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Bernard Silvi - One of the best experts on this subject based on the ideXlab platform.
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bonding changes along solid solid phase transitions using the Electron Localization function approach
2011Co-Authors: Julia Contrerasgarcia, Bernard Silvi, Miriam Marques, J. M. RecioAbstract: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
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Electron Localization function at the correlated level a natural orbital formulation
Journal of Chemical Theory and Computation, 2010Co-Authors: Ferran Feixas, Miquel Duran, Eduard Matito, Miquel Sola, Bernard SilviAbstract: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.
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Computation of Local and Global Properties of the Electron Localization Function Topology in Crystals.
Journal of chemical theory and computation, 2008Co-Authors: Julia Contreras-garcía, A. Martín Pendás, J. M. Recio, Bernard SilviAbstract: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.
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useful applications of the Electron Localization function in high pressure crystal chemistry
Journal of Physics and Chemistry of Solids, 2008Co-Authors: Julia Contrerasgarcia, Bernard Silvi, A. Martín Pendás, Manuel J RecioAbstract:Abstract The main features of a new computational code aimed at the topological analysis of the Electron Localization function (ELF) in crystals are hereby presented. Besides the complete Localization of all critical points, the code is able to determine the limiting surfaces that define the chemical regions associated with the so-found maxima (or attractors) of the ELF. Hence, integrations of density operators within these basins provide charges and volumes to cores, bonds and lone pairs. Two illustrative applications have been selected. Firstly, we examine the Z dependence of basin compressibilities in the elements of the first two rows of the periodic table, and secondly, we focus our attention on the chemical changes across the pathway of the zinc blende–rocksalt phase transition in BeO.
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understanding reaction mechanisms in organic chemistry from catastrophe theory applied to the Electron Localization function topology
Journal of Physical Chemistry A, 2008Co-Authors: Victor Polo, Juan Andres, Slawomir Berski, Luis R Domingo, Bernard SilviAbstract: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.
Slawomir Berski - One of the best experts on this subject based on the ideXlab platform.
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Electron Localization function study on intramolecular Electron transfer in the qttfq and dbttfi radical anions
Journal of Physical Chemistry A, 2011Co-Authors: Jaroslaw Kalinowski, Slawomir Berski, Agnieszka J GordonAbstract:The unsymmetrical distribution of the unpaired Electron in the ground state of the DBTTFI•– radical anion (bi(6-n-butyl-5,7-dioxo-6,7-dihydro-5H-[1,3]dithiolo[4,5-f]isoindole-2-ylidene) is theoretically predicted using the M06-2X/6-31+G(d,p) level of calculations. The results are additionally confirmed by single point calculations at B3LYP/aug-cc-pVTZ, LC-ωPBE/aug-cc-pVTZ, and M06-2X/aug-cc-pVTZ levels. DBTTFI, containing the TTF (tetrathiafulvalene) fragment, may be used in the construction of organic microElectronic devices, similarly to the radical anion of QTTFQ. The unsymmetrical distribution of spin density in (QTTFQ)•– has been confirmed using M06-2X/aug-cc-pVTZ calculations, with subsequent study using topological analysis of Electron Localization function (ELF). The reorganization of the chemical bonds during intramolecular Electron transfer in (QTTFQ)•– and (DBTTFI)•– has been analyzed using bonding evolution theory (BET). The reaction path has been simulated by the IRC procedure, and the evolut...
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oxygen bound iodine o i the Electron Localization function elf study on bonding in cis and trans iono
Chemical Physics Letters, 2011Co-Authors: Slawomir Berski, Zdzislaw Latajka, Agnieszka J GordonAbstract:Abstract The geometrical and Electronic structure of iodine nitrite, I–O–N O, have been studied using DFT/B3LYP, MP2 and CCSD(T) methods. Topological analysis of the Electron Localization Function (ELF) performed at CCSD/TZVPP//CCSD(T)/TZVPP level reveals slightly polarized covalent N O bond, the protocovalent N–O bond and mixed covalent–ionic I–O bond. The protocovalent N–O bond is described by two monosynaptic non-bonding basins, V(N) and V(O), with total basin populations of 1.1e in cis-IONO and 0.80e in trans-IONO, thus belonging to the charge-shift type. The I–O1 bond is essentially depleted with only 0.67e (cis) and 0.64e (trans).
