HOMA parameters for the boron–boron bond: How the introduction of a BB bond influences the aromaticity of selected hydrocarbons

An extension of the harmonic oscillator model of aromaticity (HOMA) model for systems with boron–boron bonds is presented. For the first time, the parameters of the HOMA model are estimated using only theoretically calculated bond lengths. The HOMA parameters obtained make geometric aromaticity studies possible for a large number of compounds containing the boron–boron bond. The derived HOMA parameters have been used to investigate how the introduction of the boron–boron moiety in the structure of selected hydrocarbons modifies their aromaticity. The conclusion is that the insertion of a boron–boron bond usually strongly decreases the aromaticity of the boron-containing compounds in comparison to their parent hydrocarbons.     

PCM study of the solvent and substituent effects on bond dissociation energies of the C?NO bond

Quantum chemical calculations are used to estimate the equilibrium C? NO bond dissociation energies (BDEs) for eight X? NO molecule (X = CCl₃, C₆F₅, CH₃, CH₃CH₂, iC₃H₇, tC₄H₉, CH₂CHCH₂, and C₆H₅CH₂). These compounds are studied by employing the hybrid density functional theory (B3LYP, B3PW91, B3P86) methods together with 6‐31G** and 6‐311G** basis sets and the complete basis set (CBS‐QB3) method. The obtained results are compared with the available experimental results. It is demonstrated that B3P86/6‐31G** and CBS‐QB3 methods are accurate for computing the reliable BDEs for the X? NO molecule. Considering the inevitably computational cost of CBS‐QB3 method and the reliability of the B3P86 calculations, B3P86 method with 6‐31G** basis set may be more suitable to calculate the BDEs of the C? NO bond. The solvent effects on the BDEs of the C? NO bond are analyzed and it is shown that the C? NO BDEs in a vacuum computed by using B3PW91/6‐311G** method are the closest to the computed values in acetontrile and the average solvent effect is 1.48 kcal/mol. Subsequently, the substituent effects of the BDEs of the C? NO bond are further analyzed and it is found that electron denoting group stabilizes the radical and as a result BDE decreases; whereas electron withdrawing group stabilizes the group state of the molecule and thus increases the BDE from the parent molecule. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2009     

The nature of the O—O bond in hydroperoxides

Quantum-chemical calculations of the H₂O₂ and F₂ molecules using different computational schemes, basis sets, and procedures for the inclusion of electron correlation were performed. High-resolution X-ray diffraction study of the electron density distribution in the crystals of 2,5-dimethyl-2,5-dihydroperoxyhexane and 2,5-dimethyl-2,5-dihydroperoxyhex-3-yne was carried out. Joint analysis of the results obtained showed that the formally covalent O—O and F—F bonds correspond to a specific type of interatomic interaction. This type is intermediate between the shared and closed-shell interactions (the latter are typical of the ionic systems and van der Waals molecules).     

Interaction of a C-F bond with the π-system of a C═C bond or "head on" with a proximate C-H bond

We describe the synthesis and preliminary study of two molecules, in which a fluorine atom is positioned proximately above the π-orbitals of a C═C bond or else wherein a C-F bond interacts in a "head on" fashion with a proximate C-H bond. The spectroscopic characteristics of these unusual interactions are documented, X-ray crystallographic analyses are reported, and theoretical calculations are employed to support the observed spectroscopy.     

Experimental and theoretical study of the dissociation enthalpy of the N–O bond on 2-hydroxypyridine N-oxide: theoretical analysis of the energetics of the N–O bond for hydroxypyrydine N-oxide isomers

The standard (p^∘=0.1 MPa) molar enthalpy of formation of crystalline 2-hydroxypyridine N-oxide was measured, at T=298.15 K, by static bomb calorimetry and the standard molar enthalpy of sublimation, at T=298.15 K, was obtained using Calvet microcalorimetry. These values were used to derive the standard molar enthalpy of formation of 2-hydroxypyridine N-oxide in gaseous phase, and to evaluate the dissociation enthalpy of the N–O bond. Additionally, high-level density functional theory calculations using the B3LYP hybrid exchange-correlation energy functional have been performed for the three isomers of hydroxypyridine N-oxide in order to confirm the experimental trend for the dissociation enthalpy of the (N–O) bond.     

