Synthesis of abasic locked nucleic acid and two seco-LNA derivatives and evaluation of their hybridization properties compared with their more flexible DNA counterparts

To investigate the structural basis of the unique hybridization properties of LNA (locked nucleic acid) three novel LNA derivatives with modified carbohydrate parts were synthesized and evaluated with respect to duplex stabilities. The abasic LNA monomer (X(L), Figure 1) with the rigid carbohydrate moiety of LNA but no nucleobase attached showed no enhanced duplex stabilities compared to its more flexible abasic DNA counterpart (X, Figure 1). These results suggest that the exceptional hybridization properties of LNA primarily originate from improved intrastrand nucleobase stacking and not backbone preorganization. Two monocyclic seco-LNA derivatives, obtained by cleavage of the C1'-O4' bond of an LNA monomer or complete removal of the O4'-furanose oxygen atom (Z(L) and dZ(L), respectively, Figure 1), were compared to their acyclic DNA counterpart (Z, Figure 1). Even though they are more constrained than Z, the seco-LNA derivatives Z(L) and dZ(L) destabilize duplex formation even more than the flexible seco-DNA monomer Z.     

C5-functionalized DNA, LNA, and α-L-LNA: positional control of polarity-sensitive fluorophores leads to improved SNP-typing

Single nucleotide polymorphisms (SNPs) are important markers in disease genetics and pharmacogenomic studies. Oligodeoxyribonucleotides (ONs) modified with 5-[3-(1-pyrenecarboxamido)propynyl]-2'-deoxyuridine monomer X enable detection of SNPs at non-stringent conditions due to differential fluorescence emission of matched versus mismatched nucleic acid duplexes. Herein, the thermal denaturation and optical spectroscopic characteristics of monomer X are compared to the corresponding locked nucleic acid (LNA) and α-L-LNA monomers Y and Z. ONs modified with monomers Y or Z result in a) larger increases in fluorescence intensity upon hybridization to complementary DNA, b) formation of more brightly fluorescent duplexes due to markedly larger fluorescence emission quantum yields (Φ(F)=0.44-0.80) and pyrene extinction coefficients, and c) improved optical discrimination of SNPs in DNA targets. Optical spectroscopy studies suggest that the nucleobase moieties of monomers X-Z adopt anti and syn conformations upon hybridization with matched and mismatched targets, respectively. The polarity-sensitive 1-pyrenecarboxamido fluorophore is, thereby, either positioned in the polar major groove or in the hydrophobic duplex core close to quenching nucleobases. Calculations suggest that the bicyclic skeletons of LNA and α-L-LNA monomers Y and Z influence the glycosidic torsional angle profile leading to altered positional control and photophysical properties of the C5-fluorophore.     

15N NMR spectroscopy. 30—structure/shift relationships of oligopeptides and copolypeptides,including gramicidin S

The ¹⁵N NMR spectra of various oligopeptide derivatives of the Z? X? Y? Y? OMe structure, where X and Y are variable amino acids and Z is the benzyloxycarbonyl group, were measured in several protic and aprotic solvents. The shift difference of the ¹⁵N of the Y? Y and X? Y bond (neighbouring residue effect) is discussed with respect to the nature of X and Y with respect to the solvent. Oligopeptides of the Z? X? Y? Y? OH and n?H₃? X? Y? Y? OMe structures were compared with the Z-pëptide esters to investigate the spectroscopic influence of the protecting groups. The methyl ester hydrochlorides of the 25 most common amino acids were measured in water and DMSO to elucidate the solvent dependence of the substituent effects. Moreover, the methyl ester hydrochlorides were compared with Z-amino acids and N-acetyl-amino acid methyl esters in DMSO to establish whether the substituent effects depend on the nature of the amino acid derivatives. In this connection the assignments of the serine, threonine and glycine signals are discussed with respect to silk proteins. Furthermore, the assignments of the signals of copolypeptides by comparison with oligo- and homo-polypeptides are discussed. Finally, it was demonstrated that intramolecular H bonds cause downfied shifts of 7–10 ppm of the acceptor amide groups.     

