Electron Domains and the VSEPR Model of Molecular Geometry

The valence shell electron pair repulsion (VSEPR) model—also known as the Gillespie–Nyholm rules—has for many years provided a useful basis for understanding and rationalizing molecular geometry, and because of its simplicity it has gained widespread acceptance as a pedagogical tool. In its original formulation the model was based on the concept that the valence shell electron pairs behave as if they repel each other and thus keep as far apart as possible. But in recent years more emphasis has been placed on the space occupied by a valence shell electron pair, called the domain of the electron pair, and on the relative sizes and shapes of these domains. This reformulated version of the model is simpler to apply, and it shows more clearly that the Pauli principle provides the physical basis of the model. Moreover, Bader and his co-workers' analysis of the electron density distribution of many covalent molecules have shown that the local concentrations of electron density (charge concentrations) in the valence shells of the atoms in a molecule have the same relative locations and sizes as have been assumed for the electron pair domains in the VSEPR model, thus providing further support for the model. This increased understanding of the model has inspired efforts to examine the electron density distribution in molecules that have long been regarded as exceptions to the VSEPR model to try to understand these exceptions better. This work has shown that it is often important to consider not only the relative locations and sizes, but also the shapes, of both bonding and lone pair domains in accounting for the details of molecular geometry. It has also been shown that a basic assumption of the VSEPR model, namely that the core of an atom underlying its valence shell is spherical and has no influence on the geometry of a molecule, is normally valid for the nonmetals but often not valid for the metals, including the transition metals. The cores of polarizable metal atoms may be nonspherical because they include nonbonding electrons or because they are distorted by the ligands, and these nonspherical cores may have an important influence on the geometry of a molecule.     

Structural chemistry of organotin(IV) complexes

The amazing structural diversity in organotin compounds is discussed in the systems containing -O and -S donor ligands. It is demonstrated that there exist a fascinating range of structural diversity for organotin(IV) complexes, including differences in coordination number and molecular geometry. The difference in structure is correlated with the nature of tin and ligand bonded R groups. Despite the large number of different structures found in organotin(IV) carboxylates, there is limited range of coordination geometries about the Sn atom. The four coordinated Sn atom in triorganotin(IV) complexes is invariably distorted tetrahedral and five coordinated Sn is distorted trigonal bipyramidal. A large range has been observed for diorganotin carboxylate structures, where five, six and seven coordinate geometries have been reported. The Sn atom in mono-organotin has only been demonstrated to exist in distorted octahedral geometries (the single exception being a pentagonal bipyramidal geometry). In the case of organotin(IV) complexes of S donor ligands, it has been shown that there exists a rich diversity in Sn atom geometries and coordination modes of the sulfur donor ligands themselves. As in related carboxylate systems, the assignment of coordination numbers to the Sn centers in some compounds is controversial. As a general trend, it has been shown that, the overall coordination number at the Sn atom decreases with the increasing number of organic substituents at the Sn atom. This phenomenon is usually achieved by increased asymmetry in the mode of coordination of the sulfur donor ligands.     

Poly[[aqua(μ7‐ethylenediaminetetraacetato)dicadmium(II)] monohydrate]

The title compound, {[Cd₂(C₁₀H₁₂N₂O₈)(H₂O)]·H₂O}_n, consists of two crystallographically independent Cd^II cations, one ethylenediaminetetraacetate (edta) tetraanion, one coordinated water molecule and one solvent water molecule. The coordination of one of the Cd atoms, Cd1, is composed of five O atoms and two N atoms from two tetraanionic edta ligands in a distorted pentagonal–bipyramidal coordination geometry. The other Cd atom, Cd2, is six‐coordinated by five carboxylate O atoms from five edta ligands and one water molecule in a distorted octahedral geometry. Two neighbouring Cd1 atoms are bridged by a pair of carboxylate O atoms to form a centrosymmetric [Cd₂(edta)₂]⁴⁻ unit located on the inversion centre, which is further extended into a two‐dimensional layered structure through Cd2—O bonds. There are hydrogen bonds between the coordinated water molecules and carboxylate O atoms within the layer. The solvent water molecules occupy the space between the layers and interact with the host layers through O—H...O and C—H...O interactions.     

