Stereochemistry of Internucleotide Bond Formation by the H-Phosphonate Method. 5. The Role of Brønsted and H-Bonding Base Catalysis in Ribonucleoside H-Phosphonate Condensation—Chemical and Stereochemical Consequences

REFERENCES

• Hall , R. H. , Todd , A. and Webb , R. F. 1957 . Nucleotides. 41. Mixed Anhydrides as intermediates in the synthesis of dinucleoside phosphates . J. Chem. Soc. , : 3291 – 3296 .
   Web of Science ®Google Scholar
• Garegg , P. J. , Regberg , T. , Stawinski , J. and Strömberg , R. 1985 . Formation Of Internucleotidic Bonds Via Phosphonate Intermediates . Chem. Scr. , 25 : 280 – 282 .
   Google Scholar
• Froehler , B. C. , Ng , P. G. and Matteucci , M. D. 1986 . Synthesis Of DNA Via Deoxynucleoside H-Phosphonate Intermediates . Nucleic Acids Res. , 14 : 5399 – 5407 .
   PubMed Web of Science ®Google Scholar
• Stawinski , J. and Kraszewski , A. 2002 . How To get the most out of two phosphorus chemistries. studies on H-phosphonates . Acc. Chem. Res. , 35 : 952 – 960 .
   PubMed Web of Science ®Google Scholar
• Kraszewski , A. and Stawinski , J. 2007 . H-Phosphonates: Versatile Synthetic precursors to biologically active phosphorus compounds . Pure Appl. Chem. , 79 : 2217 – 2227 .
   Web of Science ®Google Scholar
• Strömberg , R. and Stawinski , J. 2004 . Current Protocols In Nucleic Acid Chemistry , Edited by: Beaucage , S. L. , Bergstrom , D. E. , Glick , G. D. and Jones , R. A. New York : John Wiley & Sons .
   Google Scholar
• Garegg , P. J. , Lindh , I. , Regberg , T. , Stawinski , J. and Strömberg , R. 1986 . Nucleoside H-phosphonates. III. Chemical synthesis of oligonucleotides by the hydrogenophosphonate approach . Tetrahedron Lett. , 27 : 4051 – 4054 .
   Web of Science ®Google Scholar
• Froehler , B. C. and Matteucci , M. D. 1986 . Nucleoside H-phosphonates: Valuable intermediates in the synthesis of deoxynucleotides . Tetrahedron Lett. , 27 : 469 – 472 .
   Web of Science ®Google Scholar
• Garegg , P. J. , Regberg , T. , Stawinski , J. and Strömberg , R. 1987 . Nucleoside H-phosphonates. V. The mechanism of hydrogenophosphonate diester formation using acyl chlorides as coupling agents in oligonucleotide synthesis by the hydrogenophosphonate approach . Nucleosides Nucleotides , 6 : 655 – 662 .
   Web of Science ®Google Scholar
• Froehler , B. C. and Matteucci , M. D. 1987 . The Use of nucleoside h-phosphonates in the synthesis of deoxyoligonucleotides . Nucleosides Nucleotides , 6 : 287 – 291 .
   Web of Science ®Google Scholar
• Dubey , I. Y. , Efimov , V. A. , Lyapina , T. V. and Fedoryak , D. M. 1992 . Nucleophilic catalysts in H-phosphonate internucleotide condensation reaction . Bioorg. Khim. , 18 : 911 – 919 .
   Google Scholar
• Regberg , T. , Stawinski , J. and Strömberg , R. 1988 . Nucleoside H-phosphonates. IX. Possible side-reactions during hydrogen phosphonate diester formation . Nucleosides Nucleotides , 7 : 23 – 35 .
   Web of Science ®Google Scholar
• Troev , K. 2006 . Chemistry and Application of H-Phosphonates , Elsevier Science .
   Google Scholar
• Sigurdsson , S. and Strömberg , R. 2001 . Evaluation of several economical computational methods for geometry optimisation of phosphorus acid derivatives . Nucleosides Nucleotides Nucleic Acids , 20 : 1381 – 1384 .
   PubMed Web of Science ®Google Scholar
• Sigurdsson , S. and Strömberg , R. 2002 . The H-phosphonate approach to oligonucleotide synthesis. an investigation on the mechanism of the coupling step . J. Chem. Soc., Perkin Trans. 2 , : 1682 – 1688 .
