Travis Mackoy

Publication Date


Document Type


First Advisor

Wheeler, Ralph A.

Degree Name

Ph.D. (Doctor of Philosophy)


Department of Chemistry and Biochemistry


Chemistry--Computer simulation||Chemistry, Physical and theoretical||Materials science


Molecular dynamics (MD) simulations can be used to compute static structure factors (S(q)) and provide an interpretation of the underlying periodic atomic ordering. MD simulations complement experimentally measured S(q) by allowing qualitative assignment of peaks to various ordering, such as cation-anion ordering in ionic liquids, via decomposition of S(q) into partial S(q). Here we present a method for classifying interatomic distances that allows for quantitative peak assignment and visualization of atoms that contribute most to each peak in calculated S(q) for soft materials. The method is illustrated by investigating S(q) for the ionic liquid 1-butyl-1-methyl-pyrrolidinium bis(trifluoromethylsulfonyl)imide (C₄C₁pyrrTFSI), which shows two low-wavenumber peaks which shift to smaller wavenumber and increase their intensities with increasing temperature. The shift left corresponds to decreased density, while the greater peak intensity might seem to indicate increasing periodic atomic ordering with increasing temperature. We present MD simulations of C₄C₁pyrrTFSI at three temperatures (298, 363, and 500 K), quantify the group contributions to the peaks, and explain why peak heights increase despite decreasing periodic atomic ordering with increasing temperature. We also introduce viewSq, a Visual Molecular Dynamics (VMD) module for visualizing and quantifying periodic atomic ordering underlying S(q) from MD simulations. viewSq calculates S(q) with and without X-ray or neutron atomic form factors, radial distribution functions (g(r)), partial S(q) and partial g(r) for any atomic subsets, and decomposes S(q) and partial S(q) into positive and negative components which each indicate periodic atomic ordering. Additionally, viewSq plots the Fourier transform summands used to transform g(r) to S(q), showing where in real space around atomic centers the positive and negative components receive contributions. viewSq also ranks atoms by their contributions to S(q) for any range of wavenumbers and visualizes those atoms in descending order. Another feature allows visualization of neighboring atoms which contribute most to S(q) for any range of wavenumbers for one selected atom as the origin. Another feature prints the number and percentage of atomic distances for any two atomic sets which are associated with any range of real space distances, allowing g(r) and Fourier transform summands to be further interpreted. viewSq's utility is demonstrated for water, the protein complex Barnase-Barstar, and the ionic liquid tetradecyltrihexylphosphonium bis(trifluoromethylsulfonyl)imide.


Committee members: Gilbert, Thomas M.; Mascagni, Michael; Zheng, Chong.||Advisor: Wheeler, Ralph A.||Includes bibliographical references.


226 pages




Northern Illinois University

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