Oligonucleotides Containing Novel 4′‐C‐ or 3′‐C‐(Aminoalkyl)‐Branched Thymidines

The synthesis of four novel 3′‐C‐branched and 4′‐C‐branched nucleosides and their transformation into the corresponding 3′‐O‐phosphoramidite building blocks for automated oligonucleotide synthesis is reported. The 4′‐C‐branched key intermediate 11 was synthesized by a convergent strategy and converted to its 2′‐O‐methyl and 2′‐deoxy‐2′‐fluoro derivatives, leading to the preparation of novel oligonucleotide analogues containing 4′‐C‐(aminomethyl)‐2′‐O‐methyl monomer X and 4′‐C‐(aminomethyl)‐2′‐deoxy‐2′‐fluoro monomer Y (Schemes 2 and 3). In general, increased binding affinity towards complementary single‐stranded DNA and RNA was obtained with these analogues compared to the unmodified references (Table 1). The presence of monomer X or monomer Y in a 2′‐O‐methyl‐RNA oligonucleotide had a negative effect on the binding affinity of the 2′‐O‐methyl‐RNA oligonucleotide towards DNA and RNA. Starting from the 3′‐C‐allyl derivative 28 , 3′‐C‐(3‐aminopropyl)‐protected nucleosides and 3′‐O‐phosphoramidite derivatives were synthesized, leading to novel oligonucleotide analogues containing 3′‐C‐(3‐aminopropyl)thymidine monomer Z or the corresponding 3′‐C‐(3‐aminopropyl)‐2′‐O,5‐dimethyluridine monomer W (Schemes 4 and 5). Incorporation of the 2′‐deoxy monomer Z induced no significant changes in the binding affinity towards DNA but decreased binding affinity towards RNA, while the 2′‐O‐methyl monomer Z induced decreased binding affinity towards DNA as well as RNA complements (Table 2).     

Taxumairols X--Z,new taxoids from Taiwanese Taxus mairei

In addition to 19-dydroxybaccatin III, 1beta-hydroxy-5 alpha-deacetylbaccatin I, taxayuntin G and 13-O-deacetyltaxumairol Z (4), three new taxane diterpenoids, taxumairols X (1), Y (2), Z (3) have been isolated from extracts of the Formosan Taxus mairei (LEMEE & LEVL.) S. Y. HU. Compounds 1-2 belong to the 11(15-->1)-abeo-taxane system, having a tetrahydrofuran ring at C-2, C-3, C-4 and C-20. The new compound 3 and 4, which was misidentified previously are derivatives of 11(15-->1)-abeo-taxane with an intact oxirane system. The structures of compounds 1-4 were elucidated on the basis of extensive two dimensional (2D)-NMR analysis.     

Synthesis, structure, electrochemistry, and spectroelectrochemistry of hypervalent phosphorus(V) octaethylporphyrins and theoretical analysis of the nature of the PO bond in P(OEP)(CH(2)CH(3))(O)

A variety of phosphorus(V) octaethylporphyrin derivatives of the type [P(OEP)(X)(Y)](+)Z(-) (OEP: octaethylporphyrin) (X = CH(3), CH(2)CH(3), C(6)H(5), F; Y = CH(3), CH(2)CH(3), OH, OCH(3), OCH(2)CH(3), On-Pr, Oi-Pr, Osec-Bu, NHBu, NEt(2), Cl, F, O(-); Z = ClO(4), PF(6)) were prepared. X-ray crystallographic analysis of eleven compounds reveals that the degree of ruffling of the porphyrin core becomes greater and the average P-N bond distance becomes shorter as the axial ligands become more electronegative. Therefore, the electronic effect of the axial substituents plays a major role in determining the degree of ruffling although the steric effect of the substituents plays some role. A comparison of the (1)H NMR chemical shifts for the series of [P(OEP)(CH(2)CH(3))(Y)](+)Z(-) complexes with those of the corresponding arsenic porphyrins, which possess a planar core, indicates a much smaller ring current effect of the porphyrin core in the severely ruffled phosphorus porphyrins. The electrochemistry, spectroelectrochemistry and ESR spectroscopy of the singly reduced compounds are also discussed. The OH protons of [P(OEP)(X)(OH)](+) are acidic enough to generate P(OEP)(X)(O) by treatment with aq dilute NaOH. X-ray analysis of P(OEP)(CH(2)CH(3))(O) reveals that the PO bond length is very short (1.475(7) A) and is comparable to that in triphenylphosphine oxide (1.483 A). The features of the quite unique hexacoordinate hypervalent compounds are investigated by density functional calculation of a model (Por)P(CH(2)CH(3))(O) and (Por)P(F)(O) (Por: unsubstituted porphyrin).     

