An approximate approach to quantum mechanical study of biomacromolecules

This thesis summarizes the author's major work in Prof. John Z.H. Zhang's Threoretical Chemistry research group. In Chapter 1, we present a general description of MFCC (molecular fractionation with conjugated caps) method that has been developed in this group to treat biomacromolecules in a divide-and-conquer fashion. Then we give in detail a computational study of MFCC application to peptide/protein that contains disulfide bonds. Continued on the basis of previous MFCC tests, this study provides another numerical support for the accuracy of the MFCC approach to full quantum mechanical calculation of protein/peptide-small molecule interaction.; In Chapter 2, we further develop the MFCC scheme for quantum mechanical computation of DNA-ligand interaction energy. We study three oligonuclear acid interaction systems: dinucleotide dCG/water, trinucleotide dCGT/water and a Watson-Crick paired DNA segment dCGT/dGCA. The MFCC interaction energies are found to be in excellent agreement with the corresponding results obtained from the full system ab initio calculations. This study is an exemplification of the application of the general MFCC approach to biomacromolecules.; In Chapter 3, firstly, a MFCC-downhill simplex method is proposed to study binding structures of ligands (atoms, ions, or small molecules) in large molecular complex systems. This method employs the MFCC approach to compute the interaction energy-structure relation of the system and implements the downhill simplex algorithm for structural optimization. Secondly, this method is numerically tested on a system of [KCp(18-crown-6)], as a simplest monatomic case study, to optimize the binding position of the potassium cation in a fixed coordination Cp and 18-crown-6 coordinating sphere. The result of the MFCC-downhill simplex optimization shows good agreement with both the crystal structure and with the full-system downhill simplex optimized structure. The effects of the initial structure of the simplex and of the method/basis-set levels of the quantum chemical calculation on the MFCC-downhill simplex optimization are also discussed. Finally, the MFCC-downhill simplex method is tested, as a general multiatomic case study, on a molecular system of cyclo-AAGAGG·H 2O to optimize the binding structure of water molecule to the fixed cyclohexapeptide. The MFCC-downhill simplex optimization results in good agreement with the crystal structure. The MFCC-downhill simplex method should be applicable to optimize the structures of ligands that bind to biomacromolecules such as proteins and DNAs.; In Chapter 4, we propose a new approximate method for efficient calculation of biomacromolecular electronic properties, using a Density Matrix (DM) scheme which is integrated with the MFCC approach. In this MFCC-DM method, a biomacro-molecule such as a protein is partitioned by an MFCC scheme into properly capped fragments and concaps whose density matrices are calculated by conventional ab initio methods. These sub-system density matrices are then assembled to construct the full system density matrix which is finally employed to calculate the electronic energy, dipole moment, electronic density, electrostatic potential, etc., of the protein using Hartree-Fock or Density Functional Theory methods. By this MFCC-DM method, the self-consistent field (SCF) procedure for solving the full Hamiltonian problem is circumvented. Two implementations of this approach, MFCC-SDM and MFCC-GDM, are discussed. Systematic numerical studies are carried out on a series of extended polyglycines CH3CO-(GLY) n-NHCH3 (n=3-25) and excellent results are obtained.; In Chapter 5, we present an improvement of MFCC-DM method and introduce a pairwise interaction correction (PIC) with which the MFCC-DM method is applicable to study a real-world protein with short-range structural complexity such as hydrogen bonding and close contact. In this MFCC-DM-PIC method, a protein molecule is partitioned into properly capped f...