The Three-Center, Four-Electron Bond in Hexacoordinated AB6-Type Main Group Molecules: An Alternative Model of Bonding without d-Orbital Participation in the Central Atom

The hexacoordinated AB₆-type main group molecules have long been thought to have sp³d² hybridization on the central atom, accounting for their molecular geometry (octahedral). However, the s-p-d hybridization does not explain how an energetically unfavorable np nd excitation in an atom of nonmetallic elements, such as sulfur and phosphorus, can be achieved. In this article, the author has re-examined bonding in SF₆ and PF₆^– (O_h symmetry) and proposed that the linear F—S—F and F—P—F bonds in both species are formed via the overlap of the 3p orbital on the central atom with terminal ligand orbitals, resulting in a three-center, four-electron bond. This alternative model, which does not involve d orbitals in bonding, is supported by a partial charge analysis using Allens electronegativity approach. SF₆ or PF₆^– can be characterized by several ionic resonance structures containing a postulated SF₄²⁺ or PF₄⁺ cation (octet on sulfur or phosphorus). The three-center, four-electron bond model can also be used to study bonding in hexacoordinated AB₅E (e.g., halogen pentafluorides) and AB₄E₂ (e.g., xenon tetrafluoride) explaining well the molecular geometry. The author believes that all the results will be useful in updating chemistry texts.     

Special Features of the Geometry of the 2,2,2,4,4,4-Hexachloro-1,3-dimethyl-1,3-diaza-2,4-diphosphetane Molecule and Its Electron Distribution According to Data of ab initio Calculations

The results of a nonempirical calculation of the 2,2,2,4,4,4-hexachloro-1,3-dimethyl-1,3-diaza-2,4-diphosphetane (Cl₃PNCH₃)₂ molecule by the RHF 6-31G(d) method are in agreement with the data of X-ray structural analysis of this compound. Calculated ³⁵Cl NQR frequencies for axial and equatorial chlorine atoms are close to the experimental values. The population of the orbitals of the lone electron pairs and the p orbitals of the equatorial Cl atoms were significantly lower than those of the axial atoms. Among the MO there was no MO corresponding to a three-center bond involving a P atom and axial Cl and N atoms.     

Localized orbital calculations of the bonding in SO,SO2F2, ClO3F and SOCL2

Localized valence molecular orbitals have been obtained for SO, SO₂F₂, ClO₃F and SOCl₂ by the method due to Boys and Foster. The bonding in these molecules, in which the second row atom is exhibiting an excess valency, is discussed in terms of the form of these localized orbitals. The bonding of the second row atom to an oxygen atom is described by three bent bond orbitals, whilst bonding to a halogen atom is described by a single bond orbital. The participation of 3d functions in the various bonding and nonbonding orbitals is analysed in this localized orbital framework.     

Molecular shape,shape of the geometrically active atomic states,and hybridization

In a recent publication [C. A. Nicolaides and Y. Komninos, Int. J. Quant. Chem. 67 , 321 (1998)], we proposed that in certain classes of molecules the fundamental reason for the formation of covalent polyatomic molecules in their normal shape is to be found in the existence of a geometrically active atomic state (GAAS) of the central atom, whose shape, together with its maximum spin‐and‐space coupling to the ligands, predetermines the normal molecular shape (NMS). The shape of any atomic state was defined as that which is deduced from the maxima of the probability distribution ϱ(cos θ₁₂) of the angle formed by the position vectors of two electrons of an N‐electron atom. Because the shape of the GAAS determines the NMS and because the NMS allows the construction of corresponding hybrid orbitals, we examined and discovered the connection between the GAAS shape and Pauling's function for the strength of two equivalent orthogonal orbitals at angle θ₁₂ with one another. It is shown that the computed ϱ(cos θ₁₂) of the GAAS can be cast in a form which allows the deduction of the composition of the hybrid orbitals of maximum spin states with configurations sp³, sp³d⁵, sp³d⁵f⁷, slⁿ, s²lⁿ and the demonstration of the central atom's tendency to form bonds in directions which coincide with the nodal cones of the hybrid bond orbitals. These results not only reinforce the validity of the theory as to the fundamental “mechanism” for the formation in the normal shape of coordination compounds and covalently bonded polyatomic molecules, but also provide the justification for the relevance and importance of the hybridization model. ©1999 John Wiley & Sons, Inc. Int J Quant Chem 71: 25–34, 1999     

SYMMETRY ADAPTED LIGAND GROUP ORBITALS AND ANALYTICAL COMPOSITIONS OF HYBRID ORBITALS IN ABn TYPE MOLECULES

Abstract

A non-rigorous method of construction of SALC's for AB_n type molecules, based on the sum of the projections of the AB axes on the reference axes of the valence orbitals of the central atom, is presented. The method may be adapted to structures such as TBP where the inequivalence of the equatorial and axial ligands make the existing methods difficult to apply. A convenient method for deriving the analytical compositions of hybrid orbitals is also described.     

