Experimental and theoretical investigation of the 13C and 15N chemical shift tensors in melanostatin-exploring the chemical shift tensor as a structural probe

The determination of backbone conformations in powdered peptides using 13C and 15N shift tensor information is explored. The 13C and 15N principal shift values in natural abundance 13C and 15N melanostatin (L-Pro-L-Leu-Gly amide) are measured using the FIREMAT technique. Furthermore, the orientation of the C-N bond in the 13C shift principal axis system for the backbone carbons is obtained from the presence of the 13C-14N dipolar coupling. The Ramachandran angles for the title compound are obtained from solid-state NMR data by comparing the experimentally determined shift tensor information to systematic theoretical shielding calculations on N-formyl-L-amino acid-amide models. The effects of geometry optimization and neglect of intermolecular interactions on the theoretical shielding values in the model compounds are investigated. The sets of NMR derived Ramachandran angles are assembled in a set of test structures that are compared to the available single-crystal X-ray structure. Shift tensor calculations on the test structures and the X-ray structure are used to further assess the importance of intermolecular interactions when the shift tensor is used as a structural probe in powdered peptides.     

Revisiting the calculation of (13)C chemical shift tensors in cadmium acetate dihydrate with EIM and EIM/cluster methods

The chemical shift tensors of the acetate anions in cadmium acetate dihydrate are calculated using a cluster approach, the embedded ion method (EIM), and a combination of the two in the EIM/cluster method. The results of these calculations are compared with those completed on the isolated acetate anion and show the need for the inclusion of intermolecular interactions. The RMS difference between experiment and theory improves from over 60 ppm when the calculation is completed on an isolated anion, to below 10 ppm when interactions to nearby atoms are included. The best cluster model includes three cadmium acetate dihydrate and gives an RMS result of 4.4 ppm. The EIM method, which uses point charges to account for the intermolecular effects, achieves an RMS of 7.7 ppm on individual anions alone. A combination of the two, the EIM/cluster method, shows that the only necessary atom to explicitly add is the nearest cadmium; this addition results in an RMS of 4.1 ppm. These results are also discussed in terms of the computational cost of the different calculations.     

Solid-state (13)C NMR chemical shift anisotropy tensors of polypeptides.

Carbon-13 chemical shift anisotropy (CSA) tensors for various carbon sites of polypeptides, and for carbon sites in alpha-helical and beta-sheet conformations of poly-L-alanine, and polyglycine, are presented. The carbonyl (13)C CSA tensors were determined from one-dimensional CPMAS spectra obtained at a slow spinning speed, whereas the CSA tensors of C(alpha) and other carbons in side chains of peptides were determined using 2D PASS experiments on powder samples. The results suggest that the spans of (13)Carbonyl CSA tensors of alanine and glycine residues in various peptides are similar, even though the magnitude of individual components of the CSA tensor and the isotropic chemical shift are different. In addition, the delta(22) element is the only component of the (13)Carbonyl CSA tensor that significantly depends on the CO.HN hydrogen-bond length. Solid-state NMR experimental results also suggest that (13)Carbonyl and (13)C(alpha) CSA tensors are similar for alpha-helical and beta-sheet conformations of poly-L-alanine, which is in agreement with the reported quantum chemical calculation studies and previous solid-state NMR experimental studies on other systems. On the other hand, the (13)C(alpha) CSA tensor of the first alanine residue is entirely different from that of the second or later alanine residues of the peptide. While no clear trends in terms of the span and the anisotropic parameter were predicted for (13)C(beta) CSA tensors of alanine, they mainly depend on the conformation and dynamics of the side chain as well as on the packing interactions in the solid state of peptides.     

Ab initio study of (13)C(alpha) chemical shift anisotropy tensors in peptides

This study reports magnitudes and the orientation of the (13)C(alpha) chemical shift anisotropy (CSA) tensors of peptides obtained using quantum chemical calculations. The dependency of the CSA tensor parameters on the energy optimization of hydrogen atom positions and hydrogen bonding effects and the use of zwitterionic peptides in the calculations are examined. Our results indicate that the energy optimization of the hydrogen atom positions in crystal structures is necessary to obtain accurate CSA tensors. The inclusion of intermolecular effects such as hydrogen bonding in the calculations provided better agreement between the calculated and experimental values; however, the use of zwitterionic peptides in calculations, with or without the inclusion of hydrogen bonding, did not improve the results. In addition, our calculated values are in good agreement with tensor values obtained from solid-state NMR experiments on glycine-containing tripeptides. In the case of peptides containing an aromatic residue, calculations on an isolated peptide yielded more accurate isotropic shift values than the calculations on extended structures of the peptide. The calculations also suggested that the presence of an aromatic ring in the extended crystal peptide structure influences the magnitude of the delta(22) which the present level of ab initio calculations are unable to reproduce.     

