Pressure-induced isomerization of retinal on bacteriorhodopsin as disclosed by fast magic angle spinning NMR

Bacteriorhodopsin (bR) is a retinal protein in purple membrane of Halobacterium salinarum, which functions as a light-driven proton pump. We have detected pressure-induced isomerization of retinal in bR by analyzing 15N cross polarization-magic angle spinning (CP-MAS) NMR spectra of [zeta-15N]Lys-labeled bR. In the 15N-NMR spectra, both all-trans and 13-cis retinal configurations have been observed in the Lys N(zeta) in protonated Schiff base at 148.0 and 155.0 ppm, respectively, at the MAS frequency of 4 kHz in the dark. When the MAS frequency was increased up to 12 kHz corresponding to the sample pressure of 63 bar, the 15N-NMR signals of [zeta-15N]Lys in Schiff base of retinal were broadened. On the other hand, other [zeta-15N]Lys did not show broadening. Subsequently, the increased signal intensity of [zeta-15N]Lys in Schiff base of 13-cis retinal at 155.0 ppm was observed when the MAS frequency was decreased from 12 to 4 kHz. These results showed that the equilibrium constant of [all-trans-bR]/[13-cis-bR] in retinal decreased by the pressure of 63 bar. It was also revealed that the structural changes induced by the pressure occurred in the vicinity of retinal. Therefore, microscopically, hydrogen-bond network around retinal would be disrupted or distorted by a constantly applied pressure. It is, therefore, clearly demonstrated that increased pressure induced by fast MAS frequencies generated isomerization of retinal from all-trans to 13-cis state in the membrane protein bR.     

Observation of Diastereotopic Signals in 15N NMR Spectroscopy

The first example in the literature of a compound showing anisochronous ¹⁵N atoms resulting from diastereotopicity is described. Racemic 1,3‐dimethyl‐2‐phenyloctahydro‐1H‐benzimidazole was prepared and studied by ¹H, ¹³C and ¹⁵N NMR spectroscopy. If convenient conditions were used (monitored by theoretical calculations of ²J_N‐H spin–spin coupling constants), two ¹⁵N NMR signals were observed and corresponded to the diastereotopic atoms. GIAO/density‐functional calculations of chemical shifts were not only in good agreement with the experimental values but also served as prediction tools. This study suggests that ¹⁵N NMR spectroscopy could be used to probe chirality.     

SPONTANEOUS AGGREGATION OF BACTERIORHODOPSIN IN BROWN MEMBRANE

Abstract— Halobacterium halobium cells grown in nicotine-containing medium synthesize bacterio-opsin (bO) but little bacteriorhod-opsin (bR) because nicotine inhibits retinal synthesis. In nicotine-grown cells, bacterio-opsin is found in a specific cell membrane fraction, the brown membrane (b.m.), which consists mainly of small round sheets. Freeze-fracture of isolated brown membrane reveals a dense particle population on its cytoplasmic fracture face, with few particles on the external face. There is no apparent order in the particle distribution and the fracture faces are practically indistinguishable from those of red membrane (r.m.). The absorbance spectrum of b.m. shows peaks at 550 and 410nm, the circular dichroism (CD) spectrum a positive band around 540nm and positive and negative bands around 410nm with a cross-over at 412nm. The photoreaction cycle of bR in b.m. has the same intermediates found in purple membrane (p.m.), but the apparent kinetics resemble those of bR monomers. Addition of 13-cis-, or all-trans-retinal to b.m. induces a rapid 5- to 10-fold increase in the visible absorbance band, and the absorbance maximum shifts to 560nm in the dark. Kinetic analysis of the absorbance increase shows three first order kinetic constants with t_½= 0.5 min, 6 min and 100 min, with most of the increase contributed by the fastest component. The CD bilobal pattern typical for purple membrane appears together with the strong negative band at 320nm. Ellipticity change at 590nm is nearly as rapid as the absorbance increase; within 5 min, 85% of the negative band is formed. Electron microscopy after addition of retinal reveals structurally distinct domains in the b.m. sheets which have the characteristic appearance of p.m. However, X-ray reflections are more diffuse compared to p.m. Flash spectroscopy of reconstituted b.m. detects the same photocycle intermediates as in b.m. or p.m., but with apparent kinetics closer to those of purple membrane than before reconstitution. These results show that bO in the b.m. binds retinal to form bR which spontaneously aggregates into a lattice. However, the reconstituted bR lattice is not as well-ordered as in p.m. and some bR is still present in the form of monomers and/or small aggregates.     

