Generalized Energy-Cased Fragmentation Approach For The Water/Hydrate And Polypeptides

Water is vital for all known forms of life.And it covers 71%of Earth' s surface.Water is transparent,odorless,tasteless and ubiquitous.Though water molecule is very simple,from a chemical point of view,its behavior is quite complex.Hence,the studies of water behaviors,especially the phase transition from liquid to ice,are of great importance for our deep understanding of the complicated structures and interactions in liquid water and ice.As mixtures of methanes and waters.methane hydrates(MHs)play important roles in the energy and environmental science.The applications,such as energy recovery,store and transportation,and gas separation,give rise to extensive investigations of methane hydrates.Though it is challenging to explore the mechanism of MH nucleation,some other important information can be obtained by various experimental techniques,such as Raman spectra.The conformational study of protein is an active field,however it is very difficult to study the proteins in aqueous solutions due to their complexities.The unsolvated polypeptide provides a clean condition for the studies of polypeptides.We can clearly identify the influences of intramolecular noncovalent interactions.including hydrogen bond and dispersion interactions,on the three-dimensional structures of polypeptides.The main parts of this thesis are including:(1)investigating the accurate relative energies and binding energies of ice-liquid water systems in the melt-ing process of ice-Ih crystals with density functional theory(DFT)and accurate coupled-cluster(CC)methods:(2)evaluating the performance of various function-als in describing the interactions between methane molecule and water cages using CC methods,and then studying the structures and the C-H stretching vibrational frequencies of methane molecules in MH clusters and crystals;(3)investigating the intramolecular noncovalent interactions for unsolvated polypeptides by ab ini-tio molecular dynamics(AIMD).The main contributions of the present work can be summarized as follows:1.In chapter 3,we developed a new effective method to compute the bind-ing energies and relative energies of bulk ice-liquid water systems.In this part,ten ice-liquid 144-mers and ten periodic ice-liquid(H2O)64 systems are taken from the classical molecular dynamics simulations in the melting process of ice-Ih crystals.They are investigated at the levels of DFT,explicitly correlated sec-ond order M(?)ller-Plesset perturbation theory(MP2-F12),and CC singles and doubles with noniterative triples corrections[CCSD(T)-F12b]in the framework of generalized energy-based fragmentation(GEBF)approach.Our results show that the changing of noncovalent interactions significantly influences the perfor-mances of DFT and electron correlation methods for those systems in the melting process of ice.Various DFT functionals provide quite different results for ice and mixed ice-liquid structures but give similar results for pure liquid ones.It also explains why many DFT-based simulations lead to inaccurate densities of ice and liquid water.The CCSD(T)-F12b results suggest that the MP2-F12 method pro-vides satisfactory results and is expected to be employed to simulate the phase transitions of ice crystal.2.In chapter 4,the binding energies of CH4-water and water clusters and the Raman spectroscopy of methanes in methane hydrate are investigated.Firstly,for the binding energies of CH4-water and water clusters,we evaluate the 21 levels of DFT methods using explicitly correlated CCSD(T)(F12*)with the cc-pVDZ-F12 basis set in the framework of GEBF approach.Our results show that the B3PW91-D3 functional is the most accurate one to describe the binding energies between methane and water clusters in CH4-water and those within thee water cluster,and B97D functional could reasonably describe both the two types of binding energies.Then we use B3PW91-D3 to calculate the vibrational spectra of CH4 in MH clusters.For the clusters,the frequencies of CH4 are in good agreement with the "loose cage-tight cage" model.For MH crystals,the C-H stretching Raman spectra of methanes in the three MH crystals are investigated with PBC-GEBF approach at B3PW91-D3 and B97D levels.The B3PW91-D3 results are better than the B97D ones by comparing with the expermental values.Thus,the B3PW91-D3 functional is recommended for the investigation of the interactions and spectra of the natural gas hydrates.The PBC-GEBF approach is expected to be used to investigate the process of MH nucleation and growth.3.In chapter 5,GEBF based AIMD simulation is employed for the ultrafast conformational dynamics of two unsolvated polypeptides,310-helical Acetyl(ala)18NH2 and a subunit of DNA polymerase ?.In the GEBF-AIMD approach the ener-gies and energy gradients of subsystems are obtained with M06-2X functional,which can well describe intramolecular noncovalent interaction.The results are compared with those obtained from the simulations based on AMBER99 and CHARMM22 force fields,and semiempirical density-functional tight-binding(DFTB)and DFTB with empirical dispersion correction(DFTB-D)methods.Our re-sults show that the GEBF-M06-2X simulations may provide reasonable results for the conformational changes of the two unsolvated polypeptides due to the rea-sonable description of intramolecular noncovalent interactions.The AMBER99,CHARM22,DFTB,and DFTB-D simulations give quite different results.The GEBF-M06-2X-based AIMD simulations are expected to be applied to the fast or ultrafast conformational dynamics of large unsolvated polypeptides and to be employed for improving the empirical force fields.