Nitrogen cuts in during C-C cross-coupling.

A catalyst system diverts traditional C-C bond coupling into desired C-N bond formation.

Covalent Modification of Nucleobases using Water-Soluble Palladium Catalysts.

Nucleosides represent one of the key building blocks of biochemistry. There is significant interest in the synthesis of nucleoside-derived materials for applications as probes, biochemical models, and pharmaceuticals. Palladium-catalyzed cross-coupling reactions are effective methods for making covalent modification of carbon and nitrogen sites on nucleobases under mild conditions. Water-soluble catalysts derived from palladium and hydrophilic ligands, such as tris(3-sulfonatophenyl)phosphine trisodium (TPPTS), are efficient catalysts for a range of coupling reactions of unprotected halonucleosides. Over the past two decades, these methods have been extended to direct functionalization of halonucleotides, as well as RNA and DNA oligonucleotides (ONs) containing halogenated bases. These methods can be run under biocompatible conditions, including examples of Suzuki coupling of modified DNA in whole cells and tissue samples. In this account, development of this methodology by our group and others is highlighted along with the extension of these catalyst systems to modification of nucleotides and ONs.

Experimental and Computational Study of the Structure, Steric Properties, and Binding Equilibria of Neopentylphosphine Palladium Complexes.

Steric properties of crystallographically and computationally determined structures of linear palladium(0) and square planar palladium(II) complexes of di(tert-butyl)neopentylphosphine (P(t-Bu)2Np), tert-butyldineopentylphosphine (P(t-Bu)Np2), and trineopentylphosphine (PNp3) have been determined. Structures of linear palladium(0) complexes show that steric demand increases as tert-butyl groups are replaced with neopentyl groups (P(t-Bu)2Np < P(t-Bu)Np2 < PNp3). In square planar palladium(II) complexes, PNp3 gives the smallest steric parameters, whereas P(t-Bu)Np2 has the largest steric demand. The change in the steric demand of PNp3 compared to P(t-Bu)2Np and P(t-Bu)Np2 results from a significant conformational change in PNp3 depending on the coordination number of the metal. The steric properties of these ligands were also probed by measuring the equilibrium constant for coordination of free phosphine to dimeric [(R3P)Pd(µ-Cl)Cl]2 complexes. Binding equilibria follow the same trend as the steric parameters for square planar complexes with PNp3 having the highest binding constant. In contrast to the normal trend, the neopentylphosphines show increased pyramidalization at phosphorus with increasing steric demand. We hypothesize that this unusual dependence reflects the low back side strain of the neopentyl group, which allows the ligand to be more pyramidalized while still exerting a significant front side steric demand.

Synthesis, Structural Characterization, and Coordination Chemistry of (Trineopentylphosphine)palladium(aryl)bromide Dimer Complexes ([(Np3P)Pd(Ar)Br]2).

A series of [(PNp3)Pd(Ar)Br]2 complexes (PNp3 = trineopentylphosphine, Ar = 4-tolyl, 4-tert-butylphenyl, 2-tolyl, 4-methoxy-2-methylphenyl, 2-isopropylphenyl, and 2,6-dimethylphenyl) were synthesized and structurally characterized by X-ray crystallography and density functional theory optimized structures. The trineopentylphosphine ligand is able to accommodate coordination of other sterically demanding ligands through changes in its conformation. These conformational changes can be seen in changes in percent buried volume of the PNp3 ligand. The binding equilibria of the [(PNp3)Pd(Ar)Br]2 complexes with pyridine derivatives were determined experimentally and analyzed computationally. The binding equilibria are sensitive to the steric demand of the pyridine ligand and less sensitive to the steric demand of the aryl ligand on palladium. In contrast to previous studies, the binding equilibria do not correlate with pyridine basicity. The binding equilibria results are relevant to fundamental ligand coordination steps in cross-coupling reactions, such as Buchwald-Hartwig aminations.