   Google Scholar
• Sigurdsson , S. and Strömberg , R. 2002 . Comparison of some computational methods for geometry optimisation of phosphorus acid derivatives . Phosphorus, Sulfur Silicon Relat. Elem. , 177 : 2711 – 2724 .
   Web of Science ®Google Scholar
• Sigurdsson , S. and Strömberg , R. 2003 . Side reactions in the H-phosphonate approach to oligonucleotide synthesis: a kinetic investigation on bisacylphosphite formation and 5’-O-acylation . Nucleosides Nucleotides Nucleic Acids , 22 : 1 – 12 .
   PubMed Web of Science ®Google Scholar
• Almer , H. , Stawinski , J. and Strömberg , R. 1996 . Solid support synthesis of all-R P-oligo(ribonucleoside phosphorothioate)S . Nucleic Acids Res. , 24 : 3811 – 3820 .
   PubMed Web of Science ®Google Scholar
• Sobkowski , M. , Jankowska , J. , Stawinski , J. and Kraszewski , A. 2005 . Collection Symposium Series , Edited by: Hocek , M. 183 – 187 . Prague : Institute Of Organic Chemistry And Biochemistry, Academy Of Sciences Of The Czech Republic .
   Google Scholar
• Sobkowski , M. , Jankowska , J. , Stawinski , J. and Kraszewski , A. 2005 . Stereochemistry of internucleotide bond formation by the H-phosphonate method. 1. synthesis and 31P NMR analysis of 16 diribonucleoside (3′-5′)-H-phosphonates and the corresponding phosphorothioates . Nucleosides Nucleotides Nucleic Acids , 24 : 1469 – 1484 .
   PubMed Web of Science ®Google Scholar
• Sobkowski , M. , Kraszewski , A. and Stawinski , J. 2007 . Stereochemistry of internucleotide bond formation by the H-Phosphonate Method. 3. Investigations on a mechanism of stereoselectivity induction . Tetrahedron: Asymmetry , 18 : 2336 – 2348 .
   Google Scholar
• Sobkowski , M. , Stawinski , J. and Kraszewski , A. 2009 . Stereochemistry of internucleotide bond formation by the H-phosphonate method. 4. The role of nucleophilic catalysis in chemistry and stereochemistry of ribonucleoside H-phosphonate condensation . New. J. Chem. , 33 : 164 – 170 .
   Web of Science ®Google Scholar
• Sobkowski , M. , Stawinski , J. and Kraszewski , A. 2008 . Stereochemistry of internucleotide bond formation by the H-phosphonate method. 6. Optimization of the reaction conditions towards highest stereoselectivity . Tetrahedron: Asymmetry , 19 : 2508 – 2518 .
   Google Scholar
• Efimov , V. A. and Dubey , I. Y. 1990 . Modification Of The H-phosphonate oligonucleotide synthesis on polymer support . Bioorg. Khim. , 16 : 211 – 218 .
   PubMed Web of Science ®Google Scholar
• Sobkowski , M. , Stawinski , J. and Kraszewski , A. 2005 . A proposal for a new stereochemical notation for P-chiral nucleotide analogues and related compounds . Nucleosides Nucleotides Nucleic Acids , 24 : 1301 – 1307 .
   PubMed Web of Science ®Google Scholar
• Sobkowski , M. , Stawinski , J. and Kraszewski , A. 2006 . A proposal for a convenient notation for P-chiral nucleotide analogues. Part 2. dinucleoside monophosphate analogues . Nucleosides Nucleotides Nucleic Acids , 25 : 1363 – 1375 .
   PubMed Web of Science ®Google Scholar
• Sobkowski , M. , Stawinski , J. and Kraszewski , A. 2006 . A proposal for a convenient notation for P-chiral nucleotide analogues. Part 3. Compounds with one nucleoside residue and non-nucleosidic derivatives . Nucleosides Nucleotides Nucleic Acids , 25 : 1377 – 1389 .
   PubMed Web of Science ®Google Scholar
• Sobkowski , M. , Stawinski , J. and Kraszewski , A. 2009 . A proposal for a convenient notation for P-Chiral nucleotide analogues. Part 4. A relationship between the DP/LP notation and stereochemistry of reactions . Nucleosides Nucleotides Nucleic Acids , 28 : 29 – 42 .
