Theoretical Studies On The Colbat(Ⅲ) Complexes-DNA Interactions And Some Complexes Containing Planar Tetracoordinate Carbon Atoms

There are two parts in this thesis. In the first part, we studied the interactions between some Co(III) complexes and normal sequence as well as mismatched sequence DNA by molecular modeling methods. In the second part, the possibilities and character of some clusters containing planar tetracoordinate carbon atoms were studied by extensive computational quantum chemistry explorations.Because rapid racemization could occur automatically or in the presence of oligonucleotide (ODN) with some Co(III) complexes, the information of interactions between these kinds of Co(III) complexes and DNA will become extremely difficult to acquire for the coexistence of enantiomers and the unknown quantity of each enantiomer. To solve the difficulties and deficiencies occurring in the studies, we present in the thesis a method that analyzes the experimental and theoretical results in an efficient way. We studied the interations between [Co(phen)₂dpq]³⁺ and normal sequence DNA d(GTCGAC)2 using the method mentioned above, which solve the problem occurring in the experimental work of our work group. The work presented a feasible method to study similar systems. It should be point out that the modeling results are tally perfectly with that in the experiments and, as the theoretical studies are independent to the experimental results, the reliabilities of our modeling methods are confirmed, so it is feasible to study the similar systems without comparible experimental results with same theoretical process. In the work followed, we studied the interactions between [Co(phen)₂dpq]³⁺ and mismatched DNA containing sheared G:A base pairs and between [Co(phen)₂hpip]³⁺ (it could rapid racemize as that of [Co(phen)₂dpq]³⁺ , but the investigation on it will be more difficult in that the ligand hpip have two resonant isomers) and normal as well as sheared mismatch DNA.We sum up the main research results as well as innovations of the firstpart works as follows:1. Combined with the experimental results of our work group, modeling studies revealed an unusual phenomenon that the L-isomer of Co(III) complex [Co(phen)2dpq]3+ will be enriched when the racemic complex interacted with ODN d(GTCGAC)2. Furthermore, based on the calculating results, we could predict that the isomer of this kind of complex (could rapid racemize) that binds tighter and more stable than the other isomers with DNA will be enriched.2. In the field of the studies of interaction between macrocyclic aromatic transition metal complex with DNA, more attention has been paid to the selectivity (especially the enantio-selectivity), specificity and their mechanism during the interactions. Based on our modeling results, we clearify the information of interactions between the Co(III) complexes ([Co(phen)2dpq]3+ and [Co(phen)2hpip]3+) and DNA (normal sequence d(GTCGAC)2 and mismatched sequence d(CCGAATGAGG)2), including groove-selectivity of DNA, enantio-selectivity of complexes, the structural selectivity of hpip ligand and the site-specificity in the process of recognition of complexes to DNA. The main interaction mode for [Co(phen)2dpq]3+ and normal sequence DNA is the intercalation of dpq ligand of L-isomer to base stack in C3G4 region from DNA minor groove;that for [Co(phen)2dpq]3+ and mismatched sequence DNA is the intercalation of dpq ligand of D-isomer to base stack in A4T5 region from DNA major groove;that for [Co(phen)2hpip]3+ and normal sequence DNA is the intercalation of hpip (hydroxy oxygen atom form hydrogen bond to imidazole NH, form I) ligand of D-isomer to base stack in G5A6 region from DNA minor groove;and that for [Co(phen)2hpip]3+ and mismatched sequence DNA is the intercalation of hpip (hydroxy hydrogen atom form hydrogen bond to imidazole N, form II) ligand (the two isomers has almost the same probability) to base stack in T5G6 region from DNA major groove. Further analysis indicated that the steric interactions, especially the electrostatic interactions are the main factor that influence the characters shown in the interactions mentioned above.3. We found that both [Co(phen)2hpip]3+ and [Co(phen)2dpq]3+could repair the sheared G:A mismatch in conformational level when they interacted with mismatched DNA. Thereinto, for [Co(phen)2dpq]3+ complex, only the L-isomer could repair the sheared mismatch (both mismatched base pairs were all changed to parallel form);while for [Co(phen)2hpip]3+ complex, its four isomers all could repair the mismatch, but only the D-isomer of complex containing hpip form II could change the structure of mismatched base pairs from shared form to parallel form, the other isomers could only convert that in the intercalation site. It is noteworthy that the recognition of the [Co(phen)2hpip]3+ to sheared DNA has high specificity in that all isomers bind DNA just beside the mismatched base pairs, which, together with its photo-cleavage reactivity, could cleave the mismatched base pair from the double helical DNA. This character gives the potential possibilities to the complex to become the reagent, even the drug, to examine and cure molecular diseases concerning mismatch.In the second part, we studied the possibilities of the compound containing planar tetracoordinate carbon (PTC) atoms. In this field, most investigation are mainly focused on the species containing merely one PTC or planar hypercoordinate carbon (PHC) atom, while little attention has been paid to these with more than one PTC or PHC. We searched the possible systems of binary C-B complex and PTC-contained hydrometals, and we found some complex with more than one PTC.We sum up the main research results as well as innovations of second parts as follows:1. We found a wheel-like C6Bi22' complex, which contained six unambiguous PTCs in the center of 12-membered boron ring. In structure of this D6h complex, the six carbon atoms are equal to each other, and more significantly, the 6-membered central carbon ring and 12-membered outer boron ring could rotate quiet freely with regard to one another.2. Further analysis about the aromatic characters of the C6B]22" and related molecular reveal that they did not obey the Hiickel 4n+2 % electronrule, which is formed on the basis of single ring system, but the individual ring in the molecules maybe obey that rule.3. We found a new class of hydrometals containing more than one PTCs: CnM2n+2H2n+2 (M=Ni, Pd or Pt, n=2, 3 or 4, the numbers of PTCs in the molecules are from 2 to 4, we did not search those with more than five PTCs for the limitation of current computational resources). They all expended from the PTC-contained structural units of CM4H4, CPd4H4 and CPt4H4 in one dimension.4. Further analysis indicated that the driving force that make carbon atoms employ the planar tetracoordination is the aromaticity. Natural bond orbital (NBO) analysis revealed the obvious decrease in the occupancy of 2px orbital of PTC atoms when the structure is one-dimensional-extended, while revealed the obvious increase of 2pz orbital. The decrease in 2px orbital decreases the possibility of forming the head-to-head a bond between carbon atoms, while the increase in 2pz orbital stabilizes the whole PTC-contained structure by enhanced tt interaction. The results from nucleus-independent chemical shift (NICS) calculations confirmed that the aromaticities of the complexes ascended with the increasing number of PTC contained in the molecules.