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Theoretical Studiesof Na~+、k~+Interact with Water, Amino Acids and Dipeptides

Author: ZhangNa
Tutor: GongLiDong
School: Liaoning Normal University
Course: Physical and chemical
Keywords: the ion-biomolecule interaction the hydrated clusters of alkali metal cations quantum chemcical calculation ABEEM/MM amino acids and dipepti
CLC: O641.3
Type: Master's thesis
Year: 2013
Downloads: 15
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Abstract


Sodium ion and potassium ion are the most abundant metal ions in nature, and they playparamount roles in a wide range of biological and chemical processes. The interactions ofsodium and potassium ions with peptides and proteins facilitate many essential biologicalprocesses, so the interactions of sodium and potassium ions with some simple model systems,especially amino acids and small peptides have gained extensive attentions of scientists. Inthis dissertation, the interactions of Na+/K+with water, Serine, Threoine and six dipeptides,Glycine Dipeptide, Cysteine Dipeptide, Leucine Dipeptide, Threonine Dipeptide, TyrosineDipeptide and Valine Dipeptide, were studied by quantum chemistry and the atom-bondelectronegativity equalization fluctuating charge model （ABEEM/MM）.First of all, a high level quantum chemistry method and the ABEEM/MM model hadbeen applied to study the Na+（H2O）nand K+（H2O）n（n=16） clusters. The geometries wereoptimized and the vibration frequency were calculated by MP2/6-31++G（d,p） method; theenergies of stable conformations were calculated at the MP2/6-311++G（2d,2p） level withBSSE correction. In the spirit of ABEEM/MM, the ABEEM parameters of Na+and K+werereparameterized by fitting the charge distributions from ab inito HF/STO-3G. An accurateABEEM/MM interaction potential function for Na+/K+with H2O was constructed tocalculate the structures and binding energies of Na+（H2O）nand K+（H2O）nclusters, and theresults are consistent with the QM results. For the structure, the average absolute deviation（AAD） of the average distance between Na+/K+and the oxygen in the inner water shell, RM-O,are0.042and0.057, respectively, and the AADs of the average O-H bond length in theinner water shell, RH-O,are0.002and0.003, respectively. For the binding energy, thebiggest AADs of the total binding energy and successive binding energy are0.373kcal/moland0.052kcal/mol, for Na+（H2O）nand K+（H2O）nrespectively. The above parameters of Na+/K+were then successfully used to calculate the interactions of Na+/K+with Serine, Threoineand six dipeptides. An accurate ABEEM/MM interaction potential function for eachmodel was constructed. The charge distributions and binding energies fromABEEM/MM are consistent with those of quantum chemistry.

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CLC: > Mathematical sciences and chemical > Chemistry > Physical Chemistry ( theoretical chemistry ),chemical physics > Structural Chemistry > Molecular interactions,supramolecular chemistry
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