Reaction force constant as a descriptor of the principle of non-perfect synchronization.

CONTEXT: In this study, a small set of 1,3-dipolar cycloaddition reactions that proceed at the same exothermicity is presented. Our main objective was to extend the application of the reaction force constant concept to gain an understanding of the reactivity principles. Inspired by a recent article where we show that the Bell-Evans-Polanyi principle is fulfilled under the condition of an equal degree of (a)synchronicity, here, we demonstrate that the reaction force constant is also a suitable descriptor to quantify the principle of non-perfect synchronization proposed by Bernasconi as a way to understand deviations from the Bell-Evans-Polanyi principle. METHODS: Reaction profiles V ( ξ ) , F ( ξ ) , and κ ( ξ ) were performed at the B3LYP/6-31G(d,p) level of theory. The stabilizing interactions were characterized using the energy decomposition analysis combined with the natural orbitals for chemical valence, EDA-NOCV, method. The present work was done using Gaussian 09 and Multiwfn programs.

The Dual Descriptor Reveals the Janus-Faced Behaviour of Diiodine.

The Janus-faced ligand behavior of diiodine (I2) was evidenced after applying the dual descriptor (DD or second-order Fukui function), thus providing additional support to the work performed by Rogachev and Hoffmann in 2013. Along with its capacity to reveal sites susceptible to undergo attacks simultaneously of nucleophilic and electrophilic types, another advantage of DD lies in being an orbital-free descriptor. That means it is based only upon total electron densities when written in its most accurate operational formula. This quality is not exclusive of DD because when Fukui functions are written in terms of electron densities instead of densities of frontier molecular orbitals, they become orbital-free descriptors too. Furthermore, the present work is an application of the generalized operational formula of the dual descriptor published in 2016 that takes into account any possible degeneracy in frontier molecular orbitals. As a proof about capabilities of DD, the possible sites for a favorable interaction between I2 with two organometallic compounds [Rh2(O2CCF3)4] and [(C8H11N2)Pt (CH3)] were correctly revealed by overlapping the biggest lobe for receiving nucleophilic attacks of one molecule with the biggest lobe for receiving electrophilic attacks of the other molecule, so allowing to predict the same coordination modes as experimentally known: linear "end-on" for the [(C8H11N2)Pt (CH3)]…I2, and bent "end-on" for the [Rh2(O2CCF3)4]…I2 interactions.

Physicochemical and Theoretical Characterization of a New Small Non-Metal Schiff Base with a Differential Antimicrobial Effect against Gram-Positive Bacteria.

Searching for adequate and effective compounds displaying antimicrobial activities, especially against Gram-positive bacteria, is an important research area due to the high hospitalization and mortality rates of these bacterial infections in both the human and veterinary fields. In this work, we explored (E)-4-amino-3-((3,5-di-tert-butyl-2-hydroxybenzylidene)amino) benzoic acid (SB-1, harboring an intramolecular hydrogen bond) and (E)-2-((4-nitrobenzilidene)amino)aniline (SB-2), two Schiff bases derivatives. Results demonstrated that SB-1 showed an antibacterial activity determined by the minimal inhibitory concentration (MIC) against Staphylococcus aureus, Enterococcus faecalis, and Bacillus cereus (Gram-positive bacteria involved in human and animal diseases such as skin infections, pneumonia, diarrheal syndrome, and urinary tract infections, among others), which was similar to that shown by the classical antibiotic chloramphenicol. By contrast, this compound showed no effect against Gram-negative bacteria (Klebsiella pneumoniae, Escherichia coli, and Salmonella enterica). Furthermore, we provide a comprehensive physicochemical and theoretical characterization of SB-1 (as well as several analyses for SB-2), including elemental analysis, ESMS, 1H and 13C NMR (assigned by 1D and 2D techniques), DEPT, UV-Vis, FTIR, and cyclic voltammetry. We also performed a computational study through the DFT theory level, including geometry optimization, TD-DFT, NBO, and global and local reactivity analyses.

Analysis in silico of chemical reactivity employing the local hyper-softness in some classic aromatic compounds, boron aromatic clusters and all-metal aromatic clusters.

