Strong Conformational Preferences of Heteroaromatic Ethers and Electron Pair Repulsion

The role of the methoxy group in approved drugs

The methoxy substituent is prevalent in natural products and, consequently, is present in many natural product-derived drugs. It has also been installed in modern drug molecules with no remnant of natural product features because medicinal chemists have been taking advantage of the benefits that this small functional group can bestow on ligand-target binding, physicochemical properties, and ADME parameters. Herein, over 230 methoxy-containing small-molecule drugs, as well as several fluoromethoxy-containing drugs, are presented from the vantage point of the methoxy group. Biochemical mechanisms of action, medicinal chemistry SAR studies, and numerous X-ray cocrystal structures are analyzed to identify the precise role of the methoxy group for many of the drugs and drug classes. Although the methoxy substituent can be considered as the hybridization of a hydroxy and a methyl group, the combination of these functionalities often results in unique effects that can amount to more than the sum of the individual parts.

The pyridazine heterocycle in molecular recognition and drug discovery

The pyridazine ring is endowed with unique physicochemical properties, characterized by weak basicity, a high dipole moment that subtends π-π stacking interactions and robust, dual hydrogen-bonding capacity that can be of importance in drug-target interactions. These properties contribute to unique applications in molecular recognition while the inherent polarity, low cytochrome P450 inhibitory effects and potential to reduce interaction of a molecule with the cardiac hERG potassium channel add additional value in drug discovery and development. The recent approvals of the gonadotropin-releasing hormone receptor antagonist relugolix (24) and the allosteric tyrosine kinase 2 inhibitor deucravacitinib (25) represent the first examples of FDA-approved drugs that incorporate a pyridazine ring. In this review, the properties of the pyridazine ring are summarized in comparison to the other azines and its potential in drug discovery is illustrated through vignettes that explore applications that take advantage of the inherent physicochemical properties as an approach to solving challenges associated with candidate optimization.

Graphical Abstract

Understanding the Cis-Trans Amide Bond Isomerization of N,N'-Diacylhydrazines to Develop Guidelines for A Priori Prediction of Their Most Stable Solution Conformers

N,N'-diacylhydrazines (R1CO-NR3-NR4-COR2) are a class of small molecules with a wide range of applications in chemistry and biology. They are structurally unique in the sense that their two amide groups are connected via a N-N single bond, and as a result, these molecules can exist in eight different isomeric forms. Four of these are amide isomers [trans-trans (t-t), trans-cis (t-c), cis-trans (c-t), and cis-cis (c-c)] arising from C-N bond restricted rotation. In addition, each of these amide isomers can exist in two different isomeric forms due to N-N bond restricted rotation, especially when R3 and R4 groups are relatively bigger. Herein, we have systematically investigated the conformations of 55 N,N'-diacylhydrazines using a combination of solution NMR spectroscopy, X-ray crystallography, and density functional theory calculations. Our data suggest that when the substituents R3 and R4 on the nitrogen atoms are both hydrogens. These molecules prefer twisted trans-trans (t-t) (>90%) geometries (H-N-C═O ∼ 180°), whereas the N-alkylated and N,N'-dialkylated molecules prefer twisted trans-cis (t-c) geometries. Herein, we have analyzed the stabilization of the various isomers of these molecules in light of steric and stereoelectronic effects. We provide a guideline to a priori predict the most stable conformers of the N,N'-diacylhydrazines just by examining their substituents (R1-R4).

Structure-aided optimization of non-nucleoside M. tuberculosis thymidylate kinase inhibitors

Mycobacterium tuberculosis thymidylate kinase (MtTMPK) has emerged as an attractive target for rational drug design. We recently investigated new families of non-nucleoside MtTMPK inhibitors in an effort to diversify MtTMPK inhibitor chemical space. We here report a new series of MtTMPK inhibitors by combining the Topliss scheme with rational drug design approaches, fueled by two co-crystal structures of MtTMPK in complex with developed inhibitors. These efforts furnished the most potent MtTMPK inhibitors in our assay, with two analogues displaying low micromolar MIC values against H37Rv Mtb. Prepared inhibitors address new sub-sites in the MtTMPK nucleotide binding pocket, thereby offering new insights into its druggability. We studied the role of efflux pumps as well as the impact of cell wall permeabilizers for selected compounds to potentially provide an explanation for the lack of correlation between potent enzyme inhibition and whole-cell activity.

