It was Newton that liked a clockwork universe. The idea that everything could be calculated and put down to simple mechanics was a nice one, but today, with the advent of quantum mechanics, we know that the universe is much more complicated.
Newton's ideas were loosely based on determinism. This is the basic assumption that all events can be determined or predicted with absolute accuracy, which effectively means that 'free will' is therefore not possible, as your will is already determined for you.
Let's look at this first on a simple scale. If you had a box full of gas or liquid and you knew the exact positions and movement of all the atoms in the box, you could put all this data into a computer and easily run a program to predict what will happen to the contents at any time in the future (or the past).
This is very similar to what goes on when we look at a weather forecast. Some of the most powerful computers in the world are required to run accurate predictions of the weather. The problem is with the accuracy. It can never be perfect. Weather forecasts are always 'not quite right'. It's all to do with accumulating lots of small errors in the positions and speeds of particles over time.
Bus alas! we now know that you can never know the exact position and momentum of any particle. We can get pretty close, but Heisenberg had a theory or 'Uncertainty Principle' that stated that you could not know both with any accuracy, the more accurately you tried to find one, the less accurate the other became. A simple way to visualise this is if you were trying to find the exact position of a particle, you would have to hit it with a proton to 'see' it and this by definition would upset its speed and direction or momentum.
So these guesses and errors build up many times over and this is why we get inaccurate weather forecasts. So we can not predict what happens in the box. If we substitute the box of stuff with another arrangement of matter, say a human brain, we still have the same problem in that we cannot predict exactly what it will do at any future moment.
Due to this ambiguity, we can breathe a sigh of relief and now say that determinism is too simplistic and perhaps there is room for randomness and chaos, so our free will is therefore saved!