Experimental Chemical Shift Data Research Articles

Correlated Anion Disorder in Heteroanionic Cubic TiOF2.

Resolving anion configurations in heteroanionic materials is crucial for understanding and controlling their properties. For anion-disordered oxyfluorides, conventional Bragg diffraction cannot fully resolve the anionic structure, necessitating alternative structure determination methods. We have investigated the anionic structure of anion-disordered cubic (ReO3-type) TiOF2 using X-ray pair distribution function (PDF), 19F MAS NMR analysis, density functional theory (DFT), cluster expansion modeling, and genetic-algorithm structure prediction. Our computational data predict short-range anion ordering in TiOF2, characterized by predominant cis-[O2F4] titanium coordination, resulting in correlated anion disorder at longer ranges. To validate our predictions, we generated partially disordered supercells using genetic-algorithm structure prediction and computed simulated X-ray PDF data and 19F MAS NMR spectra, which we compared directly to experimental data. To construct our simulated 19F NMR spectra, we derived new transformation functions for mapping calculated magnetic shieldings to predicted magnetic chemical shifts in titanium (oxy)fluorides, obtained by fitting DFT-calculated magnetic shieldings to previously published experimental chemical shift data for TiF4. We find good agreement between our simulated and experimental data, which supports our computationally predicted structural model and demonstrates the effectiveness of complementary experimental and computational techniques in resolving anionic structure in anion-disordered oxyfluorides. From additional DFT calculations, we predict that increasing anion disorder makes lithium intercalation more favorable by, on average, up to 2 eV, highlighting the significant effect of variations in short-range order on the intercalation properties of anion-disordered materials.

Characterization of stereoisomeric 5-(2-nitro-1-phenylethyl)furan-2(5H)-ones by computation of 1 H and 13 C NMR chemical shifts and electronic circular dichroism spectra.

In the present work, we describe the preparation of two diastereomers from the enantioselective Michael addition of furan-2(5H)-one to (E)-(2-nitrovinyl)benzene catalyzed by a dinuclear Zn-complex. The relative configurations of the diastereomeric products were assigned by comparing nuclear magnetic resonance (NMR) experimental chemical shift data with those computed by density functional theory (DFT) methods. Corrected mean absolute error (CMAE) and CP3 analyses were used to compare the data sets. The absolute configuration of each diastereomer was initially assigned by analysis of electronic circular dichroism (ECD) data, which was consistent with that of the known X-ray crystallographic structure of the product of a related reaction, namely, (R)-5-((R)-1-(4-chlorophenyl)-2-nitroethyl)furan-2(5H)-one.

Molecular Dynamics model of peptide-protein conjugation: case study of covalent complex between Sos1 peptide and N-terminal SH3 domain from Grb2

We have investigated covalent conjugation of VPPPVPPRRRX′ peptide (where X′ denotes Nε-chloroacetyl lysine) to N-terminal SH3 domain from adapter protein Grb2. Our experimental results confirmed that the peptide first binds to the SH3 domain noncovalently before establishing a covalent linkage through reaction of X′ with the target cysteine residue C32. We have also confirmed that this reaction involves a thiolate-anion form of C32 and follows the SN2 mechanism. For this system, we have developed a new MD-based protocol to model the formation of covalent conjugate. The simulation starts with the known coordinates of the noncovalent complex. When two reactive groups come into contact during the course of the simulation, the reaction is initiated. The reaction is modeled via gradual interpolation between the two sets of force field parameters that are representative of the noncovalent and covalent complexes. The simulation proceeds smoothly, with no appreciable perturbations to temperature, pressure or volume, and results in a high-quality MD model of the covalent complex. The validity of this model is confirmed using the experimental chemical shift data. The new MD-based approach offers a valuable tool to explore the mechanics of protein-peptide conjugation and build accurate models of covalent complexes.

