Synthesis of new sandwich intermediate sitting-atop complexes between meso-tetraarylporphyrins and germanium(IV) chloride

GeCl₄ and meso-tetraarylporphyrins (H₂TAPP) react in chloroform solvent for formation sandwich intermediate sitting-atop (i-SAT) complexes, [GeCl₄(H₂TAP)₂]. The various spectral data (¹H NMR, ¹³C NMR, UV-Vis, FT-IR and elemental analysis) were used for characterization of the i-SAT complexes. In the sandwich complexes, the pyrrole rings of two porphyrin macrocycles are tilted up and down and act as electron donors by lone pairs of pyrrolic nitrogens to germanium center of GeCl₄. The spectral results of ¹H NMR and FT-IR showed that in the i-SAT complexes, the hydrogen atoms of two pyrrolic nitrogens remained still on the porphyrin macrocycles.     

Interaction between aromatic antibiotics and vitamins: 1H NMR study of heteroassociation of nicotinamide and anthracycline antitumor antibiotics

The interaction of the anthracycline antitumor antibotics daunomycin and novatrone with the vitamin nicotinamide has been studied by one-and two-dimensional ¹H NMR (500 MHz). Due to significant differences between the structures of the chromophores of interacting molecules, a two-site heteroassociation model has been developed, which implies the binding of one or several nicotinamide molecules to the chromophore of the antibiotic. The structural and thermodynamic parameters of the heteroassociation of nicotinamide with daunomycin and novatrone have been determined from the experimental concentration and temperature dependences of the ¹H NMR chemical shifts of the interacting molecules. The most favorable structures of the 1:1 nicotinamide-daunomycin and nicotinamide-novatrone heterocomplexes have been found using the molecular mechanics method (X-PLOR software) and analysis of induced proton chemical shifts. The results demonstrate that two nicotinamide molecules cannot simultaneously bind on one side of the chromophore of the daunomycin or novatrone. The 1:1 heterocomplexes of the vitamin with the antibiotics are mainly stabilized by the stacking of aromatic chromophores.     

Antifungal bis[bibenzyls] from the Chinese liverwort Marchantia polymorpha L

Bioassay-guided separation of the antifungal constituents of the Chinese liverwort Marchantia polymorpha L. (Marchantiaceae) led to the isolation of seven bis[bibenzyl]-type macrocycles. On the basis of NMR and MS analyses, the three new compounds plagiochin E (1), 13,13'-O-isoproylidenericcardin D (4), and riccardin H (7) were identified, together with four known compounds: marchantin E (2), neomarchantin A (3), marchantin A (5), and marchantin B (6). Their antifungal activities against Candida albicans were determined by TLC bioautography.     

Natural feruloyl monoglyceride macrocycles as protecting factors against free-radical damage of lipidic membranes

Nine novel natural feruloyl monoglyceride (MGs) macrocycles have been isolated from the leaves of Carex distachya, an herbaceous plant growing in the Mediterranean maquis. All the structures have been elucidated on the basis of their spectroscopic features, especially two-dimensional NMR (DQ-COSY, TOCSY, NOESY, ROESY, HSQC, HMBC, HSQC-TOCSY) and ESI-MS. All the compounds have been assayed as protecting factors against the radical damage of the lipids by using different antioxidant tests.     

New macrocyclic Schiff base complexes incorporating a phenanthroline unit: Part 1; Template synthesis of three cadmium(II) complexes and crystal structure, NMR and ab initio studies

Complexes of three Cd(II)-containing macrocyclic Schiff base complexes containing a phenanthroline ligand (L) of the type [CdLⁿ(Cl)]⁺ (n=2,3,4), have been prepared via [1+1] cyclocondensation of 2,9-dicarboxaldehyde-1,10-phenanthroline and a number of linear triamines via a metal-templated reaction and coordination features have been examined. The ligands, L, are 16-, 17-, and 18-membered pentaaza macrocycles and all the complexes incorporate a 1,10-phenanthroline unit as an integral part of their cyclic structure. The complexes have been characterized by a variety of methods including IR, ¹H, ¹³C, DEPT, COSY(H,H) and HMQC(H,C) NMR studies and MALDI mass spectrometry. The polymeric structure of was determined by X-ray crystallography, which showed that the complex cation consisted of a pentagonal bipyramidally coordinated Cd(II) ion. The seven-coordinated Cd(II) ion is ligated by the five nitrogen atoms of the macrocycle in the equatorial plane and has two bridging chloride ligands in the axial positions resulting in a ribbon of such complex ions. Supporting ab initio HF-MO calculations have been undertaken using the standard 3-21G^∗ and 6-31G^∗ basis sets.     

