NMR chemical shifts of the rhodopsin chromophore in the dark state and in bathorhodopsin: a hybrid QM/MM molecular dynamics study

We investigate nuclear magnetic resonance (NMR) parameters of the rhodopsin chromophore in the dark state of the protein and in the early photointermediate bathorhodopsin via first-principles molecular dynamics simulations and NMR chemical shift calculations in a hybrid quantum/classical (QM/MM) framework. NMR parameters are particularly sensitive to structural properties and to the chemical environment, which allows us to address different questions about the retinal chromophore in situ. Our calculations show that both the 13C and the 1H NMR chemical shifts are rather insensitive to the protonation state of Glu181, an ionizable amino acid side chain located in the vicinity of the isomerizing 11-cis bond. Thus, other techniques should be better suited to establish its protonation state. The calculated chemical shifts for bathorhodopsin further support our previously published theoretical structure, which is in very good agreement with more recent X-ray data.     

Bulk chemical shifts in hydrogen-bonded systems from first-principles calculations and solid-state-NMR

We present an analysis of bulk (1)H NMR chemical shifts for a series of biochemically relevant molecular crystals in analogy to the well-known solvent NMR chemical shifts. The term bulk shifts denotes the change in NMR frequency of a gas-phase molecule when it undergoes crystallization. We compute NMR parameters from first-principles electronic structure calculations under full periodic boundary conditions and for isolated molecules and compare them to the corresponding experimental fast magic-angle spinning solid-state NMR spectra. The agreement between computed and experimental lines is generally very good. The main phenomena responsible for bulk shifts are packing effects (hydrogen bonding and pi-stacking) in the condensed phase. By using these NMR bulk shifts in well-ordered crystalline model systems composed of biologically relevant molecules, we can understand the individual spectroscopic signatures of packing effects. These local structural driving forces, hydrogen bonding, pi-stacking, and related phenomena, stand as a model for the forces that govern the assembly of much more complex supramolecular aggregates. We show to which accuracy condensed-phase ab initio calculations can predict structure and structure-property relationships for noncovalent interactions in complex supramolecular systems.     

Chemical shifts in nucleic acids studied by density functional theory calculations and comparison with experiment

NMR chemical shifts are highly sensitive probes of local molecular conformation and environment and form an important source of structural information. In this study, the relationship between the NMR chemical shifts of nucleic acids and the glycosidic torsion angle, χ, has been investigated for the two commonly occurring sugar conformations. We have calculated by means of DFT the chemical shifts of all atoms in the eight DNA and RNA mono-nucleosides as a function of these two variables. From the DFT calculations, structures and potential energy surfaces were determined by using constrained geometry optimizations at the BP86/TZ2P level of theory. The NMR parameters were subsequently calculated by single-point calculations at the SAOP/TZ2P level of theory. Comparison of the (1) H and (13) C?NMR shifts calculated for the mono-nucleosides with the shifts determined by NMR spectroscopy for nucleic acids demonstrates that the theoretical shifts are valuable for the characterization of nucleic acid conformation. For example, a clear distinction can be made between χ angles in the anti and syn domains. Furthermore, a quantitative determination of the χ angle in the syn domain is possible, in particular when (13) C and (1) H chemical shift data are combined. The approximate linear dependence of the C1' shift on the χ angle in the anti domain provides a good estimate of the angle in this region. It is also possible to derive the sugar conformation from the chemical shift information. The DFT calculations reported herein were performed on mono-nucleosides, but examples are also provided to estimate intramolecularly induced shifts as a result of hydrogen bonding, polarization effects, or ring-current effects.     

NMR chemical shifts as a tool to analyze first principles molecular dynamics simulations in condensed phases: the case of liquid water

We present (1)H NMR chemical shift calculations of liquid water based on first principles molecular dynamics simulations under periodic boundary conditions. We focus on the impact of computational parameters on the structural and spectroscopic data, which is an important question for understanding how sensitive the computed (1)H NMR resonances are upon variation of the simulation setup. In particular, we discuss the influence of the exchange-correlation functional and the size of the basis set, the choice for the fictitious electronic mass and the use of pseudopotentials for the nuclear magnetic resonance (NMR) calculation on one hand and the underlying Car-Parrinello-type molecular dynamics simulations on the other hand. Our findings show that the direct effect of these parameters on (1)H shifts is not big, whereas the indirect dependence via the structural data is more important. The (1)H NMR chemical shifts clearly reflect the induced structural changes, illustrating once again the sensitivity of (1)H NMR observables on small changes in the local chemical structure of complex hydrogen-bonded liquids.     

