You can try the following below, here is what I added:
1) I put parentheses starting after WHERE and ending at the end of the existing statement.
2) Added ---> AND (i.Node.CustomProperties.City = 'Denver' AND i.Node.CustomProperties.Department = 'Accounting')
Please let me know if this works - full statement below:
SELECT Interfaces.Uri, Interfaces.DisplayName
FROM Orion.NPM.Interfaces AS Interfaces
LEFT JOIN Orion.TopologyConnections tc ON
(tc.SrcNodeID = Interfaces.NodeID OR tc.DestNodeID = Interfaces.NodeID)
(tc.SrcInterfaceID =Interfaces.InterfaceID OR tc.DestInterfaceID =Interfaces.InterfaceID)
tc.DestInterfaceID IS NOT NULL
AND tc.SrcInterfaceID IS NOT NULL
AND tc.LayerType = 'L2'
LEFT JOIN Orion.NPM.Interfaces i ON i.InterfaceID = tc.DestInterfaceID
OR i.InterfaceID = tc.SrcInterfaceID
WHERE (Interfaces.DuplexMode != i.DuplexMode AND Interfaces.DuplexMode > 1 AND i.DuplexMode > 1) AND (i.Node.CustomProperties.City = 'Denver' AND i.Node.CustomProperties.Department = 'Accounting')