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Slawomir Berski - One of the best experts on this subject based on the ideXlab platform.

  • the nature of multiple boron nitrogen bonds studied using Electron Localization Function elf Electron density aim and natural bond orbital nbo methods
    Journal of Molecular Modeling, 2020
    Co-Authors: Grzegorz Mierzwa, Agnieszka J Gordon, Slawomir Berski
    Abstract:

    Local nature of the boron-nitrogen (BN) bonding with different formal multiplicities (B≡N, B=N, B-N) have been investigated for 25 experimentally established organoboron molecules in both real and the Hilbert space, using topological analysis of Electron Localization Function (ELF), Electron density (AIM), and natural bond orbital (NBO) method. Each BN bond has been represented (ELF) by the bonding disynaptic attractor V(B,N), with the basin Electron population between 5.72e and 1.83e, confirming possible existence of all the three bond types. A covalent character of bonding can be associated with the dative mechanism due to the V(B,N) bonding basin formed mainly (91-96%) by the N Electron density. Similarly, the NBO method shows 2-center natural orbitals, consisting largely of the hybrids from the N atom. The AIM analysis yields the features typical for shared (H(3,-1)(r)   0) interactions. The deLocalization indices, describing Electron exchanges between B and N quantum atoms, are smaller than 1.5, even for formally very short triple B≡N bonds. Graphical abstract .

  • the nature of the t t double bond t b al ga in in dialumene and its derivatives topological study of the Electron Localization Function elf
    Journal of Molecular Modeling, 2019
    Co-Authors: Michal Michalski, Agnieszka J Gordon, Slawomir Berski
    Abstract:

    The local Electronic structure of the Al=Al bond was studied in dialumene and derivatives of dialumene in which the Al atoms were substituted by B, Ga, or In atoms. DFT calculations were performed using the B3LYP, B3PW91, PBE0, M06-L, and M06-2X Functionals. Topological analysis of the Electron Localization Function described the covalent bonds mentioned above using the disynaptic basins Vi=1,2(B,B), Vi=1,2(Al,Al), V(Ga,Ga), and Vi=1,2(In,In). The basin populations were smaller than 4 e, as expected for a double bond: B=B 2.97 e, Al=Al 3.44–3.5 e, Ga=Ga 3.58 e, and In=In 3.86 e. The Al=Al, Ga=Ga, and In=In bonds were found to be intermediate in character between single and double bonds. Topological analysis of the ρ(r) field for dialumene showed a non-nuclear attractor along the Al=Al bond, with a pseudoatom basin population of 0.937 e. NBO analysis suggested that a double bond occurred only in the molecules containing Al, Ga, or In atoms. The character of the Ga=Ga bond was observed to be strongly dependent on the effective core potential used in the calculations.

  • 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
    Chemical Communications, 2016
    Co-Authors: Juan Andres, Slawomir Berski, Bernard Silvi
    Abstract:

    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.

  • nature of the bonding in the aungx ng ar kr xe x f cl br i molecules topological study on Electron density and the Electron Localization Function elf
    Journal of Physical Chemistry A, 2015
    Co-Authors: Emilia Makarewicz, Agnieszka J Gordon, Slawomir Berski
    Abstract:

    Topological analysis of the Electron Localization Function (ELF) has been carried out for the AuNgX (Ng = Ar, Kr, Xe; X = F, Cl, Br, I) molecules using the wave Function approximated by the CCSD, MP2, and DFT(B3LYP, M062X) methods including zero-order regular approximation (ZORA). In the Ng–F bond, the bonding disynaptic attractor V(Ng,F) is missing; therefore, there are no signs of the covalent binding. The nature of the Au–Ng bond depends on the computational method used. Analysis of the ELF carried out for the AuArF and AuXeF molecules, with the wave Function approximated by the CCSD and MP2 methods, shows the V(Au,Ng) attractor possibly corresponding to a partially covalent binding between the gold and noble gas atom. However, its very small basin population (<1e) and a very large value of the variance of the basin population suggest that the Au–Ng bond has a very delocalized character. Such bond nature may be related to the charge shift concept with a resonance of the Au–+NgX, Au+–NgX hybrids. The we...