1H NMR and UV-Vis spectroscopic characterization of sulfonamide complexes of nickel(II)-carbonic anhydrase. Resonance assignments based on NOE effects.

The binding of acetazolamide, p-fluorobenzensulfonamide, p-toluenesulfonamide, and sulfanilamide to nickel(II)-substituted carbonic anhydrase II has been studied by 1H NMR and electronic absorption spectroscopies. These inhibitors bind to the metal ion forming 1:1 complexes and their affinity constants were determined. The 1H NMR spectra of the formed complexes show a number of isotropically shifted signals corresponding to the histidine ligands. The complexes with benzene-sulfonamides gave rise to very similar 1H NMR spectra. The NMR data suggest that these aromatic sulfonamides bind to the metal ion altering its coordination sphere. In addition, from the temperature dependence of 1H NMR spectra of the p-fluorobenzenesulfonamide adduct, a conformational change is suggested. The T1 values of the meta-like protons of the coordinated histidines have been measured and resonance assignments based on NOE experiments were performed.     

Chemistry of selenium/tellurium-containing Schiff base macrocycles

This paper highlights our work to establish a new class of macrocycles based on Schiff base condensation chemistry. The chemistry of a series of azomethine macrocycles, with selenium/tellurium atoms in o-positions with respect to the CN bond is discussed. These are the first Schiff base macrocycles to incorporate selenium or tellurium atom in the ring. The strong stabilization of the 10-E-3 (E = Se/Te) structures of these macrocycles by E-N coordination permits the access to these novel macrocycles by [2+2] template-free condensation of bis(aldehyde) with primary diamines. The success of cyclization has been confirmed by the usual methods of IR, NMR and X-ray structural determinations. After a brief discussion of the synthetic methods adopted for these macrocycles, their complexing abilities toward different metal ions are covered. The macrocyclic polyamine ligands, derived by reduction of the corresponding Schiff bases, readily form complexes with a range of metal ions. This allows a comparison of the properties of complexes of these ligands with those derived from the Schiff bases containing the same denticity but having a different flexibility. The selena- and tellura-macrocycles reported by other groups in the field are also included for comparison. Also discussed is the anion binding studies of some of these macrocycles.     

Nuclear magnetic resonance determination of metal-proton distances in a synthetic calcium binding site of rabbit skeletal troponin C

The binding of gadolinium to a synthetic peptide of 13 amino acid residues representing the calcium binding loop of site 3 of rabbit skeletal troponin C [AcSTnC(103-115)amide] has been studied by using proton nuclear magnetic resonance (1H NMR) spectroscopy. In particular, the proton line broadening and enhanced spin-lattice relaxation have been used to determine proton-metal ion distances for several assigned nuclei in the peptide-metal ion complex. These distances have been used in conjunction with other constraints and a distance algorithm procedure to demonstrate that the structure of the peptide-metal complex as shown by 1H NMR is consistent with the structure of the EF calcium binding loop in the X-ray structure of parvalbumin but that the available 1H NMR distances do not uniquely define the solution structure.     

A 1H NMR study of the solution conformation of the neuropeptide galanin.

The conformations of the neuropeptide galanin in water and trifluoroethanol solutions have been examined by 1H NMR spectroscopy. Analysis of two-dimensional NMR experiments enabled the assignment of virtually all the 1H resonances of galanin in trifluoroethanol solution and many of the 1H resonances in aqueous solution. Interpretation of the NMR data in structural terms suggests that in trifluoroethanol galanin is predominantly helical while in water it does not adopt a fixed conformation.     

