Aromatic Chemical Shifts Research Articles

Cytotoxic organometallic [Ru(η6-anethole)(en)(X)]PF6 (X = Br or I) complexes: Synthesis, characterization and in vitro biological evaluation

Two new organometallic compounds with the general formula [Ru(η6-anethole)(en)(X)]PF6, where X=Br (5) or I (6) and en=ethylenediamine, were synthesized and fully characterized using standard techniques (NMR, MS and elemental analysis). Displacement of the proton and carbon aromatic chemical shifts of anethole to the upper field in both compounds indicated organometallic Ru(η6-anethole) bond formation, and the characteristic “piano-stool” structure of these types of compounds was confirmed by the single crystal X-ray diffraction of compound 5. Compounds 5 and 6 exhibited interesting cytotoxicity, especially toward the human colon tumor cell line HT-29, similar to the previously studied compound [Ru(η6-anethole)(en)(Cl)]PF6 (4). A slight tendency toward cytotoxicity could be observed by varying the halogen leaving group (IC50 value): 6 (10±2μM)>5 (18±2μM)=4 (18±3μM). Compound 6 showed 3-fold more biological activity in HT-29 cells than toward the non-tumor colon cell line CCD-841, making it an interesting candidate for further studies and drug development.

Intramolecular Cooperative Effects in Multichromophoric Cavitands Exhibiting Nonlinear Optical Properties

We report on the design, synthesis, and characterization of a new class of multichromophoric cavitands based on resorcin[4]arenes. The novel compounds have exhibited high values of second-order nonlinear optical (NLO) properties, as evidenced by electric-field-induced second harmonic generation (EFISHG) measurements. Theoretical calculations indicate the presence of edge-to-face T-shaped interactions between the aromatic building blocks within these multichromophoric systems, which is further supported by the detection of hypsochromic shifts in UV-vis and upfield aromatic chemical shifts in 1H NMR. We proved for the first time that the gain in the quadratic hyperpolarizabilities of multichromophoric NLO macrocycles, originating from the near parallel orientations of the subchromophores, can be partially suppressed if the distance between the dipolar subunits falls into a specific range, where intramolecular cooperative and/or collective effects are operative. Our finding will contribute to the better understanding of the phenomenon of cooperativity in new molecular materials with promising NLO properties. (Figure Presented). © 2015 American Chemical Society.

Influence of NMR Data Completeness on Structure Determinations of Homodimeric Proteins

AbstractThe structure determination of homodimeric proteins by NMR using conventional NOESY experiments is still challenging due to the degeneracy of the chemical shifts in the identical monomers, which causes ambiguity in the NOE assignments. Residues involved in the interface between two monomers provide essential intermolecular NOEs for the structure determinations of homodimeric proteins. Hence NMR data, such as NOE peak lists and chemical shift assignments of these interface residues, play a crucial role for the successful structure determination of homodimeric proteins. This paper extends our previous report (Lin, Y.‐J.; Kirchner, D. K.; Güntert, P. J. Magn. Reson.­ 2012, 222, 96) and investigates the influence of incomplete NOESY peak lists combined with incomplete 1H chemical shift assignments of the interface residues on the structure determination of homodimeric proteins using the program CYANA. Data incompleteness was simulated by random omission of both NOESY cross peaks and interface 1H chemical shifts. Our results for three proteins with different percentages of interface residues reveal that the algorithm can tolerate about 40–50% NOESY peak omission with complete interface chemical shift assignments, which indicates that partial NOESY peak omission does not cause severe problems when the interface chemical shifts are completely assigned. Combining NOESY peak omission with incomplete interface chemical shift assignments, the tolerance for interface chemical shift omission decreases with the extent of omitted NOESY peaks. The tolerance for unassigned interface side chain, methyl and aromatic chemical shifts is affected more strongly by NOESY peak omission than that for the omission of general interface 1H chemical shifts including the backbone. In general about 10–30% peaks omission is tolerated in conjunction with missing chemical shift assignments. If more NOESY peaks are omitted calculations gradually become unstable and tend not to tolerate any missing interface chemical shifts. A large amount of omitted NOESY peaks, for instance 30% omission in our calculations, could decrease the tolerance for missing aromatic or methyl interface 1H chemical shifts to as few as 2–4 missing chemical shifts, suggesting that complete aromatic and methyl 1H chemical shift assignments are important when the NOESY peak data is significantly incomplete. Finally, for homodimeric proteins with a low percentage of interface residues, our results reveal that the omission of NOESY peaks, even at an extent of only 10%, can result in no tolerance against the omission of interface 1H chemical shifts, suggesting that the completeness of both interface 1H chemical shift assignments and NOESY peaks are important for the successful structure determination of proteins with a small homodimer interface.