A topological study of the geometry of AF6E molecules: weak and inactive lone pairs

The geometries of AF6E molecules, which may have either an O(h) or a C(3v) geometry, have been studied by means of the electron localization function. Our results show that when the molecule has a C(3v) geometry, there is a valence-shell monosynaptic V(A) basin corresponding to the presence of a lone pair in the valence shell of the central atom A. The population of this basin is, however, extensively delocalized so that the electron density has a core-valence basin character, which is consistent with an earlier suggestion of a weakly active lone pair that gives a C(3v) distorted octahedral molecule rather than the valence-shell electron-pair repulsion predicted pentagonal-pyramid geometry. In contrast, the molecules with O(h) geometry do not have a monosynaptic valence-shell basin, but they have a larger core. These results provide confirmation of a previous suggestion that in AX6E (X = Cl, Br, I) molecules with the O(h) geometry the ligands X are sufficiently closely packed around the central atom A so as to leave no space in the valence shell for the lone pair E, which remains part of the core. Among the corresponding fluorides, only BrF6- has the O(h) geometry, while the others have the C(3v) geometry because there is sufficient space in the valence shell to accommodate the lone pair, the presence of which distorts the O(h) geometry to C(3v). The energies of the O(h) and C(3v) geometries have been shown to be very similar so the observed geometries are a consequence of a very fine balance between ligand-ligand repulsions and the energy gained by the expansion of the two nonbonding electrons into the valence shell.     

Diastereopure Fe(II) and Zn(II) complexes derived from a tridentate N,N',N-bis(methyl-L-prolinate)-substituted pyridine ligand

A series of mononuclear iron(II) and zinc(II) complexes of the new chiral Py(ProMe)2 ligand (Py(ProMe)2 = 2,6-bis[[(S)-2-(methyloxycarbonyl)-1-pyrrolidinyl]methyl]pyridine) have been prepared. The molecular geometry in the solid state (X-ray crystal structures) of the complexes [FeCl2(Py(ProMe)2)] (1), [ZnCl2(Py(ProMe)2)] (2), [Fe(OTf)2(Py(ProMe)2)] (3), [Fe(Py(ProMe)2)(OH2)2](OTf)2 (4), and [Zn(OTf)(Py(ProMe)2)](OTf) (5) are reported. They all show a meridional NN'N coordination of the Py(ProMe)2 ligand. The bis-chloride derivatives 1 and 2 represent neutral isostructural five-coordinated complexes with a distorted geometry around the metal center. Unusual seven-coordinate iron(II) complexes 3 and 4 having a pentagonal bipyramidal geometry were obtained using weakly coordinating triflate anions. The reaction of Zn(OTf)2 with the Py(ProMe)2 ligand afforded complex 5 with a distorted octahedral geometry around the zinc center. All complexes were formed as single diastereoisomers. In the case of complexes 3-5, the oxygen atoms of both carbonyl groups of the ligand are also coordinated to the metal. The stereochemistry of the coordinated tertiary amine donors in complexes 3-5 is of opposite configuration as in complexes 1 and 2 as a result of the planar penta-coordination of the ligand Py(ProMe)2. Complexes 1, 2, and 5 have an overall -configuration at their metal center, while the Fe(II) ion in complexes 3 and 4 has the opposite delta-configuration (crystal structures and CD measurements). The magnetic moments of iron complexes 1, 3, and 4 correspond to that of high-spin d6 Fe(II) complexes. The solution structures of complexes 1-5 were characterized by means of UV-vis, IR, conductivity, and CD measurements and their electrochemical behavior. These studies showed that the coordination environment of 1 and 2 observed in the solid state is maintained in solution. In coordinating solvents, the triflate anion (3, 5) or water (4) co-ligands of complexes 3-5 are replaced by solvent molecules with retention of the original pentagonal bipyramidal and octahedral geometry, respectively.     

