Benchmark Theoretical and Experimental Study on 15N NMR Shifts of Oxidatively Damaged Guanine

The Ad-MD method to calculate NMR shift including effects due to conformational dynamics: The 31 P NMR shift in DNA

A method for averaging of NMR parameters by molecular dynamics (MD) has been derived from the method of statistical averaging in MD snapshots, benchmarked and applied to structurally dynamic interpretation of the ³¹ P NMR shift (δ_31P ) in DNA phosphates. The method employs adiabatic dependence of an NMR parameter on selected geometric parameter(s) that is weighted by MD-calculated probability distribution(s) for the geometric parameter(s) (Ad-MD method). The usage of Ad-MD for polymers is computationally convenient when one pre-calculated structural dependence of an NMR parameter is employed for all chemically equivalent units differing only in dynamic behavior. The Ad-MD method is benchmarked against the statistical averaging method for δ_31P in the model phosphates featuring distinctively different structures and dynamic behavior. The applicability of Ad-MD is illustrated by calculating ³¹ P NMR spectra in the Dickerson-Drew DNA dodecamer. δ_31P was calculated with the B3LYP/IGLO-III/PCM(water) and the probability distributions for the torsion angles adjacent to the phosphorus atoms in the DNA phosphates were calculated using the OL15 force field.

Systematic investigation of DFT-GIAO 15N NMR chemical shift prediction using B3LYP/cc-pVDZ: application to studies of regioisomers, tautomers, protonation states and N-oxides

The calculation of ¹⁵N NMR chemical shifts has been systematically investigated using density functional theory-gauge including/invariant atomic orbitals (DFT-GIAO) approximation at the B3LYP/cc-pVDZ level of theory. General linear regression terms for ¹⁵N chemical shift predictions were calculated for nitromethane and liquid ammonia references in DMSO. Both aliphatic and aromatic nitrogens were studied using a diverse set of molecular scaffolds. Statistical error analysis between experiment and prediction revealed that, with the exception of primary amines, 95% of linear scaled N-15 chemical shifts are within a ±9.56 ppm range. Comparison of the ¹⁵N calculated isotropic chemical shifts with the experimentally determined chemical shifts provided accurate assignment of the correct structure in cases where experimental data was ambiguous or inconclusive. Application of ¹⁵N prediction proved to be highly effective in identifying the correct regio-isomer, oxidation state, protonation state and preferred tautomer in solution.

Super high-energy density single-bonded trigonal nitrogen allotrope—a chemical twin of the cubic gauche form of nitrogen

A new ambient-pressure metastable single-bonded nitrogen allotrope was predicted using reliable theoretical methods. The predicted allotrope has a number of similarities with the experimentally detected cubic gauche nitrogen allotrope.

Two isomeric solid carbon nitrides with 1 : 1 stoichiometry which exhibit strong mechanical anisotropy

Two isomeric layered carbon nitride polymorphs are characterized using reliable theoretical methods. The NCNC phase, which is predicted for the first time, has a number of differences with the isomeric NCCN polymorph in its electronic, spectral and mechanical properties.

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

A benchmark for structural interpretation of the ³¹P NMR shift and the ²J_P,C spin–spin coupling in the phosphate group was obtained by means of theoretical calculations and measurements in diethylphosphate and 5,5-dimethyl-2-hydroxy-1,3,2-dioxaphosphinane 2-oxide.