Pentacarbonyl(di‐2‐pyridyl­amine)tungsten(0)

In the title molecular complex, (I), the W atom is in an octahedral environment with four equatorial carbonyl ligands and a fifth in an axial position trans to the monodentate dipyridyl­amine ligand. The long dimension of this last bisects the angle between two of the equatorial carbonyl groups and while the non‐bonded pyridyl N atom is directed away from the W atom, the bridging amine group is directed towards it. Thus, in addition to the N atom to which it is attached, the amino H has two nearest neighbour C atoms of equatorial carbonyl groups but does not participate in hydrogen bonding in any real or usual sense. The W—C bond distance for the axial carbonyl group is notably less than those of the equatorial groups.     

Conformational analysis of thiopeptides: (ϕ,ψ) maps of thio‐substituted dipeptides

Noncoded amino acids such as isobutyric acid have been used extensively in the process of drug design and protein engineering. This article focuses on a noncoded amino acid where the oxygen in the peptide unit is replaced with a sp² sulfur. It was hypothesized that the conformational space as well as the conformational preferences of thiopeptides will be more restricted and altered by the bulkier atom with different electrostatic properties. In vacuo conformational minima as well as associated energies for the thio‐substituted alanine dipeptides were calculated at the ab initio HF/6‐31G* level. When the bulkier sulfur atom acts as a hydrogen bond acceptor in the C₅ conformation or in the C$^{\mathrm{axial}}_{7}$ and C$^{\mathrm{equatorial}}_{7}$ conformations, the hydrogen bond lengths are much longer than that of normal peptides. Consequently, the ?, ψ dihedral angles of the C₅, C$^{\mathrm{axial}}_{7}$, and C$^{\mathrm{equatorial}}_{7}$ conformations change to accommodate the longer hydrogen bonds. The thiopeptide group is a poorer hydrogen bond acceptor and a better hydrogen bond donor than the normal peptide group. Therefore, thio‐substitution at the amino terminal leads to disfavoring of the C₇ conformations relative to the C₅ conformations and thio‐substitution at the carboxyl terminal leads to favoring of the C₇ conformations relative to the C₅ conformation. To simulate the conformations in solution, (?,ψ) conformational energy maps were calculated for the glycine and alanine dipeptides at various dielectric constants using the CFF91 force field with our previously derived parameters for the thioamide group. The results show that thio‐substitution does restrict the conformations available to amino acids residues in peptides. Thio substitution at the amino terminal introduces unfavorable interactions near ?=?120 and 120, where there are increased overlaps between S_n?1?H_β, and S_n?1?C_β atoms, respectively. Thio substitution at the carboxyl terminal restricts the conformations near ψ=60, ?60, and 180, which correspond with increase overlaps between S_n?C_β, S_n?H_β′ and S_n?N_n atoms, respectively. The effects of dithio substitutions of either the alanine or the glycine dipeptides are similar to the combined effects of the two single thio substitutions. © 2001 John Wiley & Sons, Inc. J Comput Chem 22: 1026–1037, 2001     

The Silicon Carbonyls Revisited: On the Existence of a Planar Si(CO)4

Recently, some works have focused attention on the reactivity of silicon atom with closed-shell molecules. Silicon may form a few relatively stable compounds with CO, i.e. Si(CO), Si(CO)₂, Si[C₂O₂], while the existence of polycarbonyl (n>2) silicon complexes has been rejected by current literature. In this paper, the reaction of silicon with carbonyl has been reinvestigated by density functional calculations. It has been found that the tetracoordinated planar Si(CO)₄ complex is thermodynamically stable. In Si(CO), silicon carbonyl, and Si(CO)₂, silicon dicarbonyl, the CO are datively bonded to Si; Si(CO)₄, silicon tetracarbonyl, may be viewed as a resonance between the extreme configurations (CO)₂Si + 2CO and 2CO + Si(CO)₂; while Si[C₂O₂], c-silicodiketone, is similar to the compounds formed by silicon and ethylene. A detailed orbital analysis has shown that the Si bonding with two CO is consistent with the use of sp ²-hybridized orbitals on silicon, while the Si bonding with four CO is consistent with the use of sp ² d-hybridized orbitals on silicon, giving rise to a planar structure about Si.     