Design and Identification of a GPR40 Full Agonist () Possessing a 2-Carbamoylphenyl Piperidine Moiety

GPR40/FFAR1 is a G-protein-coupled receptor expressed in pancreatic β-cells and enteroendocrine cells. GPR40 activation stimulates secretions of insulin and incretin, both of which are the pivotal regulators of glycemic control. Therefore, a GPR40 agonist is an attractive target for the treatment of type 2 diabetes mellitus. Using the reported biaryl derivative 1, we shifted the hydrophobic moiety to the terminal aryl ring and replaced the central aryl ring with piperidine, generating 2-(4,4-dimethylpentyl)phenyl piperidine 4a, which had improved potency for GPR40 and high lipophilicity. We replaced the hydrophobic moiety with N-alkyl-N-aryl benzamides to lower the lipophilicity and restrict the N-alkyl moieties to the presumed lipophilic pocket using the intramolecular π-π stacking of cis-preferential N-alkyl-N-aryl benzamide. Among these, orally available (3S)-3-cyclopropyl-3-(2-((1-(2-((2,2-dimethylpropyl)(6-methylpyridin-2-yl)carbamoyl)-5-methoxyphenyl)piperidin-4-yl)methoxy)pyridin-4-yl)propanoic acid (SCO-267) effectively stimulated insulin secretion and GLP-1 release and ameliorated glucose tolerance in diabetic rats via GPR40 full agonism.

Positively selected modifications in the pore of TbAQP2 allow pentamidine to enter Trypanosoma brucei

Mutations in the Trypanosoma brucei aquaporin AQP2 are associated with resistance to pentamidine and melarsoprol. We show that TbAQP2 but not TbAQP3 was positively selected for increased pore size from a common ancestor aquaporin. We demonstrate that TbAQP2’s unique architecture permits pentamidine permeation through its central pore and show how specific mutations in highly conserved motifs affect drug permeation. Introduction of key TbAQP2 amino acids into TbAQP3 renders the latter permeable to pentamidine. Molecular dynamics demonstrates that permeation by dicationic pentamidine is energetically favourable in TbAQP2, driven by the membrane potential, although aquaporins are normally strictly impermeable for ionic species. We also identify the structural determinants that make pentamidine a permeant although most other diamidine drugs are excluded. Our results have wide-ranging implications for optimising antitrypanosomal drugs and averting cross-resistance. Moreover, these new insights in aquaporin permeation may allow the pharmacological exploitation of other members of this ubiquitous gene family.

African sleeping sickness is a potentially deadly illness caused by the parasite Trypanosoma brucei. The disease is treatable, but many of the current treatments are old and are becoming increasingly ineffective. For instance, resistance is growing against pentamidine, a drug used in the early stages in the disease, as well as against melarsoprol, which is deployed when the infection has progressed to the brain. Usually, cases resistant to pentamidine are also resistant to melarsoprol, but it is still unclear why, as the drugs are chemically unrelated.

Studies have shown that changes in a water channel called aquaglyceroporin 2 (TbAQP2) contribute to drug resistance in African sleeping sickness; this suggests that it plays a role in allowing drugs to kill the parasite. This molecular ‘drain pipe’ extends through the surface of T. brucei, and should allow only water and a molecule called glycerol in and out of the cell. In particular, the channel should be too narrow to allow pentamidine or melarsoprol to pass through. One possibility is that, in T. brucei, the TbAQP2 channel is abnormally wide compared to other members of its family. Alternatively, pentamidine and melarsoprol may only bind to TbAQP2, and then ‘hitch a ride’ when the protein is taken into the parasite as part of the natural cycle of surface protein replacement.