Stereochemistry of lead(II) complexes containing sulfur and selenium donor atom ligands

The stereochemistry of lead(II) complexes with S- and Se-donor atom ligands, including mixed ligand complexes is reviewed with respect to the geometry of the first coordination sphere of the Pb(II) atom in these compounds and rationalized in terms of the valence shell electron-pair repulsion (VSEPR) model. The most comprehensively structurally characterized classes of lead(II) thio and seleno complexes are discussed, including monothio-, dithio(seleno)-, trithio- and tetrathio-complexes, as well as Pb(II) dialkyldithio(seleno)carbamates, alkylxanthates and dialkyl(aryl) phosphorodithio(seleno)lates. Data about the polyhedral shape of the primary coordination sphere, coordination number (CN), bond lengths (primary and secondary) and bond angles of the Pb(II) atom in the compounds under investigation are systematized in comprehensive tables. The particularities of the stereochemistry of Pb(II) complexes with S(Se)-donor atom ligands are comparatively discussed with the stereochemistry of lead(II) complexes with oxygen donor ligands.     

Compositional and structural variety of diphenyllead(IV) complexes obtained by reaction of diphenyllead dichloride with thiosemicarbazones

The reactions of PbPh(2)Cl(2) in methanol with acetophenone, salicylaldehyde, pyridine-2-carbaldehyde, 2-acetylpyridine, and 2-benzoylpyridine thiosemicarbazones (HATSC, HSTSC, HPyTSC, HAcPyTSC, and HBPyTSC, respectively) were explored. Despite the similarities among these ligands, the reactions afforded solids with very diverse compositions and structural characteristics, which were in most cases analyzed by X-ray diffractometry (as was the structure of the free ligand HBPyTSC). In the complexes [PbPh(2)Cl(2)(HATSC)](2), [PbPh(2)Cl(2)(HSTSC)(2)], [(PbPh(2)Cl(HPyTSC)(2))][PbPh(2)Cl(3)(MeOH)](2), and [PbPh(2)Cl(PyTSC)] the metal atoms are surrounded by more or less distorted octahedral coordination polyhedra; if both strong and weak interactions are considered, the lead atom in [PbPh(2)Cl(AcPyTSC)] has coordination number 7 and distorted pentagonal bipyramidal coordination geometry, while [(PbPh(2)(BPyTSC))(2)(PbPh(2)Cl(4))].2MeOH contains two different types of lead atom, one with octahedral and the other with pentagonal bipyramidal coordination. The complexes (H(2)AcPyTSC)[PbPh(2)Cl(3)] and [PbPh(2)Cl(HAcPyTSC)][PbPh(2)Cl(3)], which were also isolated, could not be crystallized. All these complexes are soluble in DMSO, and the compositions of these solutions were investigated using conductivity measurements and (1)H and (207)Pb NMR spectroscopy.     

Poly[tetra‐μ2‐l‐lactato‐indium(III)sodium(I)]

The asymmetric unit of the title compound, [InNa(C₃H₅O₃)₄]_n, consists of one In^III ion, one Na^I ion and four crystallographically independent l ‐lactate monoanions. The coordination of the In^III ion is composed of five carboxylate O and two hydroxy O atoms in a distorted pentagonal–bipyramidal coordination geometry. The Na^I ion is six‐coordinated by four carboxylate O atoms and two hydroxy O atoms from four l ‐lactate ligands in a distorted octahedral geometry. Each In^III ion is coordinated by four surrounding l ‐lactate ligands to form an [In(l ‐lactate)₄]⁻ unit, which is further linked by Na^I ions through Na—O bonds to give a two‐dimensional layered structure. Hydrogen bonds between the hydroxy groups and carboxylate O atoms are observed between neighbouring layers.     

Metal chelates of ampicillin versus amoxicillin: synthesis,structural investigation,and biological studies

Solid chelates derived from some alkaline earth and transition metal complexes with ampicillin (Hamp, a) and amoxicillin (Hamox, b) were synthesized and characterized using elemental analysis, molar conductivity, IR, magnetic susceptibility, and thermogravimetric studies. Both drugs behave as tetradentate ligands coordinating to metal through amino, imino, and carboxylate as well as through β-lactamic carbonyl. All chelates have octahedral geometry except Cu(II) complexes which have square planar structure and uranium has pentagonal bipyramidal coordination. ¹H- and ¹³C-NMR of the Zn(II) and UO₂(VI) chelates are compared with the free ligands. The antimicrobial activity of the prepared chelates was determined.     

