Scaffold diversity of exemplified medicinal chemistry space

The scaffold diversity of 7 representative commercial and proprietary compound libraries is explored for the first time using both Murcko frameworks and Scaffold Trees. We show that Level 1 of the Scaffold Tree is useful for the characterization of scaffold diversity in compound libraries and offers advantages over the use of Murcko frameworks. This analysis also demonstrates that the majority of compounds in the libraries we analyzed contain only a small number of well represented scaffolds and that a high percentage of singleton scaffolds represent the remaining compounds. We use Tree Maps to clearly visualize the scaffold space of representative compound libraries, for example, to display highly populated scaffolds and clusters of structurally similar scaffolds. This study further highlights the need for diversification of compound libraries used in hit discovery by focusing library enrichment on the synthesis of compounds with novel or underrepresented scaffolds.     

Privileged Structures Revisited

Privileged structures inspire compound library design in medicinal chemistry. We performed a comprehensive analysis of 1.4 million bioactive compounds, with the aim of assessing the prevalence of certain molecular frameworks. We used the Shannon entropy formalism to quantify the promiscuity of the most frequently observed atom scaffolds across the annotated target families. This analysis revealed an apparent inverse relationship between hydrogen-bond-acceptor count of a scaffold and its potential promiscuity. The results further suggest that chemically easily accessible scaffolds can serve as templates for the generation of bespoke compound libraries with differing degrees of multiple target engagement, and heterocyclic, sp³-rich frameworks are particularly suited for target-focused library design. The outcome of our study enables us to place some of the many narratives surrounding the concept of privileged structures into a critical context.     

Gold-catalyzed decorations of arenes and heteroarenes with C-C multiple bonds

Synthetic organic chemistry has been markedly affected by the booming of gold catalysis over the past decade. The renaissance of this coinage metal allowed unprecedented transformations to be realized in a highly selective manner and rendered "old chemistry" more accessible from a practical point of view. Particularly, organic compounds containing C-C multiple bonds benefited from the high carbophilicity of gold species, that opened access to a great chemical diversity through direct and selective π-electrophilic activations. Nowadays, the complexity of naturally occurring compounds based on functionalized aromatic frameworks continues to inspire and influence developments in synthetic chemistry. Furthermore, the ubiquitous presence of arene-based systems in pharmaceuticals, agrochemicals, and functional organic materials warrants the growing demand for mild, selective and sustainable synthetic routes to their preparation. In this context, although the peculiar aptitude of gold salts/complexes for interaction with aromatic compounds (auration process) has long been known, the direct catalytic gold decoration of arenes, has risen to prominence only recently. Here, the extensive use of electrophilic activation of C-C multiple bonds by gold species deserves a prominent mention, and the great strides made in the field over the last few years are described in this tutorial review.     

Template–Framework Interactions in Tetraethylammonium‐Directed Zeolite Synthesis

Zeolites, having widespread applications in chemical industries, are often synthesized using organic templates. These can be cost‐prohibitive, motivating investigations into their role in promoting crystallization. Herein, the relationship between framework structure, chemical composition, synthesis conditions and the conformation of the occluded, economical template tetraethylammonium (TEA⁺) has been systematically examined by experimental and computational means. The results show two distinct regimes of occluded conformer tendencies: 1) In frameworks with a large stabilization energy difference, only a single conformer was found (BEA, LTA and MFI). 2) In the frameworks with small stabilization energy differences (AEI, AFI, CHA and MOR), less than the interconversion of TEA⁺ in solution, a heteroatom‐dependent (Al, B, Co, Mn, Ti, Zn) distribution of conformers was observed. These findings demonstrate that host–guest chemistry principles, including electrostatic interactions and coordination chemistry, are as important as ideal pore‐filling.     

Amine-controlled assembly of metal-sulfite architecture from 1D chains to 3D framework

