Synthetic, structural and mechanistic studies of interactions of carbon, nitrogen, and oxygen nucleophiles with bis-pentamethylcyclopentadienyl zirconium and hafnium derivatives

The reactivity of permethylzirconocene and permethylhafnocene complexes with various nucleophiles has been investigated. Permethylzirconocene reacts with sterically hindered ketenes and allenes to afford metallacycle products. Reaction of these cummulenes with permethylzirconocene hydride complexes affords enolate and σ-allyl species, respectively. Reactions which afford enolate products are nonstereospecific, whereas reactions which afford allyl products initially give a cis-σ-allyl complex which rearranges to its trans isomer. The mechanism of these reactions is proposed to occur either by a Lewis Acid-Lewis Base interaction (ketenes) or by formation of a π-olefin intermediate (allenes).

Permethylzirconocene haloacyl complexes react with strong bases such as lithium diisopropylamide or methylene trimethylphosphorane to afford ketene compounds. Depending on the size of the alkyl ketene substituent, the hydrogenation of these compounds affords enolate-hydride products with varying degrees of stereoselectivity. The larger the substituent, the greater is the selectivity for cis hydrogenation products.

The reaction of permethylzirconocene dihydride and permethylhafnocene dihydride with methylene trimethylphosphorane affords methyl-hydride and dimethyl derivatives. Under appropriate conditions, the metallated-ylide complex 1, (η^5-C_5(CH_3)_5)_2 Zr(H)CH_2PMe_2CH_2, is also obtained and has been structurally characterized by X-ray diffraction techniques. Reaction of 1 with CO affords (η^5-C_5(CH_3)_5)_2 Zr(C,O-η^2 -(PMe_3)HC=CO)H which exists in solution as an equilibrium mixture of isomers. In one isomer (2), the η^2-acyl oxygen atom occupies a lateral equatorial coordination position about zirconium, whereas in the other isomer (3), the η-acyl oxygen atom occupies the central equatorial position. The equilibrium kinetics of the 2→3 isomerization have been studied and the structures of both complexes confirmed by X-ray diffraction methods. These studies suggest a mechanism for CO insertion into metal-carbon bonds of the early transition metals.

Permethylhafnocene dihydride and permethylzirconocene hydride complexes react with diazoalkanes to afford η^2-N, N' -hydrazonido species in which the terminal nitrogen atom of the diazoalkane molecule has inserted into a metal-hydride or metal-carbon bond. The structure of one of these compounds, Cp*_2Zr(NMeNCTol_2)OH, has been determined by X-ray diffraction techniques. Under appropriate conditions, the hydrazonido-hydride complexes react with a second equivalent of diazoalkene to afford η' -N-hydrazonido-η^2-N, N' -hydrazonido species.

Structural and mechanistic study of monoalkyl diazenes. Synthesis, characterization, and reactivity of 1,6-didehydro[10]annulene

Methodology for the preparation of allenes from propargylic hydrazine precursors under mild conditions is described. Oxidation of the propargylic hydrazines, which can be readily prepared from propargylic alcohols, with either of two azo oxidants, diethyl azodicarboxylate (DEAD) or 4-methyl 1,2-triazoline-3,5-dione (MTAD), effects conversion to the allenes, presumably via sigmatropic rearrangement of a monoalkyl diazene intermediate. This rearrangement is demonstrated to proceed with essentially complete stereospecificity. The application of this methodology to the preparation of other allenes, including two that are notable for their reactivity and thermal instability, is also described.

The structural and mechanistic study of a monoalkyl diazene intermediate in the oxidative transformation of propargylic hydrazines to allenes is described. The use of long-range heteronuclear NMR coupling constants for assigning monoalkyl diazene stereochemistry (E vs Z) is also discussed. Evidence is presented that all known monoalkyl diazenes are the E isomers, and the erroneous assignment of stereochemistry in the previous report of the preparation of (Z)-phenyldiazene is discussed.

The synthesis, characterization, and reactivity of 1,6-didehydro[10]annulene are described. This molecule has been recognized as an interesting synthetic target for over 40 years and represents the intersection of two sets of extensively studied molecules: nonbenzenoid aromatic compounds and molecules containing sterically compressed π-systems.The formation of 1,5-dehydronaphthalene from 1 ,6-didehydro[10]annulene is believed to be the prototype for cycloaromatizations that produce 1,4-dehydroaromatic species with the radical centers disposed anti about the newly formed single bond. The aromaticity of this annulene and the facility of its cycloaromatization are also analyzed.

Iso-specific Ziegler-Natta polymerization of α-olefins with a single-component organoyttrium catalyst

