Wavefunction has a great post on this subject. Here's the link: http://wavefunction.fieldofscience.com/2011/02/difference-between-chemistry-and.html
Here’s a particularly fine passage of his on the subject:
“An example more familiar to chemists which is stated by Hoffmann also vividly illustrates the problem with reducing chemistry to physics. Consider the carbonyl functional group, a workhorse of chemistry. The most important reaction that this group undergoes is nucleophilic addition. How does physics explain this process? By essentially pitching electrostatics. Physics will tell us that the carbonyl carbon has a partial positive charge and the oxygen has a partial negative one, thus attracting nucleophiles to the carbon. But a chemist would find this simple explanation deeply unsatisfying. There is much complexity associated with addition to carbonyls which goes beyond merely electrostatic attraction. There’s the angle of attack of the nucleophile- the well-known Burgi-Dunitz trajectory- which maximizes orbital overlap. There’s coordination of positively charged counterions with the oxygen which can dictate the stereochemistry. There’s also the size of groups on the attacking nucleophile which can sharply tip the distribution of products through steric effects. Then there’s the gradation of reactivity of various nucleophiles based on their size and charge. And finally, there’s the all-pervasive solvent which can drastically change product ratios and stereochemistry through solvation effects.