A novel target-promoted DNA alkylation system was designed, which consists of a DNA intercalating/alkylating quinone methide (QM) precursor, a removable amine linker, and a sequence-specific delivery. The QM in this system was regenerated by eliminating the amino linker promoted by the hydrophobic interaction between the target DNA and the intercalating QM precursor. Three alkylation model systems (methoxyl polycyclic system, intramolecular hydrogen bonding system and biaryl system) were proposed and synthesized. The potential DNA QM alkylation was investigated by deoxyadenosine (dA) and deoxyguanosine (dG) alkylation with the biaryl system. Only one deoxynucleoside adduct was observed when dA or dG reacted with quinoline or naphthalene QM precursor, in which both dA adducts degraded with time, while dG adducts remained unchanged after 72h at room temperature. The quinoline dG adduct was fully characterized as quinoline dG N1 adduct by NMR techniques. Naphthalene dG was found as a 1:1 mixture of diastereomers.

The thesis entitled "Structure and reactivity in bridged polycyclic systems: cis-trans enantiomerism, fulvene cycloadditions and crystallographic studies of bridgehead β-ketoacids " consists of two parts. Part I contains 3 chapters, and deals with cycloaddition reactions of 6-arylfulvenes with maleic anhydride and nitrones (The products in the case of maleic anhydride display cis-trans enantiomerism). Part II contains 2 chapters, and deals with resolution of racemic primary amines, racemic amino acids and the relative decarboxylation propensities of bicyclic β-ketoacids in solid state. Part I Chapter 1: A new case of the uncommon cis-trans enantiomerism is presented in the Diels-Alder cycloadducts (3 & 4) of 6-arylfulvenes (1) with maleic anhydride (2).1 The resolution of the cis-trans enantiomers were accomplished via the formation of diastereomeric imides 6 and 7 with (1S)-(naphth-1-yl)ethylamine (5), and their subsequent hydrolysis and recyclisation (Scheme 1). The enantiomers 3 and 4 were characterized spectrally, polarimetrically (including CD) and by chiral HPLC. The chiral anhydrides were also stereospecifically converted to the corresponding imides by treatment with aq. ammonia in excellent yields. The crystal structure of one of the diastereomeric imides (derived from 6-phenylfulvene) was determined, and based on the known S configuration of the naphthylethylamine moiety, the configurations of the original anhydride adducts could be assigned.2 Scheme 1 Chapter 2: In this chapter tricyclic imides (8a-c) were prepared by Diels-Alder reaction of 6-arylfulvenes (1a-c) and maleic anhydride (2),2 followed by treatment with aq. NH3. The exo isomers were found to exist as conglomerates when the aryl group was p-tolyl or p-anisyl (although not phenyl). Triage of the p-tolyl racemate (Scheme 2), followed by reaction with p-toluenesulphonyl chloride in CH2Cl2/Et3N, led to the crystalline enantiopure N-tosylimides 9 (These were also found to be conglomerates). X-ray diffraction analysis of the N-tosylimides (9) via the anomalous dispersion technique led to the assignment of the absolute configurations (as either E or Z).3, 4 The original p-tolyl imide enantiomers were found to racemise upon UV irradiation in CHCl3. Based on this, a possible second order asymmetric transformation under photochemical conditions was attempted, and indeed led to the isolation of crystalline imide with a small ee (~15%).5 Scheme 2 Chapter 3: This chapter deals with the fulvene-nitrone cycloadditions. The possibility of discovering examples of the rare (6π + 4π) cycloaddition prompted an exploration of the reaction between electron-rich nitrones and pentafulvenes. In previous reports of such cycloadditions, diazomethane or benzonitrile oxide was used as 4π component.6 Building on previous work from this laboratory,7 the reaction between a set of substituted fulvenes and electron rich nitrones were studied. Theoretical calculations indicate that the (6π + 4π) mode would be favored when the fulvene-nitrone cycloaddition is controlled by the LUMO (fulvene) – HOMO (nitrones) interaction.8 Electron withdrawing groups on the fulvene would lower the LUMO and facilitate the above orbital interaction. Therefore the reaction between electron poor fulvenes and nitrones was taken up for further study. In particular, fulvene (10) was reacted with nitrones (11). However, only a (2π + 4π) mode was observed, involving one of the endocyclic double bond of the