Crystallographic and Dynamic Aspects of Solid‐State NMR Calibration Compounds: Towards ab Initio NMR Crystallography

The excellent results of dispersion‐corrected density functional theory (DFT‐D) calculations for static systems have been well established over the past decade. The introduction of dynamics into DFT‐D calculations is a target, especially for the field of molecular NMR crystallography. Four ¹³C ss‐NMR calibration compounds are investigated by single‐crystal X‐ray diffraction, molecular dynamics and DFT‐D calculations. The crystal structure of 3‐methylglutaric acid is reported. The rotator phases of adamantane and hexamethylbenzene at room temperature are successfully reproduced in the molecular dynamics simulations. The calculated ¹³C chemical shifts of these compounds are in excellent agreement with experiment, with a root‐mean‐square deviation of 2.0 ppm. It is confirmed that a combination of classical molecular dynamics and DFT‐D chemical shift calculation improves the accuracy of calculated chemical shifts.     

Substitution effects in the 15N NMR chemical shifts of heterocyclic azines evaluated at the GIAO‐DFT level

A systematic study of the accuracy factors for the computation of ¹⁵N NMR chemical shifts in comparison with available experiment in the series of 72 diverse heterocyclic azines substituted with a classical series of substituents (CH₃, F, Cl, Br, NH₂, OCH₃, SCH₃, COCH₃, CONH₂, COOH, and CN) providing marked electronic σ‐ and π‐electronic effects and strongly affecting ¹⁵N NMR chemical shifts is performed. The best computational scheme for heterocyclic azines at the DFT level was found to be KT3/pcS‐3//pc‐2 (IEF‐PCM). A vast amount of unknown ¹⁵N NMR chemical shifts was predicted using the best computational protocol for substituted heterocyclic azines, especially for trizine, tetrazine, and pentazine where experimental ¹⁵N NMR chemical shifts are almost totally unknown throughout the series. It was found that substitution effects in the classical series of substituents providing typical σ‐ and π‐electronic effects followed the expected trends, as derived from the correlations of experimental and calculated ¹⁵N NMR chemical shifts with Swain–Lupton's F and R constants.     

Structure-based predictions of H NMR chemical shifts of sesquiterpene lactones using neural networks

In this work the prediction of ¹H NMR chemical shifts of CH_n protons of sesquiterpene lactones by means of neural networks is described. This method is based on the incorporation of experimental chemical shifts of protons of sesquiterpene lactones as additional memory of an associative neural network system previously trained with chemical shifts of other organic compounds. One advantage of this method is its ability to distinguish between CH₂ diastereotopic protons belonging to rigid substructures since stereochemistry is considered. This is achieved via the automatic conversion of the 2D structure diagram into a 3D molecular structure. The predicted ¹H NMR chemical shifts of the sesquiterpene lactones showed a high level of accuracy. This is the first report on a fully automatic proton assignment of structures of sesquiterpene lactones of an accuracy that allows its use in structure elucidation.     

Analyzing Discrepancies in Chemical-Shift Predictions of Solid Pyridinium Fumarates

Highly accurate chemical-shift predictions in molecular solids are behind the success and rapid development of NMR crystallography. However, unusually large errors of predicted hydrogen and carbon chemical shifts are sometimes reported. An understanding of these deviations is crucial for the reliability of NMR crystallography. Here, recently reported large deviations of predicted hydrogen and carbon chemical shifts of a series of solid pyridinium fumarates are thoroughly analyzed. The influence of the geometry optimization protocol and of the computational level of NMR calculations on the accuracy of predicted chemical shifts is investigated. Periodic calculations with GGA, meta-GGA and hybrid functionals are employed. Furthermore, molecular corrections at the coupled-cluster singles-and-doubles (CCSD) level are calculated. The effect of nuclear delocalization on the structure and NMR shielding is also investigated. The geometry optimization with a computationally demanding hybrid functional leads to a substantial improvement in proton chemical-shift predictions.     

