ISSN 1000-6818CN 11-1892/O6CODEN WHXUEU
Acta Phys Chim Sin >> 2013,Vol.29>> Issue(06)>> 1173-1182     doi: 10.3866/PKU.WHXB201303153         中文摘要
Site-Preference of Uracil and Thymine Hydrogen Bonding to Quercetin
WANG Chang-Sheng, LIU Peng, YU Nan
School of Chemistry and Chemical Engineering, Liaoning Normal University, Dalian 116029, Liaoning Province, P. R. China
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Exploring the binding features between small drug molecules and biomolecules is particularly important because it can provide valuable information for understanding the interaction mechanism and therefore rationally designing, modifying and screening of new drugs. In this paper, the site-preference of the nucleic acid bases uracil and thymine hydrogen bonding to the small medical molecule quercetin is investigated using the density functional theory method. Thirty stable hydrogen-bonded complexes were located at the B3LYP/6-31G(d) level of theory. The binding energies for these complexes were further evaluated at the B3LYP/6-311++G(3df,2p) level of theory with the basis set superposition error corrections. The results indicate that quercetin can interact with uracil or thymine through five binding sites, which herein we refer to as Site qu1, Site qu2, Site qu3, Site qu4, and Site qu5, and uracil (or thymine) can interact with quercetin through three binding sites, which herein we refer to as Site u1, Site u2, and Site u3 (or Site t1, Site t2, and Site t3). We found that once the binding site of quercetin is fixed, the hydrogen bonds formed through uracil Site u1 and thymine Site t1 are the strongest, while those formed through uracil Site u2 and thymine Site t2 are the weakest. When the binding site of uracil or thymine is fixed, the hydrogen bonds formed through the quercetin Site qu1 are the strongest, followed by those formed through quercetin Site qu5, while those formed through quercetin Site qu3 are the weakest. Atoms in molecules (AIM) and natural bond orbital (NBO) analyses were also carried out to explore the interaction nature of these hydrogen-bonded complexes.

Keywords: Quercetin   Uracil   Thymine   Hydrogen bond   Binding energy   Natural bond orbital analysis   Atoms in molecules analysis  
Received: 2012-12-28 Accepted: 2013-03-15 Publication Date (Web): 2013-03-15
Corresponding Authors: Email:

Fund: The project was supported by the National Natural Science Foundation of China (20973088, 21173109, 21133005), Specialized Research Fund for the Doctoral Program of Higher Education of China (20102136110001), and Program for Liaoning Excellent Talents in University, China (LR2012037).

Cite this article: WANG Chang-Sheng, LIU Peng, YU Nan. Site-Preference of Uracil and Thymine Hydrogen Bonding to Quercetin[J]. Acta Phys. -Chim. Sin., 2013,29 (06): 1173-1182.    doi: 10.3866/PKU.WHXB201303153