Whereas open-framework materials have been made in a variety of chemical compositions, few are known in which 3-connected SO3(2)- anions serve as basic building units. Here, we report four new metal-sulfite polymeric structures, (ZnSO3)Py (1, py = pyridine), (ZnSO3)2(2,2'-bipy)H2O (2, 2,2'-bipy = 2,2'-bipyridine), (ZnSO3)2(TMDPy) (3, TMDPy = 4,4'-trimethylenedipyridine), and (MnSO3)2en (4, en = ethylenediamine) that have been synthesized hydrothermally and structurally characterized. In these compounds, low-dimensional 1D and 2D inorganic subunits are assembled into higher 2D or 3D covalent frameworks by organic ligands. In addition to the structure-directing effect of organic ligands, the flexible coordination chemistry of Zn2+ and SO3(2)- also contributes to the observed structural diversity. In compounds 1-3, Zn2+ sites alternate with trigonal pyramidal SO3(2)- anions to form three types of [ZnSO3]n chains, whereas in compound 4, a 2D-corrugated [MnSO3]n layer is present. Compound 1 features a rail-like chain with pendant pyridine rings. The pi-pi interaction between 2,2'-bipy ligands is found between adjacent chains in compound 2, resulting in 2D sheets that are further stacked through interlayer hydrogen bonds. Compound 3 exhibits a very interesting inorganic [(ZnSO3)2]n chain constructed from two chairlike subunits, and such chains are bridged by TMDPy ligands into a 2D sheet. In compound 4, side-by-side helical chains permeate through 2D-corrugated [MnSO3]n layers, which are pillared by neutral ethylenediamine molecules into a 3D framework that can be topologically represented as a (3,6)-connected net. The results presented here illustrate the rich structural chemistry of metal-sulfites and the potential of sulfite anions as a unique structural building block for the construction of novel open-framework materials, in particular, those containing polymeric inorganic subunits that may have interesting physical properties such as low-dimensional magnetism or electronic properties.     

Isomerization of cyclobutane ligands in the solid state and solution

Cyclobutane compounds are a class of compounds that can be conveniently synthesized in the solid state by employing crystal engineering principles. The rctt-isomer (or the syn-dimer) is the most common form of any cyclobutene compound that is obtained in the solid state by the photochemical [2 + 2] cycloaddition reactions. However, these rctt-isomers can be converted to other less accessible forms, under some special conditions. Isomerization of cyclobutane compounds thus plays an important role in synthetic chemistry. Such isomerization of cyclobutane compounds have been reported in organic salts, metal complexes, coordination polymers and metal-organic frameworks. In this review, these fascinating examples of isomerization that occur both in the solid state and solution phase have been discussed.     

Hypercrosslinked Phenolic Polymers with Well‐Developed Mesoporous Frameworks

A soft chemistry synthetic strategy based on a Friedel–Crafts alkylation reaction is developed for the textural engineering of phenolic resin (PR) with a robust mesoporous framework to avoid serious framework shrinkage and maximize retention of organic functional moieties. By taking advantage of the structural benefits of molecular bridges, the resultant sample maintains a bimodal micro‐mesoporous architecture with well‐preserved organic functional groups, which is effective for carbon capture. Moreover, this soft chemistry synthetic protocol can be further extended to nanotexture other arene‐based polymers with robust frameworks.     

New Promises and Opportunities in 3D Printable Inks Based on Coordination Compounds for the Creation of Objects with Multiple Applications

This review focuses on the usefulness of coordination bonds to create 3D printable inks and shows how the union of chemistry and 3D technology contributes to new scientific advances, by allowing amorphous or polycrystalline solids to be transformed into objects with the desired shape for successful applications. The review clearly shows how there has been considerable increase in the manufacture of objects based on the combination of organic matrices and coordination compounds. These coordination compounds are usually homogeneously dispersed within the matrix, anchored onto a proper support or coating the printed object, without destroying their unique properties. Advances are so rapid that today it is already possible to 3D print objects made exclusively from coordination compounds without additives. The new printable inks are made mainly with nanoscale nonporous coordination polymers, metal–organic gels, or metal–organic frameworks. The highly dynamic coordination bond allows the creation of objects, which respond to stimuli, that can act as sensors and be used for drug delivery. In addition, the combination of metal–organic frameworks with 3D printing allows the adsorption or selective capacity of the object to be increased, relative to that of the original compound, which is useful in energy storage, gas separation, or water pollutant elimination. Furthermore, the presence of the metal ion can give them new properties, such as luminescence, that are useful for application in sensors or anticounterfeiting. Technological advances, the combination of various printing techniques, and the properties of coordination bonds lead to the creation of surprising, new, printable inks and objects with highly complex shapes that will close the gap between academia and industry for research into coordination compounds.     

Palladium-Catalyzed Arylfluorination of Alkenes: A Powerful New Approach to Organofluorine Compounds

Fluorine incorporation into organic molecules is often beneficial to their absorption, distribution, metabolism, and excretion (ADME) properties or bioactivity. As a consequence, organofluorine compounds have become quite common amongst drugs and agrochemicals, and their preparation is a highly important topic in both synthetic organic chemistry and pharmaceutical chemistry. One of the newly developed methods for accessing organofluorine compounds is Pd-catalyzed arylfluorination of alkenes. It is an olefin difunctionalization process that simultaneously introduces an aryl group and a fluorine atom into an alkene framework. This review provides a concise overview of this powerful and versatile method.     

