Sequence specific recognition and cleavage of DNA by synthetic molecules

DNA recognition is an essential biological process responsible for the regulation of cellular functions including protein synthesis and cell division and is implicated in the mechanism of action of some anticancer drugs. Studies directed towards defining the elements responsible for sequence specific DNA recognition through the study of the interactions of synthetic organic ligands with DNA are described.

DNA recognition by poly-N-methylpyrrolecarboxamides was studied by the synthesis and characterization of a series of molecules where the number of contiguous N-methylpyrrolecarboxamide units was increased from 2 to 9. The effect of this incremental change in structure on DNA recognition has been investigated at base pair resolution using affinity cleaving and MPE•Fe(II) footprinting techniques. These studies led to a quantitative relationship between the number of amides in the molecule and the DNA binding site size. This relationship is called the n + 1 rule and it states that a poly-N methylpyrrolecarboxamide molecule with n amides will bind n + 1 base pairs of DNA. This rule is consistent with a model where the carboxamides of these compounds form three center bridging hydrogen bonds between adjacent base pairs on opposite strands of the helix. The poly-N methylpyrrolecarboxamide recognition element was found to preferentially bind poly dA•poly dT stretches; however, both binding site selection and orientation were found to be affected by flanking sequences. Cleavage of large DNA is also described.

One approach towards the design of molecules that bind large sequences of double helical DNA sequence specifically is to couple DNA binding subunits of similar or diverse base pair specificity. Bis-EDTA-distamycin-fumaramide (BEDF) is an octaamide dimer of two tri-N methylpyrrolecarboxamide subunits linked by fumaramide. DNA recognition by BEDF was compared to P7E, an octaamide molecule containing seven consecutive pyrroles. These two compounds were found to recognize the same sites on pBR322 with approximately the same affinities demonstrating that fumaramide is an effective linking element for Nmethylpyrrolecarboxamide recognition subunits. Further studies involved the synthesis and characterization of a trimer of tetra-N-methylpyrrolecarboxamide subunits linked by β-alanine ((P4)_(3)E). This trimerization produced a molecule which is capable of recognizing 16 base pairs of A•T DNA, more than a turn and a half of the DNA helix.

DNA footprinting is a powerful direct method for determining the binding sites of proteins and small molecules on heterogeneous DNA. It was found that attachment of EDTA•Fe(II) to spermine creates a molecule, SE•Fe(II), which binds and cleaves DNA sequence neutrally. This lack of specificity provides evidence that at the nucleotide level polyamines recognize heterogeneous DNA independent of sequence and allows SE•Fe(II) to be used as a footprinting reagent. SE•Fe(II) was compared with two other small molecule footprinting reagents, EDTA•Fe(II) and MPE•Fe(II).

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.

Catalytic conversion of nitrogen to ammonia by an iron model complex

Threefold symmetric Fe phosphine complexes have been used to model the structural and functional aspects of biological N₂ fixation by nitrogenases. Low-valent bridging Fe-S-Fe complexes in the formal oxidation states Fe(II)Fe(II), Fe(II)/Fe(I), and Fe(I)/Fe(I) have been synthesized which display rich spectroscopic and magnetic behavior. A series of cationic tris-phosphine borane (TPB) ligated Fe complexes have been synthesized and been shown to bind a variety of nitrogenous ligands including N₂H₄, NH₃, and NH₂-. These complexes are all high spin S = 3/2 and display EPR and magnetic characteristics typical of this spin state. Furthermore, a sequential protonation and reduction sequence of a terminal amide results in loss of NH₃ and uptake of N₂. These stoichiometric transformations represent the final steps in potential N₂ fixation schemes.

Treatment of an anionic FeN₂ complex with excess acid also results in the formation of some NH₃, suggesting the possibility of a catalytic cycle for the conversion of N₂ to NH₃ mediated by Fe. Indeed, use of excess acid and reductant results in the formation of seven equivalents of NH₃ per Fe center, demonstrating Fe mediated catalytic N₂ fixation with acids and protons for the first time. Numerous control experiments indicate that this catalysis is likely being mediated by a molecular species.

