Ligand close packing and the geometry of the fluorides of the nonmetals of periods 3, 4, and 5

This paper discusses the geometry of the fluorides of the nonmetals of periods 3, 4, and 5 in terms of the ligand close packing (LCP) model according to which molecular geometry is determined primarily by ligand-ligand repulsions (Pauli closed shell repulsions) rather than by the bonding and lone pair Pauli repulsions of the VSEPR model. The LCP model becomes the dominant factor in determing geometry when the ligands are sufficiently crowded that they may be regarded as essentially incompressible. Ligand close packing is a modification of the VSEPR model in which ligand-ligand repulsion (Pauli closed shell repulsion) is given more emphasis than bonding and nonbonding electron pair Pauli repulsion. The nonmetals of period 3 are large enough to form octahedral six coordinated molecules in which the ligands are close packed. The larger nonmetals of period 4 also have a maximum coordination number of six and an octahedral geometry although the ligands are not close packed. Ligand radii derived from the interligand distances in the molecules of period 3 depend only on the charge of the fluorine ligands and are consistent with the previously derived radii obtained from the fluorides of the close packed tetrahedral molecules of the period 2 elements. Although the ligands in the molecules of the period 4 nonmetals are not close packed, these elements are not large enough to form molecules with a higher coordination number. However, the larger period 5 nonmetals may have coordination numbers of seven and eight. The seven coordinated molecules have a pentagonal bipyramidal geometry in which the equatorial ligands are close packed. The eight coordinated molecules have a square antiprism geometry, which is not a close packed geometry although the fluorine interligand distances are only a little larger than expected for close packing. The difference between the axial and equatorial bond lengths in the trigonal bipyramidal pentafluorides and the pentagonal bipyramidal pentafluorides can be understood on the basis of ligand close packing. Ligand packing prevents the lone pair in AF(6)E molecules from fully entering the valence shell and thereby exerting its full stereochemical effect so that these molecules have a C(3)(v)() distorted octahedral geometry rather than a geometry based on pentagonal bipyramidal seven coordination.     

Bond critical points in the electronic structures of the main group diatomic hydrides of lithium through bromine

The bond critical points and associated electronic properties of the diatomic hydrides of the twenty-one main group elements from lithium to bromine have been calculated with large basis sets. As part of a systematic study of the polarity of chemical bonds, the position of the bond critical point, the charge density at the bond critical point, the Laplacian of the charge density at the bond critical point, and the molecular dipole moment of each molecule have been calculated. Particular attention has been paid to the effect of bond length elongation and contraction on the electronic properties. Variation of the bond length reveals that with atoms of low electronegativity, the bond critical point of AH tends to follow atom A, whereas with atoms of high electronegativity, the bond critical point tends to follow the hydrogen atom as the bond lengthens. Furthermore, it is shown that some properties of the diatomic hydrides vary monotonically within each row of the periodic table, while others effect a classification according to the character of the bond.     

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.     

Effects induced by axial ligands binding to tetrapyrrole-based aromatic metallomacrocycles

The axial positions of planar metallomacrocycles are unoccupied. The positively charged metal is thus a potential binding site for electron-donating groups. The binding strength is affected by the central metal, the ligand, and the macrocycle. One ligand leads to the out-of-plane displacement of the central metal, whereas two ligands from two sides structurally neutralize each other. The axial ligand donates charge to the central metal and the macrocycle when the lone pair orients along the interaction axis. The frontier orbital levels are elevated because of the charge donated to the macrocycle. Even though the singlet-triplet gap and the absorption maximum do not change significantly upon binding, the redox chemistry is considerably affected by the shifts of orbital levels. The macrocyclic M-N bonds are weakened by the binding, but their natures remain almost unchanged. Calcium phthalocyanine is a special case, as the central calcium is too large to fit the cavity. Accordingly, multiple ligands facilely bind to the calcium from one side. The aluminum phthalocyanine halogen is another special case, as it has a halogen ligand coordinating to the aluminum through a nondative bond. This leads to some effects different from those caused by dative binding. When there is no considerable steric demand, the lone pair points along the interaction axis to facilitate the donation. When in a stacked dimer, the electron-rich group is part of a large molecule, and the orientation of the lone pair is approximately perpendicular to the interaction axis. This induces the charge loss of the central metal. Because metallomacrocycles are widespread in the biological, medical, and material sciences, the results from this study are expected to bring useful insights to these fields.     

