DNA cleavage in red light promoted by copper(II) complexes of -amino acids and photoactive phenanthroline bases

Ternary copper(II) complexes [Cu(L-trp)(B)(H2O)](NO3) ( 1–3) and [Cu(L-phe)(B)(H2O)](NO3) ( 4–6) of L-tryptophan (L-trp) and L-phenylalanine (L-phe) having phenanthroline bases (B), viz. 1,10-phenanthroline (phen, 1 and 4), dipyrido[3,2-d:2,3-f]quinoxaline (dpq, 2 and 5) and dipyrido[3,2-a:2,3-c]phenazine (dppz, 3 and 6), were prepared and characterized by physico-chemical techniques. Complexes 3 and 6 were structurally characterized by X-ray crystallography and show the presence of a square pyramidal (4 + 1) CuN3O2 coordination geometry in which the N,O-donor amino acid (L-trp or L-phe) and N,N-donor phenanthroline base bind at the equatorial plane with an aqua ligand coordinated at the elongated axial site. Complex 3 shows significant distortion from the square pyramidal geometry and a strong intramolecular – stacking interaction between the pendant indole ring of L-trp and the planar dppz aromatic moiety. All the complexes display good binding propensity to the calf thymus DNA giving an order: 3, 6 (dppz) > 2, 5 (dpq) > 1, 4 (phen). The binding constant (Kb) values are in the range of 2.1 × 104–1.1 × 106 mol-1 with the binding site size (s) values of 0.17–0.63. The phen and dpq complexes are minor groove binders while the dppz analogues bind at the DNA major groove. Theoretical DNA docking studies on 2 and 3 show the close proximity of two photosensitizers, viz. the indole moiety of L-trp and the quinoxaline/phenazine of the dpq/dppz bases, to the complementary DNA strands. Complexes 2 and 3 show oxidative DNA double strand breaks (dsb) of supercoiled (SC) DNA forming a significant quantity of linear DNA along with the nicked circular (NC) form on photoexposure to UV-A light of 365 nm and red light of 647.1 nm (Ar–Kr laser). Complexes 1, 5 and 6 show only single strand breaks (ssb) forming NC DNA. The red light induced DNA cleavage involves metal-assisted photosensitization of L-trp and dpq/dppz base resulting in the formation of a reactive singlet oxygen (1O2) species.

Towards a green synthesis of isoquinoline: Beckmann rearrangement of E,-cinnamaldoxime over H-zeolites

Isoquinoline was prepared through the Beckmann rearrangement of cinnamaldoxime over different H-zeolites, K-10 montmorillonite clay, amorphous SiO2–Al2O3 and γ-alumina under well-optimized conditions of temperature, weight hourly space velocity and catalyst loading. Cinnamaldoxime under ambient reaction conditions over the catalysts underwent migration of the anti-styryl moiety to electron deficient nitrogen (Beckmann rearrangement) followed by an intramolecular cyclization to yield isoquinoline. Cinnamo-nitrile (dehydration product) and cinnamaldehyde were formed as by-products. Isoquinoline formation was high on zeolite catalysts (ca. >86.5%) and mordenite (ca. 92.3%) was the most efficient in the series. Catalysts were susceptible for deactivation and the decrease in the percentage conversion of oxime with time is associated with a corresponding increase in the acid hydrolysis producing salicylaldehyde at later stages of the reaction. However, these catalysts retain activity considerably and can be recycled without loss of activity and change of product distribution.

Enantioselective syntheses of diquinane and (cis, anti, cis)-linear triquinanes

The enantioselective syntheses of diquinane and cis, anti, cis-linear triquinanes, starting from the readily available (S)-campholenaldehyde, employing an intramolecular rhodium carbenoid CH insertion reaction, are described. (C) 2010 Elsevier Ltd. All rights reserved.

