Description of conjugation and hyperconjugation in terms of electron distributions

Bader, R. F. W.; Slee, Tom; Cremer, Dieter; Kraka, Elfi

doi:10.1021/ja00353a035

Cited by 620 publications

(455 citation statements)

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“…The experimental ellipticities of the aromatic bonds in the phenyl ring average 0.23, compared with the theoretical value of 0.21, both in good agreement with Bader et al's 1983 HF value of 0.23, obtained for benzene with a 6-31G* basis set (40).…”

Section: Resultssupporting

confidence: 87%

Application of charge density methods to a protein model compound: Calculation of Coulombic intermolecular interaction energies from the experimental charge density

Abramov

Volkov

et al. 2002

Proc. Natl. Acad. Sci. U.S.A.

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A combined experimental and theoretical charge density study of the pentapeptide Boc-Gln-D-Iva-Hyp-Ala-Phol (Boc, butoxycarbonyl; Gln, glutamine; Iva, isovaline; Hyp, hydroxyproline; Ala, ethylalanine; Phol, phenylalaninol) is described. The experimental analysis, based on synchrotron x-ray data collected at 20 K, is combined with ab initio theoretical calculations. The topologies of the experimental and theoretical densities are analyzed in terms of the atoms in molecules quantum theory. Topological parameters, including atomic charges and higher moments integrated over the atomic basins, have been evaluated with the program TOPXD and are used to calculate the electrostatic interactions between the molecules in the crystal. The interaction energies obtained after adding dispersive and repulsive van der Waals contributions agree quite well with those based on M-B3LYP͞6 -31G** dimer calculations for two of the three dimers in the crystal, whereas for the third a larger stabilization is obtained than predicted by the calculation. The agreement with theory is significantly better than that obtained with multipole moments derived directly from the aspherical atom refinement. The convergence of the interaction as a function of addition of successively higher moments up to and including hexadecapoles (l ‫؍‬ 4) is found to be within 2-3 kJ͞mol. Although shortcomings of both the theoretical and experimental procedures are pointed out, the agreement obtained supports the potential of the experimental method for the evaluation of interactions in larger biologically relevant molecules.

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Section: Resultssupporting

confidence: 87%

Application of charge density methods to a protein model compound: Calculation of Coulombic intermolecular interaction energies from the experimental charge density

Abramov

Volkov

et al. 2002

Proc. Natl. Acad. Sci. U.S.A.

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“…Bader and co-workers [27] were also able to show a relationship between the bond order ðn B Þ and the electron density at a critical point ðr b ¼ rðr c ÞÞ such that:…”

Section: Introduction: Bond Orders and Theorymentioning

confidence: 99%

Toward an experimental bond order

Jules

Lombardi

2003

Journal of Molecular Structure: THEOCHEM

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By inverting the Guggenheimer formula relating force constant to internuclear distance we derive an experimental expression for bond order, which can be applied throughout the periodic table to diatomic molecules as well as polyatomic molecules. Only two adjustable parameters are required except they must be modified somewhat for polar molecules, most hydrides, and certain triplet ground state molecules. An alternative, suggested by Bader, depends only on the electron density at the bond critical point. It is modified to make it more generally applicable and compatible with experimental results and we compare the two approaches. q

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“…[10] The method can be applied to weak bonds as well as classical chemical bonds. [11][12][13][14][15][16] Some criteria have been proposed to enable weak interactions to be recognized, separate from the classical bonds, based on the nature of the bond critical points (BCPs).…”

Section: (O)···s*a C H T U N G T R E N N U N G (Z à C) 3c-4e Interactmentioning

confidence: 99%

“…[11][12][13][14][15][16] Some criteria have been proposed to enable weak interactions to be recognized, separate from the classical bonds, based on the nature of the bond critical points (BCPs). [10] We applied the AIM method to the extended hypervalent 5c-6e C 2 Z 2 O (Z= Se, S, and O) unit in the anthraquinone (ATQ) system, 1,8-bis(methylchalcogeno)anthraquinones (1, 2 ATQ: 1 (Z = Se), 2 (Z = S), and 3 (Z = O)) after determination of the structures by means of X-ray crystallographic analysis. Of plausible structures such as AA and BB, compounds 1-3 adopt the BB structure, according to our definition, with both ZÀC Me bonds lying in the ATQ plane, similar to the cases of I and II (Scheme 2).…”

Section: (O)···s*a C H T U N G T R E N N U N G (Z à C) 3c-4e Interactmentioning

confidence: 99%

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Atoms‐in‐Molecules Analysis of Extended Hypervalent Five‐Center, Six‐Electron (5c–6e) C₂Z₂O Interactions at the 1,8,9‐Positions of Anthraquinone and 9‐Methoxyanthracene Systems

