Ab Initio Calculations of Spin−Spin Coupling Constants in Anhydrodeoxythymidines

Toward the comprehensive calculations on the relationship between 1 H, 13 C, 31 P chemical shifts, 2 JPH , and the bonding structure of different phosphoryl benzamides

A comprehensive investigation was performed on ¹ H, ¹³ C, and ³¹ P nuclear magnetic resonance (NMR) chemical shifts (CSs) of phosphoryl benzamide derivatives (C₆ H₅ C(O)NHP(O)R₁ R₂ ), (R₁ , R₂  = aziridine [L₁ ], azetidine [L₂ ], pyrrolidine [L₃ ], piperidine [L₄ ], azepane [L₅ ], 4-methylpiperidine [L₆ ], propane-2-amine [L₇ ], and 2-methylpropane-2-amine [L₈ ]) by the gauge-independent atomic orbital method (GIAO) to find the most accordant level of theory with the experimental values. To achieve this goal, all the structures were optimized using the B3LYP, BP86, PBE1PBE, M06-2X, MPWB1K, and MP2 methods with 6-31+G* basis set. Computed structural parameters demonstrate that BP86 has the best agreement to the experimental values between the other methods. The def2-TZVP and aug-cc-pVDZ basis sets were also employed to inspect the effect of different types of basis sets with higher polarization and diffuse functions. The correlation between the empirical and computational values attests that 6-31+G* basis set is the optimum case regarding minimization of the costs and results. The comparison between calculated and experimental CSs at all mentioned combinations illustrated that in accordance with structural results, the best level of theory in CSs is also BP86/6-31+G*. Besides, ² J_PH values were computed with an acceptable agreement to experimental data at the optimum level of theory. The dependency between ² J_PH and the bonding structure of studied ligands was also scrutinized by the Natural Bond Orbital (NBO) analysis that interprets the relationship between the electronic properties and ² J_PH values.

Prediction of the 1H and 13C NMR Spectra of α-d-Glucose in Water by DFT Methods and MD Simulations

We have applied computational protocols based on DFT and molecular dynamics simulations to the prediction of the alkyl 1H and 13C chemical shifts of alpha-d-glucose in water. Computed data have been compared with accurate experimental chemical shifts obtained in our laboratory. 13C chemical shifts do not show a marked solvent effect. In contrast, the results for 1H chemical shifts provided by structures optimized in the gas phase are only fair and point out that it is necessary to take into account both the flexibility of the glucose structure and the strong effect exerted by solvent water thereupon. Thus, molecular dynamics simulations were carried out to model both the internal geometry as well as the influence of solvent molecules on the conformational distribution of the solute. Snapshots from the simulation were used as input to DFT NMR calculations with varying degrees of sophistication. The most important factor that affects the accuracy of computed 1H chemical shifts is the solute geometry; the effect of the solvent on the shielding constants can be reasonably accounted for by self-consistent reaction field models without the need of explicitly including solvent molecules in the NMR property calculation.

NMR spectra, GIAO and charge density calculations of five-membered aromatic heterocycles

The B3LYP/6-31+G(d) molecular geometry optimized structures of 17 five-membered heterocycles were employed together with the gauge including atomic orbitals (GIAO) density functional theory (DFT) method at the B3LYP/6-31+G(d,p), B3LYP/6-311++G(d,p) and B3LYP/6-311+G(2d,p) levels of theory for the calculation of proton and carbon chemicals shifts and coupling constants. The method of geometry optimization for pyrrole (1), N-methylpyrrole (2) and thiophene (7) using the larger 6-311++G(d,p) basis sets at the B3LYP/6-31+G(d,p), B3LYP/6-311++G(d,p), B3LYP/6-31+G(2d,p) and B3LYP/cc-pVTZ levels of theory gave little difference between calculated and experimental values of coupling constants. In general, the (1)H and 13C chemical shifts for all compounds are in good agreement with theoretical calculations using the smaller 6-31 basis set. The values of nJHH(n=3, 4, 5) and rmnJ(CH)(n=1, 2, 3, 4) were predicted well using the larger 6-31+G(d,p) and 6-311++G(d,p) basis sets and at the B3LYP/6-31+G(d,p), B3LYP/6-311++G(d,p), B3LYP/6-31+G(2d,2p) levels of theory. The computed atomic charges [Mülliken; Natural Bond Orbital Analysis (NBO); Merz-Kollman (MK); CHELP and CHELPG] for the B3LYP/6-311++G(d,p) geometry optimized structures of 1-17 were used to explore correlations with the experimental proton and carbon chemical shifts.