Use of oxidation-state differences and molecular orbitals to interpret bonding in the series ONXYZ (X, Y, Z=H, F, Cl), HNNX3, HNNX2Y, and HNNXY2 (X, Y=H, F) and OCX3-, OCX2Y-, and OCXY2- (X, Y=H, F)

Bonding in the series ONXYZ (X, Y, Z=H, F, Cl), HNNX3, HNNX2Y, HNNXY2 (X, Y=H, F), and OCX3-, OCX2Y-, OCXY2- (X, Y=H, F) shows evidence of a significant ionic contribution modifying the underlying covalent bonding. Increased ionic character can be correlated with oxidation-state differences between the bound atoms and is expressed in terms of shorter bond lengths. All members of the series, with the exception of ONH3, HNNH3, and OCH3-, possess a multiple O-N, N-N, or C-O bond modified by the ionic character of that bond. The O-N, N-N, and O-C single bonds in ONH3, HNNH3, and OCH3-, respectively, show some variation in length relative to "typical" single bonds of these types due to differences in ionic character. The two highest-occupied molecular orbitals in the ONXYZ or OCXYZ- (X, Y, Z=H, F) series which are piNO or piCO (when X=Y=Z=H) exhibit a distinct shift in their nodal plane as hydrogen is replaced by fluorine. The nodal plane moves from a location between the oxygen and the nitrogen or carbon to between the nitrogen or carbon and the fluorines impacting on the nature and length of the bonds joining these atoms. The pattern of N-F and C-F bond lengths in the series, ONH3-ONF3 and OCH3--OCF3-, respectively, lends support to the idea of resonance structures of the form ONXY+ F- or OCXY F- (where X, Y=H, F).     

Skeletal structures of hexa-organo substituted triatomics R3XYZR3: A rationalisation using the second-order Jahn—Teller effect

In compounds of type R₃XYZR₃ (R  phenyl, methyl, benzyl; X, Z  Al, Si, P, Ge, Sn; Y  C, N, O, F) linearity of the XYZ skeleton is predicted by the second-order Jahn—Teller effect in those examples where the valence orbitals of X and Z are much less tightly bound than those of Y. When the X and Z orbitals are bound more tightly than those of Y, the XYZ skeleton is predicted to be non linear at Y. The effects of varying R, X and Z, and the contribution of π-interactions are discussed.     

The first alpha-fluoroallenylphosphonate, the synthesis of conjugated fluoroenynes, and the stereoselective synthesis of vinylfluorophosphonates using a new multifunctional fluorine-containing building block

Limitations on current methodologies for the introduction of CF(2) and CFH in complex alpha-fluorophosphonates led to the synthesis of a fluorine-containing building block TIPS-C&tbd1;CCFXP(O)(OEt)(2), where X = H or F. This multifunctional fluorine synthon reacts with carbonyl compounds under WHE conditions to give high yields of fluorinated conjugated enynes and enediyne. When X = F, trapping of the desilylated anion with an electrophile after TIPS removal provided exclusive access to gamma-substituted derivatives of alpha-fluorophosphonates. When X = H, TBAF deprotection of the silyl group yields H(2)C=C=CFP(O)(OEt)(2) through an allenyl-propargyl resonance stabilized anion. The allene moiety has been used as template in the stereoselective synthesis of alpha-fluoro-beta, gamma-diiodopropenyl phosphonate, via electrophilic iodination, and alpha-fluoro-gamma-amino-alpha,beta-unsaturated phosphonates, including unsaturated phosphononucleosides, by nucleophilic displacement of an allylic iodide. Hydroamination of H(2)C=C=CFP(O)(OEt)(2) using secondary amines produced (Z)-alpha-fluoroenaminophosphonates, whereas Diels-Alder cycloaddition with cyclopentadiene provides the corresponding exocyclic vinylfluorophosphonate.     