Palladium-catalyzed modification of unprotected nucleosides, nucleotides, and oligonucleotides.

Synthetic modification of nucleoside structures provides access to molecules of interest as pharmaceuticals, biochemical probes, and models to study diseases. Covalent modification of the purine and pyrimidine bases is an important strategy for the synthesis of these adducts. Palladium-catalyzed cross-coupling is a powerful method to attach groups to the base heterocycles through the formation of new carbon-carbon and carbon-heteroatom bonds. In this review, approaches to palladium-catalyzed modification of unprotected nucleosides, nucleotides, and oligonucleotides are reviewed. Polar reaction media, such as water or polar aprotic solvents, allow reactions to be performed directly on the hydrophilic nucleosides and nucleotides without the need to use protecting groups. Homogeneous aqueous-phase coupling reactions catalyzed by palladium complexes of water-soluble ligands provide a general approach to the synthesis of modified nucleosides, nucleotides, and oligonucleotides.

Controlling olefin isomerization in the heck reaction with neopentyl phosphine ligands.

The use of neopentyl phosphine ligands was examined in the coupling of aryl bromides with alkenes. Di-tert-butylneopentylphosphine (DTBNpP) was found to promote Heck couplings with aryl bromides at ambient temperature. In the Heck coupling of cyclic alkenes, the degree of alkene isomerization was found to be controlled by the choice of ligand with DTBNpP promoting isomerization to a much greater extent than trineopentylphosphine (TNpP). Under optimal conditions, DTBNpP provides high selectivity for 2-aryl-2,3-dihydrofuran in the arylation of 2,3-dihydrofuran, whereas TNpP provided high selectivity for the isomeric 2-aryl-2,5-dihydrofuran. A similar complementary product selectivity is seen in the Heck coupling of cyclopentene. Heck coupling of 2-bromophenols or 2-bromoanilides with 2,3-dihydrofurans affords 2,5-epoxybenzoxepin and 2,5-epoxybenzazepins, respectively.

Trineopentylphosphine: a conformationally flexible ligand for the coupling of sterically demanding substrates in the Buchwald-Hartwig amination and Suzuki-Miyaura reaction.

Trineopentylphosphine (TNpP) in combination with palladium provides a highly effective catalyst for the Buchwald-Hartwig coupling of sterically demanding aryl bromides and chlorides with sterically hindered aniline derivatives. Excellent yields are obtained even when both substrates include 2,6-diisopropyl substituents. Notably, the reaction rate is inversely related to the steric demand of the substrates. X-ray crystallographic structures of Pd(TNpP)2, [Pd(4-t-Bu-C6H4)(TNpP)(µ-Br)]2, and [Pd(2-Me-C6H4)(TNpP)(µ-Br)]2 are reported. These structures suggest that the conformational flexibility of the TNpP ligand plays a key role in allowing the catalyst to couple hindered substrates. The Pd/TNpP system also shows good activity for the Suzuki coupling of hindered aryl bromides.

Stereospecific Suzuki, Sonogashira, and Negishi coupling reactions of N-alkoxyimidoyl iodides and bromides.

A high-yielding stereospecific route to the synthesis of single geometric isomers of diaryl oxime ethers through Suzuki coupling of N-alkoxyimidoyl iodides is described. This reaction occurs with complete retention of the imidoyl halide geometry to give single E- or Z-isomers of diaryl oxime ethers. The Sonogashira coupling of N-alkoxyimidoyl iodides and bromides with a wide variety of terminal alkynes to afford single geometric isomers of aryl alkynyl oxime ethers has also been developed. Several of these reactions proceed through copper-free conditions. The Negishi coupling of N-alkoxyimidoyl halides is introduced. The E and Z configurations of nine Suzuki-coupling products and two Sonogashira-coupling products were confirmed by X-ray crystallography.