13C and 15N NMR spectra of high‐energy polyazidocyanopyridines

¹³C and ¹⁵N NMR spectra of high‐energy 2,4,6‐triazidopyridine‐3,5‐dicarbonitrile, 2,3,5,6‐tetraazidopyridine‐4‐carbonitrile and 3,4,5,6‐tetraazidopyridine‐2‐carbonitrile are reported. The assignment of signals in the spectra was performed on the basis of density functional theory calculations. The molecular geometries were optimized using the M06‐2X functional with the 6‐311+G(d,p) basis set. The magnetic shielding tensors were calculated by the gauge‐independent atomic orbital method with the Tao–Perdew–Staroverov–Scuseria hybrid functional known as TPSSh. In all the calculations, a polarizable continuum model was used to simulate solvent effects. This approach provided accurate predictions of the ¹³C and ¹⁵N chemical shifts for all the three compounds despite complications arising due to non‐coplanar arrangement of the azido groups in the molecules. It was found that the ¹⁵N chemical shifts of the N_α atoms in the azido groups of 2,4,6‐triazidopyridines correlate with the ¹³C chemical shifts of the carbon atoms attached to these azido groups. Copyright © 2016 John Wiley & Sons, Ltd.     

1H, 13C and 15N NMR assignments for N6‐isopentenyladenosine/inosine analogues

The complete ¹H, ¹³C and ¹⁵N NMR signals assignments of some new isopentenyladenosine analogues were achieved using one‐ and two‐dimensional experiments (gs‐NOESY, gs‐HMQC and gs‐HMBC). Copyright © 2010 John Wiley & Sons, Ltd.     

Ammonolysis of 1,2‐Bis[dichloro(methyl)silyl]ethane. On the Structure of 1,3,6,8‐Tetramethyl‐2,7,11,12‐tetraaza‐1,3,6,8‐tetrasila‐tricyclo[6.2.1.13,6]‐dodecane

Ammonolysis of 1,2‐bis[dichloro(methyl)silyl]ethane afforded a crystalline tricyclic silazane along with polymeric material. The crystalline material could be isolated in pure state. It was analyzed by ¹H, ¹³C, ¹⁵N and ²⁹Si NMR spectroscopy in solution, by ¹³C, ¹⁵N and ²⁹Si MAS NMR spectroscopy in the solid state, as well as by single‐crystal and powder X‐ray diffraction. The title compound exists as a single isomer in solution, whereas in the solid state the presence of several modifications is indicated, in particular by the solid‐state MAS NMR spectra.     

13C dynamic nuclear polarization using isotopically enriched 4‐oxo‐TEMPO free radicals

The nitroxide‐based free radical 2,2,6,6‐tetramethyl‐1‐piperidinyloxy (TEMPO) is a widely used polarizing agent in NMR signal amplification via dissolution dynamic nuclear polarization (DNP). In this study, we have thoroughly investigated the effects of ¹⁵N and/or ²H isotopic labeling of 4‐oxo‐TEMPO free radical on ¹³C DNP of 3 M [1‐¹³C] sodium acetate samples in 1 : 1 v/v glycerol : water at 3.35 T and 1.2 K. Four variants of this free radical were used for ¹³C DNP: 4‐oxo‐TEMPO, 4‐oxo‐TEMPO‐¹⁵N, 4‐oxo‐TEMPO‐d₁₆ and 4‐oxo‐TEMPO‐¹⁵N,d₁₆. Our results indicate that, despite the striking differences seen in the electron spin resonance (ESR) spectral features, the ¹³C DNP efficiency of these ¹⁵N and/or ²H‐enriched 4‐oxo‐TEMPO free radicals are relatively the same compared with ¹³C DNP performance of the regular 4‐oxo‐TEMPO. Furthermore, when fully deuterated glassing solvents were used, the ¹³C DNP signals of these samples all doubled in the same manner, and the ¹³C polarization buildup was faster by a factor of 2 for all samples. The data here suggest that the hyperfine coupling contributions of these isotopically enriched 4‐oxo‐TEMPO free radicals have negligible effects on the ¹³C DNP efficiency at 3.35 T and 1.2 K. These results are discussed in light of the spin temperature model of DNP. Copyright © 2016 John Wiley & Sons, Ltd.     