fulvene, in moderate yields (Scheme 3). Structures of these adducts were assigned based on NMR and X-ray crystal structure determination. The failure to observe the (6π + 4π) mode (14) is intriguing, and it is not clear whether this is due to electronic or steric reason. Scheme 3 Part II Chapter 1 describes the resolution of racemic primary amines and racemic amino acids (16) via the formation of diastereomeric imides. For this purpose D-camphoric anhydride (15) was chosen as the chiral auxiliary for the following reasons: it is of low-molecular weight with a rigid backbone, and is also easily prepared and purified.9 Primary amine (16) was treated with D-camphoric anhydride (15) in presence of CHCl3/DCC to form the corresponding diastereomeric imides 17 and 18. (In the case of amino acids, the corresponding methyl esters were treated with D-camphoric anhydride (15) in presence of triethylamine in chloroform). The resulting diastereomeric imides 17 and 18 were separated by silica gel column chromatography (Scheme 4), and hydrolyzed to the chiral amines (or amino acids). (The by-produced camphoric acid could be reconverted to D-camphoric anhydride (15). Scheme 4 Chapter 2: The relative ease with which β-ketoacids tend to lose CO2 is intriguing and has been the focus of numerous mechanistic studies.10-12 It is generally believed that the decarboxylation of β-ketoacids occurs via a six-centered hydrogen bonded transition state (19), which leads to the formation of the enol tautomer (20) of the final ketone product (Scheme 5). Scheme 5 Scheme 6 The initial formation of the enol is apparently supported by the high thermal stability of bicyclic β-ketoacids, in which the carboxylic acid functionality is at bridgehead. In these the formation of the enol would be disfavored by Bredt’s rule, which forbids the formation of a double bond at the bridgehead (particularly in the smaller bicyclic compounds). Also, it may be expected that these trends would be manifested in the ground state. This is because there would be a stereoelectronic requirement for the decarboxylation reaction, by which the bond to the carboxylic group would need to be parallel to the C=O π bond of the keto group. Therefore, it was of interest to study the crystal structures of suitable β-ketoacids in the hope of evidencing the above structural trends (Structure for the analogs 21-23 have been reported previously (Scheme 6)).13-15 In fact, the approach pioneered by Dunitz was of particular interest in this regard. 16 In this approach crystal structures of a series of analogs were studied; these analogs possess varying degrees of strain that could be considered as leading to the transition state of a certain reaction. The bond length and related data are then employed to ‘map’ the reaction dynamics. Compound Bond* lengths (Å) Increase in the bond length compared to ketopinic acid (%) Decarboxylation temp.17 * fine bond at the bridgehead to the COOH group. In the case of the decarboxylation of β-ketoacids, a correlation between the lengthening of the bond to the COOH group and the ease of decarboxylation was sought. Therefore the set of analogs 24-26 were prepared (Scheme 6) and their crystal structures determined by X-ray diffraction (at 100K). In the case of 26, an increase of 2.47% relative to 21 in the Cα-COOH bond length was observed. However, no evidence for an intramolecular O=C-O-H…O=C H-bonding, was observed in the crystal structures of 24-26. Instead, the COOH moieties were seen to participate in intermolecular O-H…O hydrogen bonding via the well known carboxylic acid dimer motif. The β-ketoacids were also converted into their corresponding S-benzylisothiouronium salts (Scheme 6), to study the effect of destroying the COOH dimer motif. The salts 27 and 28 could be obtained in a form suitable for single crystal X-ray diffraction. The crystal structures revealed an increase in the Cα-COO- bond length to an extent of 1.97% in case of 28 relative to 27. Also, there is an increase in the relevant bond length of ~0.8% on going from 24 (m.p. 145 °C) to 26 (m.p. 132 °C). Note also that these compounds melts with decompositions. Therefore, it appears that the ease of decarboxylation of these analogs is reflected in the relative lengthening of the bond to the COOH group. Thus, this study represents an application of the Dunitz crystallographic approach to reaction dynamics,16 to the case of the decarboxylation of β-ketoacids.(For structural formula pl see the pdf file)