Determination of 13C chemical shift anisotropy tensors and molecular order of 4-hexyloxybenzoic acid

4-Alkoxy benzoic acids belong to an important class of thermotropic liquid crystals that are structurally simple and often used as starting materials for many novel mesogens. 4-Hexyloxybenzoic acid (HBA) is a homologue of the same series and exhibits an enantiotropic nematic phase. As this molecule could serve as an ideal model compound, high resolution (13)C NMR studies of HBA in solution, solid, and liquid crystalline phases have been undertaken. In the solid state, two-dimensional separation of undistorted powder patterns by effortless recoupling (2D SUPER) experiments have been carried out to estimate the magnitude of the components of the chemical shift anisotropy (CSA) tensor of all the aromatic carbons. These values have been used subsequently for calculating the orientational order parameters in the liquid crystalline phase. The CSA values computed by density functional theory (DFT) calculations showed good agreement with the 2D SUPER values. Additionally, (13)C-(1)H dipolar couplings in the nematic phase have been determined by separated local field (SLF) spectroscopy at various temperatures and were used for computing the order parameters, which compared well with those calculated by using the chemical shifts. It is anticipated that the CSA values determined for HBA would be useful for the assignment of carbon chemical shifts and for the study of order and dynamics of structurally similar novel mesogens in their nematic phases.     

Carbon-13 chemical shift tensors of disaccharides: measurement, computation and assignment

A recently developed chemical shift anisotropy amplification solid-state nuclear magnetic resonance (NMR) experiment is applied to the measurement of the chemical shift tensors in three disaccharides: sucrose, maltose, and trehalose. The measured tensor principal values are compared with those calculated from first principles using density functional theory within the planewave-pseudopotential approach. In addition, a method of assigning poorly dispersed NMR spectra, based on comparing experimental and calculated shift anisotropies as well as isotropic shifts, is demonstrated.     

13C and 15N spin–lattice relaxation and chemical shift studies of pentane-2,4-diamine

¹³C and ¹⁵N NMR chemical shift and spin–lattice relaxation data have been measured for both meso- and racemic-pentane-2,4-diamine. At high pH (12), relaxation is consistent with hindered rotation of the NH₂ group due, in part, to the formation of intramolecular hydrogen bonds. At low pH (2), relaxation is consistent with relatively unhindered rotation of the NH₃⁺ group. Rotational jump rates and barriers are reported, determined from the NT₁ ratios between ¹⁵N and ¹³C nuclei. In all cases, the ratios for the racemic diastereomer are higher than those of the meso compounds; this is interpreted in terms of conformationally more stable intramolecular hydrogen bond formation in the meso compound. Chemical shifts for the diastereomeric amines show that ¹⁵N shifts move downfield on protonation along with methyl and methylene carbons, while the methine carbon resonances move upfield.     

13C and 15N NMR chemical shifts of alkylsubstituted benzonitriles

¹³C NMR data of 14 and ¹⁵N NMR data of four alkylsubstituted benzonitriles are reported and discussed in relation to substituent effects and stereochemistry.     

Site-specific 13C chemical shift anisotropy measurements in a uniformly 15N,13C-labeled microcrystalline protein by 3D magic-angle spinning NMR spectroscopy

In this Communication, we introduce a 3D magic-angle spinning recoupling experiment that correlates chemical shift anisotropy (CSA) powder line shapes with two dimensions of site-resolved isotropic chemical shifts. The principal tensor elements from 127 ROCSA line shapes are reported, constraining 102 unique backbone and side-chain 13C sites in a microcrystalline protein (the 56 residue beta1 immunoglobulin binding domain of protein G). The tensor elements, determined by fitting to numerical simulations, agree well with quantum chemical predictions. The experiments, therefore, validate calculations of CSAs in a protein of known structure. The data will be useful for the development of side-chain CSA quantum calculations and will aid in the design and interpretation of solution NMR experiments that utilize CSA-dipole cross-correlation to constrain torsion angles or to enhance resolution and sensitivity (such as in TROSY). Furthermore, the methodology described here will enable databases of CSA data to be generated with higher efficiency, for purposes of direct protein structure refinement.     

Orientation of amide-nitrogen-15 chemical shift tensors in peptides: a quantum chemical study.

