Phenomenological description of the transition state, and the bond breaking and bond forming processes of selected elementary chemical reactions: an information-theoretic study (original) (raw)
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International Journal of Quantum Chemistry, 2012
In this work, we have investigated in position (r) and momentum (p) spaces the concurrent phenomena occurring at the vicinity of the transition state (TS) (the so-called transition region) of selected chemical reactions (such as the hydrogenic abstraction and the exchange hydrogenic reactions) by means of a broad set of single informationtheoretic functionals of the one-particle density (such as the disequilibrium (D), exponential entropy (L), Fisher information (I) and the power entropy (J)) and composite informationtheoretic measures which includes various information planes (such as the I-D, D-L, and I-J planes) and complexities of the Fisher-Shannon and L opez-Mancini-Calbet (LMC) types. The analysis of the single functionals and the information planes revealed that these information-theoretical elements can identify all the chemically significant regions, not only the reactant/product regions (R/P) and the TS but also those that are not present in the energy profile, such as the bond cleavage energy region (BCER), the bond breaking/forming regions (B-B/F) and the charge transfer complex. Moreover, the analysis of the complexities shows that in position as well as in the joint (r-p) spaces, the energy profile of the abstraction reaction bears the same information-theoretical features of the LMC and FS measures. Finally, it is shown why most of the chemical features of interest (such as e.g., BCER and B-B/F) are lost in the energy profile, being only revealed when particular information-theoretical aspects of localizability (L or J), uniformity (D) and disorder (I) are considered.
Fisher Information Study in Position and Momentum Spaces for Elementary Chemical Reactions
Journal of Chemical Theory and Computation, 2010
The utility of the Fisher information measure is analyzed to detect the transition state, the stationary points of a chemical reaction, and the bond breaking/forming regions of elementary reactions such as the simplest hydrogen abstraction and the identity S N 2 exchange ones. This is performed by following the intrinsic reaction path calculated at the MP2 and QCISD(T) levels of theory with a 6-311++G(3df, 2p) basis set. Selected descriptors of both position and momentum space densities are utilized to support the observations, such as the molecular electrostatic potential (MEP), the hardness, the dipole moment, along with geometrical parameters. Our results support the concept of a continuum of transient of Zewail and Polanyi for the transition state rather than a single state, which is also in agreement with reaction force analyses.
Information-theoretical complexity for the hydrogenic abstraction reaction
Molecular Physics, 2011
We investigate the complexity of the hydrogenic identity S N 2 exchange reaction by means of information-theoretic functionals such as disequilibrium (D), exponential entropy (L), Fisher information (I), power entropy (J) and joint information-theoretic measures, i.e., the I-D, D-L and I-J planes and the Fisher-Shannon (FS) and López-Mancini-Calbet (LMC) shape complexities. The several information-theoretic measures of the one-particle density were computed in position (r) and momentum (p) spaces. The analysis revealed that the chemically significant regions of this reaction can be identified through most of the information-theoretic functionals or planes, not only the ones which are commonly revealed by the energy, such as the reactant/product (R/P) and the transition state (TS), but also those that are not present in the energy profile such as the bond cleavage energy region (BCER), the bond breaking/forming regions (B-B/F) and the charge transfer process (CT). The analysis of the complexities shows that the energy profile of the identity S N 2 exchange reaction bears no simple behavior with respect to the LMC and FS measures. Most of the chemical features of interest (BCER, B-B/F and CT) are only revealed when particular information-theoretic aspects of localizability (L or J), uniformity (D) and disorder (I) are considered.
Reaction times, activation energies, branching ratios, yields, and many other quantitative attributes are important for precise organic syntheses and generating detailed reaction mechanisms. Often, it would be useful to be able to classify proposed reactions as fast or slow. However, quantitative chemical reaction data, especially for atom-mapped reactions, are difficult to find in existing databases. Therefore, we used automated potential energy surface exploration to generate 12,000 organic reactions involving H, C, N, and O atoms calculated at the ωB97X-D3/def2-TZVP quantum chemistry level. We report the results of geometry optimizations and frequency calculations for reactants, products, and transition states of all reactions. Additionally, we extracted atom-mapped reaction SMILES, activation energies, and enthalpies of reaction. We believe that this data will accelerate progress in automated methods for organic synthesis and reaction mechanism generation---for example, by enabl...
