Curly arrows meet electron density transfers in chemical reaction mechanisms: from electron localization function (ELF) analysis to valence-shell electron-pair repulsion (VSEPR) inspired interpretation

Probing the electron density transfers during a chemical reaction can provide important insights, making possible to understand and control chemical reactions. This aim has required extensions of the relationships between the traditional chemical concepts and the quantum mechanical ones. The present work examines the detailed chemical insights that have been generated through 100 years of work worldwide on G. N. Lewis's ground breaking paper on The Atom and the Molecule (Lewis, G. N. The Atom and the Molecule, J. Am. Chem. Soc. 1916, 38, 762–785), with a focus on how the determination of reaction mechanisms can be reached applying the bonding evolution theory (BET), emphasizing how curly arrows meet electron density transfers in chemical reaction mechanisms and how the Lewis structure can be recovered. BET that combines the topological analysis of the electron localization function (ELF) and Thom's catastrophe theory (CT) provides a powerful tool providing insight into molecular mechanisms of chemical rearrangements. In agreement with physical laws and quantum theoretical insights, BET can be considered as an appropriate tool to tackle chemical reactivity with a wide range of possible applications. Likewise, the present approach retrieves the classical curly arrows used to describe the rearrangements of chemical bonds for a given reaction mechanism, providing detailed physical grounds for this type of representation. The ideas underlying the valence-shell-electron pair-repulsion (VSEPR) model applied to non-equilibrium geometries provide simple chemical explanations of density transfers. For a given geometry around a central atom, the arrangement of the electronic domain may comply or not with the VSEPR rules according with the valence shell population of the considered atom. A deformation yields arrangements which are either VSEPR defective (at least a domain is missing to match the VSEPR arrangement corresponding to the geometry of the ligands), VSEPR compliant or pseudo VSEPR when the position of bonding and non-bonding domains are interchanged. VSEPR defective arrangements increase the electrophilic character of the site whereas the VSEPR compliant arrangements anticipate the formation of a new covalent bond. The frequencies of the normal modes which account for the reaction coordinate provide additional information on the succession of the density transfers. This simple model is shown to yield results in very good agreement with those obtained by BET.We wish to thank Professors R. J. Gillespie, Henry H. Rzepa and Patrick Chaquin and L. R. Domingo for stimulating discussions and the referees for their very constructive comment

An electron localization function and catastrophe theory analysis on the molecular mechanism of gas-phase identity SN2 reactions

A set of four reactions, XCH3+X− (X=F, Cl, Br) and ClSiH3+Cl−, is investigated by means of the joint use of the electron localization function (ELF) and catastrophe theory (CT) analysis in order to obtain newinsights into the bond breaking/forming processes for identity SN2 gas-phase reactions. Using DFT calculations at the OLYP/6-311++G(d,p) level, the effect of nucleophile (F, Cl, and Br anions) and the role of reacting centers (C or Si) on the reaction mechanisms are investigated. The charge-shift character of carbon–halogen bonds is studied by determination of the weights of the Lewis resonance structures. In all SN2 reactions at the carbon atom, there is a progressive reduction on the covalent character of the C–X bond from the reactant complex (0.41, 0.57, 0.58 for F, Cl, and Br, respectively) until the bond-breaking process, occurring before the transition structure is reached. On the other hand, the Si–Cl bond maintains its degree of covalent character (0.51) from the isolated fragments to the formation of a stable transition complex, presenting two silicon– chlorine charge-shifted bonds. The analysis of the ELF topology along the reaction path reveals that all reactions proceed via the same turning points of fold-type but the order is inverted for reactions taking place at C or Si atom

Curly arrows, electron flow, and reaction mechanisms from the perspective of the bonding evolution theory

