Molecular and crystal properties of ethyl 4,6-dimethyl-2-thioxo-1,2,3,4-tetrahydropyrimidine-5-carboxylate from experimental and theoretical electron densities

Tsirelson, Vladimir G.; Сташ, А. И.; Потемкин, В. А.; Rykounov, Alexey A.; Шуталев, А. Д.; Zhurova, Elizabeth A.; Zhurov, Vladimir V.; Pinkerton, A. Alan; Gurskaya, G. V.; Zavodnik, V. E.

doi:10.1107/s0108768106016326

Cited by 48 publications

(31 citation statements)

References 73 publications

(84 reference statements)

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“…Unfortunately, the uncertainty of 1% is too large to allow determination of intermolecular interaction energies in crystalline -N 2 O 4 . This conclusion is in agreement with other QTAIMC estimates of electronic energy in crystals (Tsirelson et al, 2006;Zhurova, Stash et al, 2006).…”

Section: Atomic Characteristics and Intramolecular Interactions: Elecsupporting

confidence: 93%

“…A similar observation has been previously reported for N-O and C-O bonds (Flaig et al, 1998;Wagner & Luger, 2001;Zhurova, Stash et al, 2006;Zhurova, Matta et al, 2006). The disagreement is a consequence of insufficient flexibility of the Hansen-Coppens multipole model in describing the covalent bonds formed by atoms with more than half-filled valence electron subshells (Tsirelson et al, 2006(Tsirelson et al, , 2007Volkov et al, 2000;Dominiak & Coppens, 2006). At the same time, the theoretical ED presented in terms of the Hansen-Coppens multipole model yields BCP parameters which are very close to the experimental ones (see line 2 of Table 2).…”

Section: Atomic Characteristics and Intramolecular Interactions: Elecsupporting

confidence: 80%

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The experimental and theoretical QTAIMC study of the atomic and molecular interactions in dinitrogen tetroxide

Tsirelson¹,

Shishkina²,

Сташ³

et al. 2009

Acta Crystallogr Sect B

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The atomic and molecular interactions in a crystal of dinitrogen tetraoxide, alpha-N2O4, have been studied in terms of the quantum topological theory of molecular structure using high-resolution, low-temperature X-ray diffraction data. The experimental electron density and electrostatic potential have been reconstructed with the Hansen-Coppens multipole model. In addition, the three-dimensional periodic electron density of crystalline alpha-N2O4 has been calculated at the B3LYP/cc-pVDZ level of theory with and without the geometry optimization. The application of the quantum theory of atoms in molecules and crystals (QTAIMC) recovered the two types of intermolecular bond paths between O atoms in crystalline alpha-N2O4, one measuring 3.094, the other 3.116 A. The three-dimensional distribution of the Laplacian of the electron density around the O atoms showed that the lumps in the negative Laplacian fit the holes on the O atoms in the adjacent molecules, both atoms being linked by the intermolecular bond paths. This shows that the Lewis-type molecular complementarity contributes significantly to intermolecular bonding in crystalline N2O4. Partial overlap of atomic-like basins created by zero-flux surfaces in both the electron density and the electrostatic potential show that attractive electrostatic interaction exists between O atoms even though they carry the same net formal charge. The exchange and correlation contributions to the potential energy density were also computed by means of the model functionals, which use the experimental electron density and its derivatives. It was found that the intermolecular interactions in alpha-N2O4 are accompanied by the correlation energy-density ;bridges' lowering the local potential energy along the intermolecular O...O bond paths in the electron density, while the exchange energy density governs the shape of bounded molecules.

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Section: Atomic Characteristics and Intramolecular Interactions: Elecsupporting

confidence: 93%

Section: Atomic Characteristics and Intramolecular Interactions: Elecsupporting

confidence: 80%

The experimental and theoretical QTAIMC study of the atomic and molecular interactions in dinitrogen tetroxide

Tsirelson¹,

Shishkina²,

Сташ³

et al. 2009

Acta Crystallogr Sect B

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“…As there is satisfactory agreement in the trend in the properties at the CP from theory and experiment, the following discussion is based on the experi-mentally determined values. The only significant differences are between values of the Laplacian obtained from the multipole model and theory, as has been previously discussed (Bianchi et al, 1996;Spackman et al, 1999;Flaig et al, 2002;Volkov et al, 2004;Zhurova et al, 2004;Henn et al, 2004;Tsirelson et al, 2006).…”

