Experimental vs. theoretical topological properties of charge density distributions. An application to the l-alanine molecule studied by X-ray diffraction at 23 K

Gatti, Carlo; Bianchi, R. M.; Destro, Riccardo; Merati, F.

doi:10.1016/0166-1280(92)85022-d

Cited by 86 publications

(86 citation statements)

References 44 publications

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“…This fact reflects the qualitative agreement between experimental and theoretical densities in the description of the hydrogen bonds, while it does not invalidate the ability of the topological analysis in also describing the intermolecular interactions. In fact, it is worth noting that almost perfect correspondence of theoretical and experimental results was found in the case of the much stronger N--H-..O hydrogen bonds of the L-alanine crystal (Gatti et al, 1992). The experimental and theoretical atomic electron populations are reported in Table 5.…”

Section: O1-mentioning

confidence: 92%

“…We would briefly comment on these points. In a previous study on L-alanine (Gatti, Bianchi, Destro & Merati, 1992) a closer agreement between experiment and theory, in the description of the polar interactions, was found when the ab initio properties were evaluated at the experimental BCP locations. A less satisfactory behavior was observed in the present case.…”

Section: Electron Densitymentioning

confidence: 96%

“…shown (Gatti et al, 1992;Gatti, MacDougall & Bader, 1988) that the effect of Coulomb correlation on the topology of the molecular charge distributions is to slightly change (by ~-,1%) the Pb values and to increase or decrease (by ---10-20%) the )-3 values for covalent and polar interactions, respectively. For the closed-shell interactions (Co--N1, Li--O1 and CmH ...O) the properties of the p(r) at the associated BCP reflect their peculiar topological characteristics: a low value of Pb and a positive V2Pb value with small and equal perpendicular curvatures ()-~ and )-2) and a dominant parallel curvature 23.…”

Section: O1-mentioning

confidence: 99%

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Theoretical and experimental (113 K) electron-density study of lithium bis(tetramethylammonium) hexanitrocobaltate(III)

Bianchi¹,

Gatti²,

Adovasio³

et al. 1996

Acta Crystallogr Sect B

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This paper presents an analysis of the crystal structure and the charge density, p(r), for lithium bis(tetramethylammonium) hexanitrocobaltate(III) determined by the rigid pseudoatom model from accurate X-ray data measured at l13K. This compound has also been investigated by an ab initio Hartree-Fock fully periodic approach. A comparison of the topological properties between the experimentally and theoretically derived density is also given. A notable agreement between experiment and theory is observed in the topological properties of the metal-ligand interaction and a close parallel between the orbital model description and the shape of the Laplacian distribution around the Co atom is outlined. The results confirm the typical 3d-electron distribution of octahedral Co nI complexes in a low-spin state and the presence of four C--H...O hydrogen bonds in the crystal structure. Important differences between experiment and theory remain for the Laplacian and the parallel curvature (23) values at the C--N and N--O bond critical points. The atomic charges derived from the Quantum Theory of Atoms in Molecules are remarkably close to the formal values.Ohba, Saito & Miyamae (1991), were based on the analysis of the deformation density (DD). These studies were mainly aimed at the determination of the asphericity of nonbonding 3d-electrons around the octahedrally coordinated transition-metal atom and of the electron-density distribution in the nitro group.In this work we perform a topological analysis (Bader & Essen, 1984;Bader, 1990) and a comparison of the total experimental density with suitable theoretical densities in order to characterize the interaction between atoms in the title crystal. By proceeding in this way experiment and theory are directly compared in terms of the properties of an observable, using an approach (Bader, 1990) rooted in quantum mechanics. Some of the problems (Ruedenberg & Schwarz, 1990) inherent to DD studies are a priori avoided; neither the choice of the most appropriate promolecule density nor the resort to a given orbital model as an interpretative tool is needed in this framework.Our study mainly focuses on the analysis of the aspherical 3d-electron distribution around the Co atom, the metal-ligand interaction, the bond nature in the coordinated NO~-group and the characteristics of the C--H.• .O interactions.