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olefin epoxidation by molybdenum peroxo compound molecular mechanism characterized by the Electron Localization function and catastrophe theory
Journal of Physical Chemistry A, 2011Co-Authors: Slawomir Berski, Juan Andres, Victor Polo, Fabricio R Sensato, V S SafontAbstract: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...
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on the multiple b n bonding in boron compounds using the topological analysis of Electron Localization function elf
New Journal of Chemistry, 2011Co-Authors: Slawomir Berski, Zdzislaw Latajka, Agnieszka J GordonAbstract:Topological analysis of the Electron Localization Function (ELF) within the framework of Quantum Chemical Topology (QCT) has been applied to study the nature of the boron–nitrogen bonds. A series of 10 compounds have been chosen, with the B–N bond length ranging between 1.698 A (B–N) and 1.258 A (BN). According to the Lewis formula three types of bonds have been recognized. These are: the single B–N bond with a basin population of 1.91 ÷ 2.09e, the double BN bond with a population of 3.78 ÷ 4.28e, and the triple BN bond with a basin population of 5.72 ÷ 5.74e. In the case of partial double bonds (BN), where formally two or more resonance hybrids have to be considered, our calculations strongly support the concept of double boron–nitrogen bonding (BN).
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understanding reaction mechanisms in organic chemistry from catastrophe theory applied to the Electron Localization function topology
Journal of Physical Chemistry A, 2008Co-Authors: Victor Polo, Juan Andres, Slawomir Berski, Luis R Domingo, Bernard SilviAbstract: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.
Patricio Fuentealba - One of the best experts on this subject based on the ideXlab platform.
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chapter 5 understanding and using the Electron Localization function
Theoretical and Computational Chemistry, 2007Co-Authors: Patricio Fuentealba, Eduardo Chamorro, Juan C SantosAbstract:Publisher Summary Electron Localization function (ELF) helps in understanding the empirical concept of Electron Localization, specially the pair Electron Localization in the spirit of Lewis structures. This chapter discusses the principal ingredients involved in the ELF and their relation with chemical concepts. A brief comparison of the ELF with other theoretical related tools, like the atoms in molecules model of Bader is discussed and also presents elementary concepts from the mathematical theory of topological analysis. One important characteristic of the ELF is its numerical stability with respect to the theoretical level at which the Electron density and the molecular orbitals are calculated. One of the first and most direct applications of the ELF is to the explanation and confirmation of the valence shell Electron pair repulsion model of Gillespie. The ELF has emerged as a powerful tool to understand in a qualitative way the behavior of the Electrons in a nuclei system. It is possible to explain a great variety of bonding situations ranging from the most standard covalent bond to the metallic bond. The ELF is a well-defined function with pragmatic characteristic. It does not depend on the method of calculation or on the basis set used. Its application to understand new bond phenomenon is already well documented and it can be used safely. Its relationship with the Pauli Exclusion Principle has been carefully studied and its consequence to understand the chemical concept of Electron pair is also been discussed in the chapter.
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understanding and using the Electron Localization function
2006Co-Authors: Patricio Fuentealba, Eduardo Chamorro, Juan C SantosAbstract:The applications of quantum mechanics to chemistry have primordially two goals. First,toprovidethenumericalvalueofobservableswhichcanbeconfrontedwithexperimentalmeasurements and, second, to help in understanding many empirical concepts widelyused in chemistry. The Electron Localization function, ELF, enters in the second goal. Ithelps in understanding the empirical concept of Electron Localization, specially the pairElectron Localization in the spirit of Lewis structures. This paper is not an attempt toreview all of the applications of the ELF, rather the aims are to explain in an easy waywith as less as possible of mathematical formalism the significances of the ELF and,more important, how to use it. Hence, from the very beginning, we give answer to acommon question of chemists in front of theoretical paper: Why should I bother tryingto understand this function, when I do not have any chance to apply it and when I do nothave any software to calculate it? Well, in this case, everybody can calculate the ELFusing the TOPMOD software developed by Silvi and co-workers
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condensation of the highest occupied molecular orbital within the Electron Localization function domains
Journal of Chemical Sciences, 2005Co-Authors: Eduardo Chamorro, William Tiznado, Juan C Santos, M Duque, Carlos Cardenas, Patricio FuentealbaAbstract:Use of regions of space defined by topological analysis of Electron Localization function (ELF) as reactivity descriptors is explored. By starting from the fact that the ELF presents high values in the regions where it is most probable to find an Electron pair and that the square of the HOMO is a good measure of the reactivity of a molecule, it is proposed that the integration of the square of the HOMO over the volumes defined by the ELF should be a local index for predicting the most nucleophilic site of a molecule. We present here some computational results on simple systems in order to get some insights about this possibility.