   PubMed Web of Science ®Google Scholar
• Sobkowski , M. 2008 . “ Diverse chemoselectivity during acylation of nucleosides ” . In Collection Symposium Series , Edited by: Hocek , M. 277 – 281 . Prague : Institute Of Organic Chemistry And Biochemistry, Academy Of Sciences Of The Czech Republic .
   Google Scholar
• Sobkowski , M. 2010 . A Convenient protection of 4-oxopyrimidine moieties in nucleosides By the pivaloyl group . Collect. Czech. Chem. Commun. , 75 : 33 – 57 .
   Google Scholar
• Efimov , V. A. , Dubey , I. Y. and Chakhmakhcheva , O. G. 1990 . NMR Study And improvement of H-phosphonate oligonucleotide synthesis . Nucleosides Nucleotides , 9 : 473 – 477 .
   Web of Science ®Google Scholar
• Sobkowski , M. , Stawinski , J. , Sobkowska , A. and Kraszewski , A. 1994 . Studies On reactions of nucleoside H-phosphonates with bifunctional reagents. 2. Stability of nucleoside h-phosphonate diesters in the presence of amino alcohols . J. Chem. Soc., Perkin Trans. 1 , : 1803 – 1808 .
   Google Scholar
• Kers , A. , Kers , I. , Stawinski , J. , Sobkowski , M. and Kraszewski , A. 1996 . Studies on aryl H-phosphonates. 3. Mechanistic investigations related to the disproportionation of diphenyl H-phosphonate under anhydrous basic conditions . Tetrahedron , 52 : 9931 – 9944 .
   Web of Science ®Google Scholar
• Hopkins , H. P. , Jahagirdar , D. V. , Moulik , P. S. , Aue , D. H. , Webb , H. M. , Davidson , W. R. and Pedley , M. D . 1984 . Basicities of the 2-, 4-, 2,4-di-, and 2,6-disubstituted tert-butyl pyridines in the gas phase and aqueous phase: Steric effects in the solvation of tert-butyl-substituted pyridines and pyridinium cations . J. Am. Chem. Soc. , 106 : 4341 – 4348 .
   Web of Science ®Google Scholar
• Benoit , R. L. , Frechette , M. and Lefebvre , D. 1988 . 2,6-Di-Tert-Butylpyridin—An unusually weak base in dimethylsulfoxide . Can. J. Chem. , 66 : 1159 – 1162 .
   Web of Science ®Google Scholar
• Augustin-Nowacka , D. and Makowski , M. 2002 . Chmurzynski, L. Potentiometric studies of cationic heteroconjugation equilibria in systems involving free and protonated pyridine derivatives in dimethyl sulfoxide . J. Chem. Thermodynamics , 34 : 391 – 400 .
   Web of Science ®Google Scholar
• Kaljurand , I. , Kutt , A. , Soovali , L. , Rodima , T. , Maemets , V. , Leito , I. and Koppel , I. A. 2005 . Extension of the self-consistent spectrophotometric basicity scale in acetonitrile to a full span of 28 Pk a units: Unification of different basicity scales . J. Org. Chem. , 70 : 1019 – 1028 .
   PubMed Web of Science ®Google Scholar
• Garrido , G. , Koort , E. , Rafols , C. , Bosch , E. , Rodima , T. , Leito , I. and Roses , M. 2006 . Acid-base equilibria in nonpolar media. absolute Pk a scale of bases in tetrahydrofuran . J. Org. Chem. , 71 : 9062 – 9067 .
   PubMed Web of Science ®Google Scholar
• Berthelot , M. , Laurence , C. , Safar , M. and Besseau , F. 1998 . Hydrogen-bond basicity Pk hb scale of six-membered aromatic N-heterocycles . J. Chem. Soc., Perkin Trans. 2 , : 283 – 290 .
   Google Scholar
• Wepster , B. M. 1957 . Steric Effects On Mesomerism. 16. Comparative investigations involving ultra-violet absorption spectra, molecular refractions, rates of reaction, and basic strengths of aromatic amines . Recl. Trav. Chim. Pays-Bas , 76 : 357 – 389 .
   Google Scholar
• Marquis , E. , Graton , J. , Berthelot , M. , Planchat , A. and Laurence , C. 2004 . Hydrogen bonding of arylamines—Competition with P and N sites . Can. J. Chem. , 82 : 1413 – 1422 .
