Weak intra- and intermolecular interactions in a binaphthol imine: an experimental charge-density study on (±)-8′-benzhydrylideneamino-1,1′-binaphthyl-2-ol

The charge density in (±)-8′-benzhydrylideneamino-1,1′-binaphthyl-2-ol (1) has been studied experimentally using Mo Kα X-ray diffraction at 100 K, and by theory using density-functional thoery (DFT) calculations at the B3LYP/6-311++G** level. The nature of the weak intramolecular peri-C...N, CH...π, H...H and C(π)...C(π) interactions has been examined by topological analysis using the Quantum Theory of Atoms in Molecules (QTAIM) approach. An analysis of the density ρ(r), the Laplacian of the density ∇2ρ(r b) and other topological properties at the bond-critical points were used to classify these interactions. The study confirms the presence of the intramolecular CH...π interaction in (1), which was previously suspected on geometrical grounds. An analysis of the ellipticity profiles along the bond paths unambiguously shows the π-delocalization between the imine unit and one N-phenyl group. The weak intermolecular interactions in the crystal of (1) were examined experimentally and theoretically through the pairwise interactions of the seven independent dimeric pairs of (1) responsible for the set of unique intermolecular interactions, and also through examination of the Hirshfeld surface d norm property. The theoretical dimeric-pair calculations used the BLYP-D functional which supplements the exchange-correlational functional with an empirical dispersion term to provide a more accurate determination of the energies for the weak intermolecular interactions.

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Intra- and intermolecular interactions in small bioactive molecules: cooperative features from experimental and theoretical charge-density analysis

Acta Crystallographica Section B Structural Science ◽

10.1107/s0108768106017393 ◽

2006 ◽

Vol 62 (4) ◽

pp. 612-626 ◽

Cited By ~ 90

Author(s):

Parthapratim Munshi ◽

Tayur N. Guru Row

Keyword(s):

Salicylic Acid ◽

Hydrogen Bonds ◽

Intermolecular Interactions ◽

Density Functional ◽

Theoretical Calculations ◽

Topological Analysis ◽

Van Der Waals Interactions ◽

Bioactive Molecules ◽

Topological Features ◽

Weak Intermolecular Interactions

The topological features of the charge densities, ρ(r), of three bioactive molecules, 2-thiouracil [2,3-dihydro-2-thioxopyrimidin-4(1H)-one], cytosine [4-aminopyrimidin-2(1H)-one] monohydrate and salicylic acid (2-hydroxybenzoic acid), have been determined from high-resolution X-ray diffraction data at 90 K. The corresponding results are compared with the periodic theoretical calculations, based on theoretical structure factors, performed using DFT (density-functional theory) at the B3LYP/6-31G** level. The molecules pack in the crystal lattices via weak intermolecular interactions as well as strong hydrogen bonds. All the chemical bonds, including the intra- and intermolecular interactions in all three compounds, have been quantitatively described by topological analysis based on Bader's quantum theory of `Atoms In Molecules'. The roles of interactions such as C—H...O, C—H...S, C—H...π and π...π have been investigated quantitatively in the presence of strong hydrogen bonds such as O—H...O, N—H...O and N—H...S, based on the criteria proposed by Koch and Popelier to characterize hydrogen bonds and van der Waals interactions. The features of weak intermolecular interactions, such as S...S in 2-thiouracil, the hydrogen bonds generated from the water molecule in cytosine monohydrate and the formation of the dimer via strong hydrogen bonds in salicylic acid, are highlighted on a quantum basis. Three-dimensional electrostatic potentials over the molecular surfaces emphasize the preferable binding sites in the structure and the interaction features of the atoms in the molecules, which are crucial for drug–receptor recognition.

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Weak Intermolecular Interactions in a Series of Bioactive Oxazoles

Molecules ◽

10.3390/molecules26103024 ◽

2021 ◽

Vol 26 (10) ◽

pp. 3024

Author(s):

Anita M. Grześkiewicz ◽

Tomasz Stefański ◽

Maciej Kubicki

Keyword(s):

Intermolecular Interactions ◽

Crystal Packing ◽

Topological Analysis ◽

Minor Role ◽

X Ray Diffraction ◽

Weak Intermolecular Interactions ◽

Nonspecific Interactions ◽

Molecule Interactions ◽

A Minor ◽

Divalent Sulfur

The intermolecular interactions in a series of nine similar 4,5-phenyl-oxazoles were studied on the basis of crystal structures determined by X-ray diffraction. The crystal architectures were analyzed for the importance and hierarchies of different, weak intermolecular interactions using three approaches: the geometrical characteristics, topological analysis (for the model based on the transfer of multipolar parameters), and energetics of the molecule–molecule interactions. The geometries of the molecules were quite similar and close to the typical values. The results of the analysis of the interactions suggest that the number of nonspecific interactions is more important than the apparent strength of the specific interactions. The interactions involving covalently bound bromine and divalent sulfur atoms were classified as secondary, they certainly did not define the crystal packing, and they played a minor role in the overall crystal cohesion energies. Incidentally, another method for confirming the degree of isostructurality, according to the topologies of the interactions, is described.

