scholarly journals Intermolecular interactions in molecular materials from the topological analysis of the electron density point of view

2004 ◽  
Vol 60 (a1) ◽  
pp. s31-s31
Author(s):  
M. Souhassou ◽  
L. Pretto ◽  
P. Gilli ◽  
S. Dahaoui ◽  
N. Claiser ◽  
...  
Keyword(s):  
Electron Density ◽  
Intermolecular Interactions ◽  
Topological Analysis ◽  
Point Of View ◽  
Density Point ◽  
Molecular Materials

A topological analysis of the interion interactions of tetraphenylphosphonium squarate

2006 ◽  
Vol 84 (5) ◽  
pp. 804-811 ◽  
Author(s):  
David Wolstenholme ◽  
Manuel AS Aquino ◽  
T Stanley Cameron ◽  
Joseph D Ferrara ◽  
Katherine N Robertson
Keyword(s):  
Hydrogen Bonding ◽  
Hydrogen Bonds ◽  
Electron Density ◽  
Intermolecular Interactions ◽  
Critical Points ◽  
Topological Analysis ◽  
Van Der Waals ◽  
Van Der Waals Interactions ◽  
Multipole Refinement ◽  
Diverse Interactions

The tetraphenylphosphonium squarate salt crystallizes with a number of diverse interactions, which all have the potential to be classified as hydrogen bonds. The squarate anions are found as dimers linked by O-H···O interactions. The multipole refinement of the tetraphenylphosphonium squarate was performed using the Hansen–Coppens model followed by topological analysis of its intermolecular interactions. A total of 28 interactions were found among the symmetry related molecules, which include a number of C-H···Cπ, C-H···O, and C-H···H-C interactions, along with the O-H···O interaction. With the criteria for hydrogen bonding proposed by Popelier and Koch, it is possible to determine which of these interactions are hydrogen bonds and which are van der Waals interactions. Both linear and exponentially dependent correlations can be seen for the properties of the bond critical points involving the intermolecular interactions that fulfill these criteria. All this leads to a better understanding of the role that hydrogen bonds play in the formation of small organic compounds.Key words: electron density, multiple refinement, hydrogen bonds.

Topological characterization of electron density, electrostatic potential and intermolecular interactions of 2-nitroimidazole: an experimental and theoretical study

2016 ◽  
Vol 72 (5) ◽  
pp. 775-786 ◽  
Author(s):  
Chinnasamy Kalaiarasi ◽  
Mysore S Pavan ◽  
Poomani Kumaradhas
Keyword(s):  
Electron Density ◽  
Intermolecular Interactions ◽  
Electrostatic Potential ◽  
Theoretical Calculations ◽  
Topological Analysis ◽  
X Ray Diffraction ◽  
Topological Characterization ◽  
Data Set ◽  
X Ray ◽  
Charge Concentration

An experimental charge density distribution of 2-nitroimidazole was determined from high-resolution X-ray diffraction and the Hansen–Coppens multipole model. The 2-nitroimidazole compound was crystallized and a high-angle X-ray diffraction intensity data set has been collected at low temperature (110 K). The structure was solved and further, an aspherical multipole model refinement was performed up to octapole level; the results were used to determine the structure, bond topological and electrostatic properties of the molecule. In the crystal, the molecule exhibits a planar structure and forms weak and strong intermolecular hydrogen-bonding interactions with the neighbouring molecules. The Hirshfeld surface of the molecule was plotted, which explores different types of intermolecular interactions and their strength. The topological analysis of electron density at the bond critical points (b.c.p.) of the molecule was performed, from that the electron density ρbcp(r) and the Laplacian of electron density ∇2ρbcp(r) at the b.c.p.s of the molecule have been determined; these parameters show the charge concentration/depletion of the nitroimidazole bonds in the crystal. The electrostatic parameters like atomic charges and the dipole moment of the molecule were calculated. The electrostatic potential surface of the molecule has been plotted, and it displays a large electronegative region around the nitro group. All the experimental results were compared with the corresponding theoretical calculations performed usingCRYSTAL09.

Experimental and theoretical charge density, intermolecular interactions and electrostatic properties of metronidazole

2019 ◽  
Vol 75 (6) ◽  
pp. 942-953 ◽  
Author(s):  
Chinnasamy Kalaiarasi ◽  
Christy George ◽  
Rajesh G. Gonnade ◽  
Venkatesha R. Hathwar ◽  
Kumaradhas Poomani
Keyword(s):  
Charge Density ◽  
Electron Density ◽  
Intermolecular Interactions ◽  
Topological Analysis ◽  
Intramolecular Hydrogen Bonding ◽  
Bond Critical Point ◽  
Monoclinic System ◽  
Electrostatic Properties ◽  
Negative Laplacian ◽  
Intramolecular Hydrogen