The synthesis of a sterically tailored ligand array (M)_2((C_5H_2-2-Si(CH_3)_3-4-C(CH_3)_3)S_2i(CH_3)_2]("M_2Bp") (M = Li, 16; K, 19) is described. Transmetallation of Li_2Bp with YCl_3(THF)_3 affords exclusively the C_2 symmetric product rac-[BpY(µ_2-Cl)_2Li(THF)_2], 20. A X-ray crystal structure of 20 has been determined; triclinic, P1, a= 13.110 (8), b = 17.163 (15), c = 20.623 (14) Å, α = 104.02 (7), β = 99.38 (5), γ = 100.24 (6)° , Z = 4, R = 0.056. Transmetallation of K_2Bp with YCl_3(THF)_3 affords the halide free complex rac-BpYCl, 23. The corresponding rac-BpLaCl, 28, is prepared in an anlogous manner. In all cases the achiral meso isomer is not obtained since only for the racemic isomers are the unfavorable steric interactions between the Si(CH3)_3 groups in the narrow portion of the [Cp-M'-Cp] wedge avoided. Alkylation of 20 or 23 with LiCH(Si(CH_3)_3)_2 affords rac-BpYCH(Si(CH_3)_3)_2, 26 in good yield. Alkylation of 28 with LiCH(Si(CH_3)_3)_2 affords rac-BpLaCH(Si(CH_3)_3)_2 29. Hydrogenation of 26 cleanly affords the bridging hydride species [BpY(µ_2-H)]_2, 27, as the homochiral (R,R) and (S,S) dimeric pairs. 26 is an efficient initiator for the polymerization of ethylene to high molecular weight linear polyethylene. 27 catalyzes the polymerization of propylene (25% v/v in methylcyclohexane) and neat samples of 1-butene, 1-pentene, 1-hexene to moderately high molecular weight polymers: polypropylene (M_n = 4,200, PDI 2.32, T_m 157 °C); poly-1-butene (M_n = 8,500, PDI 3.44, T_m 105 °C); poly-1-pentene (M_n = 20,000, PDI 1.99, T_m 73 °C); poly-1-hexene (M_n = 24,000, PDI 1.75, T_m < 25 °C). ^(13)C NMR spectra at the pentad analysis level indicates that the degree of isotacticity is 99% mmmm for all polymer samples. 27 is the first single component iso-specific α-olefin polymerization catalyst. The presumed origins of the high isospecificity are presented.

Vibrational predissociation spectroscopy of mass-selected ionic clusters

This thesis presents structural investigations of molecular ions and ionic clusters using vibrational predissociation spectroscopy. Experimentally, a pulsed beam of the mass-selected ion is crossed by a tunable infrared laser beam generated by a Nd:YAG pumped LiNbO_3 optical parametric oscillator. The resulting fragment ion is mass-analyzed and detected, with its intensity as a function of the laser wavelength being the "action" spectrum of the parent ion. In the case of SiH_7^+, we observed a vibrational band centered at 3866 cm^(-1) with clear P, Q, R branches, which is assigned as a perturbed H_2 stretch. The absence of a second H_2 band suggests that the ion forms a symmetric complex with a structure H_2•SiH_3^+•H_2 , in contrast to the species CH_7^+, which has the structure CH_5^+•H_2. The infrared spectra of NO_2^+(H_2O)_n clusters exhibit a marked change with cluster size, indicating that an intracluster reaction occurs with sufficient solvation. Specifically, in NO_2^+(H_2O)_n clusters where n≤3, H_2O binds to a nitronium ion core; but at n=4 the NO_2^+ reacts, transforming the cluster to a new structure of H_3O^+•(H_2O)_(n_2)•HNO_3. For protonated chlorine nitrate, we have observed two distinct isomers previously predicted by ab initio calculations: NO_2^+•(HOC1), the lowest energy isomer, and (ClO)(HO)NO^+, a covalently bonded isomer about 20 kcal/mol higher in energy. Both isomers decompose to NO_2^+ and HOCl upon photo-excitation. These results for HClONO_2^+ lend strong support to the involvement of an ionic mechanism in the reaction of ClONO_2 on polar stratospheric cloud surfaces, a critical step in the dramatic springtime depletion of ozone over Antarctica. Current research activities on halide-solvent clusters and metal-ligand complexes as well as technological improvements of the apparatus are also discussed.

Carbon-carbon bond forming reactions from bis(carbene)-platinum(II) complexes and olefin polymerization and oligomerization using group 4 post-metallocene complexes

A long-standing challenge in transition metal catalysis is selective C–C bond coupling of simple feedstocks, such as carbon monoxide, ethylene or propylene, to yield value-added products. This work describes efforts toward selective C–C bond formation using early- and late-transition metals, which may have important implications for the production of fuels and plastics, as well as many other commodity chemicals.

The industrial Fischer-Tropsch (F-T) process converts synthesis gas (syngas, a mixture of CO + H₂) into a complex mixture of hydrocarbons and oxygenates. Well-defined homogeneous catalysts for F-T may provide greater product selectivity for fuel-range liquid hydrocarbons compared to traditional heterogeneous catalysts. The first part of this work involved the preparation of late-transition metal complexes for use in syngas conversion. We investigated C–C bond forming reactions via carbene coupling using bis(carbene)platinum(II) compounds, which are models for putative metal–carbene intermediates in F-T chemistry. It was found that C–C bond formation could be induced by either (1) chemical reduction of or (2) exogenous phosphine coordination to the platinum(II) starting complexes. These two mild methods afforded different products, constitutional isomers, suggesting that at least two different mechanisms are possible for C–C bond formation from carbene intermediates. These results are encouraging for the development of a multicomponent homogeneous catalysis system for the generation of higher hydrocarbons.