Thermal and solvent effects on the NMR and UV parameters of some bioreductive drugs

15N NMR chemical shifts and n-->pi* electronic transition energy for metronidazole (1) has been calculated and compared with experimental data. A detailed computational study of 1 is presented, with special attention to the performance of various theoretical methods for reproducing spectroscopic parameters in solution. The most sophisticated approach involves density functional based on the Car-Parrinello molecular dynamics simulations of 1 in aqueous solution (BP86 level) and averaging chemical shifts and deltaE(n-->pi*) over snapshots from the trajectory. In the NMR and UV calculations for these snapshots (performed at the B3LYP level), a small number of discrete water molecules are retained, and the remaining bulk solution effects are included via a polarizable continuum model (PCM). A good agreement with experiment is also obtained using static geometry optimization and NMR computation of pristine 1 employing a PCM approach. Further theoretical predictions are also reported for 17O NMR and deltaE(n-->pi*) of three hydroxycinnamic acid derivatives, which suggest that it is essential to incorporate the dynamics and solvent effects for NMR and UV calculations in the condensed phase.     

Platinum-modified adenines: unprecedented protonation behavior revealed by NMR spectroscopy and relativistic density-functional theory calculations

Two novel Pt(IV) complexes of aromatic cytokinins with possible antitumor properties were prepared by reaction of selected aminopurines with K(2)PtCl(6). The structures of both complexes, 9-[6-(benzylamino)purine] pentachloroplatinate (IV) and 9-[6-(furfurylamino)purine] pentachloroplatinate (IV), were characterized in detail by using two-dimensional NMR spectroscopy ((1)H, (13)C, (15)N, and (195)Pt) in solution and CP/MAS NMR techniques in the solid state. We report for the first time the X-ray structure of a nucleobase adenine derivative coordinated to Pt(IV) via the N9 atom. The protonation equilibria for the complexes in solution were characterized by using NMR spectroscopy (isotropic chemical shifts and indirect nuclear spin-spin coupling constants) and the structural conclusions drawn from the NMR analysis are supported by relativistic density-functional theory (DFT) calculations. Because of the presence of the Pt atom, hybrid GGA functionals and scalar-relativistic and spin-orbit corrections were employed for both the DFT calculations of the molecular structure and particularly for the NMR chemical shifts. In particular, the populations of the N7-protonated and neutral forms of the complexes in solution were characterized by correlating the experimental and the DFT-calculated NMR chemical shifts. In contrast to the chemical exchange process involving the N7-H group, the hydrogen atom at N3 was determined to be unexpectedly rigid, probably because of the presence of the stabilizing intramolecular interaction N3-H···Cl. The described methodology combining the NMR spectroscopy and relativistic DFT calculations can be employed for characterizing the tautomeric and protonation equilibria in a large family of transition-metal-modified purine bases.     

Towards Accurate Predictions of Proton NMR Spectroscopic Parameters in Molecular Solids

The factors contributing to the accuracy of quantum-chemical calculations for the prediction of proton NMR chemical shifts in molecular solids are systematically investigated. Proton chemical shifts of six solid amino acids with hydrogen atoms in various bonding environments (CH, CH₂, CH₃, OH, SH and NH₃) were determined experimentally using ultra-fast magic-angle spinning and proton-detected 2D NMR experiments. The standard DFT method commonly used for the calculations of NMR parameters of solids is shown to provide chemical shifts that deviate from experiment by up to 1.5 ppm. The effects of the computational level (hybrid DFT functional, coupled-cluster calculation, inclusion of relativistic spin-orbit coupling) are thoroughly discussed. The effect of molecular dynamics and nuclear quantum effects are investigated using path-integral molecular dynamics (PIMD) simulations. It is demonstrated that the accuracy of the calculated proton chemical shifts is significantly better when these effects are included in the calculations.     

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.     

Determining valine side-chain rotamer conformations in proteins from methyl 13C chemical shifts: application to the 360 kDa half-proteasome

A method is presented for determining Val side-chain χ(1) rotamer distributions in proteins based exclusively on measured (13)C(γ1) and (13)C(γ2) chemical shifts. The approach selects an ensemble of 20 χ(1) values, calculates average methyl (13)C(γ1,γ2) chemical shifts via theoretical quantum chemical calculations and maximizes the agreement with the experimentally measured shifts using a genetic algorithm. The methodology is validated with an application involving six proteins for which (13)C(γ) chemical shifts and three-bond methyl-backbone scalar couplings are available. The utility of the methodology is demonstrated with an application to the 360 kDa 'half-proteasome' where the χ(1) rotameric distributions of Val residues are calculated on the basis of chemical shifts. For the most part the χ(1) profiles so obtained compare very well with those generated from the high-resolution (2.3 ?) X-ray structure of the proteasome. Both NMR and X-ray distributions are cross-validated by comparing calculated (1)H-(13)C methyl residual dipolar couplings with measured values, and the level of agreement is at least as good for the NMR derived χ(1) values. Notably, as the resolution of the X-ray data improves (rotamer distributions from 3.4 and 2.3 ? X-ray structures are compared with the NMR data), the agreement with the NMR gets significantly better. This emphasizes the importance of NMR approaches for the study of high molecular weight complexes that can be recalcitrant to high resolution X-ray analysis.     

