NMR “Crystallography” for Uniformly (13C, 15N)‐Labeled Oriented Membrane Proteins

In oriented‐sample (OS) solid‐state NMR of membrane proteins, the angular‐dependent dipolar couplings and chemical shifts provide a direct input for structure calculations. However, so far only ¹H–¹⁵N dipolar couplings and ¹⁵N chemical shifts have been routinely assessed in oriented ¹⁵N‐labeled samples. The main obstacle for extending this technique to membrane proteins of arbitrary topology has remained in the lack of additional experimental restraints. We have developed a new experimental triple‐resonance NMR technique, which was applied to uniformly doubly (¹⁵N, ¹³C)‐labeled Pf1 coat protein in magnetically aligned DMPC/DHPC bicelles. The previously inaccessible ¹H_α–¹³C_α dipolar couplings have been measured, which make it possible to determine the torsion angles between the peptide planes without assuming α‐helical structure a priori. The fitting of three angular restraints per peptide plane and filtering by Rosetta scoring functions has yielded a consensus α‐helical transmembrane structure for Pf1 protein.     

Through‐space 19F–19F spin–spin coupling in ortho‐fluoro Z‐azobenzene

We report through‐space (TS) ¹⁹F–¹⁹F coupling for ortho‐fluoro‐substituted Z ‐azobenzenes. The magnitude of the TS‐coupling constant (^TSJ_FF) ranged from 2.2–5.9 Hz. Using empirical formulas reported in the literature, these coupling constants correspond to non‐bonded F–F distances (d_FF) of 3.0–3.5 Å. These non‐bonded distances are significantly smaller than those determined by X‐ray crystallography or density functional theory, which argues that simple models of ¹⁹F–¹⁹F TS spin–spin coupling solely based d_FF are not applicable. ¹H, ¹³C and ¹⁹F data are reported for both the E and Z isomers of ten fluorinated azobenzenes. Density functional theory [B3YLP/6‐311++G(d,p)] was used to calculate ¹⁹F chemical shifts, and the calculated values deviated 0.3–10.0 ppm compared with experimental values. Copyright © 2015 John Wiley & Sons, Ltd.     

Long‐range 19F–15N heteronuclear shift correlation: examination of J‐modulations associated with broad range accordion excitation

The first demonstrated example of ¹⁹F–¹⁵N long‐range heteronuclear shift correlation spectroscopy at natural abundance is reported. Because of the very large variation in the size of ²J(N,F) vs ³J(N,F) long‐range heteronuclear couplings, the utilization of one of the new accordion‐optimized long‐range heteronuclear shift correlations experiments is essential if all possible correlations are to be observed in a single experiment. A modified IMPEACH‐MBC pulse sequence was used in conjunction with an optimization range from 4 to 50 Hz to demonstrate the technique using a mixture of 2‐ and 3‐fluoropyridine, which had ²J(N,F) and ³J(N,F) long‐range couplings of ?52 and 3.6 Hz, respectively. Because of the size of the ²J(N,F) long‐range coupling constant, a J‐modulation of the long‐range correlation response is observed in the spectrum resulting in a ‘doublet’ in F₁ due to amplitude modulation. The size of the ‘doublet’ is shown to be a function of the parameter selection (t_1max,T_max,T_min and spectral width in F₁). This behavior is similar to F₁ ‘skew’ associated with long‐range correlation responses in ACCORD‐HMBC spectra which has been analyzed in detail previously. Copyright © 2002 John Wiley & Sons, Ltd.     

Interpreting 2hJ(F,N), 1hJ(H,N) and 1J(F,H) in the hydrogen‐bonded FH–collidine complex

Ab initio EOM‐CCSD calculations were performed to determine ¹⁹F,¹H, ¹⁹F,¹⁵N and ¹H,¹⁵N spin–spin coupling constants in model complexes FH–NH₃ and FH–pyridine as a function of the F—H and F—N distances. The absolute value of ¹J(F,H) decreases and that of ^1hJ(H,N) increases rapidly along the proton‐transfer coordinate, even in the region of the proton‐shared F—H—N hydrogen bond. In contrast, ^2hJ(F,N) remains essentially constant in this region. These results are consistent with the recently reported experimental NMR spectra of FH–collidine which show that ^1hJ(H,N) increases and ¹J(F,H) decreases, while ^2hJ(F,N) remains constant as the temperature of the solution decreases. They suggest that the FH–collidine complex is stabilized by a proton‐shared hydrogen bond over the range of experimental temperatures investigated, being on the traditional side of quasi‐symmetric at high temperatures, and on the ion‐pair side at low temperatures. Copyright © 2002 John Wiley & Sons, Ltd.     