A second avenue of research focused on the design and synthesis of post-metallocene catalysts for olefin polymerization. The polymerization chemistry of a new class of group 4 complexes supported by asymmetric anilide(pyridine)phenolate (NNO) pincer ligands was explored. Unlike typical early transition metal polymerization catalysts, NNO-ligated catalysts produce nearly regiorandom polypropylene, with as many as 30-40 mol % of insertions being 2,1-inserted (versus 1,2-inserted), compared to <1 mol % in most metallocene systems. A survey of model Ti polymerization catalysts suggests that catalyst modification pathways that could affect regioselectivity, such as C–H activation of the anilide ring, cleavage of the amine R-group, or monomer insertion into metal–ligand bonds are unlikely. A parallel investigation of a Ti–amido(pyridine)phenolate polymerization catalyst, which features a five- rather than a six-membered Ti–N chelate ring, but maintained a dianionic NNO motif, revealed that simply maintaining this motif was not enough to produce regioirregular polypropylene; in fact, these experiments seem to indicate that only an intact anilide(pyridine)phenolate ligated-complex will lead to regioirregular polypropylene. As yet, the underlying causes for the unique regioselectivity of anilide(pyridine)phenolate polymerization catalysts remains unknown. Further exploration of NNO-ligated polymerization catalysts could lead to the controlled synthesis of new types of polymer architectures.

Finally, we investigated the reactivity of a known Ti–phenoxy(imine) (Ti-FI) catalyst that has been shown to be very active for ethylene homotrimerization in an effort to upgrade simple feedstocks to liquid hydrocarbon fuels through co-oligomerization of heavy and light olefins. We demonstrated that the Ti-FI catalyst can homo-oligomerize 1-hexene to C₁₂ and C₁₈ alkenes through olefin dimerization and trimerization, respectively. Future work will include kinetic studies to determine monomer selectivity by investigating the relative rates of insertion of light olefins (e.g., ethylene) vs. higher α-olefins, as well as a more detailed mechanistic study of olefin trimerization. Our ultimate goal is to exploit this catalyst in a multi-catalyst system for conversion of simple alkenes into hydrocarbon fuels.

Synthesis and characterization of 1,1-di-tert-butyldiazene

The synthesis and direct observation of 1,1-di-tert-butyldiazene (16) at -127°C is described. The absorption spectrum of a red solution of 1,1-diazene 16 reveals a structured absorption band with λ max at 506 run (Me_2O, -125°C). The vibrational spacing in S_1 is about 1200 cm^(-1). The excited state of 16 emits weakly with a single maximum at 715 run observed in the fluorescence spectrum (Me_2O:CD_2Cl_2, -196°C). The proton NMR spectrum of 16 occurs as a singlet at 1.41 ppm. Monitoring this NMR absorption at -94^0 ± 2°C shows that 1,1-diazene 16 decomposes with a first-order rate of 1.8 x 10^(-3) sec(-1) to form isobutane, isobutylene and hexarnethylethane. This rate is 10^8 and 10^(34) times faster than the thermal decomposition of the corresponding cis and trans 1,2-di-tert-butyldiazene isomers. The free energy of activation for decomposition of 1,1-diazene 16 is found to be 12.5 ± 0.2 kcal/mol at -94°C which is much lower than the values of 19.1 and 19.4 kcal/lmole calculated at -94°C for N-(2,2,6,6- tetramethylpiperidyl)nitrene (3) and N-(2,2,5,5- tetrarnethylpyrrolidyl)nitrene (4), respectively. This difference between 16 and the cyclic-1,1-diazenes 3 and 4 can be attributed to a large steric interaction between the tert-butyl groups in 1,1-diazene 16.

In order to investigate the nature of the singlet-triplet gap in 1,1-diazenes, 2,5-di-tert-butyl-N-pyrrolynitrene (22) was generated but was found to be too reactive towards dimerization to be persistent. In the presence of dimethylsulfoxide, however, N-pyrrolynitrene (22) can be trapped as N-(2,5-di-tert-butyl- N'-pyrrolyl)dimethylsulfoxirnine (38). N-(2,5-di-tert-butyl-N'-pyrrolyl)dimethylsulfoximine (38-d^6) exchanges with free dimethylsulfoxide at 50°C in solution, presumably by generation and retrapping of pyrrolynitrene 22.

Experimental chemical physics of droplets and clusters

Time-of-flight measurements of energetic He atoms, field ionization of cryogenic liquid helium clusters, and time-of-flight and REMPI spectroscopy of radical salt clusters were investigated experimentally. The excited He atoms were generated in a corona discharge. Two strong neutral peaks were observed, accompanied by a prompt photon peak and a charged peak. All peaks were correlated with the pulsing of the discharge. The neutral hyperthermal and metastable atoms were formed by different mechanisms at different stages of the corona discharge. Positively charged helium droplets were produced by ionization of liquid helium in an electrostatic spraying experiment. The fluid emerging from a thin glass capillary was ionized by a high voltage applied to a needle inside the capillary. Fine droplets (less than 10 µm in diameter) were produced in showers with currents as high as 0.4 µA at 2-4 kV. The high currents resulting from field ionization in helium and the low surface tension of He I, led to charge densities that greatly exceeded the Rayleigh limit, thus resulting in coulombic explosion of the liquid. In contrast, liquid nitrogen formed a well-defined Taylor cone with droplets having diameters comparable to the jet (≈100 µm) at lower currents (10 nA) and higher voltages (8 kV). The metal-halide clusters of calcium and chlorine were generated by laser ablation of calcium metal in a Ar/CCl₄ expansion. A visible spectrum of the Ca₂Cl₃ cluster was observed from 651 to 630 nm by 1 +1' REMPI. The spectra were composed of a strong origin band at 15 350.8 cm^-1 and several weak vibronic bands. Density functional calculations predicted three minimum energy isomers. The spectrum was assigned to the ²B₂ ← X ²A₁ transition of a planar C_2V structure having a ring of two Cl and two Ca atoms and a terminal Cl atom. The ring isomer of Ca₂Cl₃ has the unpaired electron localized on one Ca²⁺ ion to form a Ca⁺ chromophore. A second electronic band of Ca₂Cl₃ was observed at 720 nm. The band is sharply different from the 650 nm band and likely due to a different isomer.