  • effects of xenon insertion into hydrogen bromide comparison of the Electronic structure of the hbr co2 and hxebr co2 complexes using quantum chemical topology methods Electron Localization Function atoms in molecules and symmetry adapted perturbation
    Journal of Physical Chemistry A, 2014
    Co-Authors: Emilia Makarewicz, Agnieszka J Gordon, Zdzislaw Latajka, Krzysztof Mierzwicki, Slawomir Berski
    Abstract:

    Quantum chemistry methods have been applied to study the influence of the Xe atom inserted into the hydrogen-bromine bond (HBr → HXeBr), particularly on the nature of atomic interactions in the HBr···CO2 and HXeBr···CO2 complexes. Detailed analysis of the nature of chemical bonds has been carried out using topological analysis of the Electron Localization Function, while topological analysis of Electron density was used to gain insight into the nature of weak nonbonding interactions. Symmetry-adapted perturbation theory within the orbital approach was applied for greater understanding of the physical contributions to the total interaction energy.

Juan Andres - One of the best experts on this subject based on the ideXlab platform.

  • 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
    Chemical Communications, 2016
    Co-Authors: Juan Andres, Slawomir Berski, Bernard Silvi
    Abstract:

    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.

  • Electronic fluxes during diels alder reactions involving 1 2 benzoquinones mechanistic insights from the analysis of Electron Localization Function and catastrophe theory
    Journal of Computational Chemistry, 2012
    Co-Authors: Patricio Gonzaleznavarrete, Juan Andres, Slawomir Berski, Luis R Domingo, Bernard Silvi
    Abstract:

    By means of the joint use of Electron Localization Function (ELF) and Thom's catastrophe theory, a theoretical analysis of the energy profile for the hetero-Diels-Alder reaction of 4-methoxy-1,2-benzoquinone 1 and methoxyethylene 2 has been carried out. The 12 different structural stability domains obtained by the bonding evolution theory have been identified as well as the bifurcation catastrophes (fold and cusp) responsible for the changes in the topology of the system. This analysis permits finding a relationship between the ELF topology and the evolution of the bond breaking/forming processes and Electron pair rearrangements through the reaction progress in terms of the different ways of pairing up the Electrons. The reaction mechanism corresponds to an asynchronous Electronic flux; first, the O1C5 bond is formed by the nucleophilic attack of the C5 carbon of the Electron rich ethylene 2 on the most electrophilically activated carbonyl O1 oxygen of 1, and once the σ bond has been completed, the formation process of the second O4C6 bond takes place. In addition, the values of the local electrophilicity and local nucleophilcity indices in the framework of conceptual density Functional theory accounts for the asychronicity of the process as well as for the observed regioselectivity. © 2012 Wiley Periodicals, Inc.

  • nature of the ring closure process along the rearrangement of octa 1 3 5 7 tetraene to cycloocta 1 3 5 triene from the perspective of the Electron Localization Function and catastrophe theory
    Journal of Computational Chemistry, 2012
    Co-Authors: Juan Andres, Slawomir Berski, Luis R Domingo, Patricio Gonzaleznavarrete
    Abstract:

    We analyze the behavior of the energy profile of the ring-closure process for the transformation of (3Z,5Z)-octa-1,3,5,7-tetraene 5 to (1Z,3Z,5Z)-cycloocta-1,3,5-triene 6 through a combination of Electron Localization Function (ELF) and catastrophe theory (CT). From this analysis, concepts such as bond breaking/forming processes, formation/annihilation of lone pairs, and other Electron pair rearrangements arise naturally through the reaction progress simply in terms of the different ways of pairing up the Electrons. A relationship between the topology and the nature of the bond breaking/forming processes along this rearrangement is reported. The different domains of structural stability of the ELF occurring along the intrinsic reaction path have been identified. The reaction mechanism consists of six steps separated by fold and cusp catastrophes. The transition structure is observed in the third step, d(C1C8) = 2.342 A, where all bonds have topological signature of single bonds (CC). The “new” C1C8 single bond is not formed in transition state and respective catastrophe of the ELF field (cusp) is localized in the last step, d(C1C8) ≈ 1.97 A, where the two monosynaptic nonbonding basins V(C1) and V(C8) are joined into single disynaptic bonding basin V(C1,C8). The V(C1,C8) basin corresponds to classical picture of the C1C8 bond in the Lewis formula. In cycloocta-1,3,5-triene 6 the single C1C8 bond is characterized by relatively small basin population 1.72e, which is much smaller than other single bonds with 2.03 and 2.26e. © 2011 Wiley Periodicals, Inc. J Comput Chem, 2011

