Molecular dynamics simulation study of adsorption and patterning of DNA bases on the Au(111) surface

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Journal titleThe Journal of Physical Chemistry C
Pages2248422494; # of pages: 11
SubjectAdenine molecules; Au(111) surfaces; DNA base molecules; DNA basis; Gasphase; Gold surfaces; Hexagonal structures; Hydrogen bond interaction; Hydrogen-bonded chains; Molecular dynamics simulations; Molecular mobility; Scanning Tunneling Microscopy (stm); Self assembled structures; Surface coverages; Two-temperature; Adsorption; Binding energy; DNA; Dynamics; Hydrogen; Hydrogen bonds; Molecules; Positive ions; Scanning tunneling microscopy; Molecular dynamics
AbstractTo understand of the mechanism of self-assembly of DNA base molecules on the Au(111) surface, molecular dynamics simulations of different surface coverage of guanine, adenine, cytosine, and thymine molecules at 300 and 400 K are performed. At low coverage, guanine, adenine, and thymine form hydrogen bonded chains on the surface, while cytosine molecules cluster into islands. At larger coverage, simulations indicate that adenine molecules form ordered two-dimensional hexagonal structures, while guanine, cytosine, and thymine molecules aggregate into small random clusters. These observations agree with scanning tunneling microscopy (STM) experiments of the DNA bases on gold surfaces. The simulations show that arrangement of the molecules on the gold surface is controlled by base-base interactions. The hydrogen bond interactions and stability of base-base homopairs, which are the smallest components of the self-assembled structures on the Au(111) surface, are calculated and compared with calculations of the homopairs in the gas phase and with values available in the literature. The binding energies per base on the surface initially decrease in magnitude with increasing surface coverage and then reach a constant plateau at large coverages. The mechanisms of molecular mobility for the bases with one and two molecule coverage on the surface are analyzed at two temperatures. © 2011 American Chemical Society.
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AffiliationNational Research Council Canada (NRC-CNRC); NRC Steacie Institute for Molecular Sciences (SIMS-ISSM)
Peer reviewedYes
NPARC number21271180
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Record identifier8e38db55-5137-4113-88da-e12ed532772a
Record created2014-03-24
Record modified2017-03-23
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