Comparison of 1H–19F two‐dimensional NMR scalar coupling correlation pulse sequences

The effectiveness of hetero‐COSY, HETCOR, HMQC, and HSQC two‐dimensional NMR pulse sequences for detection of ¹⁹F–¹H correlations by scalar coupling was evaluated on monofluorinated and polyfluorinated test compounds. All four of these sequences were effective in observing ¹H–¹⁹F correlations, using either ¹⁹F or ¹H as the observe nucleus. All four sequences were amenable, to some degree, to adjustment to observe larger or smaller couplings preferentially. A 1/2J echo filter was effectively applied to remove artifacts from ²J_FF strong coupling. The HETCOR experiments afforded the best overall combination of sensitivity, resolution and selectivity for J_HF. Copyright © 2014 John Wiley & Sons, Ltd.     

Conformational dynamics of bis(BF2)‐2,2′‐bidipyrrins revealed by through‐space 13C?19F and 19F?19F couplings

The conformation of [bis‐(N,N′‐difluoroboryl)]‐3,3′‐diethyl‐4,4′,8,8′,9,9′,10,10′‐octamethyl‐2,2′‐bidipyrrin (1) in solution was studied by analyzing the ¹³C? ¹⁹F and ¹⁹F? ¹⁹F through‐space spin–spin couplings. The ¹H and ¹³C NMR spectra were assigned on the basis of nuclear Overhauser effect spectroscopy (NOESY), heteronuclear single‐quantum correlation (HSQC), and heteronuclear multiple‐bond correlation (HMBC) experiments. The ¹⁹F spectrum of 1 was compared with that of 2‐ethyl‐1,3,5,6,7‐pentamethyl‐4,4‐difluoro‐4‐bor‐3a,4a‐diaza‐s‐indacen (2). The ¹⁹F? ¹⁹F through‐space spin? spin coupling in 1 was thus assigned and the coupling constant was obtained by simulating the coupling patterns. The obtained conformation of 1 was compared with those of the known complexes [bis‐(N,N′‐difluoroboryl)]‐3,3′,8,8′,9,9′‐hexaethyl‐4,4′,10,10′‐tetramethyl‐6,6′‐(4‐methylphenyl)‐2,2′‐bidipyrrin (3)and [bis‐(N,N′‐difluoroboryl)]‐9,9′‐diethyl‐4,4′,8,8′,10,10′‐hexamethyl‐3,3′‐bis(methoxycarbonylethyl)‐2,2′‐bidipyrrin (4). The conformational dynamics of 1, 3, and 4 was surveyed by observing the temperature dependence of the through‐space coupling constants between 253 and 333 K. The ¹³C? ¹⁹F and ¹⁹F? ¹⁹F through‐space spin–spin couplings thus confirm similar conformations of different BisBODIPYs in solution in contrast to earlier findings in the solid state. Copyright © 2009 John Wiley & Sons, Ltd.     

A DFT and AIM analysis of the spin–spin couplings across the hydrogen bond in the 2‐fluorobenzamide and related compounds

In 1975 a large number of coupling constants were measured in 2‐fluorobenzamide labeled with ¹⁵N. Some of them were assigned to couplings through intramolecular N? H···F hydrogen bonds (HBs). These couplings change dramatically when CDCl₃ is replaced by DMSO‐d₆. In this theoretical paper we provide density functional theory (DFT) calculations that justify the existence of a weak HB in the absence of solvent, while solvents that act as HB acceptors break down the intramolecular hydrogen bond (IMHB) of 2‐fluorobenzamide. Atoms in molecules (AIM) analyses and Steiner‐Limbach plots were used to analyze the structure of the compounds. Copyright © 2009 John Wiley & Sons, Ltd.     