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68. LI Zhi-Feng, ZHU Yuan-Cheng, ZUO Guo-Fang, TANG Hui-An, LI Hong-Yu.Structures and Characteristics of the Abnormally Blue-Shifted Single-Electron LithiumBond Complexes Y…Li—CH3[Y=CH3, CH2CH3, CH(CH3)2, C(CH3)3] System[J]. Acta Phys. -Chim. Sin., 2010,26(02): 429-435
69. LIU Yan-Zhu, ZHANG Ling, LI Xia, LI Yong-Xiu.Comparison among the Spectral Properties ofMethyl Salicylate and Its Nitration Products by Iron (III) Nitrate[J]. Acta Phys. -Chim. Sin., 2009,25(10): 2118-2122
70. WENG Ke-Feng, WANG Hui-Gang, ZHU Xin-Ming, ZHENG Xu-Ming.Resonance Raman Spectra of Uracil and 5-Chlorouracil Dynamic Structures during 1S01S2 Transition[J]. Acta Phys. -Chim. Sin., 2009,25(09): 1799-1805
71. JIA Guo-Zhu, HUANG Ka-Ma, YANG Xiao-Qing, SONG Jian-Ping, YANG Li-Jun.Specific Phenomenon of Effective Permittivity for DMF-H2O Solution[J]. Acta Phys. -Chim. Sin., 2009,25(09): 1906-1910
72. WU Yang, ZHANG Tian-Tian, YU Ning.Interaction between 1-Ethyl-3-Methyl-Imidazolium Cation and Asparagine Anion[J]. Acta Phys. -Chim. Sin., 2009,25(08): 1689-1696
73. ZHANG Li, NIU Shu-Yun, JIN Jing, SUN Li-Ping, SHI Zhong-Feng, LI Lei.Preparation and Light-Induced Surface Electron Behavior of Ni(II) Based on Aromatic Polycarboxyl Acids[J]. Acta Phys. -Chim. Sin., 2009,25(06): 1161-1166
74. YANG Zhong-Zhi, LIU Yong-Jun.Calculation of the 9 Low-Energy Sructures of (H2O)11 Clusters Using the Accurate Ab Initio Method and the ABEEM/MM Model[J]. Acta Phys. -Chim. Sin., 2009,25(05): 928-934
75. CHEN Xin-Yuan, LV Yang, LI Shen-Min.Molecular Dynamics Simulations on the Stability of (3+1) Mixed-Type Hybrid G-quadruplex in Human Telomere[J]. Acta Phys. -Chim. Sin., 2009,25(04): 783-791
76. PAN Guo-Xiang; NI Zhe-Ming; WANG Fang; WANG Jian-Guo; LI Xiao-Nian.Molecular Dynamics Simulation on Structure, Hydrogen-Bond and Hydration Properties of Diflunisal Intercalated Layered Double Hydroxides[J]. Acta Phys. -Chim. Sin., 2009,25(02): 223-228
77. LV Feng-Zhen; PENG Zeng-Hui; ZHANG Ling-Li; YAO Li-Shuang; LIU Yan; XUAN Li.A New Type of Hydrogen-Bonded LBL Photoalignment Film for Liquid Crystal[J]. Acta Phys. -Chim. Sin., 2009,25(02): 273-277
78. XI Hai-Tao; GAO Ya-Jun; SUN Xiao-Qiang; YIN Kai-Liang; CHEN Cheng-Lung.Binding Energy of the Electron Acceptor Cyclobis (Paraquat-Phenylene) Tetracationic Cyclophane and Electron Donating Phenyl Ether Derivatives[J]. Acta Phys. -Chim. Sin., 2009,25(02): 377-381
79. YUAN Kun; LIU Yan-Zhi; ZHU Yuan-Cheng; ZHANG Ji.Hydrogen-Bonded Complex between Ozone and Thioperoxy Radical in Gas-Phase[J]. Acta Phys. -Chim. Sin., 2008,24(11): 2065-2070
80. YANG Zhen; YANG Xiao-Ning; XU Zhi-Jun.Molecular Dynamics Simulation of Structure and Dynamics Properties of Water Near an Au Nanoparticle[J]. Acta Phys. -Chim. Sin., 2008,24(11): 2047-2052
81. NI Jie; LI An-Yong; YAN Xiu-Hua.Blue- and Red-Shifted Hydrogen Bonds between HNO and (HF)1≤n≤3[J]. Acta Phys. -Chim. Sin., 2008,24(11): 2000-2006