Efficient Homogeneous Chemical Modification of Bacterial Cellulose in the Ionic Liquid 1‐N‐Butyl‐3‐methylimidazolium Chloride

Summary: Bacterial cellulose (BC), a unique type of cellulose, with high degree of polymerization of 6 500 could be dissolved easily in the ionic liquid 1‐N‐butyl‐3‐methylimidazolium chloride. For the first time, well‐soluble BC acetates and carbanilates of high degree of substitution (up to a complete modification of all hydroxyl groups) were accessible under homogeneous and mild reaction conditions. Characterization of the new BC derivatives by NMR and FTIR spectroscopy shows an unexpected distribution of the acetyl moieties in the order O‐6 > O‐3 > O‐2.

¹³C NMR spectrum (DMSO‐d₆) of a cellulose acetate with a DS of 2.25 synthesized in 1‐N‐butyl‐3‐methylimidazolium chloride.     

An Insertion or Deletion in the Extramembrane Loop Connecting Helices E and F of Archaerhodopsin-1 Affects in vitro Refolding and Slows the Photocycle

Abstract— Upon addition of retinal, archaeopsin-1 expressed in Escherichia coli (_ecaO-1002) regenerated the chromophore in dimyristoyl phosphatidylcholine (DMPC), 3-[(3-cholamidopropyl) dimethylammonio]-l-propanesulfonate (CHAPS) and sodium dodecyl sulfate(SDS) mixed micelles as efficiently as the same opsin prepared from halobacteria. Introduction of an insertion or a deletion of five amino acids into the surface loop connecting helices E and F changed the secondary and tertiary structures of _ecaO-1002 in SDS, and diminished regeneration of the chromophore. The effect of the insertion and deletion on the in vitro refolding was specific to archaeopsin because the same insertion introduced at the corresponding position of bacterioopsin (bO) did not affect chromophore regeneration. The photocycle of the regenerated _ecaR-1002 decreased in DMPC/CHAPS/SDS mixed micelles compared with that of aR-1 in the claret membrane, which was consistent with the reported behavior of bO. Unexpectedly, the insertion and deletion in loop EF perturbed the photocycle of the regenerated _ecaR-1002. The accumulation of long-lived N- and O-like intermediates suggested that the insertion and deletion slowed down the proton uptake steps at the cytoplasmic surface.     

GIAO/DFT studies on 1,2,4‐triazole‐5‐thiones and their propargyl derivatives

Density functional theory (DFT)/Becke–Lee–Yang–Parr (B3LYP) and gauge‐including atomic orbital (GIAO) calculations were performed on a number of 1,2,4‐triazole derivatives, and the optimized structural parameters were employed to ascertain the nature of their predominant tautomers. ¹³C and ¹⁵N NMR chemical shifts of 3‐substituted 1,2,4‐triazole‐5‐thiones and their propargylated derivatives were calculated via GIAO/DFT approach at the B3LYP level of theory with geometry optimization using a 6‐311++G** basis set. A good agreement between theoretical and experimental ¹³C and ¹⁵N NMR chemical shifts could be found for the systems investigated. The data generated were useful in predicting ¹⁵N chemical shifts of all the nitrogen atoms of the triazole ring, some of which could not be obtained in solution state ¹⁵N HMBC/HSQC NMR measurements. The energy profile computed for the dipropargylated derivatives was found to follow the product distribution profile of regioisomers formed during propargylation of 1,2,4‐triazole thiones. Copyright © 2013 John Wiley & Sons, Ltd.     

Characterization of 2‐aryl‐1,3,4‐oxadiazoles by 15N and 13C NMR spectroscopy

¹⁵N NMR chemical shifts of 2‐aryl‐1,3,4‐oxadiazoles were assigned on the basis of the ¹H–¹⁵N HMBC experiment. Chemical shifts of the nitrogen and carbon atoms in the oxadiazole ring correlate with the Hammett σ‐constants of substituents in the aryl ring (r² ≥ 0.966 for N atoms). ¹⁵N NMR data are a suitable and sensitive means for characterizing long‐range electronic substituent effects. Additionally, ¹³C NMR data for these compounds are presented. Copyright © 2003 John Wiley & Sons, Ltd.     

