Experimental and Theoretical Charge Density Analysis of Polymorphic Structures: The Case of Coumarin 314 Dye

Self Cite

The multipolar atom model, constructed by transferring the charge-density parameters from an experimental or theoretical database, is considered to be an easy replacement of the widely used independent atom model. The present study on a new crystal structure of quercetin monohydrate [2-(3,4-dihydroxyphenyl)-3,5,7-trihydroxy-4H-chromen-4-one monohydrate], a plant flavonoid, determined by X-ray diffraction, demonstrates that the transferred multipolar atom model approach greatly improves several factors: the accuracy of atomic positions and the magnitudes of atomic displacement parameters, the residual electron densities and the crystallographic figures of merit. The charge-density features, topological analysis and electrostatic interaction energies obtained from the multipole models based on experimental database transfer and periodic quantum mechanical calculations are found to compare well. This quantitative and comparative study shows that in the absence of high-resolution diffraction data, the database transfer approach can be applied to the multipolar electron density features very accurately.

Section: Contactssupporting

confidence: 88%

Structural analysis and multipole modelling of quercetin monohydrate – a quantitative and comparative study

Domagała¹,

Munshi²,

Ahmed³

et al. 2010

Self Cite

“…This merging of the two electron lone pairs is due to conjugation with the five-membered ring which gives a partial sp 2 character to the O3 atom. A similar effect was observed for the C-O-C ester O atom of coumarin 214 (Munshi et al, 2010) located within an aromatic cycle, both from experimental and theoretical data. The other C-O-C oxygen atom of the ethyl ester side chain shows, contrarily, two distinct lone-pair lobes.…”

Section: Deformation Electron Densitysupporting

confidence: 77%

Charge-density analysis using multipolar atom and spherical charge models: 2-methyl-1,3-cyclopentanedione, a compound displaying a resonance-assisted hydrogen bond

Nassour

Kubicki

Wright

et al. 2014

Self Cite

The experimental charge-density distribution in 2-methyl-1,3-cyclopentanedione in the crystal state was analyzed by synchrotron X-ray diffraction data collection at 0.33 Å resolution. The molecule in the crystal is in the enol form. The experimental electron density was refined using the Hansen-Coppens multipolar model and an alternative modeling, based on spherical atoms and additional charges on the covalent bonds and electron lone-pair sites. The crystallographic refinements, charge-density distributions, molecular electrostatic potentials, dipole moments and intermolecular interaction energies obtained from the different charge-density models were compared. The experimental results are also compared with the theoretical charge densities using theoretical structure factors obtained from periodic quantum calculations at the B3LYP/6-31G** level. A strong intermolecular O-H···O hydrogen bond connects molecules along the [001] direction. The deformation density maps show the resonance within the O=C-C=C-OH fragment and merged lone pair lobes on the hydroxyl O atom. This resonance is further confirmed by the analysis of charges and topology of the electron density.

“…The volume decrease from room to cryogenic temperature reaches 2.8%. By comparison, there is a similar unit cell shrinking for coumarin 314, orange and yellow crystal forms (Munshi et al, 2010), of 2.4 and 2.9% from room temperature to 100 K.…”

Section: Dihedral Angles Present Chinnakalimentioning

confidence: 91%

“…In the literature there are several reports on coumarin charge-density analyses (Howard et al, 2009;Munshi & Guru Row, 2005, 2006. In the case of 7-aminocoumarins dyes, several structural analyses have been reported (Chinnakali et al, 1989(Chinnakali et al, , 1990a(Chinnakali et al, ,b,c, 1992Chinnakali, Selladurai et al, 1990;Selladurai & Subramanian, 1992;Yip, Yaw et al, 1995;Yip et al, 1996;Honda et al, 1996;Jasinski & Woudenberg, 1994 and only one investigation on charge-density determination was performed (Munshi et al, 2010). Examination of the results of structural studies on the 7-aminocoumarin dyes quoted above shows that the amino group is in the plane of the chromen-2-one ring system.…”

Section: Introductionmentioning

confidence: 99%

Experimental and database-transferred electron-density analysis and evaluation of electrostatic forces in coumarin-102 dye

Bisseyou¹,

Bouhmaida²,

Guillot³

et al. 2012

Self Cite

The electron-density distribution of a new crystal form of coumarin-102, a laser dye, has been investigated using the Hansen-Coppens multipolar atom model. The charge density was refined versus high-resolution X-ray diffraction data collected at 100 K and was also constructed by transferring the charge density from the Experimental Library of Multipolar Atom Model (ELMAM2). The topology of the refined charge density has been analysed within the Bader `Atoms In Molecules' theory framework. Deformation electron-density peak heights and topological features indicate that the chromen-2-one ring system has a delocalized π-electron cloud in resonance with the N (amino) atom. The molecular electrostatic potential was estimated from both experimental and transferred multipolar models; it reveals an asymmetric character of the charge distribution across the molecule. This polarization effect is due to a substantial charge delocalization within the molecule. The molecular dipole moments derived from the experimental and transferred multipolar models are also compared with the liquid and gas-phase dipole moments. The substantial molecular dipole moment enhancements observed in the crystal environment originate from the crystal field and from intermolecular charge transfer induced and controlled by C-H···O and C-H···N intermolecular hydrogen bonds. The atomic forces were integrated over the atomic basins and compared for the two electron-density models.