82. FENG Jing; CHEN Jing-Chao; XIAO Bing; DU Ye-Ping; WANG Sheng-Hao; ZHANG Li-Juan.Oxidation and Thermodynamic Properties of Ag-Sn Alloy[J]. Acta Phys. -Chim. Sin., 2008,24(11): 2007-2012
83. ZHAO Zhi-Juan; LIU Fen; QIU Li-Mei; ZHAO Liang-Zhong; YAN Shou-Ke.Core Level Binding Energy Shifts Caused by Size Effect of Nanoparticles[J]. Acta Phys. -Chim. Sin., 2008,24(09): 1685-1688
84. ZHENG Bo; LI He-Xian; WANG Guo-Chang; LIU Kun; YUAN Wei; LI He; LIANG Bo.Supramolecular Complexation in Water-Methanol Mixtures[J]. Acta Phys. -Chim. Sin., 2008,24(08): 1503-1506
85. SHEN Qiu-Chan; LIANG Wan-Chun; HU Xing-Bang; LI Hao-Ran.Molecular Dynamics Simulation for Formamide Aqueous Solution[J]. Acta Phys. -Chim. Sin., 2008,24(07): 1169-1174
86. YUAN Kun; LIU Yan-Zhi; LV Ling-Ling.Red Shift Hydrogen Bond of Open-Shell (CH3)2S(O)…HOO Complexes in Gas Phase: Structures and Properties[J]. Acta Phys. -Chim. Sin., 2008,24(05): 861-867
87. WU Yang; FENG Lu; ZHANG Xiang-Dong.Theoretical Calculation on the C6H5—H…X Hydrogen-bonded Complexes[J]. Acta Phys. -Chim. Sin., 2008,24(04): 653-658
88. CHEN Dai-Wu; XIE Qing-Ji; JIANG Xue-Qin; YAO Shou-Zhuo.Interactions of Quercetin with Casein and Bovine Serum Albumin as well as Effects of Coexisting Carbon Nanotubes[J]. Acta Phys. -Chim. Sin., 2008,24(03): 379-387
89. ZHANG Rong; TAN Zai-You; ZHENG Dun-Sheng; LUO San-Lai; LI Hao-Ran.Molecular Dynamics Simulations on the Special System of TFE Aqueous Solution[J]. Acta Phys. -Chim. Sin., 2008,24(03): 428-432
90. HUANG Ka-Ma; JIA Guo-Zhu; YANG Xiao-Qing.Nonlinear Characteristics of Conductivity in Aqueous NaCl Solution at Microwave Frequency[J]. Acta Phys. -Chim. Sin., 2008,24(01): 20-24
91. LIU Hong; CHEN Yan-Qin.Nature and Structural Property of Dihydrogen-bond Complexes of BeH2 with Hydrogen Halides[J]. Acta Phys. -Chim. Sin., 2007,23(12): 1974-1978
92. WANG Dong-Dong; SUN De-Zhi; LI Lin-Wei; WEI Xin-Ting; ZHANG Ai-Mei.Interactions between 5-fluorouracil and Bovine Serum Albumin[J]. Acta Phys. -Chim. Sin., 2007,23(10): 1627-1630
93. WANG Chun; DU Xin-Zhen; DING Ning; YANG Yan; LU Xiao-Quan; CHEN Hui.Location of Solubilization of 2’-ethylhexyl Salicylate in Micelles[J]. Acta Phys. -Chim. Sin., 2007,23(09): 1337-1341
94. YANG Zhong-Zhi; CUI Bao-Qiu.Dynamic Simulations of the Hydrogen-bondings on the Proximal Side of the Heme in Terms of ABEEM/MM Method[J]. Acta Phys. -Chim. Sin., 2007,23(09): 1332-1336
95. WANG Hai-Yan; ZENG Yan-Li; ZHENG Shi-Jun; MENG Ling-Peng.Dihydrogen Bond between Pyrrole and a Series of Small Molecules[J]. Acta Phys. -Chim. Sin., 2007,23(07): 1131-1135
96. ZHENG Wen-Rui; FU Yao; LIU Lei; GUO Qing-Xiang.Hydrogen Bonding Interaction between Ureas or Thioureas and Carbonyl Compounds[J]. Acta Phys. -Chim. Sin., 2007,23(07): 1018-1024
97. YANG Zhao-Hui;ZHANG Mao-Feng;CAO Wei-Xiao.Self-assembly Films of Poly(4-diazosulfonate Styrene-co-4-vinylpyridine) with Polyaniline and Their Photoelectric Conversion Properties[J]. Acta Phys. -Chim. Sin., 2007,23(01): 1-5