Alghamdi et al. aimed to tease out these hypotheses. Computer models of the structure of the protein were paired with engineered changes in the key areas of the channel to show that, in T. brucei, TbAQP2 provides a much broader gateway into the cell than observed for similar proteins. In addition, genetic analysis showed that this version of TbAQP2 has been actively selected for during the evolution process of T. brucei. This suggests that the parasite somehow benefits from this wider aquaglyceroporin variant.

This is a new resistance mechanism, and it is possible that aquaglyceroporins are also larger than expected in other infectious microbes. The work by Alghamdi et al. therefore provides insight into how other germs may become resistant to drugs.

Photoswitchable ORG25543 Congener Enables Optical Control of Glycine Transporter 2

Glycine neurotransmission in the dorsal horn of the spinal cord plays a key role in regulating nociceptive signaling, but in chronic pain states reduced glycine neurotransmission is associated with the development of allodynia and hypersensitivity to painful stimuli. This suggests that restoration of glycine neurotransmission may be therapeutic for the treatment of chronic pain. Glycine transporter 2 inhibitors have been demonstrated to enhance glycine neurotransmission and provide relief from allodynia in rodent models of chronic pain. In recent years, photoswitchable compounds have been developed to provide the possibility of controlling the activity of target proteins using light. In this study we have developed a photoswitchable noncompetitive inhibitor of glycine transporter 2 that has different affinities for the transporter at 365 nm compared to 470 nm light.

Modulation of Conformational Preferences of Heteroaromatic Ethers and Amides through Protonation and Ionization: Charge Effect

Multiple approaches reveal the strong effects of a positive charge introduced by protonation or ionization on the conformation of o‐heteroaromatic ethers and amides. The ethers and amides containing an ortho‐N heteroatom are syn‐preferring while those containing an ortho‐O or ortho‐S heteroatom are mostly anti‐preferring. However, for all the monocyclic o‐heteroaromatic ethers and amides, the protonated ones are all anti‐preferring while the ionized ones are all syn‐preferring. Interestingly, although both the protonation and ionization introduce a positive charge, they have such different effects on molecular conformation, very informative for understanding the origin of conformational preferences. Detailed analysis shows that the population of the introduced positive charge dictates the conformational preferences via electrostatic and orbital interactions. Compared to ortho‐heteroatoms, meta‐heteroatoms have weaker effect on conformational preference. Achieved by complete inductive method, the regularity of conformational preferences and switching provides easy ways to modulate conformers (by pH or redox), and makes this kind of ether or amide bond a conformational hinge applicable to design of functional molecules (drugs and materials) and modulation of molecular biological processes.

Energy windows for computed compound conformers: covering artefacts or truly large reorganization energies?

The generation of 3D conformers of small molecules underpins most computational drug discovery. Thus, the conformer quality is critical and depends on their energetics. A key parameter is the empirical conformational energy window (ΔEw), since only conformers within ΔEw are retained. However, ΔEw values in use appear unrealistically large. We analyze the factors pertaining to the conformer energetics and ΔEw. We argue that more attention must be focused on the problem of collapsed low-energy conformers. That is due to artificial intramolecular stabilization and occurs even with continuum solvation. Consequently, the conformational energy of extended bioactive structures is artefactually increased, which inflates ΔEw. Thus, this Perspective highlights the issues arising from low-energy conformers and suggests improvements via empirical or physics-based strategies.

Discovery of Small Molecule Splicing Modulators of Survival Motor Neuron-2 (SMN2) for the Treatment of Spinal Muscular Atrophy (SMA)

Spinal muscular atrophy (SMA), a rare neuromuscular disorder, is the leading genetic cause of death in infants and toddlers. SMA is caused by the deletion or a loss of function mutation of the survival motor neuron 1 (SMN1) gene. In humans, a second closely related gene SMN2 exists; however it codes for a less stable SMN protein. In recent years, significant progress has been made toward disease modifying treatments for SMA by modulating SMN2 pre-mRNA splicing. Herein, we describe the discovery of LMI070/branaplam, a small molecule that stabilizes the interaction between the spliceosome and SMN2 pre-mRNA. Branaplam (1) originated from a high-throughput phenotypic screening hit, pyridazine 2, and evolved via multiparameter lead optimization. In a severe mouse SMA model, branaplam treatment increased full-length SMN RNA and protein levels, and extended survival. Currently, branaplam is in clinical studies for SMA.

