Validation of the GROMOS 54A7 Force Field Regarding Mixed α/β‐Peptide Molecules

A molecular‐dynamics (MD) simulation study of two heptapeptides containing α‐ and β‐amino acid residues is presented. According to NMR experiments, the two peptides differ in dominant fold when solvated in MeOH: peptide 3 adopts predominantly β‐hairpin‐like conformations, while peptide 8 adopts a 14/15‐helical fold. The MD simulations largely reproduce the experimental data. Application of NOE atom? atom distance restraining improves the agreement with experimental data, but reduces the conformational sampling. Peptide 3 shows a variety of conformations, while still agreeing with the NOE and ³J‐coupling data, whereas the conformational ensemble of peptide 8 is dominated by one helical conformation. The results confirm the suitability of the GROMOS 54A7 force field for simulation or structure refinement of mixed α/β‐peptides in MeOH.     

Synthesis and conformational analysis of efrapeptins

The efrapeptin family of peptide antibiotics produced by the fungus Tolypocladium niveum, and the neo‐efrapeptins from the fungus Geotrichum candidumare inhibitors of F₁‐ATPase with promising antitumor, antimalaria, and insecticidal activity. They are rich in C^α‐dialkyl amino acids (Aib, Iva, Acc) and contain one β‐alanine and several pipecolic acid residues. The C‐terminus bears an unusual heterocyclic cationic cap. The efrapeptins C–G and three analogues of efrapeptin C were synthesized using α‐azido carboxylic acids as masked amino acid derivatives. All compounds display inhibitory activity toward F₁‐ATPase. The conformation in solution of the peptides was investigated with electronic CD spectroscopy, FT‐IR spectroscopy, and VCD spectroscopy. All efrapeptins and most efrapeptin analogues were shown to adopt helical conformations in solution. In the case of efrapeptin C, VCD spectra proved that a 3₁₀‐helix prevails. In addition, efrapeptin C was conformationally studied in detail with NMR and molecular modeling. Besides NOE distance restraints, residual dipolar couplings (RDC) observed upon partial alignment with stretched PDMS gels were used for the conformational analysis and confirmed the 3₁₀‐helical conformation.     

Conformations of the Nine‐Membered Ring in the B‐Nor‐5,10‐secosteroids. X‐Ray and NMR Analysis

The conformations of (Z)‐ and (E)‐5‐oxo‐B‐nor‐5,10‐secocholest‐1(10)‐en‐3β‐yl acetates ( 2 and 3 , resp.) were examined by a combination of X‐ray crystallographic analysis and NMR spectroscopy, with emphasis on the geometry of the cyclononenone moiety. The ¹H‐ and ¹³C‐NMR spectra showed that the unsaturated nine‐membered ring of (E)‐isomer 3 in C₆D₆ and (D₆)acetone solution exists in a sole conformation of type B ₁ , which is similar to its solid‐state conformation. The (Z)‐isomer 2 in C₆D₆, CDCl₃, and (D₆)acetone solution, however, exists in two conformational forms of different families, with different orientation of the carbonyl group, the predominant form (85%) corresponding to the conformation of type A ₁ and the minor (15%) to the conformation A ₂ present also in the crystalline state. In this solid‐state conformations of the nine‐membered ring of both compounds, the 19‐Me and 5‐oxo groups are ‘β’‐oriented. The NMR analysis suggests that the nine‐membered ring of 4 has a conformation of type C ₁ in CDCl₃ solution.     

