Crystal Packing Interactions Research Articles

Chemical-induced formation of BZ-junction with base extrusion

The crystal structure of BZ-junction reveals that left-handed Z-DNA stabilized by Z-DNA binding domain (Zα) is continuously stacked to right-handed B-DNA with AT bases’ extrusion in the junction site. However, this structure might not fully represent the BZ-junction in solution due to the possibility of the junction formation either by crystal packing or Zα interaction. Therefore, we investigated BZ-junction in solution with chemical Z-DNA inducers using CD and 2-aminopurine base-extrusion assay. We confirmed the formation of Z-DNA and BZ-junction with base-extrusion by chemical Z-DNA inducers. However, neither typical Z-DNA nor base-extrusion could be detected with some inducers such as spermine, suggesting that the energy barrier for the formation of the BZ junction might vary depending on the Z-DNA induction conditions.

A complete characterization of vibrational IR and Raman spectra of the highly-symmetrical octathia[8]circulene

The highly-symmetrical octathia[8]circulene molecule (8S) was synthesized and well studied 10 years ago in Moscow, including X-ray diffraction, IR and Raman spectra assignment on the ground of molecular DFT calculation. Nevertheless, this comprehensive study could not explain a big number of interesting deviations from the DFT predictions based on the molecular D8h symmetry restriction being specific for a free species in a gas phase. In present work we have performed DFT optimization of the 8S tetramer starting with the X-ray diffraction analysis of a similar crystal structure. DFT calculation of IR and Raman spectra of such a huge system provides a good assignment of the crystal-field splitting and new band occurrence. The force-field distortions, electric charges and polarizability dependence on the tetramer structure are well reproduced by the B3LYP functional with the dispersion correction. Thus, the small shifts of IR and Raman bands, their splitting and intensity redistribution upon weak intermolecular interactions in crystal packing are explained and full assignment of all observed bands is presented.

Blue Phosphorescent Platinum Complexes Based on Tetradentate Bipyridine Ligands and Their Application to Organic Light-Emitting Diodes (OLEDs)

Blue phosphorescent Pt(II) complexes with 2,3′-bipyridine-based tetradentate C^N chelating ligands have been designed and synthesized. To investigate the effect of the substitution of an electron-donating/withdrawing unit on the solid-state structure and photo- and electroluminescence, either fluorine or methoxy substituents were incorporated into the C-coordinating pyridine ring. The molecular structures of all the complexes were fully characterized by different spectroscopic methods, including X-ray diffraction analysis. There are no Pt(II)···Pt(II) intermolecular interactions in crystal packing. Pt(II) complexes bearing fluorine substituents emit bright blue phosphorescence with λmax 460 nm, while methoxy-functionalized Pt(II) complexes display red-shifted and bluish green emissions with λmax 490 nm. The electron-withdrawing group at the C-coordinating pyridine ring produced a deeper HOMO (highest occupied molecular orbital) level in comparison to its electron-donating counterpart. However, the substit...

Role of halogen-involved intermolecular interactions and existence of isostructurality in the crystal packing of —CF3 and halogen (Cl or Br or I) substituted benzamides

A total of 23 benzamides are obtained through a simple reaction between chloro-/bromo-/iodoaniline and trifluoromethylbenzoyl chloride and characterized using single-crystal X-ray diffraction. Crystal structures of three series of benzamides based on N-chlorophenyl–trifluoromethyl–benzamide (nine compounds), N-bromophenyl–trifluoromethyl–benzamide (six compounds), and N-iodophenyl–trifluoromethyl–benzamide (eight compounds) are prepared to analyse the halogen-mediated noncovalent interactions. The influences of Cl/Br/I and trifluoromethyl substituents on the respective interactions are examined in the presence of a strong N—H...O hydrogen bond. This exercise has resulted in the documentation of frequently occurring supramolecular synthons involving halogen atoms in the crystal packing of benzamide molecules in the solid state. In the present study, a detailed quantitative evaluation has been performed on the nature, energetics, electrostatic contributions, and topological properties of short and directional intermolecular interactions derived from the electron density on halogenated benzamides in the solid state. Besides these, the occurrence of three-, two- and one-dimensional isostructurality in halogen (Cl or Br or I) substituted benzamide analogues is also investigated. A `region of co-existence' involving halogen-based intermolecular interactions in the vicinity of the sum of the van der Waals radii has been identified. Thus, the nature of the halogen (effective size), type of interaction and the packing characteristics via presence of additional interactions establish the subtle, yet important, role of cooperativity in intermolecular interactions in crystal packing.