Despite the usefulness of curly arrows in chemistry, their relationship with real electron density flows is still imprecise, and even their direct connection to quantum chemistry is still controversial. The paradigmatic description – from first principles – of the mechanistic aspects of a given chemical process is based mainly on the relative energies and geometrical changes at the stationary points of the potential energy surface along the reaction pathway; however, it is not sufficient to describe chemical systems in terms of bonding aspects. Probing the electron density distribution during a chemical reaction can provide important insights, enabling us to understand and control chemical reactions. This aim has required an extension of the relationships between the concepts of traditional chemistry and those of quantum mechanics. Bonding evolution theory (BET), which combines the topological analysis of the electron localization function (ELF) and Thom’s catastrophe theory (CT), provides a powerful method that offers insight into the molecular mechanism of chemical rearrangements. In agreement with the laws of physical and aspects of quantum theory, BET can be considered an appropriate tool to tackle chemical reactivity with a wide range of possible applications. In this work, BET is applied to address a long-standing problem: the ability to monitor the flow of electron density. BET analysis shows a connection between quantum mechanics and bond making/forming processes. Likewise, the present approach retrieves the classical curly arrows used to describe the rearrangements of chemical bonds and provides detailed physical grounds for this type of representation. We demonstrate this procedure using the test set of prototypical examples of thermal ring apertures, and the degenerated Cope rearrangement of semibullvalene

Describing the molecular mechanism of organic reactions by using topological analysis of electronic localization function

Here, we provide an essay on the analysis of the reaction mechanism at the molecular level; in particular, the evolution of the electron pair, as it is provided by the ELF, is used to decribe the reaction pathway. Then, the reaction mechanism is determined by the topological changes of the ELF gradient field along a series of structural stability domains. From this analysis, concepts such as bond breaking/forming processes, formation/annihilation of lone pairs and other electron pair rearrangements arise naturally along the reaction progress simply in terms of the different ways of pairing up the electrons. To visualize these results some organic reaction mechanisms (the thermal ring aperture of cyclobutene and cyclohexa-1,3-diene) have been selected, indicating both the generality and utility of this type of analysis

THEORETICAL STUDY OF CHLORINATION REACTION OF NITROBENZENE FROM DFT CALCULATIONS

The geometric parameters of stationary points on the potential surface energy of the chlorination reaction of nitrobenzene in the presence of Aluminium chloride as catalyst were investigated theoretically by hybrid DFT (Density Functional Theory) calculations in order to determine his general reaction mechanism in gas phase and in solution. The results obtained by DFT have been compared with CCSD(T) method which is the most powerful post-Hartree Fock method in terms of inclusion of dynamic correlation. Although the electrophilic substitution reaction is widely taught in most courses in organic chemistry, the mechanism has been very few studied theoretically. The results obtained in gas phase are consistent with the traditional description of these reactions: the orientation of this substitution in meta position depends on the stability of a reaction intermediate (Wheland said). Without taking in consideration the reactants and products, six stationary points are found on the potential surface energy of this reaction. The reaction has also been studied in the presence of solvent and we’ve noted that the influence of solvent decreases the electrostatic attraction on the Wheland complex, but the general reaction mechanism remains unchanged in solution

Portable LQCD Monte Carlo code using OpenACC

Varying from multi-core CPU processors to many-core GPUs, the present scenario of HPC architectures is extremely heterogeneous. In this context, code portability is increasingly important for easy maintainability of applications; this is relevant in scientific computing where code changes are numerous and frequent. In this talk we present the design and optimization of a state-of-the-art production level LQCD Monte Carlo application, using the OpenACC directives model. OpenACC aims to abstract parallel programming to a descriptive level, where programmers do not need to specify the mapping of the code on the target machine. We describe the OpenACC implementation and show that the same code is able to target different architectures, including state-of-the-art CPUs and GPUs

Molecular force field calculations by the MINDO/3 method

MINDO/3 semi empirical SCF MO method has been used to calculate the molecular force fields of a wide variety of small molecules. Calculated quadratic force constants as well as diagonal cubic and quartic stretching constants are in overall agreement with experiment

Analyse topologique de quelques interactions métal-ligand (mX (M = Sc, Ti, ..., Cu ; X = CO, N2, CN-, H2O, NH3 et F-))

PARIS-BIUSJ-Thèses (751052125) / SudocPARIS-BIUSJ-Physique recherche (751052113) / SudocSudocFranceF