Influence of intermolecular interactions on multipole-refined electron densities

1999 ◽  
Vol 55 (1) ◽  
pp. 30-47 ◽  
Author(s):  
Mark A. Spackman ◽  
Patrick G. Byrom ◽  
Maria Alfredsson ◽  
Kersti Hermansson
Keyword(s):  
Intermolecular Interactions ◽  
X Ray Diffraction ◽  
Electron Densities ◽  
Weakly Bound ◽  
X Ray ◽  
Hartree Fock ◽  
Field Gradients ◽  
Second Moments ◽  
Hydrogen Bonded Systems ◽  
Hydrogen Bonded

This work examines the effect of intermolecular interactions on molecular properties derived from simulated X-ray diffraction data. Model X-ray data are computed from a superposition of ab initio molecular electron densities in the crystal, as well as from periodic crystal Hartree–Fock electron densities, for the hydrogen-bonded systems ice VIII, formamide and urea, as well as the weakly bound acetylene. The effects of intermolecular interactions on the electron density are illustrated at both infinite and finite data resolution, and it is concluded that multipole models are capable of quantitative retrieval of the interaction density, despite the known shortcomings of the radial functions in the model. Multipole refinement reveals considerable enhancement of the molecular dipole moment for hydrogen-bonded crystals, and negligible change in molecular second moments. Electric field gradients at H nuclei are significantly reduced in magnitude upon hydrogen bonding, and this change is also faithfully represented by the rigid pseudoatom model.

Intermolecular interactions in crystals of small unsubstituted cyclic ethers and substituted epoxides

2018 ◽  
Vol 233 (9-10) ◽  
pp. 641-648 ◽  
Author(s):  
Mark A. Spackman
Keyword(s):  
Intermolecular Interactions ◽  
Cyclic Ethers ◽  
Interaction Energies ◽  
X Ray Diffraction ◽  
Weakly Bound ◽  
X Ray ◽  
Experimental Interaction ◽  
Lattice Energies ◽  
Experimental Electron Density ◽  
Careful Investigation

Abstract CE-B3LYP model energies are used to investigate intermolecular interactions in crystals of the relatively weakly bound cyclic ethers, as well as a number of substituted epoxides that have been the focus of high-quality experimental electron density studies. This approach readily provides a complete picture of all intermolecular interactions in these molecular crystals, and CE-B3LYP lattice energies for the unsubstituted cyclic ethers are in excellent agreement with available thermodynamic data. When compared with the outcomes of multipole modelling of X-ray diffraction data, these results suggest that experimental interaction energies are typically underestimated and, contrarily, experimental lattice energies are typically overestimated. These observations deserve careful investigation.

Self-Recognizing π-π Stacking Interactions Designed for the Generation of Ultrastable Mesoporous Hydrogen-Bonded Organic Frameworks

2019 ◽  
Author(s):  
KAIKAI MA ◽  
Peng Li ◽  
John Xin ◽  
Yongwei Chen ◽  
Zhijie Chen ◽  
...  
Keyword(s):  
Pore Size ◽  
Fiber Composite ◽  
Aqueous Media ◽  
Stacking Interactions ◽  
Mustard Gas ◽  
X Ray Diffraction ◽  
X Ray ◽  
Expansion Strategy ◽  
Π Stacking ◽  
Hydrogen Bonded

Creating crystalline porous materials with large pores is typically challenging due to undesired interpen-etration, staggered stacking, or weakened framework stability. Here, we report a pore size expansion strategy by self-recognizing π-π stacking interactions in a series of two-dimensional (2D) hydrogen–bonded organic frameworks (HOFs), HOF-10x (x=0,1,2), self-assembled from pyrene-based tectons with systematic elongation of π-conjugated molecular arms. This strategy successfully avoids interpene-tration or staggered stacking and expands the pore size of HOF materials to access mesoporous HOF-102, which features a surface area of ~ 2,500 m2/g and the largest pore volume (1.3 cm3/g) to date among all reported HOFs. More importantly, HOF-102 shows significantly enhanced thermal and chemical stability as evidenced by powder x-ray diffraction and N2 isotherms after treatments in chal-lenging conditions. Such stability enables the adsorption of dyes and cytochrome c from aqueous media by HOF-102 and affords a processible HOF-102/fiber composite for the efficient photochemical detox-ification of a mustard gas simulant.

