Linear-scaling Quantum Mechanical Calculations Research Articles

Molecular Dynamics Simulation of Protein Crystal with Polarized Protein-Specific Charge

The polarized force field model is indispensable in the simulation of protein crystal due to the particular electrostatic environment which is different from water solution or membrane. The polarized protein-specific charge (PPC) is fitted from in situ linear scaling quantum mechanical calculations of protein. The atomic charge for each residue is determined by its conformation and its location in the protein. Therefore, it gives a more accurate delineation of charge distribution in protein than the mean-field charge schemes in pairwise force fields do. Two 250 ns molecular simulations are carried out to study the structure and dynamics of crystal toxin protein II from the scorpion Androctonus australis Hector employing PPC, as well as the standard AMBER99SB force field, to investigate the effect of electrostatic polarization on the simulated crystal stability. Results show that PPC provides more reliable description of the monomers in the unit cell as well as the lattice in supercell with much smaller RMSDs and more realistic lattice atomic fluctuations. Most of the interactions at the interfaces among the protein units in the X-ray structure are well preserved, underscoring the important effect of polarization on maintaining the crystal stability.

Liquid water simulations with the density fragment interaction approach.

We reformulate the density fragment interaction (DFI) approach [Fujimoto and Yang, J. Chem. Phys., 2008, 129, 054102.] to achieve linear-scaling quantum mechanical calculations for large molecular systems. Two key approximations are developed to improve the efficiency of the DFI approach and thus enable the calculations for large molecules: the electrostatic interactions between fragments are computed efficiently by means of polarizable electrostatic-potential-fitted atomic charges; and frozen fragment pseudopotentials, similar to the effective fragment potentials that can be fitted from interactions between small molecules, are employed to take into account the Pauli repulsion effect among fragments. Our reformulated and parallelized DFI method demonstrates excellent parallel performance based on the benchmarks for the system of 256 water molecules. Molecular dynamics simulations for the structural properties of liquid water also show a qualitatively good agreement with experimental measurements including the heat capacity, binding energy per water molecule, and the radial distribution functions of atomic pairs of O-O, O-H, and H-H. With this approach, large-scale quantum mechanical simulations for water and other liquids become feasible.

The generalized molecular fractionation with conjugate caps/molecular mechanics method for direct calculation of protein energy

A generalized molecular fractionation with conjugate caps/molecular mechanics (GMFCC/MM) scheme is developed for efficient linear-scaling quantum mechanical calculation of protein energy. In this GMFCC/MM scheme, the interaction energy between neighboring residues as well as between non-neighboring residues that are spatially in close contact are computed by quantum mechanics while the rest of the interaction energy is computed by molecular mechanics. Numerical studies are carried out to calculate torsional energies of six polypeptides using the GMFCC/MM approach and the energies are shown to be in general good agreement with the full system quantum calculation. Among those we tested is a polypeptide containing 396 atoms whose energies are computed at the MP26-31G* level. Our study shows that using GMFCC/MM, it is possible to perform high level ab initio calculation such as MP2 for applications such as structural optimization of protein complex and molecular dynamics simulation.

New Method for Direct Linear-Scaling Calculation of Electron Density of Proteins

A new scheme for direct linear-scaling quantum mechanical calculation of electron density of protein systems is developed. The new scheme gives much improved accuracy of electron density for proteins than the original MFCC (molecular fractionation with conjugate caps) approach in efficient linear-scaling calculation for protein systems. In this new approach, the error associated with each cut in the MFCC approach is estimated by computing the two neighboring amino acids in both cut and uncut calculations and is corrected. Numerical tests are performed on six oligopeptide taken from PDB (protein data bank), and the results show that the new scheme is efficient and accurate.

Tight-Binding Theory in the Computational Materials Science

The tight-binding (TB) theory and TB molecular dynamics (TBMD) are now popular and valuable computational schemes available to materials scientists. The simplicity and transparency of the TB schemes enables us to get clear physical insights into the complicated phenomena. In the present review article, the calculational methods of the TB theory and TBMD are outlined and their applications to the important problems in the material sciences will be presented. Recently, linear scaling O(N) (order of N) TB methods have been developed for large scale computer simulations; we analyze the main ideas involved in these O(N) TB methods and their different implementations. The divide-and-conquer techniques for linear-scaling quantum mechanical calculations are reviewed, in conjunction with the catalytic activity of biological molecules. In addition, I also address the genetic and fuzzy algorithms coupled to the TB theory which allows us to find complicated final structures quite efficiently from simple initial structures.

Linear-scaling quantum mechanical calculations of biological molecules: The divide-and-conquer approach

The divide-and-conquer technique for linear-scaling quantum mechanical calculations is reviewed. The method divides a large system into many subsystems, determines the density matrix of each subsystem separately, and sums the corresponding subsystem contributions to obtain the total density matrix and the energy of the system. There is a uniform chemical potential to allow transfer of electrons between subsystems and to insure the normalization of the electron density. The implementation of the method for semiempirical quantum chemistry Hamiltonians is described. The review describes the application to the study of the catalytic mechanisms of cytidine deaminase, an enzyme which accelerates the rate of hydrolytic deamination of cytidine to uridine. The linear-scaling quantum mechanical calculations determined the active species of the ground-state complex and the structure of the reaction transition-state analog complex.