In the current work, the authors analyzed and compared the chemical behavior of some (anti)aromatic compounds. The species selected are benzene and cyclobutadiene as the aromatic and antiaromatic classical examples, respectively. Next, the anion Al 4 2 - , which is the first all-metal molecule catalogued as aromatic and its non-metallic isoelectronic analog, B 4 2 - were also analyzed. The antiaromatic clusters Al 4 4 - and B 4 4 - were studied in form of lithium salts. And the end, the non-planar B 12 boron cluster and its isoelectronic analogs ( B 11 Be - and B 11 C + ) were considered for being analyzed under the same criterium. The analysis was realized employing the following descriptors: molecular electrostatic potential and local hyper-softness to get insights concerning local reactivity when facing reagents leading to ionic or covalent interactions. The results show that all the molecules analyzed presented some specific variations in their respective local reactivity despite being labeled as aromatic compounds. This analysis provides a notion that the local reactivity is more based on the nature of the atoms and the molecular geometry than the aromatic character by itself.

The density polarization reveals directions of electron displacements due to the substituent effect: Analysis performed on a metal-organic Mo-Oxo catalyst.

Some Mo-oxo complexes bearing pyridine rings have the capability for dihydrogen production from water. However, energy barrier and overall energy vary depending on the effect exerted by several substituent groups located at different positions around one or more pyridine rings which are ligands of these compounds. Based on the Karunadasa and coworkers investigation where the para-position was experimentally tested in compounds derivatised from the 2,6-bis[1,1-bis(2-pyridil)ethyl]-pyridine oxo-molybdenum complex synthesized (Karunadasa et al., Nature, 2010, 464, 1329), we tested the combined effect of electron-withdrawing and electron-donating groups simulated as perturbations represented by point-charges. Then, we used the density polarization concept, δρ(r), a local reactivity descriptor corresponding to the partially integrated linear response function, χ(r, r') (a non-local reactivity descriptor), which is able to reveal different displacements of π-electrons on molecular structures. We perturbed the para-positions in the pentadentate ligand 2,6-bis[1,1-bis(2-pyridil)ethyl]-pyridine in the Mo-based complex by means of point-charges. They were located in three different configurations of the organic ligand (trans, geminal, and cis) which could help to explain energy barriers and overall energy of reactions catalyzed by this type of Mo-complexes. Our results indicate that the trans configuration of point-charges induces the most amount of fraction of electron shifted on the complex. A Mo-based complex bearing the same trans configuration for electron-withdrawing and electron-donating substituent groups (cyano and amino, respectively), leads to a kinetically more favorable H2 release than the cis or geminal configuration of the substituent groups aforementioned.

1,3-Dipolar Cycloadditions by a Unified Perspective Based on Conceptual and Thermodynamics Models of Chemical Reactivity.

The main aim in the present report is to gain a deeper understanding of typical 1,3-dipolar cycloadditions by means of three chemical reactivity models in a unified perspective: conceptual density functional theory, distortion/interaction, and reaction force analysis. The focus is to explore the information provided by each reactivity model and how they complement or reinforce each other. Our results showed that the Bell-Evans-Polanyi (BEP) relationship is fulfilled, which is consistent with the Hammond-Leffler postulate. The electronic chemical potential based analysis classifies the reactions as HOMO-, HOMO/LUMO-, and LUMO-controlled reactions as the activation energy increases. It seems likely that HOMO-controlled reaction shifts into LUMO-controlled one as the transition state (TS) position does from early into late. Therefore, the transition from HOMO- (and early TS) into LUMO-controlled (and late TS) is paid by shifting the overall energy change into an endothermic direction, thus supporting the fulfillment of the BEP principle. While thermodynamic models unveil that the distortion or structural rearrangements mainly drive the activation barriers rather than interaction or electronic rearrangements in accord with the distortion/interaction and reaction force analysis, respectively. It is also found that both models are consistent when energy associated with structural and electronic reordering from reaction force analysis is respectively confronted with destabilizing (distortion and Pauli repulsion) and stabilizing (electrostatic and orbital interactions) contributions from the distortion/interaction model, which, on the other hand, increases as low activation barrier and high exothermicity are converted into the high barrier and low exothermicity along with the BEP relation. Finally, the reaction force constant reveals that all 1,3-dipolar cycloaddition reactions proceed by a synchronous single-step mechanism, unveiling that the degree of synchronicity is quite the same in all reactions, confirming the statement that BEP is fulfilled for similar reactions proceeding by a quite alike degree of synchronicity.

