Conformational Polymorphism in G-tetraplex Structures: Strand Reversal by Base Flipover or Sugar Flipover

Guanine rich sequences adopt a variety of four stranded structures, which differ in strand orientation and conformation about the glycosidic bond even though they are all stabilised by Hoogsteen hydrogen bonded guanine tetrads. Detailed model building and molecular mechanics calculations have been carried out to investigate various possible conformations of guanines along a strand and different possible orientations of guanine strands in a G-tetraplex structure. It is found that for an oligo G stretch per se, a parallel four stranded structure with all guanines in anti conformation is favoured over other possible tetraplex structures. Hence an alternating syn-anti arrangement of guanines along a strand is likely to occur only in folded back tetraplex structures with antiparallel G strands. Our study provides a theoretical rationale for the observed alternation of glycosidic conformation and the inverted stacking arrangement arising from base flipover, in antiparallel G-tetraplex structures and also highlights the various structural features arising due to different types of strand orientations. The molecular mechanics calculations help in elucidating the various interactions which stabilize different G-tetraplex structures and indicate that screening of phosphate charge by counterions could have a dramatic effect on groove width in these four stranded structures.

Conformational polymorphism in G-tetraplex structures: strand reversal by base flipover or sugar flipover

Guanlne rich sequences adopt a variety of four stranded structures, which differ in strand orientation and conformation about the glycosldic bond even though they are all stabilised by Hoogsteen hydrogen bonded guanlne tetrads. Detailed model building and molecular mechanics calculations have been carried out to investigate various possible conformations of guanlnes along a strand and different possible orientations of guanlne strands In a G-tetraplex structure. It is found that for an ollgo G stretch per se, a parallel four stranded structure with all guanines In anti conformation is favoured over other possible tetraplex structures. Hence an alternating syn-anti arrangement of guanlnes along a strand is likely to occur only in folded back tetraplex structures with antiparallel G strands. Our study provides a theoretical rationale for the observed alternation of glycosldic conformation and the inverted stacking arrangement arising from base filpover, In antlparallel G-tetraplex structures and also highlights the various structural features arising due to different types of strand orientations. The molecular mechanics calculations help in elucidating the various interactions which stabilize different G-tetraplex structures and indicate that screening of phosphate charge by counterions could have a dramatic effect on groove width in these four stranded structures.

Minimizing total completion time on a batch processing machine with job families

We consider the problem of minimizing the total completion time on a single batch processing machine. The set of jobs to be scheduled can be partitioned into a number of families, where all jobs in the same family have the same processing time. The machine can process at most B jobs simultaneously as a batch, and the processing time of a batch is equal to the processing time of the longest job in the batch. We analyze that properties of an optimal schedule and develop a dynamic programming algorithm of polynomial time complexity when the number of job families is fixed. The research is motivated by the problem of scheduling burn-in ovens in the semiconductor industry

Minimizing total completion time on batch processing machines

We study the problem of minimizing total completion time on single and parallel batch processing machines. A batch processing machine is one which can process up to B jobs simultaneously. The processing time of a batch is equal to the largest processing time among all jobs in the batch. This problem is motivated by burn-in operations in the final testing stage of semiconductor manufacturing and is expected to occur in other production environments. We provide an exact solution procedure for the single-machine problem and heuristic algorithms for both single and parallel machine problems. While the exact algorithms have limited applicability due to high computational requirements, extensive experiments show that the heuristics are capable of consistently obtaining near-optimal solutions in very reasonable CPU times.

Radical Annulation Strategy to Chiral Pupukeanones: Total Synthesis of (+)-10-ex&l(- Naphthyl)pupukean-9-onea nd (+)-lO-exo-l(- Naphthyl)-5-epipupukean-9-ones1

Intramolecular alkylation reaction of the bromoenone 12, obtained from S-carvone in three steps, furnished the bicyclo[2.2.2]octenone 13. Contrary to the anticipated radical annulation reaction, the bicyclic bromides 14 and 15, obtained from the enone 13, generated exclusively the cyclopropane product 18 via a 3-exo-trig radical cyclization on reaction with nBu3SnH and AIBN, even in the presence of a large excess of a radicophile. On the other hand, bromoenone 24, synthesized from R-carvone via S-naphthylcarvone 21, underwent radical annulation reaction in the presence of radicophiles to furnish the isotwistanes 25-28 in a regio- and stereospecific manner. Hydrogenation of the olefin 34, obtained from the diketone 27 via a regiospecific Wittig reaction, furnished the naphthyl-5-epipupukean-9-one 33, whereas stereoselective hydrogenation of the enone 36, prepared from the keto ester 25 via a Grignard reaction and dehydration sequence, generated the naphthylpupukeanone 32.

