(1S,2R/1R,2S)-ainocyclohexyl glycyl thymine PNA: synthesis,monomer crystal structures,and DNA/RNA hybridization studies

[structure: see text] The synthesis of ethyl cis-(1S,2R/1R,2S)-2-aminocyclohex-1-yl-N-(thymin-1-yl-acetyl) glycinate (10a and 10b) via enzymatic resolution of the key racemic intermediate trans-2-azido cyclohexanols 3 is reported. The crystal structures of 10 show equatorial disposition of the tertiary amide group, with the torsion angle beta in the range 60-70 degrees. The PNA oligomers incorporating these show differential effects in hybridizing with complementary DNA and RNA.     

(2S,5R/2R,5S)-Aminoethylpipecolyl aepip-aegPNA chimera: synthesis and duplex/triplex stability

This article reports the design and facile synthesis of novel chiral six-membered PNA analogues (2S,5R/2R,5S)-1-(N-Boc-aminoethyl)-5-(thymin-1-yl)pipecolic acid, aepipPNA IV that upon incorporation into standard aegPNA sequences effected stabilization of complexes with complementary target DNA. Substitution of aegPNA unit by the designed monomer at the C-terminus was more effective than substitution at N-terminus. The stabilizing behaviour improved with degree of substitution and was found to be dependent on their relative positions in the sequence. The six-membered piperidine ring in the design may freeze the rigid chair conformations and the relative stereochemistry of the substituents may in effect direct the complex formation with DNA/RNA by sequence-specific nucleobase recognition. In the present aepipPNA analogues, the l-trans stereochemical disposition of the substituents seems to lead to the favorable pre-organization of the PNA oligomers for complex formation with DNA. The results reported here further expand the repertoire of cyclic PNA analogues.     

Chair/Twist-Boat Energy Gap in Monocyclic, Conformationally Unconstrained Polyalkylcyclohexanes

A conformational search procedure (HUNTER), in combination with the MM3(92) program, was used for the exploration of the conformational hypersurface of alkyl-substituted cyclohexanes and for the calculation of their chair/twist-boat (TB) energy gap. The systems studied were conformationally unconstrained polyalkylcyclohexanes (alkyl = methyl, ethyl, isopropyl, and tert-butyl) possessing either geminal and/or vicinal arrangements of the alkyl groups, but differing in the number of alkyl substituents and in their relative disposition (i.e., cis or trans). The calculations indicate that in 1,1,3,3,5,5-hexaisopropylcyclohexane the TB is the lowest energy form. Modification of the cis,trans relationship of vicinal alkyl groups changes the chair/TB energy gap, and in the minimum energy conformation of cis,trans,trans-1,2,3,4-tetraisopropylcyclohexane (23c) and cis,syn,cis-1,2,4,5-tetraisopropylcyclohexane (31c) the cyclohexyl ring adopts a TB conformation. The tetrasubstituted systems cis,syn,cis-1,2-diisopropyl-3,4-dimethylcyclohexane (46), cis,syn,cis-1,4-diisopropyl-2,5-dimethyl-cyclohexane (47), and cis,trans,trans-1,2-diisopropyl-3,4-dimethylcyclohexane (41) are the least crowded monocyclic unconstrained cyclohexanes found in which the TB conformation is of lower energy than the chair form. The present study indicates that two methyls and two isopropyl substituents are sufficient for stabilizing the TB form of a cyclohexyl ring relative to the chair form.     

Furan forming reactions of cis-2-alken-4-yn-1-ones

[reactions: see text] The cis-2-alken-4-yn-1-one, 1-phenyl-cis-2-penten-4-yn-1-one (cis-1), readily dimerizes on treatment with weak acid to give the 1,2-difurylethylenes, trans- and cis-1,2 di(2-(5-phenylfuryl))ethene (trans-1 and cis-2), in 62% and 23% yields, respectively. Trimerization of cis-1 to trans,trans-1,2,3-tri(2-(5-phenylfuryl)cyclopropane (4) occurred as a byproduct of treatment with weak acid. These reactions demonstrate the 2-furylcarbenoid reactivity of cis-2-alken-4-yn-1-ones.     

Pyrrolidine nucleic acids: DNA/PNA oligomers with 2-hydroxy/aminomethyl- 4-(thymin-1-yl)pyrrolidine-N-acetic acid

Synthesis of pyrrolidine-based chiral positively charged DNA analogues is reported. The synthesis of (2S,4S) and (2R,4R) thymin-1-ylpyrrolidine-N-acetic acid, its site specific incorporation in PNA:DNA chimera and PNA, and the study of their binding properties with complementary DNA/RNA sequences is presented.     