'Beta version' of neuroplasticity or absolute beta power in preterm infants as electroencephalographic correlate of synaptogenesis

Although numerous Schiff base complexes have been synthesized and characterized, reports on Schiff base ligands and complexes derived from amines containing terminal allyl group are rare. In this work, four halogenated Schiff base compounds were synthesized by reaction of halogenated salicylaldehydes (3,5-dichlorosalicylaldehyde, 3,5-dibromosalicylaldehyde, 3,5-diiodosalicylaldehyde and 3-bromo-5-chlorosalicylaldehyde) with allyl amine in water as green solvent at ambient temperature and characterized by elemental analyses, NMR (1H and 13C), and FT-IR spectroscopy. In continue, their Cu(II) complexes were synthesized and characterized by elemental analyses, FT-IR and single-crystal X-ray diffraction. All complexes show halogen-halogen, π–π, CH–π interactions and also metal–halogen secondary bonds in crystal packing. The coordination geometry around the Cu(II) in all reported compounds is best described as square planar with two axially elongated interactions named metal–halogen secondary bond (Cu…X), all beyond the sum of the corresponding vdW radii (3.421 Å for Cu…Cl in (Cl2L)2Cu, 3.463 Å for Cu…Br in (Br2L)2Cu, 3.486 Å for Cu…I in (I2L)2Cu and 3.467 Å for Cu…Cl in (BrClL)2Cu). The crystal structures have also been subjected to Hirshfeld surface analysis which reveals that approximately most of the close contacts correspond to relatively weak interactions. Also, all of the interactions in crystal packing have been analyzed by theoretical calculations.

4‐[(1, 3‐Dioxoisoindolin‐2‐yl)methyl]benzenesulfonamide: Full Structural and Spectroscopic Characterization and Molecular Docking with Carbonic Anhydrase II

AbstractThe structural, spectral, electronic, thermodynamic and nonlinear optical features of 4‐[(1, 3‐dioxoisoindolin‐2‐yl)methyl]benzenesulfonamide were investigated using experimental and theoretical methods. Experimental characterization was carried out via FT‐IR, Raman, carbon‐13 and proton NMR chemical shifts and UV‐Vis. spectroscopic techniques. The molecular electronic structure computations were done with DFT/B3LYP method using the 6–311++G(2d,2p) basis set. VEDA4 software was used to analyze in PED (potential energy distribution) to vibrational profile of computed harmonic frequencies. Hirshfeld surface analysis was performed to determine interactions in crystal packing of the compound. Additionally, the highest occupied molecular orbitals (HOMOs), lowest unoccupied molecular orbitals (LUMOs), nonlinear optical (NLO) analysis, molecular electrostatic potential (MEP and ESP) surfaces and thermochemical properties were studied with theoretical computational method. The localization contributions on the defined molecular groups of molecular orbitals in the electronic transitions were investigated. Enzyme‐ligand interactions of 4‐[(1, 3‐dioxoisoindolin‐2‐yl)methyl]benzenesulfonamide with carbonic anhydrase II were investigated by molecular docking analysis. The experimental and calculated structural and spectroscopic data were compared with each other. The correlation between computed results and experimental records is in a good harmony.

Understanding the solid-state emission of a trio of 1,4-diaryl-1,3-butadiynes in terms of their molecular structure and crystal packing interactions

A trio of 1,4-diaryl-1,3-butadiynes with methoxy and trifluoromethoxy substituents in the 4- and 4′-positions were prepared in useful yields (42% for one, 95+% for the others), their structures determined and their purity ascertained. Analysis of the single crystal X-ray data for the three compounds revealed that two were mostly planar with small dihedral angles of 6–9° between their aryl rings, while one existed in a twisted conformation with a dihedral angle of approximately 53° between it's aryl rings. The solid-state absorption spectra of all three compounds were similar, with structured absorptions at approximately 340 nm. One of the compounds had absorption bands at 263 and 457 nm. Two of the compounds had similar emission bands with maxima that ranged from 440 to 450 nm, while the other was quite different, with a broad emission band with a maximum at 564 nm. Each of the three compounds had excited state decay traces that were fit to tri-exponential curves which yielded three lifetimes: a longer one attributed to aggregate emission, a shorter one arising from an intermolecular charge transfer transition, and a medium one that is assigned to a locally excited transition.

