Solvent dependent photocyclization and photophysics of some 2-ethynylbiphenyls.

The spectroscopic properties and photochemical behavior of molecules having 2-ethynylbiphenyl or 2-phenyldiphenylacetylene structures are reported. These molecules undergo photocyclization reactions to yield phenanthrene and dihydrophenanthrene products via putative isophenanthrene (cyclic allene) intermediates. Phenanthrene formation from the isophenanthrene intermediates does not occur via a unimolecular sigmatropic hydrogen shift, but rather by protonation or hydrogen abstraction mechanisms involving the solvent. Cyclization efficiencies are much lower than is the case for previously-investigated 2-vinylbiphenyl systems. The 2-phenyldiphenylacetylenes have high fluorescence quantum yields and long singlet lifetimes when compared to diphenylacetylene. The 2-ethynylbiphenyls decay via a combination of fluorescence and intersystem crossing.     

Bottom-up synthesis of hyaluronan and its derivatives via enzymatic polymerization: direct incorporation of an amido functional group

This paper reports the synthesis of hyaluronan (HA) and its derivatives via the hyaluronidase-catalyzed polymerization of 2-substituted oxazoline derivative monomers designed as "transition-state analogue substrates". Polymerization of 2-methyl oxazoline monomer from N-acetylhyalobiuronate (GlcAbeta(1-->3)GlcNAc) effectively proceeded at pH 7.5 and 30 degrees C, giving rise to synthetic HA (natural type) in an optimal yield of 78% via ring-opening polyaddition under total control of regioselectivity and stereochemistry. Hyaluronidase catalysis enabled the polymerization of 2-ethyl, 2-n-propyl, and 2-vinyl monomers, affording the corresponding HA derivatives (unnatural type) with N-propionyl, N-butyryl, and N-acryloyl functional groups, respectively, at the C2 position of all glucosamine units in good yields. The 2-isopropyl oxazoline derivative provided the N-isobutyryl derivative of HA in low yields. Monomers of 2-phenyl and 2-isopropenyl oxazoline derivatives were not polymerized. The mechanism of the polymerization is discussed.     

The photochemistry and photophysics of all-trans-1,4-diindanylidenyl-2-butene, a rigid analogue of all-trans-1,6-diphenyl-1,3,5-hexatriene.

all-trans-1,4-Diindanylidenyl-2-butene (ttt-stiff-5-DPH), a torsionally constrained analogue of all-trans-1,6-diphenyl-1,3,5-hexatriene (ttt-DPH), was synthesized and studied in order to evaluate the role of phenyl-vinyl torsional motions in the photophysical and photochemical responses of the DPH chromophore. Spectroscopic and photoisomerization measurements reveal that the behavior of the rigid DPH analogue is very similar to that of the parent DPH. This similarity is obtained despite the fact that the alkyl substitution from the five-membered rings selectively lowers the energy of the 1 (1)B(u)* state, leading to inversion of the order of the 1 (1)B(u)* and 2 (1)A(g)* energy levels in hydrocarbon solvents. In stiff-5-DPH, as in DPH, an increase in solvent polarity enhances terminal over central bond photoisomerization. Analyses of fluorescence and photoisomerization quantum yields show that, as in DPH, the torsional relaxation channel on the singlet excited state manifold is inefficient, falling far short of accounting for all radiationless decay. Significant ( approximately 50 and 80% of all singlet decay in Bz and AN, respectively), photochemically unproductive, radiationless decay channels exist in both molecules. Competing one bond photoisomerizations give the two major photoproducts: tct-stiff-5-DPH and ctt-stiff-5-DPH. They were isolated in pure form and were spectroscopically characterized. Biacetyl-sensitization was used to study the behavior of the stiff-5-DPH triplet state. As in the parent DPH, stiff-5-DPH triplets undergo relatively efficient concentration dependent geometric photoisomerization.     

