Central Ring System Research Articles

Database of 4 Million Medicinal Chemistry-Relevant Ring Systems.

Central ring systems are the most important part of bioactive molecules. They determine molecule shape, keep substituents in their proper positions, and also influence global molecular properties. In the present study, a database of 4 million medicinal chemistry-relevant ring systems has been created, not by crude random enumeration but by applying a set of rules derived by analyzing rings present in bioactive molecules. The aromatic properties and tautomer stability of generated rings have also been considered to ensure that the rings in the database are stable and chemically reasonable. 99.2% of these rings are novel and not included in molecules in the ChEMBL or PubChem databases. This large database of ring systems has been created with the goal to provide support for bioisosteric design and scaffold hopping as well as to be used in generative chemistry applications. The complete set of created rings is available for download in the SMILES format from https://peter-ertl.com/molecular/data/.

Modified norcyanines enable ratiometric pH imaging beyond 1000 nm

Activatable fluorophores with emission beyond 1000 nm have the potential to enable high contrast imaging in complex in vivo settings. However, there are few scaffolds that can be applied to this challenge. Here we detail the synthesis and evaluation of benzo[c,d]indole-substituted norcyanines that enable pH responsive fluorescence imaging in the long wavelength (>1150 nm) range. A key component of our molecular design is the installation of a hydrophilic substituted quaternary amine in the central dihydropyridine ring system. A compound with a C4′-phenyl substituent, but not the C4′-protio homologue, exhibits absorbance maxima of 740 nm and 1130 nm in basic and acidic media, respectively, with evidence of J-aggregate-like properties. These two distinct absorbances enabled ratiometric imaging of probe internalization in a tumor model. Overall, these studies provide a new class of activatable long-wavelength responsive fluorophores with promising photophysical properties.

Crystal structure and Hirshfeld surface analysis of (RS)-3-hy-droxy-2-{[(3aRS,6RS,7aRS)-2-(4-methyl-phenyl-sulfon-yl)-2,3,3a,6,7,7a-hexa-hydro-3a,6-ep-oxy-1H-isoindol-6-yl]meth-yl}isoindolin-1-one.

The title compound, C24H24N2O5S, crystallizes with two independent mol-ecules (A and B) in the asymmetric unit. In the central ring systems of both mol-ecules, the tetra-hydro-furan rings adopt envelope conformations, the pyrrolidine rings adopt a twisted-envelope conformation and the six-membered ring is in a boat conformation. In mol-ecules A and B, the nine-membered groups attached to the central ring system are essentially planar (r.m.s. deviations of 0.002 and 0.003 Å, respectively). They form dihedral angles of 64.97 (9) and 56.06 (10)°, respectively, with the phenyl rings. In the crystal, strong inter-molecular O-H⋯O hydrogen bonds and weak inter-molecular C-H⋯O contacts link the mol-ecules, forming a three-dimensional network. In addition weak π-π stacking inter-actions [centroid-to centroid distance = 3.7124 (13) Å] between the pyrrolidine rings of the nine-membered groups of A mol-ecules are observed. Hirshfeld surface analysis and two-dimensional fingerprint plots were used to qu-antify the inter-molecular inter-actions present in the crystal, indicating that the environments of the two mol-ecules are very similar. The most important contributions for the crystal packing are from H⋯H (55.8% for mol-ecule A and 53.5% for mol-ecule B), O⋯H/H⋯O (24.5% for mol-ecule A and 26.3% for mol-ecule B) and C⋯H/H⋯C (12.6% for mol-ecule A and 15.7% for mol-ecule B) inter-actions.

Bi- and poly(carbyne) functionalised polycyclic aromatics

Complexes where a central polyaromatic ring system is substituted with one to four tungsten carbynes have been prepared by Pd0/AuI-mediated coupling between a tungsten stannylcarbyne and aryl halides. This strategy enables preparation of complexes with one to three carbynes substituted onto a single phenyl ring, the first anthracenyl mono- and bis-carbynes, and a tetra(carbyne) complex constructed about a central pyrene ring system.

Aromaticity and Electron Density of Hypericin.