Section: Discussionmentioning

confidence: 78%

“…Indeed, the similarities of the properties of the N-N, C-N and C-C bonds in terms of the electron density and ellipticity suggest total conjugation. However, when calculating topological bond orders from the electron density values () and the principle electron-density curvatures ( 1 , 2 , 3 ) at the bond critical points (Table 3a) (Bartashevich et al, 2006;Tsirelson et al, 2006;Howard & Lamarche, 2003), the C-N bonds are seen to have significantly lower order that the others in the five-membered rings. Although Butcher et al (2003c) noted small differences in bond lengths in the five-membered rings, there is no obvious correlation with the properties of the bond-critical points.…”

Section: Discussionmentioning

confidence: 99%

Chemical bonding and intermolecular interactions in energetic materials: 1,3,4-trinitro-7,8-diazapentalene

Chen

Сташ

Pinkerton

2007

Acta Crystallogr Sect B

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The electron density and related properties of the red-colored energetic material 1,3,4-trinitro-7,8-diazapentalene (space group Pca2(1)) have been determined from a low-temperature [90.0 (1) K] X-ray diffraction experiment. Intensity data were measured with a 2 K CCD Bruker diffractometer using Ag Kalpha radiation. One detector setting, several varphi settings, 0.15 degrees omega scans and 96 s exposure time per frame gave R(int) = 0.0188 for 31 952 (10 283 unique) reflections and (sin theta/lambda)(max) = 1.15 A(-1). The electron density was modeled using the Hansen-Coppens [(1978), Acta Cryst. A34, 909-921] multipole model and refined to R = 0.026 for 9455 unique observed reflections. The electron density, Laplacian and electrostatic potential distributions are reported and discussed. The properties of the bond (3,-1) critical points are analyzed. All results are indicative of multiple bonds in the five-membered rings. In addition, a significant number of weak intermolecular interactions (O...H, O...O, O...N, O...C) have also been characterized by the properties of their critical points. A comparison of experimental results with those obtained from theoretical calculations (periodic, CRYSTAL98; single molecule, GAUSSIAN98) is also reported.

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“…The experimental values of the electron density and its Laplacian are in good agreement with their theoretical values for single molecule and the dimers obtained by the wave function calculations by AIM2000. The di erences between the experimental and theoretical values of r 2 (r) in some cases are related to the de ciency of the multipole model description of the electron density [21,22]. The experimental properties of the strongly polarized bond are di erent from the results derived by ab initio calculations.…”

Section: Resultsmentioning

confidence: 99%

Experimental and Theoretical X-ray Charge-Density Study of 1-Cycloheptylidene-2-(2,4-dinitrophenyl)hydrazine: A Hydrazone Derivative

Sharafi

2016

Scientia Iranica

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The experimental charge density of a hydrazone derivative has been determined from low temperature (100 K) single crystal X-ray di raction data by multipolar Hansen-Coppens formalism re nement and gas phase ab initio theoretical calculations. The topology of the electron density within the molecule as well as the intramolecular and intermolecular interactions have been analyzed. The topological properties of electron density determined by the experiment were compared with the theoretical results obtained from Gaussian03 at the B3LYP/6-311++G** level of theory. The covalent nature of the bonds in the molecule has been established by (3,-1) bond critical points associated with relatively large electron densities (1.59-3.34 e. A 3) and highly negative Laplacian values (4.73-21.30 e. A 5). Numerical and analytical procedures were used to derive the charges integrated with each atomic basin. The highest charge magnitude (-0.66 e) was found in N2 and N4 atoms. The crystal packing is stabilized by the weak intermolecular ..., C-H...O and NO 2 (N)...(O)NO 2 interactions, as con rmed by the presence of critical points in the topological analysis.

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Molecular and crystal properties of ethyl 4,6-dimethyl-2-thioxo-1,2,3,4-tetrahydropyrimidine-5-carboxylate from experimental and theoretical electron densities

Cited by 48 publications

References 73 publications

The experimental and theoretical QTAIMC study of the atomic and molecular interactions in dinitrogen tetroxide

The experimental and theoretical QTAIMC study of the atomic and molecular interactions in dinitrogen tetroxide

Chemical bonding and intermolecular interactions in energetic materials: 1,3,4-trinitro-7,8-diazapentalene

Experimental and Theoretical X-ray Charge-Density Study of 1-Cycloheptylidene-2-(2,4-dinitrophenyl)hydrazine: A Hydrazone Derivative

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