X‐ray Crystallography in Open‐Framework Materials

Open‐framework materials, such as metal–organic frameworks (MOFs) and coordination polymers have been widely investigated for their gas adsorption and separation properties. However, recent studies have demonstrated that their highly crystalline structures can be used to periodically organize guest molecules and non‐structural metal compounds either within their pore voids or by anchoring to their framework architecture. Accordingly, the open framework can act as a matrix for isolating and elucidating the structures of these moieties by X‐ray diffraction. This concept has broad scope for development as an analytical tool where obtaining single crystals of a target molecule presents a significant challenge and it additionally offers potential for obtaining insights into chemically reactive species that can be stabilized within the pore network. However, the technique does have limitations and as yet a general experimental method has not been realized. Herein we focus on recent examples in which framework materials have been utilized as a scaffold for ordering molecules for analysis by diffraction methods and canvass areas for future exploration.     

A Germanosilicate Structure with 11×11×12‐Ring Channels Solved by Electron Crystallography

Zeolites have been widely used in industry owing to their ordered micropores and stable frameworks. The pore sizes and shapes are the key parameters that affect the selectivity and efficiency in their applications in catalysis, sorption, and separation. Zeolites with pores defined by 10 and 12 TO₄ tetrahedra are often used for various catalytic processes. To optimize the performance of zeolites, it is extremely desirable to fine‐tune the pore sizes/shapes. The first germanosilicate zeolite with a three‐dimensional 11×11×12‐ring channel system, PKU‐16 (PKU, Peking University) is presented. Nanosized PKU‐16 was structurally characterized by the new three‐dimensional rotation electron diffraction (RED) technique. PKU‐16 is structurally related to the zeolite β polymorph C (BEC, 12×12×12‐ring channels) by rotating half of the four‐rings in double mtw units.     

Synthesis,Spectroscopy, X‐ray Crystallography,and DFT Computations of Nanosized Phosphazenes

Nanoparticles of nine phosphazenes with general formula 4‐CH₃C₆H₄S(O)₂N=PX₃ [X = Cl ( A ), NC₄H₈ ( 1 ), NC₆H₁₂ ( 2 ), NC₄H₈N–C(O)OC₂H₅ ( 3 ), NC₄H₈N–C(O)OC₆H₅ ( 4 ), NC₄H₈O ( 5 ), NHCH₂–C₄H₇O ( 6 ), N(CH₃)(C₆H₁₁) ( 7 ), NHCH₂–C₆H₅ ( 8 ), and 2‐NH‐NC₅H₄ ( 9 )] were synthesized using ultrasonic method and characterized by ¹H, ¹³C, ³¹P NMR, FT‐IR, fluorescence, as well as UV/Vis spectroscopy and additionally with XRD, FE‐SEM, N₂ sorption, and elemental analysis. The ³¹P NMR spectra of compounds 1 – 9 reveal the most up field shift δ(³¹P) for 9 at –11.45 ppm reflecting the most electron donation of 2‐aminopyridinyl rings through resonance to the phosphorus atom. The ¹H, ¹³C NMR spectra of 7 exhibit two sets of signals for the hydrogen and carbon atoms of its two isomers present in the solution state in 1:4 ratio. The FE‐SEM micrographs illustrate that the nanoparticles of compounds 1 – 9 have spherical morphology and a size of 27–42 nm. From the XRD patterns, the crystal sizes were estimated to about 24–86 nm. The highest bandgap was measured for 3 (3.81 eV) whereas the smallest was measured for 8 (3.50 eV). The structures of two polymorphs of compound 5 ( 5 , 5′ ) were determined by X‐ray crystallography at 120 K. Both of these polymorphs are triclinic with P1 space group but 5 has a doubled unit cell volume and two symmetrically independent molecules ( 5a and 5b ). In structures 5a and 5′ , the phosphorus and all endocyclic atoms of two morpholinyl rings display disorder, whereas the molecule 5b does not show disorder. The strong intermolecular O–H ··· O hydrogen bonds plus weak intermolecular C–H ··· O and C–H ··· N interactions create three‐dimensional polymers in the crystalline networks of 5 and 5′ . The DFT computations illustrate that molecule 5b is more stable than 5a by –1.1062 and –0.9779 kcal · mol^–1 at B3LYP and B3PW91 levels, respectively. The NBO calculations presented sp³d hybridization for phosphorus and sulfur atoms and sp², sp³ hybrids for the nitrogen and oxygen atoms.     

