A solid state 13C NMR, crystallographic, and quantum chemical investigation of chemical shifts and hydrogen bonding in histidine dipeptides

We report the first solid-state NMR, crystallographic, and quantum chemical investigation of the origins of the 13C NMR chemical shifts of the imidazole group in histidine-containing dipeptides. The chemical shift ranges for Cgamma and Cdelta2 seen in eight crystalline dipeptides were very large (12.7-13.8 ppm); the shifts were highly correlated (R2= 0.90) and were dominated by ring tautomer effects and intermolecular interactions. A similar correlation was found in proteins, but only for buried residues. The imidazole 13C NMR chemical shifts were predicted with an overall rms error of 1.6-1.9 ppm over a 26 ppm range, by using quantum chemical methods. Incorporation of hydrogen bond partner molecules was found to be essential in order to reproduce the chemical shifts seen experimentally. Using AIM (atoms in molecules) theory we found that essentially all interactions were of a closed shell nature and the hydrogen bond critical point properties were highly correlated with the N...H...O (average R2= 0.93) and Nepsilon2...H...N (average R2= 0.98) hydrogen bond lengths. For Cepsilon1, the 13C chemical shifts were also highly correlated with each of these properties (at the Nepsilon2 site), indicating the dominance of intermolecular interactions for Cepsilon1. These results open up the way to analyzing 13C NMR chemical shifts, tautomer states (from Cdelta2, Cepsilon1 shifts), and hydrogen bond properties (from Cepsilon1 shifts) of histidine residue in proteins and should be applicable to imidazole-containing drug molecules bound to proteins, as well.     

Quantifying weak hydrogen bonding in uracil and 4-cyano-4'-ethynylbiphenyl: a combined computational and experimental investigation of NMR chemical shifts in the solid state

Weak hydrogen bonding in uracil and 4-cyano-4'-ethynylbiphenyl, for which single-crystal diffraction structures reveal close CH...O=C and C[triple bond]CH...N[triple bond]C distances, is investigated in a study that combines the experimental determination of 1H, 13C, and 15N chemical shifts by magic-angle spinning (MAS) solid-state NMR with first-principles calculations using plane-wave basis sets. An optimized synthetic route, including the isolation and characterization of intermediates, to 4-cyano-4'-ethynylbiphenyl at natural abundance and with 13C[triple bond]13CH and 15N[triple bond]C labeling is described. The difference in chemical shifts calculated, on the one hand, for the full crystal structure and, on the other hand, for an isolated molecule depends on both intermolecular hydrogen bonding interactions and aromatic ring current effects. In this study, the two effects are separated computationally by, first, determining the difference in chemical shift between that calculated for a plane (uracil) or an isolated chain (4-cyano-4'-ethynylbiphenyl) and that calculated for an isolated molecule and by, second, calculating intraplane or intrachain nucleus-independent chemical shifts that quantify the ring current effects caused by neighboring molecules. For uracil, isolated molecule to plane changes in the 1H chemical shift of 2.0 and 2.2 ppm are determined for the CH protons involved in CH...O weak hydrogen bonding; this compares to changes of 5.1 and 5.4 ppm for the NH protons involved in conventional NH...O hydrogen bonding. A comparison of CH bond lengths for geometrically relaxed uracil molecules in the crystal structure and for geometrically relaxed isolated molecules reveals differences of no more than 0.002 A, which corresponds to changes in the calculated 1H chemical shifts of at most 0.1 ppm. For the C[triple bond]CH...N[triple bond]C weak hydrogen bonds in 4-cyano-4'-ethynylbiphenyl, the calculated molecule to chain changes are of similar magnitude but opposite sign for the donor 13C and acceptor 15N nuclei. In uracil and 4-cyano-4'-ethynylbiphenyl, the CH hydrogen-bonding donors are sp2 and sp hybridized, respectively; a comparison of the calculated changes in 1H chemical shift with those for the sp3 hybridized CH donors in maltose (Yates et al. J. Am. Chem. Soc. 2005, 127, 10216) reveals no marked dependence on hybridization for weak hydrogen-bonding strength.     