Molecular orbital studies on the conformations of 8-amino- and 8-dimethylaminoadenosine 5'-monophosphate

The quantum mechanical PCILO method has been applied for the determination of conformational properties of 8-amino- and 8-dimethylaminoadenosine 5'-monophosphate. Contrary to other 8-substituted nucleotides the amino derivative shows a preference for an anti arrangement about the glycosidic bond. This conformation is stabilized by an intramolecular hydrogen bond between the purine and the exocyclic group. 8-dimethylamino-adenosine-5'-monophosphate adopts the syn conformation with slightly rotated dimethylamino group. There is, however, a local minimum for the anti form associated with the unusual value of chiCN = 300 degrees. This minimum is probably populated when the nucleotide is bound to lactate dehydrogenase apoenzyme. No particularly strong interactions are necessary for the stabilization of the anti form. The computations account satisfactorily for the available experimental data.     

Coupling of the guanosine glycosidic bond conformation and the ribonucleotide cleavage reaction: implications for barnase catalysis

To examine the possible relationship of guanine-dependent GpA conformations with ribonucleotide cleavage, two potential of mean force (PMF) calculations were performed in aqueous solution. In the first calculation, the guanosine glycosidic (Gchi) angle was used as the reaction coordinate, and computations were performed on two GpA ionic species: protonated (neutral) or deprotonated (negatively charged) guanosine ribose O2 '. Similar energetic profiles featuring two minima corresponding to the anti and syn Gchi regions were obtained for both ionic forms. For both forms the anti conformation was more stable than the syn, and barriers of approximately 4 kcal/mol were obtained for the anti --> syn transition. Structural analysis showed a remarkable sensitivity of the phosphate moiety to the conformation of the Gchi angle, suggesting a possible connection between this conformation and the mechanism of ribonucleotide cleavage. This hypothesis was confirmed by the second PMF calculations, for which the O2 '--P distance for the deprotonated GpA was used as reaction coordinate. The computations were performed from two selected starting points: the anti and syn minima determined in the first PMF study of the deprotonated guanosine ribose O2'. The simulations revealed that the O2 ' attack along the syn Gchi was more favorable than that along the anti Gchi: energetically, significantly lower barriers were obtained in the syn than in the anti conformation for the O--P bond formation; structurally, a lesser O2 '--P initial distance, and a better suited orientation for an in-line attack was observed in the syn relative to the anti conformation. These results are consistent with the catalytically competent conformation of barnase-ribonucleotide complex, which requires a guanine syn conformation of the substrate to enable abstraction of the ribose H2 ' proton by the general base Glu73, thereby suggesting a coupling between the reactive substrate conformation and enzyme structure and mechanism.     

Intrinsic conformational energetics associated with the glycosyl torsion in DNA: a quantum mechanical study

The glycosyl torsion (chi) in nucleic acids has long been recognized to be a major determinant of their conformational properties. chi torsional energetics were systematically mapped in deoxyribonucleosides using high-level quantum mechanical methods, for north and south sugar puckers and with gamma in the g(+) and trans conformations. In all cases, the syn conformation is found higher in energy than the anti. When gamma is changed from g(+) to trans, the anti orientation of the base is strongly destabilized, and the energy difference and barrier between anti and syn are significantly decreased. The barrier between anti and syn in deoxyribonucleosides is found to be less than 10 kcal/mol and tends to be lower with purines than with pyrimidines. With gamma = g(+)/chi = anti, a south sugar yields a significantly broader energy well than a north sugar with no energy barrier between chi values typical of A or B DNA. Contrary to the prevailing view, the syn orientation is not more stable with south puckers than with north puckers. The syn conformation is significantly more energetically accessible with guanine than with adenine in 5-nucleotides but not in nucleosides. Analysis of nucleic acid crystal structures shows that gamma = trans/chi = anti is a minor but not negligible conformation. Overall, chi appears to be a very malleable structural parameter with the experimental chi distributions reflecting, to a large extent, the associated intrinsic torsional energetics.     