Structural analyses of mannose pentasaccharide of high mannose type oligosaccharides by 1D and 2D NMR spectroscopy

NMR spectroscopy is a very important and useful method for the structural analysis of oligosaccharides, despite its low sensitivity. We first applied conventional measuring methods, 2D DQF COSY, ¹H–¹³C HSQC, and ¹H–¹³C HMBC, and also the Double Pulsed Field Gradient Spin Echo (DPFGSE)‐TOCSY and DPFGSE‐NOESY/ROESY techniques to analyze a branched mannose pentasaccharide as a model of high mannose type N‐glycans in natural abundance. The NMR spectra of the model compound are very complex and difficult to analyze owing to overlapping signals. The superior selective irradiation capability of the DPFGSE technique is useful for fine structural and conformational analyses of such complex oligosaccharides. We here introduce a novel technique called DPFGSE‐Double‐Selective Population Transfer (SPT)‐Difference and DPFGSE‐NOE/ROE‐SPT‐Difference spectroscopy. The DPFGSE‐Double‐SPT‐Difference method involves irradiation of two peaks from one proton and the subtraction of higher and lower peaks from each spectrum. The DPFGSE‐NOE/ROE‐SPT‐Difference method involves the transfer of the magnetization polarized by NOE/ROE from the nuclei to the spin‐coupled nuclei through scalar spin–spin interaction using the SPT method. Even if the signals in the NMR spectra overlap, each signal can be accurately assigned. In particular, DPFGSE‐NOE/ROE‐SPT‐Difference is very useful for identifying sugar connectivity. Copyright © 2012 John Wiley & Sons, Ltd.     

Conformational Preferences of a β‐Octapeptide as Function of Solvent and Force‐Field Parameters

The ability to design properly folded β‐peptides with specific biological activities requires detailed insight into the relationship between the amino acid sequence and the secondary and/or tertiary structure of the peptide. One of the most frequently used spectroscopic techniques for resolving the structure of a biomolecule is NMR spectroscopy. Because only signal intensities and frequencies are recorded in the experiment, a conformational interpretation of the recorded data is not straightforward, especially for flexible molecules. The occurrence of conformational and/or time averaging, and the limited amount and accuracy of experimental data hamper the precise conformational determination of a biomolecule. In addition, the relation between experimental observables with the underlying conformational ensemble is often only approximately known, thereby aggravating the difficulty of structure determination of biomolecules. The problematic aspects of structure refinement based on NMR nuclear Overhauser effect (NOE) intensities and ³J‐coupling data are illustrated by simulating a β‐octapeptide in explicit MeOH and H₂O as solvents using three different force fields. NMR Data indicated that this peptide would fold into a 3₁₄‐helix in MeOH and into a hairpin in H₂O. Our analysis focused on the conformational space visited by the peptide, on structural properties of the peptide, and on agreement of the MD trajectories with available NMR data. We conclude that 1) although the 3₁₄‐helical structure is present when the peptide is solvated in MeOH, it is not the only relevant conformation, and that 2) the NMR data set available for the peptide, when solvated in H₂O, does not provide sufficient information to derive a single secondary structure, but rather a multitude of folds that fulfill the NOE data set.     

Monitoring Conformational Changes in the NDM‐1 Metallo‐β‐lactamase by 19F NMR Spectroscopy

The New Delhi metallo‐β‐lactamase (NDM‐1) is involved in the emerging antibiotic resistance problem. Development of metallo‐β‐lactamases (MBLs) inhibitors has proven challenging, due to their conformational flexibility. Here we report site‐selective labeling of NDM‐1 with 1,1,1‐trifluoro‐3‐bromo acetone (BFA), and its use to study binding events and conformational changes upon ligand–metal binding using ¹⁹F NMR spectroscopy. The results demonstrate different modes of binding of known NDM‐1 inhibitors, including L ‐ and D ‐captopril by monitoring the changing chemical environment of the active‐site loop of NDM‐1. The method described will be applicable to other MBLs and more generally to monitoring ligand‐induced conformational changes.     