Why does cyclopropene have the acidity of an acetylene but the bond energy of methane?

The gas-phase acidity of 3,3-dimethylcyclopropene (1) has been measured by bracketing and equilibrium techniques. Consistent with simple hybridization arguments, our value (deltaH degrees (acid) = 382.7 +/- 1.3 kcal mol(-)(1)) is indistinguishable from that for methylacetylene (i.e., deltadeltaH degrees (acid)(1 - CH(3)Ctbd1;CH) = 1.6 +/- 2.5 kcal mol(-)(1)). The electron affinity of 3,3-dimethylcyclopropenyl radical (1r) was also determined (EA = 37.6 +/- 3.5 kcal mol(-)(1)), and these quantities were combined in a thermodynamic cycle to afford the homolytic C-H bond dissociation energy. To our surprise, the latter quantity (107 +/- 4 kcal mol(-)(1)) is the same as that for methane, which cannot be explained in terms of the s-character in the C-H bonds. An orbital explanation (delocalization) is proposed to account for the extra stability of 1r. All of the results are supplemented with G3 and B3LYP computations, and both approaches are in good accord with the experimental values. We also note that for simple hydrocarbons which give localized carbanions upon deprotonation there is an apparent linear correlation between any two of the following three quantities: deltaH degrees (acid), BDE, and EA. This observation could be of considerable value in many diverse areas of chemistry.     

Electrogeneration of the molybdenum-molybdenum double bond from thiolate-bridged dinuclear precursors: carbon monoxide catalysed isomerisation about the MoMo bond

The irreversible electroreduction of any of the three distinct dimolybdenum thiolate complexes [{MoCp(CO)}₂(μ-SMe)₃]⁺ and [{MoCp(CO)X}₂(μ-SMe)₂] (Cp = η⁵-C₅H₅; X = Cl or Br) gives a common intermediate which we identify as cis-[{MoCp(CO)}₂(μ-SMe)₂] (I). This intermediate slowly isomerises to the isolable product trans-[{MoCp(CO)}₂(μ-SMe)₂]; the isomerisation is catalysed by carbon monoxide, a process which we suggest takes place through CO binding across and elimination from the molybdenum-molybdenum double bond of (I).     

Enzymatic formation of an isopeptide bond involving the ε-amino group of lysine

Bacterial protease and lipase act as regioselective preparative catalysts of peptide bond synthesis in anhydrous organic solvents: when a derivative of lysine is used as the amino component, only its ε-NH₂ group reacts (to give an isopeptide linkage).     

Evolution of bond orders in the reversible reactions of alkylene oxides with R-β-hydroxyalkyl sulfides and the role of the intermolecular hydrogen bond in initiation and at intermediate reaction stages

Semiempirical (PM3) calculations of the changes in the structures and energies of the reactants, intermediates, transition states, and final products have been carried out for the reversible reaction of β-hydroxyethyl methyl sulfide with propylene oxide. The evolution of the electron density distribution during the reaction is analyzed. It is demonstrated that the transformation proceeds via two intermediate products and the O⋯H⋯O bridge persists throughout the reaction pathway.     

Elongated dihydrogen complexes: what remains of the H-H bond?

Of the several hundred examples of transition metal dihydrogen complexes that have been reported to date, the vast majority have H-H distances of less than 1.0 Angstrom. A small number of complexes have been reported with distances in the range of 1.1 to 1.5 Angstrom. These complexes have been termed elongated dihydrogen complexes. In this review, experimental methods for structure determination of such complexes are summarized, along with computational approaches which have proven useful in understanding the structures of these molecules.     

Enantioselective electrophilic bond construction to the α-carbon of α-aminoacids

In this report, we describe three possibilities for aminoacid synthesis using an enantioselective electrophilic process. Thus, enantioselective carboxylation, alkylation and protonation of Schiff bases yield optically active aminoacids with e.e. up to 76%.     

Interaction of the carbon—tin bond with beta positive charge

Participation of the CSn bond in the development of beta positive charge in aqueous trifluoroethanol does not depend on solvent nucleophilicity but does depend on SnCCX stereochemistry. These observations favor a hyperconjugative interaction and predict a phenomenal acceleration in the antiperiplanar arrangement.     