Steric repulsions, rotation barriers, and stereoelectronic effects: a real space perspective

Widely used chemical concepts like Pauli repulsion or hyperconjugation, and their role in determining rotation barriers or stereoelectronic effects, are analyzed from the real space perspective of the interacting quantum atoms approach (IQA). IQA emerges from the quantum theory of atoms in molecules (QTAIM), but is free from the equilibrium geometry constraint of the former. A framework with both electronically unrelaxed and relaxed wavefunctions is presented that leads to an approximate correspondence between the IQA concepts and those used in the EDA (energy decomposition analysis) or NBO (natural bond orbital) procedures. We show that no net force acts upon the electrons in an electronically relaxed system, so that any reasonable definition of Pauli repulsion must involve unrelaxed state functions. Using antisymmetrized fragments clarifies that Pauli repulsions are energetically connected to the IQA deformation energies, leaving footprints in the finally relaxed states. Similarly, EDA or NBO hyperconjugative stabilizations are found to be naturally related to the IQA electron delocalization patterns. Applications to the rotation barrier of ethane and other simple systems are presented, and the very often forgotten role of electrostatic contributions in determining preferred conformations is highlighted.     

Poly[[pentaaquasulfato‐μ4‐(R,R)‐tartrato‐dicadmium(II)] trihydrate]

The asymmetric unit in the title compound, {[Cd₂(C₄H₄O₆)(SO₄)(H₂O)₅]·3H₂O}_n, is composed of two cadmium cations, one (R,R)‐tartrate and one sulfate anion, five aqua ligands and three solvent water molecules. One of the cadmium ions is coordinated in an octahedral environment, whereas the second is surrounded by seven O atoms in a pentagonal–bipyramidal geometry. Both types of coordination polyhedra form two sets of perpendicular non‐intersecting polymeric chains. CdO₆ octahedra share two corners, while CdO₇ units are joined by a bridging carboxylate group. An extensive hydrogen‐bond pattern involving all of the OH groups contributes to the stabilization of the structure.     

Single-Crystal Structure of the Solvent-Separated Radical Ion Pair [9,10-diphenylanthracene.⊖][Na⊕(THF)6] and its implication for cation solvation

The one-electron transfer to large π-delocalized hydrocarbons provides an interesting possibility to crystallize solvent-separated ion-pair salts containing optimally solvated cations. Accordingly, the reduction of 9,10-diphenylanthracene in aprotic THF solution at a sodium metal mirror allows to grow dark-blue prismatic crystals of its radical anion and sixfold THF-solvated sodium cation. The structure of the radical anion is very similar to that recently published for the neutral molecule. According to AM1 hypersurface calculations based on the structural data, the phenyl twist angles obviously must be determined by lattice packing, and the negative charge is delocalized predominantly within the anthracene π system. The counter cation [Na^⊕(THF)₆], reported ordered for the first time, shows nearly octahedral coordination within a rather densily packed solvent shell. Due to the strong repulsions between the solvent molecules, its isodesmically calculated solvation enthalpy is smaller than that of the analogous dimethoxyethane complex [Na^⊕(DME)₃].     

Geometry of the Fluorides, Oxofluorides, Hydrides, and Methanides of Vanadium(V), Chromium(VI), and Molybdenum(VI): Understanding the Geometry of Non-VSEPR Molecules in Terms of Core Distortion

