Bárbara Herrera

The reaction force : Three key points along an intrinsic reaction coordinate

The concept of the reaction force is presented and discussed in detail. For typical processes with energy barriers, it has a universal form which defines three key points along an intrinsic reaction coordinate: the force minimum, zero and maximum. We suggest that the resulting four zones be interpreted as involving preparation of reactants in the first, transition to products in the second and third, and relaxation in the fourth. This general picture is supported by the distinctive patterns of the variations in relevant electronic properties. Two important points that are brought out by the reaction force are that (a) the traditional activation energy comprises two separate contributions, and (b) the transition state corresponds to a balance between the driving and the retarding forces.

Insights into the chemical meanings of the reaction electronic flux

Abstract The negative derivative of the chemical potential with respect to the reaction coordinate is called reaction electronic flux and has recently focused a wide interest to better understand chemical reactions at molecular level. After much consideration, it is now well accepted that positive REF values are associated with spontaneous processes, while negative REF ones translate unspontaneous phenomena. These characteristics of the REF are based on a thermodynamic analogy and have been shown right through computational results. In this paper, we develop two analytical expressions of the REF in both the canonical and the grand canonical ensembles. The connection between both equations is established. They are then analyzed, and some arguments are put forward to support the alleged characteristic of the REF and its ability to properly discriminate spontaneous from unspontaneous phenomena.

The role of the reaction force to characterize local specific interactions that activate the intramolecular proton transfers in DNA basis

MP2/6-311G** and B3LYP/6-311G** studies of the intramolecular proton transfer in adenine, cytosine, guanine, and thymine has been performed, with the aim of evaluating the role of the reaction force as a global descriptor of the process. It turns out that the reaction force profile is quite an interesting tool to characterize reaction mechanisms. Indeed, in adenine and cytosine the proton transfer is assisted by an increasing electronic delocalization in the adjacent ring, whereas in guanine and thymine the attractive electrostatic interaction with the acceptor oxygen atom is strong enough to promote the transfer.

Using the reaction force and the reaction electronic flux on the proton transfer of formamide derived systems.

In this work, we present a theoretical study of the mechanism of double proton transfer in formamide, formamide-thioformamide and thioformamide dimers. The reaction mechanisms were analyzed in terms of the energy profile and novel concepts such as the reaction force profile and reaction electronic flux, along with local electronic properties such as NBO analysis. All systems were characterized computationally using DFT/B3LYP 6-311G** on Gaussian09. These results show that the electronic processes take place mostly in the transition state for all the systems; in the formamide and thioformamide dimers, electron transfer has a synchronic nature, while the electron transfer is asynchronic in the formamide-thioformamide dimer.

The mechanism of chemisorption of hydrogen atom on graphene: Insights from the reaction force and reaction electronic flux

At the PBE-D3/cc-pVDZ level of theory, the hydrogen chemisorption on graphene was analyzed using the reaction force and reaction electronic flux (REF) theories in combination with electron population analysis. It was found that chemisorption energy barrier is mainly dominated by structural work (∼73%) associated to the substrate reconstruction whereas the electronic work is the greatest contribution of the reverse energy barrier (∼67%) in the desorption process. Moreover, REF shows that hydrogen chemisorption is driven by charge transfer processes through four electronic events taking place as H approaches the adsorbent surface: (a) intramolecular charge transfer in the adsorbent surface; (b) surface reconstruction; (c) substrate magnetization and adsorbent carbon atom develops a sp(3) hybridization to form the σC-H bond; and (d) spontaneous intermolecular charge transfer to reach the final chemisorbed state.

Role of water in intramolecular proton transfer reactions of formamide and thioformamide

A theoretical study of the mechanism of intramolecular proton transfer reactions in formamide and thioformamide is presented; the focus is on the characterization of the role of water in the reactions. The reaction mechanisms was analyzed with the help of energy profiles in the frame of the reaction force analysis and using the reaction electronic flux to characterize the electronic activity that takes place along the reaction. Bader’s quantum theory of atoms in molecules is used to confirm the reaction mechanism and help elucidate the specific role of water. Results at the DFT/B3LYP 6-311G** level of theory show that water catalyzes the proton transfer reaction lowering the activation energy by a factor of two. The reaction force analysis allowed the characterization of activation energies, indicating that in all four reactions, it is mostly due to structural reordering.

The mechanism of Menshutkin reaction in gas and solvent phases from the perspective of reaction electronic flux

The mechanism of Menshutkin reaction, NH3 + CH3Cl = [CH3–NH3]+ + Cl-, has been thoroughly studied in both gas and solvent (H2O and cyclohexane) phase. It has been found that solvents favor the reaction, both thermodynamically and kinetically. The electronic activity that drives the mechanism of the reaction was identified, fully characterized, and associated to specific chemical events, bond forming/breaking processes, by means of the reaction electronic flux. This led to a complete picture of the reaction mechanism that was independently confirmed by natural bond-order analysis and the dual descriptor for chemical reactivity and selectivity along the reaction path.

A Relation between Different Scales of Electrophilicity: Are the Scales Consistent Along a Chemical Reaction?

In this paper, a relationship is established between three electrophilicity scales, namely, the electrophilicity index defined by Parr, Liu, and von Szentpaly; the electron affinity; and the energy of the lowest unoccupied molecular orbital (LUMO). Profiles of electrophilicity index and LUMO energies for different kinds of chemical reactions are compared to verify if they remain consistent during a whole chemical process. It appears that the electrophilicity index and the LUMO energies are linearly correlated in almost all the cases. Besides electrophilicity scales, profiles provide valuable information about the charge-transfer stage of a chemical process.

Influence of the monoclinic and tetragonal zirconia phases on the water gas shift reaction. A theoretical study

We present a theoretical study of the water gas shift reaction taking place on zirconia surfaces modeled by monoclinic and tetragonal clusters. In order to understand the charge transfer between the active species, in this work we analyze the influence of the geometry of monoclinic and tetragonal zirconia using reactivity descriptors such as electronic che − mical potential (μ), charge transfer (