Factors Controlling Complex Morphologies of Isomorphous Metal-Organic Frameworks

We demonstrate here how nitrate salts of bivalent copper, nickel, cobalt, and manganese, along with an achiral organic ligand, assemble into various structures such as symmetrical double-decker flowers, smooth elongated hexagonal bipyramids, and hexagonal prisms. Large morphological changes occur in these structures because of different metal cations, although they maintain isomorphous hexagonal crystallographic structures. Metal cations with stronger coordination to ligands (Cu and Ni) tend to form uniform crystals with unusual shapes, whereas weaker coordinating metal cations (Mn and Co) produce crystals with more regular hexagonal morphologies. The unusual flower-like crystals formed with copper nitrate have two pairs of six symmetrical petals with hexagonal convex centers. The texture of the petals indicates dendritic growth. Two different types of morphologies were formed by using different copper nitrate-to-ligand ratios. An excess of the metal salt results in uniform and hexagonal crystals having a narrow size distribution, whereas the use of an excess of ligand results in double-decker morphologies. Mechanistically, an intermediate structure was observed with slightly concave facets and a domed center. Such structures most likely play a key role in the formation of double-decker crystals that can be formed by fusion processes. The coordination chemistry results in isostructural chiral frameworks consisting of two types of continuous helical channels. Four pyridine units from four separate ligands are coordinated to the metal center in a plane having a chiral (propeller-type) arrangement. The individual double-decker flower crystals are homochiral and a batch consists of crystals having both handedness.

Stereoisomer-dependent conversion of dinaphthothienothiophene precursor films

Soluble precursor materials of organic semiconductors are employed for fabricating solution-processable thin film devices. While the so-called precursor approach has already been tried for various organic electronic devices such as transistors and solar cells, understanding of the conversion process in the film lags far behind. Here, we report that molecular aggregation of the precursor compound significantly influences the thermal conversion reaction in the film. For this study, two stereoisomers of a dinaphthothienothiophene (DNTT) precursor that are the endo- and exo-DNTT-phenylmaleimide monoadducts are focused on. The structural change during the thermal conversion process has been investigated by a combination of infrared spectroscopy and X-ray diffraction techniques. The results show that the endo-isomer is readily converted to DNTT in the film by heating, whereas the exo-isomer exhibits no reaction at all. This reaction suppression is found to be due to the self-aggregation property of the exo-isomer accompanying the intermolecular C–H\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$\cdots$$\end{document}⋯O interactions. This finding shows a new direction of controlling the on-surface reaction, as well as the importance of analyzing the film structure at the initial stage of the reaction.

Structure–property relationship of novel supramolecular gels based on coumarins

LMWGs based on coumarins could form supramolecular gels with unusual mechanical properties explained by its interactions at theoretical level.

Discrete π Stack of a Tweezer-Shaped Naphthalenediimide-Anthracene Conjugate

The design and synthesis of a tweezer-shaped naphthalenediimide (NDI)-anthracene conjugate (2NDI) are reported. In the structure of the closed form (π_NDI ⋅⋅⋅π_NDI stack) of 2NDI, which was elucidated by single-crystal XRD, the existence of C-H⋅⋅⋅O hydrogen bonding involving the nearest carbonyl oxygen atom of an NDI unit was suggested. The tunability of π_NDI ⋅⋅⋅π_NDI interactions was studied by means of UV/Vis absorption, fluorescence and NMR spectroscopy and molecular modelling. This revealed that the π_NDI ⋅⋅⋅π_NDI interactions in 2NDI affect the absorption and emission properties depending on the temperature. Furthermore, in polar solvents, 2NDI prefers the stronger π_NDI ⋅⋅⋅π_NDI stack, whereas the π_NDI ⋅⋅⋅π_NDI interaction is diminished in nonpolar solvents. Importantly, the conformational variations of 2NDI can be reversibly switched by variation in temperature, and this suggests potential application for fluorogenic molecular switches upon temperature changes.

Weak Interactions and Conformational Changes in Core-Protonated A2- and Ax-Type Porphyrin Dications