Noncovalent intercalative complex formation and kinetic flow linear dichroism of racemic syn- and anti-benzo[a]pyrenediol epoxide-DNA solutions

In order to gain a better understanding of the molecular basis underlying the differences in biological activities of the diastereomeric syn and anti diol epoxides of benzo[a]pyrene (trans-7,8-dihydroxy-syn-9,10-epoxy-7,8,9,10-tetrahydrobenzo[a]pyrene and trans-7,8-dihydroxy-anti-9,10-epoxy-7,8,9,10-tetrahydrobenzo[a]pyrene, respectively), their interactions with DNA in aqueous solutions were studied and compared. Kinetic flow linear dichroism experiments indicate that both diastereomers (racemic mixtures) form intercalation complexes immediately after mixing; the association constant (23 degrees C, ionic strength approximately 0.005) is significantly smaller (5200 M-1) in the case of the syn than in the case of the anti diastereomer (12 200 M-1). This difference is attributed to the greater bulkiness of the 7,8,9,10 ring of the syn stereoisomer, which is in the quasi-diaxial conformation as compared to the less bulky quasi-diequatorial conformation of the anti diastereomer. In contrast, the intercalative association constants of the tetraols derived from the hydrolysis of the two diol epoxides are similar in value. Upon formation of noncovalent syn-BPDE-DNA intercalation complexes, the reaction rate constant for the formation of tetraols (approximately 98%) and covalent adducts (approximately 2%) increases from 0.009 to 0.05 s-1 at pH 9.5 in 5 mM tris(hydroxymethyl)aminomethane buffer. The conformations of the aromatic chromophores of BPDE were followed by the kinetic flow dichroism technique as a function of reaction time; while the anti diastereomer changes conformation from an intercalative to an apparently external binding site, the syn diol epoxide molecules do not appear to undergo any measurable reorientation during or after the covalent binding reaction.(ABSTRACT TRUNCATED AT 250 WORDS)     

Photoprocesses of chlorin e6 glucose derivatives

The ground and excited state processes of chlorin e6, the monomethyl ester C1, the glucose derivative C2 and the 3-heptylchlorin-glucose C3, were studied in solvents of lower and higher polarity. The excited singlet and lowest triplet states of C1-C3 were characterized by spectroscopic methods for several conditions. The quantum yields of formation of singlet molecular oxygen and the other triplet properties of the three chlorins and chlorin e6 are similar, whereas the fluorescence quantum yield decreases on going from C1 to C3. Time-resolved optoacoustic experiments revealed a ca. 30 kJ mol(-1) higher triplet level for C3 with respect to C1/2.     

Conformational studies of two isomeric ring-expanded purine nucleosides and their 5'-mono- and -diphosphate derivatives

The nucleosides Ia and IIa exist in syn and anti conformations, respectively, both in solid state and solution. Compound Ia undergoes significant conformational change, accompanied by increased population of the anti conformer, upon conversion to the corresponding 5'-mono- and- diphosphate derivatives, whereas conformation of IIa remains reasonably constant between nucleoside and nucleotides. While Ia possessed the C2'-endo-C3'-exo geometry, IIa had the opposite C2'-exo-C3'-endo conformation. The C5' of the two nucleosides bore axial and equatorial conformations, respectively.     

Photophysical properties of non-homoconjugated 1,2-dihydro, 1,2,3,4-tetrahydro and 1,2,3,4,5,6-hexahydro-C60 derivatives.

