Comparisons of NMR spectral quality and success in crystallization demonstrate that NMR and X-ray crystallography are complementary methods for small protein structure determination

X-ray crystallography and NMR spectroscopy provide the only sources of experimental data from which protein structures can be analyzed at high or even atomic resolution. The degree to which these methods complement each other as sources of structural knowledge is a matter of debate; it is often proposed that small proteins yielding high quality, readily analyzed NMR spectra are a subset of those that readily yield strongly diffracting crystals. We have examined the correlation between NMR spectral quality and success in structure determination by X-ray crystallography for 159 prokaryotic and eukaryotic proteins, prescreened to avoid proteins providing polydisperse and/or aggregated samples. This study demonstrates that, across this protein sample set, the quality of a protein's [15N-1H]-heteronuclear correlation (HSQC) spectrum recorded under conditions generally suitable for 3D structure determination by NMR, a key predictor of the ability to determine a structure by NMR, is not correlated with successful crystallization and structure determination by X-ray crystallography. These results, together with similar results of an independent study presented in the accompanying paper (Yee, et al., J. Am. Chem. Soc., accompanying paper), demonstrate that X-ray crystallography and NMR often provide complementary sources of structural data and that both methods are required in order to optimize success for as many targets as possible in large-scale structural proteomics efforts.     

Synthesis and structural characterization of new stiff rod oligomeric domains by X-ray crystallography and NMR

The monomers N,N'-dibenzylbenzene-1,4-diamine (1), N,N'-dibenzylnaphthalene-1,5-diamine (2), and N,N'-dibenzylanthracene-1,9-diamine (3) were reacted with phosgene in the presence of a base to produce the corresponding N,N'-dibenzyl-1,4-bis(chlorocarbonylamino)benzene (4), N,N'-dibenzyl-1,5-bis(chlorocarbonylamino)naphthalene (5), and N,N'-dibenzyl-9,10-bis(chlorocarbonylamino)anthracene (6). These monomers were used to create zigzag type stacks, in a stepwise fashion, of trimers and 9-mers of either 1,4-diureidobenzenes ((Phe)K(3) and (Phe)K(9)) or 1,5-diureidonaphthalenes ((Nap)K(3) and (Nap)K(9)). A byproduct in the formation of (Phe)K(9) was a cyclic hexamer (Phe)K(6). NMR gave evidence of the structure in solution while X-ray crystallographic information was obtained for 5, 6, (Nap)K(3), and the cyclic (Phe)K(6).     

Internally solvated cyclopentadienyllithium compounds: structural integrity of the Cp-Li+ moiety. NMR, dynamics, X-ray crystallography, and calculations

[Structure: see text]. N(CH2CH2OCH3)2 are as follows: T = CHCH(CH3)2, 6; T = (CH2)2, 10; T = (CH2)3, 14. The results of NOE NMR experiments for 6, 10, and 14 together with X-ray crystallography of 14 support internally coordinated monomeric structures for all three compounds. Models have been constructed for 6, 10, and 14 from modifications of an internally solvated allylic lithium compound at the B3LYP level of theory using basis set 6-311G*. The resulting structural features are very similar to those obtained from the NMR and crystallographic data. In addition, 13C NMR shifts obtained with the GIAO procedure using the results of the B3LYP/6-311G* calculations are closely similar to the experimental shifts, which validate B3LYP as a suitable model for these compounds. The Li+ centroid distance of ca. 1.9 A to 2.0 A obtained for 6, 10, and 14 is common to most crystallographic data for externally solvated Cp-Li+ compounds as well as one which incorporates a (CpLiCp)- triple ion. It is concluded that the ligand tether and the stereochemistry around Li+ accommodate to maintain the structural integrity of Cp-Li+. NMR and crystallography show 14 to be chiral. Carbon-13 NMR line shape changes are attributed to inversion via a lateral wobble mechanism with DeltaH++ = 6 kcal x mol(-1) and DeltaS++ = -2 eu. It is also shown that a 6,6-dimethylfulvene is deprotonated at methyl by LiN(CH2CH2OCH3)3 as well as by butyllithium in the presence of PMDTA producing isopropenyl Cp-Li+ compounds 24 and 25, respectively. NMR line shape changes of the sample containing 24 have been qualitatively interpreted to result from a combination of fast transfer of coordinated ligand between faces of the carbanion plane as well as a lithium-exchange process.     