A number of other phosphine ligated Fe complexes have also been tested for catalysis and suggest that a hemi-labile Fe-B interaction may be critical for catalysis. Additionally, various conditions for the catalysis have been investigated. These studies further support the assignment of a molecular species and delineate some of the conditions required for catalysis.

Finally, combined spectroscopic studies have been performed on a putative intermediate for catalysis. These studies converge on an assignment of this new species as a hydrazido(2-) complex. Such species have been known on group 6 metals for some time, but this represents the first characterization of this ligand on Fe. Further spectroscopic studies suggest that this species is present in catalytic mixtures, which suggests that the first steps of a distal mechanism for N₂ fixation are feasible in this system.

Synthesis and potency of long end-associative polymers for mist control

Long linear polymers that are end-functionalized with associative groups were studied as additives to hydrocarbon fluids to mitigate the fire hazard associated with the presence of mist in a crash scenario. These polymers were molecularly designed to overcome both the shear-degradation of long polymer chains in turbulent flows, and the chain collapse induced by the random placement of associative groups along polymer backbones. Architectures of associative groups on the polymer chain ends that were tested included clusters of self-associative carboxyl groups and pairs of hetero-complementary associative units.

Linear polymers with clusters of discrete numbers of carboxyl groups on their chain ends were investigated first: an innovative synthetic strategy was devised to achieve unprecedented backbone lengths and precise control of the number of carboxyl groups on chain ends (N). We found that a very narrow range of N allows the co-existence of sufficient end-association strength and polymer solubility in apolar media. Subsequent steady-flow rheological study on solution behavior of such soluble polymers in apolar media revealed that the end-association of very long chains in apolar media leads to the formation of flower-like micelles interconnected by bridging chains, which trap significant fraction of polymer chains into looped structures with low contribution to mist-control. The efficacy of very long 1,4-polybutadiene chains end-functionalized with clusters of four carboxyl groups as mist-control additives for jet fuel was further tested. In addition to being shear-resistant, the polymer was found capable of providing fire-protection to jet fuel at concentrations as low as 0.3wt%. We also found that this polymer has excellent solubility in jet fuel over a wide range of temperature (-30 to +70°C) and negligible interference with dewatering of jet fuel. It does not cause an adverse increase in viscosity at concentrations where mist-control efficacy exists.

Four pairs of hetero-complementary associative end-groups of varying strengths were subsequently investigated, in the hopes of achieving supramolecular aggregates with both mist-control ability and better utilization of polymer building blocks. Rheological study of solutions of the corresponding complementary associative polymer pairs in apolar media revealed the strength of complementary end-association required to achieve supramolecular aggregates capable of modulating rheological properties of the solution.

Both self-associating and complementary associating polymers have therefore been found to resist shear degradation. The successful strategy of building soluble, end-associative polymers with either self-associative or complementary associative groups will guide the next generation of mist-control technology.

Magnetic behavior of basic iron(III) compounds. I. Magnetic behavior of the basic iron sulphates and basic iron chromate. II. Magnetic behavior of delta ferric oxide hydroxide

I. The thermomagnetic behavior and infrared spectroscopic features of KFe₃(SO₄)₂(OH)₆ (jarosite), (H₃O)Fe₃(SO₄)₂ (OH)₆ (hydronium jarosite), KFe₃(CrO₄)₂ (OH)₆, Fe(OH)SO₄ (basic iron sulfate), and Fe(OH)CrO₄ (basic iron chromate) are reported. Fe(OH)CrO₄ and KFe₃(CrO₄)₂ (OH)₆ are shown to be weak ferro magnets with Curie temperatures of 73 and 71 °K, respectively. This unusual magnetic behavior is rationalized in terms of the ionic spin configurations of the phases. Exchange coupling through chromate bridging groups is shown to be weak.

II. The magnetic behavior and the influence of preparative history on the magnetic behavior of δFeO(OH) is reported. δFeO(OH) is shown to be a fine-particulate, uniaxial, magnetic species. Magnetization data for this species are shown to be consistent with the existence of magnetically inactive layers surrounding magnetic particles.