Using Side‐Chain Aromatic Proton Chemical Shifts for a Quantitative Analysis of Protein Structures

Chemical shifts are receiving renewed attention in structural biology owing to the recent introduction of novel methodologies that enable their use in protein structure determination. As these approaches have so far been mostly concerned with backbone atoms, it would be highly desirable to further generalize them to also include side-chain atoms. A major motivation for this objective is that side chains play crucial roles in determining the conformational properties of protein surfaces and interior cavities, which in most cases define the specificity of biomolecular interactions. In particular, aromatic side chains are capable of forming interactions with a variety of chemical groups through hydrophobic, p–p stacking, p–anion and p–cation interactions, and often comprise the hot spots of protein–protein and protein–ligand complex formation, and protein folding. Furthermore, aromatic side chains, as sources of ring current effects, substantially influence the chemical shifts of other nuclei, including the highly exploited backbone nuclei. However, although ring-current terms are frequently included in chemical shift predictions of backbone nuclei, aromatic chemical shifts are not normally used to define the geometry of the aromatic rings themselves. Recent advances in specific labeling technologies for aromatic side chains will soon increase the number of assigned aromatic chemical shifts, thus adding new prospects to the established methodology of aromatic chemical shift measurements. The incorporation of chemical shifts of aromatic side chains in structure-determination algorithms, in addition to the backbone atoms, would make it possible to extend the use of chemical shifts in structural studies. To achieve this goal, a chemical shift prediction method for side-chain nuclei that is based solely on the configurations of proximal atoms needs to be developed. This type of predictions, which is at variance with other currently available chemical shift predictors that provide chemical shift evaluations for side-chain nuclei, are readily differentiable with respect to the atomic coordinates, and thus enable the calculation of biasing forces for the integration of the equations of motion within a molecular dynamics scheme. Prediction of aromatic side-chain chemical shifts by differentiable functions opens new opportunities to monitor a range of important processes, and will increase the scope of chemical shift usage in determining the structures of biomolecular complexes and complex biomolecular systems. To address this challenge, we present here ArShift, a chemical shift prediction method for protein side-chain aromatic H nuclei. We then demonstrate that by using only aromatic side-chain chemical shifts, structures that do not match the state from which chemical shifts are measured can be revealed. The ArShift predictions are based on known phenomenological terms that describe the effects of ring current, magnetic anisotropy, and electric field terms, which are accompanied by a set of dihedral angle terms and distance-based polynomials (see the Supporting Information). A comprehensive analysis of the aromatic chemical shift assignments available from the BMRB database is used after filtering and re-referencing steps to reduce the number of inaccurate and artifactual entries (Figures S1 and S2 in the Supporting Information). To identify the mapping between chemical shifts and structures, only structures determined by X-ray crystallography at a resolution of 2.0 or better are considered in the derivation of the geometric terms. The combination of terms used in the predictions is then optimized through a Monte Carlo approach to decrease the number of fitted coefficients, thus increasing the significance of the remaining ones (Table S1). We assessed the accuracy of the prediction method by performing individual predictions (in leave-one-out tests) for all the chemical shift entries used for deriving the coefficients. The standard deviations of the residual errors (denoted here as standard errors) for the models implemented in the ArShift package are 0.189, 0.204, 0.256, 0.191, and 0.173 ppm for PheHd, Phe-He, Phe-Hz, Tyr-Hd, and Tyr-He nuclei, respectively (Figures S3 and S4). The comparison of the ArShift standard errors and the standard deviations of the corresponding chemical shift types in the BMRB database are presented in Figure 1. Predictions for C nuclei are not reported in this work because they do not currently provide a significant improvement over those based on the average values derived from the BMRB database. The reason for this situation is most probably the neglect of the stronger isotope effects on C [*] A. B. Sahakyan, Dr. A. Cavalli, Prof. M. Vendruscolo Department of Chemistry, University of Cambridge Lensfield Road, Cambridge CB2 1EW (UK) E-mail: mv245@cam.ac.uk Dr. W. F. Vranken European Bioinformatics Institute Wellcome Trust Genome Campus Cambridge CB10 1SD (UK) [] Current Address: Structural Biology Brussels Vrije Universiteit Brussel Pleinlaan 2, 1050 Brussel (Belgium)