Discovery and Lead Optimization of Atropisomer D1 Agonists with Reduced Desensitization

The discovery of D1 subtype-selective agonists with drug-like properties has been an enduring challenge for the greater part of 40 years. All known D1-selective agonists are catecholamines that bring about receptor desensitization and undergo rapid metabolism, thus limiting their utility as a therapeutic for chronic illness such as schizophrenia and Parkinson's disease. Our high-throughput screening efforts on D1 yielded a single non-catecholamine hit PF-4211 (6) that was developed into a series of potent D1 receptor agonist leads with high oral bioavailability and CNS penetration. An important structural feature of this series is the locked biaryl ring system resulting in atropisomerism. Disclosed herein is a summary of our hit-to-lead efforts on this series of D1 activators culminating in the discovery of atropisomer 31 (PF-06256142), a potent and selective orthosteric agonist of the D1 receptor that has reduced receptor desensitization relative to dopamine and other catechol-containing agonists.

Rapid assessment of conformational preferences in biaryl and aryl carbonyl fragments

The ability to rapidly assess the preferred conformation of key fragments in a structure “by visual inspection” is a very useful starting point in the process of drug design. With the ability to do so, one could address questions like: “How could we avoid planarity in a molecule?”, “Will a molecule change its conformational preference if we make it more or less basic?” or “How does this electronic repulsion affect the conformational preference in the system?” in timely fashion. In this paper, we describe how the conformational energy profile (CEP, plot of energy as a function of dihedral bond angle) of a fragment can be interpreted through the understanding the interplay between resonance stabilization, steric effects and electrostatic interactions. Fifty-nine biaryl and aryl carbonyl fragments present in oral drugs or which are close derivatives thereof were selected. Calculation of their CEPs using ab initio methodology allowed us to conclude the relative importance of these factors in the conformational preference of these fragments as follows: “steric repulsion > lone pair—lone pair repulsion > lone pair—fluorine repulsion > resonance stabilization” and to formulate “rules of thumb” that the practicing medicinal/organic chemist can apply when analysing molecules that contain these fragments.

Conformational preferences and isomerization upon excitation/ionization of 2-methoxypyridine and 2-N-methylaminopyridine

Conformers from the rotations of the methyl group and the methoxy or methylamino group, namely staggered (s)/eclipsed (e)-cis/trans 2-methoxypyridine (2MOP) and 2-N-methylaminopyridine (2NMP), are studied using theoretical calculations in combination with one-color resonance-enhanced two-photon ionization (1C-R2PI) and mass-analyzed threshold ionization (MATI) spectroscopies. The calculations predict that, for cis 2MOP, trans 2MOP and trans 2NMP, only the s conformers are stable in the S₀, S₁ and D₀ states. However, for cis 2NMP, the stable conformer is staggered in the S₀ state but eclipsed in the S₁ and D₀ states, indicating an isomerization upon the excitation or ionization from the S₀ state. This is experimentally supported by the 1C-R2PI and MATI spectra of 2NMP. Due to the relative instability, the number density of trans 2MOP is too low in the sample to be detected. All the bands in the 1C-R2PI and MATI spectra of 2MOP are assigned to s-cis 2MOP. The energy differences between cis and trans conformers are derived from excitation and ionization energies, indicating another conformational isomerization: stable trans 2NMP in the S₀ and S₁ states but stable cis 2NMP in the D₀ state. For 2MOP, the so-called syn preference previously found for the S₀ state is also observed in the S₁ and D₀ states. The conformational preference and isomerization are discussed with natural bond orbital calculations and reduced density gradient analysis. For 2MOP, the syn preferences are mainly caused by the exchange repulsion among several σ-orbitals of the OCH₃ group and the pyridine ring. While the relative stabilities of the s and e conformers of cis 2MOP and cis 2NMP are simultaneously influenced by steric repulsion and orbital interactions.