High-resolution solid-state 2H NMR spectroscopy of polymorphs of glycine

High-resolution solid-state (2)H MAS NMR studies of the α and γ polymorphs of fully deuterated glycine (glycine-d(5)) are reported. Analysis of spinning sideband patterns is used to determine the (2)H quadrupole interaction parameters, and is shown to yield good agreement with the corresponding parameters determined from single-crystal (2)H NMR measurements (the maximum deviation in quadrupole coupling constants determined from these two approaches is only 1%). From analysis of simulated (2)H MAS NMR sideband patterns as a function of reorientational jump frequency (κ) for the -N(+)D(3) group in glycine-d(5), the experimentally observed differences in the (2)H MAS NMR spectrum for the -N(+)D(3) deutrons in the α and γ polymorphs is attributed to differences in the rate of reorientation of the -N(+)D(3) group. These simulations show severe broadening of the (2)H MAS NMR signal in the intermediate motion regime, suggesting that deuterons undergoing reorientational motions at rates in the range κ ≈ 10(4)-10(6) s(-1) are likely to be undetectable in (2)H MAS NMR measurements for materials with natural isotopic abundances. The (1)H NMR chemical shifts for the α and γ polymorphs of glycine have been determined from the (2)H MAS NMR results, taking into account the known second-order shift. Further quantum mechanical calculations of (2)H quadrupole interaction parameters and (1)H chemical shifts reveal the structural dependence of these parameters in the two polymorphs and suggest that the existence of two short intermolecular C-H···O contacts for one of the H atoms of the >CH(2) group in the α polymorph have a significant influence on the (2)H quadrupole coupling and (1)H chemical shift for this site.     

Stereoelectronic effects on 1H nuclear magnetic resonance chemical shifts in methoxybenzenes

Investigation of all O-methyl ethers of 1,2,3-benzenetriol and 4-methyl-1,2,3-benzenetriol (3-16) by 1H NMR spectroscopy and density-functional calculations disclosed practically useful conformational effects on 1H NMR chemical shifts in the aromatic ring. While the conversion of phenol (2) to anisole (1) causes only small positive changes of 1H NMR chemical shifts (Delta delta < 0.08 ppm) that decrease in the order Hortho > Hmeta > Hpara, the experimental O-methylation induced shifts in ortho-disubstituted phenols are largest for Hpara, Delta delta equals; 0.19 +/- 0.02 ppm (n = 11). The differences are due to different conformational behavior of the OH and OCH3 groups; while the ortho-disubstituted OH group remains planar in polyphenols due to hydrogen bonding and conjugative stabilization, the steric congestion in ortho-disubstituted anisoles outweighs the conjugative effects and forces the Ar-OCH3 torsion out of the ring plane, resulting in large stereoelectronic effects on the chemical shift of Hpara. Conformational searches and geometry optimizations for 3-16 at the B3LYP/6-31G** level, followed by B3LYP/6-311++G(2d,2p) calculations for all low-energy conformers, gave excellent correlation between computed and observed 1H NMR chemical shifts, including agreement between computed and observed chemical shift changes caused by O-methylation. The observed regularities can aid structure elucidation of partly O-methylated polyphenols, including many natural products and drugs, and are useful in connection with chemical shift predictions by desktop computer programs.     

The aromaticity/antiaromaticity continuum. 1. Comparison of the aromaticity of the dianion and the antiaromaticity of the dication of tetrabenzo[5.5]fulvalene via magnetic measures

The aromaticity of the dianion (2) and the antiaromaticity of the dication (3) of tetrabenzo[5.5]fulvalene have been evaluated through magnetic criteria, (1)H NMR shifts, nucleus-independent chemical shifts, NICS, and magnetic susceptibility exaltation, Lambda. The sum of the NICS values, using the GIAO (gauge-independent atomic orbital) method, for 2 is -35.2; that of 3 is +38.2, indicating the aromaticity of 2 and the antiaromaticity of 3. Calculation of magnetic susceptibility exaltation using the CSGT (continuous set of gauge transformations) method gives a similar result, with Lambda of -81.8 ppm cgs for 2 and 95.8 ppm cgs for 3. The general validity of these values is supported by excellent agreement between the NMR shifts calculated by the GIAO and CSGT methods with experimental shifts. Comparison of 1H NMR shifts with those of model compounds allows evaluation of the magnitude of the diatropic shift in 2 and paratropic shift in 3 and supports their assignment as aromatic/antiaromatic, respectively. The agreement between calculated and experimental 1H NMR shifts is excellent for 3 in the absence of counterions but much better for 2 when counterions are included. Inclusion of counterions in the evaluation of diatropic shift for 2 gave a smaller shift than in the absence of counterions, suggesting a decreased aromaticity. When counterions were included in the calculation of Lambda, the value was also decreased, suggesting a decreased aromaticity. This observation has important consequences in the use of experimental data for the evaluation of aromaticity, and presumably antiaromaticity, of anions since, in most cases, there will be close interaction with counterions.     

