A novel catechol-based universal support for oligonucleotide synthesis.

A novel universal support for deoxyribo- and ribonucleic acid synthesis has been developed. The support, constructed from 1,4-dimethoxycatechol, represents an improvement over existing universal supports because of its ability to cleave and deprotect under mild conditions in standard reagents. Because no nonvolatile additives are required for cleavage and deprotection, the synthesized oligonucleotides do not require purification prior to use in biochemical assays. Using reverse phase HPLC and electrospray mass spectroscopy, it was determined that oligonucleotides synthesized on the universal support (UL1) 3'-dephosphorylate quickly (9 h in 28-30% ammonium hydroxide (NH4OH) at 55 degrees C, 2 h in 28-30% NH4OH at 80 degrees C, or <1 h in ammonium hydroxide/methylamine (1:1) (AMA) at 80 degrees C). Oligonucleotides used as primers for the polymerase chain reaction (PCR) assay were found to perform identically to control primers, demonstrating full biological compatibility. In addition, a method was developed for sintering the universal support directly into a filter plug which can be pressure fit into the synthesis column of a commercial synthesizer. The universal support plugs allow the synthesis of high-quality oligonucleotides at least 120 nucleotides in length, with purity comparable to non-universal commercial supports and approximately 50% lower reagent consumption. The universal support plugs are routinely used to synthesize deoxyribo-, ribo-, 3'-modified, 5'-modified, and thioated oligonucleotides. The flexibility of the universal support and the efficiency of 3'-dephosphorylation are expected to increase the use of universal supports in oligonucleotide synthesis.

Synthesis, characterization, and electrochemical studies of beta,beta'-fused metallocenoporphyrins.

Beta,beta'-Fused monoruthenocenylporphyrins, Cp*Ru(III)[1,2-[M(II)-5,10,15,20-tetrakis(3,5-di-tert-butylphenyl)-porphyrinato]-3-methyl-cyclopentadienide] (M = Ni (20), Cu (21), Zn (22)), and bisferrocenoporphyrins, Fe(II) bis[1,2-[M(II)-5,10,15,20-tetraphenylporphyrinato]-3-methyl-cyclopentadienide] (M = Ni (24), Cu (25), Zn (26)), were synthesized and characterized. A novel synthetic approach to beta,beta'-fused porphyrins through Pd(0)-catalyzed [3 + 2] cycloaddition was implemented in this work. UV-vis spectra of these compounds show largely broadened and red-shifted bands (relative to their precursors) indicating potential electronic communication between the attached organometallic moiety and the porphyrin core. The electrochemistry of these molecules suggests significant electronic interactions between the metallocene and metalloporphyrin in molecules 20 and 24. The crystal structure of the bisferrocenoporphyrin 26, Fe(II) bis[1,2-[Zn(II)-5,10,15,20-tetraphenylporphyrinato]-3-methyl-cyclopentadienide], was determined: [Cp2Fe[ZnTPP(THF)]2][Cp2Fe[ZnTPP(THF)ZnTPP(MeOH)]].3MeOH.6THF, M = 3804.35, monoclinic, space group P21/c, a = 33.327(5) A, b = 19.145(3) A, c = 29.603(5) A, beta = 106.309(2) degrees , V = 18128(5) A3, Z = 4. In this molecule, one porphyrin ring is rotated by about 72 degrees with respect to the other in the 5-fold axis of the Cp ring.

Unusual aryl-porphyrin rotational barriers in peripherally crowded porphyrins.

