Interplanar Angle Research Articles

Does Ortho-Substitution Enhance Cytotoxic Potencies in a Series of 3,5-Bis(benzylidene)-4-piperidones?

Background: A series of 3,5-benzylidene-4-piperidones, 1a-n, were prepared to evaluate the hypothesis that the placement of different groups in the ortho-location of the aryl rings led to compounds with greater cytotoxic potencies than structural analogs. Methods: The bioevaluation of 1a-n was undertaken using human Molt/4C8 and CEM cells as well as murine L1210 cells. Correlations were sought between the interplanar angles θA and θB and the cytotoxic potencies. A QSAR analysis was also undertaken. In order to evaluate whether these compounds demonstrated greater toxicity to neoplasms than non-malignant cells, 1a-n were evaluated against HSC-2, HSC-3, HSC-4 and HL60 neoplasms as well as non-malignant HGF, HPC and HPLF cells. Results: A positive correlation was noted between the interplanar angle θA of one of the aryl rings and the adjacent olefinic linkage with IC50 values in the Molt4/C8 screens. The QSAR analysis revealed a positive correlation between the Hansch pi (π) value of the aryl substituents and the IC50 values of the compounds towards the Molt4/C8 and CEM cells. The dienones in series 1 demonstrated higher tumor-selective toxicity towards HSC-2, HSC-3, HSC-4 and HL-60 neoplasms than HGF, HPC and HPLF cells. Conclusions: The bioevaluations revealed some support for greater cytotoxic potencies to be displayed by compounds having ortho-substituents.

Crystal structures of seven gold(III) complexes of the form LAuX 3 (L = substituted pyridine, X = Cl or Br).

The structures of seven gold(III) halide derivatives of general formula LAuX 3 (L = methyl-pyridines or di-methyl-pyridines, X = Cl or Br) are presented: tri-chlorido-(2-methyl-pyridine)-gold(III), [AuCl3(C6H7N)], 1 (as two polymorphs 1a and 1b); tri-bromido-(2-methyl-pyridine)-gold(III), [AuBr3(C6H7N)], 2; tri-bromido-(3-methyl-pyridine)-gold(III), [AuBr3(C6H7N)], 3; tri-bromido-(2,4-di-meth-yl-pyridine)-gold(III), [AuBr3(C7H9N)], 4; tri-chlorido-(3,5-di-methylpyridine)-gold(III), [AuCl3(C7H9N)], 5; tri-bromido-(3,5-di-methyl-pyridine)-gold(III), [AuBr3(C7H9N)], 6, and tri-chlorido-(2,6-di-methyl-pyridine)-gold(III), [AuCl3(C7H9N)], 7. Additionally, the structure of 8, the 1:1 adduct of 2 and 6, [AuBr3(C6H7N)]·[AuBr3(C7H9N)], is included. All the structures crystallize solvent-free, and all have Z' = 1 except for 5 and 7, which display crystallographic twofold rotation symmetry, and 4, which has Z' = 2. 1a and 2 are isotypic. The coordination geometry at the gold(III) atoms is, as expected, square-planar. Four of the crystals (1a, 1b, 2 and 8) were non-merohedral twins, and these structures were refined using the 'HKLF 5' method. The largest inter-planar angles between the pyridine ring and the coordination plane are observed for those structures with a 2-methyl substituent of the pyridine ring. The Au-N bonds are consistently longer trans to Br (average 2.059 Å) than trans to Cl (average 2.036 Å). In the crystal packing, a frequent feature is the offset-stacked and approximately rectangular dimeric moiety (Au-X)2, with anti-parallel Au-X bonds linked by Au⋯X contacts at the vacant positions axial to the coordination plane. The dimers are connected by further secondary inter-actions (Au⋯X or X⋯X contacts, 'weak' C-H⋯X hydrogen bonds) to form chain, double chain ('ladder') or layer structures, and in several cases linked again in the third dimension. Only 1b and 7 contain no offset dimers; these structures instead involve C-H⋯Cl hydrogen bonds combined with Cl⋯Cl contacts (1b) or Cl⋯π contacts (7). The packing patterns of seven further complexes LAuX 3 involving simple pyridines (taken from the Cambridge Structural Database) are compared with those of 1-8.

Overcrowded 14,14'-Bidibenzo[a,j]anthracenes: Challenges in Syntheses and Atypical Property of Lacking Symmetry-Breaking Charge Transfer (SBCT).