Nakanishi

Nakamoto

Hayashi

et al. 2006

Chemistry A European J

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To clarify the nature of five‐center, six‐electron (5c–6e) C2Z2O interactions, atoms‐in‐molecules (AIM) analysis has been applied to an anthraquinone, 1,8‐(MeZ)2ATQ (1 (Z=Se), 2 (Z=S), and 3 (Z=O)), and a 9‐methoxyanthracene system, 9‐MeO‐1,8‐(MeZ)2ATC (4 (Z=Se), 5 (Z=S), and 6 (Z=O)), as well as 1‐(MeZ)ATQ (7 (Z=Se), 8 (Z=S), and 9 (Z=O)) and 9‐MeO‐1‐(MeZ)ATC (10 (Z=Se), 11 (Z=S), and 12 (Z=O)). The total electronic energy density (Hb(rc)) at the bond critical points (BCPs), an appropriate index for weak interactions, has been examined for 5c–6e C2Z2O and 3c–4e CZO interactions of the np(O)⋅⋅⋅σ*(ZC) type in 1–12. Some hydrogen‐bonded adducts were also re‐examined for convenience of comparison. The total electronic energy densities varied in the following order: O⋅⋅⋅O (3: Hb(rc)=0.0028 au)=O⋅⋅⋅O (6: 0.0028 au)>O⋅⋅⋅O (9: 0.0025 au)≥NN⋅⋅⋅HF (0.0024 au)≥O⋅⋅⋅O (12: 0.0023 au)≫H2O⋅⋅⋅HOH (0.0015 au)>S⋅⋅⋅O (8: 0.0013 au)=S⋅⋅⋅O (2: 0.0013 au)≥S⋅⋅⋅O (11: 0.0012 au)=S⋅⋅⋅O (5: 0.0012 au)>HF⋅⋅⋅HF (0.0008 au)=Se⋅⋅⋅O (10: 0.0008 au)=Se⋅⋅⋅O (4: 0.0008 au)≥Se⋅⋅⋅O (1: 0.0007 au)≥Se⋅⋅⋅O (7: 0.0006 au)≫HCN⋅⋅⋅HF (−0.0013 au). Hb(rc) values for S⋅⋅⋅O were predicted to be smaller than the hydrogen bond of H2O⋅⋅⋅HOH and Hb(rc) values for Se⋅⋅⋅O are very close to or slightly smaller than that for HF⋅⋅⋅HF in both the ATQ and 9‐MeOATC systems. In the case of Z=Se and S, Hb(rc) values for 5c–6e C2Z2O interactions are essentially equal to those for 3c–4e CZO if Z is the same. The results demonstrate that two np(O)⋅⋅⋅σ*(ZC) 3c–4e interactions effectively connect through the central np(O) orbital to form the extended hypervalent 5c–6e system of the σ*(CZ)⋅⋅⋅np(O)⋅⋅⋅σ*(ZC) type for Z=Se and S in both systems. Natural bond orbital (NBO) analysis revealed that ns(O) also contributes to some extent. The electron charge densities at the BCPs, NBO analysis, and the total energies calculated for 1–12, together with the structural changes in the PhSe derivatives, support the above discussion.

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Description of conjugation and hyperconjugation in terms of electron distributions

Cited by 620 publications

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Application of charge density methods to a protein model compound: Calculation of Coulombic intermolecular interaction energies from the experimental charge density

Application of charge density methods to a protein model compound: Calculation of Coulombic intermolecular interaction energies from the experimental charge density

Toward an experimental bond order

Atoms‐in‐Molecules Analysis of Extended Hypervalent Five‐Center, Six‐Electron (5c–6e) C₂Z₂O Interactions at the 1,8,9‐Positions of Anthraquinone and 9‐Methoxyanthracene Systems

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Description of conjugation and hyperconjugation in terms of electron distributions

Cited by 620 publications

References 0 publications

Application of charge density methods to a protein model compound: Calculation of Coulombic intermolecular interaction energies from the experimental charge density

Application of charge density methods to a protein model compound: Calculation of Coulombic intermolecular interaction energies from the experimental charge density

Toward an experimental bond order

Atoms‐in‐Molecules Analysis of Extended Hypervalent Five‐Center, Six‐Electron (5c–6e) C2Z2O Interactions at the 1,8,9‐Positions of Anthraquinone and 9‐Methoxyanthracene Systems

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Atoms‐in‐Molecules Analysis of Extended Hypervalent Five‐Center, Six‐Electron (5c–6e) C₂Z₂O Interactions at the 1,8,9‐Positions of Anthraquinone and 9‐Methoxyanthracene Systems