Study of the An–Cl bond contraction in actinide trichlorides

The variation of the An–Cl bond distance in ground-state actinide trichloride (AnCl₃) molecules has been studied by density functional theory calculations using the B3LYP exchange–correlation functional in conjunction with small-core relativistic energy-consistent pseudopotentials for the actinides. The ground electronic states and the ground-state molecular properties of the trichlorides of heavy actinides (An = Bk–Lr) are reported in this paper the first time. Extending the present results with literature data on the light actinide trichlorides (AnCl₃, An = Th–Cm), the trend in the bond distance has been evaluated for the whole actinide row. The contraction is well manifested in the major part of the actinide row (An = U–Fm). The deviations at the beginning (Th, Pa) and end of the row (Md, No) have been explained by minor differences in the bonding interactions.     

N-Cα bond cleavage of the peptide backbone via hydrogen abstraction

The specific cleavage of N-C_α bonds on the peptide backbone to form the so-called ‘c’ and ‘z + 2’ products, which can be used for the rapid determination of protein amino-acid sequences, has been examined to clarify the mechanism(s) that occur during hydrogen abstraction induced by bombardment with 337-nm laser photons in matrix-assisted laser desorption/ionization (MALDI) method. Intramolecular hydrogen abstraction, which results from the hydrogen(s) on the C_α or C_β carbon, did not occur with a deuterium-labeled dodecapeptide. To confirm a proposition that intermolecular hydrogen abstraction occurs between the peptide and the MALDI matrix, a deuterium dodecapeptide embedded in a deuterium 2,5-dihydroxybenzoic acid matrix at a molar ratio of 1:7000 was analyzed. The resulting deuterium c product ions suggested that c ions form via intermolecular hydrogen abstraction, although the results obtained did not deny any other possibilities such as intramolecular transfer of labile hydrogen. A mechanism for the N-C_α bond cleavage has been proposed that the formation of hypervalent radical species and subsequent prompt bond cleavages occur. The proposed mechanism successfully rationalizes the formation of both the z + 2 and the c product ions.     

Unexpected C-C bond cleavage of α-nitroketone in the presence of TsNBr2: A new pathway for C-N bond formation

A new catalyst-free protocol for C-N bond formation via the cleavage of α-nitroketone has been developed. When α -nitroketones are treated with TsNBr₂ in the presence of potassium carbonate, unexpected cleavage of C(O)-CHNO₂ bond of α -nitroketone was observed followed by the formation of corresponding amide. Various nitroketones could be converted to corresponding amide using this procedure.     

An approximation of the Cioslowski–Mixon bond order indexes using the AlteQ approach

Fast and reliable prediction of bond orders in organic systems based upon experimentally measured quantities can be performed using electron density features at bond critical points (J Am Chem Soc 105:5061–5068, 1983; J Phys Org Chem 16:133–141, 2003; Acta Cryst B 61:418–428, 2005; Acta Cryst B 63:142–150, 2007). These features are outcomes of low-temperature high-resolution X-ray diffraction experiments. However, a time-consuming procedure of gaining these quantities makes the prediction limited. In the present work we have employed an empirical approach AlteQ (J Comput Aided Mol Des 22:489–505, 2008) for evaluation of electron density properties. This approach uses a simple exponential function derived from comparison of electron density, gained from high-resolution X-ray crystallography, and distance to atomic nucleus what allows calculating density distribution in time-saving manner and gives results which are very close to experimental ones. As input data AlteQ accepts atomic coordinates of isolated molecules or molecular ensembles (for instance, protein–protein complexes or complexes of small molecules with proteins, etc.). Using AlteQ characteristics we have developed regression models predicting Cioslowski–Mixon bond order (CMBO) indexes (J Am Chem Soc 113(42):4142–4145, 1991). The models are characterized by high correlation coefficients lying in the range from 0.844 to 0.988 dependently on the type of covalent bond, thereby providing a bonding quantification that is in reasonable agreement with that obtained by orbital theory. Comparative analysis of CMBOs approximated using topological properties of AlteQ and experimental electron densities has shown that the models can be used for fast determination of bond orders directly from X-ray crystallography data and confirmed that AlteQ characteristics can replace experimental ones with satisfactory extent of accuracy.     

