General Chemistry is a demanding course that challenges its participants who compriselargely freshman science majors. We have found that many of these students cite this class as the toughest they have to take in their first year, and they struggle to successfully complete the course. In this study, we employ Item Response Theory (IRT) to analyze previous computer administered examination data and elucidate those areas of chemistry that are problematic for students. We investigate the potential for specific questions to discriminate between students abilities and show the types of questions that will separate A and B students, B from C, etc. Additionally, it is shown that a range of these topics must be present on an examination to accurately and fairly ascribe a grade to students. To further identify difficult topics that represent a barrier for learning, we find some common misconceptions that students have about certain key concepts; without correction, these can lead to misinterpretations of theories. Specific topics are analyzed to determine for whom, and why, these topics are difficult. Armed with this analysis, the instructors modified their approach to teaching these key concepts in the 2006 and 2007 academic years. Improvement in student understanding of some of these problematic areas is accomplished.