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 molecule's 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.

Interacting Quantum Atoms Analysis of the Reaction Force: A Tool to Analyze Driving and Retarding Forces in Chemical Reactions.

The analysis of the reaction force and its topology has provided a wide range of fruitful concepts in the theory of chemical reactivity over the years, allowing to identify chemically relevant regions along a reaction profile. The reaction force (RF), a projection of the Hellmann-Feynman forces acting on the nuclei of a molecular system onto a suitable reaction coordinate, is partitioned using the interacting quantum atoms approach (IQA). The exact IQA molecular energy decomposition is now shown to open a unique window to identify and quantify the chemical entities that drive or retard a chemical reaction. The RF/IQA coupling offers an extraordinarily detailed view of the type and number of elementary processes that take reactants into products, as tested on two sets of simple reactions.

Diels-Alder reaction mechanisms of substituted chiral anthracene: A theoretical study based on the reaction force and reaction electronic flux.

Quantum chemical calculations were used to study the mechanism of Diels-Alder reactions involving chiral anthracenes as dienes and a series of dienophiles. The reaction force analysis was employed to obtain a detailed scrutiny of the reaction mechanisms, it has been found that thermodynamics and kinetics of the reactions are quite consistent: the lower the activation energy, the lower the reaction energy, thus following the Bell-Evans-Polanyi principle. It has been found that activation energies are mostly due to structural rearrangements that in most cases represented more than 70% of the activation energy. Electronic activity mostly due to changes in σ and π bonding were revealed by the reaction electronic flux (REF), this property helps identify whether changes on σ or π bonding drive the reaction. Additionally, new global indexes describing the behavior of the electronic activity were introduced and then used to classify the reactions in terms of the spontaneity of their electronic activity. Local natural bond order electronic population analysis was used to check consistency with global REF through the characterization of specific changes in the electronic density that might be responsible for the activity already detected by the REF. Results show that reactions involving acetoxy lactones are driven by spontaneous electronic activity coming from bond forming/strengthening processes; in the case of maleic anhydrides and maleimides it appears that both spontaneous and non-spontaneous electronic activity are quite active in driving the reactions.

Spectral Decomposition of the Reaction Force Constant.

Qualitative relationships between the reaction force constant κ(ξ), the second derivative of the potential energy V(ξ), and the reactive vibrational mode that drives the reaction in the transition state region have been used in the past to measure the synchronicity of key chemical events that lead a chemical reaction. In this work, we provide a formal demonstration that κ(ξ) can be expressed in terms of the frequencies of normal modes at each point of the reaction path. This produce a decomposition of κ(ξ) that is used to analyze few representatives chemical reactions, a series of intramolecular proton transfer on formic, thioformic and dithioformic acids, and an intermolecular double proton transfer in the HNS2:H2O complex. It has been found that this partitioning allows to identify unambigously the reactive mode that drives the reaction at each point along the reaction coordinate thus giving relevant and detailed information about the mechanism of the chemical reactions under study.

Theoretical study of glycine amino acid adsorption on graphene oxide.

The non-dissociative and dissociative adsorptions of zwitterionic Gly on graphene oxide (GO) was studied in the framework of DFT using a cluster model approach. In this work, the interaction with an epoxy group of GO basal plane was mainly considered. As a comparison, the non-dissociative and dissociative adsorptions of neutral Gly were also taken into account. The non-dissociative adsorption modes for zwitterionic and neutral Gly conformers show binding energies of 12.2 and 14.4 kcal mol-1, respectively. These molecules are thought to remain over the GO surface due to attractive noncovalent interactions. Two dissociative adsorption modes, for Z-Gly and N-Gly, show smaller binding energies of 7.2 and 8.4 kcal mol-1, where the deprotonated species links strongly through a C-O or C-N covalent bond to the GO surface. The results obtained in the present theoretical approach to the glycine/graphene oxide system support the fact that glycine can be attached to epoxy groups of graphene oxide basal planes in addition to the anchoring on edge oxidation groups. In summary, we conclude that glycine can be used as a reducing agent as well as a functionalizer of GO sheets.