Combining Crystallography and Hydrogen–Deuterium Exchange to Study Galectin–Ligand Complexes

The physiological significance arising from translating information stored in glycans into cellular effects explains the interest in structurally defining lectin–carbohydrate recognition. The relatively small set of adhesion/growth‐regulatory galectins in chicken makes this system attractive to study the origins of specificity and divergence. Cell binding by using glycosylation mutants reveals binding of the N‐terminal domain of chicken galectin‐8 (CG‐8N) to α‐2,3‐sialylated and galactose‐terminated glycan chains. Cocrystals with lactose and its 3′‐sialylated derivative disclose Arg58 as a key contact for the carboxylic acid and differences in loop lengths to the three homodimeric chicken galectins. Monitoring hydrogen–deuterium exchange by mass spectrometry revealed an effective reduction of deuteration after ligand binding within the contact area. In addition, evidence for changes in solvent accessibility of amide protons beyond this site was obtained. Their detection, which highlights the sensor capacity of this technique, encourages systematic studies on galectins and beyond.     

The Structure of 2‐[(1S)‐(+)‐10‐camphorsulfonamino]‐6‐aminopyridine in the Solid State and in Solution; Unprecedented Cocrystallization of Four Stereoisomers

The solid and solution structures of a new optically active aminopyridine compound, 2‐[(1S)‐(+)‐10‐camphorsulfonamino]‐6‐aminopyridine [(S)‐csaap], 1 , are reported. Crystal data: space group P2₁, a = 8.9729 (5), b = 10.9447 (6), c = 36.693 (2) Å, β = 96.435 (1)°, V = 3580.8 (3) ų, Z = 8, R₁ = 0.0673 and wR₂ = 0.1600 with I > 2σ(I). This chiral compound shows an unprecedented cocrystallization of four stereoisomers, which are characterized by X‐ray crystallography and NMR spectroscopy.     

Synthesis and Antibacterial Activities of 2‐(1‐Aryl‐5‐Methyl‐1,2,3‐triazol‐4‐yl)‐1,3,4‐Oxadiazole Derivatives

Eighteen novel 2‐(1‐aryl‐5‐methyl‐1,2,3‐triazol‐4‐yl)‐1,3,4‐oxadiazole derivatives and two acylhydrazone intermediate compounds were synthesized by various pathways starting from 1‐aryl‐5‐methyl‐1,2,3‐triazol‐4‐formhydrazide ( 1 ). All products were identified by spectroscopic analysis, and 2‐(1‐aryl‐5‐methyl‐1,2,3‐triazol‐4‐yl)‐5‐benzalthio‐1,3,4‐oxadiazole was further validated by X‐ray crystallography. Results from primary antibacterial activity tests indicated that most of the compounds were effective against E. coli, P. aeruginosa, B. subtilis and S. aureus.     

Excitation‐Wavelength‐Dependent,Ultrafast Photoinduced Electron Transfer in Bisferrocene/BF2‐Chelated‐Azadipyrromethene/Fullerene Tetrads

Donor–acceptor distance, orientation, and photoexcitation wavelength are key factors in governing the efficiency and mechanism of electron‐transfer reactions both in natural and synthetic systems. Although distance and orientation effects have been successfully demonstrated in simple donor–acceptor dyads, revealing excitation‐wavelength‐dependent photochemical properties demands multimodular, photosynthetic‐reaction‐center model compounds. Here, we successfully demonstrate donor– acceptor excitation‐wavelength‐dependent, ultrafast charge separation and charge recombination in newly synthesized, novel tetrads featuring bisferrocene, BF₂‐chelated azadipyrromethene, and fullerene entities. The tetrads synthesized using multistep synthetic procedure revealed characteristic optical, redox, and photo reactivities of the individual components and featured “closely” and “distantly” positioned donor–acceptor systems. The near‐IR‐emitting BF₂‐chelated azadipyrromethene acted as a photosensitizing electron acceptor along with fullerene, while the ferrocene entities acted as electron donors. Both tetrads revealed excitation‐wavelength‐dependent, photoinduced, electron‐transfer events as probed by femtosecond transient absorption spectroscopy. That is, formation of the Fc⁺–ADP–C₆₀^.? charge‐separated state upon C₆₀ excitation, and Fc⁺–ADP^.?–C₆₀ formation upon ADP excitation is demonstrated.     

The Structure of Bis[N‐6‐aminopyridyl‐N‐(1S)‐(+)‐10‐camphorsulfonylamino]palladium in the Solid State and in Solution

The complex, bis[N‐6‐aminopyridyl‐N‐(1S)‐(+)‐10‐camphorsulfonylamino]palladium, Pd[(S)‐APCS]₂, 1 , was prepared by reaction of 2‐[(1S)‐(+)‐10‐camphorsulfonamino]‐6‐aminopyridine with PdCl₂ in THF. Complex 1 has been characterized by spectroscopic methods and its structure has been determined by X‐ray crystallography. Crystal data: space group C2, a= 16.082 (2), b = 17.104 (2), c = 13.051 (2)Å, β = 99.95 (1)°, V = 3535.9 (8) ų, Z = 2 with final residuals R1 = 0.0491 and wR2 = 0.0944. Two independent molecules, (S,S)‐Pd[(S)‐APCS]2, 1a , and (R,R)‐Pd[(S)‐APCS]2, 1b , were found in each asymmetric unit, which exchange to each other via a series of nitrogen inversion and C‐C bond rotation. The inversion energy (ΔGc₁^≠) and the energy barrier (δGc₂^≠) were 11.5 ± 0.1 Kcal mol^?1 at 246 K and 9.8 ± 0.1 Kcal mol^?1 at 199 K, respectively, calculated by dynamic NMR data.     