Stereochemistry of peptides containing 1-aminocycloheptane-1-carboxylic acid (Ac7c)

The crystal structures of four peptides incorporating 1-aminocycloheptane-1-carboxylic acid (Ac7c) are described. Boc-Aib-Ac7c-NHMe and Boc-Pro-Ac7c-Ala-OMe adopt beta-turn conformations stabilized by an intramolecular 4----1 hydrogen bond, the former folding into a type-I/III beta-turn and the latter into a type-II beta-turn. In the dipeptide esters, Boc-Aib-Ac7c-OMe and Boc-Pro-Ac7c-OMe, the Ac7c and Aib residues adopt helical conformations, while the Pro residue remains semi-extended in both the molecules of Boc-Pro-Ac7c-OMe found in the asymmetric unit. The cycloheptane ring of Ac7c residues adopts a twist-chair conformation in all the peptides studied. 1H-NMR studies in CDCl3 and (CD3)2SO and IR studies in CDCl3 suggest that Boc-Aib-Ac7c-NHMe and Boc-Pro-Ac7c-Ala-OMe maintain the beta-turn conformations in solution.

A new glucose: Towards conformationally locked flexoses through annulation

A new family of surf ace-modified carbohydrates with locked, axial-rich conformations and bipolarofacial architectures has been developed with the aid of carbocyclic ring annulation. These novel trans-decalin-based carbohydrates have been synthesized, from simple aromatic precursors such as tetralin, through the ozonolysis of an appropriately protected allylic alcohol, followed by a cascade of intramolecular acetalizations to generate the sugar pyran moiety. The stereoselective synthesis of (racemic) cyclohexane-annulated 0-glucopyranoside and a-glucofuranoside from a common annulated trans-cyclohexadiene diol (trans-CHD) precursor under-scores the versatility of our approach. The efficacy of the annulation stratagem in generating carbohydrate diversity has been demonstrated through the synthesis of two regioisomeric annulated gulose derivatives, which differ only in the site of ring annulation on the sugar moiety. The mapping of the MLP surface and solid-state architecture of the new sugar shows that cycloalkane annulation results in surface modification and fine-tuning of sugar hydrophilicity. (© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2005).

Approaches to sesquiterpenes containing three contiguous quaternary carbon atoms. Synthesis of 3-methoxythapsene

Synthetic approach to 3-alkoxythapsane, comprising of the carbon framework of a small group of sesquiterpenes containing three contiguous quaternary carbon atoms has been described. A combination of alkylation, orthoester Claisen rearrangement and intramolecular diazoketone cyclopropanation has been employed for the creation of the three requisite contiguous quaternary carbon atoms.

Synthetic and conformational studies on dehydroalanine-containing model peptides

Three model dipeptides containing a dehydroalanine residue (Ala) at the C-terminal, Boc-X-Ala-NHCH3 [X = Ala, Val, and Phe,] have been synthesized and their solution conformations investigated by 1H-NMR, IR, and CD spectroscopy. NMR studies on these peptides in CDCl3 clearly indicate that the NH group of dehydroalanine is involved in an intramolecular hydrogen bond. This conclusion is supported by IR studies also. Nuclear Overhauser effect (NOE) studies are also accommodative of an inverse -turn-type of conformation that is characterised by conformational angles of -70° and +70° around the X residue, and a C[stack i+1 ]H-Ni+2H interproton distance of 2.5 Å. It appears that unlike dehydrophenylalanine or dehydroleucine, which tend to stabilize -turn type of structures occupying the i + 2 position of the turn, dehydroalanine favors the formation of an inverse -turn, centered at the proceeding L-residue in such solvents as CDCl3 and (CD3)2SO. A comparison of solution conformation of Boc Val-Ala-NHCH3 with the corresponding saturated analogue, Boc-Val-Ala-NHCH3, is also presented and shows that dehydroalanine is responsible for inducing the turn structure. It may be possible to design peptides with different preferred conformations using the suitable dehydroamino acid.