Synthesis of 7-azabicyclo[2.2.1]heptane and 2-oxa-4-azabicyclo[3.3.1]non-3-ene derivatives by base-promoted heterocyclization of alkyl N-(cis(trans)-3,trans(cis)-4-dibromocyclohex-1-yl)carbamates and N-(cis(trans)-3,trans(cis)-4-dibromocyclohex-1-yl)-2,2,2-trifluoroacetamides

We have studied the base-promoted heterocyclization of alkyl N-(cis(trans)-3,trans(cis)-4-dibromocyclohex-1-yl)carbamates and N-(cis(trans)-3,trans(cis)-4-dibromocyclohex-1-yl)-2,2,2-trifluoroacetamides, investigating the effect of the nitrogen protecting group and the relative configuration of the leaving group at C3 and C4 on the outcome of this reaction. We have observed that the sodium hydride-promoted heterocyclization of alkyl N-(cis-3,trans-4-dibromocyclohex-1-yl)carbamates (10, 12, 14, 16, 18) is a convenient method for the synthesis of 7-azabicyclo[2.2.1]heptane derivatives. For instance, the reaction of tert-butyl N-(cis-3,trans-4-dibromocyclohex-1-yl)carbamate (10) with sodium hydride in DMF at room temperature provides 2-bromo-7-[(tert-butoxy)carbonyl]-7-azabicyclo[2.2.1]heptane (2) (52% yield), whose t-BuOK-promoted hydrogen bromide elimination affords 7-[(tert-butoxy)carbonyl]-7-azabicyclo[2.2.1]hept-2-ene (31) in 78% yield, an intermediate in the total synthesis of epibatidine (1). However, the NaH/DMF-mediated heterocyclization of alkyl N-(trans-3,cis-4-dibromocyclohex-1-yl)carbamates (11, 13) is a more structure dependent reaction, where the nucleophilic attack of the oxygen atom of the protecting group controls the outcome of the reaction, giving rise to benzooxazolone and 2-oxa-4-azabicyclo[3.3.1]non-3-ene derivatives, respectively, from low to moderate yields, in complex reaction mixtures. Conversely, the NaH/DMF heterocyclizations of N-(cis-3,trans-4-dibromocyclohex-1-yl)-2,2,2-trifluoroacetamide (40) or N-(trans-3,cis-4-dibromocyclohex-1-yl)-2,2,2-trifluoroacetamide (42) are very clean reactions giving 7-azabicyclo[2.2.1]heptane or 2-oxa-4-azabicyclo[3.3.1]non-3-ene derivatives, respectively, in good yields. Finally, a mechanistic investigation, based on DFT calculations, has been carried out to rationalize the formation of the different adducts.     

The stereochemistry of the thermal cheletropic decarbonylation of 3-cyclopentenone as determined by multiphoton infrared photolysis/thermolysis

There are two allowed pathways for the thermal cheletropic decarbonylation of 3-cyclopentenone. The stereochemistry of decarbonylation of an unconstrained derivative (trans,trans-2,5-dimethyl-3-cyclopentenone, 4) has been determined for the first time. Under conventional pyrolysis conditions, thermal rearrangements of the initial product (trans,trans-2,4-hexadiene, 5) occur at the high temperatures required for the decarbonylation. However, by using multiphoton infrared photolysis/thermolysis to initiate decarbonylation, it was shown that the initial products from thermal decarbonylation of 4 are solely carbon monoxide and stereospecifically 5. The stereochemistry of decarbonylation is thus disrotatory, in accord with prior theoretical studies. A survey of crystal structures reveals ground-state distortions along this reaction coordinate as well.     

Stereoselective syntheses of dihydroxerulin and xerulinic acid, anti-hypocholesterolemic dyes from the fungus Xerula melanotricha

The title compounds 2 and 3, which are inhibitors of the biosynthesis of cholesterol, were synthesized in a convergent and perfectly stereoselective manner. In the key step, bromobutenolide 6 (obtained from levulinic acid in two steps) was coupled with either of the novel bis(stannanes) trans,cis,trans-35 or trans,trans,trans-35 [each accessible from 3-(tributylstannyl)allyl alcohol (17) in four steps], giving gamma-alkylidenebutenolide trans,trans,trans-32. This compound was coupled with iododiyne 42 or the bromoenediynoate 44 leading to dihydroxerulin (2) and to the (trimethylsilylethyl)ester 45 of xerulinic acid, respectively. Deprotection of the latter provided totally synthetic xerulinic acid (3) for the first time.     