Study of spontaneous E/Z isomerization of bis[(Z)‐cyanomethylidene]‐diazapentacyclodienedicarboxylates by 1H, 13C,and 15N NMR spectroscopy,X‐ray,and quantum chemical calculation data

X‐ray data show that the diethyl 6,13‐bis[(Z)‐cyanomethylidene]‐5,5,14,14‐tetramethyl‐4,15‐dioxa‐7,12‐diazapentacyclo[9.5.2.0^2,10.0^3,7.0^12,16]octadeca‐8,17‐diene‐10,17‐dicarboxylate is formed as the ZZ isomer and diastereomer with the (1R*,2R*,3R*,10S*,11R*,12R*,16R*) configuration. The ¹H, ¹³C, and ¹⁵N NMR data exhibit that on standing in chloroform‐d solution, there is a spontaneous isomerization of this compound resulting in a thermodynamically stable mixture of the ZZ, ZE, EE, and EZ isomers with the same backbone. Using the 2D [¹H–¹H] COSY, [¹H–¹³C] HSQC, and [¹H–¹³C, ¹H–¹⁵N] HMBC NMR techniques and quantum chemical calculations makes it possible a complete assignment of signals in the ¹H, ¹³C, and ¹⁵N NMR spectra of each of the isomers. Such isomerization does not occur for similar compounds with the more bulky substituents at the 1,3‐oxazolidine rings. Copyright © 2016 John Wiley & Sons, Ltd.     

The reaction of (N‐isocyanimino) triphenylphosphorane with (E)‐3‐aryl‐2‐ propenoic acid derivatives: One‐pot synthesis of 2‐[(E)‐2‐aryl‐1‐ethenyl]‐1,3,4‐oxadiazoles via intramolecular aza‐Wittig reaction

The reaction of (E)‐3‐aryl‐2‐propenoic acid derivatives with (N‐isocyanimino) triphenylphosphorane proceeds smoothly at room temperature to afford the corresponding 2‐[(E)‐2‐aryl‐1‐ethenyl]‐1,3,4‐oxadiazole via an intramolecular aza‐Wittig reaction in good yields under neutral conditions. The structures of the products were deduced from their IR, ¹H NMR, and ¹³C NMR spectra and mass spectrometry. © 2011 Wiley Periodicals, Inc. Heteroatom Chem 22:612–616, 2011; View this article online at wileyonlinelibrary.com . DOI 10.1002/hc.20701     

1H{15N} GHMQC study of 5,7‐diphenyl‐1,2,4‐triazolo[1,5‐a]pyrimidine and 1H, 13C and 15N NMR coordination shifts in Au(III) chloride complexes of 1,2,4‐triazolo[1,5‐a]pyrimidines

The ¹H{¹⁵N} NMR spectrum of 5,7‐diphenyl‐1,2,4‐triazolo[1,5‐a]‐pyrimidine ( 3 ) was measured by GHMQC, unambiguously assigned and compared with the spectra of 1,2,4‐triazolo[1,5‐a]pyrimidine ( 1 ) and 5,7‐dimethyl‐1,2,4‐triazolo[1,5‐a]pyrimidine ( 2 ). A series of Au(III) chloride complexes of general formula AuLCl₃, where L = 1 , 2 , 3 , was synthesized and studied by ¹HH{¹⁵N} GHMQC and ¹H{¹³C} GHMBC. Low‐frequency shifts of 72–74 ppm (¹⁵N) and 5–6 ppm (¹³C) were observed upon complexation by Au(III) ions for the coordination site N‐3 and adjacent C‐2, C‐3a atoms, respectively. The ¹³C signals of C‐5, C‐6, C‐7 and the ¹H resonances of H‐2, H‐6 were shifted to higher frequency. Comparison with analogous Pd(II), Pt(II) and Pt(IV) complexes revealed that in the case of Au(III) coordination the ¹⁵N shifts were relatively smaller, whereas those for ¹³C and ¹H were larger. Copyright © 2002 John Wiley & Sons, Ltd.     

Application of HSQC in the delineation of NMR signals of E and Z isomers of octadecyl p‐coumarates

Octadecyl p‐coumarates undergo E–Z isomerization in daylight. Although ¹H NMR, ¹³C NMR and ¹H–¹H COSY gave indications about this isomerization, the overlapping of some signals in the ¹H NMR of aromatic region prevented the delineation of signals of the individual isomers. However, heteronuclear spin quantum coupling correlation (HSQC) with the unique feature of two sets of nearby δ_C–δ_H correlations gave conclusive evidence for this isomerization and helped in the delineation of ¹H NMR and ¹³C NMR signals of E‐octadecyl p‐coumarate and Z‐octadecyl p‐coumarate. Copyright © 2012 John Wiley & Sons, Ltd.     