^1^5N标记邻位芳香羟肟配位体的核磁共振研究

利用稳定同位素的磁性和质量同位素效应已成为研究有机结构化学的重要手段。我们为研究部位芳香及其芝渡金属如Cu(Ⅱ),Ni(Ⅱ),Co(Ⅱ),Fe(Ⅱ)配合物的光     

Coupling of functional hydrogen bonds in pyridoxal-5'-phosphate-enzyme model systems observed by solid-state NMR spectroscopy

We present a novel series of hydrogen-bonded, polycrystalline 1:1 complexes of Schiff base models of the cofactor pyridoxal-5'-phosphate (PLP) with carboxylic acids that mimic the cofactor in a variety of enzyme active sites. These systems contain an intramolecular OHN hydrogen bond characterized by a fast proton tautomerism as well as a strong intermolecular OHN hydrogen bond between the pyridine ring of the cofactor and the carboxylic acid. In particular, the aldenamine and aldimine Schiff bases N-(pyridoxylidene)tolylamine and N-(pyridoxylidene)methylamine, as well as their adducts, were synthesized and studied using 15N CP and 1H NMR techniques under static and/or MAS conditions. The geometries of the hydrogen bonds were obtained from X-ray structures, 1H and 15N chemical shift correlations, secondary H/D isotope effects on the 15N chemical shifts, or directly by measuring the dipolar 2H-15N couplings of static samples of the deuterated compounds. An interesting coupling of the two "functional" OHN hydrogen bonds was observed. When the Schiff base nitrogen atoms of the adducts carry an aliphatic substituent such as in the internal and external aldimines of PLP in the enzymatic environment, protonation of the ring nitrogen shifts the proton in the intramolecular OHN hydrogen bond from the oxygen to the Schiff base nitrogen. This effect, which increases the positive charge on the nitrogen atom, has been discussed as a prerequisite for cofactor activity. This coupled proton transfer does not occur if the Schiff base nitrogen atom carries an aromatic substituent.     

Interpreting protein structural dynamics from NMR chemical shifts

In this investigation, semiempirical NMR chemical shift prediction methods are used to evaluate the dynamically averaged values of backbone chemical shifts obtained from unbiased molecular dynamics (MD) simulations of proteins. MD-averaged chemical shift predictions generally improve agreement with experimental values when compared to predictions made from static X-ray structures. Improved chemical shift predictions result from population-weighted sampling of multiple conformational states and from sampling smaller fluctuations within conformational basins. Improved chemical shift predictions also result from discrete changes to conformations observed in X-ray structures, which may result from crystal contacts, and are not always reflective of conformational dynamics in solution. Chemical shifts are sensitive reporters of fluctuations in backbone and side chain torsional angles, and averaged (1)H chemical shifts are particularly sensitive reporters of fluctuations in aromatic ring positions and geometries of hydrogen bonds. In addition, poor predictions of MD-averaged chemical shifts can identify spurious conformations and motions observed in MD simulations that may result from force field deficiencies or insufficient sampling and can also suggest subsets of conformational space that are more consistent with experimental data. These results suggest that the analysis of dynamically averaged NMR chemical shifts from MD simulations can serve as a powerful approach for characterizing protein motions in atomistic detail.     

A fast MAS 1H NMR study of amino acids and proteins

Fast sample spinning (up to 32 kHz) in tandem with delayed acquisition enabled resolved ¹H NMR spectra of solid amino acids to be recorded. The resulting spectra are, however, significantly dependent on sample crystallinity and on sample preparation conditions, e.g. sample drying. Sample heating leads to a marked increase in signal to noise ratio and enables groups with different dynamic properties to be identified. In addition, the observation of peak shifts as a function of heating allows the identification of hydrogen bonded sites. Spectral assignment of the ¹H MAS spectra is proposed for some examples based on relaxation properties, study of deuteriated samples and 2D NMR. The effects of molecular weight and sample complexity on the ¹H MAS spectra were investigated using tetraglycine, polyglycine and two proteins: a small protein (lysozyme) and a much larger protein (a cereal storage protein named high molecular weight subunit 1Dx5). Moderate spectral resolution was achieved for the peptides and lysozyme, but for 1Dx5, significant resolution enhancement was obtained enabling the identification of resonances in all regions of the spectra including the alpha region, the aromatic region and the NH backbone region.     