Aqueous-phase Sonogashira alkynylation to synthesize 5-substituted pyrimidine and 8-substituted purine nucleosides.

In this unit, an efficient method for the synthesis of alkyne-modified nucleosides in an aqueous solvent system is described. The method allows direct palladium-catalyzed alkynylation of readily available unprotected 8-bromo-2'-deoxyguanosine (8-BrdG), 8-bromo-2'-deoxyadenosene (8-BrdA), 8-bromoadenosine (8-BrA), and 5-iodo-2'-deoxyuridine (5-IdU) precursors. The optimal catalyst is derived from palladium acetate, tri-(2,4-dimethyl-5-sulfonatophenyl)phosphane (TXPTS), and CuI.

The conformational effect of para-substituted C8-arylguanine adducts on the B/Z-DNA equilibrium.

The B form of DNA exists in equilibrium with the Z form and is mainly affected by sequence, electrostatic interactions, and steric effects. C8-purine substitution shifts the equilibrium toward the Z form though how this interaction overcomes the unfavorable electrostatic interactions and decrease in stacking in the Z form has not been determined. Here, a series of C8-arylguanine derivatives, bearing a para-substituent were prepared and the B/Z equilibrium determined. B/Z ratios were measured by CD and conformational effects of the aryl substitution determined by NMR spectroscopy and molecular modeling. The para-substituent was found to have a significant effect on the B/Z DNA equilibrium caused by altering base-pair stacking of the B form and modifying the hydration/ion shell of the B form. A unique melting temperature versus salt concentration was observed and provides evidence relevant to the mechanism of B/Z conformational interconversion.

Synthesis and X-ray structure determination of highly active Pd(II), Pd(I), and Pd(0) complexes of di(tert-butyl)neopentylphosphine (DTBNpP) in the arylation of amines and ketones.

The air-stable complex Pd(η(3)-allyl)(DTBNpP)Cl (DTBNpP = di(tert-butyl)neopentylphosphine) serves as a highly efficient precatalyst for the arylation of amines and enolates using aryl bromides and chlorides under mild conditions with yields ranging from 74% to 98%. Amination reactions of aryl bromides were carried out using 1-2 mol % Pd(η(3)-allyl)(DTBNpP)Cl at 23-50 °C without the need to exclude oxygen or moisture. The C-N coupling of the aryl chlorides occurred at relatively lower temperature (80-100 °C) and catalyst loading (1 mol %) using the Pd(η(3)-allyl)(DTBNpP)Cl precatalyst than the catalyst generated in situ from DTBNpP and Pd(2)(dba)(3) (100-140 °C, 2-5 mol % Pd). Other Pd(DTBNpP)(2)-based complexes, (Pd(DTBNpP)(2) and Pd(DTBNpP)(2)Cl(2)) were ineffective precatalysts under identical conditions for the amination reactions. Both Pd(DTBNpP)(2) and Pd(DTBNpP)(2)Cl(2) precatalysts gave nearly quantitative conversions to the product in the α-arylation of propiophenone with p-chlorotoluene and p-bromoanisole at a substrate/catalyst loading of 100/1. At lower substrate/catalyst loading (1000/1), the conversions were lower but comparable to that of Pd(t-Bu(3)P)(2). In many cases, the tri-tert-butylphosphine (TTBP) based Pd(I) dimer, [Pd(µ-Br)(TTBP)](2), stood out to be the most reactive catalyst under identical conditions for the enolate arylation. Interestingly, the air-stable Pd(I) dimer, Pd(2)(DTBNpP)(2)(µ-Cl)(µ-allyl), was less active in comparison to [Pd(µ-Br)(TTBP)](2) and Pd(η(3)-allyl)(DTBNpP)Cl. The X-ray crystal structures of Pd(η(3)-allyl)(DTBNpP)Cl, Pd(DTBNpP)(2)Cl(2), Pd(DTBNpP)(2), and Pd(2)(DTBNpP)(2)(µ-Cl)(µ-allyl) are reported in this paper along with initial studies on the catalyst activation of the Pd(η(3)-allyl)(DTBNpP)Cl precatalyst.