Previous studies of 5,10,15,20-tetraarylporphyrins have shown that the barrier for meso aryl-porphyrin rotation (DeltaG++(ROT)) varies as a function of the core substituent M and is lower for a small metal (M = Ni) compared to a large metal (M = Zn) and for a dication (M = 4H(2+)) versus a free base porphyrin (M = 2H). This has been attributed to changes in the nonplanar distortion of the porphyrin ring and the deformability of the macrocycle caused by the core substituent. In the present work, X-ray crystallography, molecular mechanics (MM) calculations, and variable temperature (VT) (1)H NMR spectroscopy are used to examine the relationship between the aryl-porphyrin rotational barrier and the core substituent M in some novel 2,3,5,7,8,10,12,13,15,17,18,20-dodecaarylporphyrins (DArPs), and specifically in some 5,10,15,20-tetraaryl-2,3,7,8,12,13,17,18-octaphenylporphyrins (TArOPPs), where steric crowding of the peripheral groups always results in a very nonplanar macrocycle. X-ray structures of DArPs indicate differences in the nonplanar conformation of the macrocycle as a function of M, with saddle conformations being observed for M = Zn, 2H or M = 4H(2+) and saddle and/or ruffle conformations for M = Ni. VT NMR studies show that the effect of protonation in the TArOPPs is to increase DeltaG++(ROT), which is the opposite of the effect seen for the TArPs, and MM calculations also predict a strikingly high barrier for the TArOPPs when M = 4H(2+). These and other findings suggest that the aryl-porphyrin rotational barriers in the DArPs are closely linked to the deformability of the macrocycle along a nonplanar distortion mode which moves the substituent being rotated out of the porphyrin plane.

Influence of electronic and structural effects on the oxidative behavior of nickel porphyrins.

With the aim of better understanding the electronic and structural factors which govern electron-transfer processes in porphyrins, the electrochemistry of 29 nickel(II) porphyrins has been examined in dichloromethane containing either 0.1 M tetra-n-butylammonium perchlorate (TBAP) or tetra-n-butylammonium hexafluorophosphate (TBAPF(6)) as supporting electrolyte. Half-wave potentials for the first oxidation and first reduction are only weakly dependent on the supporting electrolyte, but E(1/2) for the second oxidation varies considerably with the type of supporting electrolyte. E(1/2) values for the first reduction to give a porphyrin pi-anion radical are effected in large part by the electronic properties of the porphyrin macrocycle substituents, while half-wave potentials for the first oxidation to give a pi-cation radical are affected by the substituents as well as by nonplanar deformations of the porphyrin macrocycle. The potential difference between the first and second oxidations (Delta/Ox(2) - Ox(1)/) is highly variable among the 29 investigated compounds and ranges from 0 mV (two overlapped oxidations) to 460 mV depending on the macrocycle substituents and the anion of the supporting electrolyte. The magnitude of Delta/Ox(2) - Ox(1)/ is generally smaller for compounds with very electron-withdrawing substituents and when TBAP is used as the supporting electrolyte. This behavior is best explained in terms of differences in the binding strengths of anions from the supporting electrolyte (ClO(4)(-) or PF(6)(-)) to the doubly oxidized species. A closer analysis suggests two factors which are important in modulating Delta/Ox(2) - Ox(1)/ and thus the binding affinity of the anion to the porphyrin dication. One is the type of pi-cation radical (a proxy for the charge distribution in the dication), and the other is the conformation of the porphyrin macrocycle (either planar or nonplanar). These findings imply that the redox behavior of porphyrins can be selectively tuned to display separate or overlapped oxidation processes.

Biphenyl-Strapped Diphenylporphyrins: Synthesis and Spectroscopic Characterization of a Series of Porphyrins with Ether-Linked Straps. Preliminary CO Binding Properties of Their Iron(II) Derivatives.

The synthesis of a series of meso-5,15-diphenylporphyrins strapped by 2,2'-disubstituted biphenyl units (6H(2), 7H(2), 8H(2)) is described. The biphenyl straps used are linked via their 3,3'-positions by CH(2)O groups to ortho-positions of the phenyl rings of the 5,15-diphenylporphyrins. The straps of these porphyrins have their 2,2'-positions occupied by H (6H(2)), Me (7H(2)), and OMe (8H(2)). The electronic spectral properties of these strapped porphyrins are given, and their conformational properties, which have been studied by (1)H NMR spectroscopy, are described. The synthesis and spectroscopic characterization of several iron(II) and iron(III) derivatives of these porphyrins with different axial bases are also presented. The X-ray structure of the chloroiron(III) derivative of the diphenylporphyrin dianion 6 has been determined. Violet crystals of composition 6-FeCl.CH(3)OH.CH(2)Cl(2) have been obtained by slow evaporation of CH(2)Cl(2)/MeOH solutions of 6-FeCl. These crystals belong to the monoclinic system, space group P2(1)/c, with a = 10.164(3) Å, b = 28.977(9) Å, c = 14.283(4) Å, beta = 106.22(2) degrees, and Z = 4. The iron atom of 6-FeCl is five-coordinate, high-spin. The axial chloride ligand lies opposite to the strap. The average Fe-N(p) bond distance is 2.046(6) Å, and the Fe-Cl bond length equals 2.234(2) Å. The porphyrin is slightly domed and ruffled with the iron atom lying at 0.45(1) Å out of the 4N(p) mean-plane and 0.49(1) Å out of the 24-atom core mean-plane of the porphyrin ring. Ferrous carbonyl adducts of these porphyrins have been obtained in various solvents in the presence or absence of nitrogenous bases. Their structures have been studied by (1)H NMR and IR spectroscopy. Two CO stretching vibrations differing by 20 cm(-)(1) occur in the IR spectra of 6-Fe(CO)(B) (B = py, ImH, NMeIm). The possible origin of these two nu(CO) bands is discussed.

