No abstract

One of the major challenges for nanofabrication, in particular microcontact printing (mu-CP), is the control of molecular diffusion, or "ink spreading", for the creation of nanopatterns with minimized "smudging" at pattern boundaries. In this study, fully atomistic computer simulations were used to measure the impact of naturally occurring domain boundaries on the diffusion of excess alkanethiol ink molecules on printed alkanethiol self-assembled monolayers (SAM). A periodic unit cell containing approximately one million atoms and with a surface area of 56 nm x 55 nm was used to model a hexadecanethiol SAM on Au(111), featuring SAM domain boundaries and a range of concentrations of excess hexadecanethiol ink molecules diffusing on top. This model was simulated for a total of approximately 80 ns of molecular dynamics. The simulations reveal that domain boundaries impede the diffusion of excess ink molecules and can, in some cases, permanently trap excess inks. There is competition between ink spreading and ink trapping, with the ink/SAM interaction strongly dependent on both the ink concentration and the SAM orientation at domain boundaries. SAM defects thus provide potential diffusion barriers for the control of excess ink spreading, and simulations also illustrate atom-scale mechanisms for the repair of damaged areas of the SAM via self-healing. The ability of domain boundaries to trap excess ink molecules is accounted for using an accessible volume argument, and trapping is discussed in relation to experimental efforts to reduce molecular spreading on SAMs for the creation of ultrahigh resolution nanopatterns.

Spreading of ink outside the desired printed area is one of the major limitations of microcontact printing (micro-CP) with alkanethiol self-assembled monolayers (SAMs) on gold. We use molecular dynamics (MD) computer simulations to quantify the temperature and concentration dependence of hexadecanethiol (HDT) ink spreading on HDT SAMs, modeling 18 distinct printing conditions using periodic simulation cells of approximately 7 nm edge length and printing conditions ranging from 7 ink molecules per cell at 270 K to 42 ink molecules per cell at 371K. The computed alkanethiol ink diffusion rates on the SAM are of the same order of magnitude as bulk liquid alkanethiol diffusion rates at all but the lowest ink concentrations and highest temperatures, with up to 20-30 times increases in diffusion rates at the lowest concentration-highest temperature conditions. We show that although alkanethiol surfaces are autophobic, autophobicity is not enough to pin the ink solutions on the SAM, and so any overinking of the SAM will lead to spreading of the printed pattern. Comparison of experimental and calculated diffusion data supports an interpretation of pattern broadening as a mixture of spreading on fully and partially formed SAMs, and the calculated spreading rates establish some of the fundamental limitations of mu-CP in terms of stamp contact time and desired pattern width.

'Interdigitating organic bilayers direct the short inter layer spacing in hybrid organic-inorganic layered vanadium oxide nanostructures'.Journal of Physical Chemistry B, 115 (49)

Much research has been dedicated to understanding the molecular basis of UV damage to biomolecules, yet many questions remain regarding the specific pathways involved. Here we describe a genome‐mediated mechanism that causes site‐specific virus protein cleavage upon UV irradiation. Bacteriophage MS2 was disinfected with 254 nm UV, and protein damage was characterized with ESI‐ and MALDI‐based FT‐ICR, Orbitrap, and TOF mass spectroscopy. Top‐down mass spectrometry of the products identified the backbone cleavage site as Cys46–Ser47 in the virus capsid protein, a location of viral genome–protein interaction. The presence of viral RNA was essential to inducing backbone cleavage. The similar bacteriophage GA did not exhibit site‐specific protein cleavage. Based on the major protein fragments identified by accurate mass analysis, a cleavage mechanism is proposed by radical formation. The mechanism involves initial oxidation of the Cys46 side chain followed by hydrogen atom abstraction from Ser47 Cα. Computational protein QM/MM studies confirmed the initial steps of the radical mechanism. Collectively, this study describes a rare incidence of genome‐induced protein cleavage without the addition of sensitizers.