The electron density of delocalized bonds (EDDB) applied for quantifying aromaticity

In this study the recently developed electron density of delocalized bonds (EDDB) is used to define a new measure of aromaticity in molecular rings. The relationships between bond-length alternation, electron delocalization and diatropicity of the induced ring current are investigated for a test set of representative molecular rings by means of correlation and principal component analyses involving the most popular aromaticity descriptors based on structural, electronic, and magnetic criteria. Additionally, a qualitative comparison is made between EDDB and the magnetically induced ring-current density maps from the ipsocentric approach for a series of linear acenes. Special emphasis is given to the comparative study of the description of cyclic delocalization of electrons in a wide range of organic aromatics in terms of the kekulean multicenter index KMCI and the newly proposed EDDBk indexThe research was supported in part by the Faculty of Chemistry at Jagiellonian University (grant K/DSC/001469, DS), Foundation for Polish Science (FNP START 2015, stipend 103.2015, DS), National Science Centre, Poland (NCN SONATA, grant 2015/17/ D/ST4/00558, DS) as well as the PL-Grid Infrastructure of the Academic Computer Centre CYFRONET with the calculations performed on the cluster platform ‘‘Prometheus’’. MS thanks for the support of the Ministerio de Economa y Competitividad of Spain (Project CTQ2014-54306-P), Generalitat de Catalunya (project number 2014SGR931, Xarxa de Refere`ncia en Qumica Teo`rica i Computacional, and ICREA Academia prize), and European Fund for Regional Development (FEDER grant UNGI10-4E-801

Interference of H-bonding and substituent effects in nitro- and hydroxy-substituted salicylaldehydes

Two intramolecular interactions, i.e., (1) hydrogen bond and (2) substituent effect, were analyzed and compared. For this purpose, the geometry of 4- and 5-X-substituted salicylaldehyde derivatives (X = NO2, H or OH) was optimized by means of B3LYP/6-311 + G(d,p) and MP2/aug-cc-pVDZ methods. The results obtained allowed us to show that substituents (NO2 or OH) in the para or meta position with respect to either OH or CHO in H-bonded systems interact more strongly than in the case of di-substituted species: 4- and 3-nitrophenol or 4- and 3-hydroxybenzaldehyde by ∼31%. The substituent effect due to the intramolecular charge transfer from the para-counter substituent (NO2) to the proton-donating group (OH) is ∼35% greater than for the interaction of para-OH with the proton-accepting group (CHO). The total energy of H-bonding for salicylaldehyde, and its derivatives, is composed of two contributions: ∼80% from the energy of H-bond formation and ∼20% from the energy associated with reorganization of the electron structure of the systems in question

On relation between substituent effect and aromaticity in monocyclic systems

Aromaticity/aromatic and substituent/substituent effects belong to the most commonly used terms in organic chemistry and related fields. They are used for more than a century, and so far are the subject of thousands publications a year. The quantitative description of the aromaticity of planar π-electron cyclic molecules is based on four criteria: (i) they are more stable than their acyclic unsaturated analogues, (ii) bonds have intermediate lengths between those for the single and double ones, (iii) external magnetic field induces π-electron ring current, and (iv) aromatic systems prefer reactions in which the π-electron structure is preserved. conserved. Quantitative characteristics based on these criteria, named as aromaticity indices, allow to relate aromaticity to the substituent effect. This latter can be described using either traditional Hammett-type substituent constants or characteristics based on quantum-chemistry. For this purpose, the energies of properly designed homodesmotic reactions and electron density distribution are used. In the first case, a descriptor named SESE (substituent effect stabilization energy) is obtained, while in the second case – cSAR (charge of the substituent active region), which is the sum of the charge of the ipso carbon atom and the charge of the substituent. The application of these substituent effect descriptors to a set of π-electron systems, such as: benzene, quinones, cyclopenta- and cyclohepta-dienes, as well as some azoles, allowed to draw the following conclusions: (i) The less aromatic the system, the stronger the substituent influences the π-electron system. Highly aromatic systems are resistant to the substituent effect, in line with the organic chemistry experience that aromatic compounds dislike reactions leading to changes in the π-electron structure of the ring. (ii) Intramolecular charge transfer (resonance effect) is privileged in cases where the number of bonds between the electron-attracting and electron-donating atoms is even. These effects are much weaker when this number is odd. Classically, it may be related to traditional para vs meta substituent effects in benzene derivatives. We should note that in electron-accepting groups, such as CN or NO2 (and others), electron-accepting atoms are second counting from Cipso. (iii) In all cases, when the substituent changes number of π-electrons in the ring in the direction of 4N+2, its aromaticity increases, for example electron-donating substituents in exocyclic substituted pentafulvene, or a halogen atom in complexes with heptafulvene

Characterizing strength of individual hydrogen bonds in DNA base-pairs

The main idea of the current review is to present methods useful to characterize the strength of individual hydrogen bonds in nucleic acids base-pairs. In the paper, the Authors discuss the energy definition of intermolecular interactions taking into account the presence of one intermolecular hydrogen bond (HB) as well as the situation when several intermolecular interactions (namely intermolecular hydrogen bonds) are present. In the Section 2 of the review a general overview of methods developed to estimate the strength of the individual intermolecular hydrogen bond in DNA/RNA base-pairs is presented. Thus, the reader can find detailed information on the methods used so far: the rotational method (2003), compliance constants method (2004), the EML equation application (2006), the atom replacement method (2007), the estimation of hydrogen bond energy on the basis of electron density (calculated by using the AIM theory) at BCP values (2009), the application of NBO method (2010), the comparison of HB strength based on the last two approaches (2015) and the application of coordinates interaction approach (2017). It should be emphasized, that these methods allow to estimate the strength of intermolecular interactions both in the model base-pairs and in other systems with several intermolecular hydrogen bonds. The discussion of the presented methods is supported by Tables 1-10, containing numerical values characteristics of the strength of the particular HB, and Figures 1–2. The section 3 contains a critical comparison of results based on the presented methods. Concluding remarks are given in the last Section