98. LI Rui-Hua;JIANG Zhan-Peng.Effects of Anions on OH Stretching Raman Spectra of Water[J]. Acta Phys. -Chim. Sin., 2007,23(01): 103-106
99. ZHANG Qiang;ZHANG Xia;YANG Zhong-Zhi.Modeling of Cyclic Peptides by the ABEEM/MM Fluctuating Charge Force Field[J]. Acta Phys. -Chim. Sin., 2006,22(10): 1243-1247
100. ZHANG Zhi-Qiang;QU Yi-Xin;REN Hui.Density Functional Theory Studies on Ethanol Physisorption on Ultrafine Silica[J]. Acta Phys. -Chim. Sin., 2006,22(07): 820-825
101. TONG Jian-Bo;ZHOU Peng;ZHANG Sheng-Wan;LIANG Gui-Zhao;TIAN Fei-Fei;LI Mei-Ping;LI Sheng-Shi.QSAR Studies of Anti-HIV Drug HEPT Using 3D-HoVAIF[J]. Acta Phys. -Chim. Sin., 2006,22(06): 721-725
102. ZHANG Xiao-Qing;JIA Jian-Feng;WU Hai-Shun;PEI Xiao-Qin.Theory Investigation of (BCO)n(n=1~12)[J]. Acta Phys. -Chim. Sin., 2006,22(06): 684-690
103. MENG Xiang-jun.Theoretical Study on Structures and Properties of Dihydrated Zwitterionic Glycine Complexes[J]. Acta Phys. -Chim. Sin., 2006,22(01): 98-101
104. LAN Rong; LI Hao-ran; HAN Shi-jun.Correlation of 1H NMR Chemical Shift for Alcohol + Inert Solvent Mixtures by LFHB Model[J]. Acta Phys. -Chim. Sin., 2005,21(11): 1295-1298
105. ZHANG Shu-guang; SHI Wen-yan; LEI Wu; XIA Ming-zhu; WANG Feng-yun.Molecular Dynamics Simulation of Interaction between Calcite Crystal and Water-soluble Polymers[J]. Acta Phys. -Chim. Sin., 2005,21(11): 1198-1204
106. HU Xing-bang; LI Hao-ran; LIANG Wan-chun; HAN Shi-jun.Explore the Effect Induced by Water in the Proton Transfer Process of 5-fluorouracil[J]. Acta Phys. -Chim. Sin., 2005,21(09): 952-956
107. FANG Mei-juan; LUO Shu-na; WANG He-qing; LIU Wan-yun; ZHAO Yu-fen.The Effect of Phosphoryl Oxygen on the Intermolecular Action of Alanine and Lysozyme[J]. Acta Phys. -Chim. Sin., 2005,21(09): 1042-1045
108. HE Qin; ZHOU Li-xin.Theoretical Study on the Interaction of Platinum Compounds with DNA Base Pairs[J]. Acta Phys. -Chim. Sin., 2005,21(08): 846-851
109. WANG Yong; LI Hao-Ran; WU Tao; WANG Cong-Min; HAN Shi-Jun.Reaction Mechanism Study for the Synthesis of Alkylimidazolium-based Halide Ionic Liquids[J]. Acta Phys. -Chim. Sin., 2005,21(05): 517-522
110. HUANG Yu-Cheng; HU Ying-Jie; XIAO Ji-Jun; YIN Kai-Liang; XIAO He-Ming.Molecular Dynamics Simulation of Binding Energy of TATB- based PBX[J]. Acta Phys. -Chim. Sin., 2005,21(04): 425-429
111. LI Quan;HUANG Fang-Qian.The Structure and Properties of the Hydrogen Bond between Complex of Pyridazine and Water[J]. Acta Phys. -Chim. Sin., 2005,21(01): 52-56
112. Zhang Li;Yang Zhan-Lan;Xiong Yao;Peng Teng-Teng;Weng Shi-Fu;Wu Jin-Guang.Influence of H on the Aggregation Properties of Sodium Deoxycholate Aqueous Solution[J]. Acta Phys. -Chim. Sin., 2004,20(10): 1196-1199
113. Wang Yan-Hua;Zou Jian-Wei;Hu Gui-Xiang;Zheng Ke-Wen;Yu Qing-Sen.Theoretical Studies on the Nucleophilic Additions of Mimic Compounds of Pyrroloquinoline Quinone with Ammonia[J]. Acta Phys. -Chim. Sin., 2004,20(09): 1129-1133