Hydrogenation and hydration of carbon dioxide: a detailed characterization of the reaction mechanisms based on the reaction force and reaction electronic flux analyses.

A computational DFT study of the reaction mechanism of hydrogenation and hydration of carbon dioxide is presented. It has been found that hydrogenation and hydration are endoenergetic reactions that are carried out in two steps, passing by a stable intermediate that is surrounded by energy barriers of 70 kcal/mol and 10 kcal/mol for hydrogenation and 50 kcal/mol and 10 kcal/mol for hydration. Using the reaction force analysis, we were able to characterize the physical nature of the activation barriers and found that activation energies are mostly due to structural rearrangements. An interesting difference in the reaction mechanisms disclosed by the reaction force and electronic flux analyses is that while in the hydrogenation reaction the mechanisms is conditioned by the H2 cleavage with a high energy barrier, in the hydration reaction the formation of a transient four member ring structure favoring an attractive local hydrogen bond interaction pushes the reaction toward the product with a considerably lower energy barrier.

An extension of the Marcus equation: the Marcus potential energy function.

An analytic potential function consistent with the Marcus equation for activation energy is formulated and used to reveal new insights into the activation process in chemical reactions. As for the Marcus equation, the new potential function depends only on two parameters, the reaction energy and the activation energy (or the so-called Marcus intrinsic activation energy). Combination of the Marcus potential with the reaction force analysis provides two-parameter analytic expressions for the reaction force, reaction force constant, and reaction works. Moreover, since the parameters necessary to define the Marcus potential energy function can be obtained experimentally, the present model may produce experimental analytic potentials allowing for new and interesting applications, thus emerging as a powerful tool to characterize activation processes in chemical reactions.

Reaction Electronic Flux Perspective on the Mechanism of the Zimmerman Di-π-methane Rearrangement.

The reaction electronic flux (REF) offers a powerful tool in the analysis of reaction mechanisms. Noteworthy, the relationship between aromaticity and REF can eventually reveal subtle electronic events associated with reactivity in aromatic systems. In this work, this relationship was studied for the triplet Zimmerman di-π-methane rearrangement. The aromaticity loss and gain taking place during the reaction is well acquainted by the REF, thus shedding light on the electronic nature of reactions involving dibenzobarrelenes.

Insights into the Mechanism of Ground and Excited State Double Proton Transfer Reaction in Formic Acid Dimer.

The mechanism of ground and excited state double proton transfer reaction in formic acid dimer has been analyzed with the help of reaction force and the reaction electronic flux. The separation of reaction electronic flux in terms of electronic activity and reactivity, NBO, and dual descriptor lends additional support for the mechanism. Interestingly we found that the ground state double proton transfer mechanism is concerted synchronic, whereas the excited state double proton transfer is concerted asynchronic in nature.

The influence of the metal cations and microhydration on the reaction trajectory of the N3 ↔ O2 thymine proton transfer: Quantum mechanical study.

This study involves the intramolecular proton transfer (PT) process on a thymine nucleobase between N3 and O2 atoms. We explore a mechanism for the PT assisted by hexacoordinated divalent metals cations, namely Mg2+ , Zn2+ , and Hg2+ . Our results point out that this reaction corresponds to a two-stage process. The first involves the PT from one of the aqua ligands toward O2. The implications of this stage are the formation of a hydroxo anion bound to the metal center and a positively charged thymine. To proceed to the second stage, a structural change is needed to allow the negatively charged hydroxo ligand to abstract the N3 proton, which represents the final product of the PT reaction. In the presence of the selected hexaaqua cations, the activation barrier is at most 8 kcal/mol. © 2017 Wiley Periodicals, Inc.

ETS-NOCV Decomposition of the Reaction Force: The HCN/CNH Isomerization Reaction Assisted by Water.

The partitioning of the reaction force based on the extended-transition-state natural orbital for chemical valence (ETS-NOCV) scheme has been proposed. This approach, together with the analysis of reaction electronic flux (REF), has been applied in a description of the changes in the electronic structure along the IRC pathway for the HCN/CNH isomerization reaction assisted by water. Two complementary ways of partitioning the system into molecular fragments have been considered ("reactant perspective" and "product perspective"). The results show that the ETS-NOCV picture is fully consistent with REF and bond-order changes. In addition, proposed ETS-NOCV decomposition of the reaction force allows for the quantitative assessment of the influence of the observed bond-breaking and bond-formation processes, providing detailed information about the reaction-driving and reaction-retarding force components within the assumed partitioning scheme. © 2017 Wiley Periodicals, Inc.

