Chemical reactions can be modeled by a random time-changed Poisson process on countable states. The macroscopic behaviors, such as large fluctuations, can be studied via the WKB reformulation. The WKB reformulation for the backward equation is Varadhan's discrete nonlinear semigroup and is also a monotone scheme that approximates the limiting first-order Hamilton-Jacobi equations (HJE). The discrete Hamiltonian is an m-accretive operator, which generates a nonlinear semigroup on countable grids and justifies the well-posedness of the chemical master equation (CME) and the backward equation with 'no reaction' boundary conditions. The convergence from the monotone schemes to the viscosity solution of HJE is proved by constructing barriers to overcome the polynomial growth coefficients in the Hamiltonian. This implies the convergence of Varadhan's discrete nonlinear semigroup to the continuous Lax-Oleinik semigroup and leads to the large deviation principle for the chemical reaction process at any single time. Consequently, the macroscopic mean-field limit reaction rate equation is recovered with a concentration rate estimate. Furthermore, we establish the convergence from a reversible invariant measure to an upper semicontinuous viscosity solution of the stationary HJE.