We study the fundamental mechanisms for dramatic reduction of leakage current of silicon oxide caused by the RTP-induced phonon-energy coupling enhancement (PECE). It is shown that the Si-D bonds are strengthened after RTP and deuterium anneal through characterization of hot-electron degradation of MOS transistors. The Si-O bonds are strengthened because the breakdown voltage of silicon oxide is increased after RTP. We also designed special pn junctions to examine Si-Si bonds. We found that the breakdown voltage of the silicon substrate is increased by 0.3 V after RTP anneal whereas it remains the same for diodes annealed in furnace with the same parameters as in RTP. The increase in breakdown voltage of silicon is due to its intrinsic properties, i.e. stronger SiSi bonds. The strengthening of Si-Si bonds is caused by coupling of phonon energy from silicon to thin oxide.