Prediction of reliable metal-PH3 bond energies for Ni, Pd, and Pt in the 0 and +2 oxidation states.

Phosphine-based catalysts play an important role in many metal-catalyzed carbon-carbon bond formation reactions yet reliable values of their bond energies are not available. We have been studying homogeneous catalysts consisting of a phosphine bonded to a Pt, Pd, or Ni. High level electronic structure calculations at the CCSD(T)/complete basis set level were used to predict the M-PH(3) bond energy (BE) for the 0 and +2 oxidation states for M = Ni, Pd, and Pt. The calculated bond energies can then be used, for example, in the design of new catalyst systems. A wide range of exchange-correlation functionals were also evaluated to assess the performance of density functional theory (DFT) for these important bond energies. None of the DFT functionals were able to predict all of the M-PH(3) bond energies to within 5 kcal/mol, and the best functionals were generalized gradient approximation functionals in contrast to the usual hybrid functionals often employed for main group thermochemistry.

A general synthesis of C8-arylpurine phosphoramidites.

A general scheme for the synthesis of C8-arylpurine phosphoramidites has been developed. C8-Arylation of C8-bromo-2'-deoxyguanosine is the key step and has been achieved through the use of a Suzuki coupling. Since the coupling reaction is conducted under aqueous conditions, it is unnecessary to protect and then deprotect the hydroxyl groups, thus saving several steps and improving overall yields. Once the C8-arylgroup is introduced, the glycosidic bond becomes very sensitive to acid catalyzed cleavage. Protection of the amino groups as the corresponding N,N-dimethylformamidine derivative improves stability of the derivatives. Synthetic C8-arylpurines were successfully used to prepare synthetic oligonucleotides.

Bulky alkylphosphines with neopentyl substituents as ligands in the amination of aryl bromides and chlorides.

Di(tert-butyl)neopentylphosphine (DTBNpP) in combination with palladium sources provided catalysts with comparable or better activity for the Hartwig-Buchwald amination of aryl bromides than tri(tert-butyl)phosphine (TTBP) under mild conditions. DTBNpP also provided effective catalysts for amination reactions of aryl chlorides at elevated temperatures. Further replacement of tert-butyl groups with neopentyl substituents resulted in less effective ligands for amination reactions. Computationally derived cone angles showed that replacement of a tert-butyl group with a neopentyl group significantly increased the cone angle of the phosphine. The larger cone angle of DTBNpP than TTBP appears to correlate with the higher activity of catalysts derived from DTBNpP in the amination of aryl bromides. TTBP is a stronger electron donor than DTBNpP, which may explain the higher activity for TTBP-derived catalysts toward aryl chlorides.

t-Bu-Amphos-RhCl3.3H2O: a highly recyclable catalyst system for the cross-coupling of aldehydes and aryl- and alkenylboronic acids in aqueous solvents.

The combination of t-Bu-Amphos and RhCl3.3H2O gave the first highly recyclable catalyst for the coupling of aryl- and vinylboronic acids with aldehydes in aqueous solvents.

Inhibitory effects of the guanine moiety on Suzuki couplings of unprotected halonucleosides in aqueous media.

In the Suzuki arylations of unprotected halonucleosides in aqueous media, 8-bromo-2'-deoxyguanosine (8BrdG) couplings were slower to reach completion than the corresponding 8-bromo-2'-deoxyadenosine (8BrdA) couplings. The guanine moiety has an acidic proton, which under our Suzuki conditions (pH congruent with 10) may be deprotonated to give an anion that can coordinate to palladium. The possibility that guanine coordination was responsible for the observed slower rates was explored using additive experiments in which nonhalogenated nucleosides were added to the Suzuki coupling reaction of 8BrdA or 4-bromotoluene and PhB(OH)2 and the reaction progress monitored by HPLC or GC. Adding dG slowed these reactions, and an induction period was observed. The addition of dA or 1-methyl-2'-deoxyguanosine (1MedG) to these couplings did not affect the rate of conversion to product. Guanine coordination was further explored using 13C and 31P NMR spectroscopy, which implies that guanine is coordinating to palladium through N-1 or O-6, or both. Furthermore, the presence of dG inhibited the formation of the active palladium(0) catalytic species, which may account for both the observed induction period and the sluggishness of reactions where guanine is involved.