The influence of the substituents on the geometry of the central ring system of hypericin has been analyzed. Substitution that causes flattening of the hypericin central rings is connected with introducing the aromatic character of the empty rings. All the hypericin rings have an aromatic character illustrated by the Harmonic Oscillator Measure of Aromaticity (HOMA), Nucleus Independent Chemical Shift (NICS), Fluctuation Index (FLU), and Ellipticity Index (EL) indices. Quantum Theory of Atoms in Molecules (QTAIM) and Natural Bond Orbital (NBO) analyses performed on 7,14-dihydrophenanthro[1,10,9,8-opqra]perylene, its substituted analogues, and hypericin show an influence of this substitution on electron density of the central rings.

Novel N-heterocyclic carbene silver(I) complexes: Synthesis, structural characterization, and anticancer activity

In this study, we synthesized four novel unsymmetrically substituted NHC ligands (1a-d) and their Ag(I) complexes (2a-d). All new compounds were characterized using elemental analysis, FT-IR, 1H NMR, and 13C NMR spectroscopy and X-ray crystallography. The molecular structure of complex 2d was elucidated through single crystal X-ray diffraction analyses. Single crystal structural studies for complex 2d show that the benzene rings (C9–C14) and the central benzimidazole ring system make dihedral angles of 85.65(11)°. The Ag–Cl and Ag–C single bond lengths are 2.3553(7) and 2.096(2) Å, respectively. The C–Ag–Cl bond angle is 168.27(7)°. Both salts and complexes were tested for their anti-cancer potential against three human cancer cell lines (DU-145, MCF-7, and MDA-MB-231) and non-cancer cells adipose from mouse (L-929) for 24 h, 48 h and 72 h using the MTT assays. However, the Ag(I)–NHC complexes (2a-d) showed a dose and time-dependent cytotoxic activity against all cell lines. MDA-MB-231 human breast carcinoma cells were the most sensitive to the Ag(I)–NHC complex displaying IC50 lower than 1 μM all time points. Further, the IC50s for Ag(I)–NHC were higher in non-cancer cells, suggesting that complexes possessed noteworthy selectivity for human cancer cells.

Synthesis, characterization and anticancer activity of allyl substituted N-Heterocyclic carbene silver(I) complexes

Metal N-heterocyclic carbene (NHC) complexes have attracted considerable attention in biological fields for their potential applications in cancer and antimicrobial therapies. In this study, four new benzimidazole-based N-heterocyclic carbene salts (1a-d) and their silver (I) complexes (2a-d) were synthesized. All new compounds were characterized by elemental analysis, FT-IR, 1H NMR and, 13C NMR spectroscopy. Additionally, single crystal structural studies for complex 2d show that the benzene rings (C9C14) and the central benzimidazole ring system make dihedral angles of 83.58(13)°. The AgCl and AgC single bond lengths are 2.3267(8) and 2.087(3) Å, respectively. The CAgCl bond angle is 175.20(7)°. The prop-1-ene moiety attached at the second N-atom of benzimidazole is disordered at two set of sites with an occupancy ratio of 0.592(6): 0.408(6). There is one intramolecular hydrogen bond interaction between C22A-H22A … N2. The salts and Ag-complexes were further evaluated for their in vitro anticancer activities against DU-145 human prostate cancer cells, MCF-7, MDA-MB-231 human breast cancer cells and L-929 non-cancer cell for 24 h, 48 h and 72 h using the MTT assay. The Ag(I)NHC complexes (2a-d) showed a dose and time-dependent cytotoxic activity against all cell lines. The IC50s for all Ag(I)NHC complexes lower than 1 μM for 72 h time points on cancer cells. The results showed that complex 2d exhibited the highest activity against all cancer cell lines studied. Further, the complexes had relatively higher cytotoxicity to cancer cells than to non-cancer cell lines.

π-Extension of Strained Benzenoid Macrocycles Using the Scholl Reaction

A series of bent p-terphenyl-containing macrocycles have been synthesized and then regioselectively brominated, arylated, and subsequently subjected to a Scholl-based cyclodehydrogenation reaction. Shortening the alkyloxy bridging unit of these macrocycles increases the bend in the p-terphenyl unit, as well as the strain energy (SE) of the central para-phenylene ring system. For the first time, incremental increases in SE of the macrocyclic structure of this class of benzenoid compounds have been investigated in the context of π-extension to strained polycyclic aromatic hydrocarbon systems using the Scholl reaction.