14,14'-Bidibenzo[a,j]anthracenes (BDBAs) were prepared by iridium-catalyzed annulation of 5,5'-biterphenylene with alkynes. The molecular geometries of overcrowded BDBAs were verified by X-ray crystallography. The two dibenzo[a,j]anthryl moieties are connected through the sterically hindered 14 positions, resulting in highly distorted molecular halves. The conformation with a small twist angle between two molecular halves can minimize steric conflicts between the substituents at 1 and 13 positions and the carbon atoms of the central axis, as well as steric clashes between those substituents. One such example is octafluoro-substituted BDBA, where the interplanar angle between two anthryl moieties is approximately 31° (currently the lowest reported value, cf. 81° in 9,9'-bianthracene). The intramolecular interactions and electronic couplings between two molecular halves resulted in upfield 1H NMR signals, redshifted absorption and emission bands, and a reduced HOMO-LUMO gap. Photodynamic investigations on BDBAs indicated that the formation of the conventional symmetry-breaking charge transfer (SBCT) state was suspended by restricted rocking around the central C-C bond. Such a mechanism associated with this highly constrained conformation was examined for the first time.

Lattice destabilization in electron-beam-irradiated antimony in TEM

This study investigates the effect of electron-beam heating in transmission electron microscopy (TEM) on the structure of antimony (Sb) thin films. TEM of Sb irradiated with 300 keV electrons reveals a significant deviation (2–3°) from the theoretical interplanar angle between certain planes within the irradiated region. We relate this anomaly to electron-beam heating under electron-beam irradiation. Our FEA simulations reveal localized heating within the irradiated region caused by Auger electron excitation. These simulations predict temperatures as high as 949 K, accompanied by ultrafast heating and quenching rates. This extreme thermal cycling likely induces significant thermal stress in localized regions, possibly exceeding their elastic limits. This stress is likely related to the observed structural anomalies. This work highlights the importance of considering beam heating, particularly when interpreting TEM data from nanoscale materials with reduced thermal conductivity due to surface scattering effects.

Diffraction-Based Multiscale Residual Strain Measurements.

Modern analytical tools, from microfocus X-ray diffraction (XRD) to electron microscopy-based microtexture measurements, offer exciting possibilities of diffraction-based multiscale residual strain measurements. The different techniques differ in scale and resolution, but may also yield significantly different strain values. This study, for example, clearly established that high-resolution electron backscattered diffraction (HR-EBSD) and high-resolution transmission Kikuchi diffraction (HR-TKD) [sensitive to changes in interplanar angle (Δθθ)], provide quantitatively higher residual strains than micro-Laue XRD and transmission electron microscope (TEM) based precession electron diffraction (PED) [sensitive to changes in interplanar spacing (Δdd)]. Even after correcting key known factors affecting the accuracy of HR-EBSD strain measurements, a scaling factor of ∼1.57 (between HR-EBSD and micro-Laue) emerged. We have then conducted "virtual" experiments by systematically deforming an ideal lattice by either changing an interplanar angle (α) or a lattice parameter (a). The patterns were kinematically and dynamically simulated, and corresponding strains were measured by HR-EBSD. These strains showed consistently higher values for lattice(s) distorted by α, than those altered by a. The differences in strain measurements were further emphasized by mapping identical location with HR-TKD and TEM-PED. These measurements exhibited different spatial resolution, but when scaled (with ∼1.57) provided similar lattice distortions numerically.

Crystal structure of 4-(benzo[d]thia-zol-2-yl)-1,2-dimethyl-1H-pyrazol-3(2H)-one.

In the title compound, C12H11N3OS, the inter-planar angle between the pyrazole and benzo-thia-zole rings is 3.31 (7)°. In the three-dimensional mol-ecular packing, the carbonyl oxygen acts as acceptor to four C-H donors (with one H⋯O as short as 2.25 Å), while one methyl hydrogen is part of the three-centre system H⋯(S, O). A double layer structure parallel to (01) can be recognized as a subsection of the packing.

N-(2,4-Difluorophenyl)-2-fluorobenzamide

The title compound N-(2,4-difluorophenyl)-2-fluorobenzamide (Fo24) was synthesized in high yield (1.09 g; 87%) using standard synthetic procedures from the condensation reaction of 2-fluorobenzoyl chloride with 2,4-difluoroaniline. Crystals of Fo24 were grown from CH2Cl2 at room temperature. The Fo24 crystal structure was determined using single-crystal X-ray diffraction methods at 294 (1) K in space group Pn (No. 7). Fo24 is the second regular tri-fluorinated benzamide with the formula C13H8F3N1O1 to be reported and contrasts with the more common difluorinated and tetra-fluorinated analogues. In Fo24, both aromatic rings are effectively coplanar with an interplanar angle of 0.7(2)°. The central amide group plane is oriented by 23.04(18)° and 23.69(17)° from both aromatic rings, forming an intramolecular contact with an ortho-F12 atom with H1⋯F12 = 2.12(4) Å. The primary hydrogen bonds are 1D amide–amide interactions that form along the b-axis direction. In addition, weaker C-H⋯F/O interactions are noted: a R22(12) synthon involving two C-H, a N-H and two C-F groups, with C-F⋯C ring–ring stacking contacts completing the interactions.