Chimeric peptide nucleic acids incorporating (2S,5R)-aminoethyl pipecolyl units: synthesis and DNA binding studies

The design and facile synthesis of a novel chiral six-membered PNA analogue (2S,5R )-1-(N-Boc-aminoethyl)-5-(thymin-1-yl)pipecolic acid, aepipPNA, that upon incorporation into PNA sequences effected stabilization of complexes with target complementary DNA. This is the first example where a six membered-PNA is shown to be capable of forming stable complexes with DNA and further expands the repertoire of cyclic PNA analogues.     

Synthesis of new trans-2-benzyl-3-(furan-2-yl)-4-substituted-1,2,3,4-tetrahydroisoquinolinones

The reaction of homophthalic anhydride and N-(furan-2-yl-methylidene)- benzylamine in different solvents and varying temperatures was studied in detail. Mixtures of the expected trans- and cis-1,2,3,4-tetrahydroisoquinoline-4-carboxylic acids trans-5 and cis-5, along with by-products 6 and 7 were obtained in dichloroethane or benzene. In pyridine, used for the first time, the reaction became completely diastereoselective, giving only the trans isomer. The carboxylic acid group of trans-5 was transformed in four steps into cyclic aminomethyl groups which yielded various new tetrahydroisoquinolinones trans- 11a-g, incorporating both a known fragment of pharmacological interest and various pharmacophoric substituents.     

LC diketones: synthesis, transformations and mesomorphic properties

The synthesis and chemical transformations of various diketones into liquid crystalline compounds are discussed. The diketones were prepared by the interaction of cyclohexene with acid chlorides and benzene in the presence of aluminium chloride (Nenitzescu method) or by Friedel Crafts reaction of trans-4-alkanoyl-1-phenylcyclohexanes or trans-2-alkyl-5-phenylcyclohexanones with acid chlorides, or by the condensation of corresponding Mannich salts with 2-substituted acetoacetates or acetylacetone.     

LC diketones: synthesis,transformations and mesomorphic properties

The synthesis and chemical transformations of various diketones into liquid crystalline compounds are discussed. The diketones were prepared by the interaction of cyclohexene with acid chlorides and benzene in the presence of aluminium chloride (Nenitzescu method) or by Friedel Crafts reaction of trans-4-alkanoyl-1-phenylcyclohexanes or trans-2-alkyl-5-phenylcyclohexanones with acid chlorides, or by the condensation of corresponding Mannich salts with 2-substituted acetoacetates or acetylacetone.     

Synthesis of oligomers of trans-(4S,5R)-4-carboxybenzyl 5-methyl oxazolidin-2-one: an approach to new foldamers.

The synthesis of two oligomers containing three and four residues, respectively, of trans-(4S,5R)-4-carboxy 5-methyloxazolidin-2-ones is described. The monomer is obtained by starting from benzyl-N-Boc-(3R)-aminobutanoate, by cyclization into the corresponding trans-(2S,3R)-2-carboxybenzyl-3-methyl-N-Boc-aziridine and rearrangement of the product to trans-(4S,5R)-4-carboxybenzyl-5- methyloxazolidin-2-one, catalyzed by Sn(OTf)2. The oligomers are synthesized by activating the carboxy group as its pentaflourophenyl ester. The trimer and the tetramer are obtained in good yield, and their 1H NMR spectra suggest that these molecules fold in ordered structures, where the C-4 hydrogen of a ring is always close to the carbonyl of the next ring. This result shows that the 4-carboxy-5-substituted-oxazolidin-2-ones are a new class of pseudoprolines which fully control the formation of a Xaai-1-Proi peptide bond in the trans conformation and are complementary to the pseudoprolines obtained from cyclocondensation of cysteine, serine, or threonine and aldehydes or ketones, which strongly favor the Xaai-1-Proi peptide bond in the cis conformation.     

Influence of trans-cis photoisomerizations of solubilized compounds on transition temperatures in the system cetyltrimethylammonium bromide-water: Light-induced phase transitions

Transition temperatures (TN1) from the nematic lyotropic liquid-crystalline phase to the isotropic phase were measured for the system cetyltrimethylammonium bromide (CTAB) water in the presence of small amounts of 3-stilbene carboxylic acid (3SC), 4-stilbene carboxylic acid (4SC) and Δ2/2'-bi-(2H-l,4-benzothiazine) (BT). TNI, increases as a function of trans-3SC or trans-4SC concentration, ranging from 01 to 08 wt %, by up to 12°C. A further increase in TNI between 2 and 5°C can be achieved by photochemically converting the solubilized trans stilbene derivatives to the cis isomers. Irradiation of a trans-3SC containing sample at a temperature just above TNl leads to a light-induced phase transition to the lyotropic liquid-crystalline phase. Solubilization of trans-BT causes a slight decrease of TNI while photoisomerization to cis-BT increases T_NI by 1°C.     