Z‐sinapinic acid: the change of the stereochemistry of cinnamic acids as rational synthesis of a new matrix for carbohydrate MALDI‐MS analysis

Successful application of matrix‐assisted laser desorption/ionization (MALDI) MS started with the introduction of efficient matrices such as cinnamic acid derivatives (i.e. 3,5‐dimethoxy‐4‐hydroxycinnamic acid, SA; α‐cyano‐4‐hydroxycinnamic acid). Since the empirical founding of these matrices, other commercial available cinnamic acids with different nature and location of substituents at benzene ring were attempted. Rational design and synthesis of new cinnamic acids have been recently described too. Because the presence of a rigid double bond in its molecule structure, cinnamic acids can exist as two different geometric isomers, the E‐form and Z‐form. Commercial available cinnamic acids currently used as matrices are the geometric isomers trans or E (E‐cinnamic and trans‐cinnamic acids). As a new rational design of MALDI matrices, Z‐cinnamic acids were synthesized, and their properties as matrices were studied. Their performance was compared with that of the corresponding E‐isomer and classical crystalline matrices (3,5‐dihydroxybenzoic acid; norharmane) in the analysis of neutral/sulfated carbohydrates. Herein, we demonstrate the outstanding performance for Z‐SA. Sulfated oligosaccharides were detected in negative ion mode, and the dissociation of sulfate groups was almost suppressed. Additionally, to better understand the quite different performance of each geometric isomer as matrix, the physical and morphological properties as well as the photochemical stability in solid state were studied. The influence of the E/Z photoisomerization of the matrix during MALDI was evaluated. Finally, molecular modeling (density functional theory study) of the optimized geometry and stereochemistry of E‐cinnamic and Z‐cinnamic acids revealed some factors governing the analyte–matrix interaction. Copyright © 2013 John Wiley & Sons, Ltd.     

An Alkene‐Promoted Borane‐Catalyzed Highly Stereoselective Hydrogenation of Alkynes to Give Z‐ and E‐Alkenes

The stereoselective hydrogenation of alkynes to alkenes is an extremely useful transformation in synthetic chemistry. Despite numerous reports for the synthesis of Z‐alkenes, the hydrogenation of alkynes to give E‐alkenes is still not well resolved. In particular, selective preparation of both Z‐ and E‐alkenes by the same catalytic hydrogenation system using molecular H₂ has rarely been reported. In this paper, a novel strategy of using simple alkenes as promoters for the HB(C₆F₅)₂‐catalyzed metal‐free hydrogenation of alkynes was adopted. Significantly, both Z‐ and E‐alkenes can be furnished by hydrogenation with molecular H₂ in high yields with excellent stereoselectivities. Further experimental and theoretical mechanistic studies suggest that interactions between H and F atoms of the alkene promoter, borane intermediate, and H₂ play an essential role in promoting the hydrogenolysis reaction.     

The Effect of Fluoro Substitution upon the β‐Hairpin Fold of a β‐Tetrapeptide in Methanol

The importance of β‐peptides lies in their ability to mimic the conformational behavior of α‐peptides, even with a much shorter chain length, and in their resistance to proteases. To investigate the effect of substitution of β‐peptides on their dominant fold, we have carried out a molecular‐dynamics (MD) simulation study of two tetrapeptides, Ac‐(2R,3S)‐β^2,3hVal(αMe)‐(2S)‐β²hPhe‐(R)‐β³hLys‐(2R,3S)‐β^2,3‐Ala(αMe)‐NH₂, differing in the substitution at the C_α of Phe2 (pepF with F, and pepH with H). Three simulations, unrestrained (UNRES), using ³J‐coupling biasing with local elevation in combination with either instantaneous (INS) or time‐averaging (AVE) NOE distance restraining, were carried out for each peptide. In the unrestrained simulations, we find three (pepF) and two (pepH) NOE distance bound violations of maximally 0.22 nm that involve the terminal residues. The restrained simulations match both the NOE distance bounds and ³J‐values derived from experiment. The fluorinated peptide shows a slightly larger conformational variability than the non‐fluorinated one.     

