NDLI: Molecular Modeling of a Hexacyclopeptide Dichotomin B Based on B3LYP, HF and ONIOM Methods: Comparison with Dichotomin A

Content Provider	IEEE Xplore Digital Library
Author	Xiaoqing Liu Chunli Yan Hu Teng Xiaohui Li Zhilong Xiu Ce Hao
Copyright Year	2008
Description	Author affiliation: Dept. of Biosci. & Biotechnol, Dalian Univ. of Technol., Dalian (Xiaoqing Liu; Chunli Yan; Hu Teng; Xiaohui Li; Zhilong Xiu)
Abstract	Dichotomin B shows cell growth inhibitory activities against p-388 lymphocytic leukemia cells. However, its spatial conformation and the primary factors affecting its activity are not very clear. Here we optimize the primary structure of dichotomin B at the DFT (density functional theory) with B3LYP parameterization, HF (Hartree-Fock) and ONIOM (our own N- layered integrated molecular orbital and molecular mechanics) levels of theory. As a result, all the optimized geometries contain one beta-turn and two intramolecular hydrogen bonds which presumably maintain the steady spatial arrangements of dichotomin B in solid state and contribute to its activity, while there are two beta-turns and two intramolecular hydrogen bonds in the crystal structure of dichotomin A, which may be the reason that the activity of dichotomin A is higher than that of dichotomin B. In addition, the $^{13}C$ chemical shifts of the three optimized geometries are calculated. We find that the structure obtained with HF/6-31G(d) method is the most similar to the experimental structure of dichotomin B. Furthermore, the RMS (root mean square) errors for $^{13}C$ chemical shifts relative to TMS determined using the B3LYP hybrid functional with the 6- 311G(d,p) basis set are smaller than those determined using HF at this same basis set.
Starting Page	840
Ending Page	843
File Size	190945
Page Count	4
File Format	PDF
ISBN	9781424417476
DOI	10.1109/ICBBE.2008.206
Language	English
Publisher	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Publisher Date	2008-05-16
Publisher Place	China
Access Restriction	Subscribed
Rights Holder	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Subject Keyword	Geometry Orbital calculations Peptides Hydrogen Optimization methods Hafnium Amino acids Density functional theory Nuclear magnetic resonance Chemical technology
Content Type	Text
Resource Type	Article

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