Exceptionally high in vitro antitumor activity of substituted triphenyltin benzoates including salicylates against a human mammary tumor,MCF-7, and a colon carcinoma,WiDr

Nine new substituted triphenyltin benzoates of the type Ar₃Sn? OOC? C₆H₂XYZ [X = Y = H, Z = 2-OCH₃ and 4-F; X = H, Y = 3-F, Z = 5-F; X = H, Y = 2-OH, Z = 5-Cl, 5-NH₂, 5-OCH₃ and 5-SO₃H; X = 2-OH, Y = 3-CH(CH₃)₂ and Z = 5-CH(CH₃)₂] were prepared and possess considerable in vitro antitumor activity against two human tumor cell lines (MCF-7, a mammary tumor, and WiDr, a colon carcinoma) comparable with that of mitomycin C.     

Estimation of the Anomeric Effect of the Cyano Group

ABSTRACT

The anomeric effect^1,2 is a well established phenomenon among carbohydrate derivatives, and more generally among 2-substituted tetrahydropyrans. The generalized anomeric effect¹ refers to structural moieties R-X-C-Y (where X possesses one or two lone pairs of electrons, and Y is an atom or group of high electronegativity) in both open chain or cyclic molecules. Thus hydroxyacetonitrile prefers to exist in the gauche conformation,^3,4 and several 3-cyano-perhydro-1,2-oxazine derivatives prefer conformations in which the C-3--CN bond and the lone pair of the nitrogen are coplanar.⁵ Investigation of conformational equilibria of all but one 2,6-anhydro-hexononitrile^6,7 (pentopyranosyl cyanides) left doubt relating to the anomeric effect of the cyano group, and raised the possibility of a stabilizing interaction between 1,3-diaxial cyano and acetoxy groups.     

Gas-phase protonation and deprotonation of acrylonitrile derivatives N[triple chemical bond]C--CH==CH--X (X=CH(3), NH(2), PH(2), SiH(3))

A combined experimental and theoretical study on the gas-phase basicity and acidity of a series of cyanovinyl derivatives is presented. The gas-phase basicities and acidities of (N[triple chemical bond]C--CH==CH--X, X=CH(3), NH(2)) were obtained by means of Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometry techniques. The corresponding calculated values were obtained at the G3B3 level of theory. The effects of exchanging CH(3) for SiH(3), and NH(2) for PH(2), were analyzed at the same level of theory. For the neutral molecules, the Z isomer is always the dominant species under standard gas-phase conditions at 298 K. The loss of the proton from the substituent X was found systematically to be much more favorable than deprotonation of the HC==CH linking group. The corresponding isomeric E ion is much more stable than the Z ion, so that only the former should be found in the gas phase. The most significant structural changes upon deprotonation occur for the methyl and amino derivatives because, in both cases, deprotonation of X leads to a significant charge delocalization in the corresponding anion. Protonation takes place systematically at the cyano group, whereby the isomeric E ion is again more stable than the Z ion. Push-pull effects explain the preference of aminoacrylonitrile to be protonated at the cyano group, which also explains the high basicity of this derivative relative to other members of the analyzed series that present rather similar gas-phase basicities, GB approximately 780 kJ mol(-1), indicating that the different nature of the substituents has only a weak effect on the intrinsic basicity of the cyano group. The cyanovinyl derivatives have a significantly stronger gas-phase acidity than that of the corresponding vinyl compounds CH(2)==CH--X. This acidity-strengthening effect of the cyano group is attributed to the greater stabilization of the anion with respect to the corresponding neutral compound.     

