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

<i>meso</i>-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 <i>T0</i> and <i>T0</i>^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 <i>T0</i>^4,D conformation is adopted. Importantly, conformational control of pentaphyrins can be achieved by <i>meso</i>-substituents. Two stable conformations (<i>T0</i>^4,D and <i>T0</i>^A,D) are found for the nonfused [22]­pentaphyrin, which are delicately balanced by the number of substituents. The <i>T0</i>^A,D conformation is preferred by fully <i>meso</i>-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

The Linear Response Kernel: Inductive and Resonance Effects Quantified

Calculations of conceptual density functional theory (DFT) reactivity indices are mainly restricted to global quantities and local functions, whereas values for the nonlocal kernels are rarely presented. We used a molecular orbital-based expression to calculate the atom-condensed linear response kernel. The results are the first published values of this quantity that have been obtained through a direct and generally applicable methodology. This letter focuses on the off-diagonal elements, which provide insight into the nonlocal contributions to chemical reactivity. A detailed study of a set of eight functionalized alkane and polyalkene derivatives enabled us to quantify inductive and resonance effects

() Electrostatic interaction energy (Δ) between cytosine and the substituted benzenes Ph-X (kcal/mol) versus the local hardness η()

<p><b>Copyright information:</b></p><p>Taken from "Influence of the π–π interaction on the hydrogen bonding capacity of stacked DNA/RNA bases"</p><p>Nucleic Acids Research 2005;33(6):1779-1789.</p><p>Published online 23 Mar 2005</p><p>PMCID:PMC1069514.</p><p>© The Author 2005. Published by Oxford University Press. All rights reserved</p> () Correlation part of the interaction energy (Δ) between cytosine and the substituted benzenes Ph-X (kcal/mol) versus the benzene ring polarizability divided by (see ) (a.u.)

Η() can be used for the estimation of the electrostatic interaction and the hydrogen bonding ability

<p><b>Copyright information:</b></p><p>Taken from "Influence of the π–π interaction on the hydrogen bonding capacity of stacked DNA/RNA bases"</p><p>Nucleic Acids Research 2005;33(6):1779-1789.</p><p>Published online 23 Mar 2005</p><p>PMCID:PMC1069514.</p><p>© The Author 2005. Published by Oxford University Press. All rights reserved</p

Correlation part of the interaction energy (Δ) computed for the 10 stacked DNA/RNA base dimers (kcal/mol) versus the product of the polarizabilities of each base over (see ) (a

<p><b>Copyright information:</b></p><p>Taken from "Influence of the π–π interaction on the hydrogen bonding capacity of stacked DNA/RNA bases"</p><p>Nucleic Acids Research 2005;33(6):1779-1789.</p><p>Published online 23 Mar 2005</p><p>PMCID:PMC1069514.</p><p>© The Author 2005. Published by Oxford University Press. All rights reserved</p>u.)

Extending the Scope of Conceptual Density Functional Theory with Second Order Analytical Methodologies

In the context of the growing impact of conceptual density functional theory (DFT) as one of the most successful chemical reactivity theories, response functions up to second order have now been widely applied; in recent years, among others, particular attention has been focused on the linear response function and also extensions to higher order have been put forward. As the larger part of these studies have been carried using a finite difference approach to compute these concepts, we now embarked on (an extension of) an analytical approach to conceptual DFT. With the ultimate aim of providing a complete set of analytically computable second order properties, including the softness and hardness kernels, the hardness as the simplest second order response function is scrutinized again with numerical results highlighting the difference in nature between the analytical hardness (referred to as hardness condition) and the Parr-Pearson absolute chemical hardness. The hardness condition is investigated for its capability to gauge the (de)localization error of density functional approximations (DFAs). The analytical Fukui function, besides overcoming the difficulties in the finite difference approach in treating negatively charged systems, also showcases the errors of deviating from the straight-line behavior using fractional occupation number calculations. Subsequently, the softness kernel and its atom-condensed inverse, the hardness matrix, are accessed through the Berkowitz-Parr relation. Revisiting the softness kernel confirms and extends previous discussions on how Kohn’s Nearsightedness of Electronic Matter principle can be retrieved and identified as the physicist’s version of the chemist’s “transferability of functional groups” concept. The accurate, analytical hardness matrix evaluation on the other hand provides further support for the basics of Nalewajski’s charge sensitivity analysis. Based on Parr and Liu’s functional expansion of the energy functional, a new energy decomposition is introduced with an order of magnitude analysis of the different terms for a series of simple molecules both at their equilibrium geometry and upon variation in bond length and dihedral angle. Finally, for the first time, the perturbation expansion of the energy functional is studied numerically up to second order now that all response functions and integration techniques are at hand. The perturbation expansion energies are in excellent agreement with those obtained directly from DFA calculations giving confidence in the convergence of the perturbation series and its use in judging the importance of the different terms in reactivity investigations