Metronidazole is a radiosensitizer; it crystallizes in the monoclinic system with space group P21/c. The crystal structure of metronidazole has been determined from high-resolution X-ray diffraction measurements at 90 K with a resolution of (sin θ/λ)max = 1.12 Å−1. To understand the charge-density distribution and the electrostatic properties of metronidazole, a multipole model refinement was carried out using the Hansen–Coppens multipole formalism. The topological analysis of the electron density of metronidazole was performed using Bader's quantum theory of atoms in molecules to determine the electron density and the Laplacian of the electron density at the bond critical point of the molecule. The experimental results have been compared with the corresponding periodic theoretical calculation performed at the B3LYP/6-31G** level using CRYSTAL09. The topological analysis reveals that the N—O and C—NO2 exhibit less electron density as well as negative Laplacian of electron density. The molecular packing of crystal is stabilized by weak and strong inter- and intramolecular hydrogen bonding and H...H interactions. The topological analysis of O—H...N, C—H...O and H...H intra- and intermolecular interactions was also carried out. The electrostatic potential of metronidazole, calculated from the experiment, predicts the possible electrophilic and nucleophilic sites of the molecule; notably, the hydroxyl and the nitro groups exhibit large electronegative regions. The results have been compared with the corresponding theoretical results.

scholarly journals Experimental and theoretical electron-density study of three isoindole derivatives: topological and Hirshfeld surface analysis of weak intermolecular interactions

2011 ◽  
Vol 67 (6) ◽  
pp. 569-581 ◽  
Author(s):  
Lilianna Chęcińska ◽  
Simon Grabowsky ◽  
Magdalena Małecka ◽  
Agnieszka J. Rybarczyk-Pirek ◽  
Andrzej Jóźwiak ◽  
...  
Keyword(s):  
Electron Density ◽  
Intermolecular Interactions ◽  
Crystal Packing ◽  
Theoretical Calculations ◽  
Topological Analysis ◽  
Theoretical Models ◽  
Hirshfeld Surface ◽  
Data Sets ◽  
Dft Methods ◽  
Geometric Function

A combined experimental and theoretical study of three isoindole derivatives was made on the basis of a topological analysis of their electron-density distributions. Experimental electron densities were determined from high-resolution X-ray diffraction data sets measured with synchrotron radiation at 100 K, whereas theoretical calculations were performed using DFT methods at the B3LYP\6-311++G(3df,3pd) level of approximation. Both experimental and theoretical models are in good agreement with each other. Since the analysed structures possess a variety of hydrogen-bonding interactions, weak intermolecular contacts of C—H...C(π), C,N(π)...C,N(π) and H...H types were subject to our special interest and are discussed in detail. They were characterized quantitatively and qualitatively by topological properties using Bader's Atoms in Molecules theory and by mapping the electron-density distribution, electrostatic potential and a geometric function on the Hirshfeld surface. This way the forces and directions of intermolecular interactions as present on the molecular surfaces were depicted and described. These interactions not only guide crystal packing, but are likewise important for recognition processes involving (aza)isoindole fragments in a biological environment.

X·F (X=C, N, O and S) Noncovalent Weak Intermolecular Interactions

2014 ◽  
Vol 881-883 ◽  
pp. 192-195
Author(s):  
Yan Zhi Liu ◽  
Huian Tang
Keyword(s):  
Intermolecular Interaction ◽  
Electron Density ◽  
Intermolecular Interactions ◽  
Topological Analysis ◽  
Interaction Energies ◽  
Weak Intermolecular Interaction ◽  
Weak Intermolecular Interactions ◽  
The Stability ◽  
Bsse Correction ◽  
Computational Level

A number of X···F (X=C, N, O and S) noncovalent weak intermolecular interaction systems of CH3-F···XO2 (X=C, N, O and S) has been investigated at B3LYP/6-311++G(d, p) computational level. A topological analysis of the electron density for the X···F (X=C, N, O and S) noncovalent weak bonds was performed using Baders theory of atom-in-molecules (AIM). The interaction content of the F···X in H3CF···CO2 complex would mainly represent more π property than others. The interaction energies data without (ΔE) and with (ΔEcp) BSSE correction showed that the stability of the four complexes of the H3CF···DB2 system increases in the order of H3CF···O3 < H3CF···NO2 < H3CF···CO2 < H3CF···SO2.

scholarly journals Quantitative analysis of intermolecular interactions in orthorhombic rubrene

IUCrJ ◽  
2015 ◽  
Vol 2 (5) ◽  
pp. 563-574 ◽  
Author(s):  
Venkatesha R. Hathwar ◽  
Mattia Sist ◽  
Mads R. V. Jørgensen ◽  
Aref H. Mamakhel ◽  
Xiaoping Wang ◽  
...  
Keyword(s):  
Interaction Energy ◽  
Electron Density ◽  
Intermolecular Interactions ◽  
Carrier Transport ◽  
Electronic Device ◽  
Weak Interactions ◽  
Theoretical Calculations ◽  
Topological Analysis ◽  
Lattice Energy ◽  
Covalent Interaction