GPU Accelerated Computation of Isotropic Chemical Shifts Offers New Dimension of Structure Refinement in Largescale Molecular Dynamics Simulation

Semi-empirical chemical shift prediction, where molecular coordinates and empirical data are reduced to backbone and sidechain chemical shifts through input to differentiable functions, offers a unique opportunity to validate and refine protein structure during largescale molecular dynamics (MD) simulation but poses the challenge of optimizing performance to levels comparable to modern GPU-enabled MD engines. The software PPM_One predicts backbone and sidechain chemical shifts with competitive accuracy to purely data-driven counterparts while obviating the need for deep network processing and homology assignment. To poise PPM_One for practical application in largescale biomolecular modeling, a newly optimized GPU-accelerated version of PPM_One was developed. Code refactoring and parallel GPU-processing through the directive-based OpenACC API provide a 67-fold speedup between unaccelerated and Nvidia V100 accelerated PPM_One test-cases, comparatively, in a system of 21 million protein atoms. The core functions that comprise the prediction model and compute perturbation due to Hydrogen bonding, magnetic anisotropy and ring currents were profiled at 271x, 322x, and 211x speedups, respectively. Remaining components of the predictive model saw similar individual speedups through profiling. Implementing the newly optimized functional core into NAMD is NMRForces, a global force module that enables users to compute backbone and sidechain chemical shifts at each timestep and force atoms along the prediction model's gradient with a magnitude proportional to deviance from experimental chemical shift data.

Microsecond simulations of mdm2 and its complex with p53 yield insight into force field accuracy and conformational dynamics.

The p53-MDM2 complex is both a major target for cancer drug development and a valuable model system for computational predictions of protein-ligand binding. To investigate the accuracy of molecular simulations of MDM2 and its complex with p53, we performed a number of long (200 ns to 1 µs) explicit-solvent simulations using a range of force fields. We systematically compared nine popular force fields (AMBER ff03, ff12sb, ff14sb, ff99sb, ff99sb-ildn, ff99sb-ildn-nmr, ff99sb-ildn-phi, CHARMM22*, and CHARMM36) against experimental chemical shift data, and found similarly accurate results, with microsecond simulations achieving better agreement compared to 200-ns trajectories. Although the experimentally determined apo structure has a closed binding cleft, simulations in all force fields suggest the apo state of MDM2 is highly flexible, and able to sample holo-like conformations, consistent with a conformational selection model. Initial structuring of the MDM2 lid region, known to competitively bind the binding cleft, is also observed in long simulations. Taken together, these results show molecular simulations can accurately sample conformations relevant for ligand binding. We expect this study to inform future computational work on folding and binding of MDM2 ligands.

Limiting Values of the 15N Chemical Shift of the Imidazole Ring of Histidine at High pH

Tautomeric identification by direct observation of (15)N chemical shifts of the imidazole ring of histidine (His) has become a common practice in NMR spectroscopy. However, such applications require knowledge of the "canonical" limiting values of the (15)N chemical shift of the imidazole ring of His in which each form of His, namely, the protonated (H(+)) and the tautomeric N(ε2)-H and N(δ1)-H forms, respectively, is present to the extent of 100%. So far, the adopted canonical limiting values of the (15)N chemical shift have been those available from model compounds. Whether these canonical values reflect those of the individual pure forms of His is investigated here by carrying out an analysis of the second-order shielding differences, ΔΔ = |Δ(ε) - Δ(δ) |, with Δ(ξ) (ξ = ε or δ) being the density functional theory (DFT)-computed average shielding differences between the two nitrogens of the imidazole ring of His in each pure tautomeric form. In the high-pH limit, the results indicate that (i) the ΔΔ values from the DFT-computed shielding, but not from the commonly used canonical limiting values, are in closer agreement with those obtained with experimental chemical shift data from model compounds in solution and solid-state NMR; and (ii) the commonly used canonical limiting values of the (15)N chemical shifts lead to an average tautomeric equilibrium constant that differs by a factor of ∼2.6 from the one computed by using DFT-based (15)N limiting values, raising concern about the practice of using canonical limiting (15)N values. This can be avoided by reporting tautomeric equilibrium constants computed by using only limiting (15)N values for the N(ε2)-H tautomer.

