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Jordi Poater

Publications and source records attributed to Jordi Poater.

At least 19 recordsLinked to original sources
PubMed2006

Local aromaticity in natural nucleobases and their size-expanded benzo-fused derivatives.

The influence of the insertion/addition of a benzene ring to the natural nucleic acid bases on the local aromaticity of the so-called size-expanded (xN, with N being adenine, guanine, cytosine, and thymine) bases is examined. To this end, the local aromaticity of the six- and five-membered rings in both the natural bases and their benzoderivatives is determined using HOMA, NICS, aromatic fluctuation index (FLU), and para-delocalization index (PDI) descriptors. In general, there is a good correspondence between the different indices, so that ring moieties with more negative NICS values also have larger HOMA and PDI measures and lower FLU indices. The results also point out notable differences in the aromatic character of the natural and size-expanded bases, which generally are hardly affected upon hydrogen bonding. The differences in the highest occupied molecular orbital-lowest unoccupied molecular orbital (HOMO-LUMO) gap determined for the size-expanded nucleobases show an inverse correlation with the aromaticity of the fused benzene ring, so that the larger the HOMO-LUMO gap is, the lower the destabilization experienced by the benzene upon insertion/addition to the natural bases. This finding suggests that the introduction of suitable chemical modifications in the benzene ring might be useful to modulate the HOMO-LUMO gap while enabling the design of modified DNA duplexes that are able to act as molecular wires.

Adenine↗
PubMed2006

Analysis of electron delocalization in aromatic systems: individual molecular orbital contributions to para-delocalization indexes (PDI).

Our research group has recently defined two new aromaticity indexes based on the analysis of electron delocalization in aromatic species using the quantum theory of atoms-in-molecules. One of these indexes is the para-delocalization index (PDI) that measures the electronic delocalization between para-related carbon atoms in six-membered rings. In this paper, we show that this index can be partitioned into individual molecular orbital contributions. We have applied this PDI decomposition to several polycyclic aromatic hydrocarbons showing that this partitioning provides new insight into the origin of aromaticity.

Journal Article↗
PubMed2006

Bonding in methylalkalimetals (CH(3)M)(n) (M = Li, Na, K; n = 1, 4). Agreement and divergences between AIM and ELF analyses.

The chemical bonding in methylalkalimetals (CH(3)M)(n)() (M = Li-K; n = 1, 4) has been investigated by making use of topological analyses grounded in the theory of atoms in molecules (AIM) and in the electron localization function (ELF). Both analyses describe the C-M bond as an ionic interaction. However, while AIM diagnoses a decrease of ionicity with tetramerization, ELF considers tetramers more ionic. Divergences emerge also when dealing with the bonding topology given by each technique. For the methylalkalimetal tetramers, the ELF analysis shows that each methyl carbon atom interacts through a bond pair with each of the three hydrogen atoms belonging to the same methyl group and through an ionic bond with the triangular face of the tetrahedral metal cluster in front of which the methyl group is located. On the other hand, the AIM topological description escapes from the traditional bonding schemes, presenting hypervalent carbon and alkalimetal atoms. Our results illustrate that fundamental concepts, such as that of the chemical bond, have a different, even colliding meaning in AIM and ELF theories.

Journal Article↗
PubMed2006

Hydrogen-hydrogen bonding in planar biphenyl, predicted by atoms-in-molecules theory, does not exist.

Based on an Atoms-in-Molecules (AIM) analysis, Matta et al. recently claimed evidence for the existence of hydrogen-hydrogen bonding between ortho-hydrogen atoms, pointing towards each other from adjacent phenyl groups in planar biphenyl. This AIM result is opposed to the classical view that nonbonded steric repulsion between the ortho-hydrogen atoms is responsible for the higher energy of the planar as compared to the twisted geometry of biphenyl. In the present work, we address the question if hydrogen-hydrogen bonding in biphenyl exists, as suggested by AIM, or not. To this end, we have analyzed the potential energy surface for internal rotation of biphenyl in terms of two interacting phenyl radicals using density functional theory (DFT) at BP86/TZ2P. A detailed analysis of the bonding mechanism and a quantitative bond energy decomposition in the framework of Kohn-Sham DFT show that Pauli (or overlap) repulsion, mainly between C(ortho)--H(ortho) phenyl MOs, prevents biphenyl from being planar and forces it to adopt a twisted equilibrium geometry. Furthermore, a derivative of biphenyl in which all four ortho-hydrogen atoms have been removed does adopt a planar equilibrium geometry. Thus, our results confirm the classical view of steric repulsion between ortho-hydrogen atoms in biphenyl and they falsify the hypothesis of hydrogen-hydrogen bonding.

Journal Article↗
PubMed2006

A model of the chemical bond must be rooted in quantum mechanics, provide insight, and possess predictive power.