A New, More Versatile, Optical Switching Helical Polycarbodiimide Capable of Thermally Tuning Polarizations ±359°

An in depth study of newly synthesized polycarbodiimides containing asymmetric aryl pendant groups has been performed. The focus of this study was to create new polymers capable of the low-energy, reversible, solvo-, and thermocontrollable conformational switching phenomenon previously discovered. Of the polymers synthesized, one polymer, N-(1-naphthyl)-N′-(n-octadecyl) polycarbodiimide, Poly-5, has been found to undergo reversible optical switching in various solvents, each of which alter the temperature at which the switching is observed. The switching is not due to helical inversions, but instead due to synchronous rearrangement of polyarene pendant groups around the helical backbone. This is further shown by anisotropic changes of the aromatic chemical shifts using variable temperature 1H NMR through the observed thermal switching range in THF-d8. The net change in specific optical rotation reaches a remarkable 1700° and changes in the direction of rotation. The polymer system is tunable and capable of holding the polarization output constant at constant temperature anywhere within the switching profile. Polarimetry and electronic circular dichroism (ECD) studies were performed to observe these conformational changes. Additionally reported are new polycarbodiimides that probe the effects of size and geometry of various arene pendant groups on the switching behavior of these polymer systems.

Improved pulse sequences for sequence specific assignment of aromatic proton resonances in proteins

Aromatic proton resonances of proteins are notoriously difficult to assign. Through-bond correlation experiments are preferable over experiments that rely on through-space interactions because they permit aromatic chemical shift assignments to be established independently of the structure determination process. Known experimental schemes involving a magnetization transfer across the Cbeta-Cgamma bond in aromatic side chains either suffer from low efficiency for the relay beyond the Cdelta position, use sophisticated 13C mixing schemes, require probe heads suitable for application of high 13C radio-frequency fields or rely on specialized isotopic labelling patterns. Novel methods are proposed that result in sequential assignment of all aromatic protons in uniformly 13C/15N labelled proteins using standard spectrometer hardware. Pulse sequences consist of routinely used building blocks and are therefore reasonably simple to implement. Ring protons may be correlated with beta-carbons and, alternatively, with amide protons (and nitrogens) or carbonyls in order to take advantage of the superior dispersion of backbone resonances. It is possible to record spectra in a non-selective manner, yielding signals of all aromatic residues, or as amino-acid type selective versions to further reduce ambiguities. The new experiments are demonstrated with four different proteins with molecular weights ranging from 11 kDa to 23 kDa. Their performance is compared with that of (Hbeta)Cbeta(CgammaCdelta)Hdelta and (Hbeta)Cbeta(CgammaCdeltaCepsilon)Hepsilon pulse sequences.