Direct Evidence for Methyl Group Coordination by Carbon-Oxygen Hydrogen Bonds in the Lysine Methyltransferase SET7/9

SET domain lysine methyltransferases (KMTs) are S-adenosylmethionine (AdoMet)-dependent enzymes that catalyze the site-specific methylation of lysyl residues in histone and non-histone proteins. Based on crystallographic and cofactor binding studies, carbon-oxygen (CH · · · O) hydrogen bonds have been proposed to coordinate the methyl groups of AdoMet and methyllysine within the SET domain active site. However, the presence of these hydrogen bonds has only been inferred due to the uncertainty of hydrogen atom positions in x-ray crystal structures. To experimentally resolve the positions of the methyl hydrogen atoms, we used NMR (1)H chemical shift coupled with quantum mechanics calculations to examine the interactions of the AdoMet methyl group in the active site of the human KMT SET7/9. Our results indicated that at least two of the three hydrogens in the AdoMet methyl group engage in CH · · · O hydrogen bonding. These findings represent direct, quantitative evidence of CH · · · O hydrogen bond formation in the SET domain active site and suggest a role for these interactions in catalysis. Furthermore, thermodynamic analysis of AdoMet binding indicated that these interactions are important for cofactor binding across SET domain enzymes.

De novo protein structure generation from incomplete chemical shift assignments

NMR chemical shifts provide important local structural information for proteins. Consistent structure generation from NMR chemical shift data has recently become feasible for proteins with sizes of up to 130 residues, and such structures are of a quality comparable to those obtained with the standard NMR protocol. This study investigates the influence of the completeness of chemical shift assignments on structures generated from chemical shifts. The Chemical-Shift-Rosetta (CS-Rosetta) protocol was used for de novo protein structure generation with various degrees of completeness of the chemical shift assignment, simulated by omission of entries in the experimental chemical shift data previously used for the initial demonstration of the CS-Rosetta approach. In addition, a new CS-Rosetta protocol is described that improves robustness of the method for proteins with missing or erroneous NMR chemical shift input data. This strategy, which uses traditional Rosetta for pre-filtering of the fragment selection process, is demonstrated for two paramagnetic proteins and also for two proteins with solid-state NMR chemical shift assignments.

How does β-cyclodextrin affect the aggregation of sodium perfluoroheptanoate in aqueous solution: a 19F NMR study

1H and 19F NMR spectra were recorded for D2O solutions of sodium perfluoroheptanoate with defined concentrations up to 200 mM, in the absence and presence of β-cyclodextrin (15 mM). Analysis of 1H chemical shift data obtained by the method of continuous variations (Job’s method) confirms the formation of 1:1 inclusion complexes for the perfluoroheptanote anion in β-cyclodextrin and leads to an estimate for the apparent inclusion constant (≥104 M−1). In addition, analysis of 19F chemical shift data based on two simplifying assumptions (monodisperse perfluoroheptanoate solutions below the critical micellar concentration (CMC), and a single self-associated state after the CMC) enables to interpret all the experimental chemical shift data and allows to determine CMC values for the absence and presence of β-cyclodextrin (104 and 116 mM). It is shown that the self-association of perfluoroheptanoate and its inclusion in β-cyclodextrin lead to shielding and deshielding of the fluorine atoms, respectively.

Spectral assignments for 1H,13C and 15N solution and solid‐state NMR spectra of s‐tetrazine and dihydro‐s‐tetrazine derivatives

Tetrazine-based organic species are interesting intermediates for organic synthesis and represent a source of new materials bearing specific properties with potential applications in biology and material science. 1H, 13C, 15N NMR measurements carried out in solution and in the solid-state have been used to characterize a series of 3,6-disubstituted 1,2,4,5-tetrazine/dihydrotetrazine new derivatives. Experimental results presented here provide data for the assignment of 15N chemical shifts including new organic small molecules; two polymers having the tetrazine ring in the main chain and several previously published compounds. We report apparently for the first time 15N experimental chemical shift data for tetrazine systems in the solid state.