In this response to the preceding paper by Bader, we show that the core arguments and statements presented in the latter are flawed. We argue that it is insufficient for a model of the chemical bond to be rooted in quantum mechanics. A good model must in addition provide insight and possess predictive power. Our molecular orbital (MO) model of the chemical bond, in particular, the associated energy-decomposition approach satisfies all these conditions. On the other hand, Atoms-in-Molecules (AIM) theory is only rooted in quantum mechanics as far as its mathematical framework is concerned. The physical status of its central concepts is not so clear. In particular, "bond paths" and "bond critical points" are once more confirmed not to be indicators of a stabilizing interaction. Moreover, AIM theory lacks any predictive power. We also address specific questions raised in the preceding paper. Finally, interpreting chemical bonding implies choosing a perspective on this phenomenon. That there are many perspectives is a matter of fact and this is in no way unphysical. What is unscientific is to claim uniqueness and truth for one of these choices, namely AIM, and to dismiss on this ground all other approaches.

Comment↗
PubMed2006

Role of electron density and magnetic couplings on the nucleus-independent chemical shift (NICS) profiles of [2.2]paracyclophane and related species.

The nucleus-independent chemical shifts (NICS) and electron density profiles along the inner and outer regions defined by the two stacked aromatic rings of [2.2]paracyclophane have been analyzed and compared to those of free benzene and p-xylene and benzene dimers taken as reference models. It is found that stacked aromatic rings show a reduction of the NICS indicator of aromaticity as compared to the same free aromatic systems. This decrease of the NICS values upon stacking is not due to an increase of the electron density in the inner region between the rings (as claimed in a previous work) but is related to the magnetic couplings between superimposed rings that affect this measure of local aromaticity. The increase of local aromaticity in superimposed aromatic rings indicated by NICS is not real but the result of the coupling between the magnetic fields generated by the two stacked rings. This result warns about the use of NICS as a descriptor of aromaticity for species having superimposed aromatic rings.

Electrons↗
PubMed2005

Aromaticity analysis of lithium cation/pi complexes of aromatic systems.

The changes in the local aromaticity of aromatic rings on complexation with lithium cation are discussed for a series of polycyclic aromatic hydrocarbons by using, as probes of aromaticity, the para-delocalization index (PDI), the aromatic fluctuation index (FLU), the harmonic oscillator model of aromaticity index (HOMA), and the nucleus-independent chemical shift (NICS). In most cases, changes in the electronically based PDI and FLU indices are almost irrelevant. For this reason, the analysis is carried out mainly with the more sensitive HOMA and NICS descriptors. These indices indicate that changes in the local aromatic character of the different rings are small. In general, Li+ interacts more favorably with the ring having the largest pi charge, but there is no correlation between these magnitudes. The ring directly interacting with the lithium cation suffers a slight but significant reduction of aromaticity, while the reduction of the local aromaticity of the adjacent rings is minor. For those rings located further away from the ring directly connected to Li+, we found generally a small increase in aromaticity. Although there is no clear correlation between aromaticity and Li+ binding enthalpies, there is a rough correlation between the latter and the change in the aromaticity of the ring directly interacting with the metal cation.

Journal Article↗
PubMed2005

Local aromaticity of the lowest-lying singlet States of [N]acenes (N = 6-9).

The local aromaticities of the six-membered rings in the two lowest-lying singlet states of [n]acenes (n = 6-9) have been assessed by means of three probes of local aromaticity based on structural, magnetic, and electron delocalization properties. Important differences between the local aromaticities of the closed-shell and diradical singlet electronic states are found. Thus, while the inner rings have the largest aromatic character in the closed-shell singlet states, the outer rings become the most aromatic for the diradical singlet states.

Letter↗
PubMed2005

A trinuclear Pt(II) compound with short Pt-Pt-Pt contacts. An analysis of the influence of pi-pi stacking interactions on the strength and length of the Pt-Pt bond.

In this work we report the first example of a trinuclear Pt(II) complex with Pt-Pt-Pt bonds that are not facilitated by direct intervention of bridging ligands but are partially held by the attractive pi-pi stacking interaction between the phenyl units of the 4,4'-dimethyl-2,2'-bipyridyl ligands. The effect of the pi-pi stacking interactions on the strength and length of the Pt-Pt bond has been discussed using reduced models of the interacting moieties in which the aromatic rings have been removed. The nature of the Pt-Pt bonds has been studied through energy decomposition and atoms-in-molecules analyses. The results indicate that the relatively strong (about 40 kcal mol(-1)) Pt-Pt metallic bond has similar covalent and ionic contributions.

Journal Article↗
PubMed2005

Comparison of the AIM delocalization index and the Mayer and fuzzy atom bond orders.