The photophysical properties of a novel series of non-homoconjugated 1,2-di-, 1,2,3,4-tetra-, and 1,2,3,4,5,6-hexasubstituted fullerenes (compounds 1, 2, and 3, respectively) have been systematically investigated. In this report, we examine the effect of substitution pattern of non-homoconjugated derivatized fullerenes on the ground state UV-Vis absorption, triplet state properties (lifetime, quantum yield, extinction coefficient), and singlet oxygen quantum yield. The non-homoconjugated fullerene derivatives 1-3 exhibit higher singlet oxygen quantum yield than analogous homoconjugated Bingel adducts with the same number of saturated C[double bond, length as m-dash]C bonds and exhibit decreasing quantum yield of singlet oxygen generation upon increasing the degree of functionalization on a single six member ring on the fullerene cage. This trend is similar for triplet quantum yield and triplet lifetime. The triplet extinction coefficient increases with functionalization. A detailed discussion comparing 1, 2, and 3 with functionalized homoconjugated systems and with other non-homoconjugated derivatives is presented.     

Prevalence of syn nucleobases in the active sites of functional RNAs

Biological RNAs, like their DNA counterparts, contain helical stretches, which have standard Watson-Crick base pairs in the anti conformation. Most functional RNAs also adopt geometries with far greater complexity such as bulges, loops, and multihelical junctions. Occasionally, nucleobases in these regions populate the syn conformation wherein the base resides close to or over the ribose sugar, which leads to a more compact state. The importance of the syn conformation to RNA function is largely unknown. In this study, we analyze 51 RNAs with tertiary structure, including aptamers, riboswitches, ribozymes, and ribosomal RNAs, for number, location, and properties of syn nucleobases. These RNAs represent the set of nonoverlapping, moderate- to high-resolution structures available at present. We find that syn nucleobases are much more common among purines than pyrimidines, and that they favor C2'-endo-like conformations especially among those nucleobases in the intermediate syn conformation. Strikingly, most syn nucleobases participate in tertiary stacking and base-pairing interactions: Inspection of RNA structures revealed that the majority of the syn nucleobases are in regions assigned to function, with many syn nucleobases interacting directly with a ligand or ribozyme active site. These observations suggest that judicious placement of conformationally restricted nucleotides biased into the syn conformation could enhance RNA folding and catalysis. Such changes could also be useful for locking RNAs into functionally competent folds for use in X-ray crystallography and NMR.     

Preparation of cyclic peptide libraries using intramolecular oxime formation.

A new method for the synthesis of cyclic head-to-side chain peptide libraries has been developed in which the key cyclization step involves reaction between a C-terminal ketone and an N-terminal hydroxylamine to form a macrocyclic oxime. This methodology efficiently delivers cyclic products that consist of mixtures of syn and anti isomers.     

Conformation of adenosine 3',5'-monophosphate in solution as studied by the NMR-desert method. II. Self-association and temperature-dependent glycosidic isomerization at pH 7.

A study has been made of the association and the temperature-dependent conformation of adenosine 3',5'-monophosphate (cyclic AMP) in a neutral aqueous (2H2O) solution by means of proton magnetic resonance chemical shift and relaxation. The concentration and temperature-dependent chemical shifts of H(1'), H(2), and H(8), have enabled us to estimate the self-association constant, Ka = 1.1 +/- 0.3 M-1 at 25 degrees C and thermodynamic parameters delta H = -5.8 +/- 1.5 kcal/mol and delta S (25 degrees C) = -19.0 +/- 3 cal/mol per degree. The NMR-DESERT (Deuterium Substitution Effect on Relaxation Times) method has been utilized for the determination of the syn-anti conformational equilibrium in the monomeric state and for the determination of the mutual orientation of the two adenine rings in the dimeric state of cyclic AMP. The molecules were found to coexist with nearly equimolarity or syn-anti conformers and thermal activation of the molecules perturbs the syn-anti conformational equilibrium to comprise the syn form in preference at higher temperature. The glycosidic isomerization (from anti to syn) was found to be characterized both by a positive enthalpy change and by a positive entropy change. The cyclic AMP molecules prefer to take a 'trans-stacking' conformation in the dimeric state where the two molecules are arranged in such a way that the H(2) of one molecule is close to the H(8) of the other.     

Solution conformational analysis of 2'-amino-2'deoxyadenosine, 3'-amino-3'-deoxyadenosine and puromycin by pulsed nuclear-magnetic-resonance methods.

