What can be learnt on biologically relevant systems from the topological analysis of the electron localization function?

Piquemal, Jean‐Philip; Pilmé, Julien; Parisel, Olivier; Gérard, Hélène; Fourré, Isabelle; Bergès, Jacqueline; Gourlaouen, Christophe; Lande, Aurélien de la; Severen, M.-C. van; Silvi, Bernard

doi:10.1002/qua.21711

Cited by 63 publications

(58 citation statements)

References 122 publications

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“…It also clearly indicates that the usual fixed VSEPR model used to build model force fields may not be always valid since the number of separated unbound electron pairs can vary upon electronic spatial relocation. However, it confirms the crucial importance of lone pairs Piquemal and Pilmé, 2008) in the modelling of polarization phenomenon.…”

Section: Resultssupporting

confidence: 63%

Importance of lone pair interactions/redistribution in hard and soft ligands within the active site of alcohol dehydrogenase Zn-metalloenzyme: Insights from electron localization function

Courcy

Gresh

Piquemal

2009

Interdiscip Sci Comput Life Sci

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Abstract:As a continuation of our previous work (de Courcy et al., 2008. J. Chem. Theo. Comput. 4 1659, lone pair-cation interactions were quantum-mechanically studied within the active site of the alcohol dehydrogenase Zn(II)-metalloenzyme by means of the topological analysis of the Electron Localization Function (ELF) and the Reduced Variational Space (RVS) energy decomposition analysis. Ligands lone pairs in direct interaction with the metal were shown to control the physical nature of the interaction as it appears to be dominated by polarization when the number of interacting lone pairs increases. Furthermore, we observed a peculiar behaviour of the cysteinate S − lone pairs which can redistribute and merge, thereby reducing their number to accommodate the zinc cation which also exhibits a consequent plasticity of its density outer shells which can delocalize towards ligands. Such observations should allow a deeper understanding of the usual softness/hardness concept of ions and ligands.

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Section: Resultssupporting

confidence: 63%

Importance of lone pair interactions/redistribution in hard and soft ligands within the active site of alcohol dehydrogenase Zn-metalloenzyme: Insights from electron localization function

Courcy

Gresh

Piquemal

2009

Interdiscip Sci Comput Life Sci

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“…It has been recently shown that non-VSEPR structures which occur around neutral atoms belonging to the fourth and higher periods can be explained by considering the structure of the external core shell basins16 and hereafter referred to as subvalence basins. Details about the ELF analysis can also be found in a recent review paper dealing with the application of ELF to systems of biological interest17.…”

Section: Methodsmentioning

confidence: 99%

Understanding Selectivity of Hard and Soft Metal Cations within Biological Systems Using the Subvalence Concept. 1. Application to Blood Coagulation: Direct Cation−Protein Electronic Effects versus Indirect Interactions through Water Networks

Courcy

Pedersen

Parisel

et al. 2010

J. Chem. Theory Comput.

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Following a previous study by de Courcy et al. ((2009) Interdiscip. Sci. Comput. Life Sci. 1, 55-60), we demonstrate in this contribution, using quantum chemistry, that metal cations exhibit a specific topological signature in the electron localization of their density interacting with ligands according to its “soft” or “hard” character. Introducing the concept of metal cation subvalence, we show that a metal cation can split its outer-shell density (the so-called subvalent domains or basins) according to it capability to form a partly covalent bond involving charge transfer. Such behaviour is investigated by means of several quantum chemical interpretative methods encompasing the topological analysis of the Electron Localization Function (ELF) and Bader's Quantum Theory of Atoms in Molecules (QTAIM) and two energy decomposition analyses (EDA), namely the Restricted Variational Space (RVS) and Constrained Space Orbital Variations (CSOV) approaches. Further rationalization is performed by computing ELF and QTAIM local properties such as electrostatic distributed moments and local chemical descriptors such as condensed Fukui Functions and dual descriptors. These reactivity indexes are computed within the ELF topological analysis in addition to QTAIM offering access to non atomic reactivity local index, for example on lone pairs. We apply this “subvalence” concept to study the cation selectivity in enzymes involved in blood coagulation (GLA domains of three coagulation factors). We show that the calcium ions are clearly able to form partially covalent charge transfer networks between the subdomain of the metal ion and the carboxylate oxygen lone pairs whereas magnesium does not have such ability. Our analysis also explains the different role of two groups (high affinity and low affinity cation binding sites) present in GLA domains. If the presence of Ca(II) is mandatory in the central “high affinity” region to conserve a proper folding and a charge transfer network, external sites are better stabilised by Mg(II), rather than Ca(II), in agreement with experiment. The central role of discrete water molecules is also discussed in order to understand the stabilities of the observed X-rays structures of the Gla domain. Indeed, the presence of explicit water molecules generating indirect cation-protein interactions through water networks is shown to be able to reverse the observed electronic selectivity occuring when cations directly interact with the Gla domain without the need of water.

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“…Distances corresponding to those given by the Boys localization algorithm, [20] as listed by the GAMESS software [21] in the context of the Garmer and Stevens procedure were initially adopted. More recently, upon recalibration of the method with aug-cc-pVTZ multipoles and polarizabilities, we resorted to analyses [22][23] given by the Electron Localization Function (ELF) [24][25][26] giving longer distances of the centroid to the bearer. Thus, for water O sp 3 representation of the lone pairs, with  angles of 60° and 120° instead of 90°, such that each  lone pair was actually 'shared' between the two atoms of the conjugated bond (Figure 1), enabled a better match to EX than a vertical representation.…”

Section: ) Sibfa Computationsmentioning

confidence: 99%

Importance of explicit smeared lone-pairs in anisotropic polarizable molecular mechanics. Torture track angular tests for exchange-repulsion and charge transfer contributions

et al. 2017

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What can be learnt on biologically relevant systems from the topological analysis of the electron localization function?

Cited by 63 publications

References 122 publications

Importance of lone pair interactions/redistribution in hard and soft ligands within the active site of alcohol dehydrogenase Zn-metalloenzyme: Insights from electron localization function

Importance of lone pair interactions/redistribution in hard and soft ligands within the active site of alcohol dehydrogenase Zn-metalloenzyme: Insights from electron localization function

Understanding Selectivity of Hard and Soft Metal Cations within Biological Systems Using the Subvalence Concept. 1. Application to Blood Coagulation: Direct Cation−Protein Electronic Effects versus Indirect Interactions through Water Networks

Importance of explicit smeared lone-pairs in anisotropic polarizable molecular mechanics. Torture track angular tests for exchange-repulsion and charge transfer contributions

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