Effect of the H-Bonding on Aromaticity of Purine Tautomers

Four tautomers of purine (1-H, 3-H, 7-H, and 9-H) and their equilibrium H-bonded complexes with F^– and HF for acidic and basic centers, respectively, were optimized by means of the B3LYP/6-311++G­(d,p) level of theory. Purine tautomer stability increases in the following series: 1-H < 3-H < 7-H < 9-H, consistent with increasing aromaticity. Furthermore, the presence of a hydrogen bond with HF does not change this order. For neutral H-bonded complexes, the strongest and the weakest intermolecular interactions occur (−14.12 and −10.49 kcal/mol) for less stable purine tautomers when the proton acceptor is located in the five- and six-membered rings, respectively. For 9-H and 7-H tautomers the order is reversed. The H-bond energy for the imidazole complex with HF amounts to −14.03 kcal/mol; hence, in the latter case, the fusion of imidazole to pyrimidine decreases its basicity. The ionic H-bonds of N^–···HF type are stronger by ∼10 kcal/mol than the neutral N···HF intermolecular interactions. The hydrogen bond N^–···HF energies in pyrrole and imidazole are −32.28 and −30.03 kcal/mol, respectively, and are substantially stronger than those observed in purine complexes. The aromaticity of each individual ring and of the whole molecule for all tautomers in ionic complexes is very similar to that observed for the anion of purine. This is not the case for neutral complexes and purine as a reference. The N···HF bonds perturb much more the π-electron structure of five-membered rings than that of the six-membered ones. The H-bonding complexes for 7-H and 9-H tautomers are characterized by higher aromaticity and a much lower range of HOMA variability

Hydrogen Bonding as a Modulator of Aromaticity and Electronic Structure of Selected <i>ortho</i>-Hydroxybenzaldehyde Derivatives

Properties of hydrogen bonds can induce changes in geometric or electronic structure parameters in the vicinity of the bridge. Here, we focused primarily on the influence of intramolecular H-bonding on the molecular properties in selected <i>ortho</i>-hydroxybenzaldehydes, with additional restricted insight into substituent effects. Static models were obtained in the framework of density functional theory at B3LYP/6-311+G(d,p) level. The electronic structure parameters evolution was analyzed on the basis of Atoms In Molecules (AIM) and Natural Bond Orbitals methods. The aromaticity changes related to the variable proton position and presence of substituents were studied using Harmonic Oscillator Model of Aromaticity (HOMA), Nucleus-Independent Chemical Shift (NICS) and AIM-based parameter of Matta and Hernández-Trujillo. Finally, Car–Parrinello molecular dynamics was applied to study variability of the hydrogen bridge dynamics. The interplay between effects of the substitution and variable position of the bridged proton was discussed. It was found that the hydrogen bond energies are ca. 9–10 kcal/mol, and the bridged proton exhibits some degree of penetration into the acceptor region. The covalent character of the studied hydrogen bond was most observable when the bridged proton reached the middle position between the donor and acceptor regions. The aromaticity indexes showed that the aromaticity of the central phenyl ring is strongly dependent on the bridged proton position. Correlations between these parameters were found and discussed. In the applied time-scale, the analysis of time evolution of geometric parameters showed that the resonance strengthening does not play a crucial role in the studied compounds

The role of the long-range exchange corrections in the description of electron delocalization in aromatic species

In this article, we address the role of the long-range exchange corrections in description of the cyclic delocalization of electrons in aromatic systems at the density functional theory level. A test set of diversified monocyclic and polycyclic aromatics is used in benchmark calculations involving various exchange-correlation functionals. A special emphasis is given to the problem of local aromaticity in acenes, which has been a subject of long-standing debate in the literature. The presented results indicate that the noncorrected exchange-correlation functionals significantly overestimate cyclic delocalization of electrons in heteroaromatics and aromatic systems with fused rings, which in the case of acenes leads to conflicting local aromaticity predictions from different criteriaThe research was supported in part by the Foundation for Polish Science (FNP START 2015, stipend 103.2015, DS), National Science Centre, Poland (NCN SONATA, grant 2015/17/D/ST4/ 00558, DS) as well as the PL-Grid Infrastructure of the Academic Computer Centre CYFRONET, with the calculations performed on cluster platforms Zeus and Prometheus. MS thanks for the support of the Ministerio de Economía y Competitividad of Spain (Project CTQ2014-54306-P), Generalitat de Catalunya (project number 2014SGR931, Xarxa de Referència en Química Teòrica i Computacional, and ICREA Academia prize), and European Fund for Regional Development (FEDER grant UNGI10-4E-801

Aromaticity of acenes : the model of migrating π\pi-circuits

The concept of migrating Clar's sextet is extended to explain the local aromaticity trends in linear acenes predicted by different aromaticity criteria from theoretical calculations as well as from experimental data. The electron density of delocalized bonds is used to assess the link between resonance and reactivity and to rationalize the constant-height AFM image of pentacen