Scaling factors for carbon NMR chemical shifts obtained from DFT B3LYP calculations

A linear scaling of the calculated chemical shifts is used in order to improve the accuracy of the DFT predicted ¹³C NMR chemical shifts. The widely applied method of GIAO B3LYP/6-311+G(2d,p) using the B3LYP/6-31G(d) optimized geometries is chosen, which allows cost-effective calculations of the ¹³C chemical shifts in the molecular systems with 100 and more atoms. A set of 27 ¹³C NMR chemical shifts determined experimentally for 22 simple molecules with various functional groups is used in order to determine scaling factors for reproducing experimentally measured values of ¹³C chemical shifts. The results show that the use of a simple relationship (δ_scalc = 0.95 δ_calc + 0.30, where δ_calc and δ_scalc are the calculated and the linearly scaled values of the ¹³C chemical shifts, respectively) allows to achieve a three-fold improvement in mean absolute deviations for 27 chemical shifts considered. To test the universal applicability of the scaling factors derived, we have used complex organic molecules such as taxol and a steroid to demonstrate the significantly improved accuracy of the DFT predicted chemical shifts. This approach also outperforms the recently recommended usage of the Hartree-Fock optimized geometries for the GIAO B3LYP/6-311+G(2d,p) calculations of the ¹³C chemical shifts.     

Breathing Effect via Solvent Inclusions on the Linker Rotational Dynamics of Functionalized MIL-53

The breathing effects of functionalized MIL-53-X (X=H, CH₃, NH₂, OH, and NO₂) induced by the inclusions of water, methanol, acetone, and N,N-dimethylformamide solvents were comprehensively investigated by solid-state NMR spectroscopy. 2D homo-nuclear correlation NMR provided direct experimental evidence for the host-guest interaction between the guest solvents and the MOF frameworks. The variations of the ¹H and ¹³C NMR chemical shifts in functionalized MIL-53 from the narrow pore phase transitions to large pore forms due to solvent inclusions were clearly identified. The influence of functionalized linkers and their host-guest interactions with the confined solvents on the rotational dynamics of the linkers was examined by separated-local-field MAS NMR experiments in conjunction with DFT theoretical calculations. It is found that the linker rotational dynamics of functionalized MIL-53 in narrow pore form is closely related to the computational rotational energy barrier. The BDC-NO₂ linker of activated MIL-53-NO₂ undergoes relatively faster rotation, whereas the BDC-NH₂ and BDC-OH linkers of activated MIL-53-NH₂ and MIL-53-OH exhibit relatively slower rotation. The host-guest interactions between confined solvents and MIL-53-NO₂, MIL-53-CH₃ would significantly induce an increase of the order parameters of unsubstituted carbon and reduce the rotational frequency of linkers. This study provides a spectroscopic approach for the investigation of linker rotation in functionalized MOFs at natural abundance with solvents inclusions.     

99Tc NMR as a promising technique for structural investigation of biomolecules: theoretical studies on the solvent and thermal effects of phenylbenzothiazole complex

The phenylbenzothiazole compounds show antitumor properties and are highly selective. In this paper, the ⁹⁹Tc chemical shifts based on the (^99mTc)(CO)₃(NNO) complex conjugated to the antitumor agent 2‐(4′‐aminophenyl)benzothiazole are reported. Thermal and solvent effects were studied computationally by quantum‐chemical methods, using the density functional theory (DFT) (DFT level BPW91/aug‐cc‐pVTZ for the Tc and BPW91/IGLO‐II for the other atoms) to compute the NMR parameters for the complex. We have calculated the ⁹⁹Tc NMR chemical shifts of the complex in gas phase and solution using different solvation models (polarizable continuum model and explicit solvation). To evaluate the thermal effect, molecular dynamics simulations were carried, using the atom‐centered density matrix propagation method at the DFT level (BP86/LanL2dz). The results highlight that the ⁹⁹Tc NMR spectroscopy can be a promising technique for structural investigation of biomolecules, at the molecular level, in different environments. Copyright © 2014 John Wiley & Sons, Ltd.     

