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.     

Hybridization in highly strained small ring hydrocarbons. V. Methylene and isopropylene substituted spiropentanes

Using the method of maximum overlap, the hybrids, the bond overlaps and the deviation angles as well as the interhybrid angles have been calculated for several methylene and isopropylene substituted spiropentanes. Considerably different hybrids are found for the spiro carbon when the two C₃ rings have a different number of substituants. They deviate appreciably from the usually assumed sp³ type, being as different as sp^2.70 and sp^3.34. A brief discussion and comparison of some experimental molecular properties and the corresponding calculated parameters is presented. A discussion of factors which influence the hybridization in small rings has been given with some critical remarks on the reliability of predictions of molecular geometry (bond lengths) and molecular shapes (bond angles) by the maximum overlap method.     

Crystal and molecular structures of diastereomeric 2-phosphoryl-, 2-thiophosphoryl-, and 2-selenophosphoryl-substituted 1,3-dithianes

The crystal and molecular structures of five pairs of diastereomeric cis- and trans-2-phosphoryl-, 2-thiophosphoryl-, and 2-selenophosphoryl-5-t-butyl-1,3-dithianes have been determined. For all the examined compounds, all of the basic geometrical parameters, such as bond lengths, bond and torsion angles, and the deformation of a chair conformation of the six-membered heterocyclic rings, have been established. The differences in corresponding bond lengths and valence angles in diastereomeric cis- and trans-2-P-substituted 1,3-dithianes are discussed.     

Structural model of dioxouranium(VI) with hydrazono ligands

Synthesis and characterization of several new coordination compounds of dioxouranium(VI) heterochelates with bidentate hydrazono compounds derived from 1-phenyl-3-methyl-5-pyrazolone are described. The ligands and uranayl complexes have been characterized by various physico-chemical techniques. The bond lengths and the force constant have been calculated from asymmetric stretching frequency of OUO groups. The infrared spectral studies showed a monobasic bidentate behaviour with the oxygen and hydrazo nitrogen donor system. The effect of Hammett's constant on the bond distances and the force constants were also discussed and drawn. Wilson's matrix method, Badger's formula, Jones and El-Sonbati equations were used to determine the stretching and interaction force constant from which the UO bond distances were calculated. The bond distances of these complexes were also investigated.     

Conformational analysis of nucleic acid molecules with flexible furanose rings in dihedral angle space

The computational algorithm that works in the coordinate space of dihedral angles (i.e., bond lengths and bond angles are kept fixed and only rotatable dihedral angles are treated as independent variables) is extended to deal with the pseudorotational m otion of furanose rings by introducing a variable of pseudorotation. Then, this algorithm is applied to a distance geometry calculation that generates three-dimensional (3D) structures that are consistent with given constraints of interatomic distances. This method efficiently generates 3D structures of an RNA hairpin loop which satisfy a set of experimental NMR data. © 1996 by John Wiley & Sons, Inc.     

Structure of a C26H28 alkene formed via titanium-promoted reductive dimerization of 4-(spirocyclopropyl)-pentacyclo[5.4.0.02,6.03,10.05,9]undecan-8-one

A spiro-fused C₂₆H₂₈ cage≓ dimer hydrocarbon contains two three-membered rings, two four-membered rings, eight five-membered rings, and two six-membered rings. The molecule is calculated by molecular mechanics to have 902 kJ/mol of strain energy distributed primarily between angle strain (457 kJ/mol) and torsional interactions (368 kJ/mol). Molecular mechanics calculations and a geometry-optimized ab initio calculation are used to analyze the bond lengths and bond angles in the molecule. There is one major discrepancy between observed and calculated distances.     