Hemicarbasucrose: Turning off the Exoanomeric Effect Induces Less Flexibility

Hemicarbasucrose, a close congener of sucrose in which the endocyclic oxygen atom of the glucose moiety is replaced by a methylene group was synthesized for the first time. The conformational behaviour of hemicarbasucrose was studied by a combination of molecular mechanics and NMR spectroscopy (J and NOE data). It was shown that the carbadisaccharide populates two distinct conformational families in solution, the normal syn‐ψ conformation, which is the predominating conformation of the parent natural O‐glycoside, and the anti‐ψ conformation, which has not been detected for the O‐disaccharide. Interestingly, the hemicarbasucrose is less flexible than its natural congener.     

A simple and straightforward method for determination of oxime group configuration in ethanone oximes by differential NOE experiments

Differential NOE experiments in DMSO-d₆ with pre-saturation of the N-OH protons of the oxime are described for the simple and straightforward determination of the configuration of ethanone oximes. A characteristic relative NOE of about 1% has been observed for the methyl group of E-isomers, while the Z-isomers gave an undetectable response together with an NOE interaction to the α- or β-hydrogens on the other substituent attached to oxime carbon atom.     

Photocontrol of Polar Aromatic Interactions by a Bis‐Hemithioindigo Based Helical Receptor

The first example of a bis‐hemithioindigo (bis‐HTI)‐based molecular receptor was realized. Its folding and selective binding affinity for aromatic guest molecules can be precisely controlled by visible light and heat. The thermodynamically stable state of the bis‐HTI is the s‐shaped planar Z,Z‐configuration. After irradiation with 420 nm light only the E,Z‐configuration is formed in a highly selective photoisomerization. The E,Z‐isomer adopts a helical conformation because of the implementation of repulsive steric interactions. The E,Z‐configured helix is able to recognize electron‐poor aromatic guests exclusively through polar aromatic interactions and also distinguishes between regioisomers. After heating, the Z,Z‐configuration is completely restored and the aromatic guest molecule is efficiently released.     

Linking Deltahedral Zintl Clusters with Conjugated Organic Building Blocks: Synthesis and Characterization of the Zintl Triad [R‐Ge9‐CHCH?CHCH‐Ge9‐R]4−

The accessibility of triads with deltahedral Zintl clusters in analogy to fullerene–linker–fullerene triads is another example for the close relationship between fullerenes and Zintl clusters. The compound {[K(2.2.2‐crypt)]₄[RGe₉‐CHCH CHCH‐Ge₉R]}(toluene)₂ (R=(2Z,4E)‐7‐amino‐5‐aza‐hepta‐2,4‐dien‐2‐yl), containing two deltahedral [Ge₉] clusters linked by a conjugated (1Z,3Z)‐buta‐1,3‐dien‐1,4‐diyl bridge, was synthesized through the reaction of 1,4‐bis(trimethylsilyl)butadiyne with K₄Ge₉ in ethylenediamine and crystallized after the addition of 2.2.2‐cryptand and toluene. The compound was characterized by single‐crystal structure analysis as well asNMR and IR spectroscopy.     

ss‐NMR and single‐crystal X‐ray diffraction in the elucidation of a new polymorph of bischalcone (1E,4E)‐1,5‐bis(4‐fluorophenyl)penta‐1,4‐dien‐3‐one

We report a new polymorph of (1E,4E)‐1,5‐bis(4‐fluorophenyl)penta‐1,4‐dien‐3‐one, C₁₇H₁₂F₂O. Contrary to the precedent literature polymorph with Z′ = 3, our polymorph has one half molecule in the asymmetric unit disordered over two 50% occupancy sites. Each site corresponds to one conformation around the single bond vicinal to the carbonyl group (so‐called anti or syn). The other half of the bischalcone is generated by twofold rotation symmetry, giving rise to two half‐occupied and overlapping molecules presenting both anti and syn conformations in their open chain. Such a disorder allows for distinct patterns of intermolecular C—H…O contacts involving the carbonyl and anti‐oriented β‐C—H groups, which is reflected in three ¹³C NMR chemical shifts for the carbonyl C atom. Here, we have also assessed the cytotoxicity of three symmetric bischalcones through their in vitro antitumour potential against three cancer cell lines. Cytotoxicity assays revealed that this biological property increases as halogen electronegativity increases.     