Quantum‐chemical analyses of aromaticity,UV spectra,and NMR chemical shifts in plumbacyclopentadienylidenes stabilized by Lewis bases

We carried out a series of zeroth‐order regular approximation (ZORA)‐density functional theory (DFT) and ZORA‐time‐dependent (TD)‐DFT calculations for molecular geometries, NMR chemical shifts, nucleus‐independent chemical shifts (NICS), and electronic transition energies of plumbacyclopentadienylidenes stabilized by several Lewis bases, (Ph)₂(^tBuMe₂Si)₂C₄PbL₁L₂ (L₁, L₂ = tetrahydrofuran, Pyridine, N‐heterocyclic carbene), and their model molecules. We mainly discussed the Lewis‐base effect on the aromaticity of these complexes. The NICS was used to examine the aromaticity. The NICS values showed that the aromaticity of these complexes increases when the donation from the Lewis bases to Pb becomes large. This trend seems to be reasonable when the 4n‐Huckel rule is applied to the fractional π‐electron number. The calculated ¹³C‐ and ²⁰⁷Pb‐NMR chemical shifts and the calculated UV transition energies reasonably reproduced the experimental trends. We found a specific relationship between the ¹³C‐NMR chemical shifts and the transition energies. As we expected, the relativistic effect was essential to reproduce a trend not only in the ²⁰⁷Pb‐NMR chemical shifts and J[Pb‐C] but also in the ¹³C‐NMR chemical shifts of carbons adjacent to the lead atom. © 2014 Wiley Periodicals, Inc.     

Molecular recognition in molecular tweezers systems: quantum-chemical calculation of NMR chemical shifts

Quantum-chemical calculations for molecular tweezers systems are presented, where the focus is not only on the recognition process in the host-guest systems, but on the self aggregation of the tweezers host as well. Such intermolecular interactions influence the corresponding NMR spectra strongly by up to 6 ppm for proton chemical shifts, since ring-current effects are particularly important. The quantum-chemical results allow one to reliably assign the spectra and to gain information both on the structure and on the importance of intra- and intermolecular interactions. In addition, we study the accuracy of a variety of density functionals for describing the present host-guest systems, where we observe a considerable underestimation of ring-current effects on (1)H NMR chemical shifts at the density functional theory (DFT) level using smaller basis sets such as 6-31G**, so that larger bases like TZP are required. This stands in contrast to the behavior of the Hartree-Fock scheme, where small basis sets, such as 6-31G**, provide reliable (1)H NMR shieldings for molecular tweezers systems.     

Quantum-chemical calculations of NMR chemical shifts of organic molecules: VIII. Solvation effects on 15N NMR chemical shifts of nitrogen-containing heterocycles

Effect of solvation on the accuracy of DFT quantum-chemical calculations of ¹⁵N NMR chemical shifts of pyrrole, N-methylpyrrole, and pyridine was studied. The use of continuum model is sufficient to obtain consistent theoretical σ_N values for weakly polar aprotic solvents, whereas solvation effects in strongly polar and protic solvents should be taken into account in the explicit form.     

Prediction of the 1H and 13C NMR spectra of alpha-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.     

Experimental and Theoretical Evidence of Spin-Orbit Heavy Atom on the Light Atom 1H NMR Chemical Shifts Induced through H⋅⋅⋅I− Hydrogen Bond

Spin-orbit (SO) heavy-atom on the light-atom (SO-HALA) effect is the largest relativistic effect caused by a heavy atom on its light-atom neighbors, leading, for example, to unexpected NMR chemical shifts of ¹H, ¹³C, and ¹⁵N nuclei. In this study, a combined experimental and theoretical evidence for the SO-HALA effect transmitted through hydrogen bond is presented. Solid-state NMR data for a series of 4-dimethylaminopyridine salts containing I⁻, Br⁻ and Cl⁻ counter ions were obtained experimentally and by theoretical calculations. A comparison of the experimental chemical shifts with those calculated by a standard DFT methodology without the SO contribution to the chemical shifts revealed a remarkable error of the calculated proton chemical shift of a hydrogen atom that is in close contact with the iodide anion. The addition of the relativistic SO correction in the calculations significantly improves overall agreement with the experiment and confirms the propagation of the SO-HALA effect through hydrogen bonds.     

