We have synthesized carbon nanoparticles using mandarin juice via green synthesis rout. We have doped carbon nanoparticles in liquid crystal media and studied the surface effect on self-assembly of carbon nanoclusters on ITO coated glass surface and on graphene sheet. The purpose of this study is to construct uniform nano-micro droplets for novel applications and to understand and explore the underlying science behind molecular scale reorganization in the presence of functional surfaces like graphene. We have used density functional theory approach to confirm that the carbon nanoparticles in globular structures are dispersed in presence of graphene sheet due to chemical interaction of carbon rings (or say carbon nanoparticles) with graphene carbon atoms. In order to minimize the free energy, the carbon nanoparticles leave the carbon globular structures and are dispersed to form rectangular structures in presence of LC media at graphene surface. The carbon nanoparticles are dispersed to increase contact area with graphene surface. The results are useful in construction of desired nano-micro structures for possible novel purposes in medical field since carbon nanoparticles are biocompatible. Optical microscopy, FESEM, NMR and UV spectra verifies the droplet formation and its effect on the surface and electronic properties of carbon nanoparticles.