Substituent-Induced Perturbation Symmetries and Distortions of meso-tert-Butylporphyrins.

The out-of-plane and in-plane distortions of a series of nickel(II) meso-substituted porphyrins with 0, 1, 2, or 4 tert-butyl groups [nickel(II) porphine (NiP), nickel(II) mono-tert-butylporphyrin (NiMtBuP), nickel(II) di-tert-butylporphyrin (NiDtBuP), and nickel(II) tetra-tert-butylporphyrin (NiTtBuP)] are investigated using molecular mechanics (MM) calculations, X-ray crystallography, UV-visible absorption spectroscopy, and resonance Raman spectroscopy. MM calculations are used to predict the stable conformations for this series of porphyrins. The out-of-plane distortions are then analyzed in terms of displacements along the normal coordinates of the porphyrin macrocycle using a new normal-coordinate structural decomposition method. As expected, the distortions are found to occur primarily along the lowest-frequency normal coordinate of each symmetry type and the distortions could be adequately simulated using only the lowest-frequency normal coordinates as a basis (the minimal basis). However, the distortions could be simulated significantly more accurately by extending the minimal basis by including the second-lowest-frequency normal coordinate of all symmetries. Using the extended basis is most important for the in-plane distortions. Detailed analysis of the types of distortion revealed that both the out-of-plane and the in-plane distortions depend on the perturbation symmetry of the peripheral substituents. The symmetry primarily depends on the pattern of substitution (number and positions of substituents) and the orientations of substituents. Often the perturbation symmetry can be predicted for a given porphyrin simply from the possible orientations of the substituents. Then, the main type(s) of symmetric deformation occurring for each possible molecular symmetry can be readily predicted from a D(4)(h)() correlation table. The stable conformers predicted by MM for the series of tert-butyl-substituted porphyrins confirm this simple but informative approach. Experimental verification of the calculated contributions of the symmetric deformations is provided by normal-coordinate structural decomposition of the available X-ray crystal structures of NiP, NiMtBuP, and NiDtBuP. The solid-state results are also supported by the resonance Raman and UV-visible absorption spectroscopic characterization of the porphyrins in solutions. The X-ray crystal structure of NiMtBuP is reported here for the first time.

Dihydroporphyrin Synthesis: New Methodology.

Selective formation of trans-nitrochlorins 16-19, cyclopropylchlorins 14, 15, and 20-23, or functionalized trans-chlorins 5-13 by reaction of 2-nitro-5,10,15,20-tetraphenylporphyrin 1 with "active" methylene compounds such as malonates or malononitrile in the presence of base has been achieved. Reaction control is accomplished via sequential Michael additions, followed by intramolecular nucleophilic displacement of a secondary nitro group. Steric as well as thermodynamic effects have been found to govern the selectivity of product formation. Ambient temperature or bulky carbanion substituents lead to nitrochlorins and/or cyclopropylchlorins. Increased reaction temperatures, combined with sterically less encumbered carbanion substituents, favor the formation of disubstituted trans-chlorins. Nucleophilic ring-opening reactions of cyclopropyl-derivative 14afford disubstituted trans-chlorin products 5 and 25 and provide additional mechanistic evidence for the intermediacy of the cyclopropylchlorin. Use of porphyrins with modified meso-phenyl positions illustrates the generality of this methodology and allows a novel method for the preparation of a wide range of reduced porphyrins, which may find application in fields such as the photodynamic therapy (PDT) of cancer.