Information-theoretical complexity for the hydrogenic identity SN2 exchange reaction
Journal of Mathematical Chemistry, 2012
We investigate the complexity of the hydrogenic identity S N 2 exchange reaction by means of information-theoretic functionals such as disequilibrium (D), exponential entropy (L), Fisher information (I), power entropy (J) and joint information-theoretic measures, i.e., the I-D, D-L and I-J planes and the Fisher-Shannon (FS) and López-Mancini-Calbet (LMC) shape complexities. The several information-theoretic measures of the one-particle density were computed in position (r) and momentum (p) spaces. The analysis revealed that the chemically significant regions of this reaction can be identified through most of the information-theoretic functionals or planes, not only the ones which are commonly revealed by the energy, such as the reactant/product (R/P) and the transition state (TS), but also those that are not present in the energy profile such as the bond cleavage energy region (BCER), the bond breaking/forming regions (B-B/F) and the charge transfer process (CT). The analysis of the complexities shows that the energy profile of the identity S N 2 exchange reaction bears no simple behavior with respect to the LMC and FS measures. Most of the chemical features of interest (BCER, B-B/F and CT) are only revealed when particular information-theoretic aspects of localizability (L or J), uniformity (D) and disorder (I) are considered.
Phenomenological Description of a Three-Center Insertion Reaction: An Information-Theoretic Study
Journal of Physical Chemistry A, 2010
Information-theoretic measures are employed to describe the course of a three-center chemical reaction in terms of detecting the transition state and the stationary points unfolding the bond-forming and bond-breaking regions which are not revealed in the energy profile. The information entropy profiles for the selected reactions are generated by following the intrinsic-reaction-coordinate (IRC) path calculated at the MP2 level of theory from which Shannon entropies in position and momentum spaces at the QCISD(T)/6-311++G(3df,2p) level are determined. Several complementary reactivity descriptors are also determined, such as the dipole moment, the molecular electrostatic potential (MEP) obtained through a multipole expansion (DMA), the atomic charges and electric potentials fitted to the MEP, the hardness and softness DFT descriptors, and several geometrical parameters which support the information-theoretic analysis. New density-based structures related to the bondforming and bond-breaking regions are proposed. Our results support the concept of a continuum of transient of Zewail and Polanyi for the transition state rather than a single state, which is also in agreement with reaction-force analyses.
Journal of Molecular Structure: THEOCHEM, 1991
A great deal of detailed information is available on the energy and molecular geometry changes of chemical reactions where single atoms or groups are transferred. However, much less detail is known on reactions where two or more atoms move simultaneously. In this work we deal with this type of reactions, in particular with the hydrogen-deuterium (or hydrogen-hydrogen) exchange in organic compounds. Important characteristics of these reactions can be deduced by analyzing the corresponding reaction paths. In this work, we apply ideas recently introduced, regarding relationships between potential energy and molecular shape along reaction paths, to study the H-H exchange process in benzene. We have reexamined a calculation in the literature, finding evidence of a double barrier with a very shallow minimum at the cents of the path. The changes found in molecular shape correlate exactly with this result: from minimum to minimum, four shape transitions are found, instead of two, as would be expected for a simple barrier. For comparison, we have also calculated a simpler model for the transfer: the H-H exchange between the two carbon atoms in ethene. The reaction path for this system has been computed at ab initio level with the 3-21G basis, leading to similar energy-shape interrelations along the path with and without including correlation at MP2 level. The calculated barrier shapes for benzene and ethene are similar.
Classification of reaction pathways via momentum–space and quantum molecular similarity measures
Chemical Physics Letters, 2003
For four rearrangement reactions, we evaluate (i) values of the moments of momentum 〈pn〉(−2⩽n⩽+1) for reactants, products and transition states (ii) position–space similarity indices between reactants, products and transition states using wavefunctions generated from both Hartree–Fock and density-functional theory (B3LYP). Both the momentum–space expectation values and the similarity measures can be used to distinguish Hammond and anti-Hammond behaviour. In position–space,