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

Result code in IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F00216208%3A11320%2F18%3A10378307" target="_blank" >RIV/00216208:11320/18:10378307 - isvavai.cz</a>

Result on the web

<a href="http://structbio.org/xv-discussions-structural-molecular-biology" target="_blank" >http://structbio.org/xv-discussions-structural-molecular-biology</a>

DOI - Digital Object Identifier

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Result language

angličtina

Original language name

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

Original language description

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 .

Czech name

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Czech description

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Type

O - Miscellaneous

CEP classification

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OECD FORD branch

10403 - Physical chemistry

Project

Result was created during the realization of more than one project. More information in the Projects tab.

Continuities

P - Projekt vyzkumu a vyvoje financovany z verejnych zdroju (s odkazem do CEP)

Publication year

2018

Confidentiality

S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů