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I'm designing two pairs of connectors that have same layout as RJ45 (just 2 inner pins) to have 100 ohm impedance deferentially. Seen from the side

Are there tools that allow to calculate impedance or articles/guides? There are tons of calculators that compute impedance of transmission lines on a substrate but I found out that changing substrate thickness drastically affects impedance even if I set it as air. I was thinking I could construct C and L matrices and compute characteristic impedance from there but I don't know if that's the right approach.

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There are a lot of tools to do help you do this. The substrate thickness plays a big part in the characteristic impedance, so you need this information from your board house. For a typical 0.062" thick board, a typical 4 layer stackup is 7.8mil between the outer layer and inner layers, and 47.25mil between the inner layers. This is typical but not guaranteed, so make sure you ask your vendor or specify the stackup yourself and get whatever assurance you need to feel comfortable that they'll make it as specified.

After that there's trace thickness. 1oz copper is 1.4mil, and 0.5oz is half that. Typically the outer layers are 1oz and the inner layers 0.5oz, but check with your vendor.

Now that you know your board characteristics you want to know how wide and how much space to leave between your traces to get a differential characteristic impedance of 100 ohms. This is where the online calculators come into play.

There are others. I like to run the same calculation on several calculators to make sure things line up. I recently (last week) did this, and the first two links above agreed, but eeweb gave me a number almost 40% lower than the others.

With the typical stackup and copper thickness above, I get 107 ohms differential impedance with 8mil trace and 8mil space. eeweb tells me the same stackup gives 137 ohms. YMMV, and if you are placing a ground around the traces the distance between the traces in the microstrip and the surrounding ground will affect this as well.

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