Conformation and configuration of tertiary amines via GIAO-derived (13)C NMR chemical shifts and a multiple independent variable regression analysis.

The (13)C chemical shifts of six tertiary amines of unambiguous conformational structure are compared to predicted (13)C NMR chemical shifts obtained via empirically scaled GIAO shieldings for geometries from MM3 molecular mechanics calculations. An average deviation, absolute value of Deltadelta(av), of 0.8 ppm and a maximum deviation, absolute value of Deltadelta(max), of 2.8 ppm between predicted and experimental (13)C shifts of the six tertiary amines of unambiguous structure are found. In several cases of tertiary amines subject to rapid exchange, where experimental (13)C shifts at room temperature are weighted averages of multiple conformers, a comparison of calculated (13)C shifts of all reasonable MM3 predicted conformers with experimental (13)C shifts via a multiple independent variable regression analysis provides an efficient method of determining the major and minor conformers. The examples presented are 2-methyl-2-azabicyclo[2.2.1]heptane and 1,6-diazabicyclo[4.3.1]decane, which each have two expected contributing structures, and 2-(diethylamino)propane and 1,8-diazabicyclo[6.3.1]dodecane, where ten and seven low-energy conformers, respectively, are predicted by MM3 calculations.     

Is NMR the tool to characterize the structure of C20 isomers?

We investigate the feasibility of using nuclear magnetic resonance (NMR) chemical shift calculations as a tool to provide structural information for C₂₀ fullerene type molecules. NMR chemical shifts are extremely sensitive to the local chemical environment of an atom, reflecting unambiguously its bond lengths and angles as well as its hybridization. Thus, they can distinguish between the different isomers that are candidates for the ground state of this molecule. We calculate the NMR shifts for several C₂₀ isomers and show that NMR constitutes a potential tool to discriminate and identify experimentally a particular C₂₀ molecular conformation, and also the level of theory which best describes the experimental structure.     

Stacking effect of polyfluorene on the chemical shift and electron transport

We investigate the structures, NMR chemical shifts, absorption spectra, frontier molecular orbitals, and transition density matrices of pi-stacked polyfluorenes by ab initio calculations. For F1-F4, we consider two different conformations, syn and anti. The simulated 1H NMR chemical shifts are in good agreement with the previous experiment, and the significantly upfielded chemical shifts explain that the fluorene moieties are stacked on each other. It is found that the relative stability for syn and anti conformers is almost equivalent in B3LYP calculations; however, the syn conformer becomes much more stable than the anti conformer in MP2 calculations, which is consistent with the experimental finding that only the syn conformers are relevant. The vertical detachment energy, which is linearly proportional to the ionization potential, shows the same size dependence as the previous experiment. The electron attachment energy decreases exponentially as the size increases, which implies that the electron transport would be possible even for long chains such as F3 and F4. This was evident from the frontier molecular orbitals (HOMO and LUMO). Also, it is found that the syn conformers are very favorable for electron transport through the pi-stacked fluorene moieties.     

Ab initio molecular dynamics-based assignment of the protonation state of pepstatin A/HIV-1 protease cleavage site

A recent 13C NMR experiment (Smith et al. Nature Struct. Biol. 1996, 3, 946-950) on the Asp 25-Asp25' dyad in pepstatin A/HIV-1 protease measured two separate resonance lines, which were interpreted as being a singly protonated dyad. We address this issue by performing ab initio molecular dynamics calculations on models for this site accompanied by calculations of 13C NMR chemical shifts and isotopic shifts. We find that already on the picosecond time-scale the model proposed by Smith et al. is not stable and evolves toward a different monoprotonated form whose NMR pattern differs from the experimental one. We suggest, instead, a different protonation state in which both aspartic groups are protonated. Despite the symmetric protonation state, the calculated 13C NMR properties are in good agreement with the experiment. We rationalize this result using a simple valence bond model, which explains the chemical inequality of the two C sites. The model calculations, together with our calculations on the complex, allow also the rationalization of 13C NMR properties on other HIV-1 PR/inhibitor complexes. Both putative binding of the substrate to the free enzyme, which has the dyad singly protonated (Piana, S.; Carloni, P. Proteins: Struct., Funct., Genet. 2000, 39, 26-36), and pepstatin A binding to the diprotonated form are consistent with the inverse solvent isotope effect on the onset of inhibition of pepsin by pepstatin and the kinetic iso-mechanism proposed for aspartic proteases (Cho, T.-K.; Rebholz, K.; Northrop, D.B. Biochemistry 1994, 33, 9637-9642).     

