Quantum Mechanics Approach to Hydration Energies and Structures of Alanine and Dialanine

A systematic approach to the phenomena related to hydration of biomolecules is reported at the state of the art of electronic-structure methods. Large-scale CCSD(T), MP4-SDQ, MP2, and DFT(M06-2X) calculations for some hydrated complexes of alanine and dialanine (Ala⋅13 H₂ O, Ala₂ H⁺ ⋅18 H₂ O, and Ala₂ ⋅18 H₂ O) are compared with experimental data and other elaborate modeling to assess the reliability of a simple bottom-up approach. The inclusion of a minimal number of water molecules for microhydration of the polar groups together with the polarizable continuum model is sufficient to reproduce the relative bulk thermodynamic functions of the considered biomolecules. These quantities depend on the adopted electronic-structure method, which should be chosen with great care. Nevertheless, the computationally feasible MP2 and M06-2X functionals with the aug-cc-pVTZ basis set satisfactorily reproduce values derived by high-level CCSD(T) and MP4-SDQ methods, and thus they are suitable for future developments of more elaborate and hence more biochemically significant peptides.

Unscrambling micro-solvation of –COOH and –NH groups in neat dimethyl sulfoxide: insights from 1H-NMR spectroscopy and computational studies

This study investigates the interactions of –COOH and –NH groups in neat DMSO solutions, with special focus on their thermodynamics and kinetics.

Quantum chemical studies on nucleophilic sites in calcium ion bound zwitterionic calmodulin loops

Quantum chemical calculation on Ca²⁺ bound zwitterionic calmodulin-loops shows terminal capping contributions localized near HOMO and LUMO, which decay exponentially and presence of nucleophilic site at the phenyl-ring O_h of Y99.

Interfacial water at the trialanine hydrophilic surface: a DFT electronic structure and bottom-up investigation

A model describing a network of hydrogen bonded water-trialanine has been developed to estimate hydration effects on various conformers of the peptide.