Characteristic features of interaction between atoms in chloro-substituted 1,4-dioxane fromab initio calculations

Ab initio calculations in a split-valence shell 6-31G(d) basis for the 2-chloro-1,4-dioxane (with axial and equatorial Cl atom) and 2,3-cis-dichloro-1,4-dioxane molecules with full optimization of their geometry were performed. The major contribution to the lowering of the NQR frequencies of the axial Cl atoms compared with the equatorial Cl atoms comes from the higher p-electron population of the former in these molecules. The populations of the orbitals for the unshared electron pairs of the axial and equatorial Cl atoms are identical in these molecules. But these orbitals are polarized differently, which also has some effect on the ratio of the NQR frequencies of these atoms. The differences in the electron populations of the axial and equatorial Cl atoms for the studied molecules are due to the asymmetry of the electron distribution in the Cl atoms geminal to them, which is responsible for the different polarization of the valence p-orbitals of the axial and equatorial Cl atoms.Institute of Technical Chemistry, Urals Branch, Russian Academy of Sciences, Perm' 614000, Russia; e-mail: chemist@mail.psu.ru. Translated from Khimiya Geterotsiklicheskikh Soedinenii, No. 11, pp. 1485–1490, November, 1999.     

Chemical Bonding in Silicon Carbonyl Complexes

Although silylene-carbonyl complexes are known for decades, only recently isolable examples have been accomplished. In this work, the bonding situation is re-evaluated to explain the origins of their remarkable stability within the Kohn-Sham molecular orbital theory framework. It is shown that the chemical bond can be understood as CO interaction with the silylene via a donor-acceptor interaction: a σ-donation from the σ_CO into the empty p-orbital of silicon, and a π-back donation from the sp² lone pair of silicon into the π*_CO antibonding orbitals. Notably, it was established that the driving force behind the surprisingly stable Si−CO compounds, however, is another π-back donation from a perpendicular bonding R−Si σ-orbital into the π*_CO antibonding orbitals. Consequently, the pyramidalization of the central silicon atom cannot be associated with the strength of the π-back donation, in sharp contrast to the established chemical bonding model. Considering this additional bonding interaction not only shed light on the bonding situation, but is also an indispensable key for broadening the scope of silylene-carbonyl chemistry.     

Conformational analysis of six-membered ring dioxaphosphinanes. Part 1: Anancomeric thiophosphates

A study of the conformation of a series of anancomeric axial and equatorial 2-aryloxy-2-thio-1,3,2λ⁵-dioxaphosphinanes 2-12 in solution and solid state is reported. In accord to the stereoelectronic theory, aryl thiophosphates substituted with electron-withdrawing (EW) groups will tend to occupy axial positions in chair ring conformations due to the stabilizing endo-anomeric (n_πO-σ_P-X^*) hyperconjugative interaction. The antiperiplanar orientation of the orbitals involved in the stereoelectronic interaction is a requirement that is fulfiled in the axial series of compounds when the ring adopts a chair conformation. Therefore, in the equatorial series of thiophosphates, the axial seeking characteristics of aryloxy-EW groups might render the molecule with distortion of the chair conformation. An opposite trend is anticipated for the less axial seeking aryl thiophosphates substituted with electron releasing (ER) groups. A detailed analysis of the ³J_HH, ³J_PH and ³J_CP coupling constants allowed us to conclude that there is no contribution of high energy twist-boat conformations in the equatorial thiophosphates substituted with aryl-EW groups in solution. In consequence, single chair conformations were found in solid state for aryl thiophosphates in both configurations. X-ray geometrical analysis of bond distances and bond angles supports clearly the participation of hyperconjugative endo-anomeric (n_πO-σ_P-OAr^*) effect in the stabilization of axial series of compounds and the participation of endo-anomeric (n_πO-σ_PS^*) effect in the stabilization of the equatorial thiophosphates in chair conformations.     