KID Procedure Applied on the [(PY5Me2)MoO]+ Complex.

The KID (Koopmans in DFT) protocol usually applies in organic molecules of the closed-shell type. We used the KID procedure on an open-shell Mo-based system for the first time to choose the most suitable density functional to compute global and local reactivity descriptors obtained from the conceptual density-functional theory (DFT). From a set of 18 density functionals, spread from the second until the fourth rung of Jacob's ladder: BLYP, BP86, B97-D, MN12-L, MN15-L, M06-L, M11-L, CAM-B3LYP, PBE0, B3LYP, N12-SX, M06-2X, MN15, MN12-SX, ωB97X-D, M11, LC-ωHPBE, and APFD, we concluded that CAM-B3LYP provides the best outcome, and in the second place, M06-2X. Because the vertical first ionization potential and vertical first electron affinity in the ground state (gs) are defined as follows I = E gs(N - 1) - E gs(N) and A = E gs(N) - E gs(N + 1), where E gs(N - 1), E gs(N), and E gs(N + 1) correspond to energies of the system bearing N, N + 1, and N - 1 electrons, along with Koopmans' theorem (KT) given by I ≈ -εHOMO (εHOMO, highest occupied molecular orbital energy) and A ≈ -εLUMO (εLUMO, lowest unoccupied molecular orbital energy), the deviation from the KT was performed by the use of the index, such that J I = |E gs(N - 1) - E gs(N) + εHOMO| and J A = |E gs(N) - E gs(N + 1) + εLUMO|, which are absolute deviations from the perspective of I and A, respectively. Furthermore, the εSOMO (SOMO: singly-occupied molecular orbital energy) leads us to another index given by |ΔSL| = |εSOMO - εLUMO|. Therefore, J HL and |ΔSL| are indexes defined to evaluate the quality of the KT when employed within the context of quantum chemical calculations based on DFT and not the Hartree-Fock theory. We propose the index that could be more suitable to choose the most proper density functional because the J HL and |ΔSL| are independent indexes.

Scrutinizing the substituent effect on Mo-based electrocatalysts for molecular hydrogen release through axial-equatorial decomposition: a DFT study.

Based on the experimental precedent discovered by Kuranadasa and coworkers [H. I. Karunadasa et al., Nature, 2010, 464, 1329] to produce dihydrogen from water electrocatalyzed by 2,6-bis[1,1-bis(2-pyridyl)ethyl]-pyridine oxo-molybdenum complexes, we performed an extensive analysis to study the substituent group effect of derivatised compounds coming from the before mentioned Mo-based metal-organic cations in terms of two kinds of substitutions: axial and equatorial at the para-position of pyridine rings; several conceptual tools were used to back up our conclusions. We found that each type of substituent group (electron-withdrawing and electron-donating ones) exerts an independent influence on energetic parameters (energy barrier and overall energy). This opens the chance to search for a synergistic effect by combining these opposite behaviours of these substituents located in the equatorial and axial para-positions of pyridine rings to computationally modulate the aforementioned energetic parameters. This procedure will make easier the proposal of new catalysts to favour either kinetically or thermodynamically or in both ways the production of dihydrogen from water. Additionally, we encompassed a key point: the number of solvent molecules, so that including their presence in further investigations is mandatory.

Effect of the exchange-correlation functional on the synchronicity/nonsynchronicity in bond formation in Diels-Alder reactions: a reaction force constant analysis.

