Large-scale molecular dynamics simulations of alkanethiol self-assembled monolayers

Authors

Satyavani Vemparala, Biological Computation and Visualization Center, Department of Physics & Astronomy, Louisiana State University, Baton Rouge, Louisiana 70803, USA.
Bijaya B. Karki
Rajiv K. Kalia
Aiichiro Nakano
Priya Vashishta, Department of Molecular and Cellular Medicine, College of Medicine, Texas A&M University Health Science Center, 8447 Riverside Parkway, Bryan, TX 77807, USA.
Feng Chen, High Performance Computing, 329 Frey Computing Services Center, Louisiana State University, Baton Rouge, LA 70803, USA.
Ashlin A. Naquin, Department of Chemistry, University of Louisiana at Lafayette, P.O. Box 44370, Lafayette, LA 70504, USA.
Avery C. Walton, Department of Chemistry, University of Louisiana at Lafayette, P.O. Box 44370, Lafayette, LA 70504, USA.
Peter W. Kishbaugh, Department of Chemistry, University of Louisiana at Lafayette, P.O. Box 44370, Lafayette, LA 70504, USA.
Jun-Yuan Ji, Department of Molecular and Cellular Medicine, College of Medicine, Texas A&M University Health Science Center, 8447 Riverside Parkway, Bryan, TX 77807, USA.

Document Type

Article

Publication Date

9-1-2004

Abstract

Large-scale molecular dynamics simulations of self-assembled alkanethiol monolayer systems have been carried out using an all-atom model involving a million atoms to investigate their structural properties as a function of temperature, lattice spacing, and molecular chain length. Our simulations show that the alkanethiol chains of 13-carbons tilt from the surface normal by a collective angle of 25 degrees along next-nearest-neighbor direction at 300 K. The tilt structure of 13-carbon alkanethiol system is found to depend strongly on temperature and exhibits hysteresis. At 350 K the 13-carbon alkanethiol system transforms to a disordered phase characterized by small collective tilt angle, flexible tilt direction, and random distribution of backbone planes. The tilt structure also depends on lattice spacing: With increasing lattice spacing a the tilt angle increases rapidly from a nearly zero value at a=4.7 A to as high as 34 degrees at a=5.3 A at 300 K for 13-carbon alkanethiol system. Finally, the effects of the molecular chain length on the tilt structure are significant at high temperatures.

Publication Source (Journal or Book title)

The Journal of chemical physics

First Page

4323

Last Page

30

Recommended Citation

Vemparala, S., Karki, B. B., Kalia, R. K., Nakano, A., Vashishta, P., Chen, F., Naquin, A. A., Walton, A. C., Kishbaugh, P. W., & Ji, J. (2004). Large-scale molecular dynamics simulations of alkanethiol self-assembled monolayers. The Journal of chemical physics, 121 (9), 4323-30. https://doi.org/10.1063/1.1775779