Rubrene is one of the most studied organic semiconductors to date due to its high charge carrier mobility which makes it a potentially applicable compound in modern electronic devices. Previous electronic device characterizations and first principles theoretical calculations assigned the semiconducting properties of rubrene to the presence of a large overlap of the extended π-conjugated core between molecules. We present here the electron density distribution in rubrene at 20 K and at 100 K obtained using a combination of high-resolution X-ray and neutron diffraction data. The topology of the electron density and energies of intermolecular interactions are studied quantitatively. Specifically, the presence of Cπ...Cπinteractions between neighbouring tetracene backbones of the rubrene molecules is experimentally confirmed from a topological analysis of the electron density, Non-Covalent Interaction (NCI) analysis and the calculated interaction energy of molecular dimers. A significant contribution to the lattice energy of the crystal is provided by H—H interactions. The electron density features of H—H bonding, and the interaction energy of molecular dimers connected by H—H interaction clearly demonstrate an importance of these weak interactions in the stabilization of the crystal structure. The quantitative nature of the intermolecular interactions is virtually unchanged between 20 K and 100 K suggesting that any changes in carrier transport at these low temperatures would have a different origin. The obtained experimental results are further supported by theoretical calculations.

scholarly journals Computational approaches towards crystal engineering in molecular crystals

2014 ◽  
Vol 70 (a1) ◽  
pp. C642-C642
Author(s):  
Deepak Chopra ◽  
Dhananjay Dey
Keyword(s):  
Electron Density ◽  
Intermolecular Interactions ◽  
Crystal Engineering ◽  
Crystal Packing ◽  
Topological Analysis ◽  
Molecular Crystals ◽  
Halogen Bonding ◽  
Crystal Formation ◽  
Computational Approaches ◽  
Ligand Interactions

The investigation of a large number of crystal structures has resulted in the development of the area of crystal engineering, which involves the study of intermolecular interactions in crystalline solids [1]. It is now of importance to understand the nature and energetics associated with different interactions [2] which influence the crystal packing. In this regard, different computational approaches (utilizing PIXEL and TURBOMOLE) have been developed which aid in the understanding of intra- and intermolecular interactions (for example, hydrogen and halogen bonding) in molecular crystals. This approach has been successfully applied in different classes of molecules [3]. These approaches can be combined with topological analysis of the electron density using the quantum theory of atoms in molecules (QTAIM) (in absence of high quality crystals for experimental electron density studies). In order to validate the above-mentioned methodology, we have performed a comprehensive analysis of a series of synthesized fluoro-derivatives of N'-phenylbenzimidamide to gain quantitative insights into different interactions which accompany crystal formation. The packing of the molecules has contributions from strong N-H...N, weak N-H...π [Fig 1], C-H...N, C-H...F, and C-H...π intermolecular interactions along with π-π stacking. In addition to that, ubiquitous H...H contacts are also present in the solid state. This methodology can be extended to include cocrystals, polymorphs (including solvates) and protein-ligand interactions at the active site.

Electron densities of two cyclononapeptides from invariom application

2019 ◽  
Vol 74 (11-12) ◽  
pp. 783-789
Author(s):  
Peter Luger ◽  
Birger Dittrich
Keyword(s):  
Electron Density ◽  
Intermolecular Interactions ◽  
Molecular Geometry ◽  
Electrostatic Potentials ◽  
Point Of View ◽  
Molecular Electrostatic Potentials ◽  
X Ray Diffraction ◽  
Hirshfeld Surfaces ◽  
Molecular Electron ◽  
Anti Cancer

AbstractThe nonapeptides cyclo(Val-Leu-Pro-Ile-Leu-Leu-Leu-Val-Leu) (I) and cyclo(Val-Leu-Pro-Ala-Leu-Leu-Leu-Val-Leu) (II) were identified as promising candidates for the development as potential anti-cancer drugs. We report a re-refinement of deposited single-crystal X-ray diffraction data with aspherical scattering factors from the invariom database. A subsequent evaluation of the molecular electron density distribution and of the differences in their molecular electrostatic potentials provides insight in their activities. The sequences differ only in residue 4, Ile in (I) and Ala in (II). Since the anti-tumor potency is reduced for the Ala peptide (II), the causes for the differences seen in activity between (I) and (II) were examined from a structural and from an electron density (ED) point of view. The exchange at residue 4 does not lead to significant changes in molecular geometry. Molecular Hirshfeld surfaces and electrostatic potential (ESP) isosurfaces show accumulations of intermolecular interactions in regions adjacent to the Ile/Ala residues indicating preferred interactions with a potential receptor in these regions. The concentrations of intermolecular interactions were localized on the Hirshfeld surfaces through an extended basin of ED concentration close to the Ile/Ala residues. Differences in the electrostatic potentials (ESPs) between (I) and (II) were only found at the Ile/Ala site and were very close to zero otherwise.

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