A series of novel 2,6-bis(imino)pyridyl iron catalysts: synthesis, characterization and ethylene oligomerization

A series of novel 2,6-bis(imino)pyridyl iron complexes {2,6-(2-X-4-Y-5-ZC₆H₂NCCH₃)₂C₅H₃N}FeCl₂ (X = Cl, Y = CH₃, Z = H (2); X = Br, Y = CH₃, Z = H (3); X = F, Y = H, Z = CH₃ (4); X = Cl, Y = H, Z = CH₃ (5); X = Cl, Y = F (7)) have been synthesized and characterized with elemental analysis and IR. These iron coordinative complexes, activated with methylaluminoxane (MAO), lead to highly active ethylene oligomerization (>10⁷ g/mol Fe h) and the products are mostly linear α-olefins (>90%). The catalytic activities and product properties depend on the substituents on aryl rings and the reaction conditions. As reaction temperature increases, the catalytic activities decrease rapidly and more low-molar-mass products are produced. The product distributions are almost independent of the Al/Fe molar ratio, but the catalytic activities change in different trends when the ortho-substituents on the aryl rings are different. The other three complexes have also been synthesized for comparison to investigate the steric hindrance and electronic effect on the properties of complexes. The complex with adaptable steric hindrance and electronic properties exhibits the highest catalytic activities.     

Umsetzung von 2-Dimethylamino-(1,3,2)-diox-, oxathi- und dithi-arsolanen mit Alkoholen und Thiolen

Reaction of 2-Dimethylamino-(1,3,2)-diox-, oxathi-, and dithi-arsolanes with Alcohols or Thiols The reactions of 2-dimethylamino-(l, 3,2)-diox-, oxathi- and dithi-arsolanes (CH₂)₂XYAs? N(CH₃)₂ (X = Y = O or S; X = S, Y = O) with alcohols and thiols yield by cleavage of the As? N bond in the formation of alkoxy and alkylmercaptoarsolanes (CH₂)₂XYAs? ZR (X = Y = Z = O or S; X = Y: O, Z = S; X = Y = S, Z = O; X = S, Y = O, Z = O or S), respectively. Some of these arsolanes are not stable but rearrange under formation of 1,2-Bis-(arsolanyl)ethane and arsinous acid esters.     

Infrared spectra of heterocumulenes—VII: Correlations of infrared gruop wavenumbers and integrated absorption intensities in some heterocumulenes with substituent constants

A statistical evaluation of the empirical linear relations of the ν_as(X=Y=Z) integrated absorption intensities (A) in forty various heterocumulenes with substituent constants σ and σ⁺ has been carried out. The correlations of log A with substituent constants show that the positive sign of the slopes and ⁺ has been observed, suggesting that with all heterocumulenes studied the structure of the X=Y=Z group with cumulative bonds is dominant.     

Oligodeoxynucleotides containing alpha-L-ribo configured LNA-type C-aryl nucleotides

Synthesis of 2[prime or minute]-O,4[prime or minute]-C-methylene-[small alpha]-l-ribofuranosyl derivatives containing phenyl and 1-pyrenyl aglycons, i.e., novel [small alpha]-l-ribo configured LNA-type C-aryl nucleosides, has been accomplished. Key synthetic steps included stereoselective Grignard reactions on tetrahydrofuran aldehyde, configurational inversion of the resulting alcohol into alcohol, and concomitant Mitsonobu cyclization furnishing the desired bicyclic furanosyl skeleton with a locked conformation. The phosphoramidite derivatives and were used for automated synthesis of 9-mer DNA and [small alpha]-L-LNA oligonucleotides containing the [small alpha]-L-LNA-type C-aryl monomers ([small alpha]L)Ph(L) and ([small alpha]L)Py(L) containing a phenyl and pyrenyl aglycon, respectively. Thermal denaturation studies showed universal base pairing behavior for the pyrenyl monomer ([small alpha]L)Py(L) when incorporated into a DNA or an [small alpha]-L-LNA oligonucleotide.     