Effects of Quantum Nuclear Delocalisation on NMR Parameters from Path Integral Molecular Dynamics

The influence of nuclear delocalisation on NMR chemical shifts in molecular organic solids is explored using path integral molecular dynamics (PIMD) and density functional theory calculations of shielding tensors. Nuclear quantum effects are shown to explain previously observed systematic deviations in correlations between calculated and experimental chemical shifts, with particularly large PIMD‐induced changes (up to 23 ppm) observed for carbon atoms in methyl groups. 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. An approach based on convoluting calculated shielding or coupling surfaces with probability distributions of selected bond distances and valence angles obtained from PIMD simulations is used to calculate isotope effects.     

The Stereostructure of Porphyra‐334: An Experimental and Calculational NMR Investigation. Evidence for an Efficient ‘Proton Sponge’

The mycosporine‐like amino acid (MAA) porphyra‐334 ( 1 ) is subjected to extensive ¹H‐ and ¹³C‐NMR analysis as well as to density‐functional‐theory (DFT) calculations. All ¹H‐ and ¹³C‐NMR signals of 1 are assigned, as well as the resonances of prochiral proton pairs. This is achieved by 500‐MHz standard COSY, HMQC, and HMBC experiments, as well as by one‐dimensional (DPFGSE‐NOE) and two‐dimensional (NOESY) NOE experiments. Diffusion measurements (DOSY) confirm that 1 is monomeric in D₂O solution. DFT Calculations yield ¹³C‐NMR chemical shifts which are in good agreement for species 6 which is the imino N‐protonated form of 1 . An exceptionally high proton affinity of 265.7 kcal/mol is calculated for 1 , indicating that 1 may behave as a very powerful ‘proton sponge’ of comparable strength as synthetic systems studied so far. Predictions of ¹³C‐NMR chemical shifts by the ‘NMRPredict’ software are in agreement with the DFT data. The absolute configuration at the ring stereogenic center of 1 is concluded to be (S) from NOE data as well as from similarities with the absolute configuration (S) found in mycosporine‐glycine 16 . This supports the assumption that 1 is biochemically derived from 3,3‐O‐didehydroquinic acid ( 17 ). The data obtained question the results recently published by a different research group claiming that the configuration at the imino moiety of 1 is (Z), rather than (E) as established by the here presented study.     

Investigation of structure and dynamics in a photochromic molecular crystal by NMR crystallography

A photochromic anil, N-(3,5-di-t-butylsalicylidene)-4-amino-pyridine, has been studied by single-crystal X-ray diffraction, multinuclear magic-angle spinning NMR, and first-principles density functional theory (DFT) calculations. Interpretation of the solid-state NMR data on the basis of calculated chemical shifts confirms the structure is primarily composed of molecules in the ground-state enol tautomer, whereas thermally activated cis-keto and photoisomerised trans-keto states exist as low-level defects with populations that are too low to detect experimentally. Variable temperature ¹³C NMR data reveal evidence for solid-state dynamics, which is found to be associated with fast rotational motion of t-butyl groups and 180° flips of the pyridine ring, contrasting the time-averaged structure obtained by X-ray diffraction. Comparison of calculated chemical shifts for the full crystal structure and an isolated molecule also reveals evidence for an intermolecular hydrogen bond involving the pyridine ring and an adjacent imine carbon, which facilitates the flipping motion. The DFT calculations also reveal that the molecular conformation in the crystal structure is very close to the energetic minimum for an isolated molecule, indicating that the ring dynamics arise as a result of considerable steric freedom of the pyridine ring and which also allows the molecule to adopt a favourable conformation for photochromism.     