Metal Phenoxyalkanoic Acid Interactions. XXV. The Crystal Structures of (2-Formyl-6-Methoxyphenoxy)Acetic Acid and Its Zinc(II) Complex and the Lithium, Zinc(II) and Cadmium(II) Complexes of (2-Chlorophenoxy)Acetic Acid

1987 ◽  
Vol 40 (7) ◽  
pp. 1147 ◽  
Author(s):  
EJ Oreilly ◽  
G Smith ◽  
CHL Kennard ◽  
TCW Mak
Keyword(s):  
Acetic Acid ◽  
Crystal Structures ◽  
Free Acid ◽  
Rotational Symmetry ◽  
Carboxyl Groups ◽  
X Ray Diffraction ◽  
X Ray ◽  
The Third ◽  
Planar Complex ◽  
Hydrogen Bonded

The crystal structures of (2-formyl-6-methoxyphenoxy)acetic acid (1), diaquabis [(2-formyl-6-methoxyphenoxy) acetato ]zinc(11) (2), tetraaquabis [(2-chlorophenoxy) acetato ]zinc(11) (3), triaquabis [(2-chlorophenoxy) acetato ]cadmium(11) dihydrate (4) and lithium (2-chloro- phenoxy )acetate 1.5 hydrate (5) have been determined by X-ray diffraction. The acid (1) forms centrosymmetric hydrogen-bonded cyclic dimers [O…0, 2.677(6) �] which are non-planar. Complex (2) is six-coordinate with two waters [Zn- Ow , 1.997(2) �] and four oxygens from two asymmetric bidentate carboxyl groups [Zn-O, 2.073, 2.381(2) �] completing a skew trapezoidal bipyramidal stereochemistry. Complex (5) is also six-coordinate but is octahedral, with two trans-related unidentate carboxyl oxygens [mean Zn-O, 2.134(9) �] and four waters [mean Zn-O, 2.081(9) �]. The seven-coordinate complex (4) has crystallographic twofold rotational symmetry relating two :symmetric bidentate acid ligands [ Cd -O, 2.26, 2 48(:) �] and two waters [ Cd -O, 2.34(2) �] while the third water lies on this axis [ Cd -O, 2.27(2) �]. In contrast to the monomers (2)-(4), complex (5) is polymeric with tetrahedral lithium coordinated to one water and three carboxylate oxygens [mean Li-0, 1.95(1) �]. The essential conformation of the free acid is retained in complexes (2), (3) and (4) but in (5), it is considerably changed.

scholarly journals Iron(II) Complexes with Boron Cluster Anion [B10Cl10]2-: Intermolecular Interactions according to35Cl NQR Spectroscopy and X-ray Diffraction

2017 ◽  
Vol 643 (23) ◽  
pp. 1939-1947 ◽  
Author(s):  
Eleonora A. Kravchenko ◽  
Andrei. A. Gippius ◽  
Irina N. Polyakova† ◽  
Varvara V. Avdeeva ◽  
Elena A. Malinina ◽  
...  
Keyword(s):  
Intermolecular Interactions ◽  
Cluster Anion ◽  
X Ray Diffraction ◽  
X Ray ◽  
Boron Cluster ◽  
Boron Cluster Anion

scholarly journals Construction of Two Stable Co(II)-Based Hydrogen-Bonded Organic Frameworks as a Luminescent Probe for Recognition of Fe3+ and Cr2O72− in H2O