Double Gold Activation of 1-Ethynyl-2-(Phenylethynyl)Benzene Toward 5-exo-dig and 6-endo-dig Cyclization Reactions.

In this work, a detailed characterization was carried out of the ring-closure mechanism of EPB (1-ethynyl-2-(phenylethynyl)benzene) toward the 5-exo-dig and 6-endo-dig cyclization reactions, catalyzed by two Au-N-heterocyclic carbene (NHC) moieties. It was found that the 5-exo-dig cyclization takes place with a slightly lower activation barrier and larger exothermicity compared to that of the 6-endo-dig cyclization, in agreement with the available experimental data. A phenomenological partition (structural and electronic) for rate constants computed using transition-state theory and the reaction force analysis was used to shed light into the nature of the activation rate constant. It was found that rate constants are influenced by a strong structural component, which is larger for the 5-exo-dig cyclization due to the strain to form the five-membered ring. On the other hand, the gold activation mechanism is evidenced by a σ- and π-coordination of the Au-NHC moieties to the EPB substrate. It was found that differences in the σ-coordination arise on the reaction path for the 5-exo-dig and 6-endo-dig cyclizations. Thus, in the 6-endo-dig cyclization the σ gold-EPB interaction is weakened as a consequence of the formation of the cationic aryl intermediate, while for the 5-exo-dig cyclization this interaction was found to be favored. Furthermore, although minor changes in the Au-EPB coordination occur on the reaction path, these bonds are formally established in the TS vicinity. Results support the concerted nature of the dual gold activation mechanism.

Study of antiradical mechanisms with dihydroxybenzenes using reaction force and reaction electronic flux.

Phenolic compounds represent an important category of antioxidants because they help inhibit the oxidation process of organic compounds, while also acting as antiradicals in many biological processes. In this work, we analyze the transfer mechanisms for a set of catechols and resorcinols of a single electron, proton and hydrogen, with the radical peroxyl (˙OOH) and with different electron withdrawing and donating groups as substituents. By using the M05-2X exchange correlation functional within the Density Functional Theory framework combined with the 6-311++G(d,p) basis set, we were able to compute the Gibbs free energies for all mechanisms and compounds. According to the thermodynamic results, the hydrogen atom transfer mechanism was the most favorable. Therefore, this mechanism with substituents -CH3 and -COH in catechol and resorcinol was analyzed, using the reaction force and reaction electronic flux to characterize the structural and electronic changes that take place during the reaction. Our results show that electron donating groups favor electronic changes along the reaction path, increasing the spontaneity of the hydrogen atom transfer mechanism.

The Role of Co-Activation and Ligand Functionalization in Neutral Methallyl Nickel(II) Catalysts for Ethylene Oligomerization and Polymerization.

A detailed quantum chemical study that analyzed the mechanism of ethylene oligomerization and polymerization by means of a family of four neutral methallyl NiII catalysts is presented. The role of the boron co-activators, BF3 and B(C6 F5 )3 , and the position of ligand functionalization (ortho or para position of the N-arylcyano moiety of the catalysts) were investigated to explain the chain length of the obtained polymers. The chain initialization proceeded with higher activation barriers for the ortho-functionalized complexes (≈19 kcal mol-1 ) than the para-substituted isomers (17-18 kcal mol-1 ). Two main pathways were revealed for the chain propagation: The first pathway was favored when using the B(C6 F5 )3 co-activated catalyst, and it produced long-chain polymers. A second pathway led to the ß-hydrogen complexes, which resulted in chain oligomerization; this pathway was preferred when the BF3 co-activated catalysts were used. Otherwise, the termination of longer chains occurred via a stable hydride intermediate, which was formed with an energy barrier of about 14 kcal mol-1 for the B(C6 F5 )3 co-activated catalysts. Significant new insights were made into the reaction mechanism, whereby neutral methallyl NiII catalysts act in oligomerization and polymerization processes. Specifically, the role of co-activation and ligand functionalization, which are key information for the further design of related catalysts, were revealed.