On the vibrational spectra and structural parameters of methyl, silyl, and germyl azide from theoretical predictions and experimental data

The infrared and Raman spectra of methyl, silyl, and germyl azide (XN3 where X=CH3, SiH3 and GeH3) have been predicted from ab initio calculations with full electron correlation by second order perturbation theory (MP2) and hybrid density function theory (DFT) by the B3LYP method with a variety of basis sets. These predicted data are compared to previously reported experimental data and complete vibrational assignments are provided for all three molecules. It is shown that several of the assignments recently proposed [J. Mol. Struct. (Theochem.) 434 (1998) 1] for methyl azide are not correct. Structural parameters for CH3N3 and GeH3N3 have been obtained by combining the previously reported microwave rotational constants with the ab initio MP2/6-311+G(d,p) predicted values. These "adjusted r0" parameters have very small uncertainties of +/-0.003 A for the XH distances and a maximum of +/-0.005 A for the heavy atom distances and +/-0.5 degrees for the angles. The predicted distance for the terminal NN bond which is nearly a triple bond is much better predicted by the B3LYP calculations, whereas the fundamental frequencies are better predicted by the scaled ab initio calculations. The results are discussed and compared to those obtained for some similar molecules.     

Out-of-plane deformations of cyclic polyenes : A force-field interpretation of structural data

Spectroscopic force fields of benzene are shown to be compatible with the observed non-coplanarity of benzene rings with their H- or C- substituents in strained compounds, e.g. cyclophanes. A simplified force field for annulenes and cyclophanes is discussed, and ratios of the twist and out-of-plane bending force constants involved are derived from structural data. The resistance to twisting of partial double bonds is found to increase with decreasing bond length. Various formulae to calculate out-of-plane deformation coordinates are collected in an appendix.     

Non-fused polyaromatic hydrocarbons: interactions of aromatic and antiaromatic rings through a CC bond

The interaction of the moieties of benzene, cyclobutadiene, cyclopentadinyl anion, and the cyclopentadianide cation upon each other and upon a CC bond connecting pairs of these rings is investigated computationally. The resulting non-fused bicycles include biphenyl, phenylcyclobutadiene, phenylcyclopentadienylium, phenylcyclopentadienide, pentafulvalene, cyclobutadienyl–cyclopentadienylium, cyclobutadienyl–cyclopentadienide, and bicyclobutadiene. The relative stability and aromaticity are assessed from hydrogenation energies, aromatic stabilization energies, ring separation energies, nucleus-independent chemical-shift, harmonic oscillator model of aromaticity, and natural bond orbital analysis. Calculations are performed with density functional theory (B3LYP) and Møller–Plesset perturbation theory of second order (MP2). Enthalpy quantities are also determined by G3. When both rings are aromatic in character, the bridging bond is mostly σ in character. When one or both of the rings is antiaromatic, the bridging bond has significant π character. Systems with contrasting aromaticities have CC bridging bonds of lengths between CC single bond lengths and CC double bond lengths and where the systems were charged, the charge is evenly distributed between the rings.     

3,6—二〔二甲氨基〕二苯并碘六圜氯化物的晶体和分子结构

3,6—二[二甲氨基]二苯并碘六圆氯化物的晶体呈淡黄色六棱柱状。该晶体所属的空间群是P2_1/n,晶胞参数为;a=11.073(2),b=13.766(1),c=11.229(11),β=99.36(5)°,Z=4。在CAD—4四圆衍射仪上用Mo-Kα射线收录了Ⅰ≥3σ(Ⅰ)的独立衍射数据2293个。晶体结构用重原子法解出,晶体结构参数经全矩阵最小二乘方法修正,偏离因子R=0.085。 结构测定结果表明,分子中二苯环不共面,其二面交角约为133°。值得指出的是,围绕对称心成心对称的一对分子呈二聚状态。二聚体中二碘原子、二氯原子及与碘原子毗邻的四个碳原子共处于一个平面。二聚体中I—C1间距有3.074和3.102两种,围绕碘原子的四个键角值为90°左右。在二聚体中碘原子以dsp~2。杂化轨道与周围的二氯原子、二碳原子键合。     