The application of metallointercalators in recognition of and charge transport in nucleic acids

Metal complexes that utilize the 9,10-phenanthrene quinone diimine (phi) moiety bind to DNA through the major groove. These metallointercalators can recognize DNA sites and perform reactions on DNA as a substrate. The site-specific metallointercalator Λ-1-Rh(MGP)_2phi^(5+) competitively disrupts the major groove binding of a transcription factor, yAP-1, from an oligonucleotide that contains a common binding site. The demonstration that metal complexes can prevent transcription factor binding to DNA site-specifically is an important step in using metallointercalators as therapeutics.

The distinctive photochemistry of metallointercalators can also be applied to promote long range charge transport in DNA. Experiments using duplexes with regions 4 to 10 nucleotides long containing strictly adenine and thymine sequences of varying order showed that radical migration is more dependent on the sequence of bases, and less dependent on the distance between the guanine doublets. This result suggests that mechanistic proposals of long range charge transport must involve all the bases.

RNA/DNA hybrids show charge migration to guanines from a remote site, thus demonstrating that nucleic acid stacking other than B-form can serve as a radical bridge. Double crossover DNA assemblies also provide a medium for charge transport at distances up to 100 Å from the site of radical introduction by a tethered metal complex. This radical migration was found to be robust to mismatches, and limited to individual, electronically distinct base stacks. In single DNA crossover assemblies, which have considerably greater flexibility, charge migration proceeds to both base stacks due to conformational isomers not present in the rigid and tightly annealed double crossovers.

Finally, a rapid, efficient, gel-based technique was developed to investigate thymine dimer repair. Two oligonucleotides, one radioactively labeled, are photoligated via the bases of a thymine-thymine interface; reversal of this ligation is easily visualized by gel electrophoresis. This assay was used to show that the repair of thymine dimers from a distance through DNA charge transport can be accomplished with different photooxidants.

Thus, nucleic acids that support long range charge transport have been shown to include A-track DNA, RNA/DNA hybrids, and single and double crossovers, and a method for thymine dimer repair detection using charge transport was developed. These observations underscore and extend the remarkable finding that DNA can serve a medium for charge transport via the heteroaromatic base stack.

Investigations of the origin of stereocontrol in syndiospecific Ziegler-Natta polymerizations

In order to expand our understanding of the mechanism of stereocontrol in syndiospecific α-olefin polymerization, a family of Cs-symmetric, ansa-group 3 metallocenes was targeted as polymerization catalysts. The syntheses of new ansa-yttrocene and scandocene derivatives that employ the doubly [SiMe₂]- bridged ligand array (1,2-SiMe₂)₂{C₅H-3,5-(CHMe₂)₂} (where R = t- butyl, tBuThp; where R = i-propyl, iPrThp) are described. The structures of tBuThpY(µ-Cl)₂K(THF)₂, tBuThpSc(µ-Cl)₂K(Et₂O)₂, tBuThpYCH(SiMe₃)₂, Y₂{µ₂-(tBuThp)₂}(µ₂-H)₂, and tBuThpSc(µ-CH₃)₂ have been examined by single crystal X-ray diffraction methods. Ansa-yttrocenes and scandocenes that incorporate the singly [CPh₂]-bridged ligand array (CPh₂)(C₅H₄)(C₁₃H₈)(where C₅H₄ = Cp, cyclopentadienyl; where C₁₃H₈ = Flu, fluourenyl) have also been prepared. Select meallocene alkyl complexes are active single component catalysts for homopolymerization of propylene and 1-pentene. The scandocene tetramethylaluminate complexes generate polymers with the highes molecular weights of the series. Under all conditions examined atactic polymer microstructures are observed, suggesting a chain-end mechanism for stereocontrol.

A series of ansa-tantalocenes have been prepared as models for Ziegler-Natta polymerization catalysts. A singly bridged ansa-tantalocene trimethyl complex, Me₂Si(η⁵-C₅H₄)₂TaMe₃, has been prepared and used for the synthesis of a tantalocene ethylene-methyl complex. Addition of propylene to this ethylene-methyl adduct results in olefin exchange to give a mixture of endo and exo propylene isomers. Doubly-silylene bridged ansa-tantalocene complexes have been prepared with the tBuThp ligand; a tantalocene trimethyl complex and a tantalocene methylidene-methyl complex have been synthesized and characterized by X-ray diffraction. Thermolysis of the methylidene-methyl complex affords the corresponding ethylene-hydride complex. Addition of either propylene or styrene to this ethylene-hydride compound results in olefin exchange. In both cases, only one product isomer is observed. Studies of olefin exchange with ansa-tantalocene olefin-hydride and olefin-methyl complexes have provided information about the important steric influences for olefin coordination in Ziegler-Natta polymerization.

Spectroscopic studies of gas-phase molecular clusters

Spectroscopic investigations of hydrogen-bonding and van der Waals' interactions m molecular clusters were studied by the techniques of infrared predissociation and resonance-enhanced multiphoton ionization spectroscopies (REMPI). Ab initio calculations were applied in conjunction for data interpretation.