Small carbon‐carbon couplings in monosubstituted benzenes – their signs and magnitudes determined by HCSE method

Signed values of all intra‐ring ^2,3,4J(C,C) couplings in nine monosubstituted benzenes (C₆H₅‐X where X = F, Cl, Br, CH₃, OCH₃, Si(CH₃)₃, C ≡ N, NO, NO₂) are experimentally determined as well as nine couplings to substituent carbons. It is confirmed that while all the vicinal intra‐ring ³J(C,C) are positive and all geminal ²J(C2,C4) are negative, both signs are found for geminal ²J(C1,C3) couplings. All the determined signs agree with those already predicted by theoretical calculations. Copyright © 2013 John Wiley & Sons, Ltd.     

Synthese,Strukturen, EPR‐ und ENDOR‐spektroskopische Untersuchungen an Übergangsmetallkomplexen von N,N‐Diisobutyl‐N′‐(2, 6‐difluor)benzoylselenoharnstoff

Synthesis, Structures, EPR and ENDOR Investigations on Transition Metal Complexes of N, N‐diisobutyl‐N′‐(2, 6‐difluoro)benzoyl selenourea The synthesis and the structures of the Ni^II and Pd^II complexes of the ligand N, N‐diisobutyl‐N′‐(2, 6‐difluoro)benzoylselenourea HBuⁱ₂dfbsu are reported. The ligands coordinate bidentately forming bis‐chelates. The structure of the ligand could not be obtained, however, the structure of its O‐ethyl ester will be reported. Attempts to prepare the Cu^II complex result only in the formation of oily products. However, the Cu^II complex could be incorporated into the corresponding Ni^II and Pd^II compounds. From this diamagnetically diluted powder and single‐crystal samples were obtained being suitable for EPR‐ENDOR measurements. We report X‐ and Q‐band EPR investigations on the systems [Cu/Ni(Buⁱ₂dfbsu)₂] and [Cu/Pd(Buⁱ₂dfbsu)₂] as well as a single‐crystal X‐band EPR study for [Cu/Ni(Buⁱ₂dfbsu)₂]. The obtained ^{63, 65}Cu and ⁷⁷Se hyperfine structure tensors allow a determination of the spin‐density distribution within the first coordination sphere. In addition, orientation selective ¹⁹F Q‐band pulse ENDOR investigations on powder‐samples of [Cu/Ni(Buⁱ₂dfbsu)₂] have been performed. The hyperfine structure tensors of two intramolecular ¹⁹F atoms could be determined. According to the small ¹⁹F couplings only a vanishingly small spin‐density of < 1 % was obtained for these ¹⁹F atoms.     

Magnitude of Finite‐Nucleus‐Size Effects in Relativistic Density Functional Computations of Indirect NMR Nuclear Spin–Spin Coupling Constants

A spherical Gaussian nuclear charge distribution model has been implemented for spin‐free (scalar) and two‐component (spin–orbit) relativistic density functional calculations of indirect NMR nuclear spin–spin coupling (J‐coupling) constants. The finite nuclear volume effects on the hyperfine integrals are quite pronounced and as a consequence they noticeably alter coupling constants involving heavy NMR nuclei such as W, Pt, Hg, Tl, and Pb. Typically, the isotropic J‐couplings are reduced in magnitude by about 10 to 15 % for couplings between one of the heaviest NMR nuclei and a light atomic ligand, and even more so for couplings between two heavy atoms. For a subset of the systems studied, viz. the Hg atom, Hg₂²⁺, and Tl? X where X=Br, I, the basis set convergence of the hyperfine integrals and the coupling constants was monitored. For the Hg atom, numerical and basis set calculations of the electron density and the 1s and 6s orbital hyperfine integrals are directly compared. The coupling anisotropies of TlBr and TlI increase by about 2 % due to finite‐nucleus effects.     

NMR “Crystallography” for Uniformly (13C, 15N)-Labeled Oriented Membrane Proteins

In oriented-sample (OS) solid-state NMR of membrane proteins, the angular-dependent dipolar couplings and chemical shifts provide a direct input for structure calculations. However, so far only ¹H–¹⁵N dipolar couplings and ¹⁵N chemical shifts have been routinely assessed in oriented ¹⁵N-labeled samples. The main obstacle for extending this technique to membrane proteins of arbitrary topology has remained in the lack of additional experimental restraints. We have developed a new experimental triple-resonance NMR technique, which was applied to uniformly doubly (¹⁵N, ¹³C)-labeled Pf1 coat protein in magnetically aligned DMPC/DHPC bicelles. The previously inaccessible ¹H_α–¹³C_α dipolar couplings have been measured, which make it possible to determine the torsion angles between the peptide planes without assuming α-helical structure a priori. The fitting of three angular restraints per peptide plane and filtering by Rosetta scoring functions has yielded a consensus α-helical transmembrane structure for Pf1 protein.     