Stereochemistry of peptides containing 1-aminocycloheptane-1-carboxylic acid (Ac-c)

The crystal structures of four peptides incorporating 1-aminocycloheptane-1-carboxylic acid (Ac7c) are described. Boc-Aib-Ac7c-NHMe and Boc-Pro-Ac7c-Ala-OMe adopt beta-turn conformations stabilized by an intramolecular 4----1 hydrogen bond, the former folding into a type-I/III beta-turn and the latter into a type-II beta-turn. In the dipeptide esters, Boc-Aib-Ac7c-OMe and Boc-Pro-Ac7c-OMe, the Ac7c and Aib residues adopt helical conformations, while the Pro residue remains semi-extended in both the molecules of Boc-Pro-Ac7c-OMe found in the asymmetric unit. The cycloheptane ring of Ac7c residues adopts a twist-chair conformation in all the peptides studied. 1H-NMR studies in CDCl3 and (CD3)2SO and IR studies in CDCl3 suggest that Boc-Aib-Ac7c-NHMe and Boc-Pro-Ac7c-Ala-OMe maintain the beta-turn conformations in solution.

Unfolding of Plasmodium falciparum Triosephosphate Isomerase in Urea and Guanidinium Chloride: Evidence for a Novel Disulfide Exchange Reaction in a Covalently Cross-Linked Mutant†

The conformational stability of Plasmodium falciparum triosephosphate isomerase (TIMWT) enzyme has been investigated in urea and guanidinium chloride (GdmCl) solutions using circular dichroism, fluorescence, and size-exclusion chromatography. The dimeric enzyme is remarkably stable in urea solutions. It retains considerable secondary, tertiary, and quaternary structure even in 8 M urea. In contrast, the unfolding transition is complete by 2.4 M GdmCl. Although the secondary as well as the tertiary interactions melt before the perturbation of the quaternary structure, these studies imply that the dissociation of the dimer into monomers ultimately leads to the collapse of the structure, suggesting that the interfacial interactions play a major role in determining multimeric protein stability. The C-m(urea)/C-m(GdmCl) ratio (where C-m is the concentration of the denaturant required at the transition midpoint) is unusually high for triosephosphate isomerase as compared to other monomeric and dimeric proteins. A disulfide crosslinked mutant protein (Y74C) engineered to form two disulfide cross-links across the interface (13-74') and (13'-74) is dramatically destablized in urea. The unfolding transition is complete by 6 M urea and involves a novel mechanism of dimer dissociation through intramolecular thiol-disulfide exchange.

A combined extended and helical backbone for Boc-(Ala-Leu-Ac(7)c-)(2)-OMe

The structure of the peptide Boc-Ala-Leu-Ac(7)c-Ala-Leu-Ac(7)c-OMe (Ac(7)c,1-aminocycloheptane-1-carboxylic acid) is described in crystals. The presence of two Ac(7)c residues was expected to stabilize a 3(10)-helical fold. Contrary to expectation the structural analysis revealed an unfolded amino terminus, with Ala(1) adopting an extended beta-conformation (phi = -93degrees,psi = 112degrees). Residues 2-5 form a 3(10)-helix, stabilized by three successive intramolecular hydrogen bonds. Notably, two NH groups Ala(1) and Ac(7)c(3) do not form any hydrogen bonds in the crystal. Peptide assembly appears to be dominated by packing of the cycloheptane rings that stack against one another within the molecule and also throughout the crystal in columns.

Characterization of Alkali Induced Formation of Lanthionine, Trisulfides, and Tetrasulfides from Peptide Disulfides using Negative Ion Mass Spectrometry

Peptide disulfides are unstable under alkaline conditions, resulting in the formation of products containing lanthionine and polysulfied linkages. Electrospray ionization mass spectrometry has been used to characterize major species obtained when cyclic and acyclic peptide disulfides are exposed to alkaline media. Studies on a model cyclic peptide disulfide (Boc - Cys - Pro - Leu - Cys - NHMe) and an acyclic peptide, oxidized glutathione, bis ((gamma)Glu Cys - Gly - COOH), are described. Disulfide cleavage reactions are initiated by the abstraction of (CH)-H-alpha or (CH)-H-beta protons of Cys residues, with Subsequent elimination of H2S or H2S2. The buildup of reactive thiol species which act on intermediates containing dehydroalanine residues, rationalizes the formation of lanthionine and polysulfide products. In the case of the cyclic peptide disulfide, the formation of cyclic products is facilitated by the intramolecular nature of the Michael addition reaction of thiols to the dehydroalanine residue. Mass spectral evidence for the intermediate species is presented by using alkylation of thiol groups as a trapping method. Mass spectral fragmentation in the negative ion mode of the peptides derived from trisulfides and tetrasulfides results in elimination of S-2. (J Am Soc Mass Spectrom 2009, 20, 783-791) (C) 2009 American Society for Mass Spectrometry.