A Computational and Experimental Study of the Structures and Raman and 77Se NMR Spectra of SeX3+ and SeX2 (X = Cl, Br, I): FT-Raman Spectrum of (SeI3)[AsF6

The ability of MP2, B3PW91 and PBE0 methods to produce reliable predictions in structural and spectroscopic properties of small selenium-halogen molecules and cations has been demonstrated by using 6-311G(d) and cc-pVTZ basis sets. Optimized structures and vibrational frequencies agree closely with the experimental information, where available. Raman intensities are also well reproduced at all levels of theory. Calculated GIAO isotropic shielding tensors yield a reasonable linear correlation with the experimental chemical shift data at each level of theory. The largest deviations between calculated and experimental chemical shifts are found for selenium-iodine species. The agreement between observed and calculated chemical shifts for selenium-iodine species can be improved by inclusion of relativistic effects using the ZORA method. The best results are achieved by adding spin-orbit correction terms from ZORA calculations to nonrelativistic GIAO isotropic shielding tensors. The calculated isotropic shielding tensors can be utilized in the spectroscopic assignment of the 77Se chemical shifts of novel selenium-halogen molecules and cations. The experimental FT-Raman spectra of (SeI3)[AsF6] in the solid state and in SO2(l) solution are also reported.

NMR chemical shift studies of ion association in aluminum halide-organic halide melts

The anion-cation interactions that take place in several room-temperature haloaluminate molten salts were investigated by using NMR spectroscopy. The systems studied were AlCl 3-1-(1-butyl)pyridinium chloride, AlCl 3-1-methyl-3-ethylimidazolium chloride and AlBr 3-1-methyl-3-ethylimidazolium bromide. The ion-ion associations in these systems were examined by studying the 1H and 13C chemical shifts of the nuclei on the organic cations as a function of melt composition. Investigations conducted in basic melts, i.e. those melts with an aluminium halide mole fraction less than 0.5 and where the anion-cation interactions have been found to be most extensive, suggested that, in contrast to previous work, ion-ion interactions in these solvents involve more than just simple ion-pair formation. A model is proposed which considers that each cation may interact with two or more anions and vice versa to form oligomeric chains of alternating cations and anions. The latter model is shown to provide a more realistic interpretation of the experimental chemical shift data than a model based on simple ion-pair formation.

Complete assignment of the 1H NMR spectrum of the aromatic residues of lysozyme.

Assignment of the nuclear magnetic resonance (NMR) spectrum of the 59 non-exchangeable protons of the 13 aromatic amino acid residues of lysozyme has been completed using a combination of selective spin decoupling and nuclear Overhauser experiments. The experimental chemical shift data were used to simulate the aromatic region of the NMR spectrum at 300 MHz and at 470 MHz. Excellent agreement with the experimental spectra was obtained and the simulations permitted more accurate chemical shift values and resonance linewidths to be obtained. The current set of assignments is compared with those of the assignments made previously. Evidence for the motional behaviour of the aromatic amino acid side chains is presented.

Bond-angle dependence of 13C NMR chemical shifts in some carbon sp 3 systems

Using the mathematical approach as proposed in a preceding study on 31P chemical shifts, it is found that the 13C chemical shift for molecules of the type X′CX 3, where X and X′ are different monofunctional substituents, can be related to the XCX bond angle and Z′, the number of surrounding electrons at the 13C nucleus. Taking this number to be equal to the carbon atomic number Z for the molecules under study, except those containing substituents such as Br, SCH 3, Cl, OH, OCH 3, and F for which Z′ = Z − 1, not only is a satisfactory agreement between XCX bond-angle values calculated from experimental chemical-shift data and observed values obtained, but also an expected feature concerning the dependence of the chemical shift on the effect of substituents, including their electronegativity as a major factor, appears to be discernible.

Theory of Localized Contributions to the Chemical Shift. Application to Fluorobenzenes

An expression for the magnetic shielding tensor is obtained by the use of single-determinant Hartree-Fock molecular wave functions. For nuclei of atoms in which the change in the second-order (paramagnetic) contribution is dominant, LCAO theory is employed to express the shielding in terms of localized bond parameters (ionic character, hybridization, and double bonding) and to compare it with the related treatments of the quadrupole coupling constant. Application of the formulation to the multifluorobenzenes provides an explanation of the available experimental chemical shift data and permits the prediction of shift values for other compounds. Of particular interest is the demonstration that double bonding in the C–F bond plays an important role in the fluorobenzenes. Also, the presence of an ``ortho'' effect in the shift is isolated by a comparison of experimental and theoretical results and tentatively explained in terms of charge repulsions.