which provide descriptions of a given interaction type of different accuracies will yield different electron density organizations. This gives no qualitative variations in the NCI 3D picture. But it is reflected in quantitative NCI measures even in very subtle cases. Moreover, in the case of a failure of the calculation method, NCI can also reveal the sources of its error. NCI volumes are able to locate the energetic ordering in various conformational situations, but always in a relative manner. Absolute values should not be used in comparisons, nor between compounds that do not belong to the same family.

Decabromobiphenyl (PBB-209) Activates the Aryl Hydrocarbon Receptor While Decachlorobiphenyl (PCB-209) Is Inactive : Experimental Evidence and Computational Rationalization of the Different Behavior of Some Halogenated Biphenyls

In rat H4IIE cells permanently transfected with a luciferase gene under the control of AhR, incubation with PBB-209 led to a statistically significant increase of luminescence. In this system, PCB-209 only caused a small induction of luciferase activity. In a fish cell line, only PBB-209 was able to provoke an induction of ethoxyresorufin- O-deethylase activity. Ligand binding to the AhR was studied by means of a cell-free in vitro system in which the activation of AhR is very unlikely to occur without ligand binding. None of the biphenyls studied provoked any activation of AhR in this system. To rationalize the results and to get insight into the molecular mechanism of activation of AhR by PBB-209 as compared with PCB-209, a comprehensive computational study was carried out on these congeners as well as on PCB-126 and PCB-169, two potent AhR activators through ligand binding. The calculations include (i) conformational analysis and dipole moments of each conformer, (ii) aromaticity indices, (iii) molecular electrostatic potentials, (iv) quadrupole moments, (v) electronic and reactivity descriptors, and (vi) dissociation energies of C-Cl and C-Br bonds in model aromatic compounds. It was found that some molecular features of PBB-209, such as the electrostatic potential (EP) and EP-derived descriptors (Politzers parameters), indicate that PBB-209 is more similar to PCB-126 and PCB-169 than to PCB-209, which share quite similar geometries based on the substitution pattern. The similarity between PBB-209, PCB-126, and PCB-169 seems to hint that these three compounds can share, at least partially, similar mechanisms of activation of AhR. It is unquestionable that PCB-126 and PCB-169 directly bind AhR and PBB-209 does not. We hypothesize that there are several simultaneous mechanisms for activation of AhR, and the most active compounds act for more than one mechanism.

Hydrosilylation Induced by N→Si Intramolecular Coordination: Spontaneous Transformation of Organosilanes into 1‐Aza‐Silole‐Type Molecules in the Absence of a Catalyst

Our attempts to synthesize the N→Si intramolecularly coordinated organosilanes Ph2 L(1) SiH (1 a), PhL(1) SiH2 (2 a), Ph2 L(2) SiH (3 a), and PhL(2) SiH2 (4 a) containing a CH=N imine group (in which L(1) is the C,N-chelating ligand {2-[CH=N(C6 H3 -2,6-iPr2)]C6 H4}(-) and L(2) is {2-[CH=N(tBu)]C6 H4}(-)) yielded 1-[2,6-bis(diisopropyl)phenyl]-2,2-diphenyl-1-aza-silole (1), 1-[2,6-bis(diisopropyl)phenyl]-2-phenyl-2-hydrido-1-aza-silole (2), 1-tert-butyl-2,2-diphenyl-1-aza-silole (3), and 1-tert-butyl-2-phenyl-2-hydrido-1-aza-silole (4), respectively. Isolated organosilicon amides 1-4 are an outcome of the spontaneous hydrosilylation of the CH=N imine moiety induced by N→Si intramolecular coordination. Compounds 1-4 were characterized by NMR spectroscopy and X-ray diffraction analysis. The geometries of organosilanes 1 a-4 a and their corresponding hydrosilylated products 1-4 were optimized and fully characterized at the B3LYP/6-31++G(d,p) level of theory. The molecular structure determination of 1-3 suggested the presence of a Si-N double bond. Natural bond orbital (NBO) analysis, however, shows a very strong donor-acceptor interaction between the lone pair of the nitrogen atom and the formal empty p orbital on the silicon and therefore, the calculations show that the Si-N bond is highly polarized pointing to a predominantly zwitterionic Si(+) N(-) bond in 1-4. Since compounds 1-4 are hydrosilylated products of 1 a-4 a, the free energies (ΔG298), enthalpies (ΔH298), and entropies (ΔH298) were computed for the hydrosilylation reaction of 1 a-4 a with both B3LYP and B3LYP-D methods. On the basis of the very negative ΔG298 values, the hydrosilylation reaction is highly exergonic and compounds 1 a-4 a are spontaneously transformed into 1-4 in the absence of a catalyst.