Aqueous-phase, palladium-catalyzed cross-coupling of aryl bromides under mild conditions, using water-soluble, sterically demanding alkylphosphines.

Sterically demanding, water-soluble alkylphosphines have been used in combination with various palladium salts in Suzuki, Sonogashira, and Heck couplings of aryl bromides under mild conditions in aqueous solvents. The tert-butyl-substituted ligands 2-(di-tert-butylphosphino)ethyltrimethylammonium chloride (t-Bu-Amphos) and 4-(di-tert-butylphosphino)-N,N-dimethylpiperidinium chloride (t-Bu-Pip-phos) in combination with palladium(II) salts were found to give catalysts that were significantly more active than catalysts derived from tri(3-sulfonatophenyl)phosphine trisodium (TPPTS). Suzuki couplings of unactivated aryl bromides occurred efficiently at room temperature in water/acetonitrile and water/toluene biphasic mixtures or in neat water. Notably, Suzuki couplings of hydrophilic aryl bromides gave high yields without using organic solvents for the reaction or purification. This methodology has been applied to a highly efficient synthesis of diflunisal. The catalyst derived from t-Bu-Amphos was recycled three times in Suzuki couplings in water/toluene before catalyst activity began to significantly drop. The average yield of four cycles was >80% per cycle. Heck and Sonogashira couplings were carried out under mild conditions (50 and 80 degrees C, respectively) with unactivated aryl bromides to give coupled products in high yield.

Efficient aqueous-phase Heck and Suzuki couplings of aryl bromides using tri(4,6-dimethyl-3- sulfonatophenyl)phosphine trisodium salt (TXPTS).

[reaction: see text] Sterically demanding, sulfonated arylphosphines TXPTS and TMAPTS have been applied to the aqueous-phase Heck and Suzuki coupling of aryl bromides. TXPTS provides good yields of Heck coupling products from aryl bromides at 80 degrees C, while both TMAPTS and TPPTS gave significantly less active catalysts. TXPTS is the first ligand to promote the aqueous-phase Heck coupling under such mild conditions. Both TXPTS and TMAPTS provide active catalysts for Suzuki couplings of aryl bromides at 50 degrees C.

Synthesis, properties, and NMR studies of a C8-phenylguanine modified oligonucleotide that preferentially adopts the Z DNA conformation.

Carcinogenic aryl hydrazines produce C8-arylated purine adducts. The effect of these adducts on DNA conformation and their role in hydrazine carcinogenesis are unknown. Here, we describe a new synthetic route to produce these adducts that is also compatible with the synthesis of the corresponding phosphoramidites needed for oligonucleotide synthesis. Two oligonucleotides were prepared, an unmodified oligonucleotide, d((5)(')CGCGCGCGCG(3)(')), and a C8-phenylguanine modified oligonucleotide, d((5)(')CGCGCGCGCG(3)(')) (G = 8-phenylguanine). These oligonucleotides were compared using thermal denaturation, circular dichroism, NMR, and molecular modeling. The phenyl modification destabilizes the B DNA form and stabilizes the Z DNA form such that the B:Z ratio is near one under physiological conditions. In light of recent studies that show a role for Z DNA in gene expression and cell transformation, Z DNA stabilization by C8-arylguanine formation from aryl hydrazines may be relevant to their role in carcinogenesis.