Leaving a dog alone in the backyard is not recommended, give him access to your house and family member else you rotty will be frustrated and wild. anyway there could be two reason for this either your rotty is not liking the separation or he is not properly exercised.
Best way to make him comfortable with backyard is doing it slowly. start with 15 min and then raise the time bar. Also, give your dog access to you house. Rotty are very family loving dog and loves to be around people. Give you dog freedom and time.