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

Abramov, Yu. A.

doi:10.1107/s010876739601495x

Cited by 555 publications

(445 citation statements)

References 38 publications

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“…angle of 150.9 but is, surprisingly, indicative of the lack of polarisation of the LP toward the hydrogen atom given the strength of the bond (vide infra). As suggested by Abramov 23 , the kinetic and potential energy densities (G and V) and the total energy density (H) at bond critical points in hydrogen bonds can be determined from the density property V, and thus can be used as a measure of bond strength. The ratio -G/V can also be used to estimate covalency in H-bonds: a value of between 0.5 and 1 indicates partly covalent character, while a value of greater than 1 is purely non-covalent.…”

Section: Hydrogen Atom Treatmentmentioning

confidence: 99%

Experimental and theoretical charge density distribution in Pigment Yellow 101

Váradi

Tan

et al. 2015

Phys. Chem. Chem. Phys.

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The charge density distribution in 2,2'-Dihydroxy-1,1'-naphthalazine (Pigment Yellow 101; P.Y.101) has been determined using high-resolution X-ray diffraction and multipole refinement, along with density functional theory calculations. Topological analysis of the resulting densities highlights the localisation of single/double bonds in the central C=N-N=C moiety of the molecule in its ground state. The density in the N-N is examined in detail, where we show that very small differences between experiment and theory are amplified by use of the Laplacian of the density. Quantification of hydrogen bonds highlights the importance of the intramolecular N-H…O interaction, known to be vital for retention of fluorescence in the solid state, relative to the many but weak intermolecular contacts located.However, a popular method for deriving H-bond strengths from density data appears to struggle with the intramolecular N-H…O interaction. We also show that theoretical estimation of anisotropic displacements for hydrogen atoms brings little benefit overall, and degrades agreement with experiment for one intra-molecular contact.2

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Section: Hydrogen Atom Treatmentmentioning

confidence: 99%

Experimental and theoretical charge density distribution in Pigment Yellow 101

Váradi

Tan

et al. 2015

Phys. Chem. Chem. Phys.

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“…35 Besides the electron densities  bcp and their Laplacians 2 ρ bcp , the potential energy density V bcp at the bond critical point (bcp) has previously been shown to bring additional relevant information, in particular on the strength of a given HB. [36][37][38] Thus, HB energies (E HB ) estimated from the potential energy densities V bcp according to the established relationship in Equation [2], 39 have also been computed in the present study.…”

Section: Experimental Section Computational Detailsmentioning

confidence: 99%

α‐Fluoro‐o‐cresols: The Key Role of Intramolecular Hydrogen Bonding in Conformational Preference and Hydrogen‐Bond Acidity

et al. 2016

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The conformational preferences of o-cresols driven by fluorination have been thoroughly investigated from a theoretical point of view with quantum chemical methods and compared to those recently reported for benzyl alcohols. Key conformers of both families exhibit a 6-membered intramolecular hydrogen-bond (IMHB) interaction. A significant enhancement of IMHB strength is observed in -fluoro-o-cresols, owing to the simultaneous increase of the aliphatic fluorine hydrogen-bond (HB) basicity and of the aromatic hydroxyl HB acidity, compared to o-fluorobenzyl alcohols, which are characterized by aromatic fluorine atoms and aliphatic hydroxyl groups. In the case of di-and trifluorinated derivatives, the occurrence of a three-centre hydrogen-bond is emphasised and its features discussed. The impact of these structural predilections on ocresol HB properties has been characterised from the estimation of the HB acidity parameter, pKAHY, weighted according to their conformational populations. We find that -fluorination leads to an HB acidity decrease of the hydroxyl group (in contrast with o-fluorination of benzyl alcohols), whereas ,-difluorination results in no significant variation of pKAHY. Finally, an increase of HB acidity is predicted upon methyl perfluorination, which has been confirmed experimentally. Theoretical descriptors based on AIM, NCI and NBO analyses allows rationalizing the predicted trends, and reveal a relationship with the strength of the established OHF IMHB.

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“…The associated density values (BCP), as well as the values of the second derivatives of the density, as provided through eigenvalues of the Hessian matrix and Laplacians r 2 (BCP), can be used to obtain information about the character of the interaction. Kinetic energy densities G(BCP) and potential energy densities V(BCP) as well as total energy densities H(BCP) and the ratio |V(BCP)|/G(BCP) have been calculated according to the approximate formulas of Abramov (1997), which allow these quantities to be obtained from (BCP) and r 2 (BCP).…”

Section: Computational Detailsmentioning

confidence: 99%

The active site of hen egg-white lysozyme: flexibility and chemical bonding

Held¹,

Smaalen²

2014

Acta Crystallogr D Biol Crystallogr

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Chemical bonding at the active site of hen egg-white lysozyme (HEWL) is analyzed on the basis of Bader's quantum theory of atoms in molecules [QTAIM;Bader (1994), Atoms in Molecules: A Quantum Theory. Oxford University Press] applied to electron-density maps derived from a multipole model. The observation is made that the atomic displacement parameters (ADPs) of HEWL at a temperature of 100 K are larger than ADPs in crystals of small biological molecules at 298 K. This feature shows that the ADPs in the cold crystals of HEWL reflect frozen-in disorder rather than thermal vibrations of the atoms. Directly generalizing the results of multipole studies on small-molecule crystals, the important consequence for electron-density analysis of protein crystals is that multipole parameters cannot be independently varied in a meaningful way in structure refinements. Instead, a multipole model for HEWL has been developed by refinement of atomic coordinates and ADPs against the X-ray diffraction data of Wang and coworkers [Wang et al. (2007), Acta Cryst. D63, 1254-1268], while multipole parameters were fixed to the values for transferable multipole parameters from the ELMAM2 database [Domagala et al. (2012), Acta Cryst. A68, 337-351] . Static and dynamic electron densities based on this multipole model are presented. Analysis of their topological properties according to the QTAIM shows that the covalent bonds possess similar properties to the covalent bonds of small molecules. Hydrogen bonds of intermediate strength are identified for the Glu35 and Asp52 residues, which are considered to be essential parts of the active site of HEWL. Furthermore, a series of weak C-HÁ Á ÁO hydrogen bonds are identified by means of the existence of bond critical points (BCPs) in the multipole electron density. It is proposed that these weak interactions might be important for defining the tertiary structure and activity of HEWL. The deprotonated state of Glu35 prevents a distinction between the Phillips and Koshland mechanisms.

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

Cited by 555 publications

References 38 publications

Experimental and theoretical charge density distribution in Pigment Yellow 101

Experimental and theoretical charge density distribution in Pigment Yellow 101

α‐Fluoro‐o‐cresols: The Key Role of Intramolecular Hydrogen Bonding in Conformational Preference and Hydrogen‐Bond Acidity

The active site of hen egg-white lysozyme: flexibility and chemical bonding

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