Multinuclear NMR Characterization of Cyanuric Fluoride (2,4,6‐Trifluoro‐1,3,5‐triazine)

Although 2,4,6‐trifluoro‐1,3,5‐triazine, C₃F₃N₃, is a highly symmetrical molecule, its NMR parameters can be obtained by reducing its symmetry through the introduction of ¹⁴N/¹⁵N and ¹²C/¹³C isotopomers. Experimental and computed chemical shifts of cyanuric fluoride have been obtained for ¹³C, ¹⁵N, and ¹⁹F. Spin‐spin coupling constants have been measured and compared with previous experimental data and with the complete set of computed EOM‐CCSD coupling constants.     

Synthesis and Characterization of Monomeric Aryloxo Palladium Complexes of the Type [Pd(N–N)(OAr)(C6F5)]. Crystal Structure of [Pd(tmeda)(C6F5)(OC6H4NO2‐p)]

Mononuclear palladium‐hydroxo complexes of the type [Pd(N–N)(C₆F₅)(OH)][(N–N) = 2,2′‐bipyridine (bipy), 4,4′‐dimethyl‐2,2′‐bipyridine (Me₂bipy), 1,10‐phenantroline (phen) or N,N,N′,N′‐tetramethylethylenediamine (tmeda) react with phenols ArOH in tetrahydrofuran giving the corresponding aryloxo complexes [Pd(N–N)(C₆F₅)(OAr)]. Elemental analyses and spectroscopic (IR, ¹H and ¹⁹F) methods have been used to characterize the new complexes. The X‐ray crystal structure of [Pd(tmeda)(C₆F₅)(OC₆H₄NO₂‐p)] has been determined. In the crystal packing the planes defined by two C₆H₄ rings show a parallel orientation. There are also intermolecular C–H···F and C‐H···O hydrogen bonds.     

Three derivatives of 4‐fluoro‐5‐sulfonylisoquinoline

In 4‐fluoroisoquinoline‐5‐sulfonyl chloride, C₉H₅ClFNO₂S, (I), one of the two sulfonyl O atoms lies approximately on the isoquinoline plane as a result of minimizing the steric repulsion between the chlorosulfonyl group and the neighbouring F atom. In (S)‐(−)‐4‐fluoro‐N‐(1‐hydroxypropan‐2‐yl)isoquinoline‐5‐sulfonamide, C₁₂H₁₃FN₂O₃S, (II), there are two crystallographically independent molecules (Z′ = 2). The molecular conformations of these two molecules differ in that the amine group of one forms an intramolecular bifurcated hydrogen bond with the F and OH groups, whilst the other forms only a single intramolecular N—H...F hydrogen bond. The N—H...F hydrogen bonds correspond to weak coupling between the N(H) and ¹⁹F nuclei, observed in the ¹H NMR solution‐state spectra. In (S)‐(−)‐4‐[(4‐fluoroisoquinolin‐5‐yl)sulfonyl]‐3‐methyl‐1,4‐diazepan‐1‐ium chloride, C₁₅H₁₉FN₃O₂S⁺·Cl⁻, (III), the isoquinoline plane is slightly deformed, suggestive of a steric effect induced by the bulky substituent on the sulfonyl group.     

Phosphorus NMR Characterisation of P–N Bond Rotamers of a α‐P4S3 Amide with a Conformationally Constrained Chiral Substituent

Reactions of bicyclic α‐P₄S₃I₂ with Hpthiq gave solutions containing α‐P₄S₃(pthiq)I and α‐P₄S₃(pthiq)₂, where Hpthiq is the conformationally constrained chiral secondary amine 1‐phenyl‐1,2,3,4‐tetrahydroisoquinoline. The expected diastereomers have been characterised by complete analysis of their ³¹P{¹H} NMR spectra. Hindered P–N bond rotation in the amide iodide α‐P₄S₃(pthiq)I caused greater broadening of peaks in the room‐temperature spectrum of one diastereomer than in that of the other. At 183 K, spectra of two P–N bond rotamers for each diastereomer were observed and analysed. The minor rotamers showed strong evidence for steric crowding, having large diastereomeric differences in ¹J(P–P) and ²J(P–S–P) couplings (49 Hz, 16 % of value, and 4.4 Hz, 19 % of value, respectively).     

