Jordi Poater

On the performance of some aromaticity indices: a critical assessment using a test set.

Aromaticity is a central chemical concept widely used in modern chemistry for the interpretation of molecular structure, stability, reactivity, and magnetic properties of many compounds. As such, its reliable prediction is an important task of computational chemistry. In recent years, many methods to quantify aromaticity based on different physicochemical properties of molecules have been proposed. However, the nonobservable nature of aromaticity makes difficult to assess the performance of the numerous existing indices. In the present work, we introduce a series of fifteen aromaticity tests that can be used to analyze the advantages and drawbacks of a group of aromaticity descriptors. On the basis of the results obtained for a set of ten indicators of aromaticity, we conclude that indices based on the study of electron delocalization in aromatic species are the most accurate among those examined in this work.

A Critical Assessment of the Performance of Magnetic and Electronic Indices of Aromaticity

Abstract: The lack of reference aromatic systems in the realm of inorganic aromatic compounds makes the evaluation of aromaticity in all-metal and semimetal clusters a difficult task. To date, calculation of nucleus-independent chemical shifts (NICS) has been the most widely used method to discuss aromaticity in these systems. In the first part of this work, we briefly review our previous studies, showing some pitfalls of the NICS indicator of aromaticity in organic molecules. Then, we refer to our study on the performance of some aromaticity indices in a series of 15 aromaticity tests, which can be used to analyze the advantages and drawbacks of aromaticity descriptors. It is shown that indices based on the study of electron delocalization are the most accurate among those analyzed in the series of proposed tests, while NICS(1) zz and NICS(0) πzz present the best behavior among NICS indices. In the second part, we discuss the use of NICS and electronic multicenter indices (MCI) in inorganic clusters. In particular, we evaluate the aromaticity of two series of all-metal and semimetal clusters with predictable aromaticity trends by means of NICS and MCI. Results show that the expected trends are generally better reproduced by MCI than NICS. It is concluded that NICS(0)

π Aromaticity and Three‐Dimensional Aromaticity: Two sides of the Same Coin?

A bridge between classical organic polycyclic aromatic hydrocarbons (PAH) and closo borohydride clusters is established by showing that they share a common origin regulated by the number of valence electrons in an electronic confined space. Application of the proposed electronic confined space analogy (ECSA) method to archetypal PAHs leads to the conclusion that the 4n+2 Wade-Mingos rule for three-dimensional closo boranes is equivalent to the (4n+2)π Hückel rule for two-dimensional PAHs. More importantly, use of ECSA allows design of new interesting fused closo boranes which can be a source of inspiration for synthetic chemists.

On the electron-pair nature of the hydrogen bond in the framework of the atoms in molecules theory

Delocalization indices, as defined in the atoms in molecules theory, have been calculated between hydrogen-bonded atoms in 20 molecular complexes that are formed between several H-donor and acceptor molecules. In general, the delocalization index associated to an intermolecular hydrogen bond depends on the interaction energy of the complex, but also on the nature of the H-donor and acceptor atoms. The intermolecular delocalization index appears to be strongly correlated to the orbital interaction energy term as obtained from an energy decomposition scheme based on conceptual Kohn–Sham theory. Both the atoms in molecules theory and the energy decomposition analysis allow for a characterization of the hydrogen bonds in these complexes. In general, both kinds of analysis reveal that hydrogen bonding in these systems is not an essentially electrostatic interaction. 2003 Elsevier Science B.V. All rights reserved.

Modeling the structure‐property relationships of nanoneedles: A journey toward nanomedicine

Innovative biomedical techniques operational at the nanoscale level are being developed in therapeutics, including advanced drug delivery systems and targeted nanotherapy. Ultrathin needles provide a low invasive and highly selective means for molecular delivery and cell manipulation. This article studies the geometry and the stability of a family of packed carbon nanoneedles (CNNs) formed by units of 4, 6, and 8 carbons, by using quantum chemistry computational modeling methods. At the limit of infinite‐length, these CNNs might act as semiconductors, especially when the number of terminal units is increased. CNNs are also potentially able to stabilize ions around their structure. Therefore, due to the apolar characteristics of CNNs and their ability to carry ionic species, they would be suitable to act as drug carriers through nonpolar biologic media.