The infrared predissociation spectroscopy of CN^-•(H_2O)_n (n = 2 - 6) clusters was reported in the region of 2950 - 3850 cm^(-1). The hydrogen bondings for the C-site and N-site binding, and among the water molecules were identified for n = 2 to 4. A spectral transition was observed for n = 5 and 6, implying that the anion was surface-bound onto the water aggregates in larger clusters.

The infrared predissociation spectroscopy of Br^-•(NH_3) and I^-•(NH_3)_n (n =1-3) clusters was reported in the region of 3050-3450 cm^(-1). For the Br^-•(NH_3) complex, a dominating ionic NH stretch appeared at 3175 cm^(-1), and the weaker free NH stretch appeared at 3348 cm^(-1). The observed spectrum was consistent to the structure in which there was one nearly linear hydrogen bond between Br^- and the NH_3 moiety. For the I^- •(NH_3) complex, five distinct IR absorption bands were observed in the spectrum. The spectrum was not consistent with basic frequency patterns of three geometries considered in the ab initio calculations - complex with one, two and three hydrogen bondings between I^- and the NH_3 moiety. Substantial inhomogenous broadening were displayed in the spectra for I^-•(NH_3)_n (n =2-3), suggesting the presence of multiple isomers.

The REMPI spectroscopy of the bound 4p ^2П 1/2 and ^2П 3/2 states, and the dissociative 3d ^2Σ^+ 1/2 state in the Al•Ar complex was reported. The dissociative spectrum at Al^+ channel suggested the coupling of the 4p ^2П 1/2,3/2 states to the repulsive 3d ^2Σ^+ 1/2 state. The spin-electronic coupling was further manifested in the dissociative Al^+ spectrum of the 3d ^2Σ^+ 1/2 state. Using the potential energy curves obtained from ab initio calculations, a bound → continuum Franck-Condon-intensity simulation was performed and compared with the one-photon 3d ^2Σ^+ 1/2 profile. The agreement provided evidence for the petturbation above the Al(3d)Ar dissociation limit, and the repulsive character of the 3d ^2Σ^+ 1/2 state.

Synthesis and matrix isolated photolysis of 2,3-dimethylbicyclo [2.2.0]hexa-2,5-diene-1,4-dicarboxylic acid anhydride: a potential percursor to 2,3-dimethyl-1,4-dehydrobenzene

The synthesis of the first member of a new class of Dewar benzenes has been achieved. The synthesis of 2,3- dimethylbicyclo[2.2.0]hexa-2,5-diene-1, 4-dicarboxylic acid and its anhydride are described. Dibromomaleic anhydride and dichloroethylene were found to add efficiently in a photochemical [2+2] cycloaddition to produce 1,2-dibromo- 3,4-dichlorocyclobutane-1,2-dicarboxylic acid. Removal of the bromines with tin/copper couple yielded dichloro- cyclobutenes which added to 2-butyne under photochemical conditions to yield 5,6-dichloro-2,3-dimethylbicyclo [2.2.0] hex-2-ene dicarboxylic acids. One of the three possible isomers yielded a stable anhydride which could be dechlorinated using triphenyltin radicals generated by the photolysis of hexaphenylditin.

Photolysis of argon matrix isolated 2,3-dimethylbicyclo [2.2.0]hexa-2, 5-diene-1,4-dicarboxylic acid anhydride produced traces whose strongest bands in the infrared were at 3350 and 600 cm^(-1). This suggested the formation of terminal acetylenes. The spectra of argon matrix isolated E- and Z- 3,4-dimethylhexa-1,5-diyne-3-ene and cis-and trans-octa- 2,6-diyne-4-ene were compared with the spectrum of the photolysis products. Possibly all four diethynylethylenes were present in the anhydride photolysis products. Gas chromatograph-mass spectral analysis of the volatiles from the anhydride photolysis again suggested, but did not confirm, the presence of the diethynylethylenes.

Structure-, stereochemistry-, and metal-regulated DNA binding/cleaving molecules

In the cell, the binding of proteins to specific sequences of double helical DNA is essential for controlling the processes of protein synthesis (at the level of DNA transcription) and cell proliferation (at the level of DNA replication). In the laboratory, the sequence-specific DNA binding/cleaving properties of restriction endonuclease enzymes (secreted by microorganisms to protect them from foreign DNA molecules) have helped to fuel a revolution in molecular biology. The strength and specificity of a protein:DNA interaction depend upon structural features inherent to the protein and DNA sequences, but it is now appreciated that these features (and therefore protein:DNA complexation) may be altered (regulated) by other protein:DNA complexes, or by environmental factors such as temperature or the presence of specific organic molecules or inorganic ions. It is also now appreciated that molecules much smaller than proteins (including antibiotics of molecular weight less than 2000 and oligonucleotides) can bind to double-helical DNA in sequence-specific fashion. Elucidation of structural motifs and microscopic interactions responsible for the specific molecular recognition of DNA leads to greater understanding of natural processes and provides a basis for the design of novel sequence-specific DNA binding molecules. This thesis describes the synthesis and DNA binding/cleaving characteristics of molecules designed to probe structural, stereochemical, and environmental factors that regulate sequence-specific DNA recognition.

