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Understanding the Chemistry of Lead at a Molecular Level: the Pb(II) 6S6p Lone Pair Can Be Bisdirected in Proteins

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Understanding the Chemistry of Lead at a Molecular Level: the Pb(II) 6S6p Lone Pair Can Be Bisdirected in Proteins Understanding the Chemistry of Lead at a Molecular Level: The Pb(II) 6s6p Lone Pair Can Be Bisdirected in Proteins Van Severen, Marie-Celine; Ryde, Ulf; Parisel, Olivier; Piquernal, Jean-Philip Published in: Journal of Chemical Theory and Computation DOI: 10.1021/ct300524v 2013 Link to publication Citation for published version (APA): Van Severen, M-C., Ryde, U., Parisel, O., & Piquernal, J-P. (2013). Understanding the Chemistry of Lead at a Molecular Level: The Pb(II) 6s6p Lone Pair Can Be Bisdirected in Proteins. Journal of Chemical Theory and Computation, 9(5), 2416-2424. https://doi.org/10.1021/ct300524v Total number of authors: 4 General rights Unless other specific re-use rights are stated the following general rights apply: Copyright and moral rights for the publications made accessible in the public portal are retained by the authors and/or other copyright owners and it is a condition of accessing publications that users recognise and abide by the legal requirements associated with these rights. • Users may download and print one copy of any publication from the public portal for the purpose of private study or research. • You may not further distribute the material or use it for any profit-making activity or commercial gain • You may freely distribute the URL identifying the publication in the public portal Read more about Creative commons licenses: https://creativecommons.org/licenses/ Take down policy If you believe that this document breaches copyright please contact us providing details, and we will remove access to the work immediately and investigate your claim. LUND UNIVERSITY PO Box 117 221 00 Lund +46 46-222 00 00 Understanding the toxicology of lead at a molecular level: Pb(II) 6s lone pair can be bisdirected in proteins. Marie-Céline Van Severen**, Ulf Ryde**, Olivier Parisel*, Jean-Philip Piquemal* *Laboratoire de Chimie Théorique, UPMC, CC 137, 4 place Jussieu, 75252 Paris, Cedex 05, France and CNRS, UMR 7616, CC 137, 4 place Jussieu, 75252, Paris Cedex 05, France. **Theoretical chemistry, Lund University, P.O. Box 124, 22100 Lund, Sweden. Contact author: [email protected] ABSTRACT Pb2+ complexes can attain several different topologies, depending of the shape of the Pb 6s6p lone pair. In this paper, we study structures with a bisdirected Pb lone pair with quantum mechanics (DFT) and QM/MM calculations. We study small symmetric Pb2+ models to see what factors are needed to get a bisdirected lone pair. Two important mechanisms have been found: First, the repulsion of the lone pair of Pb2+ with other lone pairs in the equatorial plan leads to a bisdirected structure. Second, a bisdirected lone pair can also arise thanks to interactions with double bonds, lone pairs, or hydrogen atoms (resembling hydrogen bond). Moreover, we have analysed Pb2+ sites in proteins and RNA (both for frozen and relaxed structure, and with sites saturated with water molecules) to see if a bisdirected lone pair can exist in an asymmetrical environment. Bisdirected lone pairs were encountered in several of them. KEYWORDS Bisdirected, RNA, QM/MM, ELF, Lead 1 The toxicity of lead is known since the antiquity and for mammals its ingestion results in the well- known disease saturnism. Experiments indicate that two types Pb2+ complexes exist: holodirected and hemidirected organizations (Figure 1)1. This structural difference is caused by the peculiar capably of the Pb 6s 6p lone pair to adapt to the presence of ligands. Hemidirected complexes arise when Pb2+ spreads the ligands in one hemisphere, letting the lone pair to expand in the opposite direction. This extension of the lone pair can cause structural variations in the protein chelation site and perturbs its native structure, leading to possible loss of activity. When this is not possible, due to strong steric and electrostatic interactions between the ligands, holodirectional complexes are recovered and the lone pair looses its stereochemical activity. Hemidirected Structure Figure 1: Schematic representation of hemi- and holodirected structures, where the arrows indicate location of ligands. In a recent paper, we showed that the lone-pair organization can be even more complex: We observed a third possible organization of the 6s lone pair, called bisdirected2 (see Figure 2c). In this case, the lone pair is split in two hemispheres. Such topological structure was obtained when Pb was bound to a plane and symmetric molecule. We showed that the topological analysis with the electron localization function (ELF) is a powerful tool to localize and visualize the domain corresponding to the valence lone pair of Pb (V(Pb)). In this study, we address answer to several questions: When will the lone pair of Pb2+ be bisdirected? What factors favour this structure? Could such a topological structure exist within proteins where the symmetry and flatness are absent? To address such issues, we analyse Pb2+- containing protein structures that are available in the protein data bank (PDB) using the ELF analysis coupled with DFT and combined quantum mechanical and molecular mechanical QM/MM calculations. 