   Web of Science ®Google Scholar
• Benoit , R. L. , Mackinnon , M. J. and Bergeron , L. 1981 . Basicity of N-substituted anilines and pyridine in dimethylsulfoxide . Can. J. Chem. , 59 : 1501 – 1504 .
   Web of Science ®Google Scholar
• Graton , J. , Besseau , F. , Berthelot , M. , Raczynska , E. and Laurence , C. 2002 . The Pk hb scale for hydrogen bonds in aliphatic tertiary amines . Can. J. Chem. , 80 : 1375 – 1385 .
   Web of Science ®Google Scholar
• Krikstopaitis , K. , Kulys , J. , Pedersen , A. H. and Schneider , P. 1998 . N-substituted P-phenylenediamines as peroxidase and laccase substrates . Acta Chem. Scand. , 52 : 469 – 474 .
   Google Scholar
• Beltrame , P. , Gelli , G. and Loi , A. 1980 . Potentiometric study of the ionisation of some nitrogen bases in acetonitrile . Gazz. Chim. Ital. , 110 : 491 – 494 .
   Google Scholar
• Nurminen , E. J. , Mattinen , J. K. and Lönnberg , H. 1999 . Alcoholysis of dialkyl tetrazolylphosphonites . J. Chem. Soc., Perkin Trans. 2 , : 2551 – 2556 .
   Google Scholar
• Kallen , R. G. and Jencks , W. P. 1966 . Equilibria for the reaction of amines with formaldehyde and protons in aqueous solution. A re-examination of the formol titration . J. Biol. Chem. , 241 : 5864 – 5878 .
   PubMed Web of Science ®Google Scholar
• Benoit , R. L. , Lefebvre , D. and Frechette , M. 1987 . Basicity Of 1,8-Bis(dimethylamino)naphthalene and 1,4-diazabicyclo[2.2.2]octane in water and dimethylsulfoxide . Can. J. Chem. , 65 : 996 – 1001 .
   Web of Science ®Google Scholar
• Coetzee , J. F. and Padmanabhan , G. R. 1965 . Properties of bases in acetonitrile as solvent. IV. Proton acceptor power and homoconjugation of mono- and diamines . J. Am. Chem. Soc. , 87 : 5005 – 5010 .
   Web of Science ®Google Scholar
• Leyden , D. E. and Mccall , J. M. Jr. 1971 . Protolysis kinetics of diamines in sulfuric acid . J. Phys. Chem. , 75 : 2400 – 2402 .
   Web of Science ®Google Scholar
• Leffek , K. T. , Pruszynski , P. and Thanapaalasingham , K. 1989 . Basicity of substituted 2-phenyl-1,1,3,3-tetramethylguanidines and other bases in acetonitrile solvent . Can. J. Chem. , 67 : 590 – 595 .
   Web of Science ®Google Scholar
• Kolthoff , I. M. , Chantoon , M. K. and Bhowmik , S. 1968 . Dissociation constants of uncharged and monovalent cation acids in dimethyl sulfoxide . J. Am. Chem. Soc. , 90 : 23 – 28 .
   Web of Science ®Google Scholar
• Cecchi , L. , De Sarlo , F. and Machetti , F. 2006 . 1,4-Diazabicyclo[2.2.2]octane (DABCO) as an efficient reagent for the synthesis of isoxazole derivatives from primary nitro compounds and dipolarophiles: The role of the base . Eur. J. Org. Chem. , : 4852 – 4860 .
   Web of Science ®Google Scholar
• Toom , L. , Kutt , A. , Kaljurand , I. , Leito , I. , Ottosson , H. , Grennberg , H. and Gogoll , A. 2006 . Substituent effects on the basicity of 3,7-diazabicyclo[3.3.1]nonanes . J. Org. Chem. , 71 : 7155 – 7164 .
   PubMed Web of Science ®Google Scholar
• Alder , R. W. 1989 . Strain effects on amine basicities . Chem. Rev. , 89 : 1215 – 1223 .
   Web of Science ®Google Scholar
• Brzezinski , B. , Schroeder , G. , Grech , E. , Malarski , Z. and Sobczyk , L. 1992 . Basicity, IR-spectra and protonation of some proton sponges in acetonitrile . J. Mol. Struct. , 274 : 75 – 82 .
