Create this stored procedure in MSDB Database : this will fetch the queries which are running more than 5 min. Long running queries information will stored in MSDB.dbo.LongRunningQuery_History table and send notification to configured mail team.
  USE MSDB
GO
CREATE  PROCEDURE sp_longRunningQueryNotification
AS 
IF (OBJECT_ID('MSDB.[dbo].[LongRunningQuery_History]') IS NULL)
BEGIN
CREATE TABLE DBAAdmin.[dbo].[LongRunningQuery_History](
 [session_id] [smallint] NOT NULL
 ,[start_time] [datetime] NOT NULL
 ,[total_elapsed_time] [int] NOT NULL
 ,[status] [nvarchar](30)
 ,[command] [nvarchar](30) NOT NULL
 ,[database_id] [VARchar](100) NOT NULL
 ,[last_wait_type] [nvarchar](100)
 ,[wait_resource] [nvarchar](256)
 ,[cpu_time] [int] NOT NULL
 ,[reads] [bigint] NOT NULL
 ,[writes] [bigint] NOT NULL
 ,[logical_reads] [bigint] NOT NULL
 ,[cmdText] [varchar] (MAX)
 ,[user_name] [varchar] (100)
 , [date] datetime
) ON [PRIMARY]
END
Declare @count varchar(100)
SELECT @count =  count(*) FROM  sys.dm_exec_requests r CROSS APPLY  sys.dm_exec_sql_text(r.sql_handle) AS t CROSS APPLY   sys.dm_exec_query_plan(r.plan_handle) AS p WHERE r.total_elapsed_time > 300000
IF (@count)>= 1 
BEGIN
  DECLARE @tableHTML  NVARCHAR(MAX) ;
  SET @tableHTML =
  N'<H1>Long Running Queries on '+ cast (@@servername as varchar(30)) +'</H1>' +
   N'<table border="1">' +
   N'<tr><th>Session_ID</th><th>Elapsed_Time_in_Mins</th><th>Command</th><th>Login_Name</th>' +
   N'<th>Database_Name</th>' +
   CAST ( ( SELECT td = CAST(r.session_id AS VARCHAR(10)), '',
        td = CAST((r.total_elapsed_time)/60000 AS VARCHAR(10)),  '',
       td = CAST(t.[text] AS VARCHAR(1000)) ,'',
       td = CAST(s.loginame AS VARCHAR(1000)) ,''
, td = CAST(DB_Name(r.database_id) AS VARCHAR(100) ),''
--, r.wait_type
--, r.last_wait_type
--, r.wait_resource
--, r.cpu_time
--, r.reads
--, r.writes
--, r.logical_reads
--, t.[text] AS [executing batch]
FROM
 sys.dm_exec_requests r
CROSS APPLY
 sys.dm_exec_sql_text(r.sql_handle) AS t
CROSS APPLY 
 sys.dm_exec_query_plan(r.plan_handle) AS p
 Left Join sys.sysprocesses s on s.spid = r.session_id
WHERE r.total_elapsed_time > 300000 
ORDER BY
 r.total_elapsed_time DESC
  FOR XML PATH('tr'), TYPE
   ) AS NVARCHAR(MAX) ) +
   N'</table>' ;
 DECLARE @vcsubject varchar(1000)
 Set @vcsubject ='Long Running Queries in ' + cast (@@servername as varchar(30))+ ', Please start monitoring'
  EXEC msdb.dbo.sp_send_dbmail @recipients='dbateam@gmail.com',
      @profile_name = 'SQLDBA_Profile',
   @subject = @vcsubject,
   @body = @tableHTML ,
   @body_format = 'HTML' ;
INSERT INTO dbo.LongRunningQuery_History SELECT  r.session_id, r.start_time, TotalElapsedTime_ms = r.total_elapsed_time, r.[status], r.command, DatabaseName = DB_Name(r.database_id),  r.last_wait_type, r.wait_resource, r.cpu_time, r.reads, r.writes, r.logical_reads, t.[text] , s.loginame, GETDATE()  FROM  sys.dm_exec_requests r CROSS APPLY  sys.dm_exec_sql_text(r.sql_handle) AS t CROSS APPLY   sys.dm_exec_query_plan(r.plan_handle) AS p  Left Join sys.sysprocesses s on s.spid = r.session_id WHERE r.total_elapsed_time > 300000 
END
DELETE FROM dbo.LongRunningQuery_History WHERE [Date] < (GETDATE() - 30)
Below is the script for creating a scheduled SQL job to monitor Long running queries.