This paper describes a study of the topology of the electron density and its Laplacian for the molecules VF(5), VMe(5), VH(5), CrF(6), CrMe(6), CrOF(4), MoOF(4), CrO(2)F(2,) CrO(2)F(4)(2)(-) and CrOF(5)(-) all of which, except VF(5,) CrF(6), and CrOF(5)(-) have a non-VSEPR geometry. It is shown that in each case the interaction of the ligands with the metal atom core causes it to distort to a nonspherical shape. In particular, the Laplacian of the electron density reveals the formation of local concentrations of electron density in the outer shell of the core, which have a definite geometrical arrangement such as four in a tetrahedral arrangement or five in a square pyramidal or trigonal bipyramidal and six in an octahedral arrangement. Ligands that are predominately covalently bonded are found opposite regions of charge depletion between these core charge concentrations. In VH(5), VMe(5), CrOF(4), and MoOF(4), these core charge concentrations have a square pyramidal arrangement, and the regions of charge depletions have the corresponding inverse square pyramidal arrangement so that these molecules have a square pyramidal geometry rather than a trigonal prism geometry. In CrMe(6), there are five core charge concentrations with a trigonal bipyramidal arrangement so that the regions of charge depletion have a trigonal prismatic arrangement and the molecule has the corresponding trigonal prism geometry rather than an octahedral geometry. In contrast, molecules in which the only ligand is the more ionically bound fluorine are less affected by core distortion and have VSEPR-predicted structures. The unexpected bond angles in CrO(2)F(2) and the preference of CrO(2)F(4)(2)(-) for a cis structure are also discussed in terms of the pattern of core charge concentrations.     

A convenient route to lanthanide triiodide THF solvates. Crystal structures of LnI(3)(THF)(4) [Ln = Pr] and LnI(3)(THF)(3.5) [Ln = Nd, Gd, Y

The reaction between 1.5 equiv of elemental iodine and rare earth metals in powder form in THF at room temperature gives the rare earth triiodides LnI(3)(THF)(n)() in good yields. Purification by Soxhlet extraction of the crude solids with THF reliably gives the THF adducts LnI(3)(THF)(4) [Ln = La, Pr] and LnI(3)(THF)(3.5) [Ln = Nd, Sm, Gd, Dy, Er, Tm, Y] as microcrystalline solids. X-ray crystallography reveals that the early, larger lanthanide iodide PrI(3)(THF)(4) crystallizes as discrete molecules having a pentagonal bipyramidal structure, whereas the later, smaller lanthanide iodides LnI(3)(THF)(3.5) [Ln = Nd, Gd, Y] crystallize as solvent-separated ion pairs [LnI(2)(THF)(5)][LnI(4)(THF)(2)] in which the cations adopt a pentagonal bipyramidal geometry and the anions adopt an octahedral geometry in the solid state.     

The geometry of nonmetal hydrides and the ligand radius of hydrogen

The aim of this paper was to investigate why the geometries of nonmetal hydrides are often not in accordance with the VSEPR model. From a consideration of interligand distances in a variety of BX(4), CX(4), and NX(4) molecules where X is a ligand or a lone pair and in which there are at least two H ligands we have shown that the hydrogen ligands are essentially close-packed. For each of the central atoms we have obtained a value for the ligand radius of hydrogen. These radii decrease with decreasing negative charge and increasing positive charge of the hydrogen ligand as the electronegativity of the central atom increases, as has been found previously for other ligands such as F and Cl. We show that ligand-ligand intractions are an important factor in determining bond angles in hydrides and that the ligand close-packing (LCP) model gives a better explanation of bond angles than the VSEPR model according to which bond angles depend on the electronegativity of the ligand rather than on its size. For example, although the very small angles in PH(3) and SH(2) are not in accord with the VSEPR model, they are consistent with the LCP model in that they are a consequence of the small size of hydrogen ligands which are pushed together by the lone pairs until they are almost close-packed.     

Synthesis,structures and Hirshfeld surface analysis of Ni(II) and Co(III) complexes with N2O donor Schiff base ligand

Two octahedral complexes [NiL(HL)]ClO₄.0.5CH₃OH and [CoL₂]ClO₄ have been synthesized with N₂O donor Schiff base ligand {((2-(phenylamino)ethyl)imino)methyl}phenol (HL) and characterized by spectroscopic techniques and single crystal X-ray diffraction studies. The molar conductivities data of the two complexes show that the complexes are 1:1 electrolyte. Single crystal X-ray diffraction data shows both Ni(II) and Co(III) complexes have distorted octahedral geometry and two ligands are coordinated to the metal centers and one ClO₄⁻ ion outside the coordination sphere. The intermolecular interactions in the complexes are evaluated by Hirshfeld surface analysis and revealed a significant contribution of non- or weakly polar interactions to the packing forces for both molecules, with crystal structure of Co(III) complex featuring short H/H contacts.     