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Revisiting the charge density analysis of 2,5-dichloro-1,4-benzoquinone at 20 K

Acta Crystallographica Section B Structural Science Crystal Engineering and Materials ◽

10.1107/s2052520617007363 ◽

2017 ◽

Vol 73 (4) ◽

pp. 654-659 ◽

Cited By ~ 3

Author(s):

Zhijie Chua ◽

Bartosz Zarychta ◽

Christopher G. Gianopoulos ◽

Vladimir V. Zhurov ◽

A. Alan Pinkerton

Keyword(s):

Charge Density ◽

Electron Density ◽

Topological Analysis ◽

Diffraction Measurement ◽

X Ray Diffraction ◽

Total Electron Density ◽

Total Electron ◽

Structure Factors ◽

Density Analysis ◽

Experimental Charge Density

A high-resolution X-ray diffraction measurement of 2,5-dichloro-1,4-benzoquinone (DCBQ) at 20 K was carried out. The experimental charge density was modeled using the Hansen–Coppens multipolar expansion and the topology of the electron density was analyzed in terms of the quantum theory of atoms in molecules (QTAIM). Two different multipole models, predominantly differentiated by the treatment of the chlorine atom, were obtained. The experimental results have been compared to theoretical results in the form of a multipolar refinement against theoretical structure factors and through direct topological analysis of the electron density obtained from the optimized periodic wavefunction. The similarity of the properties of the total electron density in all cases demonstrates the robustness of the Hansen–Coppens formalism. All intra- and intermolecular interactions have been characterized.

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

Acta Crystallographica Section B Structural Science ◽

10.1107/s0108768110041996 ◽

2010 ◽

Vol 67 (1) ◽

pp. 63-78 ◽

Cited By ~ 50

Author(s):

Sławomir Domagała ◽

Parthapratim Munshi ◽

Maqsood Ahmed ◽

Benoît Guillot ◽

Christian Jelsch

Keyword(s):

Comparative Study ◽

Charge Density ◽

Topological Analysis ◽

Atomic Displacement ◽

X Ray Diffraction ◽

Experimental Database ◽

Figures Of Merit ◽

Atom Model ◽

Atomic Displacement Parameters ◽

Model Approach

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.

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Thermal-induced transformation of glutamic acid to pyroglutamic acid and self-cocrystallization: a charge–density analysis

Acta Crystallographica Section C Structural Chemistry ◽

10.1107/s2053229621013607 ◽

2022 ◽

Vol 78 (2) ◽

Author(s):

Sehrish Akram ◽

Arshad Mehmood ◽

Sajida Noureen ◽

Maqsood Ahmed

Keyword(s):

Hydrogen Bonds ◽

Glutamic Acid ◽

Single Crystal ◽

Diffraction Data ◽

Density Functional ◽

Quantitative Estimation ◽

Topological Analysis ◽

Pyroglutamic Acid ◽

X Ray Diffraction ◽

X Ray

Thermal-induced transformation of glutamic acid to pyroglutamic acid is well known. However, confusion remains over the exact temperature at which this happens. Moreover, no diffraction data are available to support the transition. In this article, we make a systematic investigation involving thermal analysis, hot-stage microscopy and single-crystal X-ray diffraction to study a one-pot thermal transition of glutamic acid to pyroglutamic acid and subsequent self-cocrystallization between the product (hydrated pyroglutamic acid) and the unreacted precursor (glutamic acid). The melt upon cooling gave a robust cocrystal, namely, glutamic acid–pyroglutamic acid–water (1/1/1), C5H7NO3·C5H9NO4·H2O, whose structure has been elucidated from single-crystal X-ray diffraction data collected at room temperature. A three-dimensional network of strong hydrogen bonds has been found. A Hirshfeld surface analysis was carried out to make a quantitative estimation of the intermolecular interactions. In order to gain insight into the strength and stability of the cocrystal, the transferability principle was utilized to make a topological analysis and to study the electron-density-derived properties. The transferred model has been found to be superior to the classical independent atom model (IAM). The experimental results have been compared with results from a multipolar refinement carried out using theoretical structure factors generated from density functional theory (DFT) calculations. Very strong classical hydrogen bonds drive the cocrystallization and lend stability to the resulting cocrystal. Important conclusions have been drawn about this transition.