USE [msdb]
GO
/****** Object:  Job [M_SQLDBA_LongRunningQueries]    Script Date: 06/13/2014 14:10:59 ******/
BEGIN TRANSACTION
DECLARE @ReturnCode INT
SELECT @ReturnCode = 0
/****** Object:  JobCategory [[Uncategorized (Local)]]]    Script Date: 06/13/2014 14:10:59 ******/
IF NOT EXISTS (SELECT name FROM msdb.dbo.syscategories WHERE name=N'[Uncategorized (Local)]' AND category_class=1)
BEGIN
EXEC @ReturnCode = msdb.dbo.sp_add_category @class=N'JOB', @type=N'LOCAL', @name=N'[Uncategorized (Local)]'
IF (@@ERROR <> 0 OR @ReturnCode <> 0) GOTO QuitWithRollback
END
DECLARE @jobId BINARY(16)
EXEC @ReturnCode =  msdb.dbo.sp_add_job @job_name=N'M_SQLDBA_LongRunningQueries', 
  @enabled=1, 
  @notify_level_eventlog=0, 
  @notify_level_email=0, 
  @notify_level_netsend=0, 
  @notify_level_page=0, 
  @delete_level=0, 
  @description=N'No description available.', 
  @category_name=N'[Uncategorized (Local)]', 
  @owner_login_name=N'sa', @job_id = @jobId OUTPUT
IF (@@ERROR <> 0 OR @ReturnCode <> 0) GOTO QuitWithRollback
/****** Object:  Step [running]    Script Date: 06/13/2014 14:10:59 ******/
EXEC @ReturnCode = msdb.dbo.sp_add_jobstep @job_id=@jobId, @step_name=N'running', 
  @step_id=1, 
  @cmdexec_success_code=0, 
  @on_success_action=1, 
  @on_success_step_id=0, 
  @on_fail_action=2, 
  @on_fail_step_id=0, 
  @retry_attempts=0, 
  @retry_interval=0, 
  @os_run_priority=0, @subsystem=N'TSQL', 
  @command=N'Exec sp_longRunningQueryNotification', 
  @database_name=N'MSDB', 
  @flags=0
IF (@@ERROR <> 0 OR @ReturnCode <> 0) GOTO QuitWithRollback
EXEC @ReturnCode = msdb.dbo.sp_update_job @job_id = @jobId, @start_step_id = 1
IF (@@ERROR <> 0 OR @ReturnCode <> 0) GOTO QuitWithRollback
EXEC @ReturnCode = msdb.dbo.sp_add_jobschedule @job_id=@jobId, @name=N'LongRunningQueries', 
  @enabled=1, 
  @freq_type=4, 
  @freq_interval=1, 
  @freq_subday_type=4, 
  @freq_subday_interval=15, 
  @freq_relative_interval=0, 
  @freq_recurrence_factor=0, 
  @active_start_date=20140612, 
  @active_end_date=99991231, 
  @active_start_time=0, 
  @active_end_time=235959, 
  @schedule_uid=N'e7b3e53a-e7b4-4d98-b040-1ba256b7af5a'
IF (@@ERROR <> 0 OR @ReturnCode <> 0) GOTO QuitWithRollback
EXEC @ReturnCode = msdb.dbo.sp_add_jobserver @job_id = @jobId, @server_name = N'(local)'
IF (@@ERROR <> 0 OR @ReturnCode <> 0) GOTO QuitWithRollback
COMMIT TRANSACTION
GOTO EndSave
QuitWithRollback:
    IF (@@TRANCOUNT > 0) ROLLBACK TRANSACTION
EndSave:
GO