Fig. 4: Molecular dynamics simulation of analytes on SAM-functionalized gold surfaces.
From: Surface enhanced Raman scattering artificial nose for high dimensionality fingerprinting
a Snapshots of two model analytes, p-phenylenediamine (p-PDA) and 4-aminophenylacetic acid (4-APA), where the analyte–gold surface separation reaches a minimum. Analyte center-of-mass is used to measure the distance to the closest Au surface atom; % populations when analytes proximal (<0.6 nm) to a SAM/Au are calculated from MD generated equilibrium ensemble for each system: non-functionalized (bare), 1-propanethiol (3CH3), 3-mercapto-1-propanol (3OH), 3-mercaptopropionic acid (3COOH), 3-amino-1-propanethiol (3NH2), 1-undecanethiol (11CH3), 11-mercapto-1-undecanol (11OH), 11-mercaptoundecanoic acid (11COOH), 11-amino-1-undecanethiol (11NH2). Analyte orientation angles of b p-PDA and c 4-APA relative to the Au surface showing the direction of each analyte’s functional groups when proximal (<0.6 nm) to a SAM/Au. Angles < 90° indicate that the NH2 group of the analyte is pointing towards the SAM/Au surface, whereas angles > 90° specify that the charged groups (NH3+/COO−) are facing the SAM/Au. SAM and analyte protonation states are modeled based on the cognate experimental buffer conditions, i.e. p-PDA (pH 5.0) and 4-APA (pH 7.5).