114. Li Lai-Cai;Qian Yi-Ming;Zhu Yuan-Qiang;Tian An-Min.Theoretical Study on the Reaction Mechanism of the CH3 Radical with HNCO[J]. Acta Phys. -Chim. Sin., 2004,20(03): 228-232
115. Gu Feng-Cai;Zhao Zhu-Xuan;Li Ying-Hui;Men Juan;Yan Ju-Ming;Liu Rui-Xian;Zhang Li-Hua.Preparation and Characterization of SurfaceModified SnO2 Nanocrystals[J]. Acta Phys. -Chim. Sin., 2003,19(07): 621-625
116. Huang Jian-Gou;Xu Man-Cai;Li Hai-Tao;Shi Zuo-Qing;He Bing-Lin.Adsorption Thermodynamics of Macroporous Cross-linked Poly (N-methyl-N-p- vinylbenzylacetamine) Resin for Phenols from Non-aqueous System[J]. Acta Phys. -Chim. Sin., 2003,19(03): 208-211
117. Li Rui-Hua;Jiang Zhan-Peng;Shi Shao-Qi;Yang Hong-Wei.Raman Spectroscopic Study of Effect of CaCl2 and MgCl2 on Structure of Water[J]. Acta Phys. -Chim. Sin., 2003,19(02): 154-157
118. Zhou Li;Xie Jian-Chun;Ge Yu-Fang;Xu Xiao-Jie.The Application of Molecular Imprinting Technology for Hippophae Rhamnoidse Linn. Function Integrants Extraction[J]. Acta Phys. -Chim. Sin., 2002,18(09): 808-811
119. Bian Feng-Ling;Liu Ming-Zhu.The Temperature Dependence of the Viscosity of Poly (N,N-diethylacrylamide) Solutions[J]. Acta Phys. -Chim. Sin., 2002,18(09): 776-780
120. Xu Si-Chuan;Zhang Hui-Juan;Sun Zhao-Yong;Feng Juan;Ai Xi-Cheng;Zhang Qi-Yuan;Zhang Xing-Kang;Liu Yan-Qin;Han Shi-Tian.Synthesis and Spectroscopy Characteristics of 5-fluorouracil Porphyrin Compounds[J]. Acta Phys. -Chim. Sin., 2001,17(10): 879-886
121. Xie Jian-Chun;Luo Hong-Peng;Zhu Li-Li;Zhou Li;Li Chong-Xi;Xu Xiao-Jie.Extracting Active Compounds from Herbs Using Molecular Imprinting Technology[J]. Acta Phys. -Chim. Sin., 2001,17(07): 582-585
122. Zhang Yong-Hong;Mao Xi-An.Chemical Exchange and Selfdiffusion Dynamics of Quercetin in Solutions[J]. Acta Phys. -Chim. Sin., 2001,17(04): 300-304
123. Fu Xu-Chun, Yu Qing-Sen, Liang Wen-Quan.Calculation of Hydrogen-Bond Basicity by Artificial Neural Network Method[J]. Acta Phys. -Chim. Sin., 2000,16(09): 844-849
124. Shi Tu-Jin, Liu Li, Yang Da-Lin, Zhu Qi-He.Ab initio Study on Hydrogen Bonding Clusters between 1,4-dioxane and Ammonia[J]. Acta Phys. -Chim. Sin., 2000,16(05): 416-421
125. Liu Hong, Chen Zong-Zhang, Peng Jing-Cui, Chen Xiao-Hua, Bai Xiao-Jun.Short-range lnteraction in Crystals A2BC60 or A3C60[J]. Acta Phys. -Chim. Sin., 2000,16(01): 41-48
126. Feng Hai-Yan, Liu Xiao-Di, He Shu-Mei, Wu Ke-Zhong, Zhang Jian-Ling.Studies on Solid-Solid Phase Transition of Polyols and their Binary Mixtures by Infrared Spectroscopy[J]. Acta Phys. -Chim. Sin., 1999,15(09): 850-855
127. Wang Xiao-Dong, Zhang Yi-An, Li Gui-Qin, Deng Jing-Kang, Huang Jian-Dong, He Yao, Gao Nai-Fei, Wang Fang, Deng Hui, Ning Chuan-Gang, Wang Yan, Zheng Yan-You, Chen Xue-Jun.Momentum Profiles of lso-butane[J]. Acta Phys. -Chim. Sin., 1999,15(08): 676-679
128. Zhou Ping, OU Yang-Zhi-Xun, Meng Qing-An.The Second Sphere Interaction in the Supramolecular Complexes Studiey by 59Co Solid Static NMR[J]. Acta Phys. -Chim. Sin., 1999,15(06): 533-540
