The atomic configuration of C6H8 molecules chemisorbed on Si(0 0 1) surface is elucidated by the first-principles molecular dynamics method. The characteristic pattern in the STM image at similar to0.6 ML coverage is found to be reproduced by considerable thermal fluctuation of the molecules including the change in the molecular conformation. The reaction path and growth mechanism of the chemisorption region is also discussed based on static calculation of the activation barrier. (C) 2004 Elsevier B.V. All rights reserved.