Please use this identifier to cite or link to this item: http://scholarbank.nus.edu.sg/handle/10635/77736
Title: ENERGY BASED MOLECULAR FRAGMENTATION
Authors: TAN HWEE JIA
Keywords: proteins, fragmentation, chemical shifts, salt bridge, energy
Issue Date: 21-Jan-2014
Source: TAN HWEE JIA (2014-01-21). ENERGY BASED MOLECULAR FRAGMENTATION. ScholarBank@NUS Repository.
Abstract: The fragmentation method used in this thesis is an energy based fragmentation method termed the ¿combined fragmentation method (CFM)¿, and it is simple to implement and produces small fragments that are independent of conformation and size of proteins. Energy, NMR chemical shifts, and density matrices of proteins can be predicted with high accuracy using CFM. With nonbonded interactions and Coulomb field errors were significantly improved to 4 m-Eh or lower. The root mean square errors (RMSEs) of the chemical shifts of 1H, 13C, 15N, 17O, and 33S compared to the full calculation were 0.04, 0.25, 0.68, 3.48, and 0.05 ppm respectively, with the inclusion of nonbonded interactions. The close-range electrostatic interaction (salt bridge) became an issue in the process of fragmenting the proteins. For all twenty-five salt bridges, the formation of the neutral species is favoured over the ion pair structure, showing evidence of proton transfer to the carboxylate group.
URI: http://scholarbank.nus.edu.sg/handle/10635/77736
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