Simultaneous determination of the novel thiosemicarbazone anti‐cancer agent,Bp4eT,and its main phase I metabolites in plasma: Application to a pilot pharmacokinetic study in rats

Novel thiosemicarbazone metal chelators are extensively studied anti‐cancer agents with marked and selective activity against a wide variety of cancer cells, as well as human tumor xenografts in mice. This study describes the first validated LC‐MS/MS method for the simultaneous quantification of 2‐benzoylpyridine 4‐ethyl‐3‐thiosemicarbazone (Bp4eT) and its main metabolites (E/Z isomers of the semicarbazone structure, M1‐E and M1‐Z, and the amidrazone metabolite, M2) in plasma. Separation was achieved using a C₁₈ column with ammonium formate/acetonitrile mixture as the mobile phase. Plasma samples were treated using solid‐phase extraction on 96‐well plates. This method was validated over the concentration range of 0.18–2.80 μM for Bp4eT, 0.02–0.37 μM for both M1‐E and M1‐Z, and 0.10–1.60 μM for M2. This methodology was applied to the analysis of samples from in vivo experiments, allowing for the concentration–time profile to be simultaneously assessed for the parent drug and its metabolites. The current study addresses the lack of knowledge regarding the quantitative analysis of thiosemicarbazone anti‐cancer drugs and their metabolites in plasma and provides the first pharmacokinetic data on a lead compound of this class. Copyright © 2013 John Wiley & Sons, Ltd.     

Uncovering Key Structural Features of an Enantioselective Peptide‐Catalyzed Acylation Utilizing Advanced NMR Techniques

We report on a detailed NMR spectroscopic study of the catalyst‐substrate interaction of a highly enantioselective oligopeptide catalyst that is used for the kinetic resolution of trans‐cycloalkane‐1,2‐diols via monoacylation. The extraordinary selectivity has been rationalized by molecular dynamics as well as density functional theory (DFT) computations. Herein we describe the conformational analysis of the organocatalyst studied by a combination of nuclear Overhauser effect (NOE) and residual dipolar coupling (RDC)‐based methods that resulted in an ensemble of four final conformers. To corroborate the proposed mechanism, we also investigated the catalyst in mixtures with both trans‐cyclohexane‐1,2‐diol enantiomers separately, using advanced NMR methods such as T₁ relaxation time and diffusion‐ordered spectroscopy (DOSY) measurements to probe molecular aggregation. We determined intramolecular distance changes within the catalyst after diol addition from quantitative NOE data. Finally, we developed a pure shift EASY ROESY experiment using PSYCHE homodecoupling to directly observe intermolecular NOE contacts between the trans‐1,2‐diol and the cyclohexyl moiety of the catalyst hidden by spectral overlap in conventional spectra. All experimental NMR data support the results proposed by earlier computations including the proposed key role of dispersion interaction.     

The Stereostructure of Porphyra‐334: An Experimental and Calculational NMR Investigation. Evidence for an Efficient ‘Proton Sponge’

The mycosporine‐like amino acid (MAA) porphyra‐334 ( 1 ) is subjected to extensive ¹H‐ and ¹³C‐NMR analysis as well as to density‐functional‐theory (DFT) calculations. All ¹H‐ and ¹³C‐NMR signals of 1 are assigned, as well as the resonances of prochiral proton pairs. This is achieved by 500‐MHz standard COSY, HMQC, and HMBC experiments, as well as by one‐dimensional (DPFGSE‐NOE) and two‐dimensional (NOESY) NOE experiments. Diffusion measurements (DOSY) confirm that 1 is monomeric in D₂O solution. DFT Calculations yield ¹³C‐NMR chemical shifts which are in good agreement for species 6 which is the imino N‐protonated form of 1 . An exceptionally high proton affinity of 265.7 kcal/mol is calculated for 1 , indicating that 1 may behave as a very powerful ‘proton sponge’ of comparable strength as synthetic systems studied so far. Predictions of ¹³C‐NMR chemical shifts by the ‘NMRPredict’ software are in agreement with the DFT data. The absolute configuration at the ring stereogenic center of 1 is concluded to be (S) from NOE data as well as from similarities with the absolute configuration (S) found in mycosporine‐glycine 16 . This supports the assumption that 1 is biochemically derived from 3,3‐O‐didehydroquinic acid ( 17 ). The data obtained question the results recently published by a different research group claiming that the configuration at the imino moiety of 1 is (Z), rather than (E) as established by the here presented study.     