Polymorphism for a novel phosphoramidate; NMR and X-ray crystallography

Abstract  

New phosphoramidates with formula 3-NC₅H₄C(O)NHP(O)XY (X=Y=Cl (1), X=Y=NH–C(CH₃)₃ (2a,2b), X=Y=N(C₄H₉)₂ (3), X=Cl, Y=N(C₂H₅)₂ (4) were synthesized and characterized by IR, ¹H-, ¹³C-, ³¹P-NMR spectroscopy and CHN elemental analysis. Surprisingly, the reaction of compound 2a with LaCl₃, 7H₂O in 3:1 M ratio leads to a polymorph of this compound (2b). NMR spectra indicate that ² J(PNH_amide) in 2b (7.0 Hz) is very much greater than in 2a (4.1 Hz), while δ(³¹P) values are identical for both of them. In IR spectra, υ(P=O) is weaker but υ(C=O) is stronger in 2a than in 2b. The structures of 2a, 2b were determined by X-ray crystallography. These compounds form centrosymmetric dimers via two intermolecular P=O……H–N hydrogen bonds. Strong intermolecular N–H…N, N–H…O and weak C–H…O hydrogen bonds lead to a three-dimensional polymeric cluster in the 2a while intermolecular strong N–H……N and weak C–H……O hydrogen bonds form a two-dimensional polymeric chain in 2b.     

Chiolite,a case study for combining NMR crystallography,diffraction and structural simulation

Chiolite has been selected as a test case for developing a general approach to solve inorganic structures from powders by combining NMR, modeling, and X-ray diffraction. The different steps of the strategy are successfully performed, building the candidate integrant units using NMR, simulating candidate crystal structures using the computational AASBU method, and checking the consistency of the candidate structures against the diffraction data analyzed with FOX computer program.     

Chloride binding by a polyimidazolium macrocycle detected via fluorescence,NMR, and X-ray crystallography

Herein, we describe a macrocyclic polyimidazolium receptor that is preorganized for the binding of anionic guests, and particularly chloride. Additionally, diphenylimidazolium units were incorporated into this structure to enhance photophysical properties that were exploited for signal transduction of binding. In subsequent fluorescence binding studies, this receptor was found to bind a range of halides as well as phosphate with high affinity (K_a=1.8×10⁴, and 1.5×10⁴ for phosphate and chloride, respectively) in a competitive solvent mixture (1:1 water/acetonitrile). Results under these conditions were fitted to 1:1 binding curves, and indicated modest selectivity of the host for phosphate and chloride over other halides. Binding studies were also performed using ¹H NMR spectroscopy, during which the imidazolium C–H signal was observed to shift downfield upon titration with anions. These experiments were run in less polar solvent (1:9 water/acetonitrile), and could not be fitted to a 1:1 binding curve, suggesting higher order aggregates in this environment. Binding was further probed in the solid state by obtaining an X-ray crystal structure of receptor–iodide complex. In the resulting structure, two iodides were found to bind through interactions with two polyimidazolium hydrogens each. These results show that the described macrocycle is effective for anion-binding in competitive solvent, with modest selectivity for chloride over other halides, and that the nature of the binding interactions varies depending upon the solvent environment.     

A structural investigation of organic battery anode materials by NMR crystallography

Conjugated alkali metal dicarboxylates have recently received attention for applications as organic anode materials in lithium- and sodium-ion batteries. In order to understand and optimise these materials, it is important to be able to characterise both the long-range and local aspects of the crystal structure, which may change during battery cycling. Furthermore, some materials can display polymorphism or hydration behaviour. NMR crystallography, which combines long-range crystallographic information from diffraction with local information from solid-state NMR via interpretation aided by DFT calculations, is one such approach, but this has not yet been widely applied to conjugated dicarboxylates. In this work, we evaluate the application of NMR crystallography for a set of model lithium and sodium dicarboxylate salts. We investigate the effect of different DFT geometry optimisation strategies and find that the calculated NMR parameters are not systematically affected by the choice of optimisation method, although the inclusion of dispersion correction schemes is important to accurately reproduce the experimental unit cell parameters. We also observe hydration behaviour for two of the sodium salts and provide insight into the structure of an as-yet uncharacterised structure of sodium naphthalenedicarboxylate. This highlights the importance of sample preparation and characterisation for organic sodium-ion battery anode materials in particular.     

Synthesis and characterization of two cyclic organosiloxanes by multinuclear NMR spectroscopy and X-ray crystallography

1,3-[2′,6′-Pyridinebis(methyleneoxy)]-1,3-bis(diphenyl)cyclodisiloxane (9) and 2,6-pyridinebis(1,1-diphenylethoxy)diphenylsilane (11) were obtained from 2,6-pyridinediol derivatives with dichlorodiphenylsilane. An N→Si interaction is present in 2,6-pyridinebis(1,1-diphenylethoxy)diphenylsilane, which also shows fluxional behavior. The activation energy of 13.2 kcal mol⁻¹ for 11 was obtained for the intramolecular exchange between the phenyl groups from a variable-temperature ¹H-NMR study. The compounds were characterized by ¹H-, ¹³C- and ²⁹Si-NMR and their structures were established by X-ray crystallographic studies.     