The solution conformation of 2'-amino-2'-deoxyadenosine, 3'-amino-3'-deoxyadenosine, and 3'-amino-3'-deoxy-6-N,N-dimethyladenosine have been determined by nuclear magnetic resonance in aqueous and ammonia solutions. The analysis of the ribose moiety is based on the two-state S in equilibrium N model of Altona and Sundaralingam. Longitudinal proton relaxation time and nuclear Overhauser enchancement measurements have been carried out in order to characterize the orientation of the base relative to the ribose. Those studies indicate that 3'-amino-3'-deoxyadenosine and 3'-amino-3'-deoxy-6-N,N-dimethyladenosine exist in solution preferentially in the N-anti-g + conformations. On the other hand, 2'-amino-2'-deoxyadenosine adopts the S-syn-g +/t conformation families. It appears that the base is restricted to the anti conformation in the first two compounds, while in 2'-amino-2'-deoxyadenosine, one third of the molecules in the S state are in the anti range. These studies corroborate the previously proposed correlations between the N state of the ribose and the anti orientation of the base and between the S state of the ribose and the syn orientation of the base.     

Synthesis of sulfur containing dihydro-pyrrolo derivatives and their biological evaluation as antioxidants

The 1,3-dipolar cycloaddition to N-phenylmaleimide of azomethine ylides, generated in situ from sulfanyl-substituted imines of glycine esters, yields 5H-dihydro-pyrrolo products with syn diastereoselectivity. The syn (major) and anti (minor) products were isolated chromatographically and fully characterized by spectroscopic methods and in two cases also by X-ray analysis. The diastereomeric cycloadducts were tested for their antioxidant activity with good results.     

Alternating d(GA)n DNA sequences form antiparallel stranded homoduplexes stabilized by the formation of G.A base pairs.

Alternating d(GA)n DNA sequences form antiparallel stranded homoduplexes which are stabilized by the formation of G.A pairs. Three base pairings are known to occur between adenine and guanine: AH+ (anti).G(syn), A(anti).G(anti) and A(syn).G(anti). Protonation of the adenine residues is not involved in the stabilization of this structure, since it is observed at any pH value from 8.3 to 4.5; at pH < or = 4.0 antiparallel stranded d(GA.GA) DNA is destabilized. The results reported in this paper strongly suggest that antiparallel stranded d(GA.GA) homoduplexes are stabilized by the formation of alternating A(anti).G(anti) and G(anti).A(syn) pairs. In this structure, all guanine residues are in the anti conformation with their N7 position freely accessible to DMS methylation. On the other hand, adenines in one strand adopt the anti conformation, with their N7 position also free for reaction, while those of the opposite strand are in the syn conformation, with their N7 position hydrogen bonded to the guanine N1 group of the opposite strand. A regular right-handed helix can be generated using alternating G(anti).A(syn) and A(anti).G(anti) pairs.     

Photophysical properties and photodynamic activity in vivo of some tetrapyrroles

Some of the photophysical properties (stationary absorbance and fluorescence, fluorescence decay times and singlet oxygen quantum yields) of pheophorbide a, metal-free, ClAl-, Cu- and Mg-t-butyl-substituted phthalocyanines, metal-free, ClAl- and Cu-t-butyl-substituted naphthalocyanines and of a number of tetraphenylporphyrins (5,10,15,20-tetraphenylporphyrin, 5,10,15,20-tetra(m-hydroxyphenyl)porphyrin, 5,10,15,20-tetra(p-hydroxyphenyl)porphyrin) have been studied in comparison with hematoporphyrin IX in order to select potent photosensitizers for the photodynamic treatment of cancer. The photodynamic activity of these compounds was investigated using Lewis lung carcinoma in mice. As a consequence of the photophysical parameters (relatively short singlet state lifetimes, and high singlet oxygen quantum yields) the photodynamic activities of pheophorbide a, t-butyl-substituted ClAl-phthalocyanine and ClAl-naphthalocyanine were selected for study in greater detail. Under the conditions employed in the present study, pheophorbide a was found to be the most effective sensitizer, as judged from its strong absorption at the excitation wavelength as compared with the hematoporphyrin derivative and greater singlet oxygen quantum yield relative to the phthalocyanines and naphthalocyanines. The photodynamic activity was observed to be strongly dependent on the photophysical parameters of the compounds. The primary mechanism underlying the photodynamic activity of these sensitizers probably consists of energy transfer from the lowest triplet state of the dyes to molecular oxygen, resulting in the formation of singlet oxygen (type II of photosensitization).     