Characterization of Alkali Induced Formation of Lanthionine, Trisulfides, and Tetrasulfides from Peptide Disulfides using Negative Ion Mass Spectrometry

Peptide disulfides are unstable under alkaline conditions, resulting in the formation of products containing lanthionine and polysulfied linkages. Electrospray ionization mass spectrometry has been used to characterize major species obtained when cyclic and acyclic peptide disulfides are exposed to alkaline media. Studies on a model cyclic peptide disulfide (Boc - Cys - Pro - Leu - Cys - NHMe) and an acyclic peptide, oxidized glutathione, bis ((gamma)Glu Cys - Gly - COOH), are described. Disulfide cleavage reactions are initiated by the abstraction of (CH)-H-alpha or (CH)-H-beta protons of Cys residues, with Subsequent elimination of H2S or H2S2. The buildup of reactive thiol species which act on intermediates containing dehydroalanine residues, rationalizes the formation of lanthionine and polysulfide products. In the case of the cyclic peptide disulfide, the formation of cyclic products is facilitated by the intramolecular nature of the Michael addition reaction of thiols to the dehydroalanine residue. Mass spectral evidence for the intermediate species is presented by using alkylation of thiol groups as a trapping method. Mass spectral fragmentation in the negative ion mode of the peptides derived from trisulfides and tetrasulfides results in elimination of S-2. (J Am Soc Mass Spectrom 2009, 20, 783-791) (C) 2009 American Society for Mass Spectrometry.

Charge distribution in and dipole moments of some aliphatic alcohols

Using the treatment of Smith, et al.,1 charge distributions in several aliphatic alcohols and consequently their dipole moments have been evaluated. The dipole moments of trichloroethanol (2.04 D) and 1,3-dichloropropan-2-ol (2.11 D) have been measured in benzene solution at 35°. The results of evaluation and measurements are interpreted in terms of the occurrence of intramolecular interaction between the hydroxyl hydrogen and an acceptor atom X (halogen or oxygen) at the β-carbon atom.

A new glucose: Towards conformationally locked flexoses through annulation

A new family of surf ace-modified carbohydrates with locked, axial-rich conformations and bipolarofacial architectures has been developed with the aid of carbocyclic ring annulation. These novel trans-decalin-based carbohydrates have been synthesized, from simple aromatic precursors such as tetralin, through the ozonolysis of an appropriately protected allylic alcohol, followed by a cascade of intramolecular acetalizations to generate the sugar pyran moiety. The stereoselective synthesis of (racemic) cyclohexane-annulated 0-glucopyranoside and a-glucofuranoside from a common annulated trans-cyclohexadiene diol (trans-CHD) precursor under-scores the versatility of our approach. The efficacy of the annulation stratagem in generating carbohydrate diversity has been demonstrated through the synthesis of two regioisomeric annulated gulose derivatives, which differ only in the site of ring annulation on the sugar moiety. The mapping of the MLP surface and solid-state architecture of the new sugar shows that cycloalkane annulation results in surface modification and fine-tuning of sugar hydrophilicity. (© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2005).

Infra-red and raman spectra of BaCl2.2H2O and BaCl2.2D2O

The infra-red and Raman spectra of ordinary and deuterated barium chloride dihydrate have been studied to throw light on the intramolecular hydrogen bonds in these two crystals. The frequencies of the stretching, bending and librational modes observed in infra-red and Raman spectra exclude the possibility of at least one of the OH.... Cl hydrogen bonds, contrary to the results of NMR and neutron diffraction studies.