Effects of monohydration on an adenine–thymine base pair

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• 作者：Sara Watanabe ; Yudai Ogata ; Tsutomu Kawatsu…
• 关键词：Adenine–thymine base pair ; Microhydration ; Monohydration ; Nuclear quantum effect ; Path integral molecular dynamics ; Hydrogen bond ; Principal component analysis
• 刊名：Theoretical Chemistry Accounts: Theory, Computation, and Modeling (Theoretica Chimica Acta)
• 出版年：2015
• 出版时间：July 2015
• 年：2015
• 卷：134
• 期：7
• 全文大小：1,381 KB
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• 作者单位：Sara Watanabe (1)
  Yudai Ogata (1)
  Tsutomu Kawatsu (1) (2)
  Yukio Kawashima (3)
  Masanori Tachikawa (1)
  
  1. Graduate School of Nanobioscience, Yokohama City University, 22-2 Seto, Kanazawa-ku, Yokohama-City, Kanagawa, 236-0027, Japan
  2. Graduate School of Arts and Sciences, The University of Tokyo, 4-6-1 Komaba, Meguroku, Tokyo, 153-8902, Japan
  3. Computational Chemistry Research Unit, RIKEN Advanced Institute for Computational Science (RIKEN AICS), Minatojima-minami-machi, Chuo-ku, Kobe, Hyogo, 650-0047, Japan
  
• 刊物类别：Chemistry and Materials Science
• 刊物主题：Chemistry
  Theoretical and Computational Chemistry
  Inorganic Chemistry
  Organic Chemistry
  Physical Chemistry
  
• 出版者：Springer Berlin / Heidelberg
• ISSN：1432-2234

文摘

We analyzed the monohydration effect on the hydrogen-bonded structure between the adenine–thymine base pair using path integral molecular dynamics simulations including the nuclear quantum and thermal effects. We focused on two monohydration models for an adenine–thymine base pair with a water molecule bound to each adenine and thymine site. The adenine–thymine base pair without a water molecule was also discussed to reveal the role of a water molecule in monohydrated models. We found that the monohydration effect varies depending on the location of the water molecule. The monohydration effect on the inter-molecular motions is also investigated using the principle component analysis. The monohydration alters the inter-molecular motions of adenine–thymine base pair. We found that the nuclear quantum effect on the motion depends on the positions of the bound water molecule. The nuclear quantum effect on the hydrogen-bonded structure of adenine, thymine and water molecules is rather small, but we found significantly large nuclear quantum effect on the inter-molecular motions of the monohydrated base pair systems.