Chapter One introduces the DNA minor groove binding antibiotics Netropsin and Distamycin A, which are di- and tri(N-methylpyrrolecarboxamide) peptides, respectively. The method of DNA affinity cleaving, which has been employed to determine DNA binding properties of designed synthetic molecules is described. The design and synthesis of a series of Netropsin dimers linked in tail-to-tail fashion (by oxalic, malonic, succinic, or fumaric acid), or in head-to-tail fashion (by glycine, β-alanine, and γ-aminobutanoic acid (Gaba)) are presented. These Bis(Netropsin)s were appended with the iron-chelating functionality EDTA in order to make use of the technique of DNA affinity cleaving. Bis(Netropsin)-EDTA compounds are analogs of penta(N-methylpyrrolecarboxamide)-EDTA (P5E), which may be considered a head-to-tail Netropsin dimer linked by Nmethylpyrrolecarboxamide. Low- and high-resolution analysis of pBR322 DNA affinity cleaving by the iron complexes of these molecules indicated that small changes in the length and nature of the linker had significant effects on DNA binding/cleaving efficiency (a measure of DNA binding affinity). DNA binding/cleaving efficiency was found to decrease with changes in the linker in the order β-alanine > succinamide > fumaramide > N-methylpyrrolecarboxamide > malonamide >glycine, γ-aminobutanamide > oxalamide. In general, the Bis(Netropsin)-EDTA:Fe compounds retained the specificity for seven contiguous A:T base pairs characteristic of P5E:Fe binding. However, Bis(Netropsin)Oxalamide- EDTA:Fe exhibited decreased specificity for A:T base pairs, and Bis(Netropsin)-Gaba-EDT A:Fe exhibited some DNA binding sites of less than seven base pairs. Bis(Netropsin)s linked with diacids have C₂-symmmetrical DNA binding subunits and exhibited little DNA binding orientation preference. Bis(Netropsin)s linked with amino acids lack C₂-symmetrical DNA binding subunits and exhibited higher orientation preferences. A model for the high DNA binding orientation preferences observed with head-to-tail DNA minor groove binding molecules is presented.

Chapter Two describes the design, synthesis, and DNA binding properties of a series of chiral molecules: Bis(Netropsin)-EDTA compounds with linkers derived from (R,R)-, (S,S)-, and (RS,SR)-tartaric acids, (R,R)-, (S,S)-, and (RS,SR)-tartaric acid acetonides, (R)- and (S)-malic acids, N ,N-dimethylaminoaspartic acid, and (R)- and (S)-alanine, as well as three constitutional isomers in which an N-methylpyrrolecarboxamide (P1) subunit and a tri(N-methylpyrrolecarboxamide)-EDTA (P3-EDTA) subunit were linked by succinic acid, (R ,R)-, and (S ,S)-tartaric acids. DNA binding/cleaving efficiencies among this series of molecules and the Bis(Netropsin)s described in Chapter One were found to decrease with changes in the linker in the order β-alanine > succinamide > P1-succinamide-P3 > fumaramide > (S)-malicamide > N-methylpyrrolecarboxamide > (R)-malicamide > malonamide > N ,N-dimethylaminoaspanamide > glycine = Gaba = (S,S)-tartaramide = P1-(S,S)-tanaramide-P3 > oxalamide > (RS,SR)-tartaramide = P1- (R,R)-tanaramide-P3 > (R,R)-tartaramide (no sequence-specific DNA binding was detected for Bis(Netropsin)s linked by (R)- or (S)-alanine or by tartaric acid acetonides). The chiral molecules retained DNA binding specificity for seven contiguous A:T base pairs. From the DNA affinity cleaving data it could be determined that: 1) Addition of one or two substituents to the linker of Bis(Netropsin)-Succinamide resulted in stepwise decreases in DNA binding affinity; 2) molecules with single hydroxyl substituents bound DNA more strongly than molecules with single dimethylamino substituents; 3) hydroxyl-substituted molecules of (S) configuration bound more strongly to DNA than molecules of (R) configuration. This stereochemical regulation of DNA binding is proposed to arise from the inherent right-handed twist of (S)-enantiomeric Bis(Netropsin)s versus the inherent lefthanded twist of (R)-enantiomeric Bis(Netropsin)s, which makes the (S)-enantiomers more complementary to the right-handed twist of B form DNA.

Chapter Three describes the design and synthesis of molecules for the study of metalloregulated DNA binding phenomena. Among a series of Bis(Netropsin)-EDTA compounds linked by homologous tethers bearing four, five, or six oxygen atoms, the Bis(Netropsin) linked by a pentaether tether exhibited strongly enhanced DNA binding/cleaving in the presence of strontium or barium cations. The observed metallospecificity was consistent with the known affinities of metal cations for the cyclic hexaether 18-crown-6 in water. High-resolution DNA affinity cleaving analysis indicated that DNA binding by this molecule in the presence of strontium or barium was not only stronger but of different sequence-specificity than the (weak) binding observed in the absence of metal cations. The metalloregulated binding sites were consistent with A:T binding by the Netropsin subunits and G:C binding by a strontium or barium:pentaether complex. A model for the observed positive metalloregulation and novel sequence-specificity is presented. The effects of 44 different cations on DNA affinity cleaving by P5E:Fe were examined. A series of Bis(Netropsin)-EDTA compounds linked by tethers bearing two, three, four, or five amino groups was also synthesized. These molecules exhibited strong and specific binding to A:T rich regions of DNA. It was found that the iron complexes of these molecules bound and cleaved DNA most efficiently at pH 6.0-6.5, while P5E:Fe bound and cleaved most efficiently at pH 7.5-8.0. Incubating the Bis(Netropsin) Polyamine-EDTA:Fe molecules with K₂PdCl₄ abolished their DNA binding/cleaving activity. It is proposed that the observed negative metalloregulation arises from kinetically inert Bis(Netropsin) Polyamine:Pd(II) complexes or aggregates, which are sterically unsuitable for DNA complexation. Finally, attempts to produce a synthetic metalloregulated DNA binding protein are described. For this study, five derivatives of a synthetic 52 amino acid residue DNA binding/cleaving protein were produced. The synthetic mutant proteins carried a novel pentaether ionophoric amino acid residue at different positions within the primary sequence. The proteins did not exhibit significant DNA binding/cleaving activity, but they served to illustrate the potential for introducing novel amino acid residues within DNA binding protein sequences, and for the development of the tricyclohexyl ester of EDTA as a superior reagent for the introduction of EDT A into synthetic proteins.