Electronegativity based on the simple bond charge model

A single physical interpretation of the various electronegativity scales of Pauling, Mulliken and Gordy is suggested, based on the simple bond charge (SBC) model of Parr and Borkman for the covalent bond. With a charge partition determined from vibrational frequencies, the SBC model is shown to account for the covalent bond energy in single-bonded homonuclear diatomic molecules and diamond-type crystals. The binding energy to the atom of a bond-electron in the single-bonded homonuclear diatomic molecules agrees with Mulliken's electroaffinity, and provides a definition for electronegativity. Gordy's empirical relation between the bond-stretching force constant and electronegativity is explained. It is then suggested that the physical effect underlying Pauling's thermochemical formula for electronagativity is the location of the bond charge in the heteronuclear molecule. The deviation of Pauling's formula from experiment in the case of the alkali hydrides can then be explained.     

Chemical bonding in hypervalent molecules: is the octet rule relevant?

The bonding in a large number of hypervalent molecules of P, As, S, Se, Te, Cl, and Br with the ligands F, Cl, O, CH(3), and CH(2) has been studied using the topological analysis of the electron localization function ELF. This function partitions the electron density of a molecule into core and valence basins and further classifies valence basins according to the number of core basins with which they have a contact. The number and geometry of these basins is generally in accord with the VSEPR model. The population of each basin can be obtained by integration, and so, the total population of the valence shell of an atom can be obtained as the sum of the populations of all the valence basins which share a boundary with its core basin. It was found that the population of the V(A, X) disynaptic basin corresponding to the bond, where A is the central atom and X the ligand, varies with the electronegativity of the ligand from approximately 2.0 for a weakly electronegative ligand such as CH(3) to less than 1.0 for a ligand such as F. We find that the total population of the valence shell of a hypervalent atom may vary from close to 10 for a period 15 element and close to 12 for a group 16 element to considerably less than 8 for an electronegative ligand such as F. For example, the phosphorus atom in PF(5) has a population of 5.37 electrons in its valence shell, whereas the arsenic atom in AsMe5 has a population of 9.68 electrons in its valence shell. By definition, hypervalent atoms do not obey the Lewis octet rule. They may or may not obey a modified octet rule that has taken the place of the Lewis octet rule in many recent discussions and according to which an atom in a molecule always has fewer than 8 electrons in its valence shell. We show that the bonds in hypervalent molecules are very similar to those in corresponding nonhypervalent (Lewis octet) molecules. They are all polar bonds ranging from weakly to strongly polar depending on the electronegativity of the ligands. The term hypervalent therefore has little significance except to indicate that an atom in a molecule is forming more than four electron pair bonds.     

Investigation of transition metal-imido bonding in M(NBut)2(dpma)