History of X-ray crystallography

A brief account is given of the history of X-ray crystallography from its beginning in 1912 to the present time. Particular emphasis is placed on the phase problem, the major obstacle in the path leading from the observed X-ray diffraction pattern to the desired crystal structure. The essential role which mathematics plays in resolving this problem is also stressed.     

A combined solid-state NMR and X-ray crystallography study of the bromide ion environments in triphenylphosphonium bromides

Multinuclear ((31)P and (79/81)Br), multifield (9.4, 11.75, and 21.1 T) solid-state nuclear magnetic resonance experiments are performed for seven phosphonium bromides bearing the triphenylphosphonium cation, a molecular scaffold found in many applications in chemistry. This is undertaken to fully characterise their bromine electric field gradient (EFG) tensors, as well as the chemical shift (CS) tensors of both the halogen and the phosphorus nuclei, providing a rare and novel insight into the local electronic environments surrounding them. New crystal structures, obtained from single-crystal X-ray diffraction, are reported for six compounds to aid in the interpretation of the NMR data. Among them is a new structure of BrPPh(4), because the previously reported one was inconsistent with our magnetic resonance data, thereby demonstrating how NMR data of non-standard nuclei can correct or improve X-ray diffraction data. Our results indicate that, despite sizable quadrupolar interactions, (79/81)Br magnetic resonance spectroscopy is a powerful characterisation tool that allows for the differentiation between chemically similar bromine sites, as shown through the range in the characteristic NMR parameters. (35/37)Cl solid-state NMR data, obtained for an analogous phosphonium chloride sample, provide insight into the relationship between unit cell volume, nuclear quadrupolar coupling constants, and Sternheimer antishielding factors. The experimental findings are complemented by gauge-including projector-augmented wave (GIPAW) DFT calculations, which substantiate our experimentally determined strong dependence of the largest component of the bromine CS tensor, δ(11), on the shortest Br-P distance in the crystal structure, a finding that has possible application in the field of NMR crystallography. This trend is explained in terms of Ramsey's theory on paramagnetic shielding. Overall, this work demonstrates how careful NMR studies of underexploited exotic nuclides, such as (79/81)Br, can afford insights into structure and bonding environments in the solid state.     

Advanced analytical tools in proteomics

Proteomics deals with the study of proteins, their structures, localizations, posttranslational modifications, functions and interactions with other proteins. The mapping of protein structure-function holds the key to a better understanding of cellular functions under both normal and disease states, which is critical for modern drug discovery. However, the study of human proteome presents scientists with a task much more daunting than the human genome project. In fact, the estimated >100,000 different proteins expressed from 30,000 to 40,000 human genes make it extremely challenging, if not impossible with existing protein analysis techniques, to map the entire cellular functions at the translational level. Consequently, there have been rapid advances in the techniques and methods capable of large-scale proteomic studies. Among them, the recently developed high-throughput screening methods have enabled scientists to analyze proteins quickly and efficiently at an organism-wide scale. Herein, we overview some of these emerging tools for high-throughput protein analysis. In particular, we focus on recent advances in the bioassay development, which has provided sensitive and selective tools for high-throughput identification and characterizations of enzymes. Finally, the recently developed bioimaging techniques to visualize and quantify proteins in living cells are also discussed.     

Preparation,X-ray crystallography,and thermolysis of phenylenediammonium dibromide salts

Phenylenediammonium dibromide (PDADBr) salts have been prepared and characterized by X-ray crystallography. The thermal decomposition of PDADBr has been studied by thermogravimetry (TG) and differential thermal analysis (DTA). Kinetic parameters have been evaluated using model fitting and isoconversional methods. The thermolytic pathways have also been suggested which involve proton transfer as a primary step to regenerate parent amine and HBr. Interaction between amine and HBr at higher temperature yields gaseous products.     

Synthesis, glycosidase activity and X-ray crystallography of 3-amino-sugars

The cleavage of two sugar epoxides, methyl 2,3-anhydro-alpha-D-mannopyranoside and 2,3-anhydro-alpha-D-allopyranoside, with amines is presented as a method for preparing a library of 3-amino-sugars (methyl 3-amino-3-deoxy-alpha-D-altropyranosides and methyl 3-amino-3-deoxy-alpha-D-glucopyranosides) as potential glycosidase inhibitors. Several of the altropyranosides were micromolar inhibitors of bovine liver beta-galactosidase and almond beta-glucosidase. X-ray crystal structures were determined for one of the methyl 3-amino-3-deoxy-alpha-D-altropyranosides, 4t, and one of the methyl 3-amino-3-deoxy-alpha-D-glucopyranosides, 6d.     