In this paper, we assess the performance of 24 density functional theory (DFT) based methods classified into 5 categories (GGA, MGGA, HGGA, HMGGA and DHGGA) in predicting reaction energetics, transition state geometries, and the degree of synchronicity/nonsynchronicity in the formation of two new C-C single-bonds in three Diels-Alder reactions between symmetrically and unsymmetrically substituted cyanoethylenes and cyclopentadiene, which gradually proceed from fully synchronous to highly asynchronous concerted mechanisms. This important concept in reaction mechanisms is revealed by the fine structure of the reaction force constant κ(ξ) along the transition region. Some wave function theory (WFT) based methods are also assessed against the CCSD(T) and CCSD benchmarks for the energy and geometry, respectively. The results and the statistical analysis of the errors confirm the robustness of SCS-MP2 (a WFT-based method) as one of the most reliable computational approaches. Regarding DFT-based methods, hybrid exchange-correlation functionals combined with medium-range electron correlation effects or long-range corrected exchange appear as the best performing methods, highlighting both M11 and M06-2X, since a certain percentage of exact Hartree-Fock exchange could counterbalance the delocalization errors that affect pure functionals. Thus, they reliably describe energetics, geometries and the degree of synchronicity in the formation of new C-C single bonds in Diels-Alder reactions. Noticeably, moderate performance for double hybrid functionals and poor performance for the most popular B3LYP method were found as well.

Assessment of ten density functionals through the use of local hyper-softness to get insights about the catalytic activity : Iron-based organometallic compounds for ethylene polymerization as testing molecules.

Ten functionals were used to assess their capability to compute a local reactivity descriptor coming from the Conceptual Density Functional Theory on a group of iron-based organometallic compounds that have been synthesized by Zohuri, G.H. et al. in 2010; these compounds bear the following substituent groups: H-, O2N- and CH3O- at the para position of the pyridine ring and their catalytic activities were experimentally measured by these authors. The present work involved a theoretical analysis applied on the aforementioned iron-based compounds thus leading to suggest a new 2,6-bis(imino)pyridine catalyst based on iron(II) bearing a fluorine atom whose possible catalytic activity is suggested to be near the catalytic activity of the complex bearing a hydrogen atom as a substituent group by means of the so called local hyper-softness (LHS) thus opening a chance to estimate a possible value of catalytic activity for a new catalyst that has not been synthesized yet without simulating the entire process of ethylene polymerization. Since Conceptual DFT is not a predictive theory, but rather interpretative, an analysis of the used reactivity descriptor and its dependence upon the level of theory was carried in the present work, thus revealing that care should be taken when DFT calculations are used for these purposes.

Solvent effect on the degree of (a)synchronicity in polar Diels-Alder reactions from the perspective of the reaction force constant analysis.

In this work, we computationally evaluated the influence of six different molecular solvents, described as a polarizable continuum model at the M06-2X/6-31+G(d,p) level, on the activation barrier/reaction rate, overall energy change, TS geometry, and degree of (a)synchronicity of two concerted Diels-Alder cycloadditions of acrolein (R1) and its complex with Lewis acid acrolein···BH3 (R2) to cyclopentadiene. In gas-phase, we found that both exothermicity and activation barrier are only reduced by about 2.0 kcal mol-1, and the asynchronicity character of the mechanism is accentuated when BH3 is included. An increment in the solvent's polarity lowers the activation energy of R1 by 1.3 kcal mol-1, while for R2 the reaction rate is enhanced by more than 2000 times at room temperature (i.e., the activation energy decreases by 4.5 kcal mol-1) if the highest polar media is employed. Therefore, a synergistic effect is achieved when both external agents, i.e., Lewis acid catalyst and polar solvent, are included together. This effect was ascribed to the ability of the solvent to favor the encounter between cyclopentadiene and acrolein···BH3. This was validated by the asymmetry of the TS which becomes highly pronounced when either both or just BH3 is considered or the solvent's polarity is increased. Finally, the reaction force constant κ(ξ) reveals that an increment in the solvent's polarity is able to turn a moderate asynchronous mechanism of the formation of the new C-C σ-bonds into a highly asynchronous one. Graphical abstract A synergistic effect is achieved when both external agents, i.e., Lewis acid catalyst and polar solvent, are included together: lowered energy barriers and increased asynchronicities.

