Molecular Dynamics Study Of Chiral Molecule Self-assembled Monolayer And Nucleation Phenomenon In Calcium Carbonate Solution

Molecular dynamics is a simulation method to describe molecule's motion based onNewton's law. First, we build a serial of equations about the molecule's movement, andsolve them with numerical method step by step to get the coordinates and correspondingmomentum of each atom at each step, in other words, the trajectory of the molecule'smotion in the phase space, then we can calculate the macroscopic properties of the systemfrom the trajectory with various statistical methods. As the development of dynamicstheory, simulations in constant temperature, constant pressure, grand-canonical ensembleand other conditions have been implemented in many molecular dynamics packages. Com-pared to Monte Carlo method, molecular dynamics is more meticulous and e?cient, it hasbeen widely used in the simulation of chemical, biological, material and medical systems.In the past several decades, people have developed various molecular force ?elds and pack-ages for lots kinds of molecules, especially the biological macromolecule. Combined withmore accurate quantum chemistry computation methods, molecular dynamics can help usto"see"more and better in biological research which can not be achieved by experiments.This dissertation can be divided into three chapters. In the ?rst chapter, we brie?yintroduce the basic concept of molecular dynamics and review the algorithms implementedin modern molecular dynamics method. Chapter 2 and chapter 3 are two works we studiedwith molecular dynamics methods, one is about the chiral molecule self-assembled systemand the other one is on the nucleation phenomenon in calcium carbonate solution.In Chapter 1, we review the developing history of molecular dynamics method andintroduce basic theory of molecular dynamics method including the ensemble theory, in-tegration algorithms, methods of controlling the system temperature and pressure, andfree energy calculation methods in molecular dynamics simulation. At last, we brie?yintroduce several popular force ?elds and molecular dynamics packages used in our work.In chapter 2, we simulate single-stranded DNA (ssDNA) molecule's adsorption behav-ior on chiral N-isobutyryl-cysteine (NIBC) self-assembled monolayer (SAM) on Au(111)surface. In experiment,people found that ssDNA have di?erent adsorption behaviors onsuch a"chiral surface". we ?rst propose four possible self-assembled structures of NIBCmolecules on Au(111) surface, and calculate the force exerted on ssDNA by NIBC-SAMsand the water around NIBC-SAMs. We also measure the dipole moments of di?erentNIBC-SAM models. It turns out that the experimentally observed stereospeci?c adsorp- tion behavior of ssDNA on D/L-NIBC self-assembled monolayer surface mainly originatesfrom the interaction between the dipole moment of NIBC and the negative charge carriedby ssDNA.In chapter 3, we study the formation of amorphous calcium carbonate (ACC) clustersin calcium carbonate solution. Recently, both experiments and theoretic studies indi-cate that calcium carbonate crystallization can not be properly described by the classicalnucleation-crystallization model. We ?nd that ACC clusters can form spontaneously incalcium carbonate solution while there are no stable potassium carbonate clusters in potas-sium carbonate solution. Electrostatic interaction is the driving force of the formation ofCaCO3 unit, but is not the only one of ACC clusters. We also calculate the dissociationfree energy pro?les between various ions in the solution. By adding di?erent number ofsodium hydroxide molecules in the solution, we evaluate the solution's pH in?uence on theformation of ACC. We ?nd that hydroxyl ions can compete with carbonate to coordinatewith calcium and form Ca(OH)2, and moderate hydroxyl ions will promote the formationof ACC clusters in calcium carbonate solution while too much hydroxyl ions in the solutionis adverse to the formation of ACC clusters.