19F Paramagnetic Relaxation Enhancement: A Valuable Tool for Distance Measurements in Proteins

Fluorine NMR paramagnetic relaxation enhancement was evaluated as a versatile approach for extracting distance information in selectively F‐labeled proteins. Proof of concept and initial applications are presented for the HIV‐inactivating lectin cyanovirin‐N. Single F atoms were introduced at the 4‐, 5‐, 6‐ or 7 positions of Trp49 and the 4‐position of Phe4, Phe54, and Phe80. The paramagnetic nitroxide spin label was attached to Cys residues that were placed into the protein at positions 50 or 52. ¹⁹F‐T₂ NMR spectra with different relaxation delays were recorded and the transverse ¹⁹F‐PRE rate, ¹⁹F‐Γ₂, was used to determine the average distance between the F nucleus and the paramagnetic center. Our data show that experimental ¹⁹F PRE‐based distances correspond to 0.93 of the ¹H_N‐PRE distances, in perfect agreement with the gyromagnetic γ¹⁹F/γ¹H ratio, thereby demonstrating that ¹⁹F PREs are excellent alternative parameters for quantitative distance measurements in selectively F‐labeled proteins.     

Spectra edited by relative signs of homonuclear couplings of low abundance nuclei

The proposed homonuclear coupling sign edited (HCSE) experiment can detect signed homonuclear couplings between low abundant nuclei like ¹³C, ²⁹Si and ¹⁵N in linear spin systems, that is, in systems where two nuclei are coupled by the measured coupling, and one of them is coupled by a second coupling to a nucleus of different kind. The third nucleus is usually high abundant hydrogen. Two spectra are measured during the HCSE experiment. Their weighed sum and difference yield two other spectra, one containing peaks coupled only by positive measured couplings and the other having peaks coupled by negative measured couplings. The usual E.COSY‐type experiment requires all three couplings in the three spin system (triangular spin system) and not only two couplings as the HCSE experiment. The experiment was successfully tested on known carbon–carbon and silicon–silicon two bond couplings. A set of six simple siloxanes with |²J(Si‐O‐Si)| couplings ranging from 0.5 to 9.0 Hz was measured for the first time, and all the couplings were found to be positive. Copyright © 2012 John Wiley & Sons, Ltd.     

Conformational Dependence of Through‐Space Tellurium–Tellurium Spin–Spin Coupling in Peri‐Substituted Bis(Tellurides)

Three related series of peri‐substituted bis(tellurides) bearing naphthalene, acenaphthene and acenaphthylene backbones (Nap/Acenap/Aceyl(TeY)₂ (Nap=naphthalene‐1,8‐diyl N ; Acenap=acenaphthene‐5,6‐diyl A ; Aceyl=acenaphthylene‐5,6‐diyl Ay ; Y=Ph 1 ; Fp 2 ; Tol 3 ; An‐p­ 4 ; An‐o­ 5 ; Tp 6 ; Mes 7 ; Tip 8 ) have been synthesised and their solid‐state structures determined by X‐ray crystallography. Molecular conformations were classified as a function of the two C9‐C‐Te‐C(Y) dihedral angles (θ); in the solid all members adopt AB or CCt configurations, with larger Te(aryl) moieties exclusively imposing the CCt variant. Exceptionally large J(¹²⁵Te,¹²⁵Te) spin–spin coupling constants between 3289–3848 Hz were obtained for compounds substituted by bulky Te(aryl) groups, implying these species are locked in a CCt‐type conformation. In contrast, compounds incorporating smaller Te(aryl) moieties are predicted to be rather dynamic in solution and afford much smaller J values (2050–2676 Hz), characteristic of greater populations of AB conformers with lower couplings. This conformational dependence of through‐space coupling is supported by DFT calculations.