Synthesis of enantiopure trans-3,4-disubstituted piperidines. An enantiodivergent synthesis of (+)- and (-)-paroxetine

Reaction of (R)-phenylglycinol with methyl 5-oxopentanoate gave either bicyclic lactam cis-1 (the kinetic product) or its isomer trans-1 (under equilibrating conditions) as the major products, which were converted to the corresponding (cis or trans) unsaturated lactams 4 and 5. On treatment with lithium alkyl (or aryl) cyanocuprates, these chiral building blocks undergo conjugate addition to give enantiopure trans-3,4-substituted 2-piperidone derivatives in high yield and stereoselectivity. The synthetic potential of this transformation is illustrated by the synthesis of (+)-femoxetine and the two enantiomers of the known antidepressant paroxetine.     

Synthesis of photolabile o-nitroveratryloxycarbonyl (NVOC) protected peptide nucleic acid monomers

The chemical synthesis of peptide nucleic acid (PNA) monomers was accomplished using various combinations of the o-nitroveratryloxycarbonyl (NVOC) group (N-aminoethylglycine backbone) and base labile acyl-type nucleobase protecting groups (anisoyl for adenine and cytosine; isobutyryl for guanine), thus offering a photolithographic solid-phase PNA synthetic strategy compatible with photolithographic oligonucleotide synthesis conditions and allowing the in situ synthesis of PNA microarrays in an essentially neutral medium, by avoiding the use of the commonly used deprotection reagents such as trifluoroacetic acid or piperidine. Convenient methods were also explored to prepare 1-(carboxymethyl)-4-N-(4-methoxybenzoyl)cytosine and 9-(carboxymethyl)-2-N-(isobutyryl)guanine with good yields.     

Stereochemistry of the [4 + 2] cycloadditions of trans,trans- and cis,trans-2,4-hexadiene to C(60)

The [4 + 2] cycloaddition of trans,trans-2,4-hexadiene with C(60) proceeds via a concerted mechanism with retention of stereochemistry in the cycloadduct 1a. However, when cis,trans-2,4-hexadiene reacts with C(60), isomerization of the cis,trans to the thermodynamically more stable trans,trans isomer occurs. Subsequently, the cis,trans diene isomerized to the trans,trans isomer and cycloadds to C(60), to form adduct 1a. When the reaction is carried out at higher temperatures, the formation of cycloadduct 1b is also obtained. This result is consistent with a concerted cycloaddition of cis,trans-2,4-hexadiene with C(60), which is more reactive at elevated temperatures and leads to the formation of the Diels-Alder adduct 1b.     

A photoactivated trans-diammine platinum complex as cytotoxic as cisplatin

The synthesis and X-ray structure (as the tetrahydrate) of the platinum(IV) complex trans,trans,trans-[Pt(N(3))(2)(OH)(2)(NH(3))(2)] 3 are described and its photochemistry and photobiology are compared with those of the cis isomer cis,trans,cis-[Pt(N(3))(2)(OH)(2)(NH(3))(2)] 4. Complexes 4 and 3 are potential precursors of the anticancer drug cisplatin and its inactive trans isomer transplatin, respectively. The trans complex 3 is octahedral, contains almost linear azide ligands, and adopts a layer structure with extensive intermolecular hydrogen bonding. The intense azide-to-platinum(IV) charge-transfer band of complex 3 (285 nm; epsilon=19 500 M(-1) cm(-1)) is more intense and bathochromically shifted relative to that of the cis isomer 4. In contrast to transplatin, complex 3 rapidly formed a platinum(II) bis(5'-guanosine monophosphate) (5'-GMP) adduct when irradiated with UVA light, and did not react in the dark. Complexes 3 and 4 were non-toxic to human skin cells (keratinocytes) in the dark, but were as cytotoxic as cisplatin on irradiation for a short time (50 min). Damage to the DNA of these cells was detected by using the "comet" assay. Both trans- and cis-diammine platinum(IV) diazide complexes therefore have potential as photochemotherapeutic agents.     

sp carbon chains surrounded by sp(3) carbon double helices: directed syntheses of wirelike Pt(CC)(n)Pt moieties that are spanned by two P(CH(2))(m)P linkages via alkene metathesis