Stereospecific construction of multiple contiguous quaternary carbons. Total synthesis of (±)-cis,anti,cis-1,8,12,12-tetramethyl-4-oxatricyclo[6.4.0.02,6]dodecan-3-ol, a thapsane isolated from Thapsia villosa var minor

The details of the first total synthesis of a natural thapsane lg containing three contiguous quaternary carbon atoms, starting from cyclogeraniol (9) '5 described. The Claisen rearrangement of 9 with methoxypropene in the presence of a catalytic amount of propionic acid produced ketone 10. Rhodium acetate-catalyzed intramolecular cyclopropanation of a-diazo-&keto ester 12, obtained from 10 via 8-keto ester 8, furnished cyclopropyl keto ester 7. Lithium in liquid ammonia reductive cleavage of cyclopropyl compound 7 gave a 1:l mixture of hydrindanone 6 and keto1 13. Wittig methylenation of 6 furnished ester 21. Epoxidation of 21, followed by BF3-OEt2-catalyzed rearrangement of epoxide 23 afforded hemiacetal 25. Treatment of hemiacetal 25 with triethylsilane in trifluoroacetic acid furnished lactone 22, a degradation product of various thapsanes. Finally, DIBAH reduction of lactone 22 generated the thapsane

Synthesis Based on Cyclohexadienes .11. A A new total synthesis of (±)-norprezizanone

Acid catalyzed rearrangement of endo 1-methoxytricyclo[6.2.2.0(3,8)]dodec-2-en-10-ol 8c afforded the ketone 9 which has been transformed into (+/-)-norprezizanone 19 thus completing a formal synthesis of (+/-)-zizaene. A key step in this strategy is a stereospecific 1,4-addition of a methyl group

Synthesis of Isoquinolines from Indanones-Total Synthesis of Illudinine

Schmidt reaction of 5-methoxy or 7-methoxyindan-1-ones or their derivatives results exclusively in isocarbostyrils which are converted into 6-methoxy or 8-methoxyisoquinolines in good yields. This strategy has been extended to the total synthesis of illudinine methyl ester (1b) starting from methyl 8-methoxy-2,2-dimethyl-7-oxo-1,2,3,5,6,7-hexahydro-s-indacene-4-carboxylate (4).

Formal total synthesis of (+)-didemniserinolipid B

The formal total synthesis of (+)-didemniserinolipid B, a marine tunicate possessing a 6,8-dioxabicyclo3.2.1]octane framework, was accomplished starting from L-(+)-tartaric acid. The key transformations in the synthesis include the elaboration of a gamma-hydroxy-amide readily obtained by desymmetrization of tartaric acid bis-amide via the controlled addition of a Grignard reagent followed by stereoselective reduction of the resulting ketone. (C) 2010 Elsevier Ltd. All rights reserved.

Stereoselective total synthesis of (+)-synargentolide A

The stereoselective synthesis of synargentolide A, a polyhydroxy delta-lactone, has been accomplished from tartaric acid. The key steps in the synthesis involve Keck and Brown allylations and ring closing metathesis. (C) 2010 Elsevier Ltd. All rights reserved.

Modification of the sugar specificity of a plant lectin: structural studies on a point mutant of Erythrina corallodendron lectin

A mutant of Erythrina corallodendron lectin was generated with the aim of enhancing its affinity for N-acetylgalactosamine. A tyrosine residue close to the binding site of the lectin was mutated to a glycine in order to facilitate stronger interactions between the acetamido group of the sugar and the lectin which were prevented by the side chain of the tyrosine in the wild-type lectin. The crystal structures of this Y106G mutant lectin in complex with galactose and N-acetylgalactosamine have been determined. A structural rationale has been provided for the differences in the relative binding affinities of the wild-type and mutant lectins towards the two sugars based on the structures. A hydrogen bond between the O6 atom of the sugars and the variable loop of the carbohydrate-binding site of the lectin is lost in the mutant complexes owing to a conformational change in the loop. This loss is compensated by an additional hydrogen bond that is formed between the acetamido group of the sugar and the mutant lectin in the complex with N-acetylgalactosamine, resulting in a higher affinity of the mutant lectin for N-acetylgalactosamine compared with that for galactose, in contrast to the almost equal affinity of the wild-type lectin for the two sugars. The structure of a complex of the mutant with a citrate ion bound at the carbohydrate-binding site that was obtained while attempting to crystallize the complexes with sugars is also presented.

Aromatic claisen rearrangements in carbohydrates: stereocontrol of rearrangement rates in unsaturated sugar substrates

A remarkable difference is observed in the rates of [3,3]-sigmatropic rearrangement of aryl 4,6-di-O-acetyl-2,3-dideoxy-D-erythro-hex-2-enopyranosides 1 and 2; the slower reactivity of the alpha-isomers is consistent with AM1 calculated transition state energetics of model systems.

A stereoselective total synthesis of bakkenolide-a (fukinanolide)

A highly stereoselective synthesis of bakkenolide-A (fukinanolide. 1a) employing the radical mediated spirannulation methodology is described.

First total synthesis of (±)-myltayl-4(12)-ene and single-crystal X-ray structure of exo-12-normyltaylan-4-yl 4-nitrobenzoate

The total synthesis of the unusual sesquiterpene (+/-)-myltayl-4(12)-ene 3 starting from the readily available cyclogeraniol 5 and the single-crystal X-ray structure of the 4-nitrobenzoate 12 of the noralcohol 11 are described.