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Section: O1-mentioning

confidence: 92%

Section: Electron Densitymentioning

confidence: 96%

Section: O1-mentioning

confidence: 99%

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Theoretical and experimental (113 K) electron-density study of lithium bis(tetramethylammonium) hexanitrocobaltate(III)

Bianchi¹,

Gatti²,

Adovasio³

et al. 1996

Acta Crystallogr Sect B

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“…In general, quantum mechanical estimates of partial charges are thought to be correct because they agree well (Gatti et al, 1992) with those derived from high-resolution charge density crystallographic studies performed at low temperatures on small molecules, at least for nontransition metal-containing molecules.…”

Section: Explaining Amide Planaritymentioning

confidence: 92%

The partial charge of the nitrogen atom in peptide bonds

1997

Protein Science

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A majority of the standard texts dealing with proteins portray the peptide link as a mixture of two resonance forms, in one of which the nitrogen atom has a positive charge. As a consequence, it is often believed that the nitrogen atom has a net positive charge. This is in apparent contradiction with the partial negative charge on the nitrogen that is used in force fields for molecular modeling. However, charges on resonance forms are best regarded as formal rather than actual charges and current evidence clearly favors a net negative charge for the nitrogen atom. In the course of the discussion, new ideas about the electronic structure of amides and the peptide bond are presented.Keywords: a-helix; amides; electrostatics; hydrogen bonds; proteins; quantum mechanics This article begins with a listing of some estimates of the partial charges of the atoms of amides. The planarity of amides is typically explained by portraying them as two resonance forms, one of which has a nitrogen atom with a formal positive charge. However, it is chemically unsatisfactory for the nitrogen atom to have a net partial positive charge, and the reasons for this are given. The strongest evidence that the nitrogen is negative rather than positive comes from quantum mechanics. Some recent work on amides and its implications for the electronic structure of the and T orbitals of the CONH group are discussed in some detail. The effect of hydrogen bonding is then considered and, finally, the relevance of these insights for a-helices is addressed. Point charges on individual atoms:The resonance method used commonly to represent the peptide bond as in Figure 1 is often taken to imply that the nitrogen has a partial positive charge. This conflicts with the partial charges used widely in molecular mechanics force fields for modeling biological molecules. A set of calculated partial charges has been collected (Rogers, 1986), and a

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“…The latter field of application is now rapidly developing (e.g. Kapphann, Tsirelson & Ozerov, 1988;Craven & Stewart, 1990;Destro, Bianchi, Gatti & Merati, 1991;Gatti, Bianchi, Destro & Merati, 1992;Destro & Merati, 1995;Iversen, Larsen, Souhassou & Takata, 1995;Tsirelson, 1996;Tsirelson & Ozerov, 1996) owing to the possibility of analytical representation of the experimental electron density by various multipole models (Hirshfeld, 1971;Stewart, 1976;Hansen & Coppens, 1978), which allow analytical or numerical evaluation of the total electrondensity Laplacian and gradient vector field. In the present work, an attempt to develop an approach for the evaluation of electronic kinetic energy density at the bond critical-point region from the experimental electron density is described.…”

Section: Introductionmentioning

confidence: 99%

On the Possibility of Kinetic Energy Density Evaluation from the Experimental Electron-Density Distribution

Abramov¹

1997

Acta Cryst Sect A

546

422

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A simple new approach for the evaluation of the electronic kinetic energy density, G(r), from the experimental (multipole-fitted) electron density is proposed. It allows a quantitative and semi-quantitative description of the G(r) behavior at the bond critical points of compounds with closed-shell and shared interactions, respectively. This can provide information on the values of the kinetic electron energy densities at the bond critical points, which appears to be useful for quantumtopological studies of chemical interactions using experimental electron densities.

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Experimental vs. theoretical topological properties of charge density distributions. An application to the l-alanine molecule studied by X-ray diffraction at 23 K

Cited by 86 publications

References 44 publications

Theoretical and experimental (113 K) electron-density study of lithium bis(tetramethylammonium) hexanitrocobaltate(III)

Theoretical and experimental (113 K) electron-density study of lithium bis(tetramethylammonium) hexanitrocobaltate(III)

The partial charge of the nitrogen atom in peptide bonds

On the Possibility of Kinetic Energy Density Evaluation from the Experimental Electron-Density Distribution

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