(302d) Probing How Defects in Self-Assembled Monolayers Affect Protein Adsorption with Molecular Simulation

Probing how defects in self-assembled monolayers affect protein
adsorption with molecular simulation

Kayla Sprenger¹,
Jim Pfaendtner¹

¹Department
of Chemical Engineering, University of Washington, Seattle, WA, 98195, USA

ABSTRACT

The formation and characterization of self-assembled
monolayers, or SAMs, on solid surfaces has been extensively studied since the
last half of the 20^th century. The easy preparation of SAMs with
different terminal groups has made their applications far-reaching and numerous,
including bio-related technologies such as biosensors and medical implants,
nano- and microfabrication, nanodevices, and corrosion protection. Experimental
microscopy studies have long shown that SAMs have high concentrations of
defects; in some cases, as with the nanofabrication method of microcontact
printing, naturally-occurring imperfections in the
SAMs were shown to play a beneficial role in the process¹. In most
cases however, defects in the monolayers can have unexpected and perhaps
undesirable consequences. Though molecular simulation can offer unique insights
into the consequences of SAM structural imperfections and rearrangements, it has
only rarely been done; limitations of small simulation cell sizes and/or
insufficient sampling times have prevented the explicit exploration of defects in
typical SAM modeling studies.¹ Using the special enhanced sampling
method of PTMetaD-WTE^2,3 to circumvent
these challenges, we have performed a series of molecular dynamics studies of
LKa14
adsorbing on a carboxyl-terminated alkanethiol SAM with
both substrate and film naturally-occurring defects incorporated to mimic experimental
observations. With an idealized SAM as a control, three types of defects are
introduced, namely a gold depression that creates shortened alkyl chain lengths
to mimic a characteristic defect in the underlying gold substrate, and two
characteristic film defects of chains pointed towards and away from each other,
creating domain boundary effects. Binding free energies have been determined in
each case as a function of temperature to elucidate the entropic and energetic penalties
of the defects.

References

[1] Gannon, G.; Greer, J. C.; Larsson, A.; Thompson, D. Molecular
Dynamics Study of Naturally Occurring Defects in Self-Assembled Monolayer
Formation. ACS Nano 2010, 4, 921-932.

[2] Deighan, M.; Bonomi, M.; Pfaendtner, J. Efficient Simulation of
Explicitly Solvated Proteins in the Well-Tempered Ensemble. JCTC 2012, 8, 2189-2192.

[3] Deighan, M; Pfaendtner, J. 
Exhaustively Sampling Peptide Adsorption with
Metadynamics. Langmuir
2013, 29, 7999-8009.