NMR spectroscopy, molecular dynamics, and conformation of a synthetic octasaccharide fragment of the O-specific polysaccharide of Shigella dysenteriae type 1

A synthetic octasaccharide fragment (2) of the O-specific polysaccharide (1) of Shigella dysenteriae type 1 has been studied as its methyl glycoside by one- and two-dimensional homo- and heteronuclear NMR spectroscopy. Complete 1H and 13C NMR assignments have been generated, and the 13C spin-lattice relaxation times have been measured for the octasaccharide 2. A congener (6) of this octasaccharide containing one D-galactose residue with a specific 13C label at C-1 has been synthesized and used to measure interglycosidic 13C-1H coupling by the 2D J-resolved 1H NMR method. From the NMR data, three types of conformational restraints were developed: (a) 29 inter-residue, distance restraints; (b) 48 intra-residue, ring atom dihedral angle restraints, and (c) one heteronuclear, inter-residue dihedral angle restraint. The use of these restraints in a restrained molecular dynamics computation with simulated annealing yielded a conformation resembling a short, irregular spiral, with methyl substituents on the exterior.     

Metallocene basicity. VIII. Protonation of bridge substituted ferrocenophanes in strong acid media

A series of bridge substituted [3]-, [4]-, and [5]- ferrocenophanes have been prepared and characterized by ¹H NMR and mass spectroscopy. In trifluoroboric acid, HBF₃OH, solution these ferrocenophanes protonate at the iron to form long-lived species which can be studied by ¹H NMR. Analysis of the complex ¹H NMR spectra of the protonated species suggests that bridge substituents either slow or block the free oscillation of the rings and bridges. The iron-hydrogen chemical shift values have been shown to depend only on the length of the bridge and seem to be insensitive to substituents on the bridge.     

Predicting the unpredictable: Recent structure–activity studies on peptide-based macrocycles

Heterocycle-containing macrocycles are an emerging class of molecules that have therapeutic efficacy. Many biologically active natural products that have interesting biological properties fall into this class of molecules. The highly specific and selective biological activity is often attributed to the unique conformation of these macrocycles, which is affected by the elements of the macrocycles as well as its surroundings in biological systems. In this review, the structure–activity relationship studies of several recently developed biologically active heterocycle-containing macrocycles have been discussed in order to facilitate an understanding on how unpredictable structures can be controlled.     

Synthesis, crystal structure, NMR and ab initio molecular-orbital studies of some magnesium(II) macrocyclic Schiff-base complexes, with two 2-aminoethyl pendant arms

Three new Mg(II) bis(pendant arm) macrocyclic Schiff-base complexes, [MgLⁿ]²⁺(n=5, 6, 7), have been prepared via cyclocondensation of 2,6-diacetylpyridine with branched hexaamines and characterised spectroscopically. In addition, for [MgL⁵](ClO₄)₂ the crystal structure is reported. This is the first X-ray structural determination of an Mg(II) complex coordinated by seven nitrogen atoms. The ligands, L, are 15-, 16- and 17-membered pentaaza macrocycles having two 2-aminoethyl pendant arms [L⁵; 2,13-dimethyl-6,9-bis(aminoethyl)-3,6,9,12,18-pentaazabicyclo[12.3.1]octadeca-1(18), 2, 12, 14, 16-pentaene, L⁶; 2,14-dimethyl-6,10-bis(aminoethyl)-3,6,10,13,19-pentaazabicyclo[13.3.1]nonadeca-1(19), 2, 13, 15, 17-pentaene and L⁷; 2,15-dimethyl-6,11-bis(aminoethyl)-3,6,11,14,20-pentaazabicyclo[14.3.1]eicosa-1(20),2,14,16,18-pentaene]. The crystal structure of [MgL⁵](ClO₄)₂, was determined by X-ray diffraction and showed that the complex cation that had formed consisted of a pentagonal bipyramidally coordinated Mg(II) ion. All complexes were characterised by IR, ¹H NMR,¹³C NMR, COSY(H,H) and HETCOR(H,C) spectroscopy, and the data indicate that the structure is approximately pentagonal bipyramidal in each case. This structural assignment is also supported by ab initio HF-MO calculations made using the standard 3-21G* basis set.     

Production of 9-hydroxynonanoic Acid from methyl oleate and conversion into lactone monomers for the synthesis of biodegradable polylactones

The feasibility of a previously established method based on ozonolysis and hydrogenation reactions for the production of 9-hydroxynonanoic acid from oleic acid has been demonstrated. Metal catalyzed lactonization conditions have been used to convert 9-hydroxynonanoic acid into 1,11-dioxacycloicosane-2,12-dione, which is a potential monomer in the synthesis of polylactones. The structure of 9-hydroxynonanoic acid and 1,11-dioxacycloicosane-2,12-dione has been confirmed by 1H NMR, 13C NMR, and FTIR. In addition, 9-hydroxynonanoic acid was analyzed by high-resolution mass spectroscopy and 1,11-dioxacycloicosane-2,12-dione was analyzed by GC-MS. Aliphatic poly(nonanolactones) have been synthesized via ring-opening polymerization of the dilactone. The structure and number average molecular weight (M(n)) of the poly(nonanolactones) have been calculated by 1H NMR and GPC. The physical properties of these poly(nonanolactones) have been characterized by modulated differential scanning calorimetry (MDSC) and thermogravimetric analysis (TGA).     