Conformational Control in [22]- and [24]Pentaphyrins(1.1.1.1.1) by Meso Substituents and their N-Fusion Reaction

meso-Substituted pentaphyrins(1.1.1.1.1) were unexpectedly isolated as N-fused species under Rothemund-type conditions. The reaction mechanism is unknown at present, but the first example of a nonfused [22]pentaphyrin was reported in 2012. Here, the conformational preferences and N-fusion reaction of [22]- and [24]pentaphyrins have been investigated using density functional calculations, together with their aromaticity-molecular topology relationships. Two global minima are found for the unsubstituted [22]pentaphyrin corresponding to T0 and T0(4,D) Hückel structures. Möbius transition states are located in the interconversion pathways with activation barriers of 27 kcal mol(-1). Conversely, [24]pentaphyrin is able to switch between Hückel and Möbius conformers with very low activation barriers. However, nonfused [24]pentaphyrins are unstable and spontaneously undergo an N-fusion reaction driven by the strain release. On the contrary, nonfused [22]pentaphyrins could be isolated if a T0(4,D) conformation is adopted. Importantly, conformational control of pentaphyrins can be achieved by meso-substituents. Two stable conformations (T0(4,D) and T0(A,D)) are found for the nonfused [22]pentaphyrin, which are delicately balanced by the number of substituents. The T0(A,D) conformation is preferred by fully meso-aryl pentaphyrins, which is converted to the N-fused species. Interestingly, the removal of one aryl group prevents the N-fusion reaction, providing stable aromatic nonfused [22]pentaphyrins in excellent agreement with the experimental results.

Chemical applications of neural networks: aromaticity of pyrimidine derivatives

Neural networks are computational tools able to apprehend non-linear relationships between different parameters, having the capacity to order a large amount of input data and transform them into a graphical pattern of output data. We have previously reported their use for the quantification of the aromaticity through the Euclidean distance between neurons. In this article, we apply the method to a variety of pyrimidine derivatives with electron-donor and electron-withdrawing groups as substituents, with capacity to produce push-pull compounds. We have calculated the aromaticity of benzene (as a reference molecule), parent pyrimidine and other 11 pyrimidine derivatives having amino, dimethylamino and tricyanovinyl substitution. The neural network has been generated using ASE, Λ, NICS(zz)(1) and HOMA as aromaticity descriptors, since our previous work showed that the combination of these indices provided the best performance of the network. On studying the influence of the substituent on the aromaticity of the molecule, we have found that, opposite to benzene derivatives, all the substituents decrease the aromaticity of the ring. The interplay between aromaticity, planarity and push-pull properties of all the substituted pyrimidines has also been addressed. An interesting feature of the neural network to quantify aromaticity is that the importance of the reference reaction used to evaluate energy stabilization and magnetic susceptibility exaltation is minimized.

Stibinidene and Bismuthinidene as Two‐electron Donors for Transition Metals (Co and Mn).

The reaction of stibinidene and bismuthinidene ArM [where Ar=C6 H3 -2,6-(CH=NtBu)2 ; M=Sb (1), Bi (2)] with transition metal (TM) carbonyls Co2 (CO)8 and Mn2 (CO)10 produced unprecedented ionic complexes [(ArM)2 Co(CO)3 ](+) [Co(CO)4 ](-) and [(ArM)2 Mn(CO)4 ](+) [Mn(CO)5 ](-) [where M=Sb (3, 5), Bi (4, 6)]. The pnictinidenes 1 and 2 behaved as two-electron donors in this set of compounds. Besides the M→TM bonds, the topological analysis also revealed a number of secondary interactions contributing to the stabilization of cationic parts of titled complexes.