The aim of this paper is to describe a novel modeling and simulation package, connected chemistry, and assess its impact on students' understanding of chemistry. Connected chemistry was implemented inside the NetLogo modeling environment. Its design goal is to present a variety of chemistry concepts from the perspective of ldquoemergent phenomenardquo—that is, how macro-level patterns in chemistry result from the interactions of many molecules on a submicro-level. The connected chemistry modeling environment provides students with the opportunity to observe and explore these interactions in a simulated environment that enables them to develop a deeper understanding of chemistry concepts and processes in both the classroom and laboratory. Here, we present the conceptual foundations of instruction using connected chemistry and the results of a small study that explored its potential benefits. A three-part, 90-min interview was administered to six undergraduate science majors regarding the concept of chemical equilibrium. Several commonly reported misconceptions about chemical equilibrium arose during the interview. Prior to their interaction with connected chemistry, students relied on memorized facts to explain chemical equilibrium and rigid procedures to solve chemical equilibrium problems. Using connected chemistry students employed problem-solving techniques characterized by stronger attempts at conceptual understanding and logical reasoning.