Carbon Dioxide Sensitivity of Zeolitic Imidazolate Frameworks

Zeolitic imidazolate frameworks of zinc, cobalt, and cadmium, including the framework ZIF‐8 commercially sold as Basolite Z1200, exhibit surprising sensitivity to carbon dioxide under mild conditions. The frameworks chemically react with CO₂ in the presence of moisture or liquid water to form carbonates. This effect, which has been previously not reported in metal–organic framework chemistry, provides an explanation for conflicting reports on ZIF‐8 stability to water and is of outstanding significance for evaluating the potential applications of metal–organic frameworks, especially for CO₂ sequestration.     

Target family-directed exploration of scaffolds with different SAR profiles

The scaffold concept is widely applied in chemoinformatics and medicinal chemistry to organize bioactive compounds according to common core structures or associate compound classes with specific biological activities. A variety of scaffold analyses have been carried out to derive statistics for scaffold distributions, generate structural organization schemes, or identify scaffolds that preferentially occur in given compound activity classes. Herein we further extend scaffold analysis by identifying scaffolds that display defined SAR profiles consisting of multiple properties. A structural relationship-based scaffold network has been designed as the basic data structure underlying our analysis. From network representations of scaffolds extracted from compounds active against 32 different target families, scaffolds with different SAR profiles have been extracted on the basis of decision trees that capture structural and functional characteristics of scaffolds in different ways. More than 600 scaffolds and 100 scaffold clusters were assigned to 10 SAR profiles. These scaffold sets represent different activity and target selectivity profiles and are provided for further SAR investigations including, for example, the exploration of alternative analog series for a given target of target family or the design of novel compounds on the basis of scaffold(s) with desired SAR profiles.     

Anatomy of fingerprint search calculations on structurally diverse sets of active compounds

Similarity searching using molecular fingerprints is a widely used approach for the identification of novel hits. A fingerprint search involves many pairwise comparisons of bit string representations of known active molecules with those precomputed for database compounds. Bit string overlap, as evaluated by various similarity metrics, is used as a measure of molecular similarity. Results of a number of studies focusing on fingerprints suggest that it is difficult, if not impossible, to develop generally applicable search parameters and strategies, irrespective of the compound classes under investigation. Rather, more or less, each individual search problem requires an adjustment of calculation conditions. Thus, there is a need for diagnostic tools to analyze fingerprint-based similarity searching. We report an analysis of fingerprint search calculations on different sets of structurally diverse active compounds. Calculations on five biological activity classes were carried out with two fingerprints in two compound source databases, and the results were analyzed in histograms. Tanimoto coefficient (Tc) value ranges where active compounds were detected were compared to the distribution of Tc values in the database. The analysis revealed that compound class-specific effects strongly influenced the outcome of these fingerprint calculations. Among the five diverse compound sets studied, very different search results were obtained. The analysis described here can be applied to determine Tc intervals where scaffold hopping occurs. It can also be used to benchmark fingerprint calculations or estimate their probability of success.     

Rapid access to infrared reference spectra of arbitrary organic compounds: scope and limitations of an approach to the simulation of infrared spectra by neural networks

Substance identification by infrared spectroscopy is performed by comparison of the experimental spectrum with a reference spectrum from a printed compilation or a database. If the analyzed compound can not be found in a database the corresponding reference spectrum has to be simulated. In order to achieve this, several reasonable candidates of structures for the compound at hand have to be conceived and for all these, infrared spectra have to be developed. The simulated spectrum that is most similar to the experimental suggests the correct structure. A rapid spectrum prediction method based on neural networks has been developed that supplies reference spectra for any organic compound. The scope and limitations of this method will be discussed on a test set of 16 compounds representing a broad range of organic chemistry.     

Controlled Construction of Metal–Organic Frameworks: Hydrothermal Synthesis,X‐ray Structure,and Heterogeneous Catalytic Study

The role of pH in the formation of metal–organic frameworks (MOFs) has been studied for a series of magnesium‐based carboxylate framework systems. Our investigations have revealed the formation of five different zero‐dimensional (0D) to three‐dimensional (3D) ordered frameworks from the same reaction mixture, merely by varying the pH of the medium. The compounds were synthesized by the hydrothermal method and characterized by single‐crystal X‐ray diffraction. Increase of the pH of the medium led to abstraction of the imine hydrogen from the ligand and a concomitant increase in the OH^? ion concentration in the solution, facilitating the construction of higher dimensional framework compounds. A stepwise increase in pH resulted in a stepwise increase in the dimensionality of the network, ultimately leading to the formation of a 3D porous solid. A gas adsorption study of the 3D framework compound confirmed its microporosity with a BET surface area of approximately 450 m² g^?1. Notably, the 3D framework compound catalyzes aldol condensation reactions of various aromatic aldehydes with acetone under heterogeneous conditions.     

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.     