C–X···X–C vs C–H···X–C, Which One Is the More Dominant Interaction in Crystal Packing (X = Halogen)?

Three different approaches of statistical analyses, after surface area corrections, on the C–X···X–C (X = halogen) and C–H···X–C interactions have been performed. The analyses suggest that with respect to the accessible surface area on H and X, the C–H···X–C interactions are preferable over C–X···X–C interactions for all the halogens in the organic crystals. This is in contrast to the previous statistical analysis which stated that lighter halogens prefer C–H···X–C interactions whereas heavier halogens prefer C–X···X–C interactions. We have shown here the origin of the difference from the previous analysis. We also have shown here why it gives the impression that lighter halogens generally do not go for C–X···X–C interactions, but when they are replaced with the heavier halogens in the same molecule, the probability of formation of the C–X···X–C contacts increases. The preferred geometry of the C–X···X–C interactions with respect to the two ∠CXX angles and X···X distance have been shown. This study sugges...

A close insight into the nature of intra- and intermolecular interactions in new Cu(II) Schiff base complexes derived from halogenated salicylaldehydes and allylamine: Theoretical and crystallographic studies

Although numerous Schiff base complexes have been synthesized and characterized, reports on Schiff base ligands and complexes derived from amines containing terminal allyl group are rare. In this work, four halogenated Schiff base compounds were synthesized by reaction of halogenated salicylaldehydes (3,5-dichlorosalicylaldehyde, 3,5-dibromosalicylaldehyde, 3,5-diiodosalicylaldehyde and 3-bromo-5-chlorosalicylaldehyde) with allyl amine in water as green solvent at ambient temperature and characterized by elemental analyses, NMR (1H and 13C), and FT-IR spectroscopy. In continue, their Cu(II) complexes were synthesized and characterized by elemental analyses, FT-IR and single-crystal X-ray diffraction. All complexes show halogen-halogen, π–π, CH–π interactions and also metal–halogen secondary bonds in crystal packing. The coordination geometry around the Cu(II) in all reported compounds is best described as square planar with two axially elongated interactions named metal–halogen secondary bond (Cu…X), all beyond the sum of the corresponding vdW radii (3.421 Å for Cu…Cl in (Cl2L)2Cu, 3.463 Å for Cu…Br in (Br2L)2Cu, 3.486 Å for Cu…I in (I2L)2Cu and 3.467 Å for Cu…Cl in (BrClL)2Cu). The crystal structures have also been subjected to Hirshfeld surface analysis which reveals that approximately most of the close contacts correspond to relatively weak interactions. Also, all of the interactions in crystal packing have been analyzed by theoretical calculations.

Molecular docking, Hirshfeld surface, structural, spectroscopic, electronic, NLO and thermodynamic analyses on novel hybrid compounds containing pyrazole and coumarin cores

The target compound 3-(3-(4-chlorobenzoyl)-1-phenyl-1H-pyrazole-5-carbonyl)-7-methoxy-2H-chromen-2-one was characterized by FT-IR, Laser-Raman, NMR chemical shift, UV–Vis. and single-crystal X-Ray diffraction spectroscopic techniques. The molecular geometric structure, Hirshfeld surface, HOMO-LUMO, molecular electrostatic potential (MEP), non-linear optical, atomic charges, molecular docking and thermodynamic analyses were theoretically investigated to support the obtained data with experimental studies. The theoretical researches and evaluations were performed by DFT/B3LYP functional at the 6-311++G(d,p) basis set in the ground state of the compound. The assignments of computed harmonic vibrational wavenumbers were determined in terms of potential energy distribution (PED) analysis. Hirshfeld surface analysis was studied to examine intermolecular interactions in crystal packing of the compound. The experimental results on molecular geometry and spectral results were showed that the correlation between experimental and theoretical data is in good agreement. Additionally, for molecular docking study, macromolecule-ligand interactions between 3-(3-(4-chlorobenzoyl)-1-phenyl-1H-pyrazole-5-carbonyl)-7-methoxy-2H-chromen-2-one and interleukin-6 (IL-6) (PDB ID: 4NI9) were investigated by using AutoDock Vina program. All results related to title compound were evaluated in detail.