A 3D visualization of the substituent effect : A brief analysis of two components of the operational formula of dual descriptor for open-shell systems.

Six organometallic compounds coming from a basic Mo-based complex were analyzed from the perspective of the dual descriptor in order to detect subtle influences that a substituent group could exert on the reactive core at a long range. Since the aforementioned complexes are open-shell systems, the used operational formula for the dual descriptor is that one defined for those aforementioned systems, which was then compared with spin density. In addition, dual descriptor was decomposed into two terms, each of which was also applied on every molecular system. The obtained results indicated that components of dual descriptor could become more useful than the operational formula of dual descriptor because differences exerted by the substituents at the para position were better detected by components of dual descriptor rather than the dual descriptor by itself.

A generalized operational formula based on total electronic densities to obtain 3D pictures of the dual descriptor to reveal nucleophilic and electrophilic sites accurately on closed-shell molecules.

By means of the conceptual density functional theory, the so-called dual descriptor (DD) has been adapted to be used in any closed-shell molecule that presents degeneracy in its frontier molecular orbitals. The latter is of paramount importance because a correct description of local reactivity will allow to predict the most favorable sites on a molecule to undergo nucleophilic or electrophilic attacks; on the contrary, an incomplete description of local reactivity might have serio us consequences, particularly for those experimental chemists that have the need of getting an insight about reactivity of chemical reagents before using them in synthesis to obtain a new compound. In the present work, the old approach based only on electronic densities of frontier molecular orbitals is replaced by the most accurate procedure that implies the use of total electronic densities thus keeping consistency with the essential principle of the DFT in which the electronic density is the fundamental variable and not the molecular orbitals. As a result of the present work, the DD will be able to properly describe local reactivities only in terms of total electronic densities. To test the proposed operational formula, 12 very common molecules were selected as the original definition of the DD was not able to describe their local reactivities properly. The ethylene molecule was additionally used to test the capability of the proposed operational formula to reveal a correct local reactivity even in absence of degeneracy in frontier molecular orbitals. © 2016 Wiley Periodicals, Inc.

Correction: Towards the rationalization of catalytic activity values by means of local hyper-softness on the catalytic site: a criticism about the use of net electric charges.

Correction for 'Towards the rationalization of catalytic activity values by means of local hyper-softness on the catalytic site: a criticism about the use of net electric charges' by Jorge Ignacio Martínez-Araya et al., Phys. Chem. Chem. Phys., 2015, DOI: 10.1039/c5cp03822g.

Towards the rationalization of catalytic activity values by means of local hyper-softness on the catalytic site: a criticism about the use of net electric charges.

By means of the Spin-Polarized Conceptual Density Functional Theory (SP-CDFT), three 2,6-bis(imino)pyridine catalysts based on iron(II), used for polymerization of ethylene, were studied. The catalysts differed by the substituent group, bearing either -H, -NO2 or -OCH3. To date, catalytic activity, a purely experimental parameter measuring the mass of polyethylene produced per millimole of iron per time and pressure unit at a fixed temperature, has not been explained in terms of local hyper-softness. The latter is a purely theoretical parameter designed for quantifying electronic effects; it is measured using the metal atom responsible for the coordination process with the monomer (ethylene). Because steric effects are not relevant in these kinds of catalysts and only electronic effects drive the catalytic process, an interesting link is found between catalytic activity and the local hyper-softness condensed on the iron atom by means of four functionals (B3LYP, BP86, B97D, and VSXC). This work demonstrates that the use of local hyper-softness, predicted by the SP-CDFT, is a suitable parameter for explaining order relationships among catalytic activity values, thus quantifying the electronic influence of the substituent group inducing this difference; the use of only net electric charges does not lead to clear conclusions. This finding can aid in estimating catalytic activities leading to a more rational design of new catalysts via computational chemistry.

Computational nanochemistry report on the oxicams--conceptual DFT indices and chemical reactivity.