A fully-nonlocal energy-based formulation and high-performance realization of the quasicontinuum method

The quasicontinuum (QC) method was introduced to coarse-grain crystalline atomic ensembles in order to bridge the scales from individual atoms to the micro- and mesoscales. Though many QC formulations have been proposed with varying characteristics and capabilities, a crucial cornerstone of all QC techniques is the concept of summation rules, which attempt to efficiently approximate the total Hamiltonian of a crystalline atomic ensemble by a weighted sum over a small subset of atoms. In this work we propose a novel, fully-nonlocal, energy-based formulation of the QC method with support for legacy and new summation rules through a general energy-sampling scheme. Our formulation does not conceptually differentiate between atomistic and coarse-grained regions and thus allows for seamless bridging without domain-coupling interfaces. Within this structure, we introduce a new class of summation rules which leverage the affine kinematics of this QC formulation to most accurately integrate thermodynamic quantities of interest. By comparing this new class of summation rules to commonly-employed rules through analysis of energy and spurious force errors, we find that the new rules produce no residual or spurious force artifacts in the large-element limit under arbitrary affine deformation, while allowing us to seamlessly bridge to full atomistics. We verify that the new summation rules exhibit significantly smaller force artifacts and energy approximation errors than all comparable previous summation rules through a comprehensive suite of examples with spatially non-uniform QC discretizations in two and three dimensions. Due to the unique structure of these summation rules, we also use the new formulation to study scenarios with large regions of free surface, a class of problems previously out of reach of the QC method. Lastly, we present the key components of a high-performance, distributed-memory realization of the new method, including a novel algorithm for supporting unparalleled levels of deformation. Overall, this new formulation and implementation allows us to efficiently perform simulations containing an unprecedented number of degrees of freedom with low approximation error.

Heterometallic Complexes as Models of Enzymatic Active Sites

This dissertation describes studies on two multinucleating ligand architectures: the first scaffold was designed to support tricopper complexes, while the second platform was developed to support tri- and tetrametallic clusters.

In Chapter 2, the synthesis of yttrium (and lanthanide) complexes supported by a tripodal ligand framework designed to bind three copper centers in close proximity is described. Tricopper complexes were shown to react with dioxygen in a 1:1 [Cu₃]/O₂ stoichiometry to form intermediates in which the O–O bond was fully cleaved, as characterized via UV-Vis spectroscopy and determination of the reaction stoichiometry. Pre-arrangement of the three Cu centers was pivotal to cooperative O₂ activation, as mono-copper complexes reacted differently with dioxgyen. The reactivity of the observed intermediates was studied with various substrates (reductants, O-atom acceptors, H-atom donors, Brønsted acids) to determine their properties. In Chapter 3, the reactivity of the same yttrium-tricopper complex with nitric oxide was explored. Reductive coupling to form a trans-hyponitrite complex (characterized by X-ray crystallography) was observed via cooperative reactivity by an yttrium and a copper center on two distinct tetrametallic units. The hyponitrite complex was observed to release nitrous oxide upon treatment with a Brønsted acid, supporting its viability as an intermediate in nitric oxide reduction to nitrous oxide.

In Chapter 4, a different multinucleating ligand scaffold was employed to synthesize heterometallic triiron clusters containing one oxide and one hydroxide bridges. The effects of the redox-inactive, Lewis acidic heterometals on redox potential was studied by cyclic voltammetry, unveiling a linear correlation between redox potential and heterometal Lewis acidity. Further studies on these complexes showed that the Lewis acidity of the redox-inactive metals also affected the oxygen-atom transfer reactivity of these clusters. Comparisons of this reactivity with manganese systems, collaborative efforts to reassign the structures of related manganese oxo-hydroxo clusters, and synthetic attempts to access related dioxo clusters are also described.

In Appendix A, ongoing efforts to synthesize new clusters supported by the same multinucleating ligand platform are described. Studies of novel approaches towards ligand exchange in tetrametallic clusters and incorporation of new supporting and bridging ligand motifs in trinuclear complexes are presented.