Chapter Four describes the discovery and characterization of a new DNA binding/cleaving agent, [SalenMn(III)]OAc. This metal complex produces single- and double-strand cleavage of DNA, with specificity for A:T rich regions, in the presence of oxygen atom donors such as iodosyl benzene, hydrogen peroxide, or peracids. Maximal cleavage by [SalenMn(III)]OAc was produced at pH 6-7. A comparison of DNA singleand double-strand cleavage by [SalenMn(III)]⁺ and other small molecules (Methidiumpropyl-EDTA:Fe, Distamycin-EDTA:Fe, Neocarzinostatin, Bleomycin:Fe) is presented. It was found that DNA cleavage by [SalenMn(III)]⁺ did not require the presence of dioxygen, and that base treatment of DNA subsequent to cleavage by [SalenMn(III)]⁺ afforded greater cleavage and alterations in the cleavage patterns. Analysis of DNA products formed upon DNA cleavage by [SalenMn(III)] indicated that cleavage was due to oxidation of the sugar-phosphate backbone of DNA. Several mechanisms consistent with the observed products and reaction requirements are discussed.

Chapter Five describes progress on some additional studies. In one study, the DNA binding/cleaving specificities of Distamycin-EDTA derivatives bearing pyrrole N-isopropyl substituents were found to be the same as those of derivatives bearing pyrrole N-methyl substituents. In a second study, the design of and synthetic progress towards a series of nucleopeptide activators of transcription are presented. Five synthetic plasmids designed to test for activation of in vitro run-off transcription by DNA triple helix-forming oligonucleotides or nucleopeptides are described.

Chapter Six contains the experimental documentation of the thesis work.

Oxidation of Volatile Organic Compounds in Aqueous Solution and at the Air-water Interface of Aqueous Microdroplets

Isoprene (ISO),the most abundant non-methane VOC, is the major contributor to secondary organic aerosols (SOA) formation. The mechanisms involved in such transformation, however, are not fully understood. Current mechanisms, which are based on the oxidation of ISO in the gas-phase, underestimate SOA yields. The heightened awareness that ISO is only partially processed in the gas-phase has turned attention to heterogeneous processes as alternative pathways toward SOA.

During my research project, I investigated the photochemical oxidation of isoprene in bulk water. Below, I will report on the λ > 305 nm photolysis of H₂O₂ in dilute ISO solutions. This process yields C₁₀H₁₅OH species as primary products, whose formation both requires and is inhibited by O₂. Several isomers of C₁₀H₁₅OH were resolved by reverse-phase high-performance liquid chromatography and detected as MH⁺ (m/z = 153) and MH⁺-18 (m/z = 135) signals by electrospray ionization mass spectrometry. This finding is consistent with the addition of ·OH to ISO, followed by HO-ISO· reactions with ISO (in competition with O₂) leading to second generation HO(ISO)₂· radicals that terminate as C₁₀H₁₅OH via β-H abstraction by O₂.

It is not generally realized that chemistry on the surface of water cannot be deduced, extrapolated or translated to those in bulk gas and liquid phases. The water density drops a thousand-fold within a few Angstroms through the gas-liquid interfacial region and therefore hydrophobic VOCs such as ISO will likely remain in these relatively 'dry' interfacial water layers rather than proceed into bulk water. In previous experiments from our laboratory, it was found that gas-phase olefins can be protonated on the surface of pH < 4 water. This phenomenon increases the residence time of gases at the interface, an event that makes them increasingly susceptible to interaction with gaseous atmospheric oxidants such as ozone and hydroxyl radicals.

In order to test this hypothesis, I carried out experiments in which ISO(g) collides with the surface of aqueous microdroplets of various compositions. Herein I report that ISO(g) is oxidized into soluble species via Fenton chemistry on the surface of aqueous Fe(II)Cl₂ solutions simultaneously exposed to H₂O₂(g). Monomer and oligomeric species (ISO)1-8H⁺ were detected via online electrospray ionization mass spectrometry (ESI-MS) on the surface of pH ~ 2 water, and were then oxidized into a suite of products whose combined yields exceed ~ 5% of (ISO)1-8H⁺. MS/MS analysis revealed that products mainly consisted of alcohols, ketones, epoxides and acids. Our experiments demonstrated that olefins in ambient air may be oxidized upon impact on the surface of Fe-containing aqueous acidic media, such as those of typical to tropospheric aerosols.

Related experiments involving the reaction of ISO(g) with ·OH radicals from the photolysis of dissolved H₂O₂ were also carried out to test the surface oxidation of ISO(g) by photolyzing H₂O₂(aq) at 266 nm at various pH. The products were analyzed via online electrospray ionization mass spectrometry. Similar to our Fenton experiments, we detected (ISO)1-7H⁺ at pH < 4, and new m/z⁺ = 271 and m/z^- = 76 products at pH > 5.

