Two-dimensional self-assembled structures of adenine molecules: modeling and simulation
| Autor: | Keiko Shinoda, Masuhiro Mikami, Wataru Shinoda, Chee Chin Liew, Seiji Tsuzuki, Yoshitada Morikawa |
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| Rok vydání: | 2004 |
| Předmět: |
Chemistry
Surfaces and Interfaces Condensed Matter Physics Surface energy Surfaces Coatings and Films law.invention Molecular dynamics Chemical physics law Potential energy surface Materials Chemistry Molecule Physical chemistry Thermal stability Self-assembly Scanning tunneling microscope Surface states |
| Zdroj: | Surface Science. 556:109-120 |
| ISSN: | 0039-6028 |
| Popis: | Self-assembly of adenine molecules deposited on a Cu(1 1 1) surface shows some characteristic hydrogen-bonding network patterns, such as hexagonal and `double-chain'. In order to understand the emergence of energetically less favorable `double-chain' structure, in which adenine molecules form two rows, possible molecular arrangements in the `double-chain' structure are investigated by potential energy surface (PES) calculations between two single chains. A series of PES calculations elucidates that there are various stable molecular arrangements for the chain pair models: some of the models have both hexagonal and `double-chain' (I-type) hydrogen-bonding patterns, while the others have only the latter pattern (II-type). Molecular dynamics simulations starting from the obtained `double-chain' structures are also performed to assess the thermal stability of the structure. It is revealed that some of the II-type `double-chain' structures remain even at 300 K, while all I-type ones transform into hexagonal arrays. The former result reminds us that the II-type `double-chain' structures should be observed at room temperature in the STM experiment. |
| Databáze: | OpenAIRE |
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