entityManagerFactory = Persistence.createEntityManagerFactory("myPersistence-unit");
EntityManager entityManager = openEntityManager( entityManagerFactory);
entityManager.getTransaction().begin();

    String queryDropCollection = "db.Person.drop()";
    String queryDropDB = "db.dropDatabase()";

    entityManager.createNativeQuery(queryDropCollection).executeUpdate();
    entityManager.createNativeQuery(queryDropDB).executeUpdate();

entityManager.getTransaction().commit();
entityManager.close();

Exception in thread "main" com.mongodb.util.JSONParseException:
db.Person.drop()
^

Exception in thread "main" com.mongodb.util.JSONParseException:
db.dropDatabase()
^