Cyclic Hydroboration – The Structure of Perhydro‐9b‐boraphenalenes

Complete hydroboration of cyclododecatrienes was reported to give two isomers, depending on conditions. The assignment of their structure had been attempted without unequivocal proofs. We have now used NMR spectroscopy (¹¹B, ¹³C, ¹⁵N and ²³Na NMR) to study the sodium amides of these two polycyclic boranes. In addition, one of the isomeric borates could be crystallized, and the X‐ray analysis revealed a cis‐,cis‐,trans configuration of the six‐membered rings reversing the original structural assignment.     

Time‐Resolved Crystallography of the Reaction Intermediate of Nitrile Hydratase: Revealing a Role for the Cysteinesulfenic Acid Ligand as a Catalytic Nucleophile

The reaction mechanism of nitrile hydratase (NHase) was investigated using time‐resolved crystallography of the mutant NHase, in which βArg56, strictly conserved and hydrogen bonded to the two post‐translationally oxidized cysteine ligands, was replaced by lysine, and pivalonitrile was the substrate. The crystal structures of the reaction intermediates were determined at high resolution (1.2–1.3 Å). In combination with FTIR analyses of NHase following hydration in H₂¹⁸O, we propose that the metal‐coordinated substrate is nucleophilically attacked by the O(SO^?) atom of αCys114‐SO^?, followed by nucleophilic attack of the S(SO^?) atom by a βArg56‐activated water molecule to release the product amide and regenerate αCys114‐SO^?.     

α‐Peptide–Oligourea Chimeras: Stabilization of Short α‐Helices by Non‐Peptide Helical Foldamers

Short α‐peptides with less than 10 residues generally display a low propensity to nucleate stable helical conformations. While various strategies to stabilize peptide helices have been previously reported, the ability of non‐peptide helical foldamers to stabilize α‐helices when fused to short α‐peptide segments has not been investigated. Towards this end, structural investigations into a series of chimeric oligomers obtained by joining aliphatic oligoureas to the C‐ or N‐termini of α‐peptides are described. All chimeras were found to be fully helical, with as few as 2 (or 3) urea units sufficient to propagate an α‐helical conformation in the fused peptide segment. The remarkable compatibility of α‐peptides with oligoureas described here, along with the simplicity of the approach, highlights the potential of interfacing natural and non‐peptide backbones as a means to further control the behavior of α‐peptides.     

Structural polymorphism in poly(dodecamethylen‐di‐O‐methyl‐L‐tartaramide)

Structural characterization of poly(dodecamethylen‐di‐O‐methyl‐L‐tartaramide) was carried out with optical microscopy, thermal analysis, X‐ray diffraction, and electron microscopy. Two different crystalline forms were found in accordance with the thermograms, powder and fiber X‐ray diffraction diagrams. The electron microscopy allows corroboration of the morphological and crystallographic differences. Molecular modeling was used to conclude the structural analogies and differences between the two crystalline forms that were related to the chain packing and orientation in the crystal cell, respectively. © 2002 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 40: 2523–2530, 2002     

X‐Ray and Electron Diffraction Study of Poly(p‐dioxanone)

Summary: Solution‐grown lamellar crystals of poly(p‐dioxanone) (PPDX) have been crystallized isothermally from butane‐1,4‐diol at 100 °C. The crystal structure of PPDX has been determined by interpretation of X‐ray fiber diagrams of PPDX fibers and electron diffraction diagrams of lozenge‐shaped chain‐folder lamellar crystals. The unit cell of PPDX is orthorhombic with space group P2₁2₁2₁ and parameters: a = 0.970 nm, b = 0.742 nm, and c (chain axis) = 0.682 nm. There are two chains per unit cell, which exist in an antiparallel arrangement.

Transmission electron micrograph of PPDX chain‐folded lamellar crystals obtained by isothermal crystallization and its electron diffraction diagram.     

Crystallographic report: Crystal structure of tetra(4‐methyl‐5‐imidazole‐carboxyaldehyde)zinc(II) diperchlorate

The central zinc(II) atom in the title complex is tetrahedrally coordinated by four nitrogen atoms derived from 4‐methyl‐5‐imidazolecarboxyaldehyde ligands with Zn? N in the range 2.007(3) to 2.026(4) Å. Copyright © 2003 John Wiley & Sons, Ltd.