Worcester Polytechnic Institute Electronic Theses and Dissertations Collection

Title page for ETD etd-090111-115051


Document Typethesis
Author NameSA, QINA
Email Address saqina at wpi.edu
URNetd-090111-115051
TitleDeveloping the Polarizable Force Field: Focus on Amino Acid Residues
DegreeMS
DepartmentChemistry & Biochemistry
Advisors
  • George A. Kaminski, Advisor
  • Keywords
  • Polarizable Force Field
  • Date of Presentation/Defense2011-09-01
    Availability restricted

    Abstract

    Polarizable force field has been successfully used in molecular modeling for years, especially in biological and protein simulations. In this research thesis, development of a new polarizable force field ―POSSIM (POlarizable Simulations with Second order Interaction Model) involving electrostatic polarization is described and parameters for several protein residues were produced. In this research thesis, the POSSIM force field was extended to the side chains of the following residues: lysine, glutamic acid, prontonated hisidine, phenylalanine and tryptophan.

    This work involved producing parameters for methyl ammonium, acetate ion, imidazolium cation, benzene and pyrrole molecules. The parameters fitting procedure starts from the molecular complex with dipolar electrostatic probes of a many-body system to produce polarizabilities, compute the energies, then charges and Lennard-Jones parameters are produced by fitting to gas-phase dimerization calculations, followed by the torsional parameters fitting and end up with the pure liquid simulations. In all the cases, three-body energies, dimerization energies and distances agree well to the accurate quantum mechanical results. The final parameters obtained assured the error of less than 2% in the heat of vaporization and average volume results compared with the available experimental data. Unlike the quantum mechanical calculations, the polarizable force field computations require a relatively small amount of computational resources. Moreover, compared to fixed-charges empirical force fields, polarizable force fields are much more accurate in a number of energy calculations. In the following chapters, the results obtained with this particular polarizable force field are discussed.

    Files
  • (WPI)thesis_by_Qina_Sa.pdf

    (WPI) indicates that a file or directory is accessible from the WPI campus network only.


  • Browse by Author | Browse by Department | Search all available ETDs

    [WPI] [Library] [Home] [Top]

    Questions? Email etd-questions@wpi.edu
    Maintained by webmaster@wpi.edu