A Series of Lithium Pyridyl Phenolate Complexes with a Pendant Pyridyl Group for Electron-Injection Layers in Organic Light-Emitting Devices

We report a new series of lithium pyridyl phenolate complexes with a pendant pyridyl group, Li2BPP, Li3BPP, and Li4BPP, in which the pendant pyridines are substituted at the 2-, 3-, and 4-positions, respectively. The most important difference between these complexes is their molecular planarity; Li3BPP and Li4BPP adopt twisted bipyridine structures, whereas Li2BPP adopts a planar structure owing to the steric hindrance and chelating effect of bipyridine on the Li core. The planar structure leads to crystallization through π-π stacking interactions, and the small differences in the molecular structures of the pendant pyridine rings cause drastic differences in the physical properties of thin solid films of these complexes. We applied these complexes as electron-injection layers (EILs) in Ir(ppy)₃-based organic light-emitting devices. When thin EILs were used, Li3BPP and Li4BPP afforded lower driving voltages than Li2BPP; the order of the driving voltages followed the order of their electron affinity values. Moreover, the dependence of driving voltage on the EIL thickness was investigated for each complex. Among the three LiBPP derivatives, Li2BPP-based devices showed almost negligible EIL thickness dependence, which may be attributable to the high crystallinity of Li2BPP. All LiBPP-based devices also showed higher stability than conventional 8-quinolinolato lithium-based devices.

Ligand-Enabled Arylation of γ-C-H Bonds

Pd(II) -catalyzed arylation of γ-C(sp(3) )-H bonds of aliphatic acid-derived amides was developed by using quinoline-based ligands. Various γ-aryl-α-amino acids were prepared from natural amino acids using this method. The influence of ligand structure on reactivity was also systematically investigated.

Discovery of 1-{(3R,4R)-3-[({5-Chloro-2-[(1-methyl-1H-pyrazol-4-yl)amino]-7H-pyrrolo[2,3-d]pyrimidin-4-yl}oxy)methyl]-4-methoxypyrrolidin-1-yl}prop-2-en-1-one (PF-06459988), a Potent, WT Sparing, Irreversible Inhibitor of T790M-Containing EGFR Mutants

First generation EGFR TKIs (gefitinib, erlotinib) provide significant clinical benefit for NSCLC cancer patients with oncogenic EGFR mutations. Ultimately, these patients' disease progresses, often driven by a second-site mutation in the EGFR kinase domain (T790M). Another liability of the first generation drugs is severe adverse events driven by inhibition of WT EGFR. As such, our goal was to develop a highly potent irreversible inhibitor with the largest selectivity ratio between the drug-resistant double mutants (L858R/T790M, Del/T790M) and WT EGFR. A unique approach to develop covalent inhibitors, optimization of reversible binding affinity, served as a cornerstone of this effort. PF-06459988 was discovered as a novel, third generation irreversible inhibitor, which demonstrates (i) high potency and specificity to the T790M-containing double mutant EGFRs, (ii) minimal intrinsic chemical reactivity of the electrophilic warhead, (iii) greatly reduced proteome reactivity relative to earlier irreversible EGFR inhibitors, and (iv) minimal activity against WT EGFR.

Effect of water solvation on the lipophilicity of isomeric pyrimidine-carboxamides

Incorporation of nitrogen is a common medicinal chemistry tactic to reduce logD values. Neighboring group participation influences logD, so the results are isomer dependent. The logD and logP differences observed between isomeric pyrimidines 1, 2 and 3 presumably result when the carbonyl or ether lone pairs are in close proximity to a heterocyclic nitrogen lone pair, recruiting water to bridge between the electron rich atoms. Various lipophilicity calculators did not discriminate between 1 (logD=2.6) and 3 (logD=1.0), but solvation energies using Poisson-Boltzmann and 3D-RISM methods rationalize the observed differences in lipophilicity among pyrimidine carboxamide isomers.