A complete series down group 6 of the formula M(NBu(t))(2)(dpma) has been synthesized, where dpma is N,N-di(pyrrolyl-alpha-methyl)-N-methylamine. A fourth complex, Mo(NAr)(2)(dpma) (4), was also prepared, where Ar is 2,6-diisopropylphenyl. All four of these complexes display geometries in the solid state best described as square pyramidal with one imido ligand occupying the axial position and the other an equatorial site. In all cases, the axial imido ligand has a significantly smaller M-N(imido)-C bond angle with respect to the equatorial multiple-bond substituent. From the (1)H, (13)C, and (14)N NMR spectra, the axial (bent) imido appears to be more electron-rich than the equatorial and linear imido, with the differences becoming less pronounced down the column. The angular deformation energies for the axial imido ligands were studied by DFT in order to discern if and to what extent imido bond angles were important energetically. The electronic energies associated with straightening the axial imido ligand, while holding the remainder of the molecule at the ground-state geometry, for the Cr, Mo, and W derivatives were calculated as 4.5, 2.7, and 2.0 kcal/mol, respectively. A straight-line plot is found for deformation energies versus estimated electronegativity of the group 6 metals in the +6 oxidation state. The study suggests that the electronic differences between metal imido ligands of different angles are quite small; however, the effects may be more pronounced for metal centers with higher electronegativity, e.g. Cr(VI) with electron-withdrawing ligands.     

从VSEPR模型到LCP模型:价层电子对互斥理论的形成与发展

考察价层电子对互斥理论(VSEPR模型)的发展史可知,1916年路易斯提出的“原子立方体”假设为VSEPR模型的形成奠定了基础.1940年西德威克和鲍威尔的假设进一步促进了VSEPR模型的形成.1957年吉莱斯皮和尼霍尔姆拓展了西德威克和鲍威尔的假设,并于1963年正式提出价层电子对互斥理论的概念.至1988年,吉莱斯...     

Is VSEPR valid?

Summary A chief tenet of VSEPR (valence shell electron pair repulsion theory) is that very electronegative atoms or groups attached to a central atom pull electrons toward themselves. These electron pairs, being farther apart, exert less repulsion, and consequently the bond angles involving them are decreased. A comparison of 37 pairs of common compounds shows that this rule holds only for hydrogen compounds. For other molecules, the size of the attached groups determines the bond angles.

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VSEPR: ist es stichhaltig?

Zusammenfassung Ein Hauptgrundsatz der VSEPR (Valenzschalen-Elektronenpaar-Repulsion) Theorie heißt: hoch elektronegative, an einem Zentralatom angelagerte Atome oder Atomgruppen ziehen Elektronen an. Da sie weiter voneinander entfernt sind, üben diese Elektronenpaare weniger Repulsion aus. Daher werden die dazugehörigen Bindungswinkel vermindert. Ein Vergleich von 37 Paaren einfacher Verbindungen zeigt, daß diese Regel nur für Wasserstoffverbindungen gilt. In anderen Molekülen bestimmt die Größe der angelagerten Gruppen die Valenzwinkel.

     

ABEEMσπ/MM力场模型下的多肽构象

在ABEEM/MM蛋白质浮动电荷力场模型的基础上,加入孤对电子和 电荷位点,从而能够体现多肽和蛋白质分子中一些重要的各向异性极化性质,允许非化学键方向的电子转移和极化。利用从头计算数据拟合模型相关参数。计算得到的小分子团簇结合能、偶极矩、氢键键长等性质与从头计算结果符合很好。该经典极化模型力场能够重复量子场下丙氨酸二肽、丙氨酸四肽、甘氨酸三肽的各稳定构象,其稳定性顺序与精密从头计算结果相一致,其结构和能量性质较以往模型有一定提高,并优于其他力场模型。     

次级键与晶体中锑(III)螯合物配位多面体研究

考虑立体活性孤对电子附近次级键配位原子的贡献, 对文献报道的三十个氨基多羧酸锑(III)螯合物的晶体结构中配位多面体描述进行了全面的修正. 配位多面体的几何构型指定采用了单位球内截多面体的两面角判据及其相关的ANVPDA程序. 所有配位多面体几何构型的修正均得到了键价计算的有力支持.     