129. Shi Xiang-Yang, Wu Shi-Kang.A Study on the Micellar Polarity of Hydrophobic Poly(N-isopropylacrylmides)[J]. Acta Phys. -Chim. Sin., 1999,15(02): 127-132
130. Pang Wen-Ning, Gao Nai-Fei, Shang Ren-Cheng, Zhang Wen-Xin, Zheng Yan-You, Chen Xue-Jun.Investigated of Valence Orbital Electron Structure for C4H10[J]. Acta Phys. -Chim. Sin., 1998,14(11): 965-967
131. Pang Wen-Ning, Shang Ren-Cheng, Gao Nai-Fei, Zheng Yan-You, Chen Xue-Jun.Measurement of Momentum Profiles for Propane valence Orbitals(2b2)[J]. Acta Phys. -Chim. Sin., 1998,14(10): 874-876
132. Wang Yi-Xuan, Li Hong-Ping, Wang Jin-Ben, Zhang Fu-Qiang, Zhao Jian-Ping, Dai Ming.Infrared Spectroscopic Studies of Interactions of the Diols with Aprotic Solvents[J]. Acta Phys. -Chim. Sin., 1998,14(06): 514-519
133. Zhang De-Chun, Zhang Yan-Qiu, Lu Cheng-Rong.Resonance-Assisted Intramolecular Hydrogen Bonding in Substituted Phenols[J]. Acta Phys. -Chim. Sin., 1998,14(01): 63-67
134. Chen Wen-Wu,Gao Yi-Qin,Wu Guo-Sheng,Yang Da-Lin,Sheng Liu-Si,Wu Guo-Hua,Ye Wei-Q.The Study of the 6-H Pyridine Clusters[J]. Acta Phys. -Chim. Sin., 1996,12(12): 1067-1070
135. Zou Shou-Zhong,Chen Yan-Xia,Tian Zhong-Qun,Zhang Yun-Hong.Studies on the Effects of Inorganic Ions and their Concentrations on Raman Spectra of Water[J]. Acta Phys. -Chim. Sin., 1996,12(02): 130-135
136. Li Nan-Qiang, Chen Jian-Hong.Studies on the Polarographic Behaviors of Quercetin and the Catalytic Hydrogen Waves of Heavy Rare Earth Ions-quercetin System[J]. Acta Phys. -Chim. Sin., 1994,10(06): 489-494
137. Lin Hua-Kuan, Lu Xiang-Sheng, Gu Zong-Xin, Li Wei-Hong, Chen Rong-Ti.Calorimetric Study of Ni(II), Co(II), Zn(II)-N-(para-cubstitutd Pheny1) Iminodiacetic Acid[J]. Acta Phys. -Chim. Sin., 1994,10(03): 212-216
138. Zhao Liang-Zhong.Determination of O1s Binding Energies of the Alkaline Earth Oxides and Peroxide[J]. Acta Phys. -Chim. Sin., 1993,9(02): 170-174
139. Wang Jin-Ben; Wang Yi-Xuan; Zhang Fu-Qiang; Zhao Jian-Ping; Dai Ming.A Study on Association of Amine With Several Solutes by Infrared Spectrometry[J]. Acta Phys. -Chim. Sin., 1992,8(04): 481-486
140. Huang Rong-Bin; Zheng Lan-Sun; Zhu Yong-Bao; Zhang Qian-Er.Generation of a New Type of Borane Anions with Laser Ablation[J]. Acta Phys. -Chim. Sin., 1992,8(04): 438-440
141. Xu Jian-He; Sun Xian-Da; Lu Wei-Qin; Gao Hong-Jin.Study of Hydrogen Bond Association of Alcohol Molecules in Alkanes by IR Quantitative Analysis[J]. Acta Phys. -Chim. Sin., 1992,8(03): 358-363
142. LIU Shan-Shan, JI Shan, CHEN Qi-Bin, PENG Chang-Jun, LIU Hong-Lai.Surface Patterning and Force-induced Reversible Structure Transformation of Supramolecular Polymer Brush PVP-Chol[J]. Acta Phys. -Chim. Sin., 0,(): 0-0
143. WANG Yun-He, QIN Yuan, YAO Man, WANG Xu-Dong, LI Shu-Ying, WANG Dong, CHEN Ting.Molecular Dynamics Simulation of Chiral Self-assembly Structure on HOPG Surface Driven by Hydrogen Bonds for BIC and HA Systems[J]. Acta Phys. -Chim. Sin., 0,(): 0-0
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