Three-block bi-focal PLS (3BIF-PLS) and its application in QSAR

When X and Y are multivariate, the two-block partial least squares (PLS) method is often used. In this paper, we outline an extension addressing a special case of the three-block (X/Y/Z) problem, where Z sits "under" Y. We have called this approach three-block bi-focal PLS (3BIF-PLS). It views the X/Y relationship as the dominant problem, and seeks to use the additional information in Z in order to improve the interpretation of the Y-part of the X/Y association. Two data sets are used to illustrate 3BIF-PLS. Example I relates to single point mutants of haloalkane dehalogenase from Sphingomonas paucimobilis UT26 and their ability to transform halogenated hydrocarbons, some of which are found as organic pollutants in soil. Example II deals with soil remediation capability of bacteria. Whole bacterial communities are monitored over time using "DNA-fingerprinting" technology to see how pollution affects population composition. Since the data sets are large, hierarchical multivariate modelling is invoked to compress data prior to 3BIF-PLS analysis. It is concluded that the 3BIF-PLS approach works well. The paper contains a discussion of pros and cons of the method, and hints at further developmental opportunities.     

Stereochemistry of anionic vinyl polymerization

The stereochemistry of anionic polymerization of vinyl monomers: CH₂=C(R)C(Y)=X where X and Y are O, N or C and R = H or alkyl is discussed in terms of a: the geometry of the -CH₂C-(R)C(Y)=X intermediate existing as E- or Z-isomers; b: the interactions of cation (Li, Na, etc.) with the anion and coordinating groups on the penultimate or antepenultimate asymmetric carbon. The E/Z ratio appears to be determined directly by the s-trans/s-cis approach of the monomer. The nature of the coordination of the counter ion is considerably more complicated and is discussed in detail.     

New synthetic routes to biscarbonylbipyridinerhenium(I) complexes cis,trans-[Re(X2bpy)(CO)2(PR3)(Y)n+ (X2bpy = 4,4'-X2-2,2'-bipyridine) via photochemical ligand substitution reactions, and their photophysical and electrochemical properties

Photochemical ligand substitution of fac-[Re(X2bpy)(CO)3(PR3)]+ (X2bpy = 4,4'-X2-2,2'-bipyridine; X = Me, H, CF3; R = OEt, Ph) with acetonitrile quantitatively gave a new class of biscarbonyl complexes, cis,trans[Re(X2bpy)(CO)2(PR3)(MeCN)]+, coordinated with four different kinds of ligands. Similarly, other biscarbonylrhenium complexes, cis,trans-[Re(X2bpy)(CO)2(PR3)(Y)]n+ (n = 0, Y = Cl-; n = 1, Y = pyridine, PR'3), were synthesized in good yields via photochemical ligand substitution reactions. The structure of cis,trans-[Re(Me2bpy)(CO)2[P(OEt)3](PPh3)](PF6) was determined by X-ray analysis. Crystal data: C38H42N2O5F6P3Re, monoclinic, P2(1/a), a = 11.592(1) A, b = 30.953(4) A, c = 11.799(2) A, V = 4221.6(1) A3, Z = 4, 7813 reflections, R = 0.066. The biscarbonyl complexes with two phosphorus ligands were strongly emissive from their 3MLCT state with lifetimes of 20-640 ns in fluid solutions at room temperature. Only weak or no emission was observed in the cases Y = Cl-, MeCN, and pyridine. Electrochemical reduction of the biscarbonyl complexes with Y = Cl- and pyridine in MeCN resulted in efficient ligand substitution to give the solvento complexes cis,trans-[Re(X2bpy)(CO)2(PR3)(MeCN)]+.     

Efficient, one-pot transformation of indoles into functionalized oxindole and spirooxindole systems under Swern conditions

The reaction of indole derivatives bearing a 3- or 4-hydroxyalkyl chain with dimethylsulfoxide and oxalyl chloride under Swern conditions led to a one-pot, three-component process involving three different synthetic transformations, namely oxidation of indole to oxindole, introduction of a chlorine substituent at the oxindole C-3 position and substitution of the hydroxyl group in the side chain by chlorine, in good to excellent overall yields. The same conditions, applied to a 2-methylindole, afforded a 2-formylindole derivative oxidized at its side chain. The reaction starting from one indole with a 2-hydroxyalkyl chain furnished 3-(2-hydroxyalkyl)oxindoles. Finally, application of the Swern conditions to derivatives of indole-3-propionic or -butyric acid afforded 3-spirooxindole lactones.