The structure of the human retinoic acid receptor-beta DNA-binding domain determined by NMR.

The solution structure of the DNA-binding domain (DBD) of the human retinoic acid receptor-beta (hRAR-beta) has been determined by nuclear magnetic resonance (NMR) spectroscopy and distance geometry (DG). The assignments of 1H and 15N resonances were carried out by the use of 1H homonuclear and 15N-1H heteronuclear two- and three-dimensional NMR experiments. The structure of RAR DBD has been obtained on the basis of distance constrains derived from NMR experiments. The structure shows that two "zinc-finger" domains of the protein are followed by two perpendicular alpha-helices and a short beta-sheet near the N-terminus. Apolar residues in both helices form a hydrophobic core. Binding models of RAR DBD to its inverted and direct repeat response elements have been constructed based on this three-dimensional structure.     

Structural alterations of enkephalins in the presence of GM1 ganglioside micelles

The enkephalins are endogenous neurotransmitters and bind with high affinity at the delta-receptor. Gangliosides, the major glycans of nerve cells, known to interact both with receptors and ligands on the cell surface, have been implicated to modulate the actions of opioid receptors by allosteric regulation (Wu, G.; Lu, Z. H.; Wei, T. J.; Howells, R. D.; Christoffers, K.; Leeden R. W. Ann NY Acad Sci 1998, 845, 126-138). We have studied the interactions between enkephalins and monosialylated ganglioside GM1 using NMR spectroscopy and fluorescence. The structural models of enkephalins in the presence of GM1 micelles were generated using two-dimensional (1)H-ROESY experiments along with restrained molecular dynamics simulations. We report a conformational alteration of enkephalins in the presence of GM1 micelles.     

13C chemical shift map of the active cofactors in photosynthetic reaction centers of Rhodobacter sphaeroides revealed by photo-CIDNP MAS NMR

13C photo-CIDNP MAS NMR studies have been performed on reaction centers (RCs) of Rhodobacter sphaeroides wild type (WT) that have been selectively labeled with an isotope using [5-13C]-delta-aminolevulinic acid.HCl in all the BChl and BPhe cofactors at positions C-4, C-5, C-9, C-10, C-14, C-15, C-16, and C-20. 13C CP/MAS NMR and 13C-13C dipolar correlation photo-CIDNP MAS NMR provide a chemical shift map of the cofactors involved in the electron transfer process in the RC at the atomic scale. The 13C-13C dipolar correlation photo-CIDNP spectra reveal three strong components, originating from two BChl cofactors, called P1 and P2 and assigned to the special pair, as well as one BPhe, PhiA. In addition, there is a weak component observed that arises from a third BChl cofactor, denoted P3, which appears to originate from the accessory BChl BA. An almost complete set of assignments of all the aromatic carbon atoms in the macrocycles of BChl and BPhe is achieved in combination with previous photo-CIDNP studies on site-directed BChl/BPhe-labeled RCs [Schulten, E. A. M., Matysik, J., Alia, Kiihne, S., Raap, J., Lugtenburg, J., Gast, P., Hoff, A. J., and de Groot, H. J. M. (2002) Biochemistry 41, 8708-8717], allowing a comprehensive map of the ground-state electronic structure of the photochemically active cofactors to be constructed for the first time. The reasons for the anomaly of P2 and the origin of the polarization on P3 are discussed.     