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.     

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.     

An NMR, IR and theoretical investigation of (1)H chemical shifts and hydrogen bonding in phenols

The change in (1)H NMR chemical shifts upon hydrogen bonding was investigated using both experimental and theoretical methods. The (1)H NMR spectra of a number of phenols were recorded in CDCl(3) and DMSO solvents. For phenol, 2- and 4-cyanophenol and 2-nitrophenol the OH chemical shifts were measured as a function of concentration in CDCl(3). The plots were all linear with concentration, the gradients varying from 0.940 (phenol) to 7.85 (4-cyanophenol) ppm/M because of competing inter- and intramolecular hydrogen bonding. Ab initio calculations of a model acetone/phenol system showed that the OH shielding was linear with the H...O=C distance (R) for R < 2.1 A with a shielding coefficient of - 7.8 ppm/A and proportional to cos(2)phi where phi is the H...O=C--C dihedral angle. Other geometrical parameters had little effect. It was also found that the nuclear shielding profile is unrelated to the hydrogen bonding energy profile. The dependence of the OH chemical shift on the pi density on the oxygen atom was determined as ca 40 ppm/pi electron. This factor is similar to that for NH but four times the value for sp(2) hybridized carbon atoms. The introduction of these effects into the CHARGE programme allowed the calculation of the (1)H chemical shifts of the compounds studied. The CHARGE calculations were compared with those from the ACD database and from GIAO calculations. The CHARGE calculations were more accurate than other calculations both when all the shifts were considered and also when the OH shifts were excluded. The calculations from the ACD and GIAO approaches were reasonable when the OH shifts were excluded but not as good when all the shifts were considered. The poor treatment of the OH shifts in the GIAO calculations is very likely due to the lack of explicit solvent effects in these calculations.     

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.     

Spatial structure and NMR spectra of strained [2.2.2]cyclophanes

The chemical shifts and coupling constants in the NMR spectra of the title compounds are influenced by their strain and the proximity of the aromatic rings. These parameters are studied by density functional theory (DFT) calculations for 1–4 and measured for 3 and 4. We find that, in spite of the strain, the calculations reproduce the experimental values satisfactorily. This finding is of special importance for novel hypothetical molecules like hexahydrosuperphane 5 for their future identification and in searches of hydrocarbons exhibiting unusual NMR parameters. Our results demonstrate the influence of strain on the parameters studied. Most proton and carbon chemical shifts for the molecules under study having nonplanar aromatic rings differ considerably from the corresponding values for the relatively unstrained trimethylbenzenes and ethylbenzene. In addition, the calculated values of the coupling constants through three bonds in most cases do not follow Karplus relation. Copyright © 2009 John Wiley & Sons, Ltd.     

NMR Crystallography Enhanced by Quantum Chemical Calculations and Liquid State NMR Spectroscopy for the Investigation of Se-NHC Adducts**

N-heterocyclic carbene ligands (NHC) are widely utilized in catalysis and material science. They are characterized by their steric and electronic properties. Steric properties are usually quantified on the basis of their static structure, which can be determined by X-ray diffraction. The electronic properties are estimated in the liquid state; for example, via the ⁷⁷Se liquid state NMR of Se-NHC adducts. We demonstrate that ⁷⁷Se NMR crystallography can contribute to the characterization of the structural and electronic properties of NHC in solid and liquid states. Selected Se-NHC adducts are investigated via ⁷⁷Se solid state NMR and X-ray crystallography, supported by quantum chemical calculations. This investigation reveals a correlation between the molecular structure of adducts and NMR parameters, including not only isotropic chemical shifts but also the other chemical shift tensor components. Afterwards, the liquid state ⁷⁷Se NMR data is presented and interpreted in terms of the quantum chemistry modelling. The discrepancy between the structural and electronic properties, and in particular the π-accepting abilities of adducts in the solid and liquid states is discussed. Finally, the ¹³C isotropic chemical shift from the liquid state NMR and the ¹³C tensor components are also discussed, and compared with their ⁷⁷Se counterparts. ⁷⁷Se NMR crystallography can deliver valuable information about NHC ligands, and together with liquid state ⁷⁷Se NMR can provide an in-depth outlook on the properties of NHC ligands.     

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.