Individual chemical motifs are known to introduce structural distortions to the porphyrin macrocycle, be it in the core or at the periphery of the macrocycle. The interplay when introducing two or more of these known structural motifs has been scarcely explored and is not necessarily simply additive; these structural distortions have a chance to compound or negate to introduce new structural types. To this end, a series of compounds with complementary peripheral (5,15-disubstitution) and core (acidification) substitution patterns were investigated. The single-crystal X-ray structures of 18 5,15-diphenylporphyrin, 5,15-diphenylporphyrindi-ium diacid, and related compounds are reported, including the first example of a 5,15-dialkylporphyrindi-ium. Normal-coordinate structural decomposition (NSD) analysis is used for a detailed analysis of the conformation of the porphyrin subunit within the crystal structures. An elongation of porphyrin macrocycles along the C₅,C₁₅- axis (B_2g symmetry) is observed in all of the free base porphyrins and porphyrin dications; distance across the core is around 0.3 Å in the free base and diacid compounds, and more than doubled in 5,15-dipentylporphyrin and 5,15-dipentylporphyrindi-ium diacid. While the free base porphyrins are largely planar, a large out-of-plane distortion can be observed in 5,15-diphenylporphyrin diacids, with the expected “projective saddle” shape characteristic for such systems. The combination of these two distortions (B_2u and B_2g) from regular porphyrin structure results in a macrocycle best characterized in the chiral point-group D₂. A rare structural type of a cis-hydrogen bond chelate is observed for 5,15-dipentylporphyrindi-ium diacid, which adopts an achiral C_2v symmetry. Crystallographic data indicate that the protonated porphyrin core forms hydrogen bonding chelates (N-H⋯X⋯H-N) to counter-anions. Weaker interactions, such as induced intramolecular C-H⋯O interactions from the porphyrin periphery are described, with distances characteristic of charge-assisted interactions. This paper offers a conceptual framework for accessing porphyrin macrocycles with designable distortion and symmetry, useful for the selective perturbation of electronic states and a design-for-application approach to solid state porphyrin materials.

Cooperativity in alkane-1,2- and 1,3-polyols: NMR, QTAIM, and IQA study of O─H… OH and C─H… OH bonding interactions

Proton nuclear magnetic resonance chemical shifts and atom-atom interaction energies for alkanepolyols with 1,2-diol and 1,3-diol repeat units, and for their 1:1 pyridine complexes, are computed by density functional theory calculations. In the 1,3-polyols, based on a tG'Gg' repeat unit, the only important intramolecular hydrogen bonding interactions are O─H^… OH. By quantum theory of atoms in molecules analysis of the electron density, unstable bond and ring critical points are found for such interactions in 1,2-polyols with tG'g repeat units, from butane-1,2,3,4-tetrol onwards and in their pyridine complexes from propane-1,2,3-triol onwards. Several features (OH proton shifts and charges, and interaction energies computed by the interacting quantum atoms approach) are used to monitor the dependence of cooperativity on chain length: This is much less regular in 1,2-polyols than in 1,3-polyols and by most criteria has a higher damping factor. Well defined C─H^… OH interactions are found in butane-1,2,3,4-tetrol and higher members of the 1,2-polyol series, as well as in their pyridine complexes: There is no evidence for cooperativity with O─H^… OH bonding. For the 1,2-polyols, there is a tenuous empirical relationship between the existence of a bond critical point for O─H^… OH hydrogen bonding and the interaction energies of competing exchange channels, but the primary/secondary ratio is always less than unity.

Weak Intermolecular CH···N Hydrogen Bonding: Determination of 13CH-15N Hydrogen-Bond Mediated J Couplings by Solid-State NMR Spectroscopy and First-Principles Calculations

Weak hydrogen bonds are increasingly hypothesized to play key roles in a wide range of chemistry from catalysis to gelation to polymer structure. Here, ¹⁵N/¹³C spin-echo magic-angle spinning (MAS) solid-state nuclear magnetic resonance (NMR) experiments are applied to "view" intermolecular CH···N hydrogen bonding in two selectively labeled organic compounds, 4-[¹⁵N] cyano-4'-[¹³C₂] ethynylbiphenyl (1) and [¹⁵N₃,¹³C₆]-2,4,6-triethynyl-1,3,5-triazine (2). The synthesis of 2-¹⁵N₃,¹³C₆ is reported here for the first time via a multistep procedure, where the key element is the reaction of [¹⁵N₃]-2,4,6-trichloro-1,3,5-triazine (5) with [¹³C₂]-[(trimethylsilyl)ethynyl]zinc chloride (8) to afford its immediate precursor [¹⁵N₃,¹³C₆]-2,4,6-tris[(trimethylsilyl)ethynyl]-1,3,5-triazine (9). Experimentally determined hydrogen-bond-mediated ^2hJ_CN couplings (4.7 ± 0.4 Hz (1) and 4.1 ± 0.3 Hz (2)) are compared with density functional theory (DFT) gauge-including projector augmented wave (GIPAW) calculations, whereby species-independent coupling values ^2hK_CN (29.0 × 10¹⁹ kg m^-2 s^-2 A^-2 (1) and 27.9 × 10¹⁹ kg m^-2 s^-2 A^-2 (2)) quantitatively demonstrate the J couplings for these "weak" CH···N hydrogen bonds to be of a similar magnitude to those for conventionally observed NH···O hydrogen-bonding interactions in uracil (^2hK_NO: 28.1 and 36.8 × 10¹⁹ kg m^-2 s^-2 A^-2). Moreover, the GIPAW calculations show a clear correlation between increasing ^2hJ_CN (and ^3hJ_CN) coupling and reducing C(H)···N and H···N hydrogen-bonding distances, with the Fermi contact term accounting for at least 98% of the isotropic ^2hJ_CN coupling.