环多肽晶体的浮动电荷极化力场模拟

利用原子键电负性均衡结合分子力场方法(ABEEM/MM)对五种环多肽晶体进行了研究. 与传统力场相比, 该方法中的静电势包含了分子内和分子间的静电极化作用, 以及分子内电荷转移影响, 同时加入了化学键等非原子中心电荷位点, 合理地体现了分子中的电荷分布. 相对其他极化力场模型, 具有计算量较小的特点. 该模型下计算得到的环多肽分子单元相对实验测得的结构的原子位置、氢键长度和二面角的均方根偏差分别为0.009 nm、0.013 nm和5.16°, 能够很好地重复实验结果. 总体上, 其结果优于或相当于其他力场模型, 适用于对实际蛋白质体系的模拟和研究.     

Structures of Nickel(II) and Copper(II) Complexes of 14-Membered Macrocyclic Quadridentate Ligands

The structures of 41 Ni(II) and 17 Cu(II) complexes of macrocyclic quadridentate ligands have been analyzed, and are discussed about bond lengths, bond angles, conformations, and configurations, upon which many conclusions are formed. The inter- or intra-molecular hydrogen bonds exist among ligands and hydrates in many compounds and play an important role in the structures. There are exhibited two distinct peaks on the histogram of the average Ni-N distances, corresponding to four coordination and six coordination; these average Ni-N distances are 1.95(4) Å and 2.10(5) Å, respectively. The most probable structures of Ni(II) macrocyclic compounds have coordination number six for the metal ion, chair forms for six-membered rings, planar structure for the metal ion and the four donor atoms of the quadridentate ligand and an inversion center at the central metal ion.     

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.     

Study of peptide conformation in terms of the ABEEM/MM method

The ABEEM/MM model (atom-bond electronegativity equalization method fused into molecular mechanics) is applied to study of the polypeptide conformations. The Lennard-Jones and torsional parameters were optimized to be consistent with the ABEEM/MM fluctuating charge electrostatic potential. The hydrogen bond was specially treated with an electrostatic fitting function. Molecular dipole moments, dimerization energies, and hydrogen bond lengths of complexes are reasonably achieved by our model, compared to ab initio results. The ABEEM/MM fluctuating charge model reproduces both the peptide conformational energies and structures with satisfactory accuracy with low computer cost. The transferability is tested by applying the parameters of our model to the tetrapeptide of alanine and another four dipeptides. The overall RMS deviations in conformational energies and key dihedral angles for four di- or tetrapeptide, is 0.39 kcal/mol and 7.7 degrees . The current results agree well with those by the accurate ab initio method, and are comparable to those from the best existing force fields. The results make us believe that our fluctuating charge model can obtain more promising results in protein and macromolecular modeling with good accuracy but less computer cost.     

Matrix reactivity of AlF and AlCl in the presence of HCl and HBr: generation and characterization of the new Al(III) hydrides HAlFCl,HAlFBr, and HAlClBr and the monomeric mixed Al(III) halides AlX(2)Y (X,Y = F,Cl, or Br)

The spontaneous and photolytically induced reactions of AlF and AlCl in the presence of HCl and HBr in solid argon matrices were followed and the products identified and characterized by means of IR spectroscopy. Quantum mechanical calculations allow for a further evaluation of the properties of the reaction products. These are the adducts AlF.HCl, AlF.HBr, and AlCl.HBr, representing the products of spontaneous reactions, and the trivalent Al(III) hydrides HAlFCl, HAlFBr, and HAlClBr, which were formed upon photoactivation of these complexes. All three hydrides are planar molecules (C(s)() symmetry) with bond angles in agreement with the predictions of the VSEPR theory. In addition, the mixed halides AlFCl(2), AlFBr(2), and AlClBr(2) were formed upon photolysis. The bisadducts AlF.(HCl)(2) and AlF.(HBr)(2) are likely to be the precursors to these species.     

