We selected the 1N5187 because they are cheap, easy to find and they were used in similar applications with good results.
These four 1N5187 diodes are low-voltage-drop Schottky clamping diodes. The clampling diodes will prevent the input guitar signal to be more negative than –0.24V and more positive than 3.54V.
The Arduino Due ADCs can work with signals from -0.3 to 3.6, but overcoming these limits can damage the ADCs.
The series 4K7 resistors R9 and R10 will limit the current though the diodes, lowering the diodes VF to a good value to protect the ADCs. At the same time these resistors values are low enough to keep a good source impedance for the ADC (remember that the Atmel ATSAM3X A/D datasheet page 8 mentions that the source impedance must be lower than 10K)