First principles Kohn–Sham density functional theory (DFT)-based molecular dynamics (MD) is employed to investigate some physical and mechanical properties of amorphous Si (a-Si) samples, as-quenched and annealed containing dangling and floating bonds as well as distorted tetrahedral bonds. The total energy and true stress as functions of the engineering strain for a-Si samples subjected to uniaxial tensile stress as well as uniaxial extension are obtained. It is well-known that the electron density of the state of matters can be determined via ab initio DFT-based MD with high accuracy. Using this technique, such inherent properties as the elastic constants, ideal tensile strength, ultimate tensile strength, and surface and cohesive energies will be calculated. Since the employed ab initio MD, in contrast to the empirical potentials simulations, is capable of providing the evolution of the electronic charge distribution, we can afford to study the chemistry of crack initiation and reconstructed surfaces at final rupture. The calculated cohesive and surface energies are compared with the available theoretical and experimental results; Tyson’s empirical relation and universal binding energy relations (UBERs) are also examined. The calculated elastic constants using the symmetry-general scheme satisfy well the isotropic relation. To date, the ab initio MD samples of a-Si generated from the completely melted scheme were all free of three-fold-coordinated Si. In contrast, as we will show, by implementing special thermal treatments, generation of all inherent structural defects is possible. Based on the electronic charge distribution, dative bonds and trigonal prisms for, respectively, floating and dangling bonds have been observed.