I'd like to know the major changes that happened that lead to the change in thought, and what veered modern political philosophy away from the concept of city and man to the concept of natural science and history.
To the best of my knowledge there is no veering in modern political philosophy to the concepts of natural science. Natural sciences are physics, chemistry, biology, etc. These sciences deal with physical objects or the biology of humans and other animals.
At most, mathematical models enter into the discussion of political theories. A first step has been the prisoner dilemma as a model of rational decision under uncertainty.
Key players of contemporary political philosophy are e.g., David Gauthier, Robert Nozick or John Rawls. All of them advocate a liberal position. Rawls' seminal work is A Theory of Justice (1971) and its addition Justice as Fairness. A Restatement (2001). These works build on the classical contract theories as initiated by Hobbes.
One important aspect is the definition of man. Ancients like Plato and Aristotle saw man as a social animal, and thus his relation to the polis is primary. In their thought man is constitutive of the polis and is understood by reference to it (i.e. the polis is understood almost like a superorganism like the bee hive).
Modern philosophers like Descartes, Kant, Locke, and Hobbes defined the human being in a much more individualistic way. The basis of political theory became essentially a means of mediation between autonomous individuals.
Why did this happen? It's hard to say. Religious and political pluralism in Europe surely played a large role. The skepticism that Descartes introduced into mainstream philosophy and the scientific advances that helped fuel it probably led to more restricted definitions of the human being. The Protestant emphasis on the individual and Voluntaristic tendencies in philosophy and theology probably contributed as well.
(Sorry for the relative lack of sources. I don't have time to dig and this question is too old not to take a stab at)