Molecular structure, Hirshfeld surface analysis, spectroscopic (FT-IR, Laser-Raman, UV–vis. and NMR), HOMO-LUMO and NBO investigations on N-(12-amino-9,10-dihydro-9,10-ethanoanthracen-11-yl)-4-methylbenzenesulfonamide

The structural geometry, vibrational wavenumbers (FT-IR and Raman), 1H and 13C NMR chemical shifts and UV–vis. electronic absorption wavelengths of N-(12-amino-9,10-dihydro-9,10-ethanoanthracen-11-yl)-4-methylbenzenesulfonamide (C23H22N2O2S) molecule were studied using experimental and computational methods. The theoretical investigations were performed by using DFT/B3LYP functional with the 6-311G(d,p) basis set in the ground state of the title molecule. The HOMO and LUMO analyses were theoretically investigated to support electronic transitions in UV–vis. spectrum of the compound. The vibrational band assignments of the calculated harmonic wavenumbers were obtained in terms of potential energy distribution (PED) analysis by using VEDA4 program. The Hirshfeld surface analysis was done to describe intermolecular interactions in crystal packing of the compound. The NH⋯N intramolecular hydrogen bonding interaction in the compound was investigated with NBO analysis. The experimental records on molecular geometry and spectral results have been showed that the correlation between experimental and theoretical data is in a good agreement.

Unique Hydration/Dehydration-Induced Vapochromic Behavior of a Charge-Transfer Salt Comprising Viologen and Hexacyanidoferrate(II).

We successfully prepared and crystallographically characterized the first intermolecular charge-transfer (CT)-based vapochromic compound, (EV)(H3O)2[Fe(CN)6] (1-Wet, EV2+: 1,1'-diethyl-4,4'-bipyridine-1,1'-diium), an ethyl viologen-containing CT salt. 1-Wet, which is purple in color, is transformed into a brown powder (1-Dry) upon exposure to methanol vapor, drying over silica gel, or heating; 1-Dry returns to 1-Wet upon exposure to water vapor. These color changes are induced by hydration and dehydration, and gravimetric analyses suggest that 1-Dry is the dehydrated form of 1-Wet, namely, (EV)(H)2[Fe(CN)6]. Interestingly, desorption of water molecules from the oxonium ions in 1-Wet produces isolated protons (H+) that remain in 1-Dry as counter cations. Powder X-ray crystal structure analysis of 1-Dry reveals the presence of very short contacts between the nitrogen atoms of adjacent [Fe(CN)6]4- anions in the crystal. The isolated protons are trapped between the nitrogen atoms of cyanido ligands to form very short N···H···N hydrogen bonds. A detailed comparison of the crystal structures of 1-Wet and 1-Dry reveals that hydration and dehydration induce changes in crystal packing and intermolecular CT interactions, resulting in reversible color changes.

Theoretical design and exploration of novel high energy density materials based on silicon

ABSTRACTSi-based high energy density materials (HEDMs) have been theoretically studied based on density functional theory and ab initio molecular dynamics simulation. These HEDM compounds have a unique fused-heterocyclic structure centered at Si. A new theoretical technique was used to predict crystal density of HEDMs. It takes into considerations crystal packing and intermolecular interactions. The calculation predicts that the new class of HEDMs can have significantly higher densities than classical energetic materials (from 2.05 to 2.30 g/cm3). Their heats of formation are significantly higher than that of classical energetic materials. In addition, electronic structures of the chemical bonds within these HEDM compounds were theoretically determined and discussed in relation to sensitivity and stability of the compounds. The present research discovers that creatively designed substitution of C by Si in HEDMs can potentially lead to promising candidates with high performance, moderately high thermal stability, and low-impact sensitivity.

Visualising crystal packing interactions in solid-state NMR: Concepts and applications.