Conformational changes of functionalised indole receptors upon their interaction with anions

The conformational analysis of four C2-amido and C7-ureido functionalised indole anion receptors was performed by a combination of heteronuclear NMR spectroscopy and ab initio quantum mechanical calculations. NOE experiments showed that anti–anti conformation across C2–C2α and C7–N7α bonds is predominant in acetone solution in the absence of anions. Upon anion binding to receptors, syn–syn conformation becomes predominant. The conformational changes upon anion binding are in good agreement with energetic preferences established by ab initio calculations. Chemical shift changes induced by interaction of anions suggest that binding of chloride and bromide anions occurs primarily to H1 and H7α protons. Nitrate anions favour interaction with H7α and H7γ ureido protons, whereas acetate anions interact strongly with all four available hydrogen bond donor groups.     

Rotationally‐hindered furyl fulgides

Fulgides are a representative class of photochromic organic molecules which exhibit several interesting properties for diverse applications in fields such as data storage or high‐resolution spectroscopy. The crystal structures of three furyl fulgides with different steric constraints were determined and for two of the compounds both the E and Z isomer structures were defined. The compounds are 3‐[(E)‐1,3‐dimethyl‐4,5,6,7‐tetrahydro‐2‐benzofuran‐4‐ylidene]‐4‐isopropylidenetetrahydrofuran‐2,5‐dione, C₁₇H₁₈O₄, (I‐E), 3‐[(E)‐1,3‐dimethyl‐5,6,7,8‐tetrahydro‐4H‐cyclohepta[c]furan‐4‐ylidene]‐4‐isopropylidenetetrahydrofuran‐2,5‐dione, C₁₈H₂₀O₄, (II‐E), and the Z isomer, (II‐Z), and 3‐isopropylidene‐4‐[(E)‐1‐(5‐methoxy‐2‐methyl‐1‐benzofuran‐3‐yl)ethylidene]tetrahydrofuran‐2,5‐dione, C₁₉H₁₈O₅, (III‐E), with two molecules in the asymmetric unit, and the Z isomer, (III‐Z). The structures of the E and Z isomers show only little differences in the bond lengths and angles inside the hexatriene unit. Because of the strained geometry there are deviations in the torsion angles. Furthermore, small differences in the distances between the bond‐forming C atoms in the electrocyclization process give no explanation for the unequal photochromic behaviour.     

Linking Deltahedral Zintl Clusters with Conjugated Organic Building Blocks: Synthesis and Characterization of the Zintl Triad [R‐Ge9‐CHCHCHCH‐Ge9‐R]4−

The accessibility of triads with deltahedral Zintl clusters in analogy to fullerene–linker–fullerene triads is another example for the close relationship between fullerenes and Zintl clusters. The compound {[K(2.2.2‐crypt)]₄[RGe₉‐CH?CH? CH?CH‐Ge₉R]}(toluene)₂ (R=(2Z,4E)‐7‐amino‐5‐aza‐hepta‐2,4‐dien‐2‐yl), containing two deltahedral [Ge₉] clusters linked by a conjugated (1Z,3Z)‐buta‐1,3‐dien‐1,4‐diyl bridge, was synthesized through the reaction of 1,4‐bis(trimethylsilyl)butadiyne with K₄Ge₉ in ethylenediamine and crystallized after the addition of 2.2.2‐cryptand and toluene. The compound was characterized by single‐crystal structure analysis as well asNMR and IR spectroscopy.