The benchmark of 31P NMR parameters in phosphate: a case study on structurally constrained and flexible phosphate.

Jiří Fukal,Vladimír Sychrovský,Ondřej Páv,Jakub Šebera,Miloš Buděšínský

doi:10.1039/c7cp06969c

Jiří Fukal, Vladimír Sychrovský + Show 3 more

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https://doi.org/10.1039/c7cp06969c

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Abstract

A benchmark for structural interpretation of the 31P NMR shift and the 2JP,C NMR spin-spin coupling in the phosphate group was obtained by means of theoretical calculations and NMR measurements in diethylphosphate (DEP) and 5,5-dimethyl-2-hydroxy-1,3,2-dioxaphosphinane 2-oxide (cDEP). The NMR parameters were calculated employing the B3LYP, BP86, BPW91, M06-2X, PBE0, KT2, KT3, MP2, and HF methods, and the 6-31+G(d), Iglo-n (n = II, III), cc-pVnZ (n = D, T, Q, 5), aug-cc-pVnZ (n = D, T and Q), and pcS-n and pcJ-n (n = 1, 2, 3, 4) bases, including the solvent effects described with explicit water molecules and/or the implicit Polarizable Continuum Model (PCM). The effect of molecular dynamics (MD) on NMR parameters was MD-calculated using the GAFF force field inclusive of explicit hydration with TIP3P water molecules. Both the optimal geometries and the dynamic behaviors of the DEP and cDEP phosphates differed notably, which allowed a reliable theoretical benchmark of the 31P NMR parameters for highly flexible and structurally constrained phosphate in a one-to-one relationship with the corresponding experiment. The calculated 31P NMR shifts were referenced employing three different NMR reference schemes to highlight the effect of the 31P NMR reference on the accuracy of the calculated 31P NMR shift. The relative Δδ(31P) NMR shift calculated employing the MD/B3LYP/Iglo-III/PCM method differed from the experiment by 0.16 ppm while the NMR shifts referenced to H3PO4 and/or PH3 deviated from the experiment notably more, which illustrated the superior applicability of the relative NMR reference scheme. The 2JP,C coupling in DEP and cDEP calculated employing the MD/B3LYP/Iglo-III(DSO,PSO,SD)/cc-PV5Z(FC)/PCM method inclusive of correction due to explicit hydration differed from the experiment by 0.32 Hz and 0.15 Hz, respectively. The NMR calculations demonstrated that reliable structural interpretation of the 31P NMR parameters in phosphate must involve both the structural and the dynamical components.

Highlights

To date, the majority of the known structures of nucleic acids have been resolved in crystals by employing X-ray crystallography methods
The benchmark for the 31P NMR shift and the 2JP,C NMR spin–spin coupling in phosphate was obtained by means of theoretical MD/DFT calculations considering the effects of the DFT method, atomic basis, hydration and molecular dynamics in a one-to-one relationship with the NMR measurements in two distinctively different phosphates as regards their optimal geometry and dynamic behaviour
The calculations of the 31P NMR shift demonstrated that the relative referencing of the 31P NMR shift in chemically equivalent phosphates is superior to the NMR reference schemes employing H3PO4 and/or a secondary PH3 reference

Summary

Introduction

The majority of the known structures of nucleic acids have been resolved in crystals by employing X-ray crystallography methods. The NMR parameters including the Nuclear Overhauser Effect (NOE), NMR chemical shift of atom A (d(A)), indirect NMR spin–spin coupling between atoms A and B separated by n bonds (nJA,B), and residual dipolar coupling (RDC) can provide structural constraints for obtaining the 3D structure of DNA and RNA molecules.[6] probably the only method for the reliable refinement and testing of MD force fields can be currently done with structural data derived from NMR experiments.[7] knowledge of the rules for the structural.

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