In this article, we introduce and apply a methodology, based on density functional theory and the gauge-including projector augmented wave approach, to explore the effects of packing interactions on solid-state nuclear magnetic resonance (NMR) parameters. A visual map derived from a so-termed "magnetic shielding contribution field" can be made of the contributions to the magnetic shielding of a specific site-partitioning the chemical shift to specific interactions. The relation to the established approaches of examining the molecule to crystal change in the chemical shift and the nuclear independent chemical shift is established. The results are applied to a large sample of 71 molecular crystals and three further specific examples from supermolecular chemistry and pharmaceuticals. This approach extends the NMR crystallography toolkit and provides insight into the development of both cluster based approaches to the predictions of chemical shifts and for empirical predictions of chemical shifts in solids.

Quantitative characterization of new supramolecular synthons involving fluorine atoms in the crystal structures of di- and tetrafluorinated benzamides.

Strong hydrogen bonds play a significant role in crystal packing. In particular, the involvement of interactions involving fluorine in controlling the crystal packing requires appropriate attention, especially in the presence of other strong hydrogen bonds. In the present study, a detailed quantitative assessment has been performed of the nature, energetics and topological properties derived from the electron density in model compounds based on fluorinated benzamides (a total of 46 fluorine-substituted benzamides containing multiple fluorine atoms) in the solid state. The primary motivation in the design of such molecules is to enhance the acidity of the interacting H atoms in the presence of an increasing number of F atoms on the molecular scaffold, resulting in increased propensity towards the formation of intermolecular interactions involving organic fluorine. This exercise has resulted in the identification of new and frequently occurring supramolecular synthons involving F atoms in the packing of molecules in the solid state. The energetics associated with short and directional intermolecular Csp2-H...F-Csp2 interactions with significantly high electrostatic contributions is noteworthy, and the topological analysis reveals the bonding character of these ubiquitous interactions in crystal packing in addition to the presence of Csp2-F...F-Csp2 contacts.

Crystal structures, DFT calculations, and Hirshfeld surface analyses of two new copper(II) and nickel(II) Schiff base complexes derived from meso-1,2-diphenyl-1,2-ethylenediamine

Two new Ni(II) and Cu(II) complexes of a tetradentate Schiff base ligand (1 and 2, respectively), derived from the condensation of meso-1,2-diphenyl-1,2-ethylenediamine with 2-hydroxy-6-methoxy benzaldehyde, were synthesized and characterized by IR, UV–Vis, 1H NMR spectroscopy, and X-Ray crystallography. The central metal ions in both complexes are coordinated via the N2O2 coordination sphere of the ligand with square-planar geometry. DFT results revealed that the MN and MO interactions (M = Ni, Cu) are weaker than the typical covalent single bond indicating that ionic and electrostatic interactions are dominated in MN and MO bonds. Hirshfeld surface (HS) analyses of the studied structures 1 and 2 have been performed. The study using 3D HSs and 2D fingerprint plots (FPs) highlighted the dominant contacts H⋯H, C⋯H/H⋯C and O⋯H/H⋯O in both structures, and H⋯Cl in 2. The molecular assemblies held by C⋯O/O⋯C (in 1) and C⋯C (in 1 and 2) type dipole–dipole interactions are also found in the crystal packing contributing towards stability. The significant contributions arising from the mentioned interactions in crystal packing are also revealed from the Hirshfeld surface FPs showing a major contribution to total HS area for the H⋯H contacts for both structures.

A Flexible, Fused, Azomethine-Boron Complex: Thermochromic Luminescence and Thermosalient Behavior in Structural Transitions between Crystalline Polymorphs.