1,1-Insertion of substituted alkynes into the Ir-O bond of η-carboxylato iridium complexes

Alkyl-carbonyl-iridium [Ir(CH₃)(CO)(η²-O₂CR′)(PPh₃)₂]⁺ (1, R′ = CH₃, Ph, p-C₆H₄CH₃) react with alkynes (RCCH; R = Ph, p-C₆H₄CH₃) in the presence of NEt₃ to give acyl-alkynyl-iridium Ir(C(O)CH₃)(-CCR)(η²-O₂CR′)(PPh₃)₂ (4) which further react with RCCH to give alkyl-carbonyl-cis-bis(alkynyl) iridium Ir(CH₃)(CO)(CCR)₂(PPh₃)₂ (5). cis-Bis(alkenyl)iridium complexes, Ir(-CHCH₂)₂(η²-O₂CCH₃)(PPh₃)₂ (6) and (η²-O₂CCH₃)(PPh₃)₂ (7) react with substituted alkynes RCCH (R = Ph, p-C₆H₄CH₃, cyclohex-1-enyl) to give cis-bis(alkynyl) Ir(CCR)₂(η²-O₂CCH₃)(PPh₃)₂ (9) that further react with RCCH to undergo the alkyne insertion reaction into the Ir-O bond to produce iridacycles containing vinyl acetate ligands, (-CCR)₂(PPh₃)₂ (8).     

DFT study of α-maltose: influence of hydroxyl orientations on the glycosidic bond

The result of DFT geometry optimization of 68 unique α-maltose conformers at the B3LYP/6-311++G** level of theory is described. Particular attention is paid to the hydroxyl group rotational positions and their influence on the glycosidic bond dihedral angles. The orientation of lone pair electrons across the bridging hydrogen bonds are implicated in directing the glycosidic dihedral angles with for example, conformers gg-gg and gt-gt, having different minimum energy conformations for the clockwise (c) and the reverse clockwise (r) forms. Conformers tg-gg, gg-tg, tg-tg, gt-gg, and gg-gt were studied, to understand the intermediate glycosidic bond conformations. The conformation, tg-gg-c, was found to be the lowest energy structure. When the hydroxyl groups on each glucose residue were made to point in opposite directions, i.e., c/r and r/c, the optimized structures were found to have high relative energies. Several optimized ‘kink’ structures were found around (, ψ_H) ∼(−40°, −40°), the lowest relative energy conformation being ∼3 kcal/mol. “Kink” conformations are observed in crystalline CA-10 and CA-14mers. Band-flip conformations, also observed in X-ray structures of CA-26 fragments, were studied with the lowest energy α-maltose conformations ∼4.0 kcal/mol above the global energy minimum. Several trends in geometry resulting from hydroxyl rotamer directions are described. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users. Names are necessary to report factually on available data; however, the USDA neither guarantees nor warrants the standard of the product, and the use of the name by USDA implies no approval of the product to the exclusion of others that may also be suitable.     

Second-order Møller-Plesset evaluation of the bond length alternation of several series of linear oligomers

We investigate, at the second-order M?ller-Plesset level, the bond length alternation of 30 series of increasingly long linear oligomers for a total of more than 250 compounds, polyacetylene, polymethineimine, polyphosphinoborane, polyaminoborane, polyphosphazene, etc., for which, often for the first time, an accurate estimate of the polymeric bond length alternation is given. The variations induced either by chemical substitution of the backbone atoms or conformational modifications are discussed. Only three polymers present a large bond length alternation (>0.03 A). Systematic basis set effects have been unravelled, i.e., MP2/6-311G(2d) always overshoots the bond length alternation. Best estimates of the bond length alternation are provided for more than a dozen of polymers.     

Directivity of the intramolecular O→Si bond in pentacoordinate organosilicone compounds

According to the data of X-ray diffraction analysis and quantum chemical calculations, in the hypervalent silicon compounds where the coordination cycle is closed by the C=O→Si-F fragment, the O→Si interatomic distance is governed by the orientation of the silicon atom determined by the C=O→Si angle. This is an indication of a directivity of the coordination bond O→Si; a regular variation in the nature of the latter is reflected in the observed dependence of the O→Si distance on the C=O→Si angle.