Fluorescence studies of endothelin-1

Fluorescence measurements and singlet singlet energy transfer experiments on endothelin-1 provide information on the conformation of this peptide in dilute aqueous solution. The tyrosine fluorescence quantum yield in the absence of transfer (in [Phe²¹]endothelin-1) is relatively large (Φ_tyr = 0.39), indicating the side-chain is oriented away from fluorescence quenching groups such as the two disulfide bonds of the peptide. The fluorescence emission maximum (λ = 351 nm) and quantum yield (Φ_trp = 0.099) of tryptophan in endothelin-I suggests that this residue is fully accessible to the solvent and that the indole ring is not located near the fluorescence quenching histidinium moiety or the disulfide bonds.

Singlet-singlet fluorescence energy transfer measurements of the Tyr¹³/Trp²¹ intramolecular distance by both donor fluorescence quenching and relative enhancement of acceptor fluorescence yield a distance of about 12.8 ± 0.6 Å. Molecular modeling of a fully extended C-terminal hexapeptide indicates a Tyr¹³/Trp²¹ distance of about 25 Å. Thus, the C-terminal residues must bend back towards the bicyclic portion of the molecule.     

Infrared spectral studies of the non regularly alternating purine-pyrimidine hexamers d(m5CGGCM5CG), d(CBr8GGCCBr8G) and d(CGCGGC)

The oligonucleotides d(m5CGGCm5CG), d(CBr8GGCCBr8G) and d(CGCGGC) have been prepared and studied by infrared spectroscopy. The three sequences contain two GC pairs which are out of purine-pyrimidine alternation with the rest of the sequence. From the IR data of the d(m5CGGCm5CG) hexamer, it is shown that all of the dG residues adopt a syn conformation. The marker IR bands for the C3' endo syn conformation are at 1410, 1354, 1320 and 925 cm-1 whereas those for the C2' endo anti conformation at 1420, 1374 and 890 cm-1 are clearly absent. This result implies that the two adjacent guanines of the d(m5CGGCm5CG) sequence are in syn conformation. It is suggested that duplex formation occurs in d(CGCGGC) films and that all of the guanines are in syn conformation. In contrast, the central non-brominated guanine of the d(CBr8GGCCBr8G) hexamer is found in anti conformation, as expected in a Z type structure of the non-alternating region.     

Conformation, hydrogen bonding and aggregate formation of guanosine 5'-monophosphate and guanosine in dimethylsulfoxide.

The tetrabutylammonium salt of guanosine 5'-monophosphate (5'-GMP) dissolves in DMSO-d6 forming aggregated species which exhibit some properties of reverse micelles. 1H NOESY experiments show that the 5'-GMP adopts the syn conformation about the glycosidic bond. Molecular mechanics calculations reveal a stable structure with this conformation in which the phosphate group and the amino group of the base are in close enough proximity to hydrogen bond. In contrast inosine 5'-monophosphate in DMSO-d6, which has no NH2 group for hydrogen bond stabilization of the syn conformation, is shown by NMR to have the anti structure. Guanosine in DMSO-d6 behaves differently from 5'-GMP. Guanosine adopts the anti conformation and forms a symmetric dimer via hydrogen bonding between the N3 and NH2 of the bases.