Qualitative Insights into the Transport Properties of Hückel/Möbius (Anti)Aromatic Compounds: Application to Expanded Porphyrins

Expanded porphyrins have been recently identified as promising candidates for conductance switching based on aromaticity and molecular topology changes. However, the factors that control electron transport switching across the metal–molecule–metal junction still need to be elucidated. For this reason, the transport properties of Hückel/Möbius (anti)­aromatic compounds are investigated thoroughly in this work to gain qualitative understanding into the conductivity of these unique macrocycles. Starting from a polyene model, a simple counting rule is developed to predict the occurrence of quantum interference around the Fermi level at the Hückel level of theory. Next, the different approximations of Hückel theory are lifted, enabling the exploration of the influence of each of these approximations on the transport properties of expanded porphyrins. Along the way, a detailed study on the relationship between the conductance and aromaticity/topology has been undertaken. Even though it has been proposed that the π-conjugated systems of expanded porphyrins can be approximated as polyene macrocycles based on the “annulene model”, it turns out that the distortion induced by the pyrrole rings to the electronic structure of the expanded porphyrins causes the simple counting rule for the prediction of quantum interference developed for polyenes to fail in some specific situations. Nevertheless, our back-of-the-envelope approach enables an intuitive rationalization of most of the transport properties of expanded porphyrins. Our conclusions cast further doubt on the proposed negative relationship between conductance and aromaticity and highlight the importance of the connectivity on determining the shape of the transmission functions of the different states. We hope that the new insights provided here will offer experimentalists a road map toward the design of functional, multidimensional electronic switches based on expanded porphyrins

Electron-Attachment-Induced DNA Damage: Instantaneous Strand Breaks

Low energy electron-attachment-induced damage in DNA, where dissociation channels may involve multiple bonds including complex bond rearrangements and significant nuclear motions, is analyzed here. Quantum mechanics/molecular mechanics (QM/MM) calculations reveal how rearrangements of electron density after vertical electron attachment modulate the position and dynamics of the atomic nuclei in DNA. The nuclear motions involve the elongation of the P–O (P–O3′ and P–O5′) and C–C (C3′–C4′ and C4′–C5′) bonds for which the acquired kinetic energy becomes high enough so that the neighboring C3′–O3′ or C5′–O5′ phosphodiester bond may break almost immediately. Such dynamic behavior should happen on a very short time scale, within 15–30 fs, which is of the same order of magnitude as the time scale predicted for the excess electron to localize around the nucleobases. This result indicates that the C–O phosphodiester bonds can break before electron transfer from the backbone to the base

Electron-Attachment-Induced DNA Damage: Instantaneous Strand Breaks

Low energy electron-attachment-induced damage in DNA, where dissociation channels may involve multiple bonds including complex bond rearrangements and significant nuclear motions, is analyzed here. Quantum mechanics/molecular mechanics (QM/MM) calculations reveal how rearrangements of electron density after vertical electron attachment modulate the position and dynamics of the atomic nuclei in DNA. The nuclear motions involve the elongation of the P–O (P–O3′ and P–O5′) and C–C (C3′–C4′ and C4′–C5′) bonds for which the acquired kinetic energy becomes high enough so that the neighboring C3′–O3′ or C5′–O5′ phosphodiester bond may break almost immediately. Such dynamic behavior should happen on a very short time scale, within 15–30 fs, which is of the same order of magnitude as the time scale predicted for the excess electron to localize around the nucleobases. This result indicates that the C–O phosphodiester bonds can break before electron transfer from the backbone to the base

Electron-Attachment-Induced DNA Damage: Instantaneous Strand Breaks

Low energy electron-attachment-induced damage in DNA, where dissociation channels may involve multiple bonds including complex bond rearrangements and significant nuclear motions, is analyzed here. Quantum mechanics/molecular mechanics (QM/MM) calculations reveal how rearrangements of electron density after vertical electron attachment modulate the position and dynamics of the atomic nuclei in DNA. The nuclear motions involve the elongation of the P–O (P–O3′ and P–O5′) and C–C (C3′–C4′ and C4′–C5′) bonds for which the acquired kinetic energy becomes high enough so that the neighboring C3′–O3′ or C5′–O5′ phosphodiester bond may break almost immediately. Such dynamic behavior should happen on a very short time scale, within 15–30 fs, which is of the same order of magnitude as the time scale predicted for the excess electron to localize around the nucleobases. This result indicates that the C–O phosphodiester bonds can break before electron transfer from the backbone to the base