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an aromaticity scale based on the topological analysis of the Electron Localization function including σ and π contributions
Journal of Chemical Theory and Computation, 2005Co-Authors: Juan C Santos, Juan Andres, And Arie Aizman, Patricio FuentealbaAbstract:In this work, the average bifurcation value of the Electron Localization function (ELF) of both σ (ELFσ) and π (ELFπ) contributions was used to construct an aromaticity scale for chemical compounds. We have validated the scale with a series of well-known molecules and then used it to evaluate global aromaticity on aluminum based clusters, which present σ aromaticity and π antiaromaticity. The proposed scaled predicts an overall antiaromatic character for the Al4(4)(-) moiety.
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sigma pi separation of the Electron Localization function and aromaticity
Journal of Chemical Physics, 2004Co-Authors: Juan C Santos, William Tiznado, Renato Contreras, Patricio FuentealbaAbstract:The Electron Localization function (ELF) has been separated in its sigma and pi components. The topological analysis of the new ELFσ and ELFπ functions has been used to quantify the concept of resonance. The highest bifurcation values of these functions describe in a correct way the aromaticity of classical ring molecules and some new aromatic compounds as B6CO6, Al42−, and N5−. In the case of Al42−, an important σ deLocalization contribution has been found, which is in agreement with previous interpretation.
Zdzislaw Latajka - One of the best experts on this subject based on the ideXlab platform.
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hydrogen detachment driven by a repulsive 1πσ state an Electron Localization function study of 3 amino 1 2 4 triazole
Physical Chemistry Chemical Physics, 2018Co-Authors: Andrzej Bil, Zdzislaw Latajka, Malgorzata BiczyskoAbstract:Electron Localization function analysis reveals the details of a charge induced hydrogen detachment mechanism of 3-amino-1,2,4-triazole, identified recently to be responsible for phototautomerization of the molecule. In this process vertical excitation to the 1πσ* state is followed by the barrier-less migration of a H atom along the N–H bond toward the conical intersection with the S0 ground state. The most striking feature revealed for the 1πσ* state is partial ejection of σ* Electrons outside the molecule, even beyond the NH group, at the Franck–Condon point. Further gradual spatial Localization of the Electron around the proton moving along the N–H stretching coordinate gives a plausible explanation for the repulsive character of the 1πσ* potential energy surface with the proton wading through the region of space where some negative charge is accumulated (‘a virtual acceptor’), dragging some Electron density. This mechanism resembles the one postulated for the hydrogen transfer from a donor molecule (D–H) to an acceptor one (A) in a class of vertically excited molecules with a preexisting inter- or intramolecular D–H⋯A motif, even though the acceptor molecule is absent. The present analysis demonstrates also that the bond evolution and changes in the Electron density along the excited state reaction path can be effectively studied with the use of an Electron Localization function.
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oxygen bound iodine o i the Electron Localization function elf study on bonding in cis and trans iono
Chemical Physics Letters, 2011Co-Authors: Slawomir Berski, Zdzislaw Latajka, Agnieszka J GordonAbstract:Abstract The geometrical and Electronic structure of iodine nitrite, I–O–N O, have been studied using DFT/B3LYP, MP2 and CCSD(T) methods. Topological analysis of the Electron Localization Function (ELF) performed at CCSD/TZVPP//CCSD(T)/TZVPP level reveals slightly polarized covalent N O bond, the protocovalent N–O bond and mixed covalent–ionic I–O bond. The protocovalent N–O bond is described by two monosynaptic non-bonding basins, V(N) and V(O), with total basin populations of 1.1e in cis-IONO and 0.80e in trans-IONO, thus belonging to the charge-shift type. The I–O1 bond is essentially depleted with only 0.67e (cis) and 0.64e (trans).