Molecules ◽  
2021 ◽  
Vol 26 (19) ◽  
pp. 5955
Author(s):  
Qi-Ying Weng ◽  
Ya-Li Zhao ◽  
Jia-Ming Li ◽  
Miao Ouyang
Keyword(s):  
Detection Limit ◽  
Aqueous Media ◽  
Three Dimensional ◽  
Cobalt Atom ◽  
High Sensitivity ◽  
X Ray Diffraction ◽  
Chlorobenzoic Acid ◽  
X Ray ◽  
Highly Sensitive ◽  
Hydrogen Bonded

A pair of cobalt(II)-based hydrogen-bonded organic frameworks (HOFs), [Co(pca)2(bmimb)]n (1) and [Co2(pca)4(bimb)2] (2), where Hpca = p-chlorobenzoic acid, bmimb = 1,3-bis((2-methylimidazol-1-yl)methyl)benzene, and bimb = 1,4-bis(imidazol-1-ylmethyl)benzene were hydrothermally synthesized and characterized through infrared spectroscopy (IR), elemental and thermal analysis (EA), power X-ray diffraction (PXRD), and single-crystal X-ray diffraction (SCXRD) analyses. X-ray diffraction structural analysis revealed that 1 has a one-dimensional (1D) infinite chain network through the deprotonated pca− monodentate chelation and with a μ2-bmimb bridge Co(II) atom, and 2 is a binuclear Co(II) complex construction with a pair of symmetry-related pca− and bimb ligands. For both 1 and 2, each cobalt atom has four coordinated twisted tetrahedral configurations with a N2O2 donor set. Then, 1 and 2 are further extended into three-dimensional (3D) or two-dimensional (2D) hydrogen-bonded organic frameworks through C–H···Cl interactions. Topologically, HOFs 1 and 2 can be simplified as a 4-connected qtz topology with a Schläfli symbol {64·82} and a 4-connected sql topology with a Schläfli symbol {44·62}, respectively. The fluorescent sensing application of 1 was investigated; 1 exhibits high sensitivity recognition for Fe3+ (Ksv: 10970 M−1 and detection limit: 19 μM) and Cr2O72− (Ksv: 12960 M−1 and detection limit: 20 μM). This work provides a feasible detection platform of HOFs for highly sensitive discrimination of Fe3+ and Cr2O72− in aqueous media.

Quantitative Analysis of Intermolecular Interactions in 3‐Cyano‐2‐Pyridones: Evaluation through Single Crystal X‐ray Diffraction and Density Functional Theory

2018 ◽  
Vol 3 (21) ◽  
pp. 5864-5873
Author(s):  
Sunil K. Rai ◽  
Tomasz Sierański ◽  
Shaziya Khanam ◽  
Krishnan Ravi Kumar ◽  
Balasubramanian Sridhar ◽  
...  
Keyword(s):  
Density Functional Theory ◽  
Quantitative Analysis ◽  
Single Crystal ◽  
Intermolecular Interactions ◽  
Density Functional ◽  
X Ray Diffraction ◽  
Functional Theory ◽  
X Ray

scholarly journals Bottleneck Effect Explained by Le Bail Refinements: Structure Transformation of Mg-CUK-1 by Confining H2O Molecules

Materials ◽  
2020 ◽  
Vol 13 (8) ◽  
pp. 1840
Author(s):  
Elí Sánchez-González ◽  
J. Gabriel Flores ◽  
Julio C. Flores-Reyes ◽  
Ivette Morales-Salazar ◽  
Roberto E. Blanco-Carapia ◽  
...  
Keyword(s):  
Relative Humidity ◽  
Co2 Capture ◽  
Unit Cell ◽  
Structure Transformation ◽  
X Ray Diffraction ◽  
Bottleneck Effect ◽  
X Ray ◽  
Cell Parameters ◽  
Hydrogen Bonded

The structure transformation of Mg-CUK-1 due to the confinement of H2O molecules was investigated. Powder X-ray diffraction (PXRD) patterns were collected at different H2O loadings and the cell parameters of the H2O-loaded Mg-CUK-1 material were determined by the Le Bail strategy refinements. A bottleneck effect was observed when one hydrogen-bonded H2O molecule per unit cell (18% relative humidity (RH)) was confined within Mg-CUK-1, confirming the increase in the CO2 capture for Mg-CUK-1.

