Turbulence closure models that are based on a regularized deconvolution method (RDM) are proposed for application to implicitly filtered Large-Eddy Simulation (LES). This method reconstructs sub-grid scale contributions by approximately recovering filtered quantities through an optimization approach. Physical principles on the boundedness and conservation of reconstructed quantities are preserved by constraining the optimization problem. To account for effects of scales that are not resolved in implicitly filtered LES, a reconstruction method is proposed that combines sub-grid projection and energy-similarity to enrich unresolved scales. With this method, closure models are developed for turbulent scalar fluxes and turbulence-chemistry interaction that are intrinsically consistent with the LES formulation. These closure models are evaluated in application to a piloted turbulent jet flame with inhomogeneous inlet composition, in which combustion is represented by a two-scalar manifold model. The RDM-formulation is benchmarked against simulations obtained using a presumed PDF method and eddy diffusivity closure model. In partially-premixed flame regions, it is observed that RDM improves the prediction of turbulent mixing, and faster grid convergence is observed for results with RDM compared to simulations employing a presumed PDF method. (C) 2019 The Combustion Institute. Published by Elsevier Inc. All rights reserved.