Carbon quantum dots derived by direct carbonization of carbonaceous microcrystals in mesophase pitch.

Aggregation of the central aromatic ring system of asphaltene molecules due to π-π interaction can lead to the formation of carbon quantum dots (CQDs). However, to date, such a roadmap has not been demonstrated. Here, we present a simple approach to the synthesis of CQDs by direct carbonization of dispersed carbonaceous microcrystals in mesophase pitch. The size of the as-prepared CQDs is modulated by adjusting the nucleation temperature for mesophase formation. Due to the oxygen-free character, the CQDs exhibit excitation-independent fluorescent behavior with a quantum yield up to 87%. The CQDs were successfully applied to fluorescent detection of Fe3+ ions with good specificity and sensitivity. Our results not only provide a scalable production of CQDs at low cost, but also give valuable clues to understand the solidification of asphaltene at nanoscale.

3-(2,4-Difluorophenyl)-1-(pyridin-4-yl)benzo[4,5]imidazo[1,2-d][1,2,4]triazin-4(3H)-one

In the title compound, C20H11F2N5O, the central 13-membered ring system (r.m.s. deviation = 0.028 Å) makes a dihedral angle of 53.13 (7)° with the difluorophenyl ring and 79.98 (7)° with the pyridine ring. The crystal packing features aromatic π–π interactions between the 13-membered rings [shortest distance between ring centroids = 3.5682 (8) Å].

5-Benzoyl-2-(5-bromo-1H-indol-3-yl)-4-(4-methoxyphenyl)-1H-pyrrole-3-carbonitrile

In the title compound, C27H18BrN3O, the indole and central pyrrole ring systems are inclined to one another by 13.15 (15)°. The carbonitrile group is almost coplanar with its attached pyrrole ring, the C[triple-bond]N bond making a dihedral angle of 1.9 (2)° with the ring plane. The 4-methoxybenzene ring and the benzoyl ring are inclined to the central pyrrole ring by 55.1 (2) and 51.5 (2)°, respectively. The dihedral angle between these two benzene rings is 37.68 (17)°. In the crystal, molecules are linked by pairs of N—H...N hydrogen bonds, forming inversion dimers with anR22(16) ring motif. The dimers are linked by offset π–π interactions [intercentroid distance = 3.614 (2) Å], which leads to the formation of chains propagating in the [010] direction.

Crystal structure of 1,3-bis-{[4-(acetyl-sulfanyl)phenyl]ethynyl}azulene.

In the title compound, C30H20O2S2, the dihedral angles between the central azulene ring system (r.m.s. deviation = 0.039 Å) and the pendant benzene rings are 28.96 (7) and 55.15 (7)°. The dihedral angles between the benzene rings and their attached acetyl­sulfanyl groups are 59.60 (10) and 84.79 (10)°. The expected π–π stacking inter­actions are not observed in the crystal structure; instead, the packing features C—H⋯O hydrogen bonds, which link the mol­ecules into C(12) [010] chains, which are supported by weak C—H⋯π contacts.

13C NMR spectroscopy of heterocycles: 3,5-diaryl-4-bromoisoxazoles

Abstract A series of 3,5-diarylisoxazoles (1–9) underwent reaction with N-bromosuccinimide in acetic acid to yield the corresponding 3.5-diaryl-4-bromoisoxazoles (1Br–9Br) in low to moderate yield. The X-ray structure of 3-(4-chlorophenyl)-5-phenyl-4-bromoisoxazole showed torsion angles of ~40° and ~36° between the 3- and 5-aryl groups and the central ring system, respectively. Molecular modeling studies predicted the 3,5-phenylisoxazole ring system to be essentially coplanar and the 3,5-diphenyl groups of the 4-bromoisoxazole derivative to be twisted with torsional angles of 50° and 37°, respectively. Carbon-13 nuclear magnetic resonance (13C NMR) data of the 3,5-diaryl-4-bromoisoxazoles were obtained in dimethyl sulfoxide-d 6 (DMSO-d 6) at 50°C. Plots of the C4 chemical shift data for isoxazoles (1–9) vs. those for 4-bromoisoxazoles (1Br–9Br) showed a good linear correlation (r 2 = 0.974) with a slope of 0.96. Substitution on the 3-aryl group had essentially no effect on the chemical shift for C4 of the 4-bromoisoxazole, whereas that on the 5-aryl group showed an excellent correlation with σ+ values. Despite the predicted torsion angle differences, distal transmission of substituent effects in the 4-bromo ring system was essentially analogous to that in the planar 3,5-diarylisoxazoles.