A density functional theory study of eight oxicams was carried out in order to determine their global and local reactivities. These types of reactivities were measured by means of global and local reactivity descriptors coming from the conceptual density functional theory. Net electrophilicity as a global reactivity descriptor and local hypersoftness as a local reactivity descriptor were the used tools to distinguish reactivity and selectivity among these oxicams. Globally, isoxicam presents the highest electron donating capacity; meanwhile, the highest electron accepting capacity is exhibited by droxicam. Locally, two oxicams present neither nucleophilic nor electrophilic relevant reactivity in their peripheral pyridine ring, droxicam and tenoxicam, so that their more reactive zones are found on the respective fused rings. Oxicams have been divided into two subgroups in order to facilitate the local analysis of reactivity. One group is characterized because their most important condensed values for local hypersoftnes are well-separated: 4-meloxicam, lornoxicam, meloxicam, and normeloxicam. Meanwhile, the opposite situation is found in droxicam, isoxicam, piroxicam, and tenoxicam. As a whole, the nucleophilic characteristic noticeably predominates in these eight oxicams instead of an electrophilic behavior, thus meaning a greater tendency to donate electrons rather than withdrawing them; a consequence of this behavior implies a favorable interaction with a hypothetical receptor bearing one or more electron acceptor functional groups rather than electron donor functional groups; this would imply a maximization of this interaction from the covalent point of view.

Explaining reaction mechanisms using the dual descriptor: a complementary tool to the molecular electrostatic potential.

The intrinsic reactivity of cyanide when interacting with a silver cation was rationalized using the dual descriptor (DD) as a complement to the molecular electrostatic potential (MEP) in order to predict interactions at the local level. It was found that DD accurately explains covalent interactions that cannot be explained by MEP, which focuses on essentially ionic interactions. This allowed the rationalization of the reaction mechanism that yields silver cyanide in the gas phase. Other similar reaction mechanisms involving a silver cation interacting with water, ammonia, and thiosulfate were also explained by the combination of MEP and DD. This analysis provides another example of the usefulness of DD as a tool for gaining a deeper understanding of any reaction mechanism that is mainly governed by covalent interactions.

An intermediate level of approximation for computing the dual descriptor.

At present, there are two levels of approximation to compute the dual descriptor (DD). The first uses the total electronic density of the original system along with the electronic densities of the system with one more electron and one less electron, but this procedure is time consuming and normal termination of computation of total electronic densities is not guaranteed. The second level of approximation uses only the electronic densities of frontier molecular orbitals, HOMO and LUMO, to avoid the former approximation; however, the orbital relaxation implicitly included in the first level of approximation is absent in the second, thus risking an incorrect interpretation of local reactivity. Between the lowest occupied molecular orbital (LOMO) and the highest unoccupied molecular orbital (HUMO), a framework to provide an expression of the DD in terms of the electronic densities of all molecular orbitals (except HUMO and LOMO) has been proposed to be implemented by programmers as a computational code. This methodology implies another level of approximation located between the conventional approximation methods mentioned above. In this study, working equations have been oriented toward molecular closed- and open-shell systems. In addition, the mathematical expression for a closed-shell system was applied to acetylene in order to assess the capability of this approach to generate the DD.

Revisiting caffeate's capabilities as a complexation agent to silver cation in mining processes by means of the dual descriptor--a conceptual DFT approach.

Caffeic acid (C(9)H(8)O(4)) and its conjugate base C(9)H(7)O(4) (-) (anionic form-known as caffeate) were analyzed computationally through the use of quantum chemistry to assess their intrinsic global and local reactivity using the tools of conceptual density functional theory. The anionic form was found to be better at coordinating the silver cation than caffeic acid thus suggesting the use of caffeate as a complexation agent. The complexation capability of caffeate was compared with that of some of the most common ligand agents used to coordinate silver cations. Local reactivity descriptors allowed identification of the preferred sites on caffeate for silver cation coordination thus generating a plausible silver complex. All silver complexes were analyzed thermodynamically considering interaction energies in both gas and aqueous phases; the complexation free energy in aqueous phase was also determined. These results suggest that more attention be paid to the caffeate anion and its derivatives because this work has shed new light on the behavior of this anion in the recovery of silver cations that could be exploited in silver mining processes in a environmentally friendly way.