I. INTRODUCTION Self-assembled monolayers (SAMs) have attracted considerable attention as model sys- tems for many fundamental and technological investigations $^{1}$. The thiol and thiolate-based SAMs have broad applications on supramolecular assembly, wetting, tribology, corrosion in- hibition, lithography, chemical and biochemical sensors, optics, and immobilization of DNA, because of both their simplicity and stability. In particular, SAMs can simulate a biological membrane which allows adsorption of proteins to metal surfaces without denaturization $^{2–4}$. The peptide molecules with some enzymatic activity can be deposited on metal surfaces via the thiol or thiolate linkage monolayer $^{5,6}$. The deposition of a second monolayer on the top of the first adsorbed thiol or thiolate monolayer yields a bilayer system consisting of two monomolecular films. In other words, a layer of peptide molecules can be bonded to the gold surface via the linkage monolayer formed from the thioglycolic acid (HSCH$_{2}$COOH) $^{5–7}$. The chemisorption of the thioglycolic acid on the gold surface was demonstrated using surface-enhanced Raman scattering 8 and ultrafast electron crystallography $^{9}$. It was found when the higher portion of the carboxylic acid groups is deprotonated, the higher portion of the thioglycolic acid molecules adopts a trans conformation $^{8}$. It was also observed that after 2,2’-dithiodiacetic acid is deposited on the Au(111), the SCH$_{2}$COOH molecules are randomly oriented on the gold surface $^{9}$, that is, the adsorption pattern related to the SCH$_{2}$ COOH is different from that corresponding to the HSCH$_{2}$COOH. On the other hand, the swithcable SAM under the influence of an electrical potential was observed with intentionally created room for conformational changes of the molecules $^{10}$. When the external electrical potential is turned on, the hexadecanoic acid molecules (HS(CH$_{2}$)$_{15}$COO − ) bend their negatively charged COO − group towards to the positively charged gold surface $^{10}$. Simulating this swithcable SAM process via the ab initio method requires a prohibitive amount of computer time, so one has to study the simple case: the HSCH$_{2}$COO − on the Au(111) surface. It was recently observed that thiol stays intact when deposited on the regular Au(111) surface, but the S-H bond of the thiol is broken on the defected Au(111) surface $^{11,12}$. Upon the HSCH$_{2}$COOH molecules deposit on the Au(111), they can either remain intact, or turn into one of the following substances: 1) SCH$_{2}$COOH in the presence of the defect on the Au(111) $^{11,12}$; 2) HSCH$_{2}$ COO − by increasing pH value $^{8}$; 3) SCH$_{2}$ COO − by the defect and increasing pH value. To get a consistent picture of the thioglycolic acid adsorption on the 2