Crystal structure of 8-[7,8-bis-(4-chloro-benzo-yl)-7H-cyclo-penta-[a]ace-naphthylen-9-yl]naphthalene-1-carb-oxy-lic acid.

The title compound, C40H22Cl2O4, was formed by a Michael-Aldol domino reaction sequence, which coupled acenaphthene-quinone with 4-chloro-aceto-phenone in the presence of KOH in methanol. The dihedral angles between the central cyclo-penta-[a]ace-naphthyl-ene fused-ring system (r.m.s. deviation = 0.066 Å) and the 4-chloro-benzoyl rings are 62.25 (10) and 70.19 (10)°. The dihedral angle between the central ring system and the naphthoic acid grouping is 62.46 (7)°. This twisting of the pendant rings facilitates the formation of an intra-molecular aromatic π-π stacking inter-action between the 4-chloro-benzoyl and naphthoic acid rings, with centroid-centroid distances of 3.4533 (16) and 3.5311 (16) Å, and a C-H⋯π inter-action between one of the H atoms of the central moiety and the 4-chloro-benzoyl ring with an H⋯π distance of 2.57 Å. In the crystal, carb-oxy-lic acid inversion dimers generate R 2 (2)(8) loops. The dimers are linked by weak C-H⋯O and C-H⋯Cl hydrogen bonds and C-H⋯π inter-actions, generating a three-dimensional architecture.

Crystal structure of 1-acetyl-3-(4-methylphenyl)-5-phenyl-4,5-dihydro-1H-pyrazole

In the title compound, C18H18N2O, the whole molecule is not planar but the phenyl ring systems are planar individually. The central pyrazole ring system is twisted with puckering parameters Q = 0.1610(18) A and φ = 82.2(6)°. The crystallographic structure is stabilized by C-H⋯N type intramolecular hydrogen bond, generating ring motif R(5).

Crystal structure of N,N'-bis-[(pyridin-4-yl)meth-yl]naphthalene di-imide.

In the centrosymmetric title compound, C26H16N4O4 {systematic name: 6,13-bis­[(pyridin-4-yl)meth­yl]-6,13-di­aza­tetra­cyclo­[6.6.2.04,16011,15]hexa­deca-1,3,8,10,15-pantaene-5,7,12,14-tetrone}, the central ring system is essentially planar [maximum deviation = 0.0234 (8) Å] and approximately perpendicular to the terminal pyridine ring [dihedral angle = 84.38 (3)°]. The mol­ecules displays a trans conformation with the (pyridin-4-yl)methyl groups on both sides of the central naphthalene di­imide plane. In the crystal, mol­ecules are linked by π–π stacking between parallel pyridine rings [centroid–centroid distances = 3.7014 (8) and 3.8553 (8) Å] and weak C—H⋯O hydrogen bonds, forming a three-dimensional supra­molecular architecture.

Structural and antivirial studies of dipetalactone and its methyl derivative

Dipetalactone (6,6,10,10-tetramethyl-6H,10H-dipyranocoumarin) and its C4-methyl derivative have been synthesized and structurally studied. The structures of these compounds, explored on the basis of 1D and 2D NMR techniques in solution and the DFT/B3LYP calculations for the single molecule of dipetalactone, are in good agreement with those found in the crystals. In the tetracyclic dipetalactones the central coumarin ring systems are nearly planar and the pyran rings adopt a distorted sofa conformation.Both compounds crystallize with two symmetry independent molecules, A and B. The π-stacking is the main force stabilizing the pairs of centrosymmetric dimers, A⋅A and B⋅B. These dimers interact via the intermolecular CH⋯O and CH⋯π hydrogen bonds forming three-dimensional supramolecular frameworks which are nearly isostructural. The MP2 calculations reveal that the dimers of dipetalactone only slightly distort during the crystal formation as compared with those in the gas phase. The energy increase upon such a distortion was estimated as ca. 4kcalmol−1. In addition, the binding energy for the dimer was found to be ca. 20kcalmol−1.Dipetalactone and its methyl derivative were examined for cytotoxicity as well as anti-HIV activity.