From molecules to materials: molecular paddle-wheel synthons of macromolecules, cage compounds and metal-organic frameworks

Metal-organic frameworks (MOF) are becoming a more and more important class of functional materials. Yet, very often, the synthesis of MOFs is not easy to control and requires a profound knowledge and experience in solid state chemistry. One of the most frequently used metal connectors is the so-called 'paddle-wheel' (PW) unit, which is a well-known molecular compound type in inorganic coordination chemistry. Depending on the ligands, the geometry of PWs strictly directs the assembly of ordered networks. This review focuses on the question, to what extent ordered network structures can be accessed by typical molecular syntheses in solution, starting from molecular PW complexes to ordered macromolecules, finite cage compounds and finally, three-dimensional superstructures.     

含硝基咔唑类有机电催化剂的合成及其对醇的电催化氧化

有机小分子的电催化氧化是催化领域的一个重要研究内容.通过醇的选择性氧化合成相应醛或酮类化合物在精细化学品和有机化学中间体的合成领域均具有十分重要的意义.有机电催化合成用电子代替强氧化还原剂,可以使反应在比较温和的条件下进行.但在直接电氧化合成反应中,电极表面容易生成有机聚合物膜,使电极钝化,电流效率急剧下降.而在电子转移媒质作用下的有机电催化反应不仅可以避免电极表面钝化,还可以控制目标产物的过度氧化.三芳胺类化合物是一类新型的电氧化还原媒质,由于其具有较宽的电化学氧化还原电位已引起研究者的广泛关注.咔唑类化合物相比于三芳胺类具有更好的平面性,使得取代基效应更为显著.咔唑类化合物被广泛作为荧光材料,但用于电化学方面的研究很少.本文通过在咔唑类化合物中引入具有强吸电子性的硝基以提高该类化合物的氧化电位,并将其作为有机电催化媒质,采用间接电化学氧化的方式,在室温下研究醇的电化学催化氧化反应,合成相应醛类化合物.
　　我们合成了三种含硝基咔唑类有机电催化剂,通过1H NMR对其结构进行了鉴定.采用循环伏安法测试了该类有机电催化剂的电化学氧化还原性能.发现取代基的电子效应对有机电催化剂的氧化还原电位及电化学氧化还原可逆性有很大的影响,供电子基(–OCH3)的引入使氧化电位负移(0.717 V),吸电子基(–Br)的引入使氧化电位明显正移(1.282 V).同时,取代基的引入有效改善了有机电催化剂的电化学可逆性,从而可以作为有效的电氧化还原媒质应用于电化学氧化反应中.而当把化合物中的NO2还原为NH2后,咔唑类化合物的电化学氧化还原可逆性完全消失,表明硝基的引入对咔唑类有机电催化剂的电化学性能有很大的影响.
　　循环伏安结果发现,在咔唑类硝基化合物的作用下,对甲氧基苯甲醇(p-MBzOH)的电化学氧化峰电位从1.350 V降至1.286 V,表明可以在较低电位下进行电解,有效降低了电氧化反应的能耗,同时氧化峰电流明显增加,说明该类有机电催化剂对p-MBzOH具有良好的电催化性能.随着p-MBzOH浓度的增加,氧化峰电流也明显增大,说明在咔唑类有机电催化剂的作用下, p-MBzOH可以在比较高的浓度下进行电化学氧化电解.通过对不同对位取代基的苯甲醇类化合物进行循环伏安研究,发现含硝基咔唑类化合物对具有较高氧化电位的反应底物均表现出良好的电催化氧化性能.
　　在含硝基咔唑类有机电催化剂的氧化电位(1.28 V)和室温下,对不同浓度的p-MBzOH进行恒电位电解6 h,发现当催化剂的用量为底物的2.5 mol%时, p-MBzOH可以完全转化为相应的醛类目标产物.而且恒电位电解后分离回收的含硝基咔唑类有机电催化剂仍具有良好的电化学氧化还原可逆性.     

Designing,Describing and Disseminating New Materials by using the Network Topology Approach

This Concept article describes how network topology analysis is applied to different fields of solid‐state chemistry. Its usefulness is demonstrated by examples from metal–organic frameworks, group 14 allotropes and related compounds, ice polymorphs, zeolites, supramolecular (organic) solid‐state chemistry, Zintl phases, and cathode materials for Li‐ion batteries.     

Open-framework structures of transition-metal compounds

Inorganic framework solids are no longer limited to just the silicates and phosphates. Recent research has revealed that carboxylates, arsenates, sulfates, selenates, selenites, germanates, phosphites can also form such structures. One of the emerging areas combines the rich coordination chemistry of the central metal ions of many of these structures with the flexibility and functionality of the organic linkers to give rise to organic-inorganic hybrid compounds. The compounds of the transition-metals appear to provide many variations arising from their coordination preferences, ligand geometry, and the valence state. In addition, the combination of the magnetic nature of the transition metal center with the channel structure of open frameworks suggests interesting potential applications. In this Review the synthesis, structures and properties of the various transition-metal open-framework compounds are discussed.