Synthesis, growth, structure and characterization of molybdenum zinc thiourea complex crystals

2015 ◽  
Vol 71 (3) ◽  
pp. 285-292 ◽  
Author(s):  
M. Rajasekar ◽  
K. Muthu ◽  
A. Aditya Prasad ◽  
R. Agilandeshwari ◽  
SP Meenakshisundaram
Keyword(s):  
Single Crystal ◽  
Diffraction Analysis ◽  
Intermolecular Interactions ◽  
Crystal Packing ◽  
Second Harmonic ◽  
Morphological Changes ◽  
Strong Interactions ◽  
X Ray Diffraction ◽  
X Ray ◽  
Cell Parameters

Single crystals of molybdenum-incorporated tris(thiourea)zinc(II) sulfate (MoZTS) are grown by the slow evaporation solution growth technique. Crystal composition as determined by single-crystal X-ray diffraction analysis reveals that it belongs to the orthorhombic system with space groupPca21and cell parametersa= 11.153 (2),b= 7.7691 (14),c= 15.408 (3) Å,V= 1335.14 (4) Å3andZ= 4. The surface morphological changes are studied by scanning electron microscopy. The vibrational patterns in FT–IR are used to identify the functional group and TGA/DTA (thermogravimetric analysis/differential thermal analysis) indicates the stability of the material. The structure and the crystallinity of the material were confirmed by powder X-ray diffraction analysis and the simulated X-ray diffraction (XRD) closely matches the experimental one with varied intensity patterns. The band gap energy is estimated using diffuse reflectance data by the application of the Kubelka–Munk algorithm. The relative second harmonic generation (SHG) efficiency measurements reveal that MoZTS has an efficiency comparable to that of tris(thiourea)zinc(II) sulfate (ZTS). Hirshfeld surfaces were derived using single-crystal X-ray diffraction data. Investigation of the intermolecular interactions and crystal packingviaHirshfeld surface analysis reveal that the close contacts are associated with strong interactions. Intermolecular interactions as revealed by the fingerprint plot and close packing could be the possible reasons for facile charge transfer leading to SHG activity.

Exploring concomitant/conformational dimorphism in a difluoro-substituted phosphoramidate derivative

2019 ◽  
Vol 75 (4) ◽  
pp. 451-461 ◽  
Author(s):  
Avantika Hasija ◽  
Deepak Chopra
Keyword(s):  
Hydrogen Bonds ◽  
Intermolecular Interactions ◽  
Crystallization Process ◽  
X Ray Diffraction ◽  
Scanning Calorimetry ◽  
Dispersion Energy ◽  
Torsion Angles ◽  
X Ray ◽  
Electrostatic Contribution ◽  
Distinguished Contribution

The concomitant occurrence of dimorphs of diphenyl (3,4-difluorophenyl)phosphoramidate, C18H14F2NO3P, was observed via a solution-mediated crystallization process with variation in the symmetry-free molecules (Z′). The existence of two forms, i.e. Form I (block, Z′ = 1) and Form II (needle, Z′ = 2), was characterized by single-crystal X-ray diffraction, differential scanning calorimetry and powder X-ray diffraction. Furthermore, a quantitative analysis of the energetics of the different intermolecular interactions was carried out via the energy decomposition method (PIXEL), which corroborates with inputs from the energy framework and looks at the topology of the various intermolecular interactions present in both forms. The unequivocally distinguished contribution of strong N—H...O hydrogen bonds along with other interactions, such as C—H...O, C—H...F, π–π and C—H...π, mapped on the Hirshfeld surface is depicted by two-dimensional fingerprint plots. Apart from the major electrostatic contribution from N—H...O hydrogen bonds, the crystal structures are stabilized by contributions from the dispersion energy. The closely related melting points and opposite trends in the calculated lattice energies are interesting to investigate with respect to the thermodynamic stability of the observed dimorphs. The significant variation in the torsion angles in both forms helps in classifying them in the category of conformational polymorphs.

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