Structural characterization of a lipase-catalyzed copolymerization of epsilon-caprolactone and D,L-lactide

The copolymerization of epsilon-caprolactone (epsilon-CL) and d,l-lactide catalyzed by Candida antarctica lipase B was studied. Copolymerizations with different epsilon-CL-to-lactide ratios were carried out, and the product was monitored and characterized by MALDI-TOF MS, GPC, and (1)H NMR. The polymerization of epsilon-CL, which is normally promoted by C. antarctica lipase B, is initially slowed by the presence of lactide. During this stage, lactide is consumed more rapidly than epsilon-CL, and the incorporation occurs dimer-wise with regard to the lactic acid (LA) units. As the reaction proceeds, the relative amount of CL units in the copolymer increases. The nonrandom copolymer structure disappears with time, probably due to a lipase-catalyzed transesterification reaction. In the copolymerizations with a low content of lactide, macrocycles of poly(epsilon-caprolactone) and copolymers having up to two LA units in the ring were detected.     

Solution structure of a pentasaccharide representing the repeating unit of the O-antigen polysaccharide from Escherichia coli O142: NMR spectroscopy and molecular simulation studies

Conformational studies have been performed of a pentasaccharide derived from the O-polysaccharide from Escherichia coli O142. The polymer was selectively degraded by anhydrous hydrogen fluoride and reduced to yield an oligosaccharide model of its repeating unit, which in the branching region consists of four aminosugars. A comparison of (1)H and (13)C chemical shifts between the pentasaccharide and the polymer showed only minor differences, except where the cleavage had taken place, indicating that the oligomer is a good model of the repeating unit. Langevin dynamics and molecular dynamics simulations with explicit water molecules were carried out to sample the conformational space of the pentasaccharide. For the glycosidic linkages between the hexopyranoside residues, small but significant changes were observed between the simulation techniques. One-dimensional (1D) (1)H,(1)H double pulsed field gradient spin echo (DPFGSE) transverse rotating-frame Overhauser effect spectroscopy (T-ROESY) experiments were performed, and homonuclear cross-relaxation rates were obtained. Subsequently, a comparison of interproton distances from NMR experiment and the two simulation approaches showed that in all cases the use of explicit water in the simulations resulted in better agreement. Hydrogen-bond analysis of the trajectories from the molecular dynamics simulation revealed interresidue interactions to be important as a cluster of different hydrogen bonds and as a distinct highly populated hydrogen bond. NMR data are consistent with the presence of hydrogen bonding within the model of the repeating unit.     

Structural insights into the inclusion complexes between clomiphene citrate and β‐cyclodextrin: The mechanism of preferential isomeric selection

A major challenge in pharmaceuticals for clinical applications is to alter the solubility, stability, and toxicity of drug molecules in living systems. Cyclodextrins (CDs) have the ability to form host–guest inclusion complexes with pharmaceuticals for further development of new drug formulations. The inclusion complex of clomiphene citrate (CL), a poorly water‐soluble drug, with native β‐cyclodextrin (β‐CD) was characterized by a one and two‐dimensional nuclear magnetic resonance (NMR) spectroscopic approach and also by molecular docking techniques. Here we report NMR and a computational approach in preferential isomeric selection of CL, which exists in two stereochemical isomers, enclomiphene citrate (ENC; E isomer) and zuclomiphene citrate (ZNC; Z isomer) with β‐CD. β‐CD cavity protons, namely, H‐3′ and H‐5′, experienced shielding in the presence of CL. The aromatic ring protons of the CL molecule were observed to be deshielded in the presence of β‐CD. The stoichiometric ratio of the β‐CD:CL inclusion complex was observed by NMR and found to be 1:1. The overall binding constant of β‐CD:CL inclusion complexes was based on NMR chemical shifts and was calculated to be 50.21 M⁻¹. The change in Gibb's free energy (∆G) was calculated to be −9.80 KJ mol⁻¹. The orientation and structure of the β‐CD:CL inclusion complexes are proposed on the basis of NMR and molecular docking studies. 2D ¹H‐¹H ROESY confirmed the involvement of all three aromatic rings of CL in the inclusion complexation with β‐CD in the solution, confirming the multiple equilibria between β‐CD and CL. Molecular docking and 2D ¹H‐¹H ROESY provide insight into the inclusion complexation of two isomers of CL into the β‐CD cavity. A molecular docking technique further provided the different binding affinities of the E and Z isomers of CL with β‐CD and confirmed the preference of the Z isomer binding for β‐CD:CL inclusion complexes. The study indicates that the formation of a hydrogen bond between –O– of CL and the hydrogen atom of the hydroxyl group of β‐CD was the main factor for noncovalent β‐CD:CL inclusion complex formation and stabilization in the aqueous phase.