The performance of methallyl nickel complexes and boron adducts in the catalytic activation of ethylene: a conceptual DFT perspective.

In this work, global and local descriptors of chemical reactivity and selectivity are used to explain the differences in reactivities toward ethylene of methallyl nickel complexes and their B(C6F5)3 and BF3 adducts. DFT calculations were used to explain why nickel complexes alone are inactive in ethylene polymerization while their boron adducts can activate it. It is shown that chemical potential, hardness, electrophilicity and molecular electrostatic potential surfaces describe fairly well the reactivity and selectivity of these organometallic systems toward ethylene. Experimental data indicates that addition of a borane molecule to nickel complexes changes dramatically their reactivity-behavior that is confirmed computationally. Our results show that bare complexes are unable to activate ethylene-a Lewis base-because they also behave as Lewis bases. The addition of the co-catalyst-a Lewis acid-turns the adducts into Lewis acids, making them active towards ethylene.

Effects of the ionization in the tautomerism of uracil: A reaction electronic flux perspective.

The one-step tautomerization processes of uracil and its radical cation and radical anion have been investigated in the light of the reaction force and reaction electronic flux (REF) formalisms. The relative energies of the different tautomers as well as the corresponding tautomerization barriers have been obtained through the use of the G4 high-level ab initio method and by means of B3LYP/6-311+G(3df,2p)//B3LYP/6-311+G(d, p) calculations. Systematically, the enol radical cations are more stable in relative terms than the neutral, due to the higher ionization energy of the diketo forms with respect to the enolic ones. Conversely, the enol radical anions, with the only exception of the 2-keto-N1 anion, are found to be less stable than the neutral. The effects of the ionization are also sizable on the tautomerization barriers although this effect also depends on the particular tautomerization process. The reaction force analysis shows that all reactions are mainly activated through structural rearrangements that initiate the electronic activity. This electronic activity is monitored along the reaction coordinate through the REF that obeys a delicate balance between the acid and basic character of the atoms involved in the hydrogen transfer.

A detailed analysis of the mechanism of a carbocationic triple shift rearrangement.

The mechanism of a carbocationic triple shift rearrangement is analyzed within the conceptual framework of the reaction force. All the systems were characterized computationally using DFT through B3LYP/6-31+G(d,p) methodology. A complete description of the electronic activity taking place during the reaction emerged through the use of the reaction electronic flux that, together with an NBO Wiberg bond order, produces a detailed picture of the reaction mechanism in terms of chemical events that drive the reaction during the different stages of the process. It is found that a carbocation triple shift occurs asynchronously although in a concerted way.

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.

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.

Enhanced reactivity of Lys182 explains the limited efficacy of biogenic amines in preventing the inactivation of glucose-6-phosphate dehydrogenase by methylglyoxal.

This study examines the inactivation of the enzyme glucose 6-phosphate dehydrogenase (G6PD) by methylglyoxal (MG) and the eventual protection exerted by endogenous amines. To determine the protective effect of amines, the rate constant of the reaction of MG with the amino group of N-α-acetyl-lysine, carnosine, spermine and spermidine was measured at pH 7.4, and the behavior of endogenous amines was analyzed on the basis of quantum chemical reactivity descriptors. A 63% reduction in the enzyme activity was found upon incubation of G6PD with MG at pH 7.4. The inactivation of G6PD was even larger when the pH was increased to 9.4, revealing a weak protective effect by the amines. The results suggest that some basic residues of G6PD exhibit an anomalous reactivity, which likely reflects a shift in the standard pK(a) value due to the local environment in the enzyme. Under the experimental conditions used in the assays, this hypothesis was corroborated by mass spectrometry analysis, which points out that modification of Lys182 in the binding site is responsible for the inactivation of G6PD by MG. These results emphasize the need to search for more effective antiglycating agents, which can compete with basic amino acid residues possessing enhanced reactivity in proteins.