硝胺及其甲基衍生物的从头计算研究 I: 平衡几何构型的全优化

我们用移植的TEXAS梯度法从头计算程序, 选取STO-4-21G基组, 对硝胺、甲硝胺和二甲硝胺等分子的平衡几何构型进行了全优化计算。其C-N, N-H和C-H等键长的计算结果以4-21G基组的标准校正值校正之后, 所得理论预测值与实验数据良好相符, 对N-N,N-O键长以及键角、两面角等构型参数, 对照计算和实验结果进行了讨论。     

Dinitro and quinodimethane derivatives of terthiophene that can be both oxidized and reduced. Crystal structures,spectra, and a method for analyzing quinoid contributions to structure

Two new oligothiophenes, the dinitro compound 3',4'-dibutyl-5,5' '-dinitro-2,2':5',2' '-terthiophene (1) and the quinodimethane 3',4'-dibutyl-5,5' '-bis(dicyanomethylene)-5,5' '-dihydro-2,2':5',2' '-terthiophene (2), have been synthesized and studied with electrochemistry, UV-vis-NIR-IR spectroscopy, ESR, and X-ray crystallography. These compounds, designed to be both electron and hole carriers, show redox properties that are unusual for oligothiophenes. Cyclic voltammetry and spectroelectrochemistry demonstrated that each compound could be oxidized to a cation radical and reduced to an anion radical and dianion. The spectra of 2 and its three redox partners were analyzed in terms of a limiting structure in which the neutral 2 has orbitals corresponding to those of a substituted-terthiophene dication. Compound 1 crystallizes with the thiophene rings held in an unusual nonplanar, cisoid configuration in face-to-face pi-stacks, with a spacing between molecules of 3.65 A. The C-C bond lengths of the outer nitro-substituted rings have quinoid character. Compound 2 crystallizes with the thiophene rings in a planar, transoid configuration. The molecules are held in pi-stacks formed from pi-dimers with a spacing between molecules of 3.47 and 3.63 A. The C-C bond distances of the thiophene rings of 1 and 2 and other oligomers were analyzed by a principal component analysis. The analysis found that 93% of the structural variance resided in one principal component related to the quinoid structure of the oligothiophene moiety. The analysis reliably demonstrated a quinoid contribution to the structure of 1. This method should be applicable to understanding the structure of other conjugated molecules in which quinoid structures contribute.     

A naphthalene with unusual bond alternation made by annelation with bicyclo[2.1.1]hexene units: aromaticity and reactivity

An entirely new naphthalene having one six-membered ring, whose bond lengths are equalized, and another ring, whose bond lengths are alternated, has been prepared via one-electron oxidation of a benzene annelated with three bicyclo[2.1.1]hexene units. The structure has been determined by X-ray crystallography and the aromaticity of two benzene rings estimated by theoretical calculations. Although the former six-membered ring has a higher degree of aromaticity, it has been found to be more reactive toward singlet oxygen owing to the greater strain contained in it. These results have been interpreted by means of theoretical calculations.     

Novel complexes of zirconium and uranium derived from bifunctional azodyes donor ligands containing hydrogen bonds

Novel complexes of zirconium(IV) and uranium(II) with selective azodyes containing nitrogen and oxygen donor ligands have been prepared and characterized by elemental analysis, ¹H NMR and electronic spectral techniques. The important bands in the IR spectra and main ¹H NMR signals are assigned and discussed in relation to the proposed molecular structure of the complexes. The IR data of the azodye ligands suggested a bidentate binding involving azodye nitrogen and C–O/OH oxygen atom of enolic group. They also showed the presence of Cl/OAc coordinating with the metal ion. The prepared complexes of Zr(IV) fall into four types. In the stoichiometric formulae of (1:1), the chelate rings are six-membered/five coordinate; whereas in the (1:2) they are six-membered/six coordinate and all of the complexes possess non-electrolytic properties. The UO₂(II) complex, in the mean time, possesses a planar hexagonal structure with nitrogen and oxygen atoms in the axial position. The stretching vibrations and force constant interactions of the uranyl complexes have been determined and from which the U–O bond distances are calculated. These bond distances as well as the effect of Hamett’s constant are also, in turn, calculated and discussed.     