An unexpected tautomer: synthesis and crystal structure of N-[6-amino-4-(methylsulfanyl)-1,2-dihydro-1,3,5-triazin-2-ylidene]benzenesulfonamide

The title compound, C10H11N5O2S2, consists of an unexpected tautomer with a protonated nitrogen atom in the triazine ring and a formal exocyclic double bond C=N to the sulfonamide moiety. The ring angles at the unsubstituted nitrogen atoms are narrow, at 115.57 (12) and 115.19 (12)°, respectively, whereas the angle at the carbon atom between these N atoms is very wide, 127.97 (13)°. The interplanar angle between the two rings is 79.56 (5)°. The molecules are linked by three classical hydrogen bonds, forming a ribbon structure. There are also unusual linkages involving three short contacts (< 3 Å) from a sulfonamide oxygen atom to the C—NH—C part of a triazine ring.

6,7-Diphenyl-5-thia-7-aza-spiro-[2.6]nonan-8-one 5,5-dioxide.

The racemic mixture of the title compound, C19H19NO3S, crystallizes in space group P with two homochiral mol-ecules in each asymmetric unit. The seven-membered ring in both mol-ecules is in a pucker-chair conformation. The extended structure exhibits C-H⋯O hydrogen bonds, of which two connect crystallographically independent mol-ecules to generate a chain propagating along the b-axis direction. One C-H grouping of the cyclo-propyl ring is in close contact with the phenyl ring of the neighboring independent mol-ecule in C-H⋯π type inter-actions with carbon atom-ring-centroid distances of 3.544 (5) and 3.596 (4) Å. Other inter-actions are of the parallel-reciprocal type, with the chiral carbon atom of one mol-ecule donating a proton to an oxygen atom of the sulfone group of a symmetry-related mol-ecule and vice-versa. Symmetry-related mol-ecular pairs also exhibit T-type inter-actions between aromatic rings with inter-planar angles of 74.2 (2) and 69.2 (2)° and inter-centroid distances of 4.965 (4) and 5.114 (4) Å.

Analyzing the aromatic-aromatic interactions in proteins: A2ID 2.0

The Aromatic-Aromatic Interactions Database (A2ID) is a comprehensive repository dedicated to documenting aromatic-aromatic (π-π) networks observed in experimentally determined protein structures. The first version of A2ID was reported in 2011 [Int J Biol Macromol, 2011, 48, 540]. It has undergone a series of significant updates, leading to its current version, which focuses on the identification and analysis of 3,444,619 π-π networks from proteins. The geometrical parameters such as centroid-centroid distances (r) and interplanar angles (ϕ) were used to identify and characterize π-π networks. It was observed that among the 84,500 proteins with at least one aromatic π-π network, about 92.50 % of the instances are found to be either 2π (77.34 %) or 3π (15.23 %) networks. The analysis of interacting amino acid pairs in 2π networks indicated a dominance of PHE residues followed by TYR. The updated version of A2ID incorporates analysis of π-π networks based on SCOP2 and ECOD classifiers, in addition to the existing SCOP, CATH, and EC classifications. This expanded scope allows researchers to explore the characteristics and functional implications of π-π networks in protein structures from multiple perspectives. The current version of A2ID along with its extensive dataset and detailed geometric information is publicly accessible using https://acds.neist.res.in/a2idv2.

Upgraded LauePt4 for rapid recognition and fitting of Laue patterns from crystals with unknown orientations.

The LauePt program is a popular and easy-to-use crystallography tool for indexing and simulating X-ray Laue patterns, but its previous versions lack search functions for recognizing Laue patterns taken from crystals with unknown orientations. To overcome this obstacle, a major upgrade of the program, called LauePt4, is presented with three robust search schemes implemented: (i) crystal rotation along a single diffraction vector, (ii) a look-up method to search for reflection pairs matching the interplanar angle of two selected diffraction spots, and (iii) a more efficient look-up scheme to search for reflection triplets matching three interplanar angles. Extensive tests show that all these schemes, together with the convenient graphical user interfaces and highly optimized computing algorithms, are reliable and powerful for recognizing and fitting Laue patterns of any crystal taken under any diffraction geometry.