  • olefin epoxidation by molybdenum peroxo compound molecular mechanism characterized by the Electron Localization Function and catastrophe theory
    Journal of Physical Chemistry A, 2011
    Co-Authors: Slawomir Berski, Juan Andres, Victor Polo, Fabricio R Sensato, V S Safont
    Abstract:

    The oxygen atom transfer reaction from the Mimoun-type complex MoO(η2-O2)2OPH3 to ethylene C2H4 affording oxirane C2H4O has been investigated within the framework of the Bonding Evolution Theory in which the corresponding molecular mechanism is characterized by the topological analysis of the Electron Localization Function (ELF) and Thom’s catastrophe theory (CT). Topological analysis of ELF and Electron density analysis reveals that all Mo−O bonds in MoO(η2-O2)2OPH3 and MoO2(η2-O2)OPH3 belong to closed-shell type interactions though negative values of total energy densities Ee(rBCP) imply some covalent contribution. The peroxo Oi—Oj bonds are characterized as charge-shift or protocovalent species in which pairs of monosynaptic basins V3(Oi), V3(Oj) with a small Electron population of ∼0.25e each, are localized between core basins C(Oi), C(Oj). The oxygen transfer reaction from molybdenum diperoxo complex MoO(η2-O2)2OPH3 to C2H4 system can be described by the following consecutive chemical events: (a) pro...

  • understanding reaction mechanisms in organic chemistry from catastrophe theory applied to the Electron Localization Function topology
    Journal of Physical Chemistry A, 2008
    Co-Authors: Victor Polo, Juan Andres, Slawomir Berski, Luis R Domingo, Bernard Silvi
    Abstract:

    Thomʼs catastrophe theory applied to the evolution of the topology of the Electron Localization Function (ELF) gradient field constitutes a way to rationalize the reorganization of Electron pairing and a powerful tool for the unambiguous determination of the molecular mechanisms of a given chemical reaction. The identification of the turning points connecting the ELF structural stability domains along the reaction pathway allows a rigorous characterization of the sequence of Electron pair rearrangements taking place during a chemical transformation, such as multiple bond forming/breaking processes, ring closure processes, creation/annihilation of lone pairs, transformations of C−C multiple bonds into single ones. The reaction mechanism of some relevant organic reactions: Diels−Alder, 1,3-dipolar cycloaddition and Cope rearrangement are reviewed to illustrate the potential of the present approach.

Bernard Silvi - One of the best experts on this subject based on the ideXlab platform.

  • 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
    Chemical Communications, 2016
    Co-Authors: Juan Andres, Slawomir Berski, Bernard Silvi
    Abstract:

    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.

  • Electronic fluxes during diels alder reactions involving 1 2 benzoquinones mechanistic insights from the analysis of Electron Localization Function and catastrophe theory
    Journal of Computational Chemistry, 2012
    Co-Authors: Patricio Gonzaleznavarrete, Juan Andres, Slawomir Berski, Luis R Domingo, Bernard Silvi
    Abstract:

    By means of the joint use of Electron Localization Function (ELF) and Thom's catastrophe theory, a theoretical analysis of the energy profile for the hetero-Diels-Alder reaction of 4-methoxy-1,2-benzoquinone 1 and methoxyethylene 2 has been carried out. The 12 different structural stability domains obtained by the bonding evolution theory have been identified as well as the bifurcation catastrophes (fold and cusp) responsible for the changes in the topology of the system. This analysis permits finding a relationship between the ELF topology and the evolution of the bond breaking/forming processes and Electron pair rearrangements through the reaction progress in terms of the different ways of pairing up the Electrons. The reaction mechanism corresponds to an asynchronous Electronic flux; first, the O1C5 bond is formed by the nucleophilic attack of the C5 carbon of the Electron rich ethylene 2 on the most electrophilically activated carbonyl O1 oxygen of 1, and once the σ bond has been completed, the formation process of the second O4C6 bond takes place. In addition, the values of the local electrophilicity and local nucleophilcity indices in the framework of conceptual density Functional theory accounts for the asychronicity of the process as well as for the observed regioselectivity. © 2012 Wiley Periodicals, Inc.

