31 research outputs found
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 NâFusion 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]Âpentaphyrin was reported in 2012. Here, the conformational
preferences and N-fusion reaction of [22]- and [24]Âpentaphyrins have
been investigated using density functional calculations, together
with their aromaticity-molecular topology relationships. Two global
minima are found for the unsubstituted [22]Âpentaphyrin corresponding
to <i>T0</i> and <i>T0</i><sup>4,D</sup> HuĚckel
structures. MoĚbius transition states are located in the interconversion
pathways with activation barriers of 27 kcal mol<sup>â1</sup>. Conversely, [24]Âpentaphyrin is able to switch between HuĚckel
and MoĚbius conformers with very low activation barriers. However,
nonfused [24]Âpentaphyrins are unstable and spontaneously undergo an
N-fusion reaction driven by the strain release. On the contrary, nonfused
[22]Âpentaphyrins could be isolated if a <i>T0</i><sup>4,D</sup> conformation is adopted. Importantly, conformational control of
pentaphyrins can be achieved by <i>meso</i>-substituents.
Two stable conformations (<i>T0</i><sup>4,D</sup> and <i>T0</i><sup>A,D</sup>) are found for the nonfused [22]Âpentaphyrin,
which are delicately balanced by the number of substituents. The <i>T0</i><sup>A,D</sup> 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]Âpentaphyrins
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 â7.0(2) kJ mol<sup>â1</sup> 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 â12.5(1) and
â9.6(2) kJ mol<sup>â1</sup> 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 HOMOâLUMO 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 HOMOâLUMO
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 HOMOâLUMO 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 HOMOâLUMO gaps showed apparent pushâpull
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 HOMOâLUMO
gaps were obtained by introducing numerous electronegative groups
Expanding Lone PairÂˇÂˇÂˇĎ Interactions to Nonaromatic Systems and Nitrogen Bases: Complexes of C<sub>2</sub>F<sub>3</sub>X (X = F, Cl, Br, I) and TMAâ<i>d</i> <sub>9</sub>
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 Ď-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 Ď-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 (C<sub>2</sub>F<sub>3</sub>X; X = F, Cl, Br,
or I) and trimethylamineÂ(-<i>d</i>
<sub>9</sub>) were investigated.
Analysis of the spectra shows that in mixed solutions of trimethylamineÂ(-<i>d</i>
<sub>9</sub>) and C<sub>2</sub>F<sub>4</sub> or C<sub>2</sub>F<sub>3</sub>Cl lone pairÂˇÂˇÂˇĎ complex is present,
while evidence for halogen-bonded complex is found in solutions containing
trimethylamineÂ(-<i>d</i>
<sub>
9</sub>) and C<sub>2</sub>F<sub>3</sub>Cl,
C<sub>2</sub>F<sub>3</sub>Br, or C<sub>2</sub>F<sub>3</sub>I. For
all species observed, complexation enthalpies were determined, the
values varying between â4.9(1) and â24.4 kJ mol<sup>â1</sup>
Orientacni fraktograficka analyza poruseneho nosniku mostu.
Available from STL Prague, CZ / NTK - National Technical LibrarySIGLECZCzech Republi
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)<sub>2</sub>RuL]<sup><i>z</i></sup>, 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 Ď-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 PâO (PâO3Ⲡand PâO5â˛) and
CâC (C3â˛âC4Ⲡand C4â˛âC5â˛) bonds
for which the acquired kinetic energy
becomes high enough so that the neighboring C3â˛âO3Ⲡor C5â˛âO5Ⲡphosphodiester
bond may break almost immediately.
Such dynamic behavior should happen on a very short time scale, within
15â30 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 CâO 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 PâO (PâO3Ⲡand PâO5â˛) and
CâC (C3â˛âC4Ⲡand C4â˛âC5â˛) bonds
for which the acquired kinetic energy
becomes high enough so that the neighboring C3â˛âO3Ⲡor C5â˛âO5Ⲡphosphodiester
bond may break almost immediately.
Such dynamic behavior should happen on a very short time scale, within
15â30 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 CâO 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 PâO (PâO3Ⲡand PâO5â˛) and
CâC (C3â˛âC4Ⲡand C4â˛âC5â˛) bonds
for which the acquired kinetic energy
becomes high enough so that the neighboring C3â˛âO3Ⲡor C5â˛âO5Ⲡphosphodiester
bond may break almost immediately.
Such dynamic behavior should happen on a very short time scale, within
15â30 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 CâO phosphodiester bonds can
break before electron transfer from the backbone to the base