Crystal structure of 2-{[5-(methyl-sulfan-yl)-4-phenyl-4H-1,2,4-triazol-3-yl]meth-yl}benzo[d]thia-zole.

In the structure of the title compound, C17H14N4O2, the triazole ring exhibits inter-planar angles of 63.86 (2) and 76.96 (2)° with the phenyl and benzo-thia-zole planes, respectively. The C-C-C angle at the methyl-ene group is rather wide at 114.28 (4)°. The packing involves three borderline C-H⋯N contacts, two of which combine to form layers parallel to ac, and a pairing of the triazole rings across an inversion centre [inter-planar distance of 3.1852 (2) Å].

Crystal structure of 5-(β-d-gluco-pyran-osyl-thio)-N-(4-methyl-phen-yl)-1,3,4-thia-diazol-2-amine.

In the structure of the title compound, C15H19N3O5S2, the bond lengths at the linking sulfur atom are significantly different [1.7473 (17) and 1.811 (2) Å], and the angle at the exocyclic nitro-gen atom is wide at 128.45 (18)°. The inter-planar angle between the tolyl and thia-diazole rings is 9.2 (1)°. The complex hydrogen-bonding pattern, involving five donors and five acceptors, can be broken down into a one-dimensional ribbon parallel to the b axis, involving hydrogen bonds of the sugar residues only, and a two-dimensional layer structure parallel to the ab plane, based on the N-H⋯O and O-H⋯N hydrogen bonds.

Cyclic Homo- and Heterohalogen Di-λ3-diarylhalonium Structures.

In the context of the ever-growing interest in the cyclic diaryliodonium salts, this work presents synthetic design principles for a new family of structures with two hypervalent halogens in the ring. The smallest bis-phenylene derivative, [(C6H4)2I2]2+, was prepared through oxidative dimerization of a precursor bearing the ortho-disposed iodine and trifluoroborate groups. We also report, for the first time, the formation of cycles containing two different halogen atoms. These present two phenylenes linked by hetero-(I/Br) or -(I/Cl) halogen pairs. This approach was also extended to the cyclic bis-naphthylene derivative [(C10H6)2I2]2+. The structures of these bis-halogen(III) rings were further assessed through X-ray analysis. The simplest cyclic phenylene bis-iodine(III) derivative features the interplanar angle of ∼120°, while a smaller angle of ∼103° was found for the analogous naphthylene-based salt. All dications form dimeric pairs through a combination of π-π and C-H/π interactions. As the largest member of the family, a bis-I(III)-macrocycle was also assembled using the quasi-planar xanthene backbone. Its geometry enables the two iodine(III) centers to be bridged intramolecularly by two bidentate triflate anions. In a preliminary manner, the interaction of the phenylene- and naphthalene-based bis-iodine(III) dications with a new family of rigid bidentate bis-pyridine ligands was studied in solution and the solid state, with an X-ray structure showing the chelating donor bonding to just one of the two iodine centers.

A new method for calculating interplanar spacing to distinguish between similar phases in EBSD.

Commercial electron backscatter diffraction (EBSD) systems generally use interplanar angle matching for pattern indexing, and thus, they are unable to distinguish between some similar phases with close interplanar angles, such as Al and Si. The interplanar spacing is more diagnostic but generally difficult to apply in pattern indexing because it lacks precision. In this study, we proposed an efficient approach for accurately measuring interplanar spacing by correcting the reciprocal-lattice vector (RLV). The phase discrimination of Al and Si was performed by interplanar spacing matching. The Kikuchi bands were identified automatically by the self-developed method using pattern rotation combined with grey gradient recognition without the help of human eyes. The reliable RLV relationship was extracted by accurately drawing reciprocal-lattice vectors. The lengths of RLVs were corrected, and then the RLVs were used for evaluating lattice spacing. The results of five Kikuchi patterns with different clarity showed that this new method reduced the average error of interplanar spacings by 50.611% and achieved an average accuracy of 1.644% for lattice spacing calculation. The method could distinguish structures with a difference in lattice spacing of at least 3.3%. This method was also effective for fuzzy patterns and partially missing Kikuchi bands and might be used as a new strategy for improving the calculation accuracy of lattice spacing for fuzzy patterns. The method did not have additional requirements concerning the number of detected Kikuchi bands and poles. The accuracy of lattice spacing could be effectively improved by correcting the RLVs based on routine pattern recognition. This method might be used as an auxiliary approach to differentiate between similar phases and is well-adapted to the existing commercial EBSD system.