Synthesis, X-ray crystallography, and computational analysis of 1-azafenestranes

The tandem [4+2]/[3+2] cycloaddition of nitroalkenes has been employed in the synthesis of 1-azafenestranes, molecules of theoretical interest because of planarizing distortion of their central carbon atoms. The synthesis of c,c,c,c-[5.5.5.5]-1-azafenestrane was completed in good yield from a substituted nitrocyclopentene, and its borane adduct was analyzed through X-ray crystallography, which showed a moderate distortion from ideal tetrahedral geometry. The syntheses of two members of the [4.5.5.5] family of 1-azafenestranes are also reported, including one with a trans fusion at a bicyclic ring junction which brings about considerable planarization of one of the central angles (16.8 degrees deviation from tetrahedral geometry). While investigating the [4.5.5.5]-1-azafenestranes, a novel dyotropic rearrangement that converts nitroso acetals into tetracyclic aminals was discovered. Through conformational analysis, a means to prevent this molecular reorganization was formulated and realized experimentally with the use of a bulky vinyl ether in the key [4+2] cycloaddition reaction. Finally, DFT calculations on relative strain energy for the 1-azafenestranes, as well as their predicted central angles, are disclosed.     

X-ray and NMR crystallography in an enzyme active site: the indoline quinonoid intermediate in tryptophan synthase

Chemical-level details such as protonation and hybridization state are critical for understanding enzyme mechanism and function. Even at high resolution, these details are difficult to determine by X-ray crystallography alone. The chemical shift in NMR spectroscopy, however, is an extremely sensitive probe of the chemical environment, making solid-state NMR spectroscopy and X-ray crystallography a powerful combination for defining chemically detailed three-dimensional structures. Here we adopted this combined approach to determine the chemically rich crystal structure of the indoline quinonoid intermediate in the pyridoxal-5'-phosphate-dependent enzyme tryptophan synthase under conditions of active catalysis. Models of the active site were developed using a synergistic approach in which the structure of this reactive substrate analogue was optimized using ab initio computational chemistry in the presence of side-chain residues fixed at their crystallographically determined coordinates. Various models of charge and protonation state for the substrate and nearby catalytic residues could be uniquely distinguished by their calculated effects on the chemical shifts measured at specifically (13)C- and (15)N-labeled positions on the substrate. Our model suggests the importance of an equilibrium between tautomeric forms of the substrate, with the protonation state of the major isomer directing the next catalytic step.     

NMR crystallography of oxybuprocaine hydrochloride, Modification II degrees

The (13)C CPMAS spectrum is presented for the polymorph of oxybuprocaine hydrochloride which is stable at room temperature, i.e. Mod. II degrees . It shows crystallographic splittings arising from the fact that there are two molecules, with substantially different conformations, in the asymmetric unit. An INADEQUATE two-dimensional experiment was used to link signals for the same independent molecule. The chemical shifts are discussed in relation to the crystal structure. Of the four ethyl groups attached to NH(+) nitrogens, one gives rise to unusually low chemical shifts, very different from those of the other three ethyl groups. This is attributed empirically to gamma-gauche conformational effects, as is confirmed by shielding computations. These considerations allow (13)C signals to be assigned to specific carbons in the two crystallographically inequivalent molecules in the crystal structure. Indeed, information about the conformations is inherent in the NMR spectrum, which thus provides data of crystallographic significance. A (13)C/(1)H HETCOR experiment enabled resolution to be obtained in the (1)H dimension and allowed (1)H and (13)C signals for the same independent molecule to be linked.     

X-ray structural and13C NMR spectroscopic investigation of 4,7-diaminocoumarins

An x-ray structural study has been made of 7-diethylaminocoumarin and 4-morpholino-7-diethylaminocoumarin. A study has been made of the¹³C NMR spectra of these compounds and other 4,7-diaminocoumarins, in CDCl₃, and in acidic media. These studies have established that the site of first protonation is the nitrogen atom in position 7, and the site of the second protonation is the lactone oxygen atom. It is concluded that the 4-amino group is effectively conjugated with the carbonyl group in 4,7-diaminocoumarins.Translated from Izvestiya Akademii Nauk SSSR, Seriya Khimicheskaya, No. 4, pp. 802–810, April, 1991.