5 - Methylcytosine Proton Transfer And The Deaminase Reaction Mechanism

As one of the simplest and most basic phenomenons in the isomerization balance and redox reaction,proton transfer(PT)in intra- and inter- molecule plays an important role in many chemical processes,proton transfer can passed through hydrogen bonds formed between organic molecules.Such transfer is as important as energy transfer and electronic transfer which are in molecular system,almost all organic reactions have included all or part of the proton transfer process.Proton transfer plays an important role in the transmission of information between molecules.Hydrogen bond formation and proton transfer phenomena in many chemical processes are very important and common,because many chemical, physical and biological processes involve the forming and breaking of this kind of bonds.In this paper,we investigate the intramolecular or intermolecular proton transfers(PTs)isomerization under the assistant of water molecular or the six simulated acid residues compounds and the hydrolysis deamination using the density functional theory at 6-31+G^* bases set level.The main contents of the paper contain 3 parts,just as follows:1.water-catalyzed pathways of the 5—methylcytosine isomerization.Because these processes can occur in the water solution,maybe the water molecule participate in the proton transfer.When water is involved in the proton transfer,the transition state has a structure of six-member or eight-member ring.The results show that the water molecule takes part in the forming of transition state.The reaction path or mechanism is changed due to the participating of water,the proton transfer is one kind of exchange process between water and another molecule,the barrier of exchange process is much smaller than direct proton transfer.So the water plays an important role in the proton transfer of the 5—methylcytosine isomerization.2.We have chosen six kinds of compounds(CH₃COOH,CH₃CONH₂, CH₃-NH-C(NH)-NH₂,CH₃NH₂,CH₃OH,and CH₃-C₆H₄-OH)to simulate amino acid catalyzed pathways for the 5-methylcytosine isomerization.In the six compounds,the combining of the carboxyl of the CH₃COOH is most favorable for the proton transfer of 5-methylcytosine.In this proton transfer process,it must surmount a energy barrier of 16.39 KJ.mol^-1for this proton transfer process.3.5—methylcytosine have amino out of ring can be changed by hydrolysis.The products of amino hydrolysis are thymine.The hydrolysis deamination includes three steps,In the first step,5—methylcytosine isomerization with water molecules, In the second steps,the O(negative charge)of water attack the C(positive charge) of C=N and the H(positive charge)of water attack the N(negative charge)of C=N linked directly with amino,and the transition state with a new-formed four-member ring is produced.This process belongs to dipole addition reaction.In the transition state of this step,the bond of O-H and the bond of C=N are broken partly,and the bond H...N and bond O...C are formed partly.The new-formed four-member ring has a structure of plane,but it is not coplanar with base skeleton.In the third steps, the H of OH attacks the N of amino.The transition states also have a four-member ring.Accompany with the forming N-H a single bond and the bond between N of amino and C of base is weaken greatly,the skeleton of NH₃ is formed in the rough. Along with the leaving of amino,the O of hydroxyl is more and more closed to the plane of base skeleton,the products of amino hydrolysis are thymine.In summary,the research of the isomerization,the hydrolysis deamination of 5—methylcytosine unveil the information of molecule mechanism,the thermodynamic characters of these processes.