Kevin H. Shaughnessy

Hydrophilic ligands and their application in aqueous-phase metal-catalyzed reactions.

Water is truly ubiquitous. Approximately 80% of the earth’s surface is covered by water, although only 1% of this is drinkable water. Water is the solvent of life and makes up about 60% of the mass of the human body. The majority of synthetic organic chemistry carried out in research laboratories or industrial processes utilizes organic solvents, however. Organic solvents have a number of attractive features: they will dissolve a wide range of organic compounds, they come with a variety of properties, and they are often volatile and easily removed. Unfortunately, organic solvents are often toxic, flammable, and nonrenewable and have low heat capacities. In contrast, water is nontoxic and nonflammable, has a high heat capacity, and is relatively inexpensive. Of course water has some significant drawbacks as a solvent: it is a poor solvent for most organic molecules, and it is highly reactive with many classes of reagents. Because of these drawbacks, water is rarely used as a primary solvent in synthetic organic chemistry, although there is a growing body of work related to organic chemistry in water.1-3

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.

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.

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.

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.

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.

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.

Influence of water on the deprotonation and the ionic mechanisms of a Heck alkynylation and its resultant E-factors

The influence of water on deprotonation and ionic mechanisms of a Heck alkynylation and its resultant E-factors were investigated. Estimation of the Hatta modulus, MH < 0.02, in cationic deprotonation, anionic deprotonation, and the ionic mechanism each separately confirmed an infinitely slow rate of reaction with respect to the diffusive flux within the thin film of the immiscible aqueous–organic interface. As a consequence, intrinsic kinetic expressions for far-equilibrium conditions were derived from first principles for each mechanism. Analyses of Gibbs free energies revealed that water potentially switched the rate-determining steps of cationic and anionic deprotonation to any of oxidative addition of organohalide to form Pd-complex (ΔG++ = 97.6 kJ mol−1), coordination of the alkyne with the oxidative addition adduct (ΔG++ = 97.6 kJ mol−1), or ligand substitution to form the cationic Pd-complex (ΔG++ = 94.9 kJ mol−1). Hydrogen-bonding in the transfer mechanism might account for the switch. Water, in general, was found to influence which step governs each catalytic cycle and the magnitude of its Gibbs free energy. Transformation of the synthesis from batch to continuous-flow was also studied by analyses of E-factors within the thin film. The amount of waste generated, as indicted by estimations of E-factors, was less in continuous-flow operation than in batch when the fastest step of deprotonation (ligand substitution) was infinitely fast with respect to the diffusive flux. The concentration of hydrophilic phosphine ligand was observed to influence mass transport limitations and the E-factor. Increasing ligand concentrations beyond (10.5), (13.3), and (23.2) × 10−3 mol L−1 for reaction temperatures of 353, 343, and 323 K increased the E-factor above its minimum value of 4.7, and it also induced mass-transfer-limitations. The switch from intrinsic to mass-transport-limited kinetics by finite changes in the ligand concentration explains ambiguity when performing aqueous-phase catalyzed Heck alkynylations and possibly multiphase Pd-catalyzed C–C cross-couplings in general. The potential exists to inadvertently mask the reactivity of useful ligands during discovery and to force mass transport limitations during manufacture. Understanding why the E-factor can be minimized is vital to the sustainable discovery and manufacture of fine chemicals, materials, natural products, and pharmaceuticals.