I've recently had a situation come up at work where I need to protect our ASP.NET Web API 2 deployment with Windows Authentication.  We run our web client through Chrome and IE and we needed the NTLM negotiation to be handled gracefully.  There are a few things that we had to put in place to get this to go.  Here they are in list form.  The code for both the problem and the solution is here on my github.