This study describes best practices followed in my own classroom while teaching difficult concepts of organic chemistry to twelve grade students at a private high school in Pakistan using self-study research. The focus of the study is two difficult topics identified in literature and during my ownteaching learningexperiences including stability ofcarbocationand Isomerism. This self-study explores the best practices of teaching of topics perceived to be difficult by students using a relatively new genre of research. As mentioned by Loughran (2007) self-study scholars are interested in the resolution of current problems and in the achievement of short and long-term educational reformation. The main purpose ofthe study is myintrinsic motivation of improving my own classroom teaching. I am attracted towardsself-study approachbecause I want to know more about myself as a teacher. Secondly, the identification of organic chemistry as a problem area in chemistry in Pakistan and elsewhere provides the rationale for this self-study. Moreover, it is very important for teachers to explore their own best practices that enhance student’s learning within their own classrooms and self-interactions. The discourse about best practices will help other teachersto learnwhat works best for them. The data collection procedures for this study involved my own reflective journal and my own teaching portfolio consisting of lesson plans, teaching resources and student’s reflection about teaching. The analysis of the data involvedon goinganalysis of my reflective notes, critical analysis of the reflective journal and analysis of the student’s reflections using content analysis and method of constant comparison. The major findings of the study include an overarching theme of emotional pedagogy. It was found the emotional aspect of pedagogy needs to be fully understood and incorporated within whatever is taught andspeciallythe difficult topics. Moreover, it was also revealed thatteacher’s attitudetowards a topicactually becomea stimulus for student’s learning. It was found that students feel while they learn. So the pedagogies that are planned for teaching must involve both the aspects ofstudent’sthinking and student’s feelings. Another very important finding about self-study is about using informal pedagogies such as going out of classroom settings also creates enabling environment for the student’s to grasp abstract and difficult concepts in a better way which actually decrease the anxiety among students and fear pertaining to the topic itself. However, a key finding of the self-study is improving the class ecology. The class ecology includes establishing a positive relationship between students and the topics prior to teach them