Liquid Crystalline Behavior of Binary Mixtures of Structurally Dissimilar Mesogens and Nonmesogens

We have studied eight binary systems comprising three enantiotropic nematogens, namely 4-(4′-n-butyloxybenzoyloxy)phenylazo-4″-fluorobenzene, 4-(4′-n-butyloxybenzo yloxy)benzylidene-4″-fluoro aniline, and 4-(4′-n-heptyloxybenzoyloxy)phenylazo-4″-fl uorobenzene; a monotropic nematogen, viz. 4-(4′-n-dodecyloxybenzoyloxy)napthylazo-4″-fluorobenzene; and three nonmesogens, viz. 4-(4′-n-butyloxy benzoyloxy)benzalde hyde, 4-methoxybenzylidene-4′-chloroaniline, and 4-methoxybenzylidene-4′-toluidine. The central linkage, terminal group, and central ring system of the components have been varied systematically and the effect of these variations has been evaluated on the liquid crystalline properties of the binary mixtures. The mixed mesomorphic properties of these systems are discussed on the basis of their phase diagrams.

{2,7-Diethoxy-8-[(naphthalen-1-yl)carbonyl]naphthalen-1-yl}(naphthalen-1-yl)methanone

In the title compound, C36H28O4, the 1-naphthoyl groups at the 1- and 8-positions of the central 2,7-dieth­oxy­naphthalene ring system are aligned almost anti­parallel and make a dihedral angle of 76.59 (4)°. The dihedral angles between the central 2,7-dieth­oxy­naphthalene ring system and the terminal naphthalene ring systems are 86.48 (4) and 83.97 (4)°. In the crystal, C—H⋯π inter­actions between the central naphthalene ring systems and the naphthoyl groups are observed along the a axis, with the mol­ecules forming a columnar structure. The columns are linked into chains parallel to the b axis by C—H⋯O inter­actions.

Differential Furanose Selection in the Active Sites of Archaeal DNA Polymerases Probed by Fixed-Conformation Nucleotide Analogues

DNA polymerases select for the incorporation of deoxyribonucleotide triphosphates (dNTPs) using amino acid side-chains that act as a "steric-gate" to bar improper incorporation of rNTPs. An additional factor in the selection of nucleotide substrates resides in the preferred geometry for the furanose moiety of the incoming nucleotide triphosphate. We have probed the role of sugar geometry during nucleotide selection by model DNA polymerases from Sulfolobus solfataricus using fixed conformation nucleotide analogues. North-methanocarba-dATP (N-MC-dATP) locks the central ring into a RNA-type (C2'-exo, North) conformation near a C3'-endo pucker, and South-methanocarba-dATP (S-MC-dATP) locks the central ring system into a (C3'-exo, South) conformation near a C2'-endo pucker. Dpo4 preferentially inserts N-MC-dATP and in the crystal structure of Dpo4 in complex with N-MC-dAMP, the nucleotide analogue superimposes almost perfectly with Dpo4 bound to unmodified dATP. Biochemical assays indicate that the S. solfataricus B-family DNA polymerase Dpo1 can insert and extend from both N-MC-dATP and S-MC-dATP. In this respect, Dpo1 is unexpectedly more tolerant of substrate conformation than Dpo4. The crystal structure of Dpo4 bound to S-MC-dADP shows that poor incorporation of the Southern pucker by the Y-family polymerase results from a hydrogen bond between the 3'-OH group of the nucleotide analogue and the OH group of the steric gate residue, Tyr12, shifting the S-MC-dADP molecule away from the dNTP binding pocket and distorting the base pair at the primer-template junction. These results provide insights into substrate specificity of DNA polymerases, as well as molecular mechanisms that act as a barrier against insertion of rNTPs.