Reactions of trans-(C6F5)(Ph2P(CH2)m'CH=CH2)2PtCl (1; m' = a, 6; b, 7; c, 8; d, 9; e, 10) and H(CC)2H (HNEt2, cat. CuI) give trans-(C6F5)(Ph2P(CH2)m'CH=CH2)2Pt(CC)2H (3a-e, 80-95%). Oxidative homocouplings of 3a-d under Hay conditions (O2, cat. CuCl/TMEDA, acetone) yield trans,trans-(C6F5)(Ph2P(CH2)m'CH=CH2)2Pt(CC)4Pt(Ph2P(CH2)m'CH=CH2)2(C6F5) (4a-d, 64-84%). Treatment of 3c-e with excess HCCSiEt3 under Hay conditions gives trans-(C6F5)(Ph2P(CH2)m'CH=CH2)2Pt(CC)3SiEt3 (56-73%). Homocouplings (n-Bu4N+ F-, Me3SiCl, Hay conditions) afford trans,trans-(C6F5)(Ph2P(CH2)m'CH=CH2)2Pt(CC)6Pt(Ph2P(CH2)m'CH=CH2)2(C6F5) (13c-e, 59-64%). Reactions of 4a-d and 13c-e with Grubbs' catalyst, followed by hydrogenation, give mixtures of trans,trans-(C6F5)(Ph2P(CH2)mPPh2)Pt(CC)nPt(Ph2P(CH2)mPPh2)(C6F5) with termini-spanning diphosphines and trans,trans-(C6F5)(Ph2P(CH2)mPPh2)Pt(CC)nPt(Ph2P(CH2)mPPh2)(C6F5) with trans-spanning diphosphines (m = 2m' + 2; n = 4, 6). The latter (n = 4) are independently synthesized by similar metatheses/hydrogenations of 1a-d to give trans-(C6F5)(Ph2P(CH2)mPPh2)PtCl (49-59%), followed by analogous introductions of (CC)4 chains (66-77%). Crystal structures of complexes with termini-spanning diphosphines show sp3 chains with both double-helical (m/n = 20/4) and nonhelical (m/n = 20/6) conformations, and highly shielded sp chains. The sp3 chains of complexes with trans-spanning diphosphines exhibit double half-clamshell conformations. The dynamic properties of both classes of molecules are analyzed in detail.     

Methods for analysis of conjugated linoleic acids and trans-18:1 isomers in dairy fats by using a combination of gas chromatography, silver-ion thin-layer chromatography/gas chromatography, and silver-ion liquid chromatography

Conjugated linoleic acids (CLA) are octadecadienoic acids (18:2) that have a conjugated double-bond system. Interest in these compounds has expanded since CLA were found to be associated with a number of physiological and pathological responses such as cancer, metastases, atherosclerosis, diabetes, immunity, and body fat/protein composition. The main sources of these conjugated fatty acids are dairy fats. Rumen bacteria convert polyunsaturated fatty acids, especially linoleic and linolenic acids, to CLA and numerous trans- containing mono- and diunsaturated fatty acids. It has been established that an additional route of CLA synthesis in ruminants and monogastric animals, including humans, occurs via delta9 desaturation of the trans-18:1 isomers. To date, a total of 6 positional CLA isomers have been found in dairy fats, each occurring in 4 geometric forms (cis,trans; trans,cis; cis,cis; and trans,trans) for a total of 24. All of these CLA isomers can be resolved only by a combination of gas chromatography (GC), using 100 m highly polar capillary columns, and silver-ion liquid chromatography, using 3 of these 25 cm columns in series. Complete analysis of all the trans-18:1 isomers requires prior isolation of trans monoenes by silver-ion thin-layer chromatography (TLC), followed by GC analysis using the same 100 m capillary columns operated at low temperatures starting from 120 degrees C. These analytical techniques are required to assess the purity of commercial CLA preparations, because their purity will affect the interpretation of any physiological and/or biochemical response obtained. Prior assessment of CLA preparations by TLC is also recommended to determine the presence of any other impurities. The availability of pure CLA isomers will permit the evaluation and analysis of individual CLA isomers for their nutritional and biological activity in model systems, animals, and humans. These techniques are also essential to evaluate dairy fats for their content of specific CLA isomers and to help design experimental diets to increase the level of the desired CLA isomers in dairy fats. These improved techniques are further required to evaluate the CLA profile in monogastric animals fed commercial CLA preparations for CLA enrichment of animal products. This is particularly important because absorption and metabolism will alter the ingested-CLA profile in the animal fed.