Triple-Resonance Methods for Complete Resonance Assignment of Aromatic Protons and Directly Bound Heteronuclei in Histidine and Tryptophan Residues

A set of three experiments is described which correlate aromatic resonances of histidine and tryptophan residues with amide resonances in 13C/15N-labelled proteins. Provided that backbone 1H and 15N positions of the sequentially following residues are known, this results in sequence-specific assignment of histidine 1H(delta2)/13C(delta2) and 1H(epsilon1)/13C(epsilon1) as well as tryptophan 1H(delta1)/13C(delta1), 1H(zeta2)/13C(zeta2), 1H(eta2)/13C(eta2), 1H(epsilon3)/13C(epsilon3), 1H(zeta3)/13C(zeta3) and 1H(epsilon1)/15N(epsilon1) chemical shifts. In the reverse situation, these residues can be located in the 1H-(15)N correlation map to facilitate backbone assignments. It may be chosen between selective versions for either of the two amino acid types or simultaneous detection of both with complete discrimination against phenylalanine or tyrosine residues in each case. The linkages between delta-proton/carbon and the remaining aromatic as well as backbone resonances do not rely on through-space interactions, which may be ambiguous, but exclusively employ one-bond scalar couplings for magnetization transfer instead. Knowledge of these aromatic chemical shifts is the prerequisite for the analysis of NOESY spectra, the study of protein-ligand interactions involving histidine and tryptophan residues and the monitoring of imidazole protonation states during pH titrations. The new methods are demonstrated with five different proteins with molecular weights ranging from 11 to 28 kDa.

Aplicação de análise de componentes principais para verificação de atribuições de sinais nos espetros de RMN ¹H: o caso dos 3-aril (1,2,4)-oxadiazol-5-carboidrazida benzilidenos

The 1H NMR data set of a series of 3-aryl (1,2,4)-oxadiazol-5-carbohydrazide benzylidene derivatives synthesized in our group was analyzed using the chemometric technique of principal component analysis (PCA). Using the original 1H NMR data PCA allowed identifying some misassignments of the proton aromatic chemical shifts. As a consequence of this multivariate analysis, nuclear Overhauser difference experiments were performed to investigate the ambiguity of other assignments of the ortho and meta aromatic hydrogens for the compound with the bromine substituent. The effect of the 1,2,4-oxadiazol group as an electron acceptor, mainly for the hydrogens 12,13, has been highlighted.

Computerized analysis of 2D INADEQUATE spectra to assign chemical shifts in aromatic compounds

AbstractA computerized analysis of a single 2D INADEQUATE spectra assigns all of the 13C chemical shifts in fairly complex aromatic systems. Without the aid of the computer this information is often difficult, if not impossible, to retrieve owing to overlap of the signals in the double quantum dimension. In addition, the use of the computerized analysis allows for the interpretation of INADEQUATE spectra with much lower signal‐to‐noise ratios than are practical if the analysis were to be done visually. Finally, narrowing the spectral window to a subset of the entire spectrum and the companion advantages are demonstrated. The assignments of the aromatic chemical shifts in 2‐methoxydibenzofuran, 6‐methylchrysene, 1‐decylpyrene, and 7‐methylbenzo[a]pyrene illustrate the power of automated pattern recognition methods while supplying previously unavailable chemical shift assignments on these complex fused polycyclic aromatic systems.

Calculation of 13C NMR chemical shifts for aromatic carbons in polyalkylated benzenes

Abstract13C NMR spectra of a large number of polyalkylated benzenes with branched and linear aliphatic chains have been studied. This resulted in the development of a general procedure that can be used for the calculation of the aromatic chemical shifts in any polyalkylated benzene.

Aromatic chemical shifts in ar‐hydroxy‐ and ‐methoxy‐substituted indole alkaloids; reference data and substituent‐induced chemical shifts for ten different chromophoric groups

AbstractOn the basis of available 13C NMR spectral data for indole alkaloids, substituent‐induced chemical shifts have been calculated for various types of ar‐hydroxy‐ and ‐methoxy‐substituted indole alkaloids.

An NMR study of some substituted 1,3‐ and 1,4‐bistrifluoromethylbenzenes

AbstractContrary to an earlier report, the metallation of 1,3‐bistrifluoromethylbenzene with n‐butyllithium is found to take place at the 4‐ and 2‐positions. Lithiation of 1,4‐bistrifluoromethylbenzene and subsequent carboxylation gives exclusively the 2‐carboxylic acid. Structures are assigned on the basis of PMR data (100 and 220 MHz). The effects of coupling between aromatic protons and trifluoromethyl groups and the aromatic chemical shifts brought about by esterification are discussed for a series of bistrifluoromethylbenzoic acids.