   Web of Science ®Google Scholar
• Perrin , D D . 1965 . Dissociation Constants Of Organic Bases In Aqueous Solution , London : Butterworth .
   Google Scholar
• 2007 . CRC Handbook Of Chemistry And Physics , 87th Ed. , Boca Raton : CRC Press LLC .
   Google Scholar
• Taft , R. W. , Gurka , D. , Joris , L. , Von Schleyer , P. and Rakshys , J. W. 1969 . Studies Of hydrogen-bonded complex formation with P-fluorophenol. V. Linear free energy relationships with oh reference acids . J. Am. Chem. Soc. , 91 : 4801 – 4808 .
   Web of Science ®Google Scholar
• Streitwieser , A. and Kim , Y. J. 2000 . Ion pair basicity of some amines in THF: Implications for ion pair acidity scales . J. Am. Chem. Soc. , 122 : 11783 – 11786 .
   Web of Science ®Google Scholar
• Troev , K. , Tashev , E. and Borisov , G. 1981 . On the interaction between dialkyl phosphites and amine hydrochlorides . Phosphorus Sulfur , 11 : 363 – 367 .
   Web of Science ®Google Scholar
• Bryant , D. E. , Kilner , C. and Kee , T. P. 2009 . Facile one-pot mono-dealkylation of H-phosphonate esters in high yield . Inorg. Chim. Acta , 362 : 614 – 616 .
   Web of Science ®Google Scholar
• Strömberg , R. and Stawinski , J. 1987 . Evaluation of some new condensing reagents for hydrogenphosphonate diester formation . Nucleic Acids Res. Symp. Ser. , 18 : 185 – 188 .
   Google Scholar
• For the compounds presented in this paper the D P descriptor refers to a structure in which the P-H bond is directed to the right in the Fischer projection, while for the L P one, to the left. The full D P/L P notation is described in refs.[25–28]
   Google Scholar
• The same conditions as used in previous studies.[22]
   Google Scholar
• When the amount of an alcohol was reduced to 3 equiv., the above mentioned by-products appeared as trace impurities (1–2%), while for stoichiometric amounts of an alcohol, these by-products accounted for ca. 20% of the phosphorus-containing compounds present in the reaction mixtures, most likely due to decreased rates of the condensations
   Google Scholar
• When the reaction was repeated in the presence of 10 instead of 3 equiv. of DMA, a significant deacylation of the mixed anhydride 2 was observed, demonstrating the importance of the basicity of the reaction mixture on the course of reaction.
   Google Scholar
• Because analogous experiments revealed lack of deacylating activity of tosylates and hydrochlorides of the same amines, the observed deacylation of 2 should be attributed to rather unique properties (in discussed context) of the studied pivalates, while their deacylating power could be correlated with pKa values of the conjugated amines. Thus, amines of higher pKa apparently might increase nucleophilicity of pivalic acid via its more efficient deprotonation.[15]
   Google Scholar
• The reasons for low yields of esterification of the mixed anhydride 2 in the presence of powerful nucleophilic catalysts (NMI, DMAP) remain uncertain. One may speculate that the H-phosphonic onium salts formed by those nucleophilic amines during the course of the reaction[11] may react partly with the pivalate anion forming acyl onium salts (and H-phosphonate monoester 1), which subsequently might rapidly form unreactive pivalic anhydride with the next pivalate molecule. In contrast, all reactions during condensations of nucleoside H-phosphonates in the presence of moderate nucleophilic catalyst (pyridine) were evidently fully chemoselective toward H-phosphonate diester formation.
   Google Scholar
• pK HB is a measure of a relative strength of the acceptor in hydrogen-bonded complex formed with a reference acid (H-bonding basicity) and may indicate on propensity of a conjugate acid of an amine to act as a general acid catalyst. pK a and pK HB may be unrelated.[59]
   Google Scholar
• HMTA and DABCO are strong nucleophilic catalysts and the outstandingly low stereoselectivity found for these compounds were similar to those observed for N-methylimidazole and DMAP.[22] It seems that these nucleophilic catalysts, efficient for reactions at carbon and PV centers, are poor nucleofuges in H-phosphonate chemistry, and the relative stability of P-N+ intermediates makes room for side reactions and slows down their epimerization, making the DYKAT process of asymmetric induction less efficient
   Google Scholar