In this paper the behavior of three well-known electron-sharing indexes, namely, the AIM delocalization index and the Mayer and fuzzy atom bond orders are studied at the Hartree-Fock level. A large number of five-membered ring molecules, containing several types of bonding, constitute the training set chosen for such purpose. A detailed analysis of the results obtained shows that the three indexes studied exhibit strong correlations, especially for homonuclear bonds. The correlation is somewhat poorer but still significant for polar bonds. In this case, the bond orders obtained with the Mayer and fuzzy atom approaches are normally closer to the formally predicted bond orders than those given by the AIM delocalization indexes, which are usually smaller than those expected from chemical intuition. In some particular cases, the use of diffuse functions in the calculation of Mayer bond orders leads to unrealistic results. In particular, noticeable trends are found for C-C bonds, encouraging the substitution of the delocalization index by the cheaper fuzzy atom or even the Mayer bond orders in the calculation of aromaticity indexes based on the delocalization index such as the para-delocalization index and the aromatic fluctuation index.

Journal Article↗
PubMed2005

Local aromaticity of [n]acenes, [n]phenacenes, and [n]helicenes (n = 1-9).

The local aromaticity of the six-membered rings in three series of benzenoid compounds, namely, the [n]acenes, [n]phenacenes, and [n]helicenes for n = 1-9, has been assessed by means of three probes of local aromaticity based on structural, magnetic, and electron delocalization properties. For [n]acenes our analysis shows that the more reactive inner rings are more aromatic than the outer rings. For [n]phenacenes, all indicators of aromaticity show that the external rings are the most aromatic. From the external to the central ring, the local aromaticity varies in a damped alternate way. The trends for the [n]helicene series are the same as those found for [n]phenacenes. Despite the departure from planarity in [n]helicenes, only a very slight loss of aromaticity is detected in [n]helicenes as compared to the corresponding [n]phenacenes. Finally, because of magnetic couplings between superimposed six-membered rings in the higher members of the [n]helicenes series, we have demonstrated that the NICS indicator of aromaticity artificially increases the local aromaticity of their most external rings.

Journal Article↗
PubMed2004

Local aromaticity of the six-membered rings in pyracylene. A difficult case for the NICS indicator of aromaticity.

In this work, we have analyzed the local aromaticity of the six-membered rings (6-MRs) of planar and pyramidalized pyracylene species through the structurally based harmonic oscillator model of aromaticity (HOMA), the electronically based para-delocalization index (PDI), and the magnetic-based nucleus independent chemical shift (NICS) measurements, as well as with maps of ring current density. According to ring currents and PDI and HOMA indicators of aromaticity, there is a small reduction of local aromaticity in the 6-MRs of pyracylene with a bending of the molecule. In the case of NICS, the results depend on whether the NICS value is calculated at the center of the ring (NICS(0)) or at 1 A above (NICS(1)(out)) or below (NICS(1)(in)) the ring plane. While NICS(1)(out) values also indicate a slight decrease of aromaticity with bending, NICS(0) and NICS(1)(in) wrongly point out a large increase of aromaticity upon distortion. We have demonstrated that the NICS(0) reduction in the 6-MRs of pyracylene upon bending is due to (a) a strong reduction of the paratropic currents in 5-MRs and (b) the fact that, due to the distortion, the paratropic currents point their effects in other directions.

Journal Article↗
PubMed2004

Relation between the substituent effect and aromaticity.

Molecular geometries of benzene and its 18 monosubstituted derivatives were optimized at B3LYP/6-311+G** level of theory. The changes of pi-electron delocalization of the benzene fragment were estimated by use of aromatic stabilization energies (ASE) based on different homodesmotic reaction schemes, geometry-based HOMA model, magnetism-based NICS, NICS(1), NICS(1)zz, and an electronic delocalization index, PDI, derived from the AIM theory. Apart from aromatic stabilization energies the other descriptors of aromaticity vary to a very small extent, indicating high resistance of the pi-electron structure to the substituent effect. This is somewhat analogous to a tendency of benzene systems to retain their initial pi-electron structure during the reaction course that leads to aromatic substitution.

Journal Article↗
PubMed2003

An insight into the local aromaticities of polycyclic aromatic hydrocarbons and fullerenes.

In this work we quantify the local aromaticity of six-membered rings in a series of planar and bowl-shaped polycyclic aromatic hydrocarbons (PAHs) and fullerenes. The evaluation of local aromaticity has been carried out through the use of structurally (HOMA) and magnetically (NICS) based measures, as well as by the use of a new electronically based indicator of aromaticity, the para delocalization index (PDI), which is defined as the average of all the Bader delocalization indices between para-related carbon atoms in six-membered rings. The series of PAHs selected includes C(10)H(8), C(12)H(8), C(14)H(8), C(20)H(10), C(26)H(12), and C(30)H(12), with benzene and C(60) taken as references. The change in the local aromaticity of the six-membered rings on going from benzene to C(60) is analyzed. Finally, we also compare the aromaticity of C(60) with that of C(70), open [5,6]- and closed [6,6]-C(60)NH systems, and C(60)F(18).

Electrons↗