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

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

Effect of Fluorination on the Competition of Halogen Bonding and Hydrogen Bonding: Complexes of Fluoroiodomethane with Dimethyl Ether and Trimethylamine

To further rationalize the competition between halogen and hydrogen bonding, a combined experimental and theoretical study on the weakly bound molecular complexes formed between the combined halogen bond/hydrogen bond donor fluoroiodomethane and the Lewis bases dimethyl ether and trimethylamine (in standard and fully deuterated form) is presented. The experimental data are obtained by recording infrared and Raman spectra of mixtures of the compounds in liquid krypton, at temperatures between 120 and 156 K. The experiments are supported by <i>ab initio</i> calculations at the MP2/aug-cc-pVDZ-PP level, statistical thermodynamics and Monte Carlo free energy perturbation calculations. For the mixtures containing fluoroiodomethane and dimethyl ether a hydrogen-bonded complex with an experimental complexation enthalpy of −7.0(2) kJ mol^–1 is identified. Only a single weak spectral feature is observed which can be tentatively assigned to the halogen-bonded complex. For the mixtures involving trimethylamine, both halogen- and hydrogen-bonded complexes are observed, the experimental complexation enthalpies being −12.5(1) and −9.6(2) kJ mol^–1 respectively. To evaluate the influence of fluorination on the competition between halogen and hydrogen bonding, the results obtained for fluoroiodomethane are compared with those of a previous study involving difluoroiodomethane

Tuning the HOMO–LUMO Energy Gap of Small Diamondoids Using Inverse Molecular Design

Functionalized diamondoids show great potential as building blocks for various new optoelectronic applications. However, until now, only simple mono and double substitutions were investigated. In this work, we considered up to 10 and 6 sites for functionalization of the two smallest diamondoids, adamantane and diamantane, respectively, in search for diamondoid derivatives with a minimal and maximal HOMO–LUMO energy gap. To this end, the energy gap was optimized systematically using an inverse molecular design methodology based on the best-first search algorithm combined with a Monte Carlo component to escape local optima. Adamantane derivatives were found with HOMO–LUMO gaps ranging from 2.42 to 10.63 eV, with 9.45 eV being the energy gap of pure adamantane. For diamantane, similar values were obtained. The structures with the lowest HOMO–LUMO gaps showed apparent push–pull character. The push character is mainly formed by sulfur or nitrogen dopants and thiol groups, whereas the pull character is predominantly determined by the presence of electron-withdrawing nitro or carbonyl groups assisted by amino and hydroxyl groups via the formation of intramolecular hydrogen bonds. In contrast, maximal HOMO–LUMO gaps were obtained by introducing numerous electronegative groups

Expanding Lone Pair···π Interactions to Nonaromatic Systems and Nitrogen Bases: Complexes of C₂F₃X (X = F, Cl, Br, I) and TMA‑<i>d</i> ₉

The molecular electrostatic potential surface of unsaturated, locally electron-deficient molecules shows a positive region perpendicular to (a part of) the molecular framework. In recent years it has been shown both theoretically and experimentally that molecules are able to form noncovalent interactions with Lewis bases through this π-hole. When studying unsaturated perfluorohalogenated molecules containing a higher halogen atom, a second electropositive region is also observed near the halogen atom. This region, often denoted as a σ-hole, allows the molecules to interact with Lewis bases and form a halogen bond. To experimentally characterize the competition between both these noncovalent interactions, Fourier transform infrared and Raman spectra of liquefied noble gas solutions containing perfluorohalogenated ethylene derivatives (C₂F₃X; X = F, Cl, Br, or I) and trimethylamine­(-<i>d</i> ₉) were investigated. Analysis of the spectra shows that in mixed solutions of trimethylamine­(-<i>d</i> ₉) and C₂F₄ or C₂F₃Cl lone pair···π complex is present, while evidence for halogen-bonded complex is found in solutions containing trimethylamine­(-<i>d</i> ₉) and C₂F₃Cl, C₂F₃Br, or C₂F₃I. For all species observed, complexation enthalpies were determined, the values varying between −4.9(1) and −24.4 kJ mol^–1

Orientacni fraktograficka analyza poruseneho nosniku mostu.

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Scrutinizing the Noninnocence of Quinone Ligands in Ruthenium Complexes: Insights from Structural, Electronic, Energy, and Effective Oxidation State Analyses

The most relevant manifestations of ligand noninnocence of quinone and bipyridine derivatives are thoroughly scrutinized and discussed through an extensive and systematic set of octahedral ruthenium complexes, [(en)₂RuL]^<i>z</i>, in four oxidation states (<i>z</i> = +3, +2, +1, and 0). The characteristic structural deformation of ligands upon coordination/noninnocence is put into context with the underlying electronic structure of the complexes and its change upon reduction. In addition, by means of decomposing the corresponding reductions into electron transfer and structural relaxation subprocesses, the energetic contribution of these structural deformations to the redox energetics is revealed. The change of molecular electron density upon metal- and ligand-centered reductions is also visualized and shown to provide novel insights into the corresponding redox processes. Moreover, the charge distribution of the π-subspace is straightforwardly examined and used as indicator of ligand noninnocence in the distinct oxidation states of the complexes. The aromatization/dearomatization processes of ligand backbones are also monitored using magnetic (NICS) and electronic (PDI) indicators of aromaticity, and the consequences to noninnocent behavior are discussed. Finally, the recently developed effective oxidation state (EOS) analysis is utilized, on the one hand, to test its applicability for complexes containing noninnocent ligands, and, on the other hand, to provide new insights into the magnitude of state mixings in the investigated complexes. The effect of ligand substitution, nature of donor atom, ligand frame modification on these manifestations, and measures is discussed in an intuitive and pedagogical manner

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