Stereoelectronic effects dictate molecular conformation and biological function of heterocyclic amides

Heterocycles adjacent to amides can have important influences on molecular conformation due to stereoelectronic effects exerted by the heteroatom. This was shown for imidazole- and thiazole-amides by comparing low energy conformations (ab initio MP2 and DFT calculations), charge distribution, dipole moments, and known crystal structures which support a general principle. Switching a heteroatom from nitrogen to sulfur altered the amide conformation, producing different three-dimensional electrostatic surfaces. Differences were attributed to different dipole and orbital alignments and spectacularly translated into opposing agonist vs antagonist functions in modulating a G-protein coupled receptor for inflammatory protein complement C3a on human macrophages. Influences of the heteroatom were confirmed by locking the amide conformation using fused bicyclic rings. These findings show that stereoelectronic effects of heterocycles modulate molecular conformation and can impart strikingly different biological properties.

Optimizing the Physicochemical Properties of Raf/MEK Inhibitors by Nitrogen Scanning

Substituting a carbon atom with a nitrogen atom (nitrogen substitution) on an aromatic ring in our leads 11a and 13g by applying nitrogen scanning afforded a set of compounds that improved not only the solubility but also the metabolic stability. The impact after nitrogen substitution on interactions between a derivative and its on- and off-target proteins (Raf/MEK, CYPs, and hERG channel) was also detected, most of them contributing to weaker interactions. After identifying the positions that kept inhibitory activity on HCT116 cell growth and Raf/MEK, compound 1 (CH5126766/RO5126766) was selected as a clinical compound. A phase I clinical trial is ongoing for solid cancers.

Ligand-enabled γ-C-H olefination and carbonylation: construction of β-quaternary carbon centers

Monoselective γ-C–H olefination and carbonylation of aliphatic acids has been accomplished by using a combination of a quinoline-based ligand and a weakly coordinating amide directing group. The reaction provides a new route for constructing richly functionalized all-carbon quaternary carbon centers at the β-position of aliphatic acids.

The Influence of Bioisosteres in Drug Design: Tactical Applications to Address Developability Problems

The application of bioisosteres in drug discovery is a well-established design concept that has demonstrated utility as an approach to solving a range of problems that affect candidate optimization, progression, and durability. In this chapter, the application of isosteric substitution is explored in a fashion that focuses on the development of practical solutions to problems that are encountered in typical optimization campaigns. The role of bioisosteres to affect intrinsic potency and selectivity, influence conformation, solve problems associated with drug developability, including P-glycoprotein recognition, modulating basicity, solubility, and lipophilicity, and to address issues associated with metabolism and toxicity is used as the underlying theme to capture a spectrum of creative applications of structural emulation in the design of drug candidates.

Torsion angle preferences in druglike chemical space: a comprehensive guide

Crystal structure databases offer ample opportunities to derive small molecule conformation preferences, but the derived knowledge is not systematically applied in drug discovery research. We address this gap by a comprehensive and extendable expert system enabling quick assessment of the probability of a given conformation to occur. It is based on a hierarchical system of torsion patterns that cover a large part of druglike chemical space. Each torsion pattern has associated frequency histograms generated from CSD and PDB data and, derived from the histograms, traffic-light rules for frequently observed, rare, and highly unlikely torsion ranges. Structures imported into the corresponding software are annotated according to these rules. We present the concept behind the tree of torsion patterns, the design of an intuitive user interface for the management and usage of the torsion library, and we illustrate how the system helps analyze and understand conformation properties of substructures widely used in medicinal chemistry.

Inhibitors of human immunodeficiency virus type 1 (HIV-1) attachment. 12. Structure-activity relationships associated with 4-fluoro-6-azaindole derivatives leading to the identification of 1-(4-benzoylpiperazin-1-yl)-2-(4-fluoro-7-[1,2,3]triazol-1-yl-1h-pyrrolo[2,3-c]pyridin-3-yl)ethane-1,2-dione (BMS-585248)