Investigation of competitive antagonist binding to the nicotinic acetylcholine receptor using voltage-jump and light-flash techniques

1. The effect of 2,2’-bis-[α-(trimethylammonium)methyl]azobenzene (2BQ), a photoisomerizable competitive antagonist, was studied at the nicotinic acetycholine receptor of Electrophorus electroplaques using voltage-jump and light-flash techniques.

2. 2BQ, at concentrations below 3 μΜ, reduced the amplitude of voltage-jump relaxations but had little effect on the voltage-jump relaxation time constants under all experimental conditions. At higher concentrations and voltages more negative than -150 mV, 2BQ caused significant open channel blockade.

3. Dose-ratio studies showed that the cis and trans isomers of 2BQ have equilibrium binding constants (K _ᵢ) of .33 and 1.0 μΜ, respectively. The binding constants determined for both isomers are independent of temperature, voltage, agonist concentration, and the nature of the agonist.

4. In a solution of predominantly cis-2BQ, visible-light flashes led to a net cis→trans isomerization and caused an increase in the agonist-induced current. This increase had at least two exponential components; the larger amplitude component had the same time constant as a subsequent voltage-jump relaxation; the smaller amplitude component was investigated using ultraviolet light flashes.

5. In a solution of predominantly trans-2BQ, UV-light flashes led to a net trans→cis isomerization and caused a net decrease in the agonist-induced current. This effect had at least two exponential components. The smaller and faster component was an increase in agonist-induced current and had a similar time constant to the voltage-jump relaxation. The larger component was a slow decrease in the agonist-induced current with rate constant approximately an order of magnitude less than that of the voltage-jump relaxation. This slow component provided a measure of the rate constant for dissociation of cis-2BQ (k_ = 60/s at 20°C). Simple modelling of the slope of the dose-rate curves yields an association rate constant of 1.6 x 10⁸/M/s. This agrees with the association rate constant of 1.8 x 10⁸/M/s estimated from the binding constant (K_i). The Q₁₀ of the dissociation rate constant of cis-2BQ was 3.3 between 6° and 20°C. The rate constants for association and dissociation of cis-28Q at receptors are independent of voltage, agonist concentration, and the nature of the agonist.

6. We have measured the molecular rate constants of a competitive antagonist which has roughly the same K _ᵢ as d-tubocurarine but interacts more slowly with the receptor. This leads to the conclusion that curare itself has an association rate constant of 4 x 10⁹/M/s or roughly as fast as possible for an encounter-limited reaction.

Studies of dinucleoside monophosphates and monomer-polynucleotide interactions by proton magnetic resonance

The nature of the intra- and intermolecular base-stacking interactions involving several dinucleoside monophosphates in aqueous solution have been investigated by proton magnetic resonance spectrosocopy, and this method has been applied to a study of the interaction of polyuridylic acid with purine and adenosine monomers.

The pmr spectra of adenylyl (3' → 5') cytidine (ApC) and cytidylyl (3' → 5') adenosine (CpA) have been studied as a function of concentration and temperature. The results of these studies indicate that the intramolecular base-stacking interactions between the adenine and cytosine bases of these dinucleoside monophosphates are rather strong, and that the stacking tendencies are comparable for the two sequence isomers. The chemical shifts of the cytosine H₅ and adenine H₂ protons, and their variations with temperature, were shown to be consistent with stacked conformations in which both bases of the dinucleoside monophosphates are preferentially oriented in the anti conformation as in similar dApdC, and dCpdA (dA = deoxyadenosine; dC = deoxycytidine) segments in double helical DNA. The intramolecular stacking interaction was found to have a pronounced effect on the conformations of the ribose moieties, and these conformational changes are discussed. The concentration studies indicate extensive self-association of these dinucleoside monophosphates, and analysis of the concentration data facilitated determination of the dimerization constant for the association process as well as the nature of the intermolecular complexes.

The dependence of the ribose conformation upon the extent of intramolecular base-stacking was used to demonstrate that the base-base interaction in cytidylyl (3' → 5') cytidine (CpC) is rather strong, while there appears to be little interaction between the two uracil bases of uridylyl (3' → 5') uridine (UpU).

Studies of the binding of purine to several ribose and deoxyribose dinucleoside monophosphates show that the mode of interaction is base-stacking, and evidence for the formation of a purine-dinucleoside monophosphate intercalated complex is presented. The purine proton resonances are markedly broadened in this complex, and estimates of the purine linewidths in the complex and the equilibrium constant for purine intercalation are obtained.

A study of the interaction of unsubstitued purine with polyuridylic acid at 29°C by pmr indicated that purine binds to the uracil bases of the polymer by base-stacking. The severe broadening of the purine proton resonances observed provides strong evidence for the intercalation of purine between adjacent uracil bases of poly U. This interaction does not result in a more rigid or ordered structure for the polymer.

Investigation of the interaction between adenosine and polyuridylic acid revealed two modes of interaction between the monomer and the polymer, depending on the temperature. At temperatures above 26°C or so, monomeric adenosine binds to poly U by noncooperative A-U base stacking. Below this temperature, a rigid triple-stranded 1A:2U complex is formed, presumably via cooperative hydrogen-bonding as has previously been reported.

These results clearly illustrate the importance of base-stacking in non-specific interactions between bases, nucleosides and nucleotides, and also reveal the important role of the base-stacking interactions in cooperatively for med structures involving specific base-pairing where both types of interaction are possible.