The Tight Binding Method And Its Application In Charge Transfer Of DNA Helix

DNA(Deoxyribonucleic acid),the main component of chromosome and gene,is paid more attention for its physiological meanings and its potential application in nanoscale electronic devices,materials and biological synthesis.In recent years,it is found that the process of damage and repair in DNA is companied with charge transfer.Also,the potential applications in the nanoscale electronic devices are related with charge transport.So the topic of charge transfer in DNA becomes the research central in physiology,physical electronics and material science.There are many debates about the conductivity of DNA for different experimental results form superconductor,conductor,and semiconductor to insulator.However,the theoretical calculations about DNA are also different for adopted computational method.Since 1993,Barton group report that hole transfer in DNA over a distance＞4nm,a large number of experiments and theories have been advanced in the attempt to characterize the transport,mainly of a radical cation or hole.Particularly,a famous experiment was carried out by Giese on the sequence GA_nGGG,in which the hole tunnels through the first three As,then hop onto the bridge of As,where they are localized on a single A and travel further by hopping between neighboring As.Barton and Schuster groups exclaim that charge or holes can travel through more than four (A:T)s,and also holes delocalize in several bases.Meanwhile they point out that hole transport by poloraon drift in(A:T)_n(n＞3).Conwell theory group also pay attention to charge transport in DNA and study it with tight binding method.Experiments show that charge will transfer along DNA helix;however it is not clear that how the charge transfers and what is the transport mechanism.In this paper,we will try to explain the above questions for its meaningful to DNA repair,illness treatment,protein drug design,and nano device.The theoretical calculations about DNA are difficult for the ordinary quantum chemical methods(e.g.ab initio method and Density Function Theory)can't deal with such large scale system.So series of semiemperical methods are developed.The tight binding method is one of these methods that valuable ones to calculate complicate DNA molecules.The DNA structure and usual quantum chemistry(ab initio method,Density Function Theory and semiemperical method)methods are introduced,and then the difficulties in calculations are also pointed out.The tight binding method(TBM) can overcome the above limitations in virtue of fitted parameters which predigest multiple integral.The couplings between lattice displacements and charge distribution are focused on in SSH model and the model also explains some charge transport phenomena along DNA helix.Another important tight binding model is PBH model in which the interaction is the main one between the hydrogen bond stretching and charge distribution.These kind interactions also have visible effect on charge motion in DNA chain.1.In static state,the hole polaron will appear when one electron is excited from the DNA chain,in which charge distribution and lattice displacements are coupled together.Accordingly,the polaron energy level and the corresponding level come forth.In usual cases,polarons localize in the several bases with lowest onsite energy. Additionally,polaron forms at sites with initial structural fluctuations,but not ones with lowest onsite energy.2.Polaron motion becomes complicate when a DNA chain is put in an electric field.The polaron of the DNA chain composed by the same bases and the alternate ones can move along the chain under the suitable electric field until the polaron smears gradually for the lattices fluctuations.In the DNA chain made up of the same bases or alternate bases,the polaron can move along the chain in the direction of the electric field until smearing under the electric field.We discuss the DNA chains composed of different quantum wells and potential barriers detailedly.When polaron localizes at quantum wells,it will smear under an electric field;the polaron localizing at other sites will move forward until it localizes at the wells.The wells with deep potential energy can hold the polaron until it smears. The polaron at shallower wells will move forward further,such as in A₃₀TA₆₉.The DNA chains in which potential barriers are existed are also discussed.The results show that hole polaron can't tunnel through single barrier under weak field,but it can go through the barrier when the electric field is enlarged.It is interested that the polaron will divided into two halves.One is small polaron and the other is the remain one.The small one will move forward and the remain one will smear under the electric field.To the case there are 3 or more barriers in a DNA chain,the tunneling can't be observed though larger electric field.It is interested that polaron can transfer in the chains of three segments (?)R_N-R′_M-R″_p(?) by annihilating and creating.Polaron can annihilate gradually, meanwhile new polaron will be created at other sites with lowest onsite energy.The charge transport method can be finished in several picoseconds,or more rapidly. From the transport of charge and system energy,we speculate the result can be explained by two aspects:one is the coupling between charges and lattices;the other is the strong interaction of hydrogen bond of complementary bases.In the forth chapter,the environmental factors on a static polaron and a dynamic one are also simulated in SSH model.The calculations are realized based on emphasis that the environmental influences are due to structural fluctuations.The results show that the environmental factors have an effect on charge distribution,lattice displacements and energy band structure.Also,these factors can slow the polaron velocity at the same conditions,contrast to the one with no environmental effect.In brief,in virtue of polaron and quantum well theory,we investigate charge transfer in different DNA chains with SSH and PBH model.The two models are focused on adjacent space and hydrogen bond coupling with electrons respectively.They are all valuable models in our research topic.Additionally,the simulations of environmental effect on charge transport are also considered with SSH model.The next research topics are showed as following:Model calculations can give a few valuable information,but results rely on model parameters heavily.As we all known,DNA molecules are complicate and its structure are subtle when environmental factors are considered.So good parameters describing the above effect are essential in further research.The research is also relied on polaron model heavily.We can't investigate charge transfer when polaron smears under an electric field.In our research,polaron can be named as 'space poalron',because it forms by the interaction between electrons and lattices.In recent years,some research groups found that the tight binding energy of a polaron is about 0.5eV in water,differently form our calculated polaron model.This kind of polaron is called 'solvent polaron'.In next work,the solvent polaron should also be considered.