13 research outputs found
Understanding the Physics and Chemistry of Reaction Mechanisms from Atomic Contributions: A Reaction Force Perspective
Studying chemical reactions involves the knowledge of
the reaction
mechanism. Despite activation barriers describing the kinetics or
reaction energies reflecting thermodynamic aspects, identifying the
underlying physics and chemistry along the reaction path contributes
essentially to the overall understanding of reaction mechanisms, especially
for catalysis. In the past years the reaction force has evolved as
a valuable tool to discern between structural changes and electronsâ
rearrangement in chemical reactions. It provides a framework to analyze
chemical reactions and additionally a rational partition of activation
and reaction energies. Here, we propose to separate these energies
further in atomic contributions, which will shed new insights in the
underlying reaction mechanism. As first case studies we analyze two
intramolecular proton transfer reactions. Despite the atom based separation
of activation barriers and reaction energies, we also assign the participation
of each atom in structural changes or electronsâ rearrangement
along the intrinsic reaction coordinate. These participations allow
us to identify the role of each atom in the two reactions and therfore
the underlying chemistry. The knowledge of the reaction chemistry
immediately leads us to suggest replacements with other atom types
that would facilitate certain processes in the reaction. The characterization
of the contribution of each atom to the reaction energetics, additionally,
identifies the reactive center of a molecular system that unites the
main atoms contributing to the potential energy change along the reaction
path
Theoretical Study of Cytosine Deamination from the Perspective of the Reaction Force Analysis
International audienc
Etude théorique d'une étape complexe de la désamination de la cytosine
International audienc
How Does Pin1 Catalyze the CisâTrans Prolyl Peptide Bond Isomerization? A QM/MM and Mean Reaction Force Study
Pin1 represents an enzyme that specifically catalyzes
the isomerization
of peptide bonds between phosphorylated threonine or serine residues
and proline. Despite its relevance as molecular timer in a number
of biological processes related to cancer and Alzheimer disease, a
detailed understanding of the factors contributing to the catalysis
is still missing. In this study, we employ extensive QM/MM molecular
dynamics simulations in combination with the mean reaction force (MRF)
to discern the influence of the enzyme on the reaction mechanism and
the origin of the catalysis. As a recently introduced method, the
MRF separates the activation free energy barrier to reach the transition
state into structural and electronic contributions providing a more
detailed description of the enzymeâs function. As a reference,
we first study the isomerization starting from the cis form in solution
and obtain a free energy barrier and a reaction free energy, which
are in agreement with previous studies and experiment. With the new
mean reaction force method, intramolecular hydrogen bonds in the peptide
were identified that stabilize the transition state and reduce the
electronic contribution to the free energy barrier. To elucidate the
mechanism of catalysis of Pin1, the reaction in solution and in the
catalytic cavity of the enzyme were compared. Both yield the same
free energy barrier for the isomerization of the cis form, but with
different decomposition in structural and electronic contributions
by the mean reaction force. The enzyme reduces the energy required
for structural rearrangements to reach the transition state, pointing
to a destabilization of the reactant, but increases the electronic
contribution to the barrier through specific enzymeâpeptide
hydrogen bonds. In the reverse reaction, the isomerization of the
trans form, the enzyme alters the energetics and the mechanism of
the reaction considerably. Unfavorable enzymeâpeptide interactions
in the catalytic cavity during the isomerization change the reaction
coordinate, resulting in two minima with small energy differences
to the transition state. These small free energy barriers should in
principle make the reaction feasible at room temperature once the
conformer is bound in the right conformation
Catalytic Mechanism of H<sub>2</sub> Activation by a Carbenoid Aluminum Complex
The catalytic mechanism of H<sub>2</sub> activation by a carbenoid
aluminum compound is analyzed in great detail. On the basis of the
reaction force analysis, the electronic activity that takes place
during the chemical reaction was identified and characterized through
the reaction electronic flux and rationalized in terms of chemical
events that drive the reaction. Successive transformation of the nucleophilic
or electrophilic character of the reagents along the reaction coordinate
monitored through the dual descriptor allows us to obtain a very complete
and detailed description of the reaction mechanism that proceeds through
a two-stage mechanism in a one-kinetic-step process
Basis Electronic Activity of Molecular Systems. A Theory of Bond Reactivity
In this paper, we present a new finding, the basis electronic
activity
(BEA) of molecular systems; it corresponds to the significant, although
nonreactive, vibrationally induced electronic activity that takes
place in any molecular system. Although the moleculeâs BEA
is composed of an equal number of local contributions as the vibrational
degrees of freedom, our results indicate that only stretching modes
contribute to it. To account for this electronic activity, a new descriptor,
the bond electronic flux (BEF), is introduced. The BEF combined with
the force constant of the potential well hosting the electronic activity
gives rise to the effective bond reactivity index (EBR), which turns
out to be the first density functional theory-based descriptor that
simultaneously accounts for structural and electronic effects. Besides
quantifying the bond reactivity, EBR provides a basis to compare the
reactivities of bonds inserted in different chemical environments
and paves the way for the exertion of selective control to enhance
or inhibit their reactivities. The new concepts formulated in this
paper and the associated computational tools are illustrated with
characterization of the BEA of a set of representative molecules.