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on the multiple b n bonding in boron compounds using the topological analysis of Electron Localization function elf
New Journal of Chemistry, 2011Co-Authors: Slawomir Berski, Zdzislaw Latajka, Agnieszka J GordonAbstract:Topological analysis of the Electron Localization Function (ELF) within the framework of Quantum Chemical Topology (QCT) has been applied to study the nature of the boron–nitrogen bonds. A series of 10 compounds have been chosen, with the B–N bond length ranging between 1.698 A (B–N) and 1.258 A (BN). According to the Lewis formula three types of bonds have been recognized. These are: the single B–N bond with a basin population of 1.91 ÷ 2.09e, the double BN bond with a population of 3.78 ÷ 4.28e, and the triple BN bond with a basin population of 5.72 ÷ 5.74e. In the case of partial double bonds (BN), where formally two or more resonance hybrids have to be considered, our calculations strongly support the concept of double boron–nitrogen bonding (BN).
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quantum chemical topology description of the hydrogen transfer between the ethynyl radical and ammonia c2h nh3 the Electron Localization function study
Chemical Physics Letters, 2006Co-Authors: Slawomir Berski, Zdzislaw LatajkaAbstract:Abstract The topological analysis of the Electron Localization Function (ELF) has been carried out for the hydrogen abstraction pathway between ethynyl radical (HCC ) and ammonia (NH 3 ). The IRC path, minima (HCC⋯HNH 2 , HCCH⋯NH 2 ) and transition structure have been calculated at the UB3LYP/6-311++G(2d, 2p) computational level. The ‘closed-shell’ and ‘spin-polarized’ formula of ELF are used for an analysis. A detailed study of the topology of ELF (the basin population and spin density redistribution) shows that the reaction consists of three main steps distinguished on the IRC path. First, the N–H bond in ammonia is broken, then the hydrogen atom with a population of ca. 0.7 e is transferred and finally the C–H bond in acetylene is formed. It is interesting to note that all chemically important changes occur after the transition state.
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bonding in hypohalous acids hox x f cl br and i from the topological analysis of the Electron Localization function
Journal of Chemical Physics, 1999Co-Authors: Slawomir Berski, Bernard Silvi, Zdzislaw Latajka, Jerzy LeszczynskiAbstract:The bonding in hypohalous acids has been investigated from the topological analysis of the Electron Localization function (ELF) at the Becke3LYP and Hartree–Fock levels. The interaction between halogen and oxygen atoms has been characterized by the presence of bonding, disynaptic attractors V(O,X) X=F, Cl, Br, and I with the mean Electron population N of 0.32, 0.61, 0.45, and 0.35e, respectively. In the case of HOBr, the possibility of a strong contribution of 3d bromine core Electrons to the valence shell has been observed. On the base of the bonding evolution theory (BET), the O–F bond has been recognized as a covalent, polarized one whereas, the bonding between O and Cl, Br, and I atoms is of the Electron donor–acceptor-type with halogen donating the Electron density to valence shell of oxygen. The observed difference between HO+F− and HO−X+ (X=Cl, Br, and I) polarizations is reflected in topology of ELF maps with a large Localization domain surrounding the V(F) and V(F,O) attractors in HOF and a comm...
Juan C Santos - One of the best experts on this subject based on the ideXlab platform.
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substituent effects in the mechanism of mono substituted acetylene trimerization a topological analysis of the Electron Localization function
Chemical Physics Letters, 2009Co-Authors: Oscar Donosotauda, Arie Aizman, Carlos Escobar, Juan C SantosAbstract:The reaction mechanism of the mono-substituted acetylenes trimerization has been analysed by means of the Electron Localization function (ELF). The trimerization reactions were characterized in six domains of structural stability of ELF along the IRC pathway. Substituent effects are shown to be varied and important along the IRC. Among the substituent considered in this study (F, CN, COH and OH), Formyl, the most relevant, promotes reactant stabilization by hydrogen interaction, decreases close shell interactions, increases the distortion energy in the first step, and provides the highest stabilization by aromaticity.