This manuscript reports the multi-functional boron complex presenting aggregation-induced emission (AIE), crystallization-induced emission enhancement (CIEE), and thermosalient behavior accompanying thermochromic luminescence during crystal-crystal transitions by employing the fused azomethine ligand. In particular, we propose that these properties can be explained by molecular "flexibility" toward external stimuli, including temperature changes and photo-excitation, and two types of crystal polymorphs with different absorption and luminescent properties were obtained. Optical measurements indicated that both polymorphs showed individual AIE and strong CIEE properties. From the investigations, the boron complex showed large structural relaxation and formed the bent structure in the excited state, followed by emission annihilation in the absence of structural restriction. In addition, it was shown that interconversion between these polymorphs could be reversibly induced by heating and cooling. The data from the single-crystal X-ray analyses suggested that alteration of crystal packing and intermolecular interaction should influence the luminescent chromism. Moreover, we also found that the crystals showed unusual mechanical behavior, such as hopping and fragmentation by heating and cooling, respectively, which is called thermosalient behavior. It was suggested that the loosely-fused structure could be responsible for expressing unique optical and mechanical properties.

Synthesis, Structural Characterization, Hirshfeld Surface and Antioxidant Activity Analysis of a Novel Organic Cation Antimonate Complex

A new organic–inorganic hybrid material of formula (C10H15N2)7 Sb2Cl10 Sb2Cl9 (SbCl5)2 SbCl4 2Cl·7H2O was synthesized and characterized by an X-ray diffraction analysis. It crystallizes in the triclinic system with the P $$\bar{1}$$ space group and the following unit cell parameters a = 11.8127(3) A, b = 15.7557(4) A, c = 35.4511(8) A, α = 89.409(1)°, β = 84.04(1)°, γ = 71.116(1)°, Z = 2 and V = 6207.3(3) A3. The examination of the structure shows that the two dimensional frameworks are produced by O–H Cl, N–H⋯Cl and N–H⋯O hydrogen bonding. In addition, the most important features of crystal packing and intermolecular interactions in the title complex were quantified via Hirshfeld surface analysis. Differential scanning calorimetry has revealed a dehydration phenomenon at around 348 K. The investigation of the antioxidant activity of the title compound was carried out using the 2,2-diphenyl-1-picrylhydrazyl and ferrous iron chelating methods.

Room temperature structure of human IgG4-Fc from crystals analysed in situ.

The Fc region of IgG antibodies (Cγ2 and Cγ3 domains) is responsible for effector functions such as antibody-dependent cell-mediated cytotoxicity and phagocytosis, through engagement with Fcγ receptors, although the ability to elicit these functions differs between the four human IgG subclasses. A key determinant of Fcγ receptor interactions is the FG loop in the Cγ2 domain. High resolution cryogenic IgG4-Fc crystal structures have revealed a unique conformation for this loop, which could contribute to the particular biological properties of this subclass. To further explore the conformation of the IgG4 Cγ2 FG loop at near-physiological temperature, we solved a 2.7Å resolution room temperature structure of recombinant human IgG4-Fc from crystals analysed in situ. The Cγ2 FG loop in one chain differs from the cryogenic structure, and adopts the conserved conformation found in IgG1-Fc; however, this conformation participates in extensive crystal packing interactions. On the other hand, at room temperature, and free from any crystal packing interactions, the Cγ2 FG loop in the other chain adopts the conformation previously observed in the cryogenic IgG4-Fc structures, despite both conformations being accessible. The room temperature human IgG4-Fc structure thus provides a more complete and physiologically relevant description of the conformation of this functionally critical Cγ2 FG loop.

Role of intermolecular interaction in crystal packing: A competition between halogen bond and electrostatic interaction

To investigate the competition between halogen bond and electrostatic interaction and their influence on the crystal packing, four novel solvates of 1,3,5-trichloro-2,4,6-trinitrobenzene (TCTNB) and 1,3,5-tribromo-2,4,6-trinitrobenzene (TBTNB) were synthesized while the intermolecular forces and the contribution of each interaction were analyzed quantitatively. The electrostatic interaction is the main link between TCTNB, TBTNB and 1,4-dioxane respectively, while π-π interaction dominates in these two solvates of TCTNB/1,4-dimethylbenzene (PX) and TCTNB/mesitylene. The solvate interaction changes and varieties were illuminated by Hirshfeld surface analysis, and the group contributions were illustrated respectively. Molecular electrostatic potential surface (MEPs) with density functional theory (DFT) calculation was performed to compare the relative strength of electrostatic interaction and halogen bond. The result shows that MEPs can be used as a descriptor for determining the most possible intermolecular interaction under certain circumstances. The study presented here may provide the guidance for the design and synthesis of the complex with desired properties.