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Efficient NMR crystallography of nucleic acid systems

Final Report Summary - DNAMET (Efficient NMR crystallography of nucleic acid systems)

The primary aim of the proposed work has been to develop efficient protocols for characterising H-atom positions in solids derived from small organic molecules. We used the Cambridge Structural Database to determine a suitable set of structures for calculation, plus a subset suitable for experimental work. These range from simple systems with a few resonances (nucleic acid bases cytosine and thymine, amino acids glycine and alanine, and amino acid hydrochlorides) to more challenging systems with disordered water molecules and sodium ions (thymine monohydrate, disordered sodium salt hydrates of guanosine-5’-monophosphate and uridine-5’-monophosphate). The crystalline samples were obtained in collaboration with IOCB, Prague and the crystal structures were verified/re-determined by Durham X-ray service. We performed DFT calculations on the structures of interest, and synthesised theoretical spectra including spectra of quadrupolar nuclei 35Cl, 23Na, and deuterium.
We characterized the selected samples by a large number of solid-state NMR experiments (including 1H, 2H, 13C, 15N, 23Na, and 35Cl experiments, static and magic angle spinning experiments, variable temperature experiments, T1 relaxation times determination). The experimental data provided evidence of the importance of molecular motion in the studied samples.
We have studied the influence of fast molecular motion on NMR parameters in detail on a set of amino acids and nucleic acid bases. A combination of DFT molecular dynamics and calculations of shielding and electric field gradient (EFG) tensors revealed the impact of vibrational motions on isotropic chemical shifts, chemical shift anisotropies (CSAs) and quadrupolar interactions. We demonstrated that molecular motion has a significant effect on average molecular structures, and that neglecting the effects of motion on crystal structures derived by diffraction methods may lead to significant errors of calculated isotropic chemical shifts. Re-orientation of the NMR tensors by molecular motion reduces the magnitudes of the NMR anisotropies, and inclusion of molecular dynamics can significantly improve the agreement between calculated quadrupolar couplings and experimental values. The results of this study have been published [1].
We have also explored the influence of nuclear delocalisation on NMR chemical shifts in molecular organic solids using path integral molecular dynamics (PIMD) and calculations of shielding tensors. We demonstrated that nuclear quantum effects explain previously observed systematic deviations in correlations between calculated and experimental chemical shifts. The PIMD approach also enables isotope substitution effects on chemical shifts and J couplings to be predicted in excellent agreement with experiment for both isolated molecules and molecular crystals. This paper has been highlighted by the reviewers and the editor as very important paper[2].

The other focus of the project was the characterisation of the role of coordinated water around phosphate units and metal ions. We observed dynamical behaviour of water molecules and sodium ions in the samples of thymine monohydrate and sodium salt hydrates of guanosine-5’-monophosphate and uridine-5’-monophosphate. In thymine monohydrate, the water molecule is disordered over two non-equivalent sites but at room temperature the exchange between these two sites is fast and averaged NMR spectra can be observed. However, at low temperature (below -80 ˚C), the water motion is slowed down and two sets of signals can be observed. Water and sodium ion dynamics in the nucleotide salts represent much more complicated examples of dynamical behaviour in solid materials. For example, only one nucleotide molecule with heavily disordered water and sodium ions were found in the asymmetric unit of uridine-5’-monophosphate structure determined by X-ray diffraction. However, we observed multiple sets of signals in the 13C and 23Na NMR spectra of this compound at low temperature indicating that the hydration shell dynamics leads to lower symmetry of the system than observed by diffraction techniques.
We have characterised the labile solvent molecules using 2H NMR, and with the use of molecular dynamics (MD) simulations to link NMR observations with molecular level behaviour in solids. The samples have been prepared in collaboration with IOCB, Prague.We performed a number of MD simulations of nucleotide and oligonucleotide systems, both in the solid state and solution. The computational predictions have been linked to the experimental results. Parts of the results of water and ion dynamics around oligonucleotides in solution were summarised in two papers [3,4]. We are currently finalising another manuscript, which deals with the water and sodium dynamics in solid nucleotides.

[1] Dracínský M., Hodgkinson P.: A molecular dynamics study of the effects of fast molecular motions on solid-state NMR parameters. CrystEngComm 2013, 15, 8705-8712.

[2] Dracínský M., Hodgkinson P.: Effects of quantum nuclear delocalisation on NMR parameters from path integral molecular dynamics. Chem. Eur. J. 2014, in press

[3] Towards Reproducing Sequence Trends in Phosphorus Chemical Shifts for Nucleic Acids by MD/DFT Calculations, J. Chem. Theory Comput. 2013, 9, 1641-1656

[4] Dracínský M., Möller H., Exner T.: Conformational Sampling by Ab Initio Molecular Dynamics Simulations Improves NMR Chemical Shift Predictions, J. Chem. Theory Comput. 2013, 9, 3806-3815.

[4] Dračínský M., Möller H., Exner T.: Conformational Sampling by Ab Initio Molecular Dynamics Simulations Improves NMR Chemical Shift Predictions, J. Chem. Theory Comput. 2013, 9, 3806-3815.