Study On The Properties Of The Hydrogen Bonds In Biology

The nature of the hydrogen bond has gained increasing attention because of itssignificance in physical, chemistry and biology processes. The solute-solvent interactionsplay a fundamental role in the optical properties, structures and functions of the biologymolecules. However, how does the hydrogen bond cause the changes of the opticalphenomenon? How does it exert the effects on the structures and functions of themacromolecules? The best measure aiming to resolve these questions is to study in detail theultrafast dynamics of the hydrogen bond. In the present work, employing DFT, TDDFT andMD methods, we performed some theoretical calculation to investigate the dynamicproperties of hydrogen bond.The time-dependent density functional theory and the density functional theory wereused to investigate the nature of hydrogen bonds formed by the derivative of the coumarin(TFKC) and the water molecules. The ground-state geometry optimizations, electronicexcited energies and corresponding oscillation strengths were fully calculated. It is foundthat, upon photoexcitation, the weaker hydrogen bond in the ground state is affected by therelatively large impact for TFKC in the water. For better understanding the properties of thehydrogen bonds in the excited states, the frontier molecular orbitals of the S0and S1stateswere investigated, and it is found an obvious electron density transitions form the watermolecules to the TFKC monomer, which is expected to be the reason the hydrogen bonddynamics happens.The hydrogen bonding dynamics of6-aminocoumarin (6AC) in the water wereinvestigated by the time-dependent density functional theory and density functional theorymethods. According to the analysis of the molecular structure, it is demonstrated that AHB isthe strongest hydrogen bonds among three ones formed between6AC and water moleculesin the ground state. By means of the analysis of the electronic excitation energies and theoscillation strengths, it is found that the dynamic properties of the hydrogen bond vary from stateto state greatly. Upon the photoexcitation, AHB is proved to be extremely weakened which is significantly greater than the strengthening of BHB and CHB in S1states. This is expected tobe the theoretical explanation for the unusual blue-shift of a long-wavelength band inabsorption spectra for6AC in the water observed in the experiment. The results of thefrontier molecular orbitals showed obvious photo-induced electron redistribution, which isthe basic reason for the weakening of AHB.The time-dependent density functional theory method was employed to investigate thenature of the excited-state intramolecular proton transfer (ESIPT) for a white-lightingmaterial (HHBF). Firstly, the comparison of calculated and experimental emission spectraprovided that direct evidence for the occurrence of the ESIPT. Analysis of the results alsoshowed that the intramolecular hydrogen bond of HHBF is strengthened from E to E*.According to the results of the frontier molecular orbitals, electron density swing betweenthe proton acceptor and donor was found, which provides the driving forces for the forwardand backward ESIPT, enabling the excited-state equilibrium to be established. Meanwhile,the photoexcitation and the interchange of position for electron-donating andelectron-withdrawing groups are demonstrated to be the main reasons for the electron densityswing. The potential energy curves provided the further thermodynamic explanation for theequilibrium of ESIPT.The dynamics nature of a new ZFP-DNA binding pattern was investigated using themolecular dynamics (MD) simulations and the steered molecular dynamics (SMD)simulations. The roles of the four base contacts at the ZFP-DNA surface were clearly shown.In particular, the affinity between the ZFP and DNA mainly derives from the interactions ofR471-N1-2and D473-N2-6. Meanwhile, the combined actions of S472-N2-6, D473-N2-1and H474-N1-2drive the enlarged-major-groove DNA conformation which is crucial forlimiting the number of fingers that contact neighboring sub-sites. All the related resultsprovide the theoretical basis for the biological experiments.