The maximum clock frequency of the TM4C123AH6PMI7R is 80 MHz, but it can be overclocked to 120 MHz with some limitations.
The pin muxing on the TM4C123AH6PMI7R can be configured using the Pin Mux Utility tool provided by Texas Instruments, or by writing code to configure the GPIO registers directly.
The main difference between the TM4C123AH6PMI7R and the TM4C1294NCPDT is that the TM4C1294NCPDT has more flash memory (1MB vs 256KB) and more peripherals, such as a USB OTG interface and a CAN interface.
The ADC on the TM4C123AH6PMI7R can be used by configuring the ADC registers, selecting the input channel, and triggering the conversion. The ADC result can then be read from the ADC FIFO.
Yes, the TM4C123AH6PMI7R can be used with an operating system such as TI-RTOS, FreeRTOS, or Linux. However, the operating system must be ported to the specific microcontroller and configured to use the available peripherals.