Knowledge of the orientation of the nitrogen-15 chemical shift anisotropy (CSA) tensor is critical for a variety of experiments that provide information on protein structure and dynamics in the solid and solution states. Unfortunately, the methods available for determining the orientation of the CSA tensor experimentally have inherent limitations. Rotation studies of a single crystal provide complete information but are tedious and limited in applicability. Solid-state NMR studies on powder samples can be applied to a greater range of samples but suffer from ambiguities in the results obtained. Density functional gauge-including-atomic-orbitals (GIAO) calculations of the orientations of (15)N CSA tensors in peptides are presented here as an independent source of confirmation for these studies. A comparison of the calculated (15)N CSA orientations with the available experimental values from single-crystal and powder studies shows excellent agreement after a partial, constrained optimization of some of the crystal structures used in the calculation. The results from this study suggest that the orientation as well as the magnitudes of (15)N CSA tensors may vary from molecule to molecule. The calculated alpha(N) angle varies from 0 degrees to 24 degrees with the majority in the 10 degrees to 20 degrees range and the beta(N) angle varies from 17 degrees to 24 degrees in good agreement with most of the solid-state NMR experimental results. Hydrogen bonding is shown to have negligible effect on the orientation of (15)N CSA tensor in accordance with recent theoretical predictions. Furthermore, it is demonstrated that the orientation of the (15)N CSA can be calculated accurately with much smaller basis sets than is needed to calculate the chemical shift, suggesting that the routine application of ab initio calculations to the determination of (15)N CSA tensor orientations in large biomolecules might be possible.     

Multinuclear (13C, 15N) NMR study of polyethyleneimine-based polymers

Representative polyethyleneimine-based polymers have been studied by ¹³C- and ¹⁵N-nuclear magnetic resonance spectroscopy and an extensive set of chemical shift assignments has been proposed for the complex spectra obtained. The samples in question represent a complex mixture of both protonated and nonprotonated primary, secondary, and tertiary as well as quaternary monomeric units.     

Acetylenic carbon-13 chemical shift tensors for diphenylacetylene and (eta2-Diphenylacetylene)Pt(PPh3)2: a solid-state NMR and theoretical study

The structure of (eta2-diphenylacetylene)Pt(PPh3) (2), as well as those of its dichloromethane and benzene solvates, is determined via X-ray crystallography. An investigation of the chemical shift (CS) tensors of the 13C-labeled carbons in Ph13C13CPh and (eta2-Ph13C13CPh)Pt(PPh3)2.(C6H6) is carried out via analysis of 13C NMR spectra from stationary solid samples. The principal components of the CS tensors as well as their orientations with respect to the 13C,13C internuclear vector are determined. DFT calculations of these CS tensors are in close agreement with the experimental values. For diphenylacetylene (tolane), the orientations and principal-component magnitudes of the alkynyl carbon CS tensors are comparable to those for other alkynyl carbons, although the CS tensor is not axially symmetric in this case. Coordination to platinum causes a change in the CS tensor orientation and a net increase in the isotropic chemical shift, resulting from a significant increase in two principal components (delta11 and delta33) while the third (delta22) decreases only slightly. The measured carbon CS tensors in the platinum complex bear a striking similarity to those of the alkenyl carbons in trans-Ph(H)C=C(H)Ph, and a short theoretical discussion of these observations is presented.     

Long-range 19F-15N distance measurements in highly-13C, 15N-enriched solid proteins with 19F-dephased REDOR shift (FRESH) spectroscopy

We present a novel rotational-echo double resonance (REDOR) method for detection of multiple (19)F-(15)N distances in solid proteins. The method is applicable to protein samples containing a single (19)F label, in addition to high levels of (13)C and (15)N enrichment. REDOR dephasing pulses are applied on the (19)F channel during an indirect constant time chemical shift evolution period on (15)N, and polarization is then transferred to (13)C for detection, with high-power (1)H decoupling throughout the sequence. This four-channel experiment reports site-specifically on (19)F-(15)N distances, with highly accurate determinations of approximately 5 A distances and detection of correlations arising from internuclear distances of at least 8 A. We demonstrate the method on the well-characterized 56-residue model protein GB1, where the sole tryptophan residue (Trp-43) has been labeled with 5-(19)F-Trp, in a bacterial growth medium also including (13)C-glucose and (15)N ammonium chloride. In GB1, 11 distances are determined, all agreeing within 20% of the X-ray structure distances. We envision the experiment will be utilized to measure quantitative long-range distances for protein structure determination.     

13C chemical shielding tensors in single crystals of tetraacetylethane

The orientations of the principal axes of the ¹³C chemical shielding tensor of the double-bonded C5 carbon nucleus in single crystals of 1,1,2,2-tetraacetylethane are essentially identical with those of an aromatic carbon nucleus. That observation and the similarities between the tensors of the carbonyl and the enolic carbon nuclei result from strong intramolecular hydrogen bonding.     