Quantitative and qualitative 1H, 13C,and 15N NMR spectroscopic investigation of the urea–formaldehyde resin synthesis

Urea–formaldehyde resins are bulk products of the chemical industry. Their synthesis involves a complex reaction network. The present work contributes to its elucidation by presenting results from detailed NMR spectroscopic studies with different methods. Besides¹H NMR and¹³C NMR,¹⁵N NMR spectroscopy is also applied.¹⁵N‐enriched urea was used for the investigations. A detailed NMR signal assignment and a model of the reaction network of the hydroxymethylation step of the synthesis are presented. Because of its higher spectral dispersion and the fact that all key reactions directly involve the nitrogen centers,¹⁵N NMR provides a much larger amount of detail than do¹H and¹³C NMR spectroscopy. Symmetric and asymmetric dimethylol urea can be clearly distinguished and separated from monomethylol urea, trimethylol urea, and methylene‐bridged urea. The existence of hemiformals of methylol urea is confirmed. 1,3,5‐Oxadiazinan‐4‐on (uron) and its derivatives were not found in the reaction mixtures investigated here but were prepared via alternative routes. The molar ratios of formaldehyde to urea were 1, 2, and 4, the pH values 7.5 and 8.5, and the reaction temperature 60 °C. Copyright © 2014 John Wiley & Sons, Ltd.     

Imines in the Titanium Coordination Sphere – Transformation of Imidoyl Chlorides to Nitrilium Ions

In the reaction of TiCl₄ in benzene as solvent with the imidoyl chloride p‐Tolyl(Cl)C=NPh ( 1 ) the abstraction of the chloride substituent is observed, leading to the nitrilium salt [p‐Tolyl–C≡N–Ph]⁺[Ti₂Cl₉]^– ( 2 ) in quantitative yield. The highly electrophilic salt 2 is characterized by IR‐ and NMR spectroscopy. The observed band for the C≡N stretching mode of 2 clearly indicates the formation of a nitrilium ion. Especially a characteristic line broadening of the ¹³C{¹H}‐NMR signals related to carbon atoms next to the nitrogen is observed. By ¹⁵N,¹H‐HMBC NMR experiments it is shown that the nitrogen signal of 2 is significantly shifted to high‐field in relation to nitriles and imines. The molecular structure of 2 was confirmed by single‐crystal X‐ray diffraction. The C≡N bond length and the linearity of the C–C≡N–C unit in 2 confirm the triple bond character of this bond.     

Comparison of GIAO and CSGT for calculating 13C and 15N nuclear magnetic resonance chemical shifts of substituent neutral 5‐aminotetrazole and 5‐nitrotetrazole compounds

The comparison of the gauge‐including atomic orbital (GIAO) and the continuous set of gauge transformation methods for calculating nuclear magnetic chemical shifts (CSs) mainly at density functional levels of theory are presented. Isotropic ¹³ C and ¹⁵ N magnetic CS for 14 compounds of tetrazoles are reported. Compared with establishing a convenient and consistent protocol to be employed for confirming the experimental ¹³ C and ¹⁵ N NMR spectra of tetrazole compounds, different combinations of functionals and basis sets were considered. The most reliable results were obtained at GIAO/B3LYP/aug‐cc‐pVDZ with integral equation formulation for the polarizable continuum model (PCM), which has the smallest root mean square errors and can be used to calculate ¹³ C and ¹⁵ N NMR CS with a very high accuracy for tetrazoles. These results show that the accurately calculated ¹⁵N NMR CS of tetrazoles could be used for the evaluation of the intrinsic relationship between structure and explosive properties. Copyright © 2012 John Wiley & Sons, Ltd.     

The Studies of Structure of 2N‐(3‐phenyl‐allyl‐)(5‐phenyl‐[1,3,4] Thiadiazol‐2‐yl) Amine in Solution

2N‐(3‐phenyl‐allyl‐)(5‐phenyl‐[1,3,4] thiadiazol‐2‐yl) amine was studied by means of the ¹H, ¹³C, ¹⁵N NMR spectroscopy and DFT calculations. On the basis of the one‐dimensional ¹H, ¹³C, ¹⁵N‐NMR and two‐dimensional ¹H‐¹³C HMQC, ¹H‐¹³C HMBC, ¹H‐¹⁵N HMQC, ¹H¹H NOESY, ¹H¹H COSY correlation spectra the amine‐type and the imine‐type tautomers have been determined in the solution. Variety of structural forms including: biradical, ionic–biradical, and ionic structures of the amine‐type a and of the imine‐type b , c tautomers exist in the solution. According to the DFT computations the differences in the total energy between a and b , a and c , and b and c tautomers are equal to 1.5 kJ/mol, 1.2 kJ/mol, and 0.3 kJ/mol, respectively.