High resolution 13C NMR spectroscopy V—structure dependence of the 13C,H coupling constants in aceheptylene,azulene and 5-azaazulene

In order to study the structure dependence of the ¹³C,H coupling constants in polycyclic conjugated π electron systems with 5-and 7-membered rings, the ¹H coupled ¹³C NMR spectra of aceheptylene, azulene and 5-azaazulene have been analysed. The results are discussed, including published data of monocyclic reference compounds, and are compared to theoretical values calculated by the FPT-INDO method. It is shown that, first, the geminal ¹³C,H couplings in the unsaturated 5-membered carbocycles are predominantly dependent on CC bond lengths. Second, the vicinal ¹³C,H coupling constants in 5- as well as in 7-membered unsaturated carbocyclic rings can be linearly related to the lengths of the central CC bonds. Third, the vicinal inter-ring couplings show a large variation and give information on ring junction, thus being of special value in structure determination and are governed mainly by the bond angles. Fourth, the calculated ¹³C,H couplings across one and two bonds are totally useless for practical purposes; those across three bonds, however, at least reflect the experimental trends.     

Orbital overlap and chemical bonding

The chemical bonds in the diatomic molecules Li(2)-F(2) and Na(2)-Cl(2) at different bond lengths have been analyzed by the energy decomposition analysis (EDA) method using DFT calculations at the BP86/TZ2P level. The interatomic interactions are discussed in terms of quasiclassical electrostatic interactions DeltaE(elstat), Pauli repulsion DeltaE(Pauli) and attractive orbital interactions DeltaE(orb). The energy terms are compared with the orbital overlaps at different interatomic distances. The quasiclassical electrostatic interactions between two electrons occupying 1s, 2s, 2p(sigma), and 2p(pi) orbitals have been calculated and the results are analyzed and discussed. It is shown that the equilibrium distances of the covalent bonds are not determined by the maximum overlap of the sigma valence orbitals, which nearly always has its largest value at clearly shorter distances than the equilibrium bond length. The crucial interaction that prevents shorter bonds is not the loss of attractive interactions, but a sharp increase in the Pauli repulsion between electrons in valence orbitals. The attractive interactions of DeltaE(orb) and the repulsive interactions of DeltaE(Pauli) are both determined by the orbital overlap. The net effect of the two terms depends on the occupation of the valence orbitals, but the onset of attractive orbital interactions occurs at longer distances than Pauli repulsion, because overlap of occupied orbitals with vacant orbitals starts earlier than overlap between occupied orbitals. The contribution of DeltaE(elstat) in most nonpolar covalent bonds is strongly attractive. This comes from the deviation of quasiclassical electron-electron repulsion and nuclear-electron attraction from Coulomb's law for point charges. The actual strength of DeltaE(elstat) depends on the size and shape of the occupied valence orbitals. The attractive electrostatic contributions in the diatomic molecules Li(2)-F(2) come from the s and p(sigma) electrons, while the p(pi) electrons do not compensate for nuclear-nuclear repulsion. It is the interplay of the three terms DeltaE(orb), DeltaE(Pauli), and DeltaE(elstat) that determines the bond energies and equilibrium distances of covalently bonded molecules. Molecules like N(2) and O(2), which are usually considered as covalently bonded, would not be bonded without the quasiclassical attraction DeltaE(elstat).     