13C carbonyl chemical shielding tensors: Comparing SCF,MBPT (2), and DFT predictions to experiment

In this work, we calculate the ¹³C nuclear magnetic resonance chemical shielding tensors for 18 carbonyl-containing compounds. The many-body perturbation theory (MBPT), self-consistent field (SCF), and density functional theory (DFT) formalisms were used with gauge including atomic orbitals (GIAO) to calculate the shielding tensors. Our data suggest that shielding tensors can be efficiently estimated by performing one MBPT(2) correlated calculation (e.g., at a reference geometry) and SCF-level calculations at other geometries and taking the SCF-to-correlated tensor element differences to be geometry independent. That is, the correlation contribution to the chemical shielding seems to be relatively constant over a considerable range of distortions. Treatment of correlation using DFT methods is shown to not be as systematically reliable as with MBPT(2). Data on 18 carbonyl compounds show that the single largest influence on the shielding tensor is the presence of nearby electron-withdrawing or electron-donating groups. Finally, although good agreement with powder or single-crystal experimental data is achieved for two or three tensor eigenvalues, systematic differences remain for one element; the origins of these differences are discussed. © 1997 John Wiley & Sons, Inc. Int J Quant Chem 63: 875–894, 1997     

Synthesis of 13C and 15N labelled (S)-Tryptophan

(R,S)-serine-1-¹³C was incubated in a culture of $\text{Escherichia}$$\text{coli}$ cells to produce (S)-trytophan-1-¹³C. Bromoacetyl bromide-2-¹³C was converted to bromoacetanilide and cyclization of the anilide, followed by reduction and dehydrogenation furnished indole-3-¹³C. Indole-¹⁵N was synthesized by known sequences. These ¹³C and ¹⁵N isotomers of indole were converted by commercially available, lyophilized $\text{E}$. $\text{coli}$ to furnish (S)-tryptophan-γ-¹³C and (S)-tryptophan-indole-¹⁵N, respectively.     

Solventless protocol for efficient bis-N-boc protection of adenosine, cytidine, and guanosine derivatives

A solvent-free reaction employing a simple low-energy ball mill apparatus converts the amino groups of adenosine, 2-deoxyadenosine, cytidine, 2-deoxycytidine, guanosine, and 2-deoxyguanosine as well as some of their ribosyl O-protected derivatives to the corresponding bis-N-Boc carbamates. In the case of guanosine compounds, the carbonyl group of the base moiety was also blocked as its O-Boc enol carbonate. A variation of this approach using transient in situ O-silylation permitted the preparation of bis-N-Boc nucleosides in which the sugar hydroxyls were unprotected. The ball mill reactions were rapid, convenient, and very high-yielding except in the case of the guanosine compounds. This highly efficient method protects the amino groups of these nucleosides with a base stable and acid labile group suitable for further synthetic manipulation.     

Theoretical 13C chemical shift, 14N, and 2H quadrupole coupling- constant studies of hydrogen bonding in L-alanylglycine dipeptide

(13)C chemical shieldings and (14)N and (2)H electric field gradient (EFG) tensors of L-alanylglycine (L-alagly) dipeptide were calculated at RHF/6-31 + + G** and B3LYP/6-31 + + G** levels of theory respectively. For these calculations a crystal structure of this dipeptide obtained from X-ray crystallography was used. Atomic coordinates of different clusters containing several L-alagly molecules were used as input files for calculations. These clusters consist of central and surrounding L-alagly molecules, the latter forming short, strong, hydrogen bonds with the central molecule. Since the calculations did not converge for these clusters, the surrounding L-alagly molecules were replaced by glycine molecules. In order to improve the accuracy of calculated chemical shifts and nuclear quadrupole coupling constants (NQCCs), different geometry-optimization strategies were applied for hydrogen nuclei. Agreement between calculated and experimental data confirms that our optimized coordinates for hydrogen nuclei are more accurate than those obtained by X-ray diffraction.     

NMR investigations on alanyl-[15% 13C, 95% 15N]-proline: 15N chemical shifts and 13C?15N coupling constants

The dipeptide alanylproline has been prepared with the proline residue both ¹³C (15%) and ¹⁵N (95%) enriched. ¹⁵N NMR spectra of alanylproline reveal signals for both possible conformations—cis and trans—of the dipeptide backbone in solution. Different pK values for both conformers are obtained from the pH dependence of the ¹⁵N chemical shifts using a least square programme based on the Henderson–Hasselbach equation. These different values are discussed in terms of interaction between the α-amino group and the carboxylate group and between the carboxylate oxygen and the carbonyl oxygen of the dipeptide via hydrogen bonding. Further evidence for these interactions is obtained from the pH dependence of the ratio of the ¹⁵N NMR signal intensities of the two conformers. One, two or three bonded ¹³C? ¹⁵N coupling constants measured in the ¹³C NMR high resolution spectra have different values in the cis and trans isomers of alanylproline and thus indicate different geometry in the pyrrolidine ring.