CH3SH…HOO开壳型氢键复合物的结构及其电子密度拓扑性质

在DFT-B3LYP/6-311++G**水平下求得CH3SH…HOO复合物势能面上的稳定构型. 计算结果表明, 在HOO以其O8—H7作为质子供体与CH3SH分子中的S5原子为质子受体形成的氢键复合物1和2中, O8—H7明显被“拉长”, 且其伸缩振动频率发生显著的红移, 红移值分别为330.1和320.4 cm-1; 在CH3SH分子以其S5—H6作为质子供体与HOO的端基O9原子为质子受体形成的氢键复合物3和4中, 也存在类似的情况, 但S5—H6伸缩振动频率红移不大. 经MP2/6-311++G**水平计算的4种复合物含BSSE校正的相互作用能分别为-20.81, -20.10, -4.46和-4.52 kJ/mol. 自然键轨道理论(NBO)分析表明, 在CH3SH…HOO复合物1和2中, 引起H7—O8键长增加的因素包括两种电荷转移, 即孤对电子n1(S5)→σ*(H7—O8)和孤对电子n2(S5)→σ*(H7—O8), 其中后者为主要作用. 在复合物3和4中也有相似的电荷转移情况, 但轨道间的相互作用要弱一些. AIM理论分析结果表明, 4个复合物中的S5…H7间和O9…H6间都存在键鞍点, 且其Laplacian量▽2ρ(r)都是很小的正值, 说明这种相互作用介于共价键和离子键之间, 偏静电作用为主.     

Ligands of low electronegativity in the VSEPR model: The structures of singlet carbenes

Equilibrium structures and force constants for skeletal bending from linearity have been calculated, in the MNDO approximation, for twenty five singlet carbenes CX₂. When the substituent X bears neither vacant orbitals nor lone pairs, the force constant becomes steadily more negative as the electronegativity of X increases; when X bears vacant orbitals, the C→ X π bond order and the force constant both increase with the electronegativity of X. When X bears lone pairs, the force constant parallels the HOMO—LUMO gap at linearity. Previous discussions of the structures of singlet carbenes are shown to be inadequate: the reported results support the interpretation in terms of the second-order Jahn-Teller effect of the observed stereochemical inactivity of lone pairs in the presence of ligands of low electronegativity.     

Ligand close packing and the geometries of A(XY)4 and some related molecules

Molecules of the type A(OX)₄, A(NX₂)₄ and A(CY₂X)₄ are not regularly tetrahedral about the central atom A. Two of the angles about this central atom are smaller than tetrahedral and four are larger, or four are smaller and two larger. By considering that the ligand atom (O, N or C) that is bonded to the central atom A has three intramolecular ligand radii and minimising the number of ligand–ligand contact distances, as described in the theory of ligand close packing, we are able to account for the S₄ and D_2d geometries observed for C(OCH₃)₄, C(OPh)₄ and CEE₄ and related molecules. The ligand close packing model also rationalises the C₂ geometries of SO₂(OR)₂ molecules and the differences in O–C–R angles and C–R bond lengths in R₃COX molecules. The lengths of these interligand radii can be determined either by calculating the molecular geometry or by deriving them from experimental geometries. The radii depend on the charge of the ligand, the sizes of the Y and Z groups and the angle A–X–Z. The relative sizes of these radii determine the preference for D_2d or S₄ geometries and the degree of distortion of the bond angles from the ideal tetrahedral angle.     

Intramolecular Reactivity of π-Coordinated P-Heterocycles: How to Form Five-Membered Rings out of Phosphaalkynes

Experimental and theoretical evidence is presented for a novel metal-dependent intramolecular reactivity of ~ -bonded, unsaturated P-heterocycles like 1,3-diphosphete and 1,3,5-triphosphinine. The nucleophilic attack of a P lone pair of 1,3-diphosphete toward a neighboring ligand leads to new bicyclic ligands with unique structural features. A metal-initiated intramolecular hydrogen transfer and C--C bond formation are observed for (1,3,5-triphosphinine)(COD)Fe to result in the formation of [(CO) 5 Cr(4,5,6-trihydro-1,3,5-triphosphinine)(trihydropentalene)Fe].