20 research outputs found
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
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 (Î) between cytosine and the substituted benzenes Ph-X (kcal/mol) versus the local hardness Ρ()
<p><b>Copyright information:</b></p><p>Taken from "Influence of the ĎâĎ 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>Š The Author 2005. Published by Oxford University Press. All rights reserved</p> () Correlation part of the interaction energy (Î) between cytosine and the substituted benzenes Ph-X (kcal/mol) versus the benzene ring polarizability divided by (see ) (a.u.)
Î() 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 ĎâĎ 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>Š The Author 2005. Published by Oxford University Press. All rights reserved</p
Correlation part of the interaction energy (Î) 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 ĎâĎ 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>Š 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 Kohnâs Nearsightedness
of Electronic Matter principle can be retrieved and identified as
the physicistâs version of the chemistâs âtransferability
of functional groupsâ concept. The accurate, analytical hardness
matrix evaluation on the other hand provides further support for the
basics of Nalewajskiâs charge sensitivity analysis. Based on
Parr and Liuâs 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 HuĚckel/MoĚbius (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 metalâmoleculeâmetal
junction still need to be elucidated. For this reason, the transport
properties of HuĚckel/MoĚbius (anti)Âaromatic 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 HuĚckel
level of theory. Next, the different approximations of HuĚckel
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 Ď-conjugated systems of expanded porphyrins
can be approximated as polyene macrocycles based on the âannulene
modelâ, 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 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