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Accurate determination of band gaps within density functional formalism

Physical Review B ◽

10.1103/physrevb.87.235110 ◽

2013 ◽

Vol 87 (23) ◽

Cited By ~ 9

Author(s):

Prashant Singh ◽

Manoj K. Harbola ◽

Biplab Sanyal ◽

Abhijit Mookerjee

Keyword(s):

Density Functional ◽

Accurate Determination ◽

Band Gaps ◽

Functional Formalism

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Charge density analysis of paracetamol, acetotoluidine and methacetin

Acta Crystallographica Section A Foundations and Advances ◽

10.1107/s2053273314094583 ◽

2014 ◽

Vol 70 (a1) ◽

pp. C541-C541

Author(s):

Dmitry Druzhbin ◽

Tatiana Drebushchak ◽

Elena Boldyreva

Keyword(s):

Charge Density ◽

Topological Analysis ◽

Intramolecular Interactions ◽

Amide Bond ◽

Electrostatic Energy ◽

X Ray Diffraction ◽

Methyl Group ◽

Point Of Interest ◽

Density Analysis ◽

Topological Characteristics

Paracetamol (p-hydroxyacetanilide, Pbca), acetotoluidine (p-methylacetanilide, P21/c) and methacetin (p-methoxyacetanilide, Pbca) contain acetamide group included in molecular fragments, which play an important role in many drugs and proteins. As all of them are derivatives of acetanilide used in medicine, and due to the presence of the amide bond, their charge density analysis is important for better understanding amide infinite peptide chains. Thus, comparing the data obtained for paracetamol with acetotoluidine and with methacetin charge density data can provide deeper insight into NH···O bonding. Another point of interest is the possibility of methyl group rotation that remains to be ambiguous in these acetanilide molecule based compounds. In the present study we have attempted to elucidate these problems using precise X-ray diffraction at 100K with subsequent charge density topological analysis. All charge density refinements were based on the Hansen and Coppens multipolar atom model. The topologies of the inter- and intramolecular interactions are carefully analyzed for compounds. The atomic charges, bond orders, and the electrostatic energy in molecules are discussed. The topological characteristics in the critical point of the NH···O bond of paracetamol, acetotoluidine and methacetin are shown in the table below. In contrast to similarity in NH···O bonds for all studied compounds, intermolecular interactions between the double bonded oxygen atom and the hydrogen of dimer's methyl group are different. In acetotoluidine and methacetin the (3, –1) critical points with the same topological characteristics were detected between these atoms. In comparison to them, paracetamol with disordered methyl group [1, 2] has no such point. That can be related to the absence of the methyl group disorder in acetotoluidine and methacetin.

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A method for the accurate determination of crystal truncation rod intensities by X-ray diffraction

Journal of Applied Crystallography ◽

10.1107/s0021889892011592 ◽

1993 ◽

Vol 26 (2) ◽

pp. 166-171 ◽

Cited By ~ 17

Author(s):

E. D. Specht ◽

F. J. Walker

Keyword(s):

Accurate Determination ◽

X Ray Diffraction ◽

X Ray ◽

Crystal Truncation Rod

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Doxycycline hydrate and doxycycline hydrochloride dihydrate – crystal structure and charge density analysis

Zeitschrift für Kristallographie - Crystalline Materials ◽

10.1515/zkri-2018-2058 ◽

2018 ◽

Vol 233 (9-10) ◽

pp. 649-661 ◽

Cited By ~ 1

Author(s):

Daniel Tchoń ◽

Anna Makal ◽

Matthias Gutmann ◽

Krzysztof Woźniak

Keyword(s):

Charge Density ◽

Topological Analysis ◽

Crystal Form ◽

X Ray Diffraction ◽

Neutron Data ◽

Distribution Models ◽

Crystal Forms ◽

Density Analysis ◽

Resonance Assisted Hydrogen Bond ◽

Amide Nitrogen Atom

Abstract High-resolution low-temperature X-ray diffraction experiments for doxycycline monohydrate and hydrochloride dihydrate have been performed. Translation-Libration-Screw (TLS) analysis for both crystal forms as well as the data from neutron diffraction experiment for hydrochloride combined with the Hansen-Coppens formalism resulted in precise charge density distribution models for both the zwitterionic monohydrate and a protonated hydrochloride crystal forms. Their detailed topological analysis suggested that the electron structure of doxycycline’s amide moiety undergoes significant changes during protonation due to formation of a very strong resonance-assisted hydrogen bond. A notably increased participation of amide nitrogen atom and hydrogen-accepting oxygen atom in the resonance upon doxycycline protonation was observed. A comparison of TLS- and neutron data-derived hydrogen parameters confirmed the experimental neutron data to be vital for proper description of intra- and inter-molecular interactions in this compound. Finally, calculated lattice and interaction energies quantified repulsive Dox-Dox interactions in the protonated crystal form of the antibiotic, relating with a good solubility of doxycycline hydrochloride relative to its hydrate.

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