Nuclear magnetic resonance chemical shifts with the statistical average of orbital-dependent model potentials in Kohn–Sham density functional theory

In this paper, an orbital-dependent Kohn–Sham exchange-correlation potential, the so-called statistical average of (model) orbital potentials, is applied to the calculation of nuclear magnetic resonance chemical shifts of a series of simple molecules containing H, C, N, O, and F. It is shown that the use of this model potential leads to isotropic chemical shifts which are substantially improved over both local and gradient-corrected functionals, especially for nitrogen and oxygen atoms. This improvement in the chemical shift calculations can be attributed to the increase in the gap between highest occupied and lowest unoccupied orbitals, thus correcting the excessively large paramagnetic contributions, which have been identified to give deficient chemical shifts with both the local-density approximation and with gradient-corrected functionals. This is in keeping with the improvement by the statitical average of orbital model potentials for response properties in general and for excitation energies in part...

Selectivity in DNA replication. Interplay of steric shape, hydrogen bonds, π-stacking and solvent effects

Our dispersion-corrected DFT computations reveal key factors behind the intrinsic affinity of a DNA template-primer complex to select the correct nucleotide.

An Analysis of the Isomerization Energies of 1,2-/1,3- Diazacyclobutadiene, Pyrazole/Imidazole, and Pyridazine/Pyrimidine with the Turn-Upside-Down Approach

The isomerization energies of 1,2- and 1,3-diazacyclobutadiene, pyrazole and imidazole, and pyridazine and pyrimidine are 10.6, 9.4, and 20.9 kcal/mol, respectively, at the BP86/TZ2P level of theory. These energies are analyzed using a Morokuma-like energy decomposition analysis in conjunction with what we have called turn-upside-down approach. Our results indicate that, in the three cases, the higher stability of the 1,3-isomers is not due to lower Pauli repulsions but because of the more favorable σ-orbital interactions involved in the formation of two C-N bonds in comparison with the generation of C-C and N-N bonds in the 1,2-isomers.

Examining the Planarity of Poly(3,4-ethylenedioxythiophene): Consideration of Self-Rigidification, Electronic, and Geometric Effects

The intramolecular interactions responsible for the planarity observed in poly(3,4-ethylenedioxythiophene) and small 3,4-ethylenedioxythiophene-containing oligomers have been investigated using quantum mechanical methods. Specifically, the relative influence of electron-donating effects, pi-conjugation, and geometric restrictions induced by the cyclic substituent and attractive S...O intramolecular noncovalent interactions, which were proposed to be the most relevant factor for such planarity on the self-rigidification observed in these compounds, have been examined considering a wide number of model compounds. Results evidenced that noncovalent S...O interactions, which were postulated on the basis that the nonbonded distances between sulfur and oxygen atoms belonging to neighboring repeating units are significantly shorter than the sum of the van der Waals radii of sulfur and oxygen, are slightly repulsive destabilizing the planar anti conformation. In contrast, the latter arrangement is favored by the pi-conjugation produced by both geometric restrictions imposed by the cyclic substituent and the electron-donating effects provided by the oxygen atoms attached to positions three and four of each tiophene ring. Therefore, these factors produce gain in aromaticity and favorable electrostatic interactions when the planarity is reached, compensating the Pauli repulsions between the shared electron pairs of the sulfur and oxygen atoms.

Analysis of the Effects of N-Substituents on Some Aspects of the Aromaticity of Imidazoles and Pyrazoles

The influence of the N-substituent on the aromaticity of azoles is a subject that has not yet been addressed in detail, in contrast to the good understanding of the corresponding C-substitution. In the present work, we analyze the aromaticities of a series of 1,2- and 1,3-azoles (pyrazoles and imidazoles, respectively) with the N-substituents NH(2), OH, Cl, SH, H, NO(2), CN, SO(2)F, SO(2)CF(3), and N(SO(2)CF(3))(2), which are also compared with the aromaticities of the corresponding substituted benzene series. The larger stabilitiy of the imidazole ring is due not to a higher aromaticity, but rather to the weakness of the N-N bond in the pyrazole series. The aromaticity of azoles was found to be significantly less robust to N-substitutions than that of their C-substituted benzene counterparts.