2 V(Pb) V(Pb) V(Pb) 2+ 2+ a) [Pb(HNCO)3] b) [Pb(HNCO)6] c) HCOH Hemidirected structure Holodirected structure Bisdirected structure Figure 2: Three different topological structures of the lone pair of Pb2+. (The red colour is used for a basin that belongs to only one atom, the green colour is used for basin shared by two atoms and the blue colour is for the hydrogen + the covalent bond H-X with X=any atoms. On the right the basin of Pb2+ and the basin of H are not coloured) Results In this article, we will study bisdirected Pb2+ 6s6p lone pairs in various structures with the aim to understand where and why this topology arises. We will first study a series of model complexes to understand when bisdirected lone pairs arise. Then, we will study Pb2+ in protein structures to see if bisdirected structures are encountered in biological systems. Bisdirected lone pairs in model complexes Figure 2c shows a bisdirected lone pair in the complex of Pb2+ with the chelating ligand 1,4,7,10,13,16- hexaoxa-cyclooctadeca-2,5,8,11,14,17 hexaene (HCOH), which consists of six oxygen atoms alternating with six C=C double bonds. One can ask whether it is the oxygen atoms or the double bond that give rise to this bisdirected lone pair. To answer this question, we deleted the double bonds of HCOH replaced and the carbon atoms by hydrogen atoms ( a) H of H2O are in the plane of the molecule b) H of H2O are out of the plane of the molecule Figure 3). Thus, the complex is now formed by six water molecules with the oxygen atoms located in the same place as the oxygen atoms in HCOH in Figure 2c. a) H of H2O are in the plane of the molecule b) H of H2O are out of the plane of the molecule Figure 3: ELF representation of HCOH replaced by six water molecules. 3 From the ELF analysis in Figure 3a, it is obvious that the lone pair of Pb2+ is still bisdirected. It seems that this structure is caused by the repulsion of the lone pairs of oxygen atoms creating a hole in the lone pair of Pb2+. To exclude the possibility that the bisdirected structure is linked to the direction of the lone pairs of the oxygen atoms, another calculation was carried out with the hydrogen atoms directed vertically to plane with the Pb and O atoms (Figure 3b). However, the ELF analysis shows that the lone pair of Pb2+ is still bisdirected. This indicates that the Pb lone pair will be bisdirected in structures where some atoms induce repulsion in a plane. Ligand Pb(p) O(p) H(s) HCOH 0.50 4.96 0.73 (H2O)6 planar 0.19 5.27 0.45 (H2O)6 perpendicular H 0.22 5.32 0.40 Table 1: NBO analysis of the bisdirected structures in Figures 2 and 3 for only one O and one H in the different system. Table 1 shows electronic populations of the donor orbitals: 2p of O and 1s of H and the acceptor 6p orbitals of Pb2+. As the 6s of Pb2+ is already full the occupation of 6p orbitals are important because they will receive the electron for the environment. It can be seen that the lone pair of Pb2+ in the HCOH complex has a higher population than in the complexes with water molecules. The oxygen orbitals of this complex have lower populations than the water complexes because of the more polar bonds in the water molecules. Consequently, the populations on the hydrogen atoms are higher in the HCOH complex than in the two water complexes. This is comprehensible, considering that in the HCOH ring there are more electrons available, thanks to double bonds, so the oxygen atoms take electrons form the hydrogen atoms in one case and from the C=C double bonds in the other case. This example is not enough to settle why the bisdirected structure is observed. Further evidence can be obtained by using a molecule that does not cut the lone pair of Pb2+ in its middle. Therefore, we studied 2+ the Pb(C16H16O16) complex (complex A) in a) Ball and stick representation b) Side view c) Top view Figure 4. b) Ball and stick representation b) Side view c) Top view Figure 4: Schematic and ELF representations of complex A. (Violet colour is for the basin of Pb2+, the pink colour for the basin of the oxygens that point inside the cycle and the blue colour for the basin of oxygens that point outside the cycle.) 4 As can be seen from the ELF analysis, again the lone pair of Pb2+ is bisdirected.
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