The Physical Mechanism of the Chemical Bond

First the interplay of kinetic and potential energy via the uncertainty relation is described with the aid of a variational function for the ground state of the H atom. The H ion is used to illustrate the physical mechanism of the occurrence of the chemical bond. The formation of the chemical bond can be divided into three steps: 1. the quasi-classical (electrostatic) interaction of the unchanged electronic charges of the separate atoms; 2. the interference of the atomic orbitals, which (in the case of positive interference) leads to a displacement of charge into the bonding region and to a decrease in the kinetic energy; 3. deformation of the molecular orbitals to restore the correct balance of kinetic and potential energy. In simple models, it is often sufficient to consider just the second step. A two-electron bond is not fundamentally different from a one-electron bond. In larger molecules it is possible to distinguish between long-range and short-range interatomic contributions to the chemical bond. If the former are small, i. e. in molecules with non-polar bonds, a one-electron molecular orbital theory can be justified. Finally, the possibility of describing molecules by localized bonds is discussed.     

The role of the sulfur 3d orbitals in bond formation in sulfur-containing compounds

The role of the sulfur 3d orbitals in bond formation is discussed by taking into account the influence of the environment on the orbitals of the sulfur atom in the molecules. The calculation results of a series of prototype molecules containing sulfur such as SF₂ SF₄, NSF₃, SF₀, H₂S are reported. It is convincingly shown that in highly electronegative environment the energy levels of the sulfur 3d orbitals are reduced to the vicinity of those of the ligand valence orbitals and their spatial distributions are contracted to the bonding area, and therefore they can participate in bond formation to a certain extent, which is enhanced by the formation of the d-p π back bonds. It seems that the result reported in this paper is helpful for the solution of the long-standing debate about the sulfur 3d orbital participation in bond formation.     

Etude par Résonance Magnétique Nucléaire de dioxaphosphorinanes-1,3,2 à liaison P?N extracyclique. Exemple de changement d'orientation de la liaison P?N

The ¹H NMR spectra of several 1,3,2-dioxaphosphorinanes bearing an extracyclic P? N bond have been analysed. The ³J(POCH) couplings are strongly dependent upon the orientation of the bond around the phosphorus atom. Depending upon the nature of the bonds attached to the nitrogen atom, the dioxaphosphorinane ring may adopt either a fixed chair conformation with the P? N bond in the axial or equatorial orientation, or it may be in equilibrium between two chair conformations where the P? N bond is alternately axial or equatorial. The equilibrium is fast on the NMR time scale.     

Potential Functions of Internal Rotation around the Csp2-X Bonds and Intermolecular Interactions in the Compounds CH2 = CHXCH3 (X = O,S, Se)

The potential functions of internal rotation around the Csp ²-X bonds in the CH₂ = CHXCH₃ molecules (X = O, S, Se) were determined by MP2/6-31G* and MP2/6-31G** calculations. The stationary points were identified by solution of vibrational problems. The rotation barriers were evaluated taking into account the zero-point vibration energy. The intramolecular interactions were considered in terms of the method of natural bond orbitals. The degrees of hybridization, energies, and populations of the orbitals of the lone electron pairs of the O, S, and Se atoms, the energies of their donor-acceptor interaction with the antibonding * and * orbitals of the double bond, and the natural atomic charges in various conformations were determined.     

Comparative Infrared,Raman, and Natural‐Bond‐Orbital Analyses of King's Sultam

By means of ¹H‐NOESY‐ and Raman‐spectroscopic analyses, we experimentally demonstrated the presence of the equatorial N? Me conformer of King's sultam 4b in solution, resulting from a rapid equilibrium. As a consequence, the value of the N lone‐pair anomeric stabilization should be revised to 1.5–1.6 kcal/mol. Independently from the N tilting, natural bond orbital (NBO)‐comparative analyses suggest that the S d* orbitals do not appear as primordial and stereospecific acceptors for the N lone pair. Second, the five‐membered‐ring sultams do not seem to be particularly well‐stabilized by the S? C σ* orbital in the N‐substituted pseudo‐axial conformation, as opposed to an idealized anti‐periplanar situation for the six‐membered‐ring analogues. In this latter case, the other anti‐periplanar C? C σ* and C(1′)? H/C(2′) σ*orbitals are as important, if not more, when compared to the S? C σ* participation. In the pseudo‐equatorial conformation, γ‐sultams particularly benefit from the N lone‐pair hyperconjugation with the anti‐periplanar S? O₁ σ* and C(2)? H/C or C(1′)? H/C σ* orbitals. This is also the case for δ‐sultams when the steric requirement of the N‐substituent exceeds 1.6 kcal/mol. When both axial and equatorial conformations are sterically too exacting, the N‐atom is prone to sp² hybridization or/and conformational changes (i.e., 12c ). In that case also, the mode of stereoelectronic stabilization differs from γ‐ to δ‐sultams.     