Structural elucidation of nitro-substituted five-membered aromatic heterocycles utilizing GIAO DFT calculations

The GIAO (Gauge Including Atomic Orbitals) DFT (Density Functional Theory) method is applied at the B3LYP/6-31+G(d,p)//B3LYP/6-31+G(d), B3LYP/6-311++G(d,p)//B3LYP/6-31+G(d), B3LYP/6-311+G (2d,p)//B3LYP/6-31+G(d) and B3LYP/6-311++G(d,p)//B3LYP/6-311++G(d,p) levels of theory for the calculation of proton and carbon chemicals shifts and coupling constants for 25 nitro-substituted five-membered heterocycles. Difference (1D NOE) spectra in combination with long-range gHMBC experiments were used as tools for the structural elucidation of nitro-substituted five-membered heterocycles. The assigned NMR data (chemical shifts and coupling constants) for all compounds were found to be in good agreement with theoretical calculations using the GIAO DFT method. The magnitudes of one-bond (1JCH) and long-range (nJCH, n>1) coupling constants were utilized for unambiguous differentiation between regioisomers of nitro-substituted five-membered heterocycles.

Toward the Complete Prediction of the1H and13C NMR Spectra of Complex Organic Molecules by DFT Methods: Application to Natural Substances

The NMR parameters (1H and 13C chemical shifts and coupling constants) for a series of naturally occurring molecules have been calculated mostly with DFT methods, and their spectra compared with available experimental ones. The comparison includes strychnine as a test case, as well as some examples of recently isolated natural products (corianlactone, daphnipaxinin, boletunone B) featuring unusual and/or crowded structures and, in the case of boletunone B, being the subject of a recent revision. Whenever experimental spectra were obtained in polar solvents, the calculation of NMR parameters was also carried out with the Integral Equation-Formalism Polarizable Continuum Model (IEF-PCM) continuum method. The computed results generally show a good agreement with experiment, as judged not only by statistical parameters but also by visual comparison of line spectra. The origin of the remaining discrepancies is attributed to the incomplete modeling of conformational and specific solvent effects.

Experimental and DFT 1H NMR study of conformational equilibria in trans-4',7-dihydroxyisoflavan-4-ol and trans-isoflavan-4-ol

The solution-state conformational equilibria of trans-4',7-dihydroxyisoflavan-4-ol (1) and trans-isoflavan-4-ol (2) were assessed based on the temperature dependence of their vicinal coupling constants J(H)(-)(2)(alpha)(,H)(-)(3) and J(H-3,H)(-)(4) in comparison to values calculated with density functional theory (DFT) methods at the B3LYP/cc-pVTZ//B3LYP/6-31G(d,p) level of theory. For each half-chair conformer, several rotamers with respect to the C-4 hydroxyl and C-3 phenyl were calculated and the overall diequatorial-to-diaxial ratio at 298 K was assessed as 66:34 for 1 and 73:27 for 2. The syntheses of 1 and 2 are described.

Modeling NMR parameters by DFT methods as an aid to the conformational analysis of cis-fused 7a(8a)-methyl octa(hexa)hydrocyclopenta[d][1,3]oxazines and [3,1]benzoxazines

The energies of the preferred conformations of four 7a-methyl octa(or hexa)hydrocyclopenta[d][1,3]oxazines, five 8a-methyl octa(or hexa)hydro[3,1]benzoxazines, and 8a-methyl hexahydro[1,3]benzoxazinone, all cis-fused, were investigated by DFT methods. Following geometry optimization at the B3LYP/6-31G(d,p) level, both the proton chemical shifts and the vicinal coupling constants between H-4a and the H-4 and H-5 protons were calculated at the B3LYP/cc-pVTZ level and compared to the previously experimentally measured values. The agreement between the calculated and the experimental chemical shifts was found to be good. Similarly, the agreement between the calculated and the experimental vicinal coupling constants was also found to be good, thus providing a methodology for determining the conformational equilibria of such systems that is comparable in many respects to experimental approaches such as variable-temperature NMR or to the use of model coupling constant values, when available, from analogous compounds.

Complete Prediction of the1H NMR Spectrum of Organic Molecules by DFT Calculations of Chemical Shifts and Spin-Spin Coupling Constants

1H NMR chemical shifts and coupling constants for several aromatic and aliphatic organic molecules have been calculated with DFT methods. In some test cases (furan, o-dichlorobenzene and n-butyl chloride) the performance of several functionals and basis sets has been analyzed, and the various contributions to spin-spin coupling (Fermi-contact, diamagnetic and paramagnetic spin-orbit) have been evaluated. The latter two components cancel each other, so that the calculation of the contact term only is sufficient for an accurate evaluation of proton-proton couplings. Such calculated values are used to simulate the 1H NMR spectra of organic molecules with complicated spin systems (e.g. naphthalene, o-bromochlorobenzene), obtaining a generally very good agreement with experimental spectra with no prior knowledge of the involved parameters.