Cementitious materials (cement paste) are highlyheterogeneous and hierarchical material systems. Processesand features at the nanometer sized morphological structures affect theperformance, deformation/failure behavior at larger length scales. Further, cement paste undergo chemical and morphological changes gaining strengthduring transient hydration process. Mechanical properties, deformation and failureare thus influenced by starting material genome chemistry structures, theirevolution to microstructures and engineering scale.Particlebased methods via Molecular Dynamics (MD) modeling is a viable methodology tostudy and characterize material systems based on nanoscale and chemistry level features.The present paper presents our research on the material modeling of stiffness anddeformation characteristics of cement paste material constituents. Inparticular, MD modeling of shear deformation of hydrated cement paste constituentcalcium-silicate-hydrate (C-S-H) is discussed. Computational C-S-H molecularstructure (Jennite) is subjected to shear deformation resulting in the predictedshear stress - strain behavior along its main crystalline orientations, and an estimationof shear modulus and strength. Energy changes and nano structural features suchas interatomic distances and bonding angles are analyzed to define andcharacterize the molecular structural level changes during deformation. MDbased material chemistry level modeling allows a predictive understanding ofthe effect of material chemistry, and additive changes on the mechanical propertiesand deformation behavior.