In all cases, the BEFs follow the same linear pattern, whose slopes
indicate the intensity of the electronic activity and quantify the
reactivity of chemical bonds
Basis Electronic Activity of Molecular Systems. A Theory of Bond Reactivity
In this paper, we present a new finding, the basis electronic
activity
(BEA) of molecular systems; it corresponds to the significant, although
nonreactive, vibrationally induced electronic activity that takes
place in any molecular system. Although the moleculeâs BEA
is composed of an equal number of local contributions as the vibrational
degrees of freedom, our results indicate that only stretching modes
contribute to it. To account for this electronic activity, a new descriptor,
the bond electronic flux (BEF), is introduced. The BEF combined with
the force constant of the potential well hosting the electronic activity
gives rise to the effective bond reactivity index (EBR), which turns
out to be the first density functional theory-based descriptor that
simultaneously accounts for structural and electronic effects. Besides
quantifying the bond reactivity, EBR provides a basis to compare the
reactivities of bonds inserted in different chemical environments
and paves the way for the exertion of selective control to enhance
or inhibit their reactivities. The new concepts formulated in this
paper and the associated computational tools are illustrated with
characterization of the BEA of a set of representative molecules.
In all cases, the BEFs follow the same linear pattern, whose slopes
indicate the intensity of the electronic activity and quantify the
reactivity of chemical bonds
Mechanisms of Formation of Hemiacetals: Intrinsic Reactivity Analysis
The reaction mechanism of the hemiacetal formation from
formaldehyde
and methanol has been studied theoretically at the B3LYP/6-311++GÂ(d,p)
level. In addition to the study of the reaction between the isolated
reactants, three different kinds of catalysis have been explored.
The first one examines the use of assistants, especially bridging
water molecules, in the proton transfer process. The second one attempts
to increase the local electrophilicity of the carbon atom in formaldehyde
with the presence of a BrĂžnsted acid (H<sup>+</sup> or H<sub>3</sub>O<sup>+</sup>). The last one considers the combined effect
of both catalytic strategies. The reaction force, the electronic chemical
potential, and the reaction electronic flux have been characterized
for the reaction path in each case. In general, it has been found
that structural rearrangements represent an important energetic penalty
during the activation process. The barriers for the reactions catalyzed
by BrĂžnsted acids show a high percentage of electronic reorganization
contribution. The catalytic effects for the reactions assisted by
water molecules are due to a reduction of the strain in the transition
state structures. The reaction that includes both acid catalysis and
proton assistance transfer shows the lowest energy barrier (25.0 kJ
mol<sup>â1</sup>)
Binding of Trivalent Arsenic onto the Tetrahedral Au<sub>20</sub> and Au<sub>19</sub>Pt Clusters: Implications in Adsorption and Sensing
The
interaction of arsenicÂ(III) onto the tetrahedral Au<sub>20</sub> cluster
was studied computationally to get insights into the interaction
of arsenic traces (presented in polluted waters) onto embedded electrodes
with gold nanostructures. Pollutant interactions onto the vertex,
edge, or inner gold atoms of Au<sub>20</sub> were observed to have
a covalent character by forming metalâarsenic or metalâoxygen
bonding, with adsorption energies ranging from 0.5 to 0.8 eV, even
with a stable physisorption; however, in aqueous media, the Auâvertexâpollutant
interaction was found to be disadvantageous. The substituent effect
of a platinum atom onto the Au<sub>20</sub> cluster was evaluated
to get insights into the changes in the adsorption and electronic
properties of the adsorbentâadsorbate systems due to chemical
doping. It was found that the dopant atom increases both the metalâpollutant
adsorption energy and stability onto the support in a water media
for all interaction modes; adsorption energies were found to be in
a range of 0.6 to 1.8 eV. All interactions were determined to be accompanied
by electron transfer as well as changes in the local reactivity that
determine the amount of transferred charge and a decrease in the HOMOâLUMO
energy gap with respect to the isolated substrate