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COMPUTATIONAL STUDIES ON THE STUCTURE OF β-CHITIN AND OTHER POLYSACCHARIDES

Zafer, Aliya (2001) COMPUTATIONAL STUDIES ON THE STUCTURE OF β-CHITIN AND OTHER POLYSACCHARIDES. PhD thesis, University of Karachi, Karachi.

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Abstract

The purpose of the present work is to study the structure of β-chitin and cellulose 1 by using modern computer facilities now available. The unit cell for β-chitin is monoclinic with dimensions a =4.85Ǻ, b = 10.38 Ǻ (fiber axis), c = 9.26 Ǻ and β = 97.5 the space group is P21 The location of water molecule in the β-chitin structure is varied along with other parameters (P1, P3, P4, P5, P6, P7, P8). The R-value was found to be 0.268. The structure was then refined using following parameters P1=236.628, P3 = 2.296, P4 = 3.9, P5 = -4, P6 = 0.087, P7 = 2.484, P8 = 0.1198532 and the position of water molecule (Xw, Yw, Zw). The R-value is reduced to 0.246 from 0.246. The Ǿ-value was found to be 38.491 The values of the parameters after refinement were found to be P1 = 236.628, P3 = 2.296, P4 = 3.90, P5 = -4, P6 = 0.087, P7 = 2.484, P8 = 0.1198532. The co-ordinates of water molecule, after refinement by least squares method are found to be Xw = 2.832, Yw = 4.790, Zw = 2.511 Difference fourier synthesis map for the model of β-chitin with water, after refinement by least squares method indicates the improvement of structure The chains possess three H-bonds; O3 (II residue)-H…Ow has distance 2.41Ǻ;O5 (III resideue)-H…Ow has distance about 2.91Ǻ and O3 (IV residue)-H…Ow has distance about 3.02Ǻ. Total potential energy by Kitaigorodsky (1961) function was then computed. The minimum potential energy was found to be at Ǿ = 220 for (K1) and 240 for (K2). This value is very close to the value obtained by least squares refinement (Ǿ = 236.62). The above calculations suggest that O6 atom in the structure of β-chitin does not lie in gt conformation (Gardner and Blackwell, 1975) The structure of cellulose 1 has been determined using the intensity data from alga Valonia ventricosa and rigid body least squares method. The unit cell is monoclinic with dimensions a = 817Ǻ and β = 97. The space group is P21. Four geometrical parameters )P1 = 130.190, P2 = 80.00, P3 = -6.328, P4 = -7.504 and temperature factor (P5 = -1.243) and scaling factor (P6 = 0.457) were used to refine the structure by least squares method. R-values were reduced from 0.334 to 0.271 and Ǿ-value wasd found to be 1625.020 respectively The chains posses two intra-chain hydrogen bonds O5 (1 chain)-H…O3 (II chain) (2.64Ǻ), O6 (II chain)-H…O2 (I chain) (2.53Ǻ) and one inter-chain hydrogen bond O6 (I chain)-H…O3 (III chain) (3.08Ǻ) Potential energy calculations involving orientation of O6 atom indicate that O6 atom can adopt different conformations in different chains in the monoclinic unit cell which are related to the symmetry. Different orientations of the O6 atom might give statistical model for cellulose 1 By the help of least squares method, the best position of O6 atom was redetermined, and values are found to be Ǿ = 130.19 (first chain) and Ǿ = 80 (Center chain). At this position, R and Ǿ-values are found to be 0.271 and 1625.020 respectively. The present calculations suggest parallel down model for cellulose 1 (1β)

Item Type:Thesis (PhD)
Uncontrolled Keywords:β-chitin, polysaccharides, cellulose
Subjects:Physical Sciences (f) > Chemistry(f2) > Biochemistry(f2.1)
ID Code:1340
Deposited By:Mr. Muhammad Asif
Deposited On:27 Jan 2007
Last Modified:04 Oct 2007 21:06

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