The ultimate goal of much of physics, chemistry and biology is to understand molecular interactions at a level that allows useful predictions. A complete understanding of interactions of RNA would allow predictions of structure and perhaps function from sequence. For the hydrogen molecule, quantum mechanics is enough to predict all its properties. For a complex molecule like RNA, however, it is not possible to use the rigorous equations of quantum mechanics. The large number of atoms in an RNA molecule forces the use of an approximate method that makes use of force fields. Inclusion of Quantum Mechanical effects in Molecular Dynamics simulations will improve the calculations in order to reconcile experiments with computational results and thus provide insight into molecular interactions.

GA base pairs play important roles in the structure, dynamics, and stability of RNA. In internal RNA loops, GA base pairs often occur in tandem arrangements and their structure is context and sequence dependent. In this thesis, the amber99 force field is tested using the Thermodynamic Integration (TI) approach by comparing computational predictions of free energy differences with the free energy differences expected on the basis of NMR determined structures of the RNA duplexes (5'-GCGGACGC-3') ₂, (5'-GCiGGAiCGC-3')₂, (5'-GGC GAGCC-3')₂, and (5'-GGiCGAiGCC-3') ₂. iG and iC represent isoguanosine and isocytidine, which have amino and carbonyl groups transposed relative to guanosine and cytidine. The NMR structures show that the GA base pairs adopt either imino (cis Watson-Crick/Watson-Crick A-G) or sheared (trans Hoogsteen/Sugar edge A-G) conformations depending on the identity and orientation of the adjacent base pair. A new mixing function for the TI approach is developed that allows alchemical transitions in which atoms can disappear in both the initial and final states. The amber99 force field was modified to partially include pyramidalization effects of the unpaired amino group of guanosine in imino GA base pairs. For the (5'-GCG GACGC-3')₂ to (5'-GCiGGAiCGC-3') ₂ transformation, the nonplanarity has a ∼0.6 kcal/mol effect in the direction favoring the structures observed by NMR. For the transformation of (5'-GGCGAGCC-3')₂ to (5'-GGiC GAiGCC-3')₂, the computational free energy difference predictions for both amber99 and modified amber99 force fields are essentially identical and favor the structures determined by NMR. For the transformations, the free energy change favoring the NMR structures, however, is underestimated by about 3 and 2 kcal/mol, respectively. In an independent set of calculations, the duplexes were restrained to sample around experimentally determined NMR structures. This also improved the computational free energy difference predictions. The results suggest that the free energy changes associated with amino group nonplanarity are underestimated when approximated by a simple force field and that other factors such as stacking and backbone effects are also important in determining local structure. Nevertheless, the calculations are close to reproducing expectations from the experimental results and are thus capable of providing useful qualitative insights complementing the NMR experiments.