  • bonding changes along solid solid phase transitions using the Electron Localization Function approach
    2011
    Co-Authors: Julia Contrerasgarcia, Bernard Silvi, Miriam Marques, J. M. Recio
    Abstract:

    Recent computational developments on the application of the Electron Localization Function in the solid state allow to perform a rich characterization of chemical changes along phase transitions induced by thermodynamic variables in crystals. Chemical entities, in the sense of the Lewis theory, can be idengified and classified according to the role they play in these processes. Covalent (SiO2), ionic (BeO), molecular (CO2, O2), and metallic (Na, K) systems have been selected to illustrate the ability of ELF to gain insight into the global understanding of the transformations. Detailed topological analysis of the bonding reconstruction process clearly distinguishes transitions where the bonding nature of the solid is not altered, and just a reorganization takes place, to those where the chemical pattern suffers a dramatic change. We have highlighted the close relationship between energy, structure and bonding across several transition pathways and how ELF can be of help to anticipate pressure induced emerging structures and to discard among competitive transition mechanism

  • Electron Localization Function at the correlated level a natural orbital formulation
    Journal of Chemical Theory and Computation, 2010
    Co-Authors: Ferran Feixas, Miquel Duran, Eduard Matito, Miquel Sola, Bernard Silvi
    Abstract:

    In this work we present a 2-fold approximation for the calculation of the Electron Localization Function (ELF) which avoids the use of the two-particle density (2-PD). The first approximation is used for the calculation of the ELF itself and the second one is used to approximate pair populations integrated in the ELF basins. Both approximations only need the natural orbitals and their occupancies, which are available for most methods used in Electronic structure calculations. In this way, methods such as CCSD and MP2 can be used for the calculation of the ELF despite the lack of a pertinent definition of the 2-PD. By avoiding the calculation of the 2-PD, the present formulation provides the means for routine calculations of the ELF in medium-size molecules with correlated methods. The performance of this approximation is shown in a number of examples.

  • Computation of Local and Global Properties of the Electron Localization Function Topology in Crystals.
    Journal of chemical theory and computation, 2008
    Co-Authors: Julia Contreras-garcía, A. Martín Pendás, J. M. Recio, Bernard Silvi
    Abstract:

    We present a novel computational procedure, general, automated, and robust, for the analysis of local and global properties of the Electron Localization Function (ELF) in crystalline solids. Our algorithm successfully faces the two main shortcomings of the ELF analysis in crystals: (i) the automated identification and characterization of the ELF induced topology in periodic systems, which is impeded by the great number and concentration of critical points in crystalline cells, and (ii) the Localization of the zero flux surfaces and subsequent integration of basins, whose difficulty is due to the diverse (in many occasions very flat or very steep) ELF profiles connecting the set of critical points. Application of the new code to representative crystals exhibiting different bonding patterns is carried out in order to show the performance of the algorithm and the conceptual possibilities offered by the complete characterization of the ELF topology in solids.

Patricio Gonzaleznavarrete - One of the best experts on this subject based on the ideXlab platform.

  • Electronic fluxes during diels alder reactions involving 1 2 benzoquinones mechanistic insights from the analysis of Electron Localization Function and catastrophe theory
    Journal of Computational Chemistry, 2012
    Co-Authors: Patricio Gonzaleznavarrete, Juan Andres, Slawomir Berski, Luis R Domingo, Bernard Silvi
    Abstract:

    By means of the joint use of Electron Localization Function (ELF) and Thom's catastrophe theory, a theoretical analysis of the energy profile for the hetero-Diels-Alder reaction of 4-methoxy-1,2-benzoquinone 1 and methoxyethylene 2 has been carried out. The 12 different structural stability domains obtained by the bonding evolution theory have been identified as well as the bifurcation catastrophes (fold and cusp) responsible for the changes in the topology of the system. This analysis permits finding a relationship between the ELF topology and the evolution of the bond breaking/forming processes and Electron pair rearrangements through the reaction progress in terms of the different ways of pairing up the Electrons. The reaction mechanism corresponds to an asynchronous Electronic flux; first, the O1C5 bond is formed by the nucleophilic attack of the C5 carbon of the Electron rich ethylene 2 on the most electrophilically activated carbonyl O1 oxygen of 1, and once the σ bond has been completed, the formation process of the second O4C6 bond takes place. In addition, the values of the local electrophilicity and local nucleophilcity indices in the framework of conceptual density Functional theory accounts for the asychronicity of the process as well as for the observed regioselectivity. © 2012 Wiley Periodicals, Inc.