New diorganotin(IV) complexes of Schiff base derived from 4‐amino‐3‐hydrazino‐5‐mercapto‐4H‐1,2,4‐triazole: Synthesis,structural characterization,density functional theory studies,atoms‐in‐molecules analysis and antifungal activity

New diorganotin(IV) complexes of a Schiff base (HL) having general formula R₂Sn(L)Cl (where L is the monoanion of HL and R = n‐Bu or Ph) have been synthesized and characterized using elemental analysis, infrared, NMR (¹H, ¹³C, ¹¹⁹Sn) and UV–visible spectroscopies and mass spectrometry. These investigations suggest that in these 1:1 monomeric derivatives the Schiff base ligand acts in a monoanionic bidentate manner coordinating through the O_phenolic and N_azomethine, with proposed distorted trigonal bipyramidal geometry around tin with O_phenolic and two organic groups in the equatorial plane and the N_azomethine and the third organic group in axial positions. The proposed structures have been validated by density functional theory (DFT)‐based quantum chemical calculations at the B3LYP/6‐31G(d,p)/Def2‐SVP (Sn) level of theory. The simulated UV–visible spectrum was obtained with the time‐dependent DFT method in the gas phase and in the solvent field with the integral equation formalism–polarizable continuum model. A comparative analysis of the experimental vibrational frequencies and simulated harmonic frequencies indicates a good correlation between them. An insight into the intramolecular bonding and interactions among bonds in organotin(IV) complexes of HL was obtained by means of natural bond orbital analysis. The topological and energetic properties of the electron density distribution for the tin–ligand interaction in R₂Sn(L)Cl have been theoretically calculated at the bonds around the central tin atom in terms of atoms‐in‐molecules theory. The R₂Sn(L)Cl complexes were screened for their in vitro antifungal activity against chosen fungal strains.     

Synthesis,crystal structure and properties of a novel di-μ2-aqua bridged binuclear manganese(III) Schiff base complex [Mn(vanen)(H2O)2]2(ClO4)2 · 2H2O

The preparation and isolation of the binuclear manganese(III) complex, [Mn(vanen)(H₂O)₂]₂(ClO₄)₂ · 2H₂O was accomplished by air oxidation of a solution containing H₂vanen^**, Et₃N, and Mn(ClO₄)₂ · 6H₂O in absolute EtOH. The crystal structure of complex was determined by X-ray crystallography, and consists of two molecules bridged by two water molecules through hydrogen bonding. The manganese atom is six-coordinate and presents a distorted octahedral coordination sphere, which consists of the two imine N atoms and two phenolic O atoms of vanen^2– ligand in the equatorial plane, with Mn–N bond distances of 1.975 and 1.987 Å, and Mn–O distances of 1.867 and 1.876 Å, respectively. The non-bonding interatomic MnMn distance is 4.79 Å. In the axial direction, the elongated Mn–O(H₂O) bond distances of 2.255 and 2.381 Å, respectively, are due to Jahn–Teller distortion at the d⁴ metal center. The presence of lattice and coordinate water molecules were also confirmed by the t.g. study and the i.r. spectra. Upon irradiation using visible light in water in the presence of p-benzoquinone, the complex demonstrates its ability to split water.     

Electronic and Spatial Structure of Piperidine and Its Substituted Derivatives from the Results of ab initio Calculations

The results of non empirical quantum-chemical calculations using the RHF/6-31G(d) and MP2/6-31G(d) methods do not agree with proposals for the axial position of the H atom on the N atom in the piperidine molecule. According to RHF/6-31G(d) calculations for the N-methylpiperidine molecule and its chloro-substituted derivatives an equatorially placed methyl group is energetically more favored than an axial. The axial C-Cl and C-H bonds in these molecules are longer than the equatorial. The ³⁵ Cl NQR frequencies for the axial Cl atoms are lower than the equatorial. The ³⁵ Cl NQR frequency of the axial chlorine atom in 2-chloro-1-methylpiperidine is anomalously low. This is chiefly due to the high population density of its p σ-orbital and this is a result of the polarization of the C-Cl bond via the N atom unshared electron pair directly through the field. The effect of a similar unshared electron pair on the parameters of the C-Cl bond in the ClCH₂NH₂ molecule has been studied by the RHF/6-31(g) method for different angles of rotation of the ClCH₂ group around the C-N bond. __________ Translated from Khimiya Geterotsiklicheskikh Soedinenii, No. 7, pp. 1044–1052, July, 2005.