Quantitative mapping of strain and displacement fields over HR-TEM and HR-STEM images of crystals with reference to a virtual lattice

A method for the reciprocal space treatment of high-resolution transmission electron microscopy (HR-TEM) and high-resolution scanning transmission electron microscopy (HR-STEM) images has been developed. Named “Absolute strain” (AbStrain), it allows for quantification and mapping of interplanar distances and angles, displacement fields and strain tensor components with reference to a user-defined Bravais lattice and with their corrections from the image distortions specific to HR-TEM and HR-STEM imaging. We provide the corresponding mathematical formalism. AbStrain goes beyond the restriction of the existing method known as geometric phase analysis by enabling direct analysis of the area of interest without the need for reference lattice fringes of a similar crystal structure on the same field of view. In addition, for the case of a crystal composed of two or more types of atoms, each with its own sub-structure constraint, we developed a method named “Relative displacement” for extracting sub-lattice fringes associated to one type of atom and measuring atomic columns displacements associated to each sub-structure with reference to a Bravais lattice or to another sub-structure. The successful application of AbStrain and Relative displacement to HR-STEM images of functional oxide ferroelectric heterostructures is demonstrated.

Crystal structure of 3-(benzo[d]thia-zol-2-yl)-6-methyl-2H-chromen-2-one.

The mol-ecule of the title compound, C17H11NO2S, is almost planar, with an inter-planar angle of 3.01 (3)° between the benzo-thia-zole and chromene ring systems. A short intra-molecular S⋯O=C contact of 2.727 (2) Å is observed. The crystal packing involves a layer structure parallel to (211), containing dimeric inversion-symmetric units connected by a 'weak' C-H⋯O=C hydrogen bond.

Syntheses and characterization of dithienyl-blocked hexapyrrin and its mononuclear complexes

With the purpose to develop long chain-conjugated oligopyrrin-like compounds and their metal complexes, and thus achieve tunable near-infrared absorption, a dithienyl-blocked hexapyrrane [Formula: see text] was synthesized by acid-catalyzed [2+4+2] condensation, followed by oxidation with DDQ to afford dithiaoctapyrrin 1, and its mononuclear metal complexes 1-Cu and 1-Zn were synthesized by treating 1 with Cu(II) and Zn(II) acetates. All the compounds were systematically characterized by NMR/EPR, and HRMS. The crystal structures revealed that 1 adopts a double hook-like conformation. Whereas, both complexes 1-Cu and 1-Zn adopt spiral-hook hybrid conformations, showing smaller interplanar angles between the rings within the spiral part, compared with those in the hook-like counterpart of molecule 1, which is favorable for red-shifting the absorption. As expected, the absorption band edges for complexes 1-Cu and 1-Zn are red-shifted to ca. 1560 nm, compared with that of 1260 nm observed for 1.

Difluoroborate-based bichromophores: Symmetry relaxation and two-photon absorption

Given potential applications of multiphoton absorbers, in the present work we have studied the symmetry-relaxation effects in one- and two-photon absorption spectra in two bichromophore systems based on difluoroborate core linked by biphenylene or bianthracene moieties. We have employed a palette of experimental methods (synthesis, one- and two-photon spectroscopy, X-ray crystallography) and state-of-the-art computational methods to shed light on how symmetry relaxation, a result of twisting of building blocks, affects one- and two-photon absorption of the two studied fluorescent dyes. Electronic-structure calculations revealed that the planarity of central biphenyl moiety, as well as deviations from planarity up to 30–40 deg., ensure maximum values of two-photon transition strengths. Perpendicular arrangement of phenylene units in biphenylene moiety leads to 20% drop in the two-photon transition strengths. More detailed studies demonstrated that equilibrium structures of both compounds in chloroform solution show very different values of two-photon absorption cross sections at absorption band maxima, i.e. 224 GM for and 134 GM for biphenyle and bianthracene linkers, respectively. The latter value is in good agreement with experimental value obtained using Z-scan method. The difference in two-photon absorption cross section between both compounds can be rationalized based on equilibrium geometry differences, i.e. interplanar angle is 35 deg and 91 deg in the case of biphenylene and bianthracene moiety, respectively. It is thus not beneficial to introduce conformationally locked central linker based on bianthracene moiety.

A Family of Bisnaphthyl C2-Symmetric and Asymmetric Clefts: Synthesis, Solid-State Structure, and Calculation of the Interplanar Angle.

The synthesis of a new family of naphthalenoid C2-symmetric clefts has been realized through a four-step synthetic sequence giving three C2-symmetric clefts and a rare nonsymmetric example. Subsequently, stereoselective reduction of the carbonyl groups at C-8 and C-16 then provides cleft molecules with hydrogen bonding potential. Using single-crystal X-ray and computational analysis, the cleft angle of the dione has been determined.