  • nature of the ring closure process along the rearrangement of octa 1 3 5 7 tetraene to cycloocta 1 3 5 triene from the perspective of the Electron Localization Function and catastrophe theory
    Journal of Computational Chemistry, 2012
    Co-Authors: Juan Andres, Slawomir Berski, Luis R Domingo, Patricio Gonzaleznavarrete
    Abstract:

    We analyze the behavior of the energy profile of the ring-closure process for the transformation of (3Z,5Z)-octa-1,3,5,7-tetraene 5 to (1Z,3Z,5Z)-cycloocta-1,3,5-triene 6 through a combination of Electron Localization Function (ELF) and catastrophe theory (CT). From this analysis, concepts such as bond breaking/forming processes, formation/annihilation of lone pairs, and other Electron pair rearrangements arise naturally through the reaction progress simply in terms of the different ways of pairing up the Electrons. A relationship between the topology and the nature of the bond breaking/forming processes along this rearrangement is reported. The different domains of structural stability of the ELF occurring along the intrinsic reaction path have been identified. The reaction mechanism consists of six steps separated by fold and cusp catastrophes. The transition structure is observed in the third step, d(C1C8) = 2.342 A, where all bonds have topological signature of single bonds (CC). The “new” C1C8 single bond is not formed in transition state and respective catastrophe of the ELF field (cusp) is localized in the last step, d(C1C8) ≈ 1.97 A, where the two monosynaptic nonbonding basins V(C1) and V(C8) are joined into single disynaptic bonding basin V(C1,C8). The V(C1,C8) basin corresponds to classical picture of the C1C8 bond in the Lewis formula. In cycloocta-1,3,5-triene 6 the single C1C8 bond is characterized by relatively small basin population 1.72e, which is much smaller than other single bonds with 2.03 and 2.26e. © 2011 Wiley Periodicals, Inc. J Comput Chem, 2011

  • an Electron Localization Function and catastrophe theory analysis on the molecular mechanism of gas phase identity sn2 reactions
    Theoretical Chemistry Accounts, 2008
    Co-Authors: Victor Polo, Bernard Silvi, Patricio Gonzaleznavarrete, Juan Andres
    Abstract:

    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 new insights 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 atoms.

Luis R Domingo - One of the best experts on this subject based on the ideXlab platform.

  • complementarity of reaction force and Electron Localization Function analyses of asynchronicity in bond formation in diels alder reactions
    Physical Chemistry Chemical Physics, 2014
    Co-Authors: Diana Yepes, Luis R Domingo, Jane S Murray, Patricia Perez, Peter Politzer, Pablo Jaque
    Abstract:

    We have computationally compared three Diels-Alder cycloadditions involving cyclopentadiene and substituted ethylenes; one of the reactions is synchronous, while the others are slightly or highly asynchronous. Synchronicity and weak asynchronicity are characterized by the reaction force constant κ(ξ) having just a single minimum in the transition region along the intrinsic reaction coordinate ξ, while for high asynchronicity κ(ξ) has a negative maximum with minima on both sides. The Electron Localization Function (ELF) shows that the features of κ(ξ) can be directly related to the formation of the new C-C bonds between the diene and the dienophile. There is thus a striking complementarity between κ(ξ) and ELF; κ(ξ) identifies the key points along ξ and ELF describes what is happening at those points.

  • Electronic fluxes during diels alder reactions involving 1 2 benzoquinones mechanistic insights from the analysis of Electron Localization Function and catastrophe theory
    Journal of Computational Chemistry, 2012
    Co-Authors: Patricio Gonzaleznavarrete, Juan Andres, Slawomir Berski, Luis R Domingo, Bernard Silvi
    Abstract:

    By means of the joint use of Electron Localization Function (ELF) and Thom's catastrophe theory, a theoretical analysis of the energy profile for the hetero-Diels-Alder reaction of 4-methoxy-1,2-benzoquinone 1 and methoxyethylene 2 has been carried out. The 12 different structural stability domains obtained by the bonding evolution theory have been identified as well as the bifurcation catastrophes (fold and cusp) responsible for the changes in the topology of the system. This analysis permits finding a relationship between the ELF topology and the evolution of the bond breaking/forming processes and Electron pair rearrangements through the reaction progress in terms of the different ways of pairing up the Electrons. The reaction mechanism corresponds to an asynchronous Electronic flux; first, the O1C5 bond is formed by the nucleophilic attack of the C5 carbon of the Electron rich ethylene 2 on the most electrophilically activated carbonyl O1 oxygen of 1, and once the σ bond has been completed, the formation process of the second O4C6 bond takes place. In addition, the values of the local electrophilicity and local nucleophilcity indices in the framework of conceptual density Functional theory accounts for the asychronicity of the process as well as for the observed regioselectivity. © 2012 Wiley Periodicals, Inc.