A series of highly potent HIV-1 attachment inhibitors with 4-fluoro-6-azaindole core heterocycles that target the viral envelope protein gp120 has been prepared. Substitution in the 7-position of the azaindole core with amides (12a,b), C-linked heterocycles (12c-l), and N-linked heterocycles (12m-u) provided compounds with subnanomolar potency in a pseudotype infectivity assay and good pharmacokinetic profiles in vivo. A predictive model was developed from the initial SAR in which the potency of the analogues correlated with the ability of the substituent in the 7-position of the azaindole to adopt a coplanar conformation by either forming internal hydrogen bonds or avoiding repulsive substitution patterns. 1-(4-Benzoylpiperazin-1-yl)-2-(4-fluoro-7-[1,2,3]triazol-1-yl-1H-pyrrolo[2,3-c]pyridin-3-yl)ethane-1,2-dione (BMS-585248, 12m) exhibited much improved in vitro potency and pharmacokinetic properties than the previous clinical candidate BMS-488043 (1). The predicted low clearance in humans, modest protein binding, and good potency in the presence of 40% human serum for 12m led to its selection for human clinical studies.

Total synthesis of the marine metabolite (±)-polysiphenol via highly regioselective intramolecular oxidative coupling

(±)-Polysiphenol (1), an atropisomerically stable 4,5-dibrominated 9,10-dihydrophenanthrene from Polysiphonia ferulacea, was prepared by a biomimetically inspired highly regioselective intramolecular oxidative coupling of a dibrominated dihydrostilbene. The installation of the two bromine atoms prior to oxidative coupling prevents further oxidation to a planar aromatized phenanthrene. By this strategy, the synthesis of (±)-polysiphenol was achieved in four steps in 70% overall yield. Synthesis of the naturally occurring 5,5'-(ethane-1,2-diyl)bis(3-bromobenzene-1,2-diol) (2) (the likely biogenetic precursor of polysiphenol) and 5,5'-(ethane-1,2-diyl)bis(3,4,6-tribromobenzene-1,2-diol) (9) are also reported. The origins of the regioselectivity in the oxidative coupling are explored.

Syntheses and structures of isomeric diaminotriazinyl-substituted 2,2'-bipyridines and 1,10-phenanthrolines

Isomeric 2,2'-bipyridines 4a-6a and 1,10-phenanthrolines 7a-9a with two diaminotriazinyl (DAT) substituents were synthesized to explore their dual ability to direct association by the chelation of metals and the characteristic hydrogen bonding of DAT groups. Crystals of compounds 4a-6a and 7a-9a were grown under diverse conditions, and their structures were solved by X-ray crystallography. Analysis revealed multiple shared features analogous to those observed in the structures of simpler DAT-substituted pyridines 1-3. For example, the bipyridines and phenanthrolines favor flattened conformations except in the cases of compounds 8a and 9a, where the patterns of substitution prevent the DAT groups from lying in the plane of the phenanthroline core. As expected, the DAT groups form approximately coplanar hydrogen bonds according to standard motifs I-III, which play a key role in directing molecular organization. However, the structures of simple pyridines 1-3, which favor efficiently packed chains and sheets, differ predictably from those of bipyridines 4a-6a and phenanthrolines 7a-9a in two ways: (1) The larger number of DAT groups in compounds 4a-9a typically leads to complex three-dimensional networks held together by a larger number of hydrogen bonds per molecule, and (2) the need to respect multiple directional interactions prevents compounds 4a-9a from forming closely packed structures, and significant quantities of guests are included. Together, these observations confirm the effectiveness of incorporating special groups such as DAT within more complex molecular structures to control association according to reliable patterns. Bipyridines 4a-6a and phenanthrolines 7a-9a promise to be particularly rich sources of new supramolecular chemistry because they have well-defined molecular topologies and a dual ability to direct association by chelating metals and by engaging in multiple hydrogen bonds according to reliable patterns.

Ring transformation of unsaturated N-bridgehead fused pyrimidin-4(3H)-ones: role of repulsive electrostatic nonbonded interaction

Thermal ring transformation ability of unsaturated N-bridgehead fused pyrimidin-4(3H)-ones A is governed by both the steric and the electrostatic interactions between the oxygen of the carbonyl group and the substituent in the peri position.