NMR hyperfine shifts in blue copper proteins: a quantum chemical investigation

We present the results of the first quantum chemical investigations of 1H NMR hyperfine shifts in the blue copper proteins (BCPs): amicyanin, azurin, pseudoazurin, plastocyanin, stellacyanin, and rusticyanin. We find that very large structural models that incorporate extensive hydrogen bond networks, as well as geometry optimization, are required to reproduce the experimental NMR hyperfine shift results, the best theory vs experiment predictions having R2 = 0.94, a slope = 1.01, and a SD = 40.5 ppm (or approximately 4.7% of the overall approximately 860 ppm shift range). We also find interesting correlations between the hyperfine shifts and the bond and ring critical point properties computed using atoms-in-molecules theory, in addition to finding that hyperfine shifts can be well-predicted by using an empirical model, based on the geometry-optimized structures, which in the future should be of use in structure refinement.     

Multinuclear magnetic resonance and theoretical calculations in the study of structure and tautomerism of some 2-amino-N'-(aryl)-benzamidines

1H, 13C and 15N NMR spectra of eight 2-amino-N'-(aryl)-benzamidines and of the parent compound were recorded, and unequivocal chemical shift assignments through the use of COSY, 1H-J resolved, HETCOR and COLOC sequences were performed. 1H and 13C chemical shifts for the nuclei of the benzamidine aromatic ring were not affected by the substituents present at N'-phenyl group, while the substituent effects in the chemical shifts of the same nuclei of N'-phenyl ring were very similar to the ones reported for the corresponding monosubstituted benzenes, indicating that there is no interaction between the two aromatic rings. 15N NMR spectra (DEPT sequence) show just two hydrogenated nitrogen atoms, which confirm that the amino form is the most stable tautomer, but the observation of a sharp signal and two broad signals (15N decoupled spectra), and the corresponding broad signal for the =C-NH(2) protons (in the 1H spectra), indicates the occurrence of tautomerism between the amino and imino forms, observable for some of the studied benzamidines. Theoretical calculations lead to the conclusion that these compounds occur mostly as the amino tautomer with Z configuration, which is stabilized by hydrogen bonding.     

1H NMR chemical shift calculations as a probe of supramolecular host-guest geometry

The self-assembled supramolecular host [Ga(4)L(6)](12-) (1; L = 1,5-bis[2,3-dihydroxybenzamido]naphthalene) can encapsulate cationic guest molecules within its hydrophobic cavity and catalyze the chemical transformations of bound guests. The cavity of host 1 is lined with aromatic naphthalene groups, which create a magnetically shielded interior environment, resulting in upfield shifted (1-3 ppm) NMR resonances for encapsulated guest molecules. Using gauge independent atomic orbital (GIAO) DFT computations, we show that (1)H NMR chemical shifts for guests encapsulated in 1 can be efficiently and accurately calculated and that valuable structural information is obtained by comparing calculated and experimental chemical shifts. The (1)H NMR chemical shift calculations are used to map the magnetic environment of the interior of 1, discriminate between different host-guest geometries, and explain the unexpected downfield chemical shift observed for a particular guest molecule interacting with host 1.     

氧氟沙星的核磁共振波谱性质研究

结合1H, 13C NMR, DEPT, COSY, HSQC, HMBC谱和碳氟偶合裂分行为, 对酸性及碱性溶液中氧氟沙星(Ofloxacin, OFL)的1H和13C谱分别进行归属, 研究了哌嗪环亚甲基构成的AA'BB'复杂自旋体系中各H的化学位移. 发现噁嗪环上的甲基处于直立键; 5H在酸性溶液中化学位移移向低场, 这可能与形成C—H…O弱氢键有关; 在碱性溶液中, OFL的羧基变为羧酸根, 造成羧基和羰基周围碳原子上π电子重新分布, 导致相应C的化学位移和碳氟偶合常数发生明显变化.     

Natural-abundance solid-state 2H NMR spectroscopy at high magnetic field

High-resolution solid-state (2)H NMR spectroscopy provides a method for measuring (1)H NMR chemical shifts in solids and is advantageous over the direct measurement of high-resolution solid-state (1)H NMR spectra, as it requires only the application of routine magic angle sample spinning (MAS) and routine (1)H decoupling methods, in contrast to the requirement for complex pulse sequences for homonuclear (1)H decoupling and ultrafast MAS in the case of high-resolution solid-state (1)H NMR. However, a significant obstacle to the routine application of high-resolution solid-state (2)H NMR is the very low natural abundance of (2)H, with the consequent problem of inherently low sensitivity. Here, we explore the feasibility of measuring (2)H MAS NMR spectra of various solids with natural isotopic abundances at high magnetic field (850 MHz), focusing on samples of amino acids, peptides, collagen, and various organic solids. The results show that high-resolution solid-state (2)H NMR can be used successfully to measure isotropic (1)H chemical shifts in favorable cases, particularly for mobile functional groups, such as methyl and -N(+)H(3) groups, and in some cases phenyl groups. Furthermore, we demonstrate that routine (2)H MAS NMR measurements can be exploited for assessing the relative dynamics of different functional groups in a molecule and for assessing whole-molecule motions in the solid state. The magnitude and field-dependence of second-order shifts due to the (2)H quadrupole interaction are also investigated, on the basis of analysis of simulated and experimental (1)H and (2)H MAS NMR spectra of fully deuterated and selectively deuterated samples of the α polymorph of glycine at two different magnetic field strengths.     