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chapter 5 understanding and using the Electron Localization function
Theoretical and Computational Chemistry, 2007Co-Authors: Patricio Fuentealba, Eduardo Chamorro, Juan C SantosAbstract:Publisher Summary Electron Localization function (ELF) helps in understanding the empirical concept of Electron Localization, specially the pair Electron Localization in the spirit of Lewis structures. This chapter discusses the principal ingredients involved in the ELF and their relation with chemical concepts. A brief comparison of the ELF with other theoretical related tools, like the atoms in molecules model of Bader is discussed and also presents elementary concepts from the mathematical theory of topological analysis. One important characteristic of the ELF is its numerical stability with respect to the theoretical level at which the Electron density and the molecular orbitals are calculated. One of the first and most direct applications of the ELF is to the explanation and confirmation of the valence shell Electron pair repulsion model of Gillespie. The ELF has emerged as a powerful tool to understand in a qualitative way the behavior of the Electrons in a nuclei system. It is possible to explain a great variety of bonding situations ranging from the most standard covalent bond to the metallic bond. The ELF is a well-defined function with pragmatic characteristic. It does not depend on the method of calculation or on the basis set used. Its application to understand new bond phenomenon is already well documented and it can be used safely. Its relationship with the Pauli Exclusion Principle has been carefully studied and its consequence to understand the chemical concept of Electron pair is also been discussed in the chapter.
-
understanding and using the Electron Localization function
2006Co-Authors: Patricio Fuentealba, Eduardo Chamorro, Juan C SantosAbstract:The applications of quantum mechanics to chemistry have primordially two goals. First,toprovidethenumericalvalueofobservableswhichcanbeconfrontedwithexperimentalmeasurements and, second, to help in understanding many empirical concepts widelyused in chemistry. The Electron Localization function, ELF, enters in the second goal. Ithelps in understanding the empirical concept of Electron Localization, specially the pairElectron Localization in the spirit of Lewis structures. This paper is not an attempt toreview all of the applications of the ELF, rather the aims are to explain in an easy waywith as less as possible of mathematical formalism the significances of the ELF and,more important, how to use it. Hence, from the very beginning, we give answer to acommon question of chemists in front of theoretical paper: Why should I bother tryingto understand this function, when I do not have any chance to apply it and when I do nothave any software to calculate it? Well, in this case, everybody can calculate the ELFusing the TOPMOD software developed by Silvi and co-workers
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an Electron Localization function study of the trimerization of acetylene reaction mechanism and development of aromaticity
Chemical Physics Letters, 2005Co-Authors: Juan C Santos, Victor Polo, Juan AndresAbstract:Abstract The reaction mechanism and the development of the aromaticity along the trimerization of acetylene to yield benzene have been analyzed by means of use of the Electron Localization function (ELF) and the catastrophe theory. The Electronic rearrangements associated to bond breaking/forming processes are characterized by four catastrophes, which determine five domains of structural stability of the ELF topology along the intrinsic reaction path. The analysis of the ELF separated into in-plane (σ) and out-of-plane (π) contributions shows that the transition structure (TS) has a low σ Electron deLocalization, being π-aromaticity developed at the final stage of the reaction.
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condensation of the highest occupied molecular orbital within the Electron Localization function domains
Journal of Chemical Sciences, 2005Co-Authors: Eduardo Chamorro, William Tiznado, Juan C Santos, M Duque, Carlos Cardenas, Patricio FuentealbaAbstract:Use of regions of space defined by topological analysis of Electron Localization function (ELF) as reactivity descriptors is explored. By starting from the fact that the ELF presents high values in the regions where it is most probable to find an Electron pair and that the square of the HOMO is a good measure of the reactivity of a molecule, it is proposed that the integration of the square of the HOMO over the volumes defined by the ELF should be a local index for predicting the most nucleophilic site of a molecule. We present here some computational results on simple systems in order to get some insights about this possibility.