What is the preferred geometry of sulfur–disulfide interactions?

Combined crystallographic and quantum chemical studies showed that in most cases, in crystal structures, interactions between sulphur atoms and disulphide bonds are bifurcated.

A Million Crystal Structures: The Whole Is Greater than the Sum of Its Parts

The founding in 1965 of what is now called the Cambridge Structural Database (CSD) has reaped dividends in numerous and diverse areas of chemical research. Each of the million or so crystal structures in the database was solved for its own particular reason, but collected together, the structures can be reused to address a multitude of new problems. In this Review, which is focused mainly on the last 10 years, we chronicle the contribution of the CSD to research into molecular geometries, molecular interactions, and molecular assemblies and demonstrate its value in the design of biologically active molecules and the solid forms in which they are delivered. Its potential in other commercially relevant areas is described, including gas storage and delivery, thin films, and (opto)electronics. The CSD also aids the solution of new crystal structures. Because no scientific instrument is without shortcomings, the limitations of CSD research are assessed. We emphasize the importance of maintaining database quality: notwithstanding the arrival of big data and machine learning, it remains perilous to ignore the principle of garbage in, garbage out. Finally, we explain why the CSD must evolve with the world around it to ensure it remains fit for purpose in the years ahead.

Model molecules to classify CHO hydrogen-bonds

We developed a set of conformationally locked molecules each of which makes a single CHO H-bond/short contact and has different electron density at the acceptor oxygen atom. The downfield shift of the 1H NMR signals due to the hydrogen involved in the CHO H-bond varied from 0.93-1.6 ppm, and the magnitude of Δδ is in correlation with the hybridization state of the acceptor oxygen and with the CHO H-bond strengths quantified using a computational method.

Strong CH/O interactions between polycyclic aromatic hydrocarbons and water: Influence of aromatic system size

Energies of CH/O interactions between water molecule and polycyclic aromatic hydrocarbons with a different number of aromatic rings were calculated using ab initio calculations at MP2/cc-PVTZ level. Results show that an additional aromatic ring in structure of polycyclic aromatic hydrocarbons significantly strengthens CH/O interactions. Calculated interaction energies in optimized structures of the most stable tetracene/water complex is -2.27 kcal/mol, anthracene/water is -2.13 kcal/mol and naphthalene/water is -1.97 kcal/mol. These interactions are stronger than CH/O contacts in benzene/water complex (-1.44 kcal/mol) while CH/O contacts in tetracene/water complex are even stronger than CH/O contacts in pyridine/water complexes (-2.21 kcal/mol). Electrostatic potential maps for different polycyclic aromatic hydrocarbons were calculated and used to explain trends in the energies of interactions.

The trans/cis photoisomerization in hydrogen bonded complexes with stability controlled by substituent effects: 3-(6-aminopyridin-3-yl)acrylate case study

The association of aminopyridine-based acrylic acid and its salt was studied by NMR titration experiments. The AA (acceptor, acceptor) hydrogen-bonding pattern present in the salt forms a complex readily with a DD (donor, donor) hydrogen-bonding pattern of the substituted ureas even in polar and competitive environment. The double carbon–carbon bond in the acrylic acid derivative is subjected to photoisomerization. This is dependent on the association with substituted urea derivatives. The substituent in ureas influences the trans/cis isomerization kinetics and position of the photostationary state. Two mechanisms that influence the photoisomerization were proposed. To the best of our knowledge, the trans/cis photoisomerization influenced by the substituent in such a hydrogen-bonding pattern has not observed previously. It was shown that interaction with urea derivatives causes lowering of the trans-to-cis photoreaction rates.

The association of aminopyridine-based acrylic acid and its salt was studied by NMR titration experiments.

Electrostatic Constraints Assessed by 1H MAS NMR Illuminate Differences in Crystalline Polymorphs

Atomically resolved crystal structures not only suffer from the inherent uncertainty in accurately locating H atoms but also are incapable of fully revealing the underlying forces enabling the formation of final structures. Therefore, the development and application of novel techniques to illuminate intermolecular forces in crystalline solids are highly relevant to understand the role of hydrogen atoms in structure adoption. Novel developments in ¹H NMR MAS methodology can now achieve robust measurements of ¹H chemical shift anisotropy (CSA) tensors which are highly sensitive to electrostatics. Herein, we use ¹H CSA tensors, measured by MAS experiments and characterized using DFT calculations, to reveal the structure-driving factors between the two polymorphic forms of acetaminophen (aka Tylenol or paracetamol) including differences in hydrogen bonding and the role of aromatic interactions. We demonstrate how the ¹H CSAs can provide additional insights into the static picture provided by diffraction to elucidate rigid molecules.

C–H/O interactions of nucleic bases with a water molecule: a crystallographic and quantum chemical study

The C–H/O interactions of nucleic bases are substantially stronger than the C–H/O interactions of benzene and pyridine. These results can be very important for molecular recognition of DNA and RNA.