  • nature of the ring closure process along the rearrangement of octa 1 3 5 7 tetraene to cycloocta 1 3 5 triene from the perspective of the Electron Localization Function and catastrophe theory
    Journal of Computational Chemistry, 2012
    Co-Authors: Juan Andres, Slawomir Berski, Luis R Domingo, Patricio Gonzaleznavarrete
    Abstract:

    We analyze the behavior of the energy profile of the ring-closure process for the transformation of (3Z,5Z)-octa-1,3,5,7-tetraene 5 to (1Z,3Z,5Z)-cycloocta-1,3,5-triene 6 through a combination of Electron Localization Function (ELF) and catastrophe theory (CT). From this analysis, concepts such as bond breaking/forming processes, formation/annihilation of lone pairs, and other Electron pair rearrangements arise naturally through the reaction progress simply in terms of the different ways of pairing up the Electrons. A relationship between the topology and the nature of the bond breaking/forming processes along this rearrangement is reported. The different domains of structural stability of the ELF occurring along the intrinsic reaction path have been identified. The reaction mechanism consists of six steps separated by fold and cusp catastrophes. The transition structure is observed in the third step, d(C1C8) = 2.342 A, where all bonds have topological signature of single bonds (CC). The “new” C1C8 single bond is not formed in transition state and respective catastrophe of the ELF field (cusp) is localized in the last step, d(C1C8) ≈ 1.97 A, where the two monosynaptic nonbonding basins V(C1) and V(C8) are joined into single disynaptic bonding basin V(C1,C8). The V(C1,C8) basin corresponds to classical picture of the C1C8 bond in the Lewis formula. In cycloocta-1,3,5-triene 6 the single C1C8 bond is characterized by relatively small basin population 1.72e, which is much smaller than other single bonds with 2.03 and 2.26e. © 2011 Wiley Periodicals, Inc. J Comput Chem, 2011

  • understanding reaction mechanisms in organic chemistry from catastrophe theory applied to the Electron Localization Function topology
    Journal of Physical Chemistry A, 2008
    Co-Authors: Victor Polo, Juan Andres, Slawomir Berski, Luis R Domingo, Bernard Silvi
    Abstract:

    Thomʼs catastrophe theory applied to the evolution of the topology of the Electron Localization Function (ELF) gradient field constitutes a way to rationalize the reorganization of Electron pairing and a powerful tool for the unambiguous determination of the molecular mechanisms of a given chemical reaction. The identification of the turning points connecting the ELF structural stability domains along the reaction pathway allows a rigorous characterization of the sequence of Electron pair rearrangements taking place during a chemical transformation, such as multiple bond forming/breaking processes, ring closure processes, creation/annihilation of lone pairs, transformations of C−C multiple bonds into single ones. The reaction mechanism of some relevant organic reactions: Diels−Alder, 1,3-dipolar cycloaddition and Cope rearrangement are reviewed to illustrate the potential of the present approach.

  • the joint use of catastrophe theory and Electron Localization Function to characterize molecular mechanisms a density Functional study of the diels alder reaction between ethylene and 1 3 butadiene
    Journal of Physical Chemistry A, 2003
    Co-Authors: Slawomir Berski, Juan Andres, And Bernard Silvi, Luis R Domingo
    Abstract:

    The catastrophe theory has been used to investigate the reorganization of the Localization basins, within the Electron Localization Function formalism, along the intrinsic reaction coordinate associated with the reaction pathway of the Diels−Alder reaction between ethylene and 1,3-butadiene. There are distinguished seven phases (I−VII) characterized by a decay and formation of the double bonds, an accumulation of the nonbonding Electron density on the C atoms involved in the formation of two sigma bonds and a ring closure processes. During the reaction 10 catastrophes occur belonging to two elementary types:  fold and cusp. The transition structure is located in phase III, being determined by a “reduction” of the double CC bond of ethylene to the single bond, and it is not associated with any special event on the intrinsic reaction coordinate path. For the first time, it is shown that formation of two new sigma C−C bonds between ethylene and 1,3-butadiene begins in phase VI at 2.044A.