The synthesis and crystal structure of [NiL(NCS)2] (L=3-hydroxyethyl-1,3,5,8,12-pentaazacyclotetradecane)

The reaction of H2CO and H2NCH2CH2OH with the nickel(II) complex of 1,9-diamino-3,7-diazanonane (2,3,2-tet) in the presence of Et3N gives the nickel(II) complex of the macrocycle 3-hydroxyethyl-1,3,5,8,12-pentaazacyclotetradecane (L), which can be readily isolated as the perchlorate salt. The reaction of KCNS with the perchlorate salt in aqueous solution gives [NiL(NCS)2] and the crystal structure of this complex has been determined. The complex is octahedral and trans with the two N-bonded thiocyanates in the axial sites with Ni-NCS bond lengths of 2.106 and 2.145AÅ. The equatorial sites are occupied by N2, N5, N8 and N12 with Ni-N bond distances of 2.053 to 2.076AÅ, which are typical for octahedral nickel(II) complexes. The ligand has a trans III configuration of the sec-NH centres, leading to chair six-membered rings and gauche five-membered rings. The hydroxyethyl group on N3 is axial. There is no evidence for hydrogen-bonding interactions involving the hydroxyethyl group in the crystal lattice.     

Structural and electronic effects involving pyridine rings in 4-methylpyridine Cu4OX6L4 complexes. II. Correlations based on molecular structure of the Cu4OCl6(4-Mepy)4 complex

Correlations involving bond lengths and bond angles in the molecular structure of the Cu₄OCl₆(4-Mepy)₄ complex (4-Mepy = 4-methylpyridine) with four symmetrically independent molecules present in the unit cell showed that the donor-acceptor behavior involving the π-back donation into the pyridine rings of the 4-Mepy ligands is most effectively stimulated by a suitable orientation of the pyridine rings in the trigonal bipyramidal geometry. The pyridine ring planes are almost in parallel orientation with one of the three Cu-Cl bonds. The bond lengths of these Cu-Cl bonds are in a significant linear correlation with the Cu-N bond lengths and the bonds lengths of the pyridine rings. The pyridine rings orientation is affected by distortion of the trigonal bipyramidal geometry to tetragonal pyramidal coordination, by out-of plane pyridine rings deviation and in-plane pyridine rings tilting, by puckering of the pyridine rings and by the effects of the methyl groups. The pyridine rings in at least seven of the sixteen trigonal bipyramidal coordinations exhibit an orientation supporting the π-back bonding between the Cu(II) atoms and the pyridine rings.     

Hybridization in fulvene and some related cycloalkenes by the iterative maximum overlap approximation

The hybrid orbitals in cyclopentadiene, fulvene and 6,6-dimethylfulvene were calculated by the iterative maximum overlap method. The hybridization parameters obtained were then used for the calculation of the proton chemical shifts and spin-spin coupling constants J(¹³C-¹H) of the directly bonded carbon and hydrogen nuclei. They can be favourably compared with available experimental data. The predicted bond lengths and bond angles are compared with the results of the more sophisticated semiempirical MINDO/2 and MINDO/3 methods. It is shown that the iterative maximum overlap method gives equally good, or sometimes even better, agreement with experiment. The calculated bond lengths and angles have been used for prediction of molecular diamagnetic susceptibilities by using the additivity formulae of Maksi? and Bloor. The results are within experimental error.     

Magic electron counts and bonding in tubular boranes

Ring stacking in some closo-borane dianions and the hypothetical capped borane nanotubes, predicted to be stable earlier, is analyzed in a perturbation theoretic way. A "staggered" building up of rings to form nanotubes is explored for four- and five-membered B(n)H(n) rings. Arguments are given for the stacking of B(5)H(5) rings being energetically more favorable than the stacking of B(4)H(4) rings. Elongated B[bond]B distances in the central rings are predicted for some nanotubes, and the necessity to optimize ring-cap bonding is found to be responsible for this elongation. This effect reaches a maximum in B(17)H(17)(2-); the insertion of additional rings will reduce this elongation. These closo-borane nanotubes obey Wade's n + 1 rule, but the traditional explanation based on a partitioning into radial/tangential molecular orbitals is wanting.