Heptacoordinated diphenyllead; hexa- and pentacoordinated triphenyllead and tin compounds derived from 5H-benzimidazo[1,2-c]quinazoline-6-thione

Heptacoordinated diphenyllead; hexa- and pentacoordinated triphenyllead and tin compounds derived from 5H-benzimidazo[1,2-c]quinazoline-6-thione are reported. The same molecular structures were found in solution by ¹¹⁹Sn and ²⁰⁷Pb NMR and in the solid state by X-ray diffraction analysis. The ligand was bound through S and N giving a four-membered ring. Due to the tension of the chelate ring in the penta- and hexacoordinated compounds, the nitrogen approaches the metal atom from an oblique direction giving a weak coordination. Hexacoordinated metal atoms were obtained by Lewis bases coordination to the polycyclic tin and lead compounds, which was possible because the M-phenyl groups form a cavity that allows the bases to approach from the opposite direction to the sulfur atom. In some crystals, two molecules formed a cavity where a solvent molecule was included. A heptacoordinated diphenyllead bound to two ligands and having the less common pentagonal bipyramidal geometry and cis-mer configuration with two sulfur atoms lying very close together was obtained.     

Crystallographic report: Bis(acetato‐O,O′){4‐[N,N‐bis(2‐cyanoethyl)amino] pyridine}bis(methanol)cadmium(II), [Cd(C11H12N4) (CH3CO2)2(CH3OH)2]

The cadmium atom is coordinated in distorted pentagonal bipyramidal geometry by the pyridine‐nitrogen atom of the 4‐[N,N‐bis(2‐cyanoethyl)amino]pyridine ligand, two oxygen atoms of two methanol molecules and four oxygen atoms of two acetate groups. Copyright © 2005 John Wiley & Sons, Ltd.     

Crystallographic report: Aquadicylcohexyltin(IV) bis(2‐picolinate) ethanol solvate

The tin atom in the title compound is in a distorted pentagonal bipyramidal geometry defined by two sets of nitrogen and oxygen donors derived from the carboxylate ligands, two carbon atoms from the cyclohexyl substituents and an oxygen atom from the coordinated water molecule; C? Sn? C 170.85(15)°. Extensive hydrogen bonding occurs in the lattice. Copyright © 2004 John Wiley & Sons, Ltd.     

A two‐dimensional cadmium(II) coordination polymer based on 5‐(pyridin‐4‐yl)isophthalic acid: poly[[tetraaquabis[μ3‐5‐(pyridin‐4‐yl)isophthalato]dicadmium(II)] pentahydrate]

The title Cd^II compound, {[Cd₂(C₁₃H₇NO₄)₂(H₂O)₄]·5H₂O}_n, was synthesized by the hydrothermal reaction of Cd(NO₃)₂·4H₂O and 5‐(pyridin‐4‐yl)isophthalic acid (H₂L). The asymmetric unit contains two crystallographically independent Cd^II cations, two deprotonated L²⁻ ligands, four coordinated water molecules and five isolated water molecules. One of the Cd^II cations adopts a six‐coordinate octahedral coordination geometry involving three O atoms from one bidentate chelating and one monodentate carboxylate group of two different L²⁻ ligands, one N atom of another L²⁻ ligand and two coordinated water molecules. The second Cd^II cation adopts a seven‐coordinate pentagonal–bipyramidal coordination geometry involving four O atoms from two bidentate chelating carboxylate groups of two different L²⁻ ligands, one N atom of another L²⁻ ligand and two coordinated water molecules. Each L²⁻ ligand bridges three Cd^II cations and, likewise, each Cd^II cation connects to three L²⁻ ligands, giving rise to a two‐dimensional graphite‐like 6³ layer structure. These two‐dimensional layers are further linked by O—H...O hydrogen‐bonding interactions to form a three‐dimensional supramolecular architecture. The photoluminescence properties of the title compound were also investigated.