Atomic-Scale Investigations Of The Interaction Mechanism Between Nucleobases And Salt,Metal,and Water

It is well known that nucleic acids contain detailed genetic information for most livings,which makes them as an important research focus in the field.Nucleobases molecules,including adenine(A),guanine(G),cytosine(C),thymine(T),and uracil(U),are important components of nucleic acids.In the absence of polymerase,complementary pairing induced by hydrogen bond interactions is considered to be the key to the recognition of nucleobases,and the polymerization of the first oligonucleotide.In addition to the influence of noncovalent interaction within the DNA structure,the influence of the environment(solvent and metal ions)on nucleobases should not be underestimated.Metal ions are of great significance in biological processes such as the formation of noncovalent bonds,which also act as adhesives.As one of the most important small molecules in living bodies,water plays an important role in regulating the function and structures of biomolecules,as well as driving their self-assembly.Although the investigations of water have been performed before,interactions between water and biomolecules are so complicated that has not been fully revealed yet.The main reason is the lack of characterization and regulation methods at the scale of a single atom or single molecule.In this thesis,based on the surface science strategy under an ultra-high vacuum condition,we try to investigate the interactions and self-assembly of nucleobases with metals,water,and salts,by utilization of highresolution scanning tunneling microscope(STM),single bond resolution non-contact atomic force microscope(nc-AFM),X-ray photoelectron spectra(XPS),and density functional theory(DFT)calculation.The main results are summarized as follows:(1)Interactions between uracil(U)and different metals on the surface: By investigating the interaction between uracil molecules and alkali metals on the surface,we demonstrate that the on-surface reversible structural transformations of metalorganic nanostructures are composed of ionic bonds.On this basis,we have successfully fabricated two novel bimetallic two-dimensional(2D)metal-organic nanostructures through the synergy and competition among noncovalent interactions.In addition,the 2D metal-organic structures can be transformed by the ratio between the metal atoms and U molecules.(2)Interactions between cytosine(C)and water molecules on different surfaces:By investigating the interactions between cytosine molecules and water molecules on the different surfaces,we found that water molecules can selectively break the weak hydrogen-bonded dimers,while the strongly hydrogen-bonded dimers remain.The hydrated chain segments connect by forming strong hydrogen bonds and the water molecules are released spontaneously.In addition,the water molecules can also significantly reduce the energy barrier of the silver atoms escaping from the Ag(111)and Ag(110)surfaces.(3)Interactions between uracil(U)and water molecules on different surfaces: By investigating the interaction between uracil molecules and water molecules on the different surfaces,we found that the racemic U self-assembled structures can be transformed to homochiral water-involved structures in the presence of water molecules,resulting in an unexpected chiral separation on the surface and it is revealed that the preferential binding between the specific site of U molecules and water molecules is the origin of chiral separation.On Ag(111)surface,the amorphous-to-crystalline phase transformation can also be catalyzed by water molecules.(4)The interactions between salts and water molecules on the surface: By comparing the dissolution process of a variety of salts,we found that halogen anion is hydrated preferentially in the process of salt solution.In addition,the results are consistent with the electrode potentials of metal cations,which is a key point of the hydration process of halogen anion.The higher the electrode potential is,the easier halogen anion is to be hydrated.