神东2-2煤镜质组大分子结构模型13C-NMR谱的构建与修正

利用浮沉离心法得到了神东原煤的镜质组（SDV）,并对其进行了固体¹3C-CP/MAS NMR测试和元素分析。由¹3C-NMR实验得到了SDV中碳原子的结构分布特征和12种结构参数。结果表明,在SDV的结构中芳香碳原子的存在形式主要是缩合程度为2的萘,其余则是以苯环和含杂原子的芳香环。利用结构参数和元素分析的结果构建了SDV的大分子结构模型, 并运用¹3C-NMR预测软件ACD/CNMR predictor计算了SDV大分子结构模型的¹3C 化学位移。根据计算结果对SDV的大分子结构模型进行了修正,获得了能和实验谱图吻合较好的大分子结构模型。     

2-Dimensional and computational analysis of the 1H NMR spectrum of the bis(2,2′-bipyridine)carbonatocobalt(III) ion†

The use of COSzY and NOESY ¹H NMR techniques allows for the assignment of ¹H NMR chemical shifts for the bis(2,2′-bipyridine)carbonatocobalt(III) ion. These assignments are further confirmed by DFT GIAO-NMR calculations using the model chemistry B3LYP/6-31G(d,p) and invoking the IEF-PCM representing acetone. These computations also allow for initial quantification of a cis influence on the chemical shift due to anisotropic ring currents and a much less pronounced trans influence on the chemical shift due to inductive effects. The computational model employed is also compared to previously accepted models for anisotropic effects.     

Solid‐state NMR characterization of oxygen sites in organically modified aluminosilicate xerogels

Solid‐state NMR characterization of hybrid aluminosilicate xerogels, by ¹⁷O magic angle spinning (MAS) and triple quantum magic angle spinning (MQMAS) techniques, evidences Si—O—Si and Si—O—Al oxygen sites, spectrally separated in MQMAS experiments. Inversion of the MQMAS spectra allows the measurement of quadrupolar parameters, isotropic chemical shifts, distribution of chemical shift and discussion of the mobility of the structural units. Copyright © 2003 John Wiley & Sons, Ltd.     

An investigation of weak CH...O hydrogen bonds in maltose anomers by a combination of calculation and experimental solid-state NMR spectroscopy

Two-dimensional (1)H-(13)C MAS-J-HMQC solid-state NMR spectra of the two anomeric forms of maltose at natural abundance are presented. The experimental (1)H chemical shifts of the CH and CH(2) protons are assigned using first-principles chemical shift calculations that employ a plane-wave pseudopotential approach. Further calculations show that the calculated change in the (1)H chemical shift when comparing the full crystal and an isolated molecule is a quantitative measure of intermolecular C-H...O weak hydrogen bonding. Notably, a clear correlation between a large chemical shift change (up to 2 ppm) and both a short H...O distance (<2.7 A) and a CHO bond angle greater than 130 degrees is observed, thus showing that directionality is important in C-H...O hydrogen bonding.     

Origins of linewidth in 1H magic-angle spinning NMR

A detailed study of the factors determining the linewidth (and hence resolution) in 1H solid-state magic-angle spinning NMR is described. Although it has been known from the early days of magic-angle spinning (MAS) that resolution of spectra from abundant nuclear spins, such as 1H, increases approximately linearly with increasing sample rotation rate, the difficulty of describing the dynamics of extended networks of coupled spins has made it difficult to predict a priori the resolution expected for a given sample. Using recently developed, highly efficient methods of numerical simulation, together with experimental measurements on a variety of test systems, we propose a comprehensive picture of 1H resolution under MAS. The "homogeneous" component of the linewidth is shown to depend primarily on the ratio between an effective local coupling strength and the spin rate, modified by geometrical factors which loosely correspond to the "dimensionality" of the coupling network. The remaining "inhomogeneous" component of the natural linewidth is confirmed to have the same properties as in dilute-spin NMR. Variations in the NMR frequency due to chemical shift effects are shown to have minimal impact on 1H resolution. The implications of these results for solid-state NMR experiments involving 1H and other abundant-spin nuclei are discussed.     

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.