Understanding sterol-membrane interactions part I: Hartree-Fock versus DFT calculations of 13C and 1H NMR isotropic chemical shifts of sterols in solution and analysis of hydrogen-bonding effects

1H and 13C NMR chemical shifts are exquisitely sensitive probes of the local environment of the corresponding nuclei. Ultimately, direct determination of the chemical shifts of sterols in their membrane environment has the potential to reveal their molecular interactions and dynamics, in particular concerning the hydrogen-bonding partners of their OH groups. However, this strategy requires an accurate and efficient means to quantify the influence of the various interactions on chemical shielding. Herein the validity of Hartree-Fock and DFT calculations of the 13C and 1H NMR chemical shifts of cholesterol and ergosterol are compared with one another and with experimental chemical shifts measured in solution at 500 MHz. A computational strategy (definition of basis set, simpler molecular models for the sterols themselves and their molecular complexes) is proposed and compared with experimental data in solution. It is shown in particular that the effects of hydrogen bonding with various functional groups (water as a hydrogen-bond donor and acceptor, acetone) on NMR chemical shifts in CDCl3 solution can be accurately reproduced with this computational approach.     

NMR,MP2, and DFT study of thiophenoxyketenimines (o‐thio‐Schiff bases): Determination of the preferred form

Five new thiophenoxyketinimines have been synthesized. ¹H and ¹³C NMR spectra as well as deuterium isotope effects on ¹³C chemical shifts are determined, and spectra are assigned. DFT and MP2 calculations of both structures, chemical shifts, and isotope effects on chemical shifts are done. The combined analysis reveals that the compounds are primarily on a zwitterionic form with an NH⁺ and a S⁻ group and with a little of the neutral form mixed in. Very strong intramolecular hydrogen bonding is found and very high NH chemical shifts are observed. The theoretical calculations show that calculations at the MP2 level are best to obtain correct “C═S” chemical shifts.     

Etude de divers types de diastereotopie par RMN de 1H et de 13C dans les series du ferrocene et du titanocene

The influence of a chiral group on the ¹H and ¹³C NMR parameters of ferrocenes and titanocenes is studied. The difference of screening due to the diastereotopy of the cyclopentadienyl carbon nuclei is usually larger than the non-equivalence of corresponding proton chemical shifts. If the chiral group is the titanium atom itself a diastereotopy is also introduced into the cyclopentadienyl ring. Proton spectra obtained at 250 MHz, INDOR and off-resonance experiments, using chemical shift reagents permit a complete analysis of the proton and carbon spectra of some derivatives, especially ferrocene with a CH(CH₃)(CH₂CO bridge and titanocene with a CH(CH₃)CH₂CH₂ bridge. The result give information on the stereochemistry, and preferred conformations are identified.     

Benzene dilution shifts and steric interactions in N,N-dialkylamides

The NMR spectra of ten disubstituted amides have been recorded at 0°C in carbon tetrachloride and in benzene solutions. The benzene dilution shifts (ASIS) and proton spin decoupling were used to make the chemical shift assignments. A time-averaged solvent cluster model for the association between the amide and benzene is consistent with the observed ASIS values. The assignments for the N-methine and N-methyl resonance peaks in RCON[CH(CH₃)₂]₂, where R is methyl, ethyl or propyl are inverted from the assignments for N,N-diisopropylformamide (R ? H).     

Computing the (1)H NMR spectrum of a bulk ionic liquid from snapshots of car-parrinello molecular dynamics simulations.

We have investigated the performance of several computational protocols in predicting the NMR spectrum of a molecular ion in a complex liquid phase such as an ionic liquid. To do this, we computed the proton NMR chemical shifts of the 1-ethyl-3-methylimidazolium cation [emim](+) in [emim][Cl]. Environmental effects on the imidazolium ring proton chemical shifts are quite significant and must be taken into account explicitly. Calculations performed on the isolated imidazolium cation as well as on the [emim][Cl] ion pair grossly